Дисертації: "Phylogeography"

1

Montano-Rendon, Mauricio. "Phylogeography of littorinid snails." Thesis, University of Sheffield, 2016. http://etheses.whiterose.ac.uk/13328/.

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Interactions between evolutionary forces such as natural selection, genetic drift and gene flow are complex. Natural selection can lead to parallel formation of phenotypes under similar environmental conditions. Phylogenetic relationships can be inferred from the accumulation of genetic variation caused by genetic drift, regardless of phenotypes. Gene flow between populations can sometimes facilitate the formation of species by natural selection. In this thesis, two groups of marine snails in the diverse subfamily Littorininae were studied. The three rocky-shore species Littorina saxatilis, Littorina arcana and Littorina compressa form one such group, whereas the two sister-species Littoraria cingulata and Littoraria filosa form the other group. Previous studies of the L. saxatilis complex have shown high levels of phenotypic and genetic diversity both at local and broader scales. Previous studies of L. cingulata and L. filosa have found some of the typical signatures of reinforcement. Chapters II and III focused on analysing morphological and genetic variation, respectively, within and among species in the Littorina saxatilis complex from the British Isles. Geometric morphometrics analyses revealed a diversity of shell shape among species, but especially so within L. saxatilis. Shell shape was better explained by environment rather than by geography. Molecular data obtained by high-throughput targeted capture showed the opposite pattern, i.e. genetic variation showed a strong phylogeographic pattern. Chapter IV focused on testing whether reinforcement had contributed towards speciation between Littoraria cingulata and Littoraria filosa. Approximate Bayesian computation analysis supported absence of gene flow between the species in sympatry, suggesting that reinforcement did not contribute towards speciation. However, the results need to be validated and more complex models tested. This thesis highlights the relevance of marine snails in the subfamily Littorininae as model species for addressing a wide range of evolutionary questions. It also provides a wealth of data for many potential follow-up studies.

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2

Haughey, Michael D. "Phylogeography of the Spring Salamander, Gyrinophilus porphyriticus: Historic and Contemporary River System's Influence on Phylogeographic History." Ohio University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1422367075.

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3

Rönkä, N. (Nelli). "Phylogeography and conservation genetics of waders." Doctoral thesis, Oulun yliopisto, 2016. http://urn.fi/urn:isbn:9789526211633.

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Abstract Many waders are in decline, and the number of endangered species and populations is increasing. Their protection and management requires knowledge of both ecological and genetic state of the populations. In this thesis, I studied the distribution-wide genetic variation, structure and phylogeography of the Temminck’s Stint (Calidris temminckii) and Terek Sandpiper (Xenus cinereus) using microsatellites and sequence data from the mitochondrial control region and cytochrome oxidase I gene. I compared these regionally endangered species to other waders with varying evolutionary histories, breeding systems and habitat preferences to examine the levels of genetic variation and structure at different spatial scales. In addition, I studied the genetic structure of the endangered Baltic population of the Southern Dunlin (Calidris alpina schinzii) with microsatellites. I used genetic information in all three study species to determine units for conservation. The Temminck’s Stint and Terek Sandpiper, both not restricted to the Arctic, had low distribution-wide structuring. They also had quite low levels of variation when compared to other species breeding at similar latitudes, indicating reductions in population sizes during past climate changes. Especially the peripheral breeding populations were differentiated and showed signs of inbreeding and genetic drift when compared to the main range. The Temminck’s Stint populations at the Bothnian Bay and Yakutia, and Terek Sandpiper populations in Finland and Belarus, should be treated as separate management units. The broader interspecific comparison of waders suggests that habitat availability, mating system and the extent of philopatry may affect the genetic composition of species. The genetic analyses of the Southern Dunlin indicated strong effects of philopatry and inbreeding throughout the range. Local subpopulations at the Bothnian Bay and in Sweden need to be considered as separate management units. Management efforts at the Baltic should be focused on increasing connectivity and providing large enough breeding habitats for potential immigrants and recruits Tiivistelmä Useat kahlaajapopulaatiot ovat pienentyneet ja uhanalaistuneet maailmanlaajuisesti. Lajien ja populaatioiden ekologiaa ja genetiikkaa on tunnettava, jotta suojelutoimia voidaan kohdistaa oikein. Tutkin väitöskirjassani lapinsirrin (Calidris temminckii) ja rantakurvin (Xenus cinereus) geneettistä rakennetta, muuntelua ja fylogeografiaa levinneisyysalueen laajuisesti mikrosatelliittien ja mitokondrion kontrollialueen ja sytokromioksidaasi I -geenin sekvenssien avulla. Tutkin, mitkä tekijät vaikuttavat geneettisen rakenteeseen ja muunteluun vertaamalla näitä lajeja muihin kahlaajiin, joilla on erilaisia lisääntymisstrategioita, jotka pesivät vaihtelevissa ympäristöissä ja joista monet eroavat toisistaan myös fylogeografialtaan. Lisäksi tutkin Itämeren rannalla pesivän etelänsuosirrin (Calidris alpina schinzii) geneettistä populaatiorakennetta mikrosatelliittien avulla. Käytin geneettistä tietoa hyväksi luonnonsuojeluyksikköjen määrittämisessä kaikille kolmelle tutkimuslajilleni. Lapinsirrin ja rantakurvin fylogeografinen historia oli samankaltainen. Geneettisen muuntelun määrä oli vähäisempää verrattuna muihin, samankaltaisissa ympäristöissä pesiviin kahlaajiin. Molemmat lajit ovat todennäköisesti kärsineet historiallisten ilmaston-muutosten aiheuttamasta populaatioiden pienenemisestä. Erityisesti levinneisyysalueen reunoilla pesivät populaatiot olivat erilaistuneita, ja niissä näkyi sukusiitoksen ja geneettisen satunnaisajautumisen merkkejä. Perämeren ja Jakutian lapinsirri- sekä Valko-Venäjän ja Suomen rantakurvipopulaatioita tulee kohdella erillisinä suojeluyksiköinään. Vertailu muihin kahlaajiin osoitti, että niin pesimä- ja talvehtimisalueiden laajuus kuin lisääntymisstrategiat ja paikkauskollisuus voivat vaikuttaa lajien geneettiseen koostumukseen. Etelänsuosirrin geneettiset analyysit paljastivat merkkejä sukusiitoksesta, joita paikkauskollisuus ja populaatioiden pienuus ovat voimistaneet. Perämeren ja Ruotsin populaatioita tulee kohdella erillisinä suojeluyksiköinään. Suojelutoimet on kohdistettava tarpeeksi suurien, hyvälaatuisten pesimäpaikkaverkostojen ylläpitämiseen

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4

Kvist, L. (Laura). "Phylogeny and phylogeography of European Parids." Doctoral thesis, University of Oulu, 2000. http://urn.fi/urn:isbn:9514255364.

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Abstract Mitochondrial DNA sequences were used to study the phylogeny, population structure and colonisation history of Parus species. The phylogenetic relationships of seven European and three American species were examined by sequencing a part of the cytochrome b gene. Phylogenetically the closest species were the great tit (Parus major) and the blue tit (P. caeruleus). Subgenus Poecile was divided into two clades, one consisting of the Siberian tit (P. cinctus), the Carolina chickadee (P. carolinensis) and the Black-capped chickadee (P. atricapillus) and the other consisting of the marsh tit (P. palustris) and the willow tit (P. montanus). The coal tit (P. ater) and the crested tit (P. cristatus) did not group with any of the species studied. The population structure and the colonisation history of the willow tit, the great tit and the blue tit were examined by using control region sequences. The results suggest that the historical effective population size in the willow tit has been large and not contracted by the last ice age. Current gene flow must also be extensive as no population structuring was detected. No population structuring was evident either in the great tit and the populations showed distinctive signs of a recent population expansion. The patterns of genetic variation probably reflect a population bottleneck during the ice age, and a recolonisation of the European continent thereafter, presumably from a refugium situated in the Balkans. Two maternal lineages were found in the blue tit. The southern lineage was restricted to the Iberian peninsula whereas the northern lineage was detected from all the populations. The colonisation history has been similar to the one suggested for the great tit. The southern lineage, however, may have survived the ice age in a different refugium in the Iberian peninsula and was not as successful as the northern lineage in colonising available regions when the ice retreated. Both, the blue tit and the great tit have continued to expand their distribution northwards during this century and gene flow plays an important role in homogenising the populations.

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5

Kuo, Hao-Chi. "Phylogeography and diversification of Taiwanese bats." Thesis, Queen Mary, University of London, 2012. http://qmro.qmul.ac.uk/xmlui/handle/123456789/8493.

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Gene flow is a central evolutionary force that largely determines the level of differentiation among populations of organisms and thus their potential for divergence from each other. Identifying key factors that influence gene flow among populations or closely related taxa can thus provide valuable insights into how new species arise and are maintained. I undertook a comparative study of the factors that have shaped range-wide intraspecific differentiation in four related and broadly co-distributed Taiwanese bat species of the genera Murina and Kerivoula. Bats were sampled from sites across Taiwan and sequenced at two mitochondrial genes as well as genotyped at newly developed and/or existing multi-locus microsatellite markers. To improve phylogeographic inference of existing patterns of population genetic structure, I undertook spatial distribution modeling of the focal species at both the present time and at the Last Glacial Maximum. Genetic data were analysed using traditional and new methods, including Bayesian clustering, coalescent-based estimation of gene flow, and haplotype network reconstruction. My findings revealed contrasting signatures of population subdivision and demographic expansion that appear in part to reflect differences in the altitudinal ranges of the focal taxa. Mitochondrial analyses also revealed a putative sister relationship between two of the Taiwanese endemic taxa - M. gracilis and M. recondita, which - given the fact both are restricted to Taiwan - presents an unusual case of potential non-allopatric divergence. To dissect this divergence process in more detail, I used 454-Pyrosequencing to obtain ten nuclear loci sequences of these two taxa, and a third taxon from mainland Asia, M. eleryi. Based on these loci, Bayesian isolation-migration models provided no strong evidence of post-split gene flow and, therefore, did not support speciation within Taiwan. Instead, the divergence process reconstructed from ncDNA loci was found to be incompatible with the mtDNA tree, with M. recondita showing a sister relationship with M. eleryi. This conflict is best explained by the ancient introgression of mtDNA between the two insular species following their colonization of Taiwan at different times.

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6

Darrock, David John. "Phylogeography of two lusitanian sea stars." Thesis, Cardiff University, 2010. http://orca.cf.ac.uk/55099/.

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The first comprehensive genetic study of North East Atlantic and Mediterranean sea stars, Asterina gibbosa and Asterina phylactica, is presented here, based on mitochondrial DNA (mtDNA) and Amplified Fragment Length Polymorphism (AFLP) data. MtDNA analysis revealed that the two putative species are distinct however there is incomplete lineage sorting, with the two most common haplotypes being shared across both species. MtDNA revealed low divergence between populations especially among most Atlantic populations, with no significant differentiation between the two basins. Although, both species possessed private haplotypes within both basins, the most common haplotype within both species is found throughout the entire geographical range of both species. Two mitchondrial haplogroups were identified, both of which showed evidence for a population expansion, occurring during the Pleistocene epoch. Haplogroup 1 was dominated by A. gibbosa (88%) whereas haplogroup 2 was dominated by A. phylactica (84%). The mtDNA results tentatively suggest that one Asterina population may descend from a population that survived the last glacial maximum (LGM) in one or more northern refugium. The AFLP data showed that A. gibbosa and A. phylactica are genetically distinct, with no apparent hybridization between species, with the possible exception of a single individual found at Rovinj, Croatia which was identified as being an A. phylactica individual at the time of sampling, but the allocation test assigned it to the Naples, Italy, A. gibbosa population. This could be the result of introgression or the individual could have been incorrectly classified as A. phylactica at the time of sampling. The AFLP data showed that there is gene flow occurring but it appears to be restricted, particularly within the Mediterranean basin, with no apparent gene flow occurring between the Atlantic and Mediterranean basins. There was no evidence with either marker to conclude that the brooding behaviour of A. phylactica provides a different pattern of genetic diversity within populations or differentiation between populations to the crawl away behaviour of A. gibbosa. The analysis suggests that gene flow is slightly more restricted for A. phylactica than A. gibbosa and, for A. gibbosa, it is more restricted in the Mediterranean than the Atlantic. The study identifies both A. phylactica and A. gibbosa populations that would be suitable to receive conservation status, based upon their unique genetic characteristics.

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7

Martinez, Araneda Camila. "Plant phylogeography in southern South America." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5041.

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This thesis is a phylogeographic investigation into plant species from Patagonia, and aims to infer their past distributions from the study of genealogical lineages. These species have gone through several events such as glacial periods, volcanism and topographical change which are expected to contribute to the divergence of genetic lineages by shaping distributions, isolating populations and therefore changing their genetic structure. So understanding how these processes have affected populations is important to get information on how the biodiversity in the region has been assembled, to identify hotspots of intra-specific diversity and therefore to establish potential conservation priorities. Several multi-species phylogeographic studies have been done in the northern hemisphere, but only few are published for South America and even less for the studied area. Patagonia is an area of a great interest because is the only area in the southern hemisphere apart from Antarctica that have been covered buy a thick layer of ice within the glacial periods. It has high levels of endemism, due to its natural boundaries and environmental processes, and is a biodiversity hotspot for conservation. Its varied topography (two big mountain ranges with a north-south distribution divided by a low flat area) also makes Patagonia interesting to study, due to the likelihood of this impacting on phylogeographic patterns. This study encompass seven different Patagonian species of which one is a range restricted conifer and the rest are all angiosperms and include trees, shrubs and herbs with a broad distributions. The reason why I have chosen so many different species is to look for general phylogeographic patterns in species in this region. The thesis was constructed in five chapters. The first is an introductory chapter that provides background to the study system and concepts. Chapters 2, 3, and 4 are empirical phylogeographic studies. These are written as self-contained chapters with the intention that each will be submitted as a separate paper. This leads to some repetition between chapters, but this is intentional as each will need to ‘stand alone’ when submitted for publication. Chapter 2 is a general investigation into five different Patagonian plant species: Discaria chacaye, Donatia fascicularis, Escallonia virgata, Tepualia stipularis and Weinmannia trichosperma. Chapter 3 describes the phylogeographic structure of Gentianella magellanica an annual, cold tolerant species with a wide distribution throughout Patagonia. This species was treated separately and in more detail than the previous five species due to its marked phylogeographic structure. Chapter 4 describes the phylogeographic structure of a Chilean endemic conifer Prumnopitys andina. This has a small distribution in the Andes and only one known population in the coastal cordillera. It was treated separately due to its restricted distribution and different mode of chloroplast inheritance (paternal). Chapter 5, is a general summary, bring all of the results together and giving a wider explanation of the phylogeographic patterns for all species and an outline of future research areas.

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8

Maddock, S. T. "Systematics and phylogeography of Seychelles amphibians." Thesis, University College London (University of London), 2016. http://discovery.ucl.ac.uk/1476198/.

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This thesis investigates evolutionary patterns of variation in endemic amphibians from the Seychelles archipelago. Focal groups include the treefrog (Tachycnemis seychellensis), and a radiation of caecilians in three genera (Grandisonia, Hypogeophis and Praslinia), and attempts to place these into a phylogenetic context. The introduction (Chapter 1) discusses the importance of islands in the study of evolution and examines patterns of intraspecific variation that have been reported in other Seychelles organisms. Chapter 2 provides the first intraspecific molecular study of the monotypic Seychelles treefrog Tachycnemis, implementing a species tree approach in order to investigate its relationship with its closest living relatives (Heterixalus) from Madagascar and test whether its ancestor colonised the Seychelles via overseas dispersal. Chapters 3 and 4 explore variation in the six species of Seychelles caecilian, all of which overlap in range on at least one island. To assess within- and among-island intraspecific variation in these subterranean amphibians, Chapter 3 uses genetic data from both mitochondrial and nuclear markers, while Chapter 4 uses morphometric and meristic data. Differing patterns of geographic structure was observed among the caecilian species. The final two data chapters analyse species-level relationships among the Seychelles caecilians. Chapter 5 utilises Next Generation Sequencing to obtain mitogenomic data, and multiple approaches to infer phylogeny, and the effectiveness of alternative methods are evaluated. Chapter 6 attempts to resolve relationships of the island caecilians using 11 nuclear loci and multiple methods of phylogenetic inference. Chapter 7 discusses how the thesis has increased knowledge of the study taxa and of the evolution of amphibians on islands, particularly the Seychelles.

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9

Last, Mariana P. "Intraspecific Phylogeography of Cycladenia humilis (Apocynaceae)." BYU ScholarsArchive, 2009. https://scholarsarchive.byu.edu/etd/2287.

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Cycladenia humilis (Apocynaceae) is a rare perennial herb native to western North America and has a fragmented distribution in California, Utah, and Arizona. Populations in Utah and Arizona are federally listed as threatened, while there is no conservation status applied to California populations. Using genetic (three chloroplast and two nuclear DNA loci) and morphological characters, intraspecific variation between populations of C. humilis and current taxonomic conventions were assessed. Nested Clade Phylogeographic Analysis and Bayesian phylogenies were used to assess patterns within C. humilis and supported three main population groupings: a northern California, southern California, and Colorado Plateau group. The northern California populations represent a distinct group and include populations from the Santa Lucia Mountains contrary to current classifications. The southern California group consistently includes populations in the San Gabriel and Inyo Mountains and was unique from any other region. The Colorado Plateau represents a group distinct from all other groups. The resilience of C. humilis on the Colorado Plateau to human threats remains unknown, but based on its frequency being comparable to California and our findings that considerable genetic variation exists within the species and within populations on the Colorado Plateau, we recommend that the threatened status of C. humilis be lifted.

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10

Sole, Catherine Lynne. "Phylogeography of Scarabaeus (Pachysoma) macleay (Scarabaidae : scarabaeinae)." Pretoria : [s.n.], 2005. http://upetd.up.ac.za/thesis/available/etd-01302006-123900.

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11

Jones, Rhys. "British reptitle conservation : phylogeography and translocation studies." Thesis, Cardiff University, 2009. http://orca.cf.ac.uk/54886/.

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This thesis reviews the availability and suitability of non-invasive samples for examining genetic diversity of reptiles. Such samples were used to examine the phylogeography of British snakes, namely Natrix natrix, Vipera berus and Coronella austriaca. In addition, Anguis fragilis was used as a model reptile to assess the impact of land development and consequent habitat loss on present day reptile populations. For the first time, we demonstrate that snake faecal, egg and foetal tissues, as well as sloughed skin and carcasses, are valuable sources of non-invasively sampled (NIS) material permitting genetic studies with minimal disturbance to the individual and its population. Using mitochondrial cytochrome b primers, 500 and 758 bp length sequences were successfully amplified from a variety of NIS tissues. Furthermore, a new method was developed for obtaining snake faeces in the field. Non-invasively collected samples supplied sufficient quality DNA to reconstruct cyt b mtDNA phylogenetic histories for V. berus (434 bp), C. austriaca (141 bp) and N. natrix (265 bp). Median spanning networks, Bayesian inference and Neighbour joining analyses grouped all three British snake species within Italian lineages. V. berus showed greater genetic variability (5 haplotypes) than the other two monophyletic British snake species. It is likely that V. berus survived in British Younger Dryas refugia whilst both C. austriaca and N. natrix retreated to more southerly European refugia. Using the common slow worm, Anguis fragilis, as a model species, the impact of land development on present day reptile populations was calculated by accessing the success of established translocation protocols. During monitoring, we achieved a slow worm recapture rate of 24% with all animals maintaining or increasing body condition in the first year following translocation. We recommend a minimum of 5 year post-translocation monitoring of receptor site with preferably four receptor site visits per year. This number of visits is a compromise between ideal recapture rate and mitigation costs. The effect of parasitic load on translocated slow worm populations was investigated though the first British record and field study of Neoxysomatium brevicaudatum (83% prevalence, n=100). Increased parasite load negatively affected slow worm body condition with parasitic loads varying amongst host populations. We discuss the value of post-translocation monitoring and disease surveillance as an important conservation tool in preserving threatened reptile species.

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12

Kidd, David Michael. "Applications of geographical information systems to phylogeography." Thesis, University of St Andrews, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.675412.

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13

Kohli, Brooks A. "Stock Structure, Management, and Phylogeography of Muskellunge." Ohio University Honors Tutorial College / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=ouhonors1275666981.

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14

Runnels, Cora. "Phylogeography and Species Status of Ramphogordius sanguineus." VCU Scholars Compass, 2013. http://scholarscompass.vcu.edu/etd/3165.

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Ramphogordius sanguineus (Rathke 1799) is a gregarious nemertean with a worldwide distribution and found mainly on hard substrates associated with mussels, oysters and other organisms of the fouling community. Asexual reproduction occurs by spontaneous fragmentation and only anecdotal accounts of sexual reproduction exist. This is the first phylogeographic study of R. sanguineus as well as the first species delimitation analyses employing DNA markers. Analysis of the mitochondrial gene nad6 and nuclear ISSR markers showed little diversity among geographically widespread populations, but AMOVA analyses of both markers revealed moderate to high genetic differentiation. Populations from Maine and Massachusetts exhibited the highest level of differentiation. These findings are consistent with predictions for invertebrates lacking a planktonic larval stage. Results of the nad6 tree-based delimitation analysis were in agreement with modern morphological and histocompatibility observations, suggesting that R. sanguineus is a single species and that a former division into four separate species was solely based on geographic location.

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15

Cooke, Elizabeth Laura. "The phylogeography and systematics of Cardamine hirsuta." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:22573e44-881c-456b-a571-d398a04c876a.

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Cardamine hirsuta L. is an emerging model system in developmental genetics, where natural genetic variation within C. hirsuta provides the means to investigate the genetic basis of morphological traits. This thesis investigates the geographical structure and genealogical history of genetic variation within C. hirsuta and identifies its closest relatives. This will enable the accurate selection of species for comparison with C. hirsuta when making interpretations of evolutionary processes, and provide a better understanding of morphological character evolution in C. hirsuta. The phylogeographic history of C. hirsuta was reconstructed using multiple chloroplast and nuclear markers and widespread accession sampling from across its native range. A distinct group was identified within C. hirsuta, restricted to the high mountains of East Africa. Climate suitability modelling showed that Pleistocene glacial dynamics have had a strong effect on the distribution of genetic variation within C. hirsuta. The phylogeographical data generated here was used to investigate the origin of C. hirsuta in the Azores, an oceanic archipelago. The Azores are dominated by an endemic chloroplast haplotype which is associated with an endemic phenotype. Thus, C. hirsuta appears to have diversified in situ in the Azores. Phylogenetic analyses of Cardamine, restricted to diploid species to remove the confounding effects of polyploids, found that C. hirsuta is most closely related to C. oligosperma, a western North American species. Multiple loci and extensive intraspecific sampling were brought to bear to demonstrate that C. hirsuta and C. oligosperma are reciprocally monophyletic. Cardamine pattersonii, a restricted endemic from north-west Oregon is likely to be an allopolyploid, with C. oligosperma as the maternal parent and possibly C. nuttallii as the paternal parent.

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16

Smith, Ashley D. "Intraspecific Phylogeography of Graptemys ouachitensis." Ohio : Ohio University, 2008. http://www.ohiolink.edu/etd/view.cgi?ohiou1213565776.

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17

Haney, Todd Allen. "Taxonomy and phylogeography of the leptostracan crustacea." Diss., Restricted to subscribing institutions, 2008. http://proquest.umi.com/pqdweb?did=1781954281&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.

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18

Kontula, Tytti. "Phylogeography and evolution of freshwater cottid fishes." Helsinki : University of Helsinki, 2003. http://ethesis.helsinki.fi/julkaisut/mat/ekolo/vk/kontula/.

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19

Palo, Jukka. "Genetic diversity and phylogeography of landlocked seals." Helsinki : University of Helsinki, 2003. http://ethesis.helsinki.fi/julkaisut/mat/ekolo/vk/palo/.

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20

Cottle, Ceaira. "A Tale of Two Islands: Long Distance Dispersal to Oceanic Islands and the Influence of Dispersal Potential on Large-Scale Phylogeographic Patterns." Thesis, Griffith University, 2014. http://hdl.handle.net/10072/367140.

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Comparative phylogeography seeks to compare phylogeographic patterns of multiple co-distributed species in order to examine levels of temporal and spatial congruence. Comparative assessments can lead to reconstructions of major trends in the recent histories of dispersal of a region and can provide significant advances in understanding how behaviour, demography and natural histories of species and populations can influence phylogeographic patterns. When common spatial patterns of evolutionary sub-division are found between co-distributed species they are thought to share a biogeographic history. Although concordant phylogeographic patterns have been found across multiple taxa, not all comparative phylogeographic studies have found evidence of congruence. The influence of dispersal potential on the phylogeographic structuring of multiple co-distributed species was the main focus of this thesis. The main goal was to explore how dispersal potential, based on life history characteristics, influenced phylogeographic structure on a large-scale in multiple co-distributed species, and in particular how this influenced oceanic island populations. Whilst there are disagreements in the biogeographic literature as to whether vicariant or dispersal processes best explain the geographic distribution of a species, the colonisation and accumulation of biotic assemblages on oceanic islands is unequivocally the result of transoceanic dispersal. The biotic communities present on oceanic islands therefore inevitably consist of species that are able to disperse well. Genetic variation within island populations is directly influenced by the dispersal potential of the species in question. Species that disperse frequently will be more closely related to the source population due to continual migration to the islands from mainland (or other island) sources; whereas species that do not disperse as often will be more genetically distinct and divergent from the source population. Thesis (PhD Doctorate) Doctor of Philosophy (PhD) Griffith School of Environment Science, Environment, Engineering and Technology Full Text

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21

Vodă, Raluca. "Biodiversity and comparative phylogeography of western Mediterranean butterflies." Doctoral thesis, Universitat Autònoma de Barcelona, 2015. http://hdl.handle.net/10803/329006.

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Esta tesis doctoral se basa en un enfoque macroecológico y en análisis de grandes conjuntos de datos para el estudio de la biodiversidad y filogeografía de las mariposas mediterráneas occidentales. Una de las contribuciones más importantes y originales de esta tesis doctoral fue la creación de una extensa colección de ADN y tejidos de mariposas del Mediterráneo occidental, así como la reunión de datos de presencia sobre las comunidades de las islas y del continente. Actualmente en Europa no existen conjuntos de datos similares disponibles para grupos taxonómicos enteros con tan amplia distribución y con una resolución espacial comparable. En el primer capítulo investigamos los patrones de la beta-diversidad de las mariposas del Mediterráneo occidental y proporcionamos nueva evidencia de la efectividad de diferentes medidas para la beta diversidad. Se demuestra que ningún índice por sí mismo puede recuperar amplios patrones biogeográficos simultáneamente para las islas y el continente. Por lo tanto, se propone comparar y combinar los resultados obtenidos usando los dos tipos de índices, particionados y no particionados, para obtener conclusiones válidas. En el segundo capítulo definimos objetivamente las especies crípticas y producimos una lista de grupos crípticos para todas las mariposas del Mediterráneo occidental. Se demuestra que los patrones de distribución ‘chequered’ dentro de los grupos crípticos son mucho más frecuentes que entre especies no crípticas congéneres y que preponderantemente se producen entre las especies no hermanas con una divergencia genética sustancial. Estos patrones de distribución son un fenómeno general de las especies crípticas de mariposas en el Mediterráneo occidental pero también podría ser el caso para otros organismos. En el tercer capítulo investigamos las causas potenciales que pueden producir patrones de distribución ‘chequered’, utilizando un enfoque multidisciplinario para dos pares de especies crípticas. Se demuestra que éste es un fenómeno multifacético que no puede ser explicado por hipótesis simples y establecemos algunos de los factores clave, incluyendo las interacciones entre especies, que suelen ser olvidadas en ecología dada la dificultad de evaluar su importancia. En el cuarto capítulo, proporcionamos un nuevo método para comparar directamente los diferentes tipos de marcadores, incluso si los datos disponibles para cada marcador sólo en parte se superponen, y discutimos las implicaciones biogeográficas de las concordancias y discrepancias observadas. Una de las aplicaciones más importantes de este método es que puede ser utilizado para una amplia variedad de marcadores y taxones. En el quinto y último capítulo se investigan los mecanismos que determinan y mantienen la comunidad de mariposas de las islas circum-sicilianas. Se demuestra que las poblaciones insulares tienen historias muy diferentes y presentan diferentes probabilidades de recolonización tras extinciones locales. Estos resultados tienen grandes implicaciones para centrar los esfuerzos de conservación en ciertas islas. Los resultados de esta tesis doctoral contribuyen a una mejor comprensión de la diversidad de mariposas en el Mediterráneo occidental y también proporcionan un marco para futuros estudios que investiguen no sólo las mariposas, si no también otros organismos. El trabajo realizado durante esta tesis doctoral aporta nuevos datos para la investigación (una completa colección de especímenes, datos de presencia y secuencias de ADN), herramientas originales para filogeografía comparada (algoritmos mejorados, funciones R), resultados descriptivos (mapas zoogeográficos, patrones filogeográficos) y aportaciones conceptuales (exclusión mutua, las propiedades únicas de la biodiversidad críptica, las islas como individuos, los procesos que determinan las comunidades insulares i el valor filogeográfico de las poblaciones para la priorización de la conservación). This PhD thesis consists in a comprehensive macroecological approach and in analyses of large datasets to study the biodiversity and phylogeography of western Mediterranean butterflies. One of the most important and original contributions of this PhD was creating a comprehensive butterfly DNA and tissues collection for the western Mediterranean and improving the occurrence data for island and mainland communities. Currently in Europe there are no other similar datasets available for an entire taxonomic group with such a wide distribution and with a comparable spatial resolution. In the first chapter we investigate patterns of the butterfly beta-diversity in the western Mediterranean and provide new evidence for the effectiveness of different measures of beta diversity. We demonstrate that no index by itself is able to retrieve comprehensive biogeographical patterns simultaneously for islands and mainland and the results should be compared and combined by using both unpartitioned and partitioned indices to obtain comprehensive results. In the second chapter we objectively define cryptic species and produce a list of cryptic groups for all the butterflies in the western Mediterranean. We show that chequered patterns of distribution within cryptic groups are much more frequent than among congeneric non-cryptic species and they preponderantly occur between non-sister species with substantial genetic divergence. These patterns of distribution are a general phenomenon for cryptic butterfly taxa in the western Mediterranean as could also be the case for other organisms. In the third chapter we investigate the potential causes producing such chequered distribution patterns by using a multidisciplinary approach for two pairs of cryptic species. We show that this is a multifaceted phenomenon that cannot be explained by simple hypotheses and we pinpoint some of the key players, including species interactions, which are usually forgotten in ecology given the difficulty to assess their importance. In the fourth chapter we provide a new method to directly compare different types of markers even if data available for each marker only partially overlap and discuss the biogeographic implications of the observed concordances and discrepancies. One of the most important applications of this method is that it can be used for a wide array of markers and taxa. In the fifth and last chapter we investigate the mechanisms determining and maintaining the butterfly community that occurs on the circum-Sicilian islands. We show that island populations have very different histories and are subjected to different recolonization probabilities following local extinctions. These findings have great implications for focusing conservation efforts on particular islands. The results of this PhD thesis contribute to a better understanding of the butterfly diversity in the western Mediterranean and they also provide a framework for future studies that investigate not only butterflies, but other organisms as well. The work performed during this PhD brings novel data for research (a comprehensive collection of specimens, presence data and DNA sequences), original tools for comparative phylogeography (improved algorithms, R functions), descriptive results (zoogeographic maps, phylogeographic patterns) and conceptual contributions (mutual exclusion, unique properties of cryptic biodiversity, islands as individuals, processes that determine island communities, the phylogeographic value of populations for conservation prioritization).

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22

Carlsson, Martin. "Phylogeography of the Adder, Vipera berus." Doctoral thesis, Uppsala universitet, Institutionen för evolutionsbiologi, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3477.

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The phylogeography of a wide ranging temperate species, the adder, Vipera berus, was investigated using several genetic tools, with special emphasis on the post-glacial colonisation pattern of Fennoscandia. The area was colonised from two directions by adder populations representing different glacial refugia. The two populations meet in three places and the main contact zone is situated in Northern Finland. The two other contact zones are the result of dispersal across the Baltic Sea to the Umeå archepelago and South-Western Finland. Asymmetrically distributed nuclear genetic variation compared to mitochondrial DNA in the northern contact zone suggests a skewed gene flow from the east to the west across the zone. This pattern might reflect differences in dispersal among sexes and lineages, or may be accounted for by a selective advantage for nuclear variation of eastern origin among Fennoscandian adders. The phylogeographic pattern for adders across the entire species range was addressed by sequencing part of the mitochondrial genome and scoring microsatellite markers. The adder can be divided into three major genetic groups. One group is confined to the Balkan peninsula harbouring the distribution range of V. b. bosniensis. A second, well differentiated group is restricted to the Southern Alps. These two areas have probably served as refugia for adders during a number of ice ages for the adders. The third group is distributed across the remainder of the species’ range, from extreme Western Europe to Pacific Russia and can be further divided into one ancestral group inhabiting the Carpathians refugial area, and three more recent groups inhabiting areas west, north and east of the Alps. The adder provides an example of a species where the Mediterranean areas are housing endemic populations, rather than the sources for post-glacial continental colonisation. Continent-wide colonisation has instead occurred from up to three cryptic northern refugia.

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23

Villaverde, Hidalgo Tamara M. "Systematics and Phylogeography of "Carex capitata" Complex (Cyperaceae)." Thesis, Université d'Ottawa / University of Ottawa, 2012. http://hdl.handle.net/10393/23368.

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Only thirty known species have populations at high latitudes in both hemispheres, this is, a bipolar distribution. Five of them belong to the genus Carex. Before attempting to elucidate the origins of such distributions, we need to resolve taxonomical problems that are typically encountered in such species. We focus on the Carex capitata complex, which includes Carex arctogena as a bipolar species, in worldwide scope sampling. A morphometric study and phylogenetic analyses based on maximum parsimony, Bayesian inference and Statistical Parsimony have revealed: a) C. capitata and C. arctogena are different species; b) C. anctarctogena is a synonym of C. arctogena and c) a great biodiversity previously undetected in western North America that could lead to the description of three new taxa (“Carex cayouetteana”, Carex sp. nov. 1 and 2) comprised in the so called “C. cayouetteana” lineage. More studies are needed in some C. capitata samples from Russia that appears in the molecular analyses in a strongly supported clade.

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24

Fraser, Ceridwen, and n/a. "Phylogeography of the kelp genus Durvillaea (Phaeophyceae: Fucales)." University of Otago. Department of Zoology, 2009. http://adt.otago.ac.nz./public/adt-NZDU20091002.131226.

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Durvillaea, a kelp genus occurring only in the Southern Hemisphere, presents an ideal system for studies of marine connectivity and postglacial recolonisation. Durvillaea contains five currently-recognised species, four of which are non-buoyant. Whereas all non-buoyant species are restricted to the south-western Pacific, the sole buoyant species (D. antarctica) has a far wider, circumpolar distribution, strongly suggesting that long-distance dispersal in D. antarctica is achieved by rafting. This contrast in predicted dispersal ability among Durvillaea species provides an opportunity for natural phylogeographic comparisons, thereby assessing the effectiveness of rafting as a long-distance dispersal mechanism. Additionally, the inability of D. antarctica to survive in ice-affected areas, combined with its broad distribution, make it an ideal candidate for studies of postglacial recolonisation. Phylogenetic and biogeographic relationships within Durvillaea were here assessed using sequence data from mitochondrial (COI), chloroplast (rbcL) and nuclear (18S) DNA. Genetic data were obtained from more than 500 specimens, including representatives from across the geographic range of each recognised species of Durvillaea. Mitochondrial data for Durvillaea were found to be highly phylogenetically informative, with 117 variable sites observed over a 629 bp fragment of COI. Chloroplast and nuclear markers, on the other hand, showed less variation than COI, but nonetheless contributed useful phylogenetic information. Phylogenetic analyses were performed using both Maximum Likelihood and Bayesian approaches. Contrasting patterns of genetic diversity were observed across the range of D. potatorum in Australia, with genetic homogeneity throughout western sites versus relatively high levels of diversity in eastern populations. Based on these results, I hypothesise that D. potatorum recolonised much of the western part of its range postglacially, perhaps being entirely eliminated from western Tasmania during the last glacial period by altered oceanographic systems. Additionally, 'western' and 'eastern' D. potatorum haplotypes formed deeply-divergent clades, likely reflecting geographic isolation on either side of the Bassian Isthmus during Pleistocene marine regressions. Substantial genetic diversity was observed across the range of the circumpolar species D. antarctica. Within New Zealand, phylogenetic and morphological analyses of D. antarctica indicate that two morphotypes ('cape' and 'thonged' forms) likely represent reproductively isolated species, with the 'cape' lineage apparently restricted to southern New Zealand. Whereas the 'cape' lineage showed little genetic variation throughout its range, the 'thonged' lineage exhibited marked phylogeographic structure, with high genetic diversity and a clear north - south genetic disjunction delineated by the Canterbury Bight. On a broader, circumpolar scale, D. antarctica showed contrasting patterns of genetic diversity, with high levels of variation in low-latitude regions (e.g., continental coasts of New Zealand and Chile), versus near-homogeneity at high, subantarctic latitudes. These phylogeographic contrasts strongly suggest that D. antarctica recolonised much of the subantarctic region only recently, most plausibly following extirpation by ice scour at the Last Glacial Maximum (LGM). Locations of putative recolonised islands relative to 'refugial' areas indicate that Antarctic sea ice was likely more extensive at the LGM than previous studies have suggested. Latitudinal contrasts in genetic diversity were also observed among Chilean populations of D. antarctica, with a single mitochondrial haplotype detected throughout Chilean Patagonia versus high diversity in central Chile (32�-42�S). The Patagonian populations appear to have recolonised the region postglacially, following recession of the Patagonian Ice Sheet after the LGM. These populations show transoceanic ancestry, with a closer relationship to populations in the subantarctic and southern New Zealand regions than to those in central Chile. Substantial phylogeographic structure was evident across small spatial scales in central Chile, and the correspondence of major genetic disjunctions among central Chilean sites with the presence of long stretches of unsuitable substrate (beaches) strongly suggests that habitat discontinuity drives genetic isolation in this dispersive species. Broad-scale molecular phylogenetic analyses indicate that the current taxonomy of Durvillaea species requires substantial revision. Previously-recognised 'morphotypes' of Durvillaea (of D. potatorum in Australia, and D. antarctica in New Zealand), for example, were here found to be genetically distinct, likely representing reproductively-isolated species. This phylogeographic research on Durvillaea kelp sheds new light on the historical impacts of climate change on Southern Hemisphere marine environments, and on the processes driving evolution in a marine macroalga.

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25

Fouquet, Antoine. "Diversity and phylogeography of eastern Guiana Shield frogs." Thesis, University of Canterbury. School of Biological Sciences, 2008. http://hdl.handle.net/10092/2693.

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The Guiana Shield is a sub-region of Amazonia, one of the richest areas on earth in terms of species number. It is also one of the most pristine areas and is still largely unexplored. Species number, distribution, boundaries and their evolutionary histories remain at least unclear but most of the time largely unknown. This is the case for most Anurans, a group which is recognized as threatened globally and is disappearing even from pristine tropical forests. Given the pace of forest destruction and the growing concerns about climate change it is urgently necessary to obtain a better estimate of regional biodiversity in Amazonian frogs as well as a better understanding of the origin and distribution of Anuran diversity. Furthermore, given their sensitivity to climatic conditions, amphibians are a good model to investigate the influence of paleoclimatic events on Neotropical diversification which was supposedly the driving force on biotic evolution during Pleistocene in the Guiana Shield. I first test species boundaries in two species Scinax ruber and Rhinella margaritifera. These species are widely distributed, abundant and largely recognized as species complexes. I used an original species delineation method based on the combined use of mitochondrial and nuclear DNA in phylogenetic and phylogeographic analyses. Phylogenetic analyses demonstrated the polyphyly of Scinax ruber and Rhinella margaritifera. These species consist of multiple lineages that may all merit species status. Conflicting signals of mitochondrial and nuclear markers indicated the possibility of ongoing hybridization processes. Phylogeographic analyses added further information in support of the specific status of these lineages. Our results highlight the utility of combining phylogenetic and phylogeographic methods, as well as the use of both mitochondrial and nuclear markers within one study. This approach helped to better understand the evolutionary history of taxonomically complex groups of species. The assessment of the geographic distribution of genetic diversity in tropical amphibian communities can lead to conclusions that differ strongly from prior analyses based on the occurrence of currently recognized species alone. Such studies, therefore, hold the potential to contribute to a more objective assessment of amphibian conservation priorities in tropical areas. Subsequently, I tested if these first results on cryptic species are generalisable, questioning what would potentially be a minimum estimate of the number of cryptic frog species in Amazonia and the Guiana Shield, using mtDNA with multiple complementary approaches. I also combined isolation by distance, phylogenetic analyses, and comparison of molecular distances to evaluate threshold values for the identification of candidate species among these frogs. In most cases, geographically distant populations belong to genetically highly distinct lineages that could be considered as candidate new species. This was not universal among the taxa studied and thus widespread species of Neotropical frogs really do exist, contra to previous assumptions. Moreover, the many instances of paraphyly and the wide overlap between distributions of inter- and intra-specific distances reinforce the hypothesis that many cryptic species remain to be described. In our data set, pairwise genetic distances below 0.02 are strongly correlated with geographical distances. This correlation remains statistically significant until genetic distance is 0.05, with no such relation thereafter. This suggests that for higher genetic distances allopatric and sympatric cryptic species prevail. Based on our analyses, we propose a more inclusive pairwise genetic distance of 0.03 between taxa to target lineages that could correspond to candidate species. Using this approach, we identify 129 candidate species, two-fold greater than the 60 species included in the current study. This leads to estimates of around 170 to 460 frog taxa unrecognized in Amazonia-Guianas. As a consequence the global amphibian decline detected especially in the Neotropics may be worse than realised. The Rhinella margaritifera complex is characterisized by the presence of many cryptic species throughout its wide distribution, ranging from Panama to Bolivia and almost entire Amazonia. French Guiana has long been thought to harbor two species of this group, though molecular data analysed in previous chapters indicated as many as five lineages. I tested whether morphological measurements are correlated or not with genetic data using discriminant analysis and if diagnostic characteristics among the previously determined lineages can be used to describe these new species. This is a novel integrative method which can lead to a facilitation of the description of cryptic species that have been detected by phylogenetic and/or phylogeographic studies. These analyses, combined with published data of other Rhinella species, indicated that two of these lineages represent previously unnamed species. Two of the remaining are allocable to R. margaritifera while the status of the fifth is still unclear because so far it is morphologically indistinguishable from R. castaneotica. Determining if codistributed species responded to climate change in an independent or concerted manner is a basic objective of comparative phylogeography. Species boundaries, histories, ecologies and their geographical ranges are still to be explored in the Guiana Shield. According to the refugia hypothesis this region was supposed to host a forest refugium during climatic oscillations of the Pleistocene but the causes and timing for this have been criticized. We investigated patterns of genetic structure within 18 frog species in the eastern Guiana Shield to explore species boundaries and their evolutionary history. We used mtDNA and nuclear DNA and complementary methods to compare the genetic diversity spatially and temporally. With one exception all the species studied diversified repeatedly within the eastern Guiana Shield during the last 4 million years. Instead of one Pleistocene forest refugium the Guiana Shield has probably hosted multiple refugia during late Pliocene and Pleistocene. Most of these Pleistocene refugia were probably situated on the coast of French Guiana, Amapà, Suriname and Guyana. This diversification likely resulted from forest fragmentation. Many species deserve taxonomic revisions and their ranges to be reconsidered. The local endemism of the Anuran fauna of the Guiana Shield is likely to be much higher and some areas consequently deserve more conservation efforts. Specifically I questioned whether major intraspecific diversification started before the Pleistocene and occurred within the Guiana Shield or ex situ. According to ecological characteristics of the species involved I will test different diversification hypotheses. The consequences on the diversity and the endemism of the Guiana Shield will be explored. My results demonstrate that we have been grossly underestimating local biological diversity in the Guiana Shield but also in Amazonia in general. The order of magnitude for potential species richness means that the eastern Guiana Shield hosts one of the richest frog fauna on earth. In most of the species studied high levels of mtDNA differentiation between populations call for a reassessment of the taxonomic status of what is being recognised as single species. Most species display deep divergence between eastern Guiana Shield populations and Amazonian ones. This emphasizes that the local endemism in the Guiana Shield of these zones is higher than previously recognized and must be prioritised elements taken into account in conservation planning. Nevertheless, a few other species appear widely distributed showing that widespread species do exist. This underlines the fact that some species have efficient dispersal abilities and that the frog fauna of the eastern Guiana Shield is a mixture of old Guianan endemic lineages that diversified in situ mostly during late Pliocene and Pleistocene and more recently exchanged lineages with the rest of Amazonia. Recognizing this strong historical component is necessary and timely for local conservation as these zones are likely to be irremediably modified in the near future.

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26

Paulo, Octavio Fernando de Sousa Salgueiro Godinho. "The phylogeography of reptiles of the Iberian peninsula." Thesis, Queen Mary, University of London, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.251650.

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27

Quijada, MascarenÌƒas Jesus AdriaÌn. "Molecular phylogeography of the neotropical rattlesnake Crotalus durissus." Thesis, Bangor University, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.428835.

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28

Techow, N. M. S. Mareile. "Phylogeny and phylogeography of four southern ocean petrels." Doctoral thesis, University of Cape Town, 2007. http://hdl.handle.net/11427/4339.

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Includes bibliographical references (leaves 199-212) This thesis investigates the phylogeography of four southern ocean petrel species in an attempt to resolve taxonomic uncertainties and phylogeography in these species. A large proportion of petrel and albatross species are listed as threatened under Red List criteria, in many cases as a result of threats at sea. Most albatrosses and petrels breed in discrete island colonies and exhibit strong natal philopatry. They may thus be expected to show population divergence, but published studies show that this is not always the case. Most studies to date have concentrated on northern hemisphere species, with mostly albatrosses studied within the southern oceans. White-chinned (Procel/aria aequinoctialis), Spectacled (P. conspicillata) and giant petrels (Macronectes giganteus and M. hal/I) are southern ocean species of Procellariiformes. All four species are threatened by accidental mortality in long line and other fisheries, as well as by introduced predators at their breeding colonies. In order to adequately conserve these species, species limits need to be resolved. Taxonomic uncertainties are an important issue in conservation because often only recognised species receive protection. In addition, islands of origin for birds killed at sea need to be identified. This thesis examines the species status of the Spectacled Petrel (Procel/aria conspicillata), which has been separated from the White-chinned Petrel (P. aequinoctialis) based on morphology and vocalisations, as well as examining the taxonomic status of the two forms of giant petrel, and their phylogeography. Cytochrome b was used to confirm the species rank of the Spectacled Petrel. The decision to support separate species status was based on the lack of shared haplotypes, six fixed mutational differences between the closest haplotypes of the White-chinned and Spectacled Petrel and a sequence divergence of 1.74%. Within Procel/aria, Whitechinned and Spectacled Petrels are sister species, closely related to the wide-ranging Grey Petrel. Within the White-chinned Petrel, two regional populations were found corresponding to colonies in the New Zealand region and the Indian/Atlantic Ocean.Evidence of population expansions were detected in both species and both regional populations of the White-chinned Petrel. Between these two regional populations, the greatest genetiC diversity was within the New Zealand regional population. This result is consistent with the White-chinned Petrel originating in the New Zealand area.

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29

Furtner, Genevieve. "Phylogeography of Highlands walleye in eastern North America." Ohio University Honors Tutorial College / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ouhonors1429887556.

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30

Papadopoulou, Anna. "Phylogeography of Tenebrionid beetles in the Aegean archipelago." Thesis, Imperial College London, 2009. http://hdl.handle.net/10044/1/5504.

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The Aegean archipelago, which has a mostly continental origin, provides a ‘natural laboratory’ to explore the effects of dispersal limitation on population and community structure. This thesis investigated the phylogeographic, genetic diversity and species richness patterns of the darkling beetles (Coleoptera: Tenebrionidae) of the central Aegean islands. Sampling was conducted on 30 islands and the corresponding coasts of Greece and Turkey and several individuals per taxon and locality were sequenced for mitochondrial and nuclear markers. The generated sequence data were used to: reconstruct phylogenies, calculate population genetic parameters, apply DNA-based species delineation methods, estimate substitution rates and assess macroecological patterns. The results show that many of the existing taxonomic names do not reflect the genetic diversification processes in the archipelago. The majority of the morphological species are split into several geographically confined clades, recognised as ‘independently coalescing entities’. Habitat preference and wing development were identified as two major factors affecting phylogeographic structure, genetic diversity and macroecological patterns. Differences in dispersal propensity were observed between psammophilic taxa inhabiting ephemeral coastal sandy habitats and geophilic taxa associated with presumably stable compact-soil habitats. The widespread geophilic lineages were found to be deeply subdivided along the biogeographic barrier of the ‘mid-Aegean trench’, and the age of this geological event was used as a calibration point to estimate substitution rates and reassess the ‘standard' insect mitochondrial molecular clock. A positive species – genetic diversity correlation was recorded, driven primarily by island sizes and geographic distances, while certain macroecological regularities such as the species – area curve and the distance – decay of similarity relationship could be described at both species and haplotype level. This study demonstrated how palaeogeography, contemporary geography and habitat persistence interact with stochastic processes at population and community level to shape the observed diversity patterns of the Aegean tenebrionid fauna.

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31

Whinnett, Alaine Jean. "The phylogeography and molecular evolution of ithomiine butterflies." Thesis, University College London (University of London), 2006. http://discovery.ucl.ac.uk/1445953/.

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This thesis uses molecular techniques to investigate aspects of the evolution of ithomiine butterflies (Lepidoptera: Nymphalidae: Ithomiinae). 1) This thesis takes a comparative phylogeographic approach to investigate the diversification of ithomiines collected across an Amazonian suture zone in N. E. Peru. High variability of mitochondrial DNA (mtDNA) and triosephosphate isomerase (Tpi) sequence divergences was recovered, which, i) suggested that diversification of the ithomiines studied here was inconsistent with predictions of the Pleistocene forest refugia theory, one of the leading hypotheses used to explain the record richness of Amazonian biodiversity, and ii) challenged the categorisation of taxa based purely on DNA divergence thresholds, as proposed by DNA barcoding. 2) This thesis also investigates the contribution of ecological adaptation versus allopatric differentiation in explaining the distribution patterns of 4 subspecies belonging to the ithomiine species Hyposcada anchiala. The mtDNA sequence data revealed that the most recent radiations were consistent with allopatric divergence during the Pleistocene. 3) In addition, this thesis generates gene genealogies for the ithomiine tribe Oleriini, based on regions of mtDNA, wingless and elongation factor /-a. In nearly all cases individuals were clustered by species into the four recognised genera. However, the relationships between the genera remains undetermined. These data contribute to a complete Oleriini phylogeny, which will be used to examine aspects of the evolution of this tribe. 4) Finally, this thesis contributes to the development of nuclear loci for PCR in Lepidoptera. Tpi had previously been used for phylogenetics, but here was further developed so that a longer region could be amplified. Primers were also developed for a novel region, Tektin, which is shown to have phylogenetic utility at the genus, tribe and subfamily levels.

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32

Schmidt, Daniel J. "Congeneric Phylogeography of Australian Ogyris Butterflies (Lepidoptera: Lycaenidae)." Thesis, Griffith University, 2007. http://hdl.handle.net/10072/366723.

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This study investigated spatial genetic structuring of two groups of Australian Ogyris butterflies (Lycaenidae). Ogyris represents one of several Australian endemic butterfly radiations that is well characterised in terms of basic biology but lacking in data useful for discriminating among the potential factors promoting divergence and speciation. A phylogeographic approach was used to document structuring in mitochondrial DNA markers (mtDNA) across the geographic range of two groups of closely related taxa. These include a pair of sister species: Ogyris zosine and O. genoveva, and the polytypic species O. amaryllis which is comprised of four subspecies. Topological relationships among recognised taxonomic units were tested and polyphyletic patterns investigated as a potential source of information relating to divergence and speciation. Sister species Ogyris zosine and O. genoveva were found to exhibit a polyphyletic relationship based on mtDNA. The deepest divergence within the group separated allopatric populations of O. zosine in northern Australia which do not correspond to a recognised taxonomic entity. The distribution of O. zosine and O. genoveva is parapatric along the east coast and additional sampling in this area along with evidence from allozyme markers revealed that the polyphyletic pattern can be explained by past mtDNA introgression at the current contact zone. The two species engage in an obligate mutualistic association with different suites of Camponotus ant species. It is hypothesised that this association may be involved in maintaining differentiation between the taxa through ant-mediated selection against hybrids. The distribution of a blue/purple wing colour polymorphism in female O. zosine is consistent with the role of wing colour as a prezygotic isolating mechanism in the contact zone although other explanations cannot be excluded. Genetic relationships were examined among four nominal taxa of the polytypic species Ogyris amaryllis which have a combined distribution spanning most of mainland Australia. Mitochondrial sequence data recovered a putatively ancestral and polyphyletic inland subspecies with several peripheral subspecies showing reduced variation within this topology. Analysis of spatiotemporal patterns of variation for the inland subspecies indicated a recurrent history of restricted gene flow and range expansion through the Pleistocene, while peripheral subspecies are characterised by higher levels of population structure and a history of population fragmentation. High levels of variation and population differentiation observed for allozyme markers were not consistent with subspecies boundaries. Partitioning of allozyme variation was explained better by arranging populations according to their larval host plant. Genetic data, combined with information on distribution and ecology, are consistent with a pattern of peripheral isolation associated with host plant specialisation of coastal populations in the O. amaryllis complex. Thesis (PhD Doctorate) Doctor of Philosophy (PhD) School of Environmental Science Science, Environment, Engineering and Technology Full Text

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33

Miller, Becky Akiko. "The Phylogeography of Prosopium in Western North America." BYU ScholarsArchive, 2006. https://scholarsarchive.byu.edu/etd/1002.

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The mountain whitefish (Prosopium williamsoni) has been largely overlooked in population genetic analyses despite its wide distribution in discrete drainage basins in western North America for over four million years. Its closest sister taxa the Bear Lake whitefish (P. abyssicola), Bonneville cisco (P. gemmifer), and Bonneville whitefish (P. spilonotus) are found only in Bear Lake Idaho-Utah and were also included in the analyses. A total of 1,334 cytochrome b and 1,371 NADH dehydrogenase subunit 2 sequences from the Bonneville Basin, the Columbia River Sub-basin, the lower Snake River Sub-basin, the upper Snake River Sub-basin, the Green River Basin, the Lahontan Basin, and the Missouri Basin were examined to test for geographically based genetic differentiation between drainage basins and sub-basins and phylogeographic relationships to determine the invasion route of Prosopium into western North America and to aid in understanding current relationships. Prosopium entered the region via the Missouri River connection to Hudson Bay and moved in two waves: one colonized the lower Snake River Sub-basin, Columbia River Sub-basin, and the Lahontan Basin; the second wave colonized the upper Snake River Sub-basin, Bonneville Basin, Green River Basin, and established the Bear Lake Prosopium. Mountain whitefish exhibit a large amount of geographical genetic differentiation based on drainage basin except between the upper Snake River and the Bonneville Basin while the Bear Lake Prosopium show large amounts of gene flow between the three species. The apparent paraphyly of the mountain whitefish and the limited genetic structure of the Bear Lake Prosopium warrant recognition in the management of Prosopium and raise questions regarding species definitions in the group.

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34

Freudmann, Anita. "Phylogeography, habitat and resource use of Nyctimene robinsoni." Thesis, Queensland University of Technology, 2020. https://eprints.qut.edu.au/203859/1/Anita_Freudmann_Thesis.pdf.

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Fruit-eating bats play important roles in maintaining ecosystem health by contributing to seed dispersal and pollination. The current research aims to provide fundamental knowledge on the ecology and behaviour of the Queensland tube-nosed fruit bat (Nyctimene robinsoni). A field-based study investigated genetic variation across the currently known distribution range, and described habitat use, roosting ecology, foraging behaviour and dietary spectrum to evaluate the species' role as a seed disperser. Research outcomes contribute to a better understanding of the poorly understood group of Tube-nosed fruit bats, and findings can serve to support their conservation and species management.

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McKay, Bailey D. "Geographic variation in the Yellow-throated warbler (Dendroica Dominica)." Auburn, Ala., 2007. http://repo.lib.auburn.edu/07M%20Theses/MCKAY_BAILEY_29.pdf.

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36

Lunt, David H. "mtDNA differentiation across Europe in the meadow grasshopper Chorthippus parallelus (Orthoptera: acrididae)." Thesis, University of East Anglia, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.298311.

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This thesis examines the European phylogeography of the meadow grasshopper Chorthippus paralleJus. This common species has a very large range covering Europe, southern Scandinavia, Turkey and Russia, with two recognized subspecies. These are c.p.erythropus in Spain and c.p.paraJ1eJus in other regions. This species has been studied using mtDNA RFLPs and sequence data. The greatest levels of genetic subdivision were found to occur between southern Spain, southern Italy and the Balkans. No subdivision was detected between Balkan populations and those in central and northern Europe. These data were interpreted as indications that at least three refugia existed in Europe during the last glaciation. The historical locations of these refugia can be inferred to have been in southern Spain, southern Italy and the Balkans. Furthermore, postglacial expansion from the Balkan refugium is indicated as the origin of central and northern European populations of C.paralleJus. A phylogeny of common European Chorthippus species, and closely related genera, is presented from analysis of mtDNA sequence data. This analysis indicates that, although there are many similarities to the traditional morphological taxonomic arrangement, several revisions need to be considered and investigated further. These include the position of the monospecific genus Stauroderus outside of the Chorthippus clade and the division of these Chorthippus species into 3 subgenera. Finally, the evolutionary patterns of the cytochrome oxidase subunit I (COl) gene, which was used for the Chorthippus studies, are investigated for insects in general. The patterns of amino acid variability indicate regions of very different substitutional rates within this gene. These regions are discussed in terms of the known and assumed functional constraints on gene function. The variety of evolutionary rates in adjacent regions are considered further with regard to their utility in different levels of phylogenetic study, and conserved insect primers for the exploitation of these regions are presented.

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Goldson, Andrew James. "Genetic and phenotypic variation in two marine bryozoans." Thesis, Bangor University, 1998. https://research.bangor.ac.uk/portal/en/theses/genetic-and-phenotypic-variation-in-two-marine-bryozoans(458dcb15-cca6-478f-b197-61b720709a2f).html.

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Chronic copper toxicity was found to result in growth hormesis in both C. hvalina and E. pilosa. Tolerance levels of the bryozoans to copper contamination were found to be high in comparison with those of other marine organisms. Generally, both genotype and copper dosage affected growth and sexual functions, but genotype had no affect on organism response to copper. Nonetheless, large differences in responses were detected between the two E. pilosa populations examined. Variation in tentacle number of C. hyalina colonies was found to be very limited and dietary regime was not observed to have a marked influence upon this trait. In contrast, colonies of E. pilosa were found to produce more tentacles per lophophore in optimal dietary conditions. Significant differences were detected between two E. pilosa populations in astogeny, sexual maturity and tentacle number. Laboratory experiments designed to identify the cue for induction of extended (long) medium proximal spines in E. pilosa colonies were unsuccessful. Differences in spine growth were again identified between the two E. pilosa populations from contrasting sites. Reciprocal transplantation demonstrated that `long' spine formation was triggered in colonies previously possessing only `short' spines and vice versa. Flume observations of particle path trajectories imply that spine formation may result in near-colony flow conditions which are more favourable to feeding in high flow velocities. Demographic analysis using the RAPD technique for both C. hyalina and E. pilosa indicate population structuring corresponding to their contrasting modes of larval dispersal. Populations of C. hyalina appear to exhibit considerable genetic differentiation over distancesa s small as 100 m, whereasE . pilosa is characterisedb y high levels of genetic heterogeneity over much larger spatial scales. E. pilosa population differentiation is observed at a site some 80 Km distance, which may be a consequenceo f hydrographic features. Evidence from analysis of mtDNA (COI) and observations on reproductive isolation and morphological differentiation indicate high levels of cryptic speciation amongst globally distributed populations of C. hyalina. It is suggested that the Chilean C. hyalina population is sufficiently different from all other populations examined to be considered a separate species.

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Steele, Craig A. "Speciation, phylogeography, and gene flow in giant salamanders (Dicamptodon)." Online access for everyone, 2006. http://www.dissertations.wsu.edu/Dissertations/Fall2006/C_Steele_091106.pdf.

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39

Martin, Holly R. "Intraspecific phylogeography of the Least brook lamprey (Lampetra aepyptera)." Ohio : Ohio University, 2006. http://www.ohiolink.edu/etd/view.cgi?ohiou1141746230.

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40

Chubb, Tanya L. A. "Phylogeography and Hybridisation of the New Zealand House Mouse." The University of Waikato, 2008. http://hdl.handle.net/10289/2479.

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Three subspecies of house mice of different geographic origins have reached New Zealand; M. m. domesticus (10 haplotypes), M. m. musculus (1 haplotype) both from Europe, and M. m. castaneus (3 haplotypes) from Asia. Identifying the sources of the multiple historical introductions of the house mouse is a complex issue, particularly during the peak colonisation period of 1830-1880. The early European settlers came with many bags, crates, plants, seed and livestock, which provided ample travel opportunities for stowaway rats and mice. With the assistance of volunteers, I have collected mice from various locations throughout the New Zealand region, to confirm the previously recorded haplotypes and to look for evidence of hybridisation between the colonising subspecies. Morphological characteristics traditionally used for identification of subspecies were compared with genetic characters, to establish whether the use of morphology is still a viable method of identifying subspecific distinctions between mice in New Zealand. While no M. m. musculus haplotypes were found among these samples, some mice still had the coat colouration typical of M. m. musculus. Data from mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) markers revealed some surprising results. I have found six new M. m. domesticus haplotypes, and three new M. m. castaneus haplotypes. The data have also revealed extensive hybridisation, particularly between M. m. domesticus and M. m. castaneus. The finding of the new haplotypes supports the previous assumption that there were multiple introductions of mice into New Zealand, but the finding of M. m. castaneus in inland towns and cities does not support the associated assumption that European mice were initially the only mice present in New Zealand. Rather, the wide distribution of M. m. castaneus suggests that this subspecies probably arrived during the early nineteenth century. The house mouse has long been recognised as an ideal organism for hybridisation studies, and the finding of a hybrid zone within New Zealand would provide an excellent opportunity to extend our knowledge of hybridisation and gene transfer. Previous studies found M. m. domesticus in Napier, and a M. m. musculus/M. m. castaneus hybrids in Wellington. A systematic sampling programme was undertaken between Wellington and Napier following State Highway 2 (SH2), in an attempt to locate a hybrid zone. Analysis of mtDNA and nDNA showed that, M. m. castaneus was found as far North as Dannevirke, and M. m. domesticus as far South as Featherston. There was also extensive evidence of integration of M. m. domesticus nDNA markers into mice with M. m. castaneus mtDNA. There was no clear support for a hybrid zone, but this does not mean that one has not existed in the past and that it has since been overrun by movement of mice with humans and their goods. Identification of subspecies by morphological characteristics, while used with confidence in other countries, is of little use in New Zealand. Extensive hybridisation/and or introgression between the subspecies has long since blurred any morphological distinctions the colonising mice may have had. I propose that these physical characters should be used in support of genetic analysis of the subspecies. The official classification of the New Zealand house mouse currently stands as M. m. musculus, however, data collected does not support this and it is proposed that the official classification should be changed to M. m. domesticus.

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Marshall, H. Dawn. "Molecular evolution and phylogeography of common chaffinches (Fringilla coelebs)." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape16/PQDD_0012/NQ28010.pdf.

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42

Dueck, Gregory S. "Genetic relations and phylogeography of woodland and barrenground caribou." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp01/MQ34355.pdf.

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Lourie, Sara Anne. "Phylogeography of Southeast Asian seahorses in a conservation context." Thesis, McGill University, 2004. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=84284.

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This thesis investigates the potential role of historical isolation of ocean basins in promoting diversification among marine organisms in Southeast Asia. It also questions the possible effects of Pleistocene exposure of the Sunda Shelf on present day marine distributions and genetic diversity. Four species of exploited seahorses (genus Hippocampus), with differing ecological parameters, are used to test historical hypotheses. The results (based on cytochrome b DNA sequencing) suggest that significant phylogeographic structure does exist among seahorse populations in Southeast Asia, but that the patterns are only partially concordant across species. Distinct phylogeographic breaks are seen in H. barbouri, H. kuda, and H. trimaculatus, whereas greater spatial overlap of haplotypes in H. spinosissimus indicates more extensive gene flow. The phylogeographic history of the two shallow water species (H. barbouri and H. kuda) appears to have been primarily shaped by fragmentation and/or long-distance colonisation events. Both species show patterns consistent with hypotheses of divergence mediated by ocean basins separations. The deeper water species (H. spinosissimus and H. trimaculatus) show more evidence of range expansion and isolation by distance. Hippocampus trimaculatus shows a deep east-west phylogeographic division at right angles to that predicted by the separation of the Indian versus Pacific Ocean basins and instead parallels the terrestrial division known as Wallace's Line. Different species have also responded differently to the reflooding of the Sunda Shelf at the end of the last Ice Age: the two deeper water species have colonised it extensively suggesting limited barriers to movement, whereas the shallow water species have not. It is possible that the populations of H. kuda now inhabiting the shelf may stem from populations that found refuge in brackish water lakes when the shelf was exposed to the air. All four species are heav

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44

Grindon, Adele. "Mitochondrial phylogeography of three European helicid land snail species." Thesis, University of Nottingham, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.523072.

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45

Chan, Hon-ki, and 陳翰奇. "Phylogeography and cryptic diversity of occidozyga lima (gravenhorst 1829)." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hub.hku.hk/bib/B50605835.

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The anuran fauna has been found to harbor substantial cryptic diversity, and chronic, low-level population declines in evolutionarily significant units can be masked by a lack of resolution on this diversity. Numerous species previously believed to be common and widespread have been found to represent cryptic species complexes consisting of distinct genetic lineages with restricted ranges. Most research on cryptic diversity has focused on high elevation areas because they usually harbor higher diversity and levels of endemism; thus cryptic diversity from lowland areas remains poorly understood. This study investigated the population divergence of the pearly-skinned floating frog (Occidozyga lima), a lowland wetland species broadly distributed throughout Southeast Asia and considered common throughout its range. I analyzed six DNA regions (Histone H3, Tyrosinase exon-1, 28S, 16S, ND1 and 12S; a total of 4,650 base pairs) to reconstruct the phylogenetic relationships among populations. Morphometric analyses were conducted to test for morphological differentiation. Both genetic and morphological data revealed substantial lineage divergence in O. lima. I found that sympatric lineages are not sister lineages, a common feature of cryptic species complexes. The current status of O. lima as a single species should be rejected. Three candidate species were delineated based on 5% mitochondrial 16S genetic divergence. The name O. lima should be restricted to populations in the type locality, Java, Indonesia (candidate species I), and two new species should be assigned to populations from South China to Northern Indochina (candidate species II) and Southern Indochina to Myanmar (candidate species III). Resolving the widely-distributed species complex into three valid species requires reassessment of the IUCN conservation status. Given observed population declines in South China and Indonesia, the new species are likely to belong to a higher threat category. Species considered to be common and widespread are under-represented in current conservation planning because conservation priority has been biased toward rare and range-restricted species. Increasing evidence suggests that species whose populations are considered stable are declining at rates exceeding those of rare species. Using habitat availability as a proxy for their occurrence, it appears that the three clades are threatened to varying degrees because of habitat loss. Populations from South China and Indonesia are the most threatened due to massive development of lowland habitats. In addition, conversion of wet agriculture to permanent dry crops and the predicted increases in persistent droughts pose threats to amphibian populations in lowland habitats. The extirpated O. lima populations should be restored in Hong Kong by means of reintroduction. A study of the reproductive ecology of O. lima followed by experimental reintroduction is necessary to restore populations and may serve as a model for public education about amphibian conservation. Given the rapid decline of this species in South China, a reintroduction plan and resources to initiate a reintroduction are urgently needed. published_or_final_version Biological Sciences Master Master of Philosophy

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Reynolds, Terry Veronica. "Phylogeny and phylogeography of South African barnacles (Thoracica; Cirripedia)." Thesis, Stellenbosch : Stellenbosch University, 2011. http://hdl.handle.net/10019.1/18121.

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Thesis (MSc)--Stellenbosch University, 2011. ENGLISH ABSTRACT: South Africa is known for its high marine invertebrate diversity but the evolutionary histories of these species are largely unknown. The present study contributes to the growing body of phylogeographic studies of southern African coastal species. The main aim is to better understand the colonization and diversification of South African barnacles. To investigate the phylogeographic pattern in the southern African volcano barnacle, Tetraclita serrata, 410 individuals from 20 sampling localities were analyzed. In addition, to understand the colonization and diversification patterns of South African barnacle species, nine taxa were included in a molecular phylogeny derived from the nuclear gene, 18S rRNA. With only a limited number of 18S sequences available on GenBank, a separate phylogenetic tree, for the mitochondrial gene, was constructed to determine whether the genus Tetraclita is monophyletic. Restricted gene flow in some geographical areas was hypothesized for T. serrata based on oceanic circulation patterns; known biogeographic regions; and features such as the Agulhas Bank, which has shaped the population genetic structure of several other South African marine organisms. The population genetic structure was investigated using the mitochondrial cytochrome oxidase subunit 1 (CO1) and nuclear internal transcribed spacer 1 (ITS1) genes. Phylogenetic and population genetic analyses of the CO1 gene revealed two distinct genetic clades with overlapping distributions. The nuclear ITS1 data performed on a subset of individuals drawn from both mtDNA clades revealed a single lineage. The pattern observed can be ascribed to a historical event that may have been responsible for the formation of allopatric lineages that have since come into secondary contact. On the other hand, the pattern observed may be as result of incomplete sorting of nDNA alleles, in which case, given that the two mtDNA clades are not geographically isolated, could be explained by selective pressures acting on the species due to ecological constraints. No clear phylogeographic structure was found within each of these clades and the direction of gene flow of T. serrata individuals can be linked to the oceanographic features found along the South African coast. In contrast to most other South African marine species studied to date, the haplotype network, mismatch distributions and time since expansion suggest that the effective population size of T. serrata was not severely affected by the Last Glacial Maximum. It is proposed that further investigations into the phylogeography of coastal marine species, particularly obligatory sessile species such as barnacles, are required to determine whether the patterns observed in T. serrata is a rare history, or not. Neighbour-joining, maximum parsimony and Bayesian analyses on the CO1 gene provide evidence for the monophyly of the genus Tetraclita; however, Tetraclita species found in South Africa do not share a common ancestry suggesting multiple colonization events. This study has also accidently led to the discovery of an introduced species, Balanus perforatus, native to Europe, and I discuss the potential of the alien becoming invasive on the east coast of South Africa where it was found. AFRIKAANSE OPSOMMING: Suid-Afrika is bekend vir sy hoë mariene ongewerwelde diversiteit, maar die evolusionêre geskiedenis van hierdie spesies is grootliks onbekend. Hierdie studie is gedoen om by te dra tot die filografiese studies van suider Afrikaanse kus spesies en om die kolonisasie en diversifikasie van die Suid-Afrikaanse eendmossels beter te verstaan. Om die genetiese struktuur van die bevolkings van die vulkaan eendmossel, Tetraclita serrata, wat langs die Suid-Afrikaanse kuslyn voorkom, te bestudeer, was 410 individue van 20 lokaliteite ontleed. Daarbenewens, om die kolonisasie en diversifikasie van Suid-Afrikaanse eendmossels te verstaan, was nege spesies ingesluit in 'n molekulêre filogenie wat gebaseer is op die kern geen, 18s rRNA. Met slegs 'n beperkte aantal 18s DNS volgordes beskikbaar op GenBank,is 'n aparte filogenetiese boom, vir die mitochondriale geen COI, gekonstrueer om te bepaal of die genus Tetraclita monofileties is. Beperkte geen-vloei in sommige geografiese gebiede was verwag vir T. serrrata gebaseer op oseaniese sirkulasiepatrone; bekende biogeografiese streke, en kenmerke soos die Agulhas Bank, wat die filogeografiese struktuur van verskeie ander Suid- Afrikaanse mariene organismes beïnvloed het. Die genetiese struktuurvan die bevolkings is geondersoek met behulp van die mitochondriale sitochroom oksidase subeenheid 1 (COI) en kern interne getranskripeerde spasieërder 1 (ITS1) gene. Geen duidelike bevolkings genetiese struktuur is gevind nie en die rigting van geenvloei van T. serrata individue kan gekoppel word aan die oseanografiese kenmerke wat langs die Suid-Afrikaanse kus voorkom. Filogenetiese en bevolking genetiese ontleding van die COI geen openbaar twee afsonderlike klades maar met oorvleuelende geografiese verspruidings. Die ITS1 data-analise wat uitgevoer was op 'n subset van individue wys op 'n enkele spesie. Die waargenome patroon dui op 'n belangrike historiese verskil tussen die twee klades. 'n Geskiedkundige gebeurtenis was dalk verantwoordelik vir die vorming van twee evolusionêre lyne wat sederdien sekondêre kontak het. Aan die ander kant, kan die patroon waargeneem word as gevolg van die onvolledige sortering van nDNA allele, in welke geval, gegee dat die twee mtDNA clades nie geografies geïsoleer is nie, dit verduidelik kan word deur selektiewe druk wat op die spesie was as gevolg van fisiologiese of ekologiese beperkings. Die statistiese parsimonie netwerk, ongelyksoortige verspreidings en tyd sedert die bevolkingsuitbreiding dui daarop dat T. serrata die laaste ysagtige maksimum tydperk oortleef het. Tot op hede het geen Suid- Afrikaanse mariene spesies so 'n patroon gewys nie. So, verdere ondersoeke in die filogeografie van die kus mariene spesies, veral verpligte sittende spesies soos eendmossels, word vereis om te bepaal of die patroon waargeneem in T. serrata 'n seldsame geskiedenis het, of nie. Buur-aansluiting, maksimum parsimonie en Bayesian afleiding op die CO1 geen het bewyse verskaf vir die monofiletiese afkoms van die genus Tetraclita, maar Tetraclita spesies wat in Suid Afrika gevind is, deel nie ‘n gemeenskaplike afkoms nie, wat weer bewyse verskaf vir verskeie kolonisasie gebeure. Hierdie studie het gelei tot die ontdekking van 'n eksotiese spesie, Balanus perforatus, inheems aan Europa, en die potensiaal van die indringer om ontwykend te raak aan die ooskus van Suid-Afrika waar dit gevind is word bespreek. The South African National Research Foundation (NRF) and Stellenbosch University

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47

Duguid, R. A. "Population genetics and phylogeography of brown trout (Salmo truttal)." Thesis, Queen's University Belfast, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.269048.

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48

Gosney, Louise Mary. "Phylogeography and population structure of carabid beetle Pterostichus melanarius." Thesis, University of East Anglia, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.247110.

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Hsu, Yuan-yuan, and 許媛媛. "Phylogeography of Microphysogobio alticorpus." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/75919245604205216665.

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碩士 國立臺南大學 生態科學與技術學系環境生態碩士班 101 In this study, make ues of the mitchondrial DNA cytochrome b and D-loop gene to explore Taiwan freshwater fish phylogeographic pattern and phylogeographical analyses on Microphysogobio alticorpus samples from six rivers in Taiwan were conducted for biogeographic studies. A total of 12 haplotypes were genotyped for mtDNA D-loop gene and 17 haplotypes were genotyped for mtDNA cytochrome b gene in 90 specimens. Three major phylogenetic haplotype groups were revealed via phylogenetic analysis. Population differentiation analyses indicated significant genetic structure (FST = 0.78 and 0.89).Mismatch distribution analysis, neutrality tests and Bayesian skyline plots indicated the river is highly differentiated , but no significant population expansion for Microphysogobio alticorpus. This study suggests that the size and stability of population ,and the water body size as the major reason.

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Lin, Chung-Jian, and 林宗鍵. "Phylogeography of Hemibarbus labeo (Cyprinidae)." Thesis, 2008. http://ndltd.ncl.edu.tw/handle/45694825359786136768.

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博士 國立成功大學 生命科學系碩博士班 96 Nucleotide sequences of the D-loop control region of mtDNA were used to assess the genetic structure and phylogeography of Hemibarbus labeo in Mainland China and Taiwan. A hierarchical analysis of molecular variance of populations in 11 major streams from three geographical regions revealed significant structuring among populations and among geographical regions. High levels of nucleotide diversity (π= 1.88%) and haplotype diversity (h= 0.96 ± 0.009) suggested a large effective population size. A neighbor-joining tree based on the mtDNA variation identified two ancient mtDNA lineages, which coalesced to the most recent common ancestor (TMRCA) approximately 0.39 million years ago. Overlapping distribution of the major lineages displayed low correspondence with geographical regions and reflected a scenario of secondary mergence after long isolation. Gene genealogy and IM simulations of demographic dynamics revealed a unidirectional, northward migration; mismatch distributions also supported a recent demographic expansion. Nevertheless, there existed a phylogeographical structure that agreed with a biogeographical hypothesis. That is, within each lineage, a close phylogeny between populations of the River-Campagna and East-Pacific regions was supported by the mtDNA gene genealogy. The degree of genetic differentiation was correlated with geographical distances between populations, displaying a pattern of ‘isolation by distance’. Gene genealogy of mtDNA revealed that Yangtzejiang population may act as a divergence center of H. labeo. In addition, Taiwan population was colonized via a recent a founder event, likely from population GS (Yangtzejiang) about 30,500 years before present. Low haplotype number and genetic variability also suggested possible bottleneck events in the ZO and DZ populations.

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