Dissertations / Theses on the topic 'Species divergence'
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Madsen, Susan M. "Divergence in repetitive DNA sequences among three sitopsis wheat species /." free to MU campus, to others for purchase, 1998. http://wwwlib.umi.com/cr/mo/fullcit?p9901260.
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Colbeck, Gabriel Joseph. "Phylogeography, song divergence and reproductive isolation in two species of songbird." Pullman, Wash. : Washington State University, 2009. http://www.dissertations.wsu.edu/Dissertations/Spring2009/g_colbeck_042009.pdf.
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Henry, Amanda Ann (Shaffer). "Clarkia genetic basis of sister species divergence Clarkia concinna x Clarkia breweri /." Thesis, Montana State University, 2006. http://etd.lib.montana.edu/etd/2006/henry/HenryA0806.pdf.
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Ross, Rebecca Isabel Charlotte. "Local adaptation and adaptive divergence in a hybrid species complex in Senecio." Thesis, University of Oxford, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.543007.
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FitzGerald, Alyssa. "Speciation and Ecological Niche Divergence of a Boreal Forest Bird Species Complex." Thesis, State University of New York at Albany, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10276556.
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Evolutionary biologists are supremely interested in the events that cause populations to diverge and speciate, and the mechanisms that maintain divergence over time. Here, I investigate the evolutionary history of a boreal bird species complex. Boreal bird species are co-distributed, diverged during the Pleistocene, and generally have patterns of genetic divergence that are consistent with a single “boreal” clade in northern and eastern North America. The Gray-cheeked Thrush species complex, however, shows a possible species break in eastern North America between the Bicknell’s Thrush ( Catharus bicknelli) and Gray-cheeked Thrush (Catharus minimus ). Using population genetic and genomic analyses of the largest sampling to-date of either species, I find that the eastern break indeed coincides with a species-level divergence, although low levels of admixture in a few individuals and one probable hybrid hint at the possibility of occasional hybridization. Species distribution models (SDMs) of the Last Glacial Maximum revealed that divergence may have been maintained by residence in different late-Pleistocene refugia. However, because speciation occurred mid-Pleistocene, I examined the geographical context of divergence of the Bicknell’s Thrush and Gray-cheeked Thrush using multivariate analyses and ecological niche modeling techniques of local-scale habitat data and broad-scale climate and tree species distributions. Local-scale habitat analyses reveal that the thrushes breed at sites with unique tree species composition, physiognomy (forest structure), and ground cover characteristics; furthermore broad-scale analyses reveal that niche divergence, rather than conservatism, was the predominant pattern for these species, suggesting that ecological divergence has played a role in their speciation. This dissertation supports the hypothesis that the Bicknell’s Thrush and Gray-cheeked Thrush are distinctive species that breed in divergent local- and broad-scale niches and emphasizes that this species-level divergence seems unique among boreal bird species.
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Herrig, Danielle Kay. "Evaluating gene flow, gene expression divergence, and hybrid expression in Drosophila sister species." Diss., University of Iowa, 2016. https://ir.uiowa.edu/etd/2222.
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A primary goal of evolutionary biology is to elucidate the factors necessary for a single interbreeding species to become two independent species. Observations and data collected and recorded since the 6th century B.C. have added to our comprehension of the “the origin of species—that mystery of mysteries” (DARWIN 1859). To continue to add to our knowledge of how speciation occurs and how species interact, it is crucial to determine 1) how different categories of genes evolve as species diverge, 2) what happens to hybrids of two species, and 3) if genetic exchange is allowed between species, where it is located.
In the first research aim of my dissertation, I look for population genetic trends and signatures of gene flow in a minimally studied set of Drosophila sister species using sequences of 26 nuclear and mitochondrial regions in 29 isofemale lines of D. subobscura and D. madierensis. Standard population genetic tests revealed that the X chromosome evolves faster than the autosomes in these species. We also find evidence of genetic exchange for some autosomal genes while both the sex chromosomes and mitochondrial genomes remain distinct between species.
In the second research aim of my dissertation, I assess the rates of gene expression evolution for sex-biased genes located on the X chromosome and autosomes. We find that gene expression evolves faster in males than females and find evidence of faster-X evolution that is exclusive to genes expressed at higher levels in males. The X chromosome has previously been shown to have a disproportionately large influence on hybrid male sterility compared to autosomes. I investigate this trend and find that the sex chromosomes have a large influence on autosomal expression levels in hybrid males and hybrid females. Specifically, uniparental inheritance of the X chromosome results in greater differences between reciprocal hybrids and higher levels of hybrid misexpression.
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Oyakawa, Chisako. "Species-specific Acoustic Structures Organizing Population Divergence and Acoustic Individuality in Wild Agile Gibbons." 京都大学 (Kyoto University), 2008. http://hdl.handle.net/2433/124359.
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Mercader, Rodrigo J. "Species ranges, host selection, and hybridization how increased hybridization is leading to host use divergence in a polyphagous sibling species pair /." Diss., Connect to online resource - MSU authorized users, 2008.
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Thesis (Ph.D.)--Michigan State University. Dept. of Entomology and Program in Ecology, Evolutionary Biology, and Behavior, 2008.Title from PDF t.p. (viewed on July 17, 2009) Includes bibliographical references (p. 115-126). Also issued in print.
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Zhou, Y. (Yongfeng). "Demographic history and climatic adaptation in ecological divergence between two closely related parapatric pine species." Doctoral thesis, Oulun yliopisto, 2014. http://urn.fi/urn:isbn:9789526206769.
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Abstract Both demographic histories and natural selection complicate the speciation process. There is a need to jointly study the effects of natural selection on so called magic traits that can cause reproductive isolation such as climatic adaptation, and its interaction with neutral demographic histories. Closely related incipient coniferous species offer us a great system for this effort. I used genetic variation at one set of climate-related candidate genes and another set of reference loci and cytoplasmic genomic fragments of two closely related parapatric pine species: Pinus massoniana Lamb. and Pinus hwangshanensis Hisa. Population genetic analyses were used to measure genetic variation and detect signals of ancient and recent selection. Speciation parameters including migration rates and divergence times at candidate genes and reference loci were compared under the Isolation with migration model. Hierarchical Approximate Bayesian Computation (ABC) was used to define demographic and speciation models. Intra- and interspecific genetic variation at cytoplasmic and nuclear intronic sequences were compared between parapatric populations and allopatric populations to distinguish the effects of introgression and incomplete lineage sorting in generating shared genetic variation between the species. The results showed that ancient selection were shared by the lineages leading to the species while recent selection has been species-specific. Candidate genes had significant lower migration rates compared to reference loci. Recent differential climatic selection might counteract against gene flow at underlying genes, which therefore favors divergence between the two pines through ecological speciation. Shared mitotypes were randomly distributed across species’ ranges, which therefore supported the incomplete lineage sorting hypothesis, but the shared nuclear intronic variation distributed more frequently in parapatric populations than in allopatric populations, supported the introgression hypothesis. ABC and species’ distribution modeling also supported the secondary gene flow model. The three genomes had different rates of mutation and gene flow might mirror different phases of the speciation continuum. The results in this thesis are valuable for understanding evolution in general and for other applied purposes such as tree breeding and climate change adaptationTiivistelmä Luonnonvalinta ja populaatioiden historian demografia tekevät lajiutumisesta monimutkaisen tapahtumaketjun. Luonnonvalinnan ja demografisten tekijöiden vuorovaikutusta on paras tutkia samanaikaisesti, kun tarkastellaan lajiutumiseen vaikuttavia ominaisuuksia. Tällaisia ovat esimerkiksi ilmastoon sopeutumiseen liittyvät ominaisuudet. Lähisukuiset havupuulajit tarjoavat erinomaiset mahdollisuudet tähän työhön. Tutkin geneettistä muuntelua yhtäältä ilmastosopeutumiseen liittyvissä ns. ehdokasgeeneissä ja toisaalta neutraaleiksi oletetuissa verrokkigeeneissä sekä sytoplasman genomeissa kahdessa lähisukuisessa mäntylajissa Pinus massoniana Lamb. ja Pinus hwangshanensis Hisa, joiden populaatiot esiintyvät joskus erillään toisistaan (allopatrisesti), toisinaan vierekkäin (parapatrisesti). Mittasin muuntelun määrää ja etsin merkkejä valinnan vaikutuksesta. Vertasin erilaisia lajiutumismallien parametrejä verrokki- ja ehdokasgeeneissä. Käytin simulaatioita etsiäkseni parhaat demografiset ja lajiutumiseen liittyvät mallit. Vertasin kloroplastien ja mitokondrioiden genomien sekvenssien lajinsisäistä ja lajien välistä muuntelua allopatrisissa ja parapatrisissa populaatioissa tutkiakseni onko lajien yhteinen muuntelu seurausta siitä että lajien eriytymisestä on kulunut vain vähän aikaa vai siitä että sen jälkeen on tapahtunut geenivirtaa. Kauan sitten tapahtunut valinta on vaikuttanut samalla tavalla kumpaankin lajiin, osin koska tutkimus kohdistui myös niiden yhteiseen edeltäjälinjaan. Äskettäinen valinta taas oli suuremmassa määrin kummallekin lajille ominaista. Viime aikojen ilmastoon liittyvä valinta on voinut vähentää geenivirtaa ehdokasgeeneissä, mikä voisi edistää ekologista lajiutumista. Tuman DNA:n muuntelu jakautuminen tuki sitä mahdollisuutta että lajien yhteinen geneettinen muuntelu johtuu äskettäisestä geenivirrasta, ei vain siitä että lajiutuminen on niin varhaisessa vaiheessa. Mitokondrioiden geeneissä lajeilla yhtä paljon yhteistä muuntelua sekä allopatrisissa että parapatrisissa populaatioissa, mikä tukee sen sijaan eriytymisen jälkeistä epätäydellistä muuntelun erilaistumista. Eri genomit heijastavat lajiutumisprosessin eri vaiheita. Väitöskirjan tulokset ovat osaltaan tuottaneet uutta tietoa lajiutumisesta ja valinnasta. Lisäksi niillä on merkitystä ilmastomuutoksen vaikutusten ymmärtämisessä ja metsänjalostuksessa
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Wyatt, Kimberly M. "Rapid morphological divergence among subpopulations of the introduced common wall lizard, Podarcis muralis." University of Cincinnati / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1377874890.
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Bunt, Thomas Michael. "Reproductive Isolation and Genetic Divergence in a Young "Species Flock" of Pupfishes (Cyprinodon sp.) from San Salvador Island, Bahamas." Thesis, Virginia Tech, 2001. http://hdl.handle.net/10919/31212.
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The study of the process of speciation is instrumental to understanding the species diversity observed today. Diverging populations are intriguing, because speciation has not reached an endpoint, yet the process that may eventually lead to distinct species can be studied. Systems that contain many putative species and/or parallel divergences, such as many species flocks and species pairs, are extraordinary examples of divergence and therefore are critical to the understanding of the speciation process. A "miniature" species flock of pupfish (Cyprinodon variegatus) discovered in lakes on San Salvador Island, Bahamas has evolved in less than 6 000 years, and is, therefore, important to the study of the pace of evolutionary processes. The San Salvador Island pupfish flock is composed of a normal form, which resembles coastal C. variegatus, and bulldog and bozo morphs, which diverge ecologically and morphologically from the normal morph.
In Chapter 1, I sequenced the mtDNA control region and used haplotype frequency analyses to assess the level of differentiation between sympatric normals and bulldogs sampled from Osprey Lake and Little Lake on San Salvador Island. The bozo morph was too rare to include in the study. I also included samples of normals that occur in lakes without bulldog and bozo morphs to assess any differences between lakes on the island. All haplotype frequency comparisons for sympatric normals and bulldogs were highly significant, which suggests these morphs are distinct populations in sympatry and, therefore, have characteristics of biological species. Further, an estimation of Time for Speciation supports geological data that suggest this fauna is very young (6 000 years). The San Salvador Island pupfish species flock is, therefore, the youngest known species flock and presents an important model system for the study of how morphological and ecological divergence can promote speciation in Cyprinodon.
In Chapter 2, I first compared the San Salvador Island pupfishes to other Bahamian C. variegatus populations to assess the level of inter- and intra-island pupfish population differentiation in the Bahamas. The mtDNA control region was sequenced for bulldogs and normals from San Salvador Island and normals sampled from New Providence and Exuma Islands. San Salvador Island bulldogs were found to be distinct from all normal populations sampled, and comparisons of shared haplotypes suggest they originated on San Salvador Island rather than any of the other islands sampled. This was intriguing, because a "bulldog-like" morph has recently been observed in a lake on New Providence Island, which suggests parallel divergences may be occurring throughout the Bahamas. I also sequenced the mtDNA cytochrome b gene to assess the phylogeography of C. variegatus. Populations were sampled from the Bahamas and the east coast of North America, and the results suggest the Bahamas were only recently colonized by the Southern coastal lineage of C. variegatus. A distinct Northern lineage of C. variegatus, which may warrant species designation, was also supported by the cytochrome b data. Overall, the results supported a San Salvador Island origin for the Little Lake and Osprey Lake bulldog morphs, and also suggest the Bahamian C. variegatus populations are very young.Master of Science
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Dhami, Kirandeep K. "AMONG-LOCUS HETEROGENEITY IN GENETIC DIVERSITY AND DIVERGENCE IN TWO PAIRS OF DUCK SPECIES (GENUS: ANAS)." Wright State University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=wright1357230023.
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Metegnier, Gabriel. "From gene expression to genetic adaptation : insights into the spatio-temporal dynamics of Alexandrium minutum cryptic species complex." Thesis, Sorbonne université, 2018. http://www.theses.fr/2018SORUS200/document.
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Les populations naturelles sont confrontées à des changements environnementaux. Pour y faire face, différentes réponses ont été sélectionnées au cours de l'évolution. Parmi elles se trouvent la plasticité phénotypique et l'adaptation génétique. Etudier les liens existants entre elles est une manière de comprendre les dynamiques des populations et de prévoir leurs réponses à un environnement changeant. Dans la présente étude, je me suis attaché à étudier ces liens à plusieurs échelles (intra- et interspécifique), chez le complexe d'espèces cryptiques de la micro-algue Alexandrium minutum, et ce à la fois in vitro et in situ. En ce qui concerne la plasticité phénotypique, ces deux espèces proches montrent de profondes différences, soulignant les liens entre divergence génétique et écologique. Au niveau intraspécifique, il apparaît que face à des variations de facteurs abiotiques, les populations ajustent les niveaux d'expression de certains gènes (notamment impliqués dans des fonctions de motilité et d'interactions intercellulaires dans des environnements froids à faible salinité). D'autre part, les populations montrent de la différentiation génétique à la fois à faible échelle spatiale, au cours du temps, et lorsque la communauté change. Pour conclure, il existe une interaction directe entre divergence génétique et changements d'expression de gènes. En plus de poser de nombreuses questions quant aux capacités de réponse des populations, ces résultats soulignent comment plasticité phénotypique et changements génétique sont liés et interagissent. Ils offrent une perspective nouvelle sur les mécanismes qui sous-tendent les réponses des populations à leur environnementNatural populations face environmental changes. In this context, different responses were evolutionnary selected. Among them are phenotypic plasticity and genetic adaptation. Studying the links between these two types of response is a way to understand population dynamics and to predict how they may respond to a changing environment. In the present Ph.D thesis, I focused on studying these links at several scales (intra- and interspecific), in the cryptic species complex of the microalga Alexandrium minutum, both in vitro and in situ. With respect to phenotypic plasticity, these two closely related species show profound differences, highlighting the links between genetic and ecological divergence. At the intraspecific level, it appears that, when facing abiotic factors variations, populations adjust the expression levels of certain genes (notably involved in motility related functions and intercellular interactions under low-salinity and cold environments). On the other hand, populations show genetic differentiation at both small spatial scale, over time, and when the community changes. To conclude, there is a direct interaction between genetic divergence and changes in gene expression. In addition to asking many questions about the response capabilities of populations, these results highlight how phenotypic plasticity and genetic changes are linked and interact. They offer new perspectives on the mechanisms underlying population responses to their environment
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Bunt, Thomas M. "Reproductive isolation and genetic divergence in a young "species flock" of pupfishes (Cyprinodon sp.) from San Salvador Island, Bahamas." Connect to this title online, 2001. http://scholar.lib.vt.edu/theses/available/etd-02122002-153708/.
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McCreary, Cheryl S. "Genetic Relationships, Morphological Divergence and Ecological Correlates in Three Species of the Viola canadensis Complex in Western North America." View online, 2005. http://etd.ohiolink.edu/send-pdf.cgi/McCreary%20Cheryl%20S.pdf?acc_num=ohiou1133550610.
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Wang, Zhen, Ruiguang Yang, Upendra K. Devisetty, Julin N. Maloof, Yang Zuo, Jingjing Li, Yuxiao Shen, Jian Zhao, Manzhu Bao, and Guogui Ning. "The Divergence of Flowering Time Modulated by FT/TFL1 Is Independent to Their Interaction and Binding Activities." FRONTIERS MEDIA SA, 2017. http://hdl.handle.net/10150/624058.
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FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1) proteins share highly conserved amino acid residues but they play opposite regulatory roles in promoting and repressing the flowering response, respectively. Previous substitution models and functional analysis have identified several key amino acid residues which are critical for the promotion of flowering. However, the precise relationship between naturally occurring FT/TFL1 homologs and the mechanism of their role in flowering is still unclear. In this study, FT/TFL1 homologs from eight Rosaceae species, namely, Spiraea cantoniensis, Pyracantha fortuneana, Photinia serrulata, Fragaria ananassa, Rosa hybrida, Prunus mume, Prunus persica and Prunus yedoensis, were isolated. Three of these homologs were further characterized by functional analyses involving site-directed mutagenesis. The results showed that these FT/TFL1 homologs might have diverse functions despite sharing a high similarity of sequences or crystal structures. Functional analyses were conducted for the key FT amino acids, Tyr-85 and Gln-140. It revealed that TFL1 homologs cannot promote flowering simply by substitution with key FT amino acid residues. Mutations of the IYN triplet motif within segment C of exon 4 can prevent the FT homolog from promoting the flowering. Furthermore, physical interaction of FT homologous or mutated proteins with the transcription factor FD, together with their lipid-binding properties analysis, showed that it was not sufficient to trigger flowering. Thus, our findings revealed that the divergence of flowering time modulating by FT/TFL1 homologs is independent to interaction and binding activities.
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Santos, Santos Javier H. "Ecomorphological discrimination of vertebrate sister species with recent phylogenetic divergence using novel non-destructive morphometric methods = Discriminación ecomorfológica de especies hermanas de vertebrados con divergencia filogenética reciente utilizando nuevos métodos morfométricos no-destructivos." Doctoral thesis, Universitat de Barcelona, 2019. http://hdl.handle.net/10803/666609.
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The thesis "Ecomorphological discrimination of vertebrate sister species with recent phylogenetic divergence using novel non-destructive morphometric methods” compares morphological evolution during syntopic adaptive radiation between two vertebrate classes: the model African cichlid fish and the non-model Malagasy mantellid frogs. In Section I the ontogenetic body shape development of two Lake Victoria haplochromine cichlid sister species (Haplochromis fischeri and H. piceatus) and their non-natural hybrid is described by means of landmark-based Geometric Morphometrics. Chapter 1 relates divergent shape changes in the parental species to their respective trophic specializations and discloses associated shape variation linked to their respective locomotor specializations along the benthic-limnetic axis. Chapter 2 observes their hybrid to display a mosaic of parental and unique morphological features and discusses the influence of hybridization in the radiation of East African cichlids. In Section II computed-tomography (CT) techniques are used to study the musculoskeletal anatomy of mantellid frogs, genus Blommersia. Chapter 3 provides the ecological, morphological, and phylogenetic description of two new species of Blommersia (B. alexi and B. nataliae) found on the Comorian island of Mayotte thought to have evolved in sympatry and to be undergoing opposite processes of gigantism and nanism, respectively, in relation to their most recent common ancestor. Chapter 4 provides the first complete skeletal description for any mantellid species, B. alexi, and reveals genus-specific osteological features that are predicted to be implicated in their locomotion and unique reproductive behavior. Chapter 5 presents a custom soft-tissue contrast staining technique used prior to CT-scanning and applies the recently developed featureless Geometric Morphometric technique of Generalized Procrustes Surface Analysis to compare pelvic shape across seven species of the genus Blommersia, relating observed patterns of shape variation to their phylogenetic relationships and pelvic muscular architecture. In Section III the biomechanics of anuran locomotion are evaluated. Chapter 6 explores biomechanical performance during jumping and swimming locomotion in the wood frog (Rana sylvatica), putting special emphasis on the hindleg musculature implicated in thrust production during both locomotor modes, and reveals incredible physiological resilience as reflected by their relatively unaltered biomechanical performance before and after freezing. Overall, cichlid fish morphological evolution appears to be influenced to a larger degree by trophic ecological pressures, whereas in mantellid frogs it is body size variation and locomotor performance that condition species' divergence.La tesis "Discriminación ecomorfológica de especies hermanas de vertebradas con divergencia filogenética reciente utilizando nuevos métodos morfométricos no destructivos" compara la evolución morfológica durante la radiación adaptativa sintópica entre dos clases de vertebrados: los peces cíclidos africanos modelo y las ranas mantélidas malgaches no modelo. En la Sección I, el desarrollo ontogenético de la forma del cuerpo de dos especies hermanas de cíclidos haplochrominos del Lago Victoria (Haplochromis fischeri y H. piceatus) y de su híbrido no-natural se describe mediante métodos de Geometría Morfométrica basado en landmarks. El Capítulo 1 relaciona los cambios divergentes en forma entre las especies parentales a sus respectivas especializaciones tróficas y revela variación en forma asociada a sus respectivas especializaciones locomotoras según el eje bentónico-limnético. El capítulo 2 muestra que su híbrido presenta un mosaico de características morfológicas parentales y únicas, y discute la influencia de la hibridación en la radiación de los cíclidos africanos. En la Sección II, se utilizan técnicas de tomografía computarizada (CT) para estudiar la anatomía musculo-esquelética de las ranas mantélidas, género Blommersia. El Capítulo 3 proporciona la descripción ecológica, morfológica, y filogenética de dos nuevas especies de Blommersia (B. alexi y B. nataliae) halladas en la isla comorana de Mayotte, que se cree evolucionaron en simpatría y que están sufriendo procesos opuestos de gigantismo y nanismo, respectivamente, en relación a su ancestro común más reciente. El Capítulo 4 proporciona la primera descripción esquelética completa para cualquier especie de mantélido, B. alexi, y revela características osteológicas específicas del género que se predice que están implicadas en su locomoción y comportamiento reproductivo único. El Capítulo 5 presenta una técnica personalizada de tinción de contraste de tejidos blandos para utilización antes de la CT y aplica la técnica recientemente desarrollada de Geometría Morfométrica para estructuras lisas llamada Generalized Procrustes Surface Analysis para comparar la forma pélvica entre siete especies del género Blommersia, de esta forma relacionando los patrones observados de variación en forma con sus relaciones filogenéticas y arquitectura muscular pélvica. En la Sección III, se evalúa la biomecánica en la locomoción de los anuros. El capítulo 6 explora el rendimiento biomecánico durante la locomoción de salto y natación en la Rana sylvatica, poniendo especial énfasis en la musculatura de la pata trasera implicada en la producción de empuje durante ambos modos locomotores, y revela una increíble resistencia fisiológica reflejada por su rendimiento biomecánico relativamente inalterado antes y después de ser congelado En general, la evolución morfológica en los peces cíclidos parece estar influenciada en mayor medida por las presiones ecológicas tróficas, mientras que en las ranas mantélidas es la variación del tamaño corporal y el rendimiento locomotor lo que condiciona la divergencia de las especies.
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Brett, Christy Donna. "Testing the effectiveness of the mt DNA Cytochrome c oxidase subunit 1 (COI) gene locus for identifying species of Polychaete worm (Polychaeta: Annelida) in New Zealand." The University of Waikato, 2006. http://hdl.handle.net/10289/2425.
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The ability to accurately identify species is fundamental to ecological research and environmental monitoring. Current taxonomic identifications often rely on differentiation of morphologically ambiguous characters, and a process of categorization which is tedious and often leads to misidentifications. This is compounded by the presence of cryptic taxa, which may be prevalent among Polychaete worms (Polychaeta: Annelida). With increased access to genetic techniques, Cytochrome c oxidase subunit I has been suggested as a possible aid to assist in the discrimination of species resources. In this study, I tested the hypothesis that the mtDNA COI gene locus is effective in discriminating morphologically recognised species of Polychaete worms. A 543 base-pair fragment of the COI locus was successfully extracted for 111 individuals from 16 out of 20 morphologically recognised species. Average intraspecific divergences were 0.8 %, ranging from 0 % to 5 %. Average interspecific variation was 26.4 %, ranging from 13.8 % to 36.8 %. The lowest divergences were found between two Nereid species (13.8 %), and two Glycera americana species (17.2 %). Relatively high maximum divergences of over 30 % suggest that some species may have reached a divergence saturation level, which may partially explain why familial groupings in constructed trees were not monophyletic. Divergences within the different Nereid species - a group previously known to have morphologically cryptic species - did not reveal the presence of any cryptic taxa. Pairwise comparisons showed a clear divide between percentages of intra- and interspecific divergences, and the suggested threshold of 11 % is effective for the taxa investigated here. On the basis of these results, I conclude that sequence variation in the mtDNA COI gene locus is effective in discriminating morphologically recognised species of Polychaete worms, but may not be appropriate for deeper (e.g. generic or familial) phylogenetic relationships among taxa.
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Carvalho, Edvanda Andrade Souza de. "Variabilidade genética e morfológica em populações de Trichodactylus fluviatilis Latreille, 1828 (Brachyura, Trichodactylidae) no Brasil." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/59/59139/tde-01112013-083827/.
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O caranguejo de água doce Trichodactylus fluviatilis Latreille, 1828 apresenta uma considerável variabilidade morfológica, aliada a uma ampla distribuição geográfica e ocupação de ambientes costeiros e continentais. Tal variabilidade tem gerado, em alguns casos, dúvidas quanto à delimitação da espécie. O presente trabalho tem como objetivo averiguar se as populações de T. fluviatilis apresentam divergências morfológicas e genéticas compatíveis com o nível intraespecífico avaliando-se a hipótese de validade deste táxon. Para isto, foi realizada a análise da variabilidade genética entre as populações e uma revisão taxonômica. O material analisado foi obtido por meio de coletas, visitas e empréstimos de coleções carcinológicas do Brasil. Foram analisados caracteres descritos na literatura e obtidas sequências parciais dos genes mitocondriais 16S rRNA e citocromo c oxidase subunidade I (COI). Dentre os caracteres morfológicos analisados alguns tiveram muita variação, enquanto outros se mostraram bem informativos para alguns grupos. O resultado da análise molecular mostrou a formação de clados internos com altas divergências genéticas entre eles, tanto para o gene 16S quanto para o COI. Além disso, a espécie T. petropolitanus foi alocada entre os clados reconhecidos morfologicamente como T. fluviatilis. Tais estruturações genéticas, aliada ao polimorfismo morfológico, mostraram claramente que a espécie reconhecida morfologicamente como T. fluviatilis não forma um grupo monofilético, podendo ser considerada um complexo de espécies, que precisa de ajustes taxonômicos consideráveis.The freshwater crab Trichodactylus fluviatilis Latreille, 1828 presents a considerable morphological variability, as well as a wide geographical distribution and occupancy of coastal and continental environments. Such variability has generated, in some cases, doubts concerning the species delimitation. The present work aims to investigate whether the populations of T. fluviatilis exhibit morphological and genetic divergence compatible with the intraspecific level, assessing the hypothesis of validity of this taxon. Therefore, we have performed the analysis of genetic variability among populations and a taxonomic revision. The material analyzed was obtained from field expeditions, visits and loans from carcinological collections. We analyzed morphological characters described in the literature as well as obtained partial sequences of the 16S rRNA and cytochrome c oxidase subunit I (COI) mitochondrial genes. Some morphological characters analyzed had a wide variation, while others were well informative for some groups. The results of molecular analysis showed the formation of internal clades with high genetic divergence among them, both for 16S and COI. Moreover, the species T. petropolitanus was allocated among clades recognized morphologically as T. fluviatilis. Such genetic structuration and morphological polymorphism clearly indicate that the species morphologically recognized as T. fluviatilis does not form a monophyletic group. Therefore, it must be considered as a species complex, which claims for huge taxonomic adjustments.
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Ruskey, Jennifer Anne. "Morphological stasis and genetic divergence without reproductive isolation in the Rhinichthys cataractae species complex : insights from a zone of secondary contact in the lower Fraser Valley, British Columbia." Thesis, University of British Columbia, 2014. http://hdl.handle.net/2429/50920.
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The Nooksack dace (Rhinichthys cataractae putative subspecies; NSD) and longnose dace (R. cataractae; LND) form a zone of post-glacial secondary contact in three streams in British Columbia's lower Fraser River valley, providing a valuable opportunity to study contact between populations separated during the Pleistocene glaciations. They are morphologically cryptic, despite an estimated 2-3 million years of separation. The NSD is currently listed as Endangered under Canada's Species at Risk Act (SARA) and my study clarifies its taxonomic and conservation status. NSD and LND have highly divergent mitochondrial DNA types, and dace carrying each mtDNA type have been found in roughly equal numbers in the zone of secondary contact. However, it was unknown whether this represented ongoing hybridization or reproductive isolation in sympatry. I conducted a morphological analysis using 11 morphometric measurements and two meristic characters (N = 582, 23 sampling locations) to uncover any subtle variation between the two dace, as well as to test for morphological intermediacy in the zone of sympatry. I then employed a 10-locus microsatellite DNA assay (N = 374, 12 sampling locations) to test for introgression between LND and NSD in the zone of secondary contact. I found that the two dace could not be reliably distinguished: there was overlap in all morphological characters measured, and both morphological and microsatellite analyses showed a greater effect of location than mtDNA clade, even when restricted to allopatric populations. There was no evidence of population structure within the sympatric populations, indicating complete admixture. The LND and NSD provide an example of "ephemeral speciation" - two lineages which, despite long separation, have developed no apparent barriers to reproduction and have collapsed into a single interbreeding population where they come into secondary contact. The zone of secondary contact should ideally be conserved for its evolutionary significance, and is a good illustration of the complicated patterns of diversification caused by the Pleistocene glaciations. However, while the NSD should be protected as a distinct designatable unit, it should not be considered a separate species, or even subspecies.Science, Faculty of
Zoology, Department of
Graduate
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Tucker, Derek B. "Molecular Studies of South American Teiid Lizards (Teiidae: Squamata) from Deep Time to Shallow Divergences." BYU ScholarsArchive, 2016. https://scholarsarchive.byu.edu/etd/6419.
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I focus on phylogenetic relationships of teiid lizards beginning with generic and species relationship within the family, followed by a detailed biogeographical examination of the Caribbean genus Pholidoscelis, and end by studying species boundaries and phylogeographic patterns of the widespread Giant Ameiva Ameiva ameiva. Genomic data (488,656 bp of aligned nuclear DNA) recovered a well-supported phylogeny for Teiidae, showing monophyly for 18 genera including those recently described using morphology and smaller molecular datasets. All three methods of phylogenetic estimation (two species tree, one concatenation) recovered identical topologies except for some relationships within the subfamily Tupinambinae (i.e. position of Salvator and Dracaena) and species relationships within Pholidoscelis, but these were unsupported in all analyses. Phylogenetic reconstruction focused on Caribbean Pholidoscelis recovered novel relationships not reported in previous studies that were based on significantly smaller datasets. Using fossil data, I improve upon divergence time estimates and hypotheses for the biogeographic history of the genus. It is proposed that Pholidoscelis colonized the Caribbean islands through the Lesser Antilles based on biogeographic analysis, the directionality of ocean currents, and evidence that most Caribbean taxa originally colonized from South America. Genetic relationships among populations within the Ameiva ameiva species complex have been poorly understood as a result of its continental-scale distribution and an absence of molecular data for the group. Mitochondrial ND2 data for 357 samples from 233 localities show that A. ameiva may consist of up to six species, with pairwise genetic distances among these six groups ranging from 4.7–12.8%. An examination of morphological characters supports the molecular findings with prediction accuracy of the six clades reaching 72.5% using the seven most diagnostic predictors.
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Gholami, Zeinab. "Ecological plasticity and divergence processes of the Iranian inland species of Aphanius (Teleostei, Cyprinodontidae), with focus on A. sophiae and A. farsicus in the Kor River and Maharlu Lake basins, Southwestern Iran." Diss., Ludwig-Maximilians-Universität München, 2014. http://nbn-resolving.de/urn:nbn:de:bvb:19-175728.
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Gholami, Zeinab [Verfasser], and Bettina [Akademischer Betreuer] Reichenbacher. "Ecological plasticity and divergence processes of the Iranian inland species of Aphanius (Teleostei, Cyprinodontidae), with focus on A. sophiae and A. farsicus in the Kor River and Maharlu Lake basins, Southwestern Iran / Zeinab Gholami. Betreuer: Bettina Reichenbacher." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2014. http://d-nb.info/1060978687/34.
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Relich, Ryan F. "Gliding Motility Mechanisms in Divergent Mycoplasma Species." Miami University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=miami1316482073.
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Bradwell, Katie. "Genomic comparisons and genome architecture of divergent Trypanosoma species." VCU Scholars Compass, 2016. http://scholarscompass.vcu.edu/etd/4598.
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Virulent Trypanosoma cruzi, and the non-pathogenic Trypanosoma conorhini and Trypanosoma rangeli are protozoan parasites with divergent lifestyles. T. cruzi and T. rangeli are endemic to Latin America, whereas T. conorhini is tropicopolitan. Reduviid bug vectors spread these parasites to mammalian hosts, within which T. rangeli and T. conorhini replicate extracellularly, while T. cruzi has intracellular stages. Firstly, this work compares the genomes of these parasites to understand their differing phenotypes. Secondly, genome architecture of T. cruzi is examined to address the effect of a complex hybridization history, polycistronic transcription, and genome plasticity on this organism, and study its highly repetitive nature and cryptic genome organization. Whole genome sequencing, assembly and comparison, as well as chromosome-scale genome mapping were employed. This study presents the first comprehensive whole-genome maps of Trypanosoma, and the first T. conorhini strain ever sequenced. Original contributions vii to knowledge include the ~21-25 Mbp assembled genomes of the less virulent T. cruzi G, T. rangeli AM80, and T. conorhini 025E, containing ~10,000 to 13,000 genes, and the ~36 Mbp genome assembly of highly virulent T. cruzi CL with ~24,000 genes. The T. cruzi strains exhibited ~74% identity to proteins of T. rangeli or T. conorhini. T. rangeli and T. conorhini displayed greater complex carbohydrate metabolic capabilities, and contained fewer retrotransposons and multigene family copies, e.g. mucins, DGF-1, and MASP, compared to T. cruzi. Although all four genomes appear highly syntenic, T. rangeli and T. conorhini exhibited greater karyotype conservation. T. cruzi genome architecture studies revealed 66 maps varying from 0.13 to 2.4 Mbp. At least 2.6% of the genome comprises highly repetitive repeat regions, and 7.4% exhibits repetitive regions barren of labels. The 66 putative chromosomes identified are likely diploid. However, 20 of these maps contained regions of up to 1.25 Mbp of homology to at least one other map, suggestive of widespread segmental duplication or an ancient hybridization event that resulted in a genome with significant redundancy. Assembled genomes of these parasites closely reflect their phylogenetic relationships and give a greater context for understanding their divergent lifestyles. Genome mapping provides insight on the genomic evolution of these parasites.
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Gilchrist, Derek S. "Structure and mechanism of DNA gyrase from divergent bacterial species." Thesis, University of Liverpool, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.484289.
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McCullagh, Bonnie. "Sequence evolution among divergent mitochondrial haplotypes within species of Junonia butterflies." Journal of Asia-Pacific Entomology, 2015. http://hdl.handle.net/1993/31105.
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The New World Junonia butterflies include well-studied model organisms yet their phylogeny remains unresolved by traditional cox1 DNA barcodes. Sixteen Junonia mitochondrial genomes were sequenced using next generation MiSeq technology. Junonia lemonias, an Old World species, has mitochondrial genome features typical of Ditrysian Lepidoptera, and synteny is maintained throughout Junonia. Analysis of Junonia mitogenomes produced a robust phylogeny that was used with biogeographic information to infer that Junonia crossed the Pacific Ocean to invade the New World on 3 separate occasions. Junonia vestina, a high elevation species from the Andes Mountains, shows high altitude adaptation in the mitochondrial protein coding loci atp6, atp8, cox1, cob, nad1, and nad2, with the strongest effects seen in cox1 and nad1. There is some overlap between these genes with human loci that have disease associations with the same amino acid positions which could help elucidate the function of high elevation mutations in J. vestina.February 2016
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Li, Yuanzhi. "Structure et dynamique d'occupation de l'espace fonctionnel à travers des gradients spatiaux et temporels." Thèse, Université de Sherbrooke, 2017. http://hdl.handle.net/11143/11615.
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Les modèles d'occupation de niche au sein des communautés locales, la variabilité spatiale de la biodiversité le long des gradients environnementaux du stress et des perturbations, et les processus de succession végétale sont plusieurs sujets fondamentaux en écologie. Récemment, l'approche basée sur les traits est apparue comme un moyen prometteur de comprendre les processus structurant les communautés végétales et cette approche a même été proposée comme méthode pour reconstruire l'écologie communautaire en fonction des traits fonctionnels. Par conséquent, lier ces thèmes fondamentaux en utilisant une lentille fonctionnelle devrait nous donner un aperçu de certaines questions fondamentales en écologie et sera l'objectif principal de ma thèse. En général, mon projet de doctorat vise à étudier les structures de l'occupation de l'espace fonctionnel dans les gradients spatio-temporels. Plus précisément, l'objectif du chapitre 2 est (i) d'étudier les modèles d'occupation de la niche fonctionnelle en calculant trois métriques clés de niche (le volume total de niche fonctionnelle , le chevauchement des niches fonctionnelles et le volume de niche fonctionnel moyen) des communautés pauvres en espèces aux communautés riches en espèces et (ii) de déterminer le principal facteur de la structure observée de l'occupation de la niche fonctionnelle dans les communautés végétales du monde entier. Dans le chapitre 3, je vise à prédire et à expliquer la variation de la richesse en espèces selon les gradients de stress et de perturbation, en reliant le modèle d'équilibre dynamique et l'occupation de la niche fonctionnelle en fonction du cadre développé au chapitre 2. L'objectif du chapitre 4 est de tester expérimentalement l’application d'une méthode d'ordination CSR évaluée globalement en fonction de trois traits de feuilles (surface foliaire, teneur en matière sèche des feuilles et surface foliaire spécifique) dans les études locales. Enfin, l'objectif du chapitre 5 est de tester expérimentalement les hypothèses qui concilient les points de vue déterministes et historiquement contingents de la succession végétale, en étudiant la variation des divergences taxonomiques et fonctionnelles entre les communautés selon des gradients de stress et de perturbation.
L'étude globale (chapitre 2) est basée sur une collection de 21 jeux de données, couvrant les biomes tropicaux et tempérés, et se compose de 313 communautés végétales représentant différentes formes de croissance. Les études locales (chapitre 3, 4 et 5) sont basées sur le même système expérimental constitué de 24 mésocosmes présentant différents niveaux de stress et de perturbation. L'expérience a commencé en 2009 avec le même mélange de graines de 30 espèces herbacées semées sur les 24 mésocosmes et s'est terminée en 2016. Nous avons permis la colonisation naturelle de graines de la banque commune de graines de sol et de l'environnement pendant la succession de sept ans. Dix traits ont été mesurés sur cinq individus (échantillonnés directement à partir des mésocosmes) par espèce par mésocosme en 2014 (chapitre 3 et 4). Un autre ensemble de traits (16 traits, y compris certains traits qui ne pouvaient pas être mesurés directement dans les mésocosmes), ont été mesurés au niveau de l'espèce (valeurs moyennes des traits) pour les 34 espèces les plus abondantes (certaines espèces disparues dans les mésocosmes) au cours des sept Ans, en les regroupant séparément pour une saison de croissance.
Au chapitre 2, nous avons constaté que les communautés étaient plus diverses en termes fonctionnels (une augmentation du volume fonctionnel total) dans les communautés riches en espèces et que les espèces se chevauchaient davantage au sein de la communauté (augmentation du chevauchement fonctionnel), mais ne divisaient pas plus finement l'espace fonctionnel (aucune réduction du volume fonctionnel moyen). En outre, le filtrage de l'habitat est un processus répandu qui conduit à la caractérisation de l'occupation de niche fonctionnelle dans les communautés végétales. Dans le chapitre 3, nous avons trouvé un modèle similaire d'occupation de niche fonctionnelle sur un système expérimental avec une taille spatiale communautaire constante et un effort d'échantillonnage des traits, qui, avec le chapitre 2, nous a fourni une image plus complète et plus solide de l'occupation de niche fonctionnelle dans les communautés végétales. De plus, nous avons réussi à relier le modèle de l'occupation de la niche fonctionnelle et le modèle d'équilibre dynamique et avons constaté que le filtrage concurrentiel était le processus dominant qui détermine le mode d'occupation de la niche fonctionnelle et la richesse des espèces le long du stress et de la perturbation des gradients. Au chapitre 4, nous fournissons un soutien empirique à une méthode d'ordination CSR calibrée globalement en montrant une relation entre l'abondance relative d'espèces en croissance dans les mésocosmes ayant différents niveaux de fertilité du sol et mortalité indépendante de la densité et leur classification CSR. Au chapitre 5, nous avons montré que la succession d'installations au cours de sept ans dans ces mésocosmes était plus déterministe d'un point de vue fonctionnel, mais plus historiquement contingent d'un point de vue taxonomique et que l'importance relative de la contingence historique a diminué à mesure que l'environnement devenait plus stressé ou perturbé.
En conclusion, les structures de l'occupation de l'espace fonctionnel dans (le volume fonctionnel total, le chevauchement fonctionnel et le volume fonctionnel moyen, les Chapitre 2 et 3) ou entre les communautés locales (dissimilarité fonctionnelle, chapitre 5) sont déterministes plutôt que neutres (ou contingence historique ). Les espèces tolératrices de stress sont plus avantagées dans les mésocosmes moins fertiles tandis que les espèces rudérales sont plus avantagées dans les mésocosmes avec plus de mortalité indépendante de la densité.Abstract : The patterns of niche occupancy within local communities, the spatial variability of biodiversity along environmental gradients of stress and disturbance, and the processes of plant succession are several fundamental topics in ecology. Recently, the trait-based approach has emerged as a promising way to understand the processes structuring plant communities and has even been proposed as a method to rebuild community ecology based on functional traits. Therefore, linking these fundamental themes through a functional lens should give us more insight into some basic questions in ecology and will be the main objective of my thesis. Generally, my PhD project is to investigate the structures of functional space occupancy along both spatial and temporal gradients. Specifically, the objective of Chapter 2 is to investigate the patterns of functional niche occupancy by calculating three key niche metrics (the total functional niche volume, the functional niche overlap and the average functional niche volume) from speciespoor communities to species-rich communities and to determine the main driver of the observed pattern of functional niche occupancy across plant communities worldwide. In Chapter 3, I aim to predict and explain the variation of species richness along gradients of stress and disturbance, by linking the dynamic equilibrium model and functional niche occupancy based on the framework developed in Chapter 2. The objective of Chapter 4 is to experimentally test the application of a globally calibrated CSR ordination method based on three leaf traits (leaf area, leaf dry matter content and specific leaf area) in local studies. Finally, the aim of Chapter 5 is to experimentally test the hypotheses reconciling the deterministic and historically contingent views of plant succession, by investigating the variation of taxonomic and functional dissimilarities between communities along gradients of stress and disturbance. The global study (Chapter 2) is based on a collection 21 trait datasets, spanning tropical to temperate biomes, and consisting of 313 plant communities representing different growth forms. The local studies (Chapter 3, 4 and 5) are based on the same experimental system consisting of 24 mesocosms experiencing different levels of stress and disturbance. The experiment started in 2009 with the same seed mixture of 30 herbaceous species broadcast over the 24 mesocosms and ended in 2016. We allowed natural colonization of seeds from the common soil seed bank and from the surroundings during the seven-year succession. Ten traits were measured on five individuals (sampled directly from the mesocosms) per species per mesocosms in 2014 (Chapter 3 and 4). Another set of traits (16 traits including some traits that were not able to measured directly in the mesocosms) were measured at the species level (species mean traits values) for the 34 most abundant species (some species disappeared in the mesocosms) over the seven years, by regrowing them separately for one growing season. In Chapter 2, we found communities were more functionally diverse (an increase in total functional volume) in species-rich communities, and species overlapped more within the community (an increase in functional overlap) but did not more finely divide the functional space (no decline in average functional volume). Moreover, habitat filtering is a widespread process driving the pattern of functional niche occupancy across plant communities. In Chapter 3, we found a similar pattern of functional niche occupancy on an experimental system with a constant community spatial size and trait-sampling effort, which together with Chapter 2 provided us a more comprehensive and robust picture of functional niche occupancy across plant communities. In addition, we succeeded in linking the pattern of functional niche occupancy and the dynamic equilibrium model and found that habitat filtering was the dominant process determining the pattern of functional niche occupancy and species richness along the gradients stress and disturbance. In Chapter 4, we provide empirical support for a globally calibrated CSR ordination method by showing a relationship between the relative abundance of species growing in mesocosms having different levels of soil fertility and density-independent mortality and their CSR classification. In Chapter 5, we showed that plant succession over seven years in these mesocosms was more deterministic from a functional perspective but more historically contingent from a taxonomic perspective, and that the relative importance of historical contingency decreased as the environment became more stressed or disturbed. In conclusion, the structures of functional space occupancy within (the total functional volume, the functional overlap and the average functional volume; Chapter 2 and 3) or between local communities (functional dissimilarity, Chapter 5) are deterministic rather than neutral (or historical contingency). Stress-tolerators were more favored in high stress communities, while ruderals are more favored in high disturbed mesocosms (Chapter 4).
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Bewley, Marie Suzy. "CFTR from divergent species respond differently to the channel inhibitors CFTRinh-172, glibenclamide, and GlyH-101." Yale University, 2010. http://ymtdl.med.yale.edu/theses/available/etd-05202010-073459/.
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Studies of widely diverse species of a protein are a powerful tool to gain information on the structure and function of the protein. We investigated the response of human, pig, shark and killifish cystic fibrosis trans-membrane conductance regulator (CFTR) to specific inhibitors of the channel: CFTRinh-172, GlyH-101, and glibenclamide. In several expression systems, including isolated perfusions of the rectal gland, primary cell cultures of rectal gland tubules and oocyte expression, we observed fundamental differences in the sensitivity to inhibition by these CFTR blockers. We used primarily two-electrode voltage clamping of cRNA microinjected Xenopus laevis oocytes. In oocyte studies, shark CFTR was insensitive to CFTRinh-172 (maximum inhibition 8 ± 1.4% at 20µM), pCFTR was insensitive to Glibenclamide (maximum inhibition 12.8 ± 4.2% at 200µM), and all species were sensitive to GlyH-101 (maximum inhibition with pCFTR of 80.2 ± 3.6% at 20µM). Shark CFTR was completely insensitive to inhibition by CFTRinh-172 in short circuit current experiments (2.5 ± 0.15 % inhibition of chloride secretion) compared to inhibition with GlyH-101 (56.5 ± 6.56 % inhibition of chloride secretion). Perfusion studies confirmed these results. These experiments demonstrate a profound difference in the sensitivity of different CFTR species to inhibition by CFTR blockers. However, the amino acid residues that have been proposed by site directed mutagenesis studies to be responsible for inhibitor binding are uniformly conserved in all four isoforms studied. Therefore, the differences cannot be explained by simply targeting one amino acid for site-directed mutagenesis. Rather, the potency of the inhibitory actions of CFTRinh-172, Gly-H101 and glibenclamide on the CFTR molecule is dictated by the local environment and the three dimensional structure of residues that form the vestibule and the chloride pore.
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au, p. coulson@murdoch edu, and Peter Coulson. "The biology of three teleost species with divergent life cycle characteristics and their implications for fisheries management." Murdoch University, 2008. http://wwwlib.murdoch.edu.au/adt/browse/view/adt-MU20090324.143252.
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The overall aim of this thesis was to determine the size and age compositions, growth and reproductive biology of Western Blue Groper (Achoerodus gouldii), Blue Morwong (Nemadactylus valenciennesi) and Yellowtail Flathead (Platycepahlus endrachtensis) in south-western Australian waters, in which these three species have divergent life cycle characteristics. As A. gouldii and N. valenciennesi are commercially and recreationally important in coastal waters and P. endrachtensis is one of the most recreationally important species in the Swan River Estuary, these biological data were then used to produce estimates of mortality and spawning stock biomass per recruit for each of these species. The biological data and stock assessment parameters were finally employed comparatively to ascertain whether any of the three species possessed characteristics that would make them particularly susceptible to the effects of fishing and whether there was evidence that any of the species is fully or even overexploited.
Achoerodus gouldii typically uses reefs in protected inshore waters along the coast and around neighbouring islands as a nursery habitat and then, as it increases in size, moves to deeper, offshore reefs, where it spawns between early winter and mid-spring. The maximum total length and age of A. gouldii were 1162 mm and 70 years, the latter being the greatest age by far yet recorded for any species of labrid. However, most growth occurs in the first 20 years of life. Histological and demographic analyses demonstrated that all individuals begin life as females and, after attaining maturity, many become males, i.e. A. gouldii is a monandric protogynous hermaphrodite. The L50 at maturity and sex change were 653 and 821 mm, respectively, which correspond to ages of c. 17 and 37 years, respectively. As sex change took place over a narrower range in lengths (650 to 900 mm) than in ages (15 to 49 years), that change is apparently related more to size than age. Since sex change is typically accompanied by a change from green to blue, body colour can be used as a proxy for determining the length (L50) at which females change to males. von Bertalanffy growth curves fitted to the lengths at age of individuals of each sex of this hermaphroditic species using a novel technique demonstrated that, with increasing age, the lengths of males became increasingly greater than those of females. Thus, at ages 15, 30 and 60 years, the estimated lengths at age of females were c. 600, 670 and 680 mm, respectively, whereas those of males were c. 695, 895 and 975 mm, respectively.
As A. gouldii is very long-lived and sexual maturity, and even more particularly sex change, occur late, this labrid is potentially very susceptible to overfishing. Thus, because the mortality estimates and per recruit analyses indicated that, at present, this species is close to or fully exploited, fisheries managers will need to take a precautionary and watchful approach to managing and thus conserving the stocks of this species.
As with A. gouldii, N. valenciennesi moves to deeper, offshore waters as it increases in size and then matures and spawns in those waters. Although N. valenciennesi has a maximum length of nearly 1 m and thus, like A. gouldii, is moderately large, it has a far shorter life span, i.e. 19 vs 70 years. While female N. valenciennesi does not grow to as large a size as its males (max. lengths = 846 and 984 mm, respectively), the maximum age of both sexes was 19 years. From the growth curves, the females by ages 3, 6 and 10 years havd attained, on average, lengths of 435, 587 and 662 mm, respectively, compared with 446, 633 and 752 mm, respectively, for males. Both sexes grew little after 10 years of age.
Juvenile N. valenciennesi < 400 mm in total length were found exclusively in shallow, coastal waters on the south coast, whereas their adults were abundant in offshore waters of both the south and lower west coasts. The females and males typically mature in offshore waters of the south coast at lengths of c. 600-800 mm and ages of c. 7-9 years. In contrast, the vast majority of females caught in offshore waters of the lower west coast (where they were of a similar length and age range to those in offshore waters on the south coast) became mature at lengths of 400-600 mm and 3-4 years of age. The attainment of maturity by N. valenciennesi at far lesser lengths and ages on the lower west coast than south coast suggests that the former coast provides better environmental conditions for the gonadal maturation and spawning of this species. Furthermore, the contrast between the almost total absence of the juveniles of N. valenciennesi in nearshore waters on the lower west coast and their substantial numbers in comparable waters on the south coast indicates that the larvae of this species produced on the lower west coast are transported southwards to the south coast, where they become juveniles. As spawning occurs between mid-summer and late autumn, the larvae, which spend a protracted period in the plankton, would be exposed, on the lower west coast, to the influence of the southwards-flowing Leeuwin Current at the time when that current is at its strongest.
Although N. valenciennesi is caught by recreational line fishing and commercial gillnet fishing when they are as young as 3-4 years old, they do not become fully vulnerable to these fisheries until they are about 9 years old. Consequently, the individuals of this species can potentially breed over a number of years before they become particularly prone to capture by fishers. Mortality estimates and per recruit analyses suggested that N. valenciennesi in south-western Australia is not currently overfished. A greater resilience to fishing by N. valenciennesi than A. gouldii presumably reflects, in part, its far shorter lifespan, earlier maturity and possession of gonochorism rather than hermaphroditism.
Platycephalus endrachtensis spawns in the Swan River Estuary between late spring and early autumn and completes the whole of its life cycle in this system. Although females attain a far larger length (615 mm) than males (374 mm), females and males were present in each age class. These data, together with a detailed examination of histological sections of a wide size and age range of individuals, demonstrated that this species, unlike some of its relatives, is not a protandrous hermaphrodite, i.e. it does not change from male to female with increasing body size. The combination of the presence of females and males in all age classes and the observation that all of the large number of individuals between 374 and 615 mm were females shows that the far greater length attained by that sex is largely related to its faster growth rate. The fact that females outnumbered males in each age class of P. endrachtensis in which the sample size was substantial, i.e. > 25, with the overall sex ratio being 2.7 females: 1 male, indicate that there has been strong selection for egg production in this species. As the minimum legal length for retention of P. endrachtensis is 300 mm, and relatively few males exceeded this length, the recreational fishery which targets this species is based largely on its females.
The estimates of mortality and results of per recruit analyses provided no evidence that P. endrachtensis is currently overfished. From a management point of view, it is advantageous that the current size limit for this species exceeds the average length at which its females (259 mm) attain maturity. Furthermore, this species appears to be resilient to capture and release.
The data presented in this thesis demonstrate that A. gouldii possesses biological characteristics which make it potentially more prone to the effects of fishing than is the case with either N. valenciennesi or P. endrachtensis. This presumably accounts, at least in part, for the indications that A. gouldii is the only one of these three species that is likely to be close to or at full exploitation.
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Coulson, Peter Graham. "The biology of three teleost species with divergent life cycle characteristics and their implications for fisheries management." Thesis, Coulson, Peter Graham (2008) The biology of three teleost species with divergent life cycle characteristics and their implications for fisheries management. PhD thesis, Murdoch University, 2008. https://researchrepository.murdoch.edu.au/id/eprint/481/.
Full textAbstract:
The overall aim of this thesis was to determine the size and age compositions, growth and reproductive biology of Western Blue Groper (Achoerodus gouldii), Blue Morwong (Nemadactylus valenciennesi) and Yellowtail Flathead (Platycepahlus endrachtensis) in south-western Australian waters, in which these three species have divergent life cycle characteristics. As A. gouldii and N. valenciennesi are commercially and recreationally important in coastal waters and P. endrachtensis is one of the most recreationally important species in the Swan River Estuary, these biological data were then used to produce estimates of mortality and spawning stock biomass per recruit for each of these species. The biological data and stock assessment parameters were finally employed comparatively to ascertain whether any of the three species possessed characteristics that would make them particularly susceptible to the effects of fishing and whether there was evidence that any of the species is fully or even overexploited.
Achoerodus gouldii typically uses reefs in protected inshore waters along the coast and around neighbouring islands as a nursery habitat and then, as it increases in size, moves to deeper, offshore reefs, where it spawns between early winter and mid-spring. The maximum total length and age of A. gouldii were 1162 mm and 70 years, the latter being the greatest age by far yet recorded for any species of labrid. However, most growth occurs in the first 20 years of life. Histological and demographic analyses demonstrated that all individuals begin life as females and, after attaining maturity, many become males, i.e. A. gouldii is a monandric protogynous hermaphrodite. The L50 at maturity and sex change were 653 and 821 mm, respectively, which correspond to ages of c. 17 and 37 years, respectively. As sex change took place over a narrower range in lengths (650 to 900 mm) than in ages (15 to 49 years), that change is apparently related more to size than age. Since sex change is typically accompanied by a change from green to blue, body colour can be used as a proxy for determining the length (L50) at which females change to males. von Bertalanffy growth curves fitted to the lengths at age of individuals of each sex of this hermaphroditic species using a novel technique demonstrated that, with increasing age, the lengths of males became increasingly greater than those of females. Thus, at ages 15, 30 and 60 years, the estimated lengths at age of females were c. 600, 670 and 680 mm, respectively, whereas those of males were c. 695, 895 and 975 mm, respectively.
As A. gouldii is very long-lived and sexual maturity, and even more particularly sex change, occur late, this labrid is potentially very susceptible to overfishing. Thus, because the mortality estimates and per recruit analyses indicated that, at present, this species is close to or fully exploited, fisheries managers will need to take a precautionary and watchful approach to managing and thus conserving the stocks of this species.
As with A. gouldii, N. valenciennesi moves to deeper, offshore waters as it increases in size and then matures and spawns in those waters. Although N. valenciennesi has a maximum length of nearly 1 m and thus, like A. gouldii, is moderately large, it has a far shorter life span, i.e. 19 vs 70 years. While female N. valenciennesi does not grow to as large a size as its males (max. lengths = 846 and 984 mm, respectively), the maximum age of both sexes was 19 years. From the growth curves, the females by ages 3, 6 and 10 years havd attained, on average, lengths of 435, 587 and 662 mm, respectively, compared with 446, 633 and 752 mm, respectively, for males. Both sexes grew little after 10 years of age.
Juvenile N. valenciennesi < 400 mm in total length were found exclusively in shallow, coastal waters on the south coast, whereas their adults were abundant in offshore waters of both the south and lower west coasts. The females and males typically mature in offshore waters of the south coast at lengths of c. 600-800 mm and ages of c. 7-9 years. In contrast, the vast majority of females caught in offshore waters of the lower west coast (where they were of a similar length and age range to those in offshore waters on the south coast) became mature at lengths of 400-600 mm and 3-4 years of age. The attainment of maturity by N. valenciennesi at far lesser lengths and ages on the lower west coast than south coast suggests that the former coast provides better environmental conditions for the gonadal maturation and spawning of this species. Furthermore, the contrast between the almost total absence of the juveniles of N. valenciennesi in nearshore waters on the lower west coast and their substantial numbers in comparable waters on the south coast indicates that the larvae of this species produced on the lower west coast are transported southwards to the south coast, where they become juveniles. As spawning occurs between mid-summer and late autumn, the larvae, which spend a protracted period in the plankton, would be exposed, on the lower west coast, to the influence of the southwards-flowing Leeuwin Current at the time when that current is at its strongest.
Although N. valenciennesi is caught by recreational line fishing and commercial gillnet fishing when they are as young as 3-4 years old, they do not become fully vulnerable to these fisheries until they are about 9 years old. Consequently, the individuals of this species can potentially breed over a number of years before they become particularly prone to capture by fishers. Mortality estimates and per recruit analyses suggested that N. valenciennesi in south-western Australia is not currently overfished. A greater resilience to fishing by N. valenciennesi than A. gouldii presumably reflects, in part, its far shorter lifespan, earlier maturity and possession of gonochorism rather than hermaphroditism.
Platycephalus endrachtensis spawns in the Swan River Estuary between late spring and early autumn and completes the whole of its life cycle in this system. Although females attain a far larger length (615 mm) than males (374 mm), females and males were present in each age class. These data, together with a detailed examination of histological sections of a wide size and age range of individuals, demonstrated that this species, unlike some of its relatives, is not a protandrous hermaphrodite, i.e. it does not change from male to female with increasing body size. The combination of the presence of females and males in all age classes and the observation that all of the large number of individuals between 374 and 615 mm were females shows that the far greater length attained by that sex is largely related to its faster growth rate. The fact that females outnumbered males in each age class of P. endrachtensis in which the sample size was substantial, i.e. > 25, with the overall sex ratio being 2.7 females: 1 male, indicate that there has been strong selection for egg production in this species. As the minimum legal length for retention of P. endrachtensis is 300 mm, and relatively few males exceeded this length, the recreational fishery which targets this species is based largely on its females.
The estimates of mortality and results of per recruit analyses provided no evidence that P. endrachtensis is currently overfished. From a management point of view, it is advantageous that the current size limit for this species exceeds the average length at which its females (259 mm) attain maturity. Furthermore, this species appears to be resilient to capture and release.
The data presented in this thesis demonstrate that A. gouldii possesses biological characteristics which make it potentially more prone to the effects of fishing than is the case with either N. valenciennesi or P. endrachtensis. This presumably accounts, at least in part, for the indications that A. gouldii is the only one of these three species that is likely to be close to or at full exploitation.
32
Coulson, Peter Graham. "The biology of three teleost species with divergent life cycle characteristics and their implications for fisheries management." Coulson, Peter Graham (2008) The biology of three teleost species with divergent life cycle characteristics and their implications for fisheries management. PhD thesis, Murdoch University, 2008. http://researchrepository.murdoch.edu.au/481/.
Full textAbstract:
The overall aim of this thesis was to determine the size and age compositions, growth and reproductive biology of Western Blue Groper (Achoerodus gouldii), Blue Morwong (Nemadactylus valenciennesi) and Yellowtail Flathead (Platycepahlus endrachtensis) in south-western Australian waters, in which these three species have divergent life cycle characteristics. As A. gouldii and N. valenciennesi are commercially and recreationally important in coastal waters and P. endrachtensis is one of the most recreationally important species in the Swan River Estuary, these biological data were then used to produce estimates of mortality and spawning stock biomass per recruit for each of these species. The biological data and stock assessment parameters were finally employed comparatively to ascertain whether any of the three species possessed characteristics that would make them particularly susceptible to the effects of fishing and whether there was evidence that any of the species is fully or even overexploited.
Achoerodus gouldii typically uses reefs in protected inshore waters along the coast and around neighbouring islands as a nursery habitat and then, as it increases in size, moves to deeper, offshore reefs, where it spawns between early winter and mid-spring. The maximum total length and age of A. gouldii were 1162 mm and 70 years, the latter being the greatest age by far yet recorded for any species of labrid. However, most growth occurs in the first 20 years of life. Histological and demographic analyses demonstrated that all individuals begin life as females and, after attaining maturity, many become males, i.e. A. gouldii is a monandric protogynous hermaphrodite. The L50 at maturity and sex change were 653 and 821 mm, respectively, which correspond to ages of c. 17 and 37 years, respectively. As sex change took place over a narrower range in lengths (650 to 900 mm) than in ages (15 to 49 years), that change is apparently related more to size than age. Since sex change is typically accompanied by a change from green to blue, body colour can be used as a proxy for determining the length (L50) at which females change to males. von Bertalanffy growth curves fitted to the lengths at age of individuals of each sex of this hermaphroditic species using a novel technique demonstrated that, with increasing age, the lengths of males became increasingly greater than those of females. Thus, at ages 15, 30 and 60 years, the estimated lengths at age of females were c. 600, 670 and 680 mm, respectively, whereas those of males were c. 695, 895 and 975 mm, respectively.
As A. gouldii is very long-lived and sexual maturity, and even more particularly sex change, occur late, this labrid is potentially very susceptible to overfishing. Thus, because the mortality estimates and per recruit analyses indicated that, at present, this species is close to or fully exploited, fisheries managers will need to take a precautionary and watchful approach to managing and thus conserving the stocks of this species.
As with A. gouldii, N. valenciennesi moves to deeper, offshore waters as it increases in size and then matures and spawns in those waters. Although N. valenciennesi has a maximum length of nearly 1 m and thus, like A. gouldii, is moderately large, it has a far shorter life span, i.e. 19 vs 70 years. While female N. valenciennesi does not grow to as large a size as its males (max. lengths = 846 and 984 mm, respectively), the maximum age of both sexes was 19 years. From the growth curves, the females by ages 3, 6 and 10 years havd attained, on average, lengths of 435, 587 and 662 mm, respectively, compared with 446, 633 and 752 mm, respectively, for males. Both sexes grew little after 10 years of age.
Juvenile N. valenciennesi < 400 mm in total length were found exclusively in shallow, coastal waters on the south coast, whereas their adults were abundant in offshore waters of both the south and lower west coasts. The females and males typically mature in offshore waters of the south coast at lengths of c. 600-800 mm and ages of c. 7-9 years. In contrast, the vast majority of females caught in offshore waters of the lower west coast (where they were of a similar length and age range to those in offshore waters on the south coast) became mature at lengths of 400-600 mm and 3-4 years of age. The attainment of maturity by N. valenciennesi at far lesser lengths and ages on the lower west coast than south coast suggests that the former coast provides better environmental conditions for the gonadal maturation and spawning of this species. Furthermore, the contrast between the almost total absence of the juveniles of N. valenciennesi in nearshore waters on the lower west coast and their substantial numbers in comparable waters on the south coast indicates that the larvae of this species produced on the lower west coast are transported southwards to the south coast, where they become juveniles. As spawning occurs between mid-summer and late autumn, the larvae, which spend a protracted period in the plankton, would be exposed, on the lower west coast, to the influence of the southwards-flowing Leeuwin Current at the time when that current is at its strongest.
Although N. valenciennesi is caught by recreational line fishing and commercial gillnet fishing when they are as young as 3-4 years old, they do not become fully vulnerable to these fisheries until they are about 9 years old. Consequently, the individuals of this species can potentially breed over a number of years before they become particularly prone to capture by fishers. Mortality estimates and per recruit analyses suggested that N. valenciennesi in south-western Australia is not currently overfished. A greater resilience to fishing by N. valenciennesi than A. gouldii presumably reflects, in part, its far shorter lifespan, earlier maturity and possession of gonochorism rather than hermaphroditism.
Platycephalus endrachtensis spawns in the Swan River Estuary between late spring and early autumn and completes the whole of its life cycle in this system. Although females attain a far larger length (615 mm) than males (374 mm), females and males were present in each age class. These data, together with a detailed examination of histological sections of a wide size and age range of individuals, demonstrated that this species, unlike some of its relatives, is not a protandrous hermaphrodite, i.e. it does not change from male to female with increasing body size. The combination of the presence of females and males in all age classes and the observation that all of the large number of individuals between 374 and 615 mm were females shows that the far greater length attained by that sex is largely related to its faster growth rate. The fact that females outnumbered males in each age class of P. endrachtensis in which the sample size was substantial, i.e. > 25, with the overall sex ratio being 2.7 females: 1 male, indicate that there has been strong selection for egg production in this species. As the minimum legal length for retention of P. endrachtensis is 300 mm, and relatively few males exceeded this length, the recreational fishery which targets this species is based largely on its females.
The estimates of mortality and results of per recruit analyses provided no evidence that P. endrachtensis is currently overfished. From a management point of view, it is advantageous that the current size limit for this species exceeds the average length at which its females (259 mm) attain maturity. Furthermore, this species appears to be resilient to capture and release.
The data presented in this thesis demonstrate that A. gouldii possesses biological characteristics which make it potentially more prone to the effects of fishing than is the case with either N. valenciennesi or P. endrachtensis. This presumably accounts, at least in part, for the indications that A. gouldii is the only one of these three species that is likely to be close to or at full exploitation.
33
Hollar, Amy Rebecca. "Cloning and developmental expression of thyroid hormone receptors from three species of spadefoot toads with divergent larval period durations." University of Cincinnati / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1291050160.
Full text
34
Marjanović, David. "Phylogeny of the limbed vertebrates with special consideration of the origin of the modern amphibians." Paris 6, 2010. http://www.theses.fr/2010PA060690.
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Zetterquist, Henrik. "The use of molecular techniques for identification of genetic divergence in transplantation : with special reference to MHC genes and HLA typing /." Stockholm, 1998. http://diss.kib.ki.se/1998/91-628-3267-0/.
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Buyukates, Yesim. "Characterization of the plankton community in the lower Rincon Delta: Investigations regarding new approaches to management." Diss., Texas A&M University, 2003. http://hdl.handle.net/1969.1/1312.
Full textAbstract:
In light of increasing harmful algal blooms and the need to protect human health and aquatic resources, proactive management approaches merit further study. For this purpose I conducted field samplings to characterize plankton community composition and laboratory experiments to test some approaches to new management schemes in the lower Rincon Delta. On site measurements and microscopic analysis showed that environmental parameters and plankton community composition varied considerably among sampling stations and sampling dates. A recent modeling study suggested that manipulation of freshwater inflow to estuaries might prevent phytoplankton blooms and enhance secondary productivity. To test this theory I conducted three semi-continuous design and flow-through incubation design experiments using natural plankton assemblages. I investigated the effect of two different pulsing regimes of inflow and nutrient loading on zooplankton densities, and phytoplankton biomass and diversity. Despite differences in zooplankton structure and phytoplankton community composition between the two experiment designs, the results confirmed that pulsed inflows might alter plankton dynamics. My findings showed that 3-day pulse treatments consistently supported greater zooplankton densities and higher phytoplankton species diversity when compared to 1-day pulse treatments. In addition, accumulation of phytoplankton biovolume remained low during 3-day pulse treatments. Differences in zooplankton performance between 3-day pulse and 1-day pulse inflow treatments were likely due to the ability of phytoplankton to uptake and store greater amounts of nutrients under conditions of 3-day pulse inflow. This resulted in food of higher quality for zooplankton, and might have supported greater zooplankton population growth rates. Additionally, in an attempt to understand the mechanisms leading to high biodiversity in aquatic ecosystems, I built a resource-storage model and studied the effects of resource-storage on competition of multiple phytoplankton species on multiple abiotic resources. I compared this model with a well-established multi-species competition model. My results showed that for certain species combinations a resource-storage-based model can generate dissimilar outcomes when compared to a model without resource-storage.
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梁博凱. "Postglacial population bottleneck and species divergence in Rhododendron pseudochrysanthum species complex." Thesis, 2011. http://ndltd.ncl.edu.tw/handle/42163889133214074538.
Full textAbstract:
碩士國立臺灣師範大學
生命科學研究所
99
Rhododendron pseudochrysanthum species complex constitutes of R. pseudochrysanthum, R. morii, R. rubropunctatum and R. hyperythrum. Species in the R. pseudochrysanthum complex are all endemics to Taiwan and they are morphologically similar. Previous studies revealed that R. rubropunctatum was the origin of this species complex in which Pleistocene range expansion was found and population fragmentation occurred since the last glacial maximum. Aims of this study were to gather information to trace the effect of bottleneck that resulted in reduction of effective population size and genetic structure. Based on expressed sequenced tag (EST)-derived simple sequence repeats (SSRs) marker system, genotyping data of 27 EST-SSRs were analyzed and population genetic parameters were estimated. Severe bottleneck was found in the R. rubropunctatum populations and high level of genetic divergence in comparison with populations of other species in the R. pseudochrysanthum complex. In addition, high level of genetic divergence is associated with local climatic factors and resulted in local adaptation.
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Chou, Shih-Yin, and 周詩縈. "Genetic divergence between Keteleeria species (Pinaceae) using multilocus analysis." Thesis, 2014. http://ndltd.ncl.edu.tw/handle/fnzm7e.
Full textAbstract:
碩士國立中山大學
生物科學系研究所
102
Speciation is an important issue in evolutionary biology and species complex is a good model to test the pattern of speciation. Keteleeria (Pinaceae) is an Asian gymnosperm genus and restricted to subtropical to north tropical hill regions of South China, Taiwan, and Hainan. Fossil records have been wild distributed in Northern Hemisphere. Current distribution indicates that apparently affected by Quaternary climate shifts and almost extinction. The definition of species is difficult to consensus because taxonomists had different opinions based on morphological similarities. In this study, we build a transcriptome based on high-throughput Illumina RNA-seq sequencing technique using K. davidiana var. formosana as target taxa. We surveyed sequence variation for 4 chloroplast (cp) DNA fragments, and 27 nuclear genes among 91 individuals sampled from 12 taxa of Keteleeria. The assignment test based on STRUCTURE show the best clustering was assumed at K=2, DE group in Yunnan and other species include in FP group. The RASP based on S-DIVA indicates the divergence because vicariance events and IMa suggesting low level of gene flow (2.7-8.7 ∗ 10-8) among group. The divergence time estimates c. 3.3-0.5 mya, a timescale with recent uplift of Qinghai-Tibet Plateau and the formation Hengduan Mountains. Pleistocene glaciation in Hengduan Mountains is relatively warm and rainy, became a refuge of DE group. FP group associated with the extinctive species of North America, and the refugia of glaciation located in Guizhou and Guangxi that have high genetic diversity of species. The RASP analysis inferred species expansion from west to east and north to south in southeast China. Keteleeria davidiana var. formosana in Taiwan and K. hainanensis in Hainan have unique genotype in assignment test respectively. Two species suggesting low level of gene flow (1.55-9.3 ∗ 10-10, 26-1.6 ∗ 10-10), small effective population size (70-270 k, 12-6 k), diverged c. 70 and 18 ka with FP group by IMa and the vicariance events inferred by RASP. The period of continental shelf was almost free of marine influence, these islands provided refugia for northern species that migrated south during glacial periods. Keteleeria revealed species evolving through glacial cycles and caused separation, migration, and extinction as well as accelerating speciation.
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Li, Ying, and 黎罃. "Genetic divergence between Tsuga species (Pinaceae) using multilocus analyses." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/yzpkk7.
Full textAbstract:
碩士國立中山大學
生物科學系研究所
106
Tsuga (Pinaceae) is an important coniferous taxon in the subalpine zone. The fossil record of Tsuga indicates that this genus was distributed throughout North America and Eurasia during the Late Cretaceous to the Plio-Pleistocene. However, currently, Tsuga exhibits a disjunctive distribution pattern across North America through East Asia island arcs and continental China. A total of 9 extant species recognized in Farjon (1990), including Tsuga chinensis (Franchet) E. Pritzel, Tsuga dumosa (D. Don) Eichler, Tsuga chinensis var. forrestii (Downie) Silba, Tsuga diversifolia (Maxim.) Mast, Tsuga sieboldii Carrière, Tsuga canadensis (Linnaeus) Carrière, Tsuga caroliniana Engelmann, Tsuga heterophylla (Rafinesque) Sargent, Tsuga mertensiana (Bongard) Carrière. In addition, we also sampled Tsuga chinensis var. formosana (Hayata) H.L.Li & H.Keng and Tsuga ulleungensis from Taiwan and Ullung Island, respectively; due to the unique distribution pattern such as vicariance. In the present study, we established a functional genomic database from Tsuga chinensis var. formosana then designed primers to amplified DNA sequences from 89 individuals which were sampled from 11 species. Eventually, we successfully conduct several amplification, including two mitochondria spacers, four chloroplast spacers and sixteen nuclear loci. Our result demonstrated that Tsuga has low level of genetic diversity, indicated recent divergence of Tsuga and do not have enough time to accumulate mutations in the population. In STURCTURE assignment test based on chloroplast and nuclear loci show the best clustering at K=2 and K=7, North America, China, East Asia island have difference special genetic ingredient. The most recently common ancestor of Tsuga was at 90 mya, which is corresponding to the evidence of older Tsuga fossil (90 mya). Using RASP analysis to inferred events of dispersal, vicariance and extinction that from common ancestor nodes. The results suppose Tsuga may originate from North America that spread from Western North America to Eastern North America. Asia regional species common ancestors were from Eastern North America, that spread to two different path: one was proceed to North Japan and formatted Tsuga diversifolia , the other was proceed to China and formatted the Tsuga dumosa / Tsuga chinensis var. formosana common ancestor. The path in China spread from Eastern China to Western China even arrive at Taiwan and South Japan. The Tsuga ulleungensis was dispersal by Tsuga diversifolia from North Japan to Korea and they had closely relationship showed on the phylogenetic tree and assignment test. Overview the results of divergence time analysis and fossil record, it can be inferred that Tsuga may have originated from North America and dispersed to Asia through the Bering Corridor. The fossil record proved the Tsuga widely distributed in Europe in the pass, years later the Tsuga became extinct cause by not suitable temperature and humidity for survival (1.8 mya). The disjunct distribution of Tsuga can be a result of speciation that can be resolved by multiple speciation models.
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Barkan, Charlotte Barkan. "Evolution of Xenopus Vocal Patterns: Retuning a Hindbrain Circuit During Species Divergence." Thesis, 2017. https://doi.org/10.7916/D8862TQP.
Full textAbstract:
Circuits underlying motor patterns of closely related species provide an ideal framework in which to study how evolution shapes behavioral variation. Male African clawed frogs (Xenopus and Silurana) advertisement call to attract female mates and silence male rivals. Males of each species produce a unique vocal pattern that serves as a species-identifier. Xenopus laevis is the most well-studied species in terms of its vocal behavior and underlying anatomy and physiology. The clade that includes X. laevis, or X. laevis senso lato, also includes 3 other species that diverged ~8.5 million years ago. All 4 of these species produce advertisement calls that include fast trills – trains of fast rate (~60 Hz) sound pulses. However, their calls differ substantially between species in measures of trill duration and period. I examined the premotor circuit underlying vocal patterning in three of these species: X. laevis, X. petersii, and X. victorianus. I used extracellular recordings to find that a premotor nucleus, DTAM, which is part of the vocal central pattern generator, is the likely source of species-variation of vocal patterns. Species-specific trill duration and period are intrinsic to the region of the hindbrain that includes DTAM. Next, I used blind whole-cell patch recordings in DTAM of X. laevis and X. petersii to examine the cells that encode trill duration and period. I identified homologous populations of premotor vocal cells in both species that code for trill duration and period in a species-specific manner. Together, these results support an autonomous role of the DTAM circuit for generation of species variation in call duration and period.
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Ribeiro, Ana Luisa Emauz Leite. "Is empathy consistent across species? Exploring factors that may explain convergence/divergence." Doctoral thesis, 2017. http://hdl.handle.net/10071/14592.
Full textAbstract:
PsycINFO Codes: 2360 Motivation and Emotion; 2560 PsychophysiologyThe aim of this study was to understand the relationship between human-directed empathy (HDE) and animal directed empathy (ADE), an under known and investigated relationship. Previous studies indicated a weak association, and there was scarce information about the factors that could explain one and the other forms of empathy as well as their convergence or divergence. Chapter 1 reviews the literature on HDE and ADE, how they develop, relate, and what factors influence them together or separately. Chapter 2 presents the study of the adaptation and validation for the Portuguese population of the Animal Empathy Scale. Chapter 3 reports an investigation in which predictors of HDE and ADE were explored in two populations (Lusophone and Anglo-Saxon), showing that the two forms of empathy are influenced by different predictors. The study also confirms the existence of a weak correlation between HDE and ADE. Chapter 4 reports an experimental study with presentation of emotional stimuli in videos, where participants showed some capacity to correctly identify the emotional valence in distinct species (humans, chimpanzees and dogs), also exhibiting an electromyographic activity congruent with the emotions exhibited in the stimuli of the target species, especially when it came to dogs and humans. Finally, Chapter 5 discusses the results, their limitations and contexts, seeking to provide clues for future studies on the one hand, and also to draw some guidelines for the practice of those who work with animals.
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Papenrecht, Elisabeth Aletta van. "Nucleotide and functional divergence in esterase 6 amongst sibling species of drosophila." Phd thesis, 1995. http://hdl.handle.net/1885/142357.
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Hei, Yu Shu, and 游淑惠. "Genetic divergence of Acanthopagrus berda species complex in the surrounding waters of Taiwan." Thesis, 2000. http://ndltd.ncl.edu.tw/handle/31553840473657161744.
Full textAbstract:
碩士國立臺灣師範大學
生物研究所
88
The genetic structure among the Acanthopagrus berda from surrounding waters of Taiwan is carried out by isozyme electrophoresis. The available inbreeding coefficient (Fis) of 0.374, and fixed index (Fst) of 0.410, indicate there are significant differentiation among the overall samples examined. The interpopulational genetic distance estimated was far greater than that between species, when the A. schlegeli who used as an outgroup. Genotypes of most indivuals examined were found to have a strong linkage effect with loci ADH*、 G6PDH*、 GPI-A*、 sMDH*. The above four loci were fixed differently between samples of Dapong bay and those from other localities, due to reproduction isolation. Thus the above mentioned typical Dapong sample(= A. sp.) can be considered as a valid cryptic species. With the exclusion of Acanthopagrus sp,the remaining 336 real berda from 7 localities, scored three polymorphic loci(P95) (sAAT* 、GPI-B*、IDH-2*), with a redution of fixed index(Fst) to 0.017, indicating an extremely low level of differentiation (P=0.227>0.05), among them Chi-square contigency table analysis showed the genetic structure among different samples was homogenous, suggestion that there are strong gene flow among the samples .
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Tseng, Wan-Hsuan, and 曾婉瑄. "Speciation and Genetic Divergence of Amentotaxus argotaenia Species Complex based on Multilocus Analysis." Thesis, 2015. http://ndltd.ncl.edu.tw/handle/90553790097363838866.
Full textAbstract:
碩士國立屏東科技大學
森林系所
103
Amentotaxus, representing an ancient lineage of relic species, is a gymnosperm genus. Amentotaxus argotaenia species complex, including A. argotaenia Pilg., A. formosana H. L. Li, A. yunnanensis H. L. Li and A. poilanei (Ferr#westeur042# &; Rouane) D. K. Ferguson, was distributed in the Southeast Asia. In this study, we used multilocus (8 organelle loci, and 32 nuclear loci) to assess phylogenies and speciation models of this species complex. Amentotaxus formosana (π=0.0245；θ=0.0248) and A. yunnanensis (π=0.0215；θ=0.0230) exhibited the highest nucleotide diversity, and higher levels reflected features of a refugium. Only 3 genes tree showed the consistent topology with species tree, and most gene trees displayed various tree topologies. The incongruence of gene tree and species tree resulted from ancestral polymorphism or gene flow. IMa2 was used to estimate effective population size and gene flow of this species complex. The results indicated effective population sizes of ancient and extant populations have similar pattern, ancient gene flow is higher than recent gene flow. We suggested that allopatric speciation is the predominant mode for A. formosana. However, high levels of ancient and recent gene flow were detected among A. argotaenia, A. yunnanensis and A. poilanei and effective population size for extant population was lower than ancient population for these species. Both results suggested that parapatric speciation is likely for these species.
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Smith, Geneviève Kathleen. "The coexistence of ecologically similar species." 2013. http://hdl.handle.net/2152/23186.
Full textAbstract:
The biological diversity on planet Earth is astounding. Understanding the origins of this diversity, and how it is maintained, are the twin goals of ecology and evolutionary biology. An early and oft-repeated insight in this investigation is that that similar organisms cannot coexist indefinitely. Theory predicts that individuals and species will compete for limited resources and whichever has even a slight advantage will drive all others extinct in a process known as ‘competitive exclusion’. By diversifying, species avoid competition, thereby ‘stabilizing’ their coexistence. Yet natural systems often display levels of diversity that are surprisingly high, given this theory and investigations of how the similarity of coexisting species is maintained have received much less attention. Using a combination of field studies and experiments I demonstrate that highly similar species of freshwater amphipods may compete for resources without resulting in competitive exclusion. These findings suggest that there exist a range of interactions among Hyalella amphipods, ranging from strong stabilizing effects due to ecological trade-offs, to weakly stabilizing effects, to a total lack of stabilizing effects among various pairs of species in this system. These findings demonstrate how the relative strength of stabilizing forces may vary among coexisting species.
Although much effort has been dedicated to enumerating and classifying the ways in which ecological and evolutionary forces promote diversity among species, there has been far less attention paid to mechanisms such as convergent evolution, habitat filtering, competition for non-substitutable resources, and non-ecological speciation, among others. I surveyed current theory that may explain the high levels of similarity among species often found in natural systems. I describe how several ecological and evolutionary mechanisms may operate to promote the coexistence of similar species and present results from new theoretical combinations of mechanisms to demonstrate how they may further act in concert with one another.text
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Chen, Kun-Mu, and 陳琨木. "Phylogeography of Cephalotaxus inferred from SSR loci: insights into species divergence and genetic diversity." Thesis, 2019. http://ndltd.ncl.edu.tw/handle/m8arn5.
Full textAbstract:
碩士國立中山大學
生物科學系研究所
107
The existing species of Cephalotaxus (Cephalotaxaceae) are mainly distributed in East Asia. In the fossil evidence, it can be inferred that the rough inhabited the Russian Far East during the Cretaceous period to the Pliocene, and migrated to the south during the Oligocene, and finally extended to Yunnan, Guangxi, and Japan in the Miocene. In this study, four species and three variants of Cephalotaxus fortunei, C. harringtonii, C. harringtonii var. nana, C. harringtonii var. wilsoniana, C. oliveri, C. hainanensis and C. harringtonii var. koreana were used, for a total of 360 individuals, and 20 polymorphic microsatellite loci were used for experimental and genetic analyses. Genetic analysis showed that the heterozygous observations (HO=0-0.79) were smaller than the heterozygous expected values (HE =0.45-0.90). Results of AMOVA showed that the group of genetic variation are among populations within species (68.82%) existence, and all of the populations had significant genetic differentiation (FST=0.107, P<0.01), significant inbreeding (FIS=0.771, P<0.01), and all ethnic groups significantly deviated from the Hardy-Weinberg equilibrium (P<0.001). Moreover, the IMa3 analysis result indicated that the effective population size of the ethnic group (CO, HN, CN) in East Asia (303-40350) and the population of Japan and its variants (SJP, NJP, KC, TW) (92-12292) were greater than the size of ancestral population (23-3086). It also demonstrated that the effective population size of the ethnic group (CO, HN, CN) in East Asia (303-40350) and the population of Japan and its variants (SJP, NJP, KC, TW) (92-12292) had expanded. Futhermore, the results of STRUCTURE analysis was K=5 which indicated that Japan (SJP) had the same genetic grouping as its Taiwan (TW) variant and nana (NJP) variant. The Korean variant had no identical genotype, which could be used to identify that Korean varieties should be classified differently from the Japanese species and it also could be used as a basis for the future Korean variants to move out of this taxonomic group.
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Ho, Chuan-Wen, and 何瓊紋. "The sequence divergence of mitochondrial COI gene indicate a sibling species in Octopus marginatus (Cephalopoda: Octopodidae) from Taiwan." Thesis, 2001. http://ndltd.ncl.edu.tw/handle/92302773786884270249.
Full textAbstract:
碩士國立臺灣大學
海洋研究所
89
Abstract Sibling species are relatively common among major marine taxa, and the failure in diagnosing sibling species is often caused by lack of effective genetic markers. In this study, we examine the sequence divergence and molecular evolution of the mitochondrial cytochrome c oxidase subunit I (mtCOI) gene in octopods, and diagnose the relationship among Octopus marginatus and its morphologically similar species, O. cf. marginatus. The analysis of phylogenetic relationship includes O. aegina from the same species complex, and sequences from Genbank (O. tetricus, Hapalochlaena maculosa [Octopodinae], Graneledone verrucosa [Graneledoninae], Vitreledonella richardi [Vitreledonellidae] as an outgroup). Analysis of transitional (ts) and transversional (tv) substitutions at three codon positions of the mtCOI gene among Octopus (657 bp) and other genera show a saturated pattern (ts/tv<1) at the level above genera, but not between species (ts/tv>2), which suggests that the mtCOI gene is suitable for reconstructing species phylogeny of Octopus. Reconstructing the phylogenetic tree by maximum parsimony, neighbor joining, and maximum likelihood methods indicated distinct genetic differentiation between O. marginatus and O. cf. marginatus. The sequence divergence (9.44%) reaches up to species level. After translating mtCOI DNA sequences to amino acid sequences, it also has one substitution between O. marginatus and O. cf. marginatus. Based on the mtCOI phylogeny the sibling status of the above two taxa is supported, indicating the existence of a new species of Octopus.
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Rego, Carla José Azevedo. "Evolutionary divergence between two closely related species: Drosophila madeirensis and D. subobscura : quantitative genetic differentiation, reproductive barriers and evolutionary potential." Doctoral thesis, 2007. http://hdl.handle.net/10451/1680.
Full textAbstract:
Tese de doutoramento em Biologia (Biologia Evolutiva), apresentada à Universidade de Lisboa através da Faculdade de Ciências, 2008Speciation and species differentiation are very important issues in Evolutionary Biology. This thesis focuses several aspects related with the differentiation between two closely related species, Drosophila madeirensis and Drosophila subosbcura, namely the contribution of additive and non-additive genetic effects to that differentiation, the contribution of assortative mating to their reproductive isolation, the analysis of hybrid developmental problems expressed as higher fluctuating asymmetry and their underlying causes (developmental noise), and the implications of species differentiation in terms of adaptation to a novel, common environment. The results indicate that negative dominance and epistasis are both involved in the genetic differentiation between these species. Both species present assortative mating, conspecific matings being more likely. Furthermore, the two reciprocal cross directions apparently present different reproductive barriers. In the cross involving D. madeirensis females the barrier is mostly prezygotic, with mating being hard to observe, however, this cross direction yields a high number of hybrids with an even sex-ratio. On the other hand, mating in the reciprocal cross is easy to observe but produces fewer hybrids with a male-biased sex ratio. The analysis comparing fluctuating asymmetry levels between hybrids and parental species indicates that, although hybridization disrupts developmental buffering, hybrid females presenting higher asymmetry, this disruption does not reflect higher developmental noise, as fluctuating asymmetry levels are similar to parental species. The results comparing species differences in life history traits and evolutionary dynamics indicate that these closely related species differ in the adaptation to new conditions (captivity). These findings have important implications for several fields, namely Evolutionary Biology, Speciation, Development and Conservation, which are discussed at the end of this thesis.
FCT (PhD Fellowship: PRAXIS XXI/BD/21479/99)
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Lemmon, Alan Richard 1976. "Analytical, computational, and statistical approaches to studying speciation." Thesis, 2007. http://hdl.handle.net/2152/3324.
Full textAbstract:
Two of the most challenging goals of evolutionary biology are to reconstruct the evolutionary relationships among all extant species and to understand the process by which new species form. Accomplishing these goals will require accurate computational methods for reconstructing phylogenetic trees, general analytic models of speciation, and powerful statistical tools for studying the process of speciation in natural systems. In the first chapter, I study the effects of improper model assumption on estimates of phylogeny. Using DNA sequence data simulated under a variety of models of sequence evolution, I demonstrate that use of oversimplified models can result in erroneous phylogeny estimates. This result suggests that if the models currently utilized are oversimplified then current estimates of phylogeny may be inaccurate and more complex models need to be developed and employed. In the second and third chapters, I study one process thought to be important in completing the final stages of speciation: reinforcement. Using simulations of a hybrid zone, I show that the process of reinforcement can result in patterns other than reproductive character displacement. I also show that speciation by reinforcement is more likely when the genes involved in reproductive isolation are sex-linked. In the fourth chapter, I develop a statistical method of quantifying the degree of isolation between species undergoing divergence. Using genotype data obtained from natural hybrid zones, this novel method can be used to estimate the fitness of hybrids during different stages of their life cycle. This approach offers a new approach to empirical biologists studying extrinsic postzygotic isolation in natural systems.
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"Structure-Function Study of Telomerase RNA from Evolutionary Disparate Species: Remarkable Divergence in Gross Architecture with the Preservation of Critical Universal Structural Elements." Doctoral diss., 2015. http://hdl.handle.net/2286/R.I.29772.
Full textAbstract:
abstract: Telomerase enzyme is a truly remarkable enzyme specialized for the addition of short, highly repetitive DNA sequences onto linear eukaryotic chromosome ends. The telomerase enzyme functions as a ribonucleoprotein, minimally composed of the highly conserved catalytic telomerase reverse transcriptase and essential telomerase RNA component containing an internalized short template region within the vastly larger non-coding RNA. Even among closely related groups of species, telomerase RNA is astonishingly divergent in sequence, length, and secondary structure. This massive disparity is highly prohibitive for telomerase RNA identification from previously unexplored groups of species, which is fundamental for secondary structure determination. Combined biochemical enrichment and computational screening methods were employed for the discovery of numerous telomerase RNAs from the poorly characterized echinoderm lineage. This resulted in the revelation that--while closely related to the vertebrate lineage and grossly resembling vertebrate telomerase RNA--the echinoderm telomerase RNA central domain varies extensively in structure and sequence, diverging even within echinoderms amongst sea urchins and brittle stars. Furthermore, the origins of telomerase RNA within the eukaryotic lineage have remained a persistent mystery. The ancient Trypanosoma telomerase RNA was previously identified, however, a functionally verified secondary structure remained elusive. Synthetic Trypanosoma telomerase was generated for molecular dissection of Trypanosoma telomerase RNA revealing two RNA domains functionally equivalent to those found in known telomerase RNAs, yet structurally distinct. This work demonstrates that telomerase RNA is uncommonly divergent in gross architecture, while retaining critical universal elements.Dissertation/Thesis
Doctoral Dissertation Molecular and Cellular Biology 2015