Academic literature on the topic 'Molecular species delimitation'

Here, we test the current generic delimitation of Rostania (Collemataceae, Peltigerales, Ascomycota) utilizing molecular phylogeny and morphological investigations. Using DNA sequence data from the mitochondrial SSU rDNA and two nuclear protein-coding genes (MCM7 and β-tubulin) and utilizing parsimony, maximum likelihood and Bayesian phylogenetic methods, Rostania is shown to be non-monophyletic in the current sense. A new generic delimitation of Rostania is thus proposed, in which the genus is monophyletic, and three species (Rostaniacoccophylla, R.paramensis, R.quadrifida) are excluded and transferred to other genera. Rostaniaoccultata is further non-monophyletic, and a more detailed investigation of species delimitations in Rostania s. str. is needed. The new combinations Leptogiumparamense and Scytiniumquadrifidum are proposed.

Capparis spinosa L. (Capparidaceae) is the largest genus of the family Capparaceae, distributed in pantropical region. C. spinosa is known as a medicinal plant species. In Iran, different parts of caper bush plants are used as diuretics, tonics and in treatment of malaria and joint disease. Till present time, there has been no detailed information available on molecular phylogeny and genetic structure of these species in the country. Therefore, the present study was conducted with the aim to investigate species delimitation by both morphological and molecular data and to reveal genetic diversity and population structure in these five of Capparis species. For this study, 108 randomly collected plants from 20 geographical populations in of Capparis species were used. We encountered extensive within species genetic and morphological diversity. ISSR molecular markers could delimit the studied species. STRUCTURE analysis revealed the occurrence gene flow between these species. The Mantel test showed correlation between genetic distance and geographical distance of the populations studied. Phylogenetic tree was constructed based on ITS data set which separated out-groups from the studied species. Genetic affinity of the studied species have been discussed.

Abstract Brittle stars (Echinodermata: Ophiuroidea) comprise over 2, 000 species, all of which inhabit marine environments and can be abundant in the deep sea. Morphological plasticity in number and shape of skeletal parts, as well as variable colors, can complicate correct species identification. Consequently, DNA sequence analysis can play an important role in species identification. In this study we compared the genetic variability of the mitochondrial cytochrome c subunit I gene (COI) and the nuclear small subunit ribosomal DNA (SSU, 18S rDNA) to morphological identification of 66 specimens of 11 species collected from the North Atlantic in Icelandic waters. Also two species delimitation tools, Automatic Barcode Gap Discovery (ABGD) and General Mixed Yule Coalescence Method (GMYC) were performed to test species hypotheses. The analysis of both gene fragments was successful to discriminate between species and provided new insights into some morphological species hypothesis. Although less divergent than COI, it is helpful to use the SSU region as a complementary fragment to the barcoding gene.

AbstractEumerusis one of the most diverse genera of hoverfly worldwide. Species delimitation within genus is considered to be difficult due to: (a) lack of an efficient key; (b) non-defined taxonomical status of a large number of species; and (c) blurred nomenclature. Here, we present the first molecular study to delimit species of the genus by using a fragment of the mitochondrial cytochrome-c oxidase subunit I gene (COI) gene. We assessed 75 specimens assigned to 28 taxa originating from two biogeographic zones: 22 from the western Palaearctic and six from the Afrotropical region. Two datasets were generated based on different sequence lengths to explore the significance of availability of more polymorphic sites for species delimitation; dataset A with a total length of 647 bp and dataset B with 746 bp. Various tree inference approaches and Poisson tree processes models were applied to evaluate the putative ‘taxonomical’ vs. ‘molecular’ taxa clusters. All analyses resulted in high taxonomic resolution and clear species delimitation for both the dataset lengths. Furthermore, we revealed a high number of mitochondrial haplotypes and high intraspecific variability. We report two major monophyletic clades, and seven ‘molecular’ groups of taxa formed, which are congruent with morphology-based taxonomy. Our results support the use of the mitochondrial COI gene in species diagnosis ofEumerus.

The accurate identification of an organism is the basis of all biological disciplines. Although there have been many different species concepts and methods proposed, researchers generally choose the most appropriate concept according to their interests. However, each species concept has both advantages and disadvantages. In such cases, an integrated concept based on evidence obtained from different species concepts and methods is suitable for the accurate delimitation of a species. The biggest dilemma of integrated species delimitation methods is the inconsistency between species concepts and methods. Herein, the congruency of the different concepts and methods was tested to reveal the relationship of the Noccaea densiflora species complex. Nuclear ribosomal internal transcribed spacer, chloroplast trnL-F, and trnQ-5′rps16 regions were used for species delimitation using the multispecies coalescent model as implemented in two developed Bayesian methods. Internal transcribed spacer and trnL-F regions were also used for Templeton, Crandall, and Singh haplotype network analyses. In addition to morphological measurements from different populations and vouchers, specific bioclimatic data values were also used for the principal component analysis. Based on the analyses, it was determined that only one population of N. densiflora (Boiss. & Kotschy) F.K. Mey. and one of Noccaea microstyla (Boiss.) F.K. Mey. were clearly distinct, whereas the rest of the specimens remain taxonomically uncertain.

Sri Lanka is an amphibian hotspot of global significance. Its anuran fauna is dominated by the shrub frogs of the genus Pseudophilautus. Except for one small clade of four species in Peninsular India, these cool-wet adapted frogs, numbering some 59 extant species, are distributed mainly across the montane and lowland rain forests of the island. With species described primarily by morphological means, the diversification has never yet been subjected to a molecular species delimitation analysis, a procedure now routinely applied in taxonomy. Here we test the species boundaries of Pseudophilautus in the context of the phylogenetic species concept (PSC). We use all the putative species for which credible molecular data are available (nDNA–Rag-1; mt-DNA– 12S rRNA, 16S rRNA) to build a well resolved phylogeny, which is subjected to species delimitation analyses. The ABGD, bPTP, mPTP and bGMYC species delimitation methods applied to the 16S rRNA frog barcoding gene (for all species), 12S rRNA and Rag-1 nDNA grouped P. procax and P. abundus; P. hallidayi and P. fergusonianus; P. reticulatus and P. pappilosus; P. pleurotaenia and P. hoipolloi; P. hoffmani and P. asankai; P. silvaticus and P. limbus; P. dilmah and P. hankeni; P. fulvus and P. silus.. Surprisingly, all analyses recovered 14 unidentified potential new species as well. The geophylogeny affirms a distribution across the island’s aseasonal ‘wet zone’ and its three principal hill ranges, suggestive of allopatric speciation playing a dominant role, especially between mountain masses. Among the species that are merged by the delimitation analyses, a pattern leading towards a model of parapatric speciation emerges–ongoing speciation in the presence of gene flow. This delimitation analysis reinforces the species hypotheses, paving the way to a reasonable understanding of Sri Lankan Pseudophilautus, enabling both deeper analyses and conservation efforts of this remarkable diversification. http://zoobank.org/urn:lsid:zoobank.org:pub:DA869B6B-870A-4ED3-BF5D-5AA3F69DDD27.

The genus Xanthoparmelia is the largest genus of lichen- forming fungi with about 800 species worldwide. Xanthoparmelia is also common in the deserts of central Mexico, but only a few molecular studies exist on its species’ diversity in this region. In this study, we sampled 38 Xanthoparmelia species from around the world including species from the xerophytic scrubs of central Mexico to assess the diversity using an integrative approach. Molecular phylogenetic analyses were performed using a combination of the ITS, mtSSU and nuLSU genetic markers. We evaluated our phylogenetic results in a context of traditional morphological and chemical characters. The combined evidence of molecular, morphological, and chemical data identified a total of 18 Xanthoparmelia species-level lineages occurring in central Mexico. However, numerous traditionally circumscribed species did not form monophyletic groups in the molecular phylogenetic reconstructions. This conflict indicates that taxonomy and species delimitation in the genus Xanthoparmelia requires revision and emphasizes the importance of molecular evidence for more robust species delimitations in this genus.

Accurate species description in the marine environment is critical for estimating biodiversity and identifying genetically distinct stocks. Analysis of molecular data can potentially improve species delimitations because they are easily generated and independent, and yield consistent results with high statistical power. We used classical phylogenetic (maximum likelihood and Bayesian inference) and coalescent-based methods (divergence dating with fossil calibrations and coalescent-based species delimitation) to resolve the phylogeny of the spiny lobster Panulirus homarus subspecies complex in the Indo-West Pacific. Analyses of mitochondrial data and combined nuclear and mitochondrial data recovered Panulirus homarus homarus and Panulirus homarus rubellus as separately evolving lineages, while the nuclear data trees were unresolved. Divergence dating analysis also identified Panulirus homarus homarus and Panulirus homarus rubellus as two distinct clades which diverged from a common ancestor during the Oligocene, approximately 26 million years ago. Species delimitation using coalescent-based methods corroborated these findings. A long pelagic larval life stage and the influence of ocean currents on post-larval settlement patterns suggest that a parapatric mode of speciation drives evolution in this subspecies complex. In combination, the results indicate that Panulirus homarus rubellus from the Southwest Indian Ocean is a separately evolving lineage and possibly a separate species.

Integrative taxonomy is crucial for discovery, recognition, and species delimitation, especially in underestimated species complex or cryptic species, by incorporating different sources of evidence to construct rigorous species hypotheses. The spider genus Physocyclus Simon, 1893 (Pholcidae, Arteminae) is composed of 37 species, mainly from North America. In this study, traditional morphology was compared with three DNA barcoding markers regarding their utility in species delimitation within the genus: 1) Cytochrome c Oxidase subunit 1 (CO1), 2) Internal Transcribed Spacer 2 (ITS2), and 3) Ribosomal large subunit (28S). The molecular species delimitation analyses were carried out using four methods under the corrected p-distances Neighbor-Joining (NJ) criteria: 1) Automatic Barcode Gap Discovery (ABGD), 2) Assemble Species by Automatic Partitioning (ASAP), 3) General Mixed Yule Coalescent model (GMYC), and 4) Bayesian Poisson Tree Processes (bPTP). The analyses incorporated 75 terminals from 22 putative species of Physocyclus. The average intraspecific genetic distance (p-distance) was found to be < 2%, whereas the average interspecific genetic distance was 20.6%. The ABGD, ASAP, and GMYC methods were the most congruent, delimiting 26 or 27 species, while the bPTP method delimited 33 species. The use of traditional morphology for species delimitation was congruent with most molecular methods, with the male palp, male chelicerae, and female genitalia shown to be robust characters that support species-level identification. The barcoding with CO1 and 28S had better resolution for species delimitation in comparison with ITS2. The concatenated matrix and traditional morphology were found to be more robust and informative for species delimitation within Physocyclus.

The plant family Gesneriaceae is represented in Sri Lanka by six genera: Aeschynanthus, Epithema, Championia, Henckelia, Rhynchoglossum and Rhynchotechum, with 13 species (plus one subspecies/variety) of which ten are endemic including the monotypic genus Championia, according to the last revision in 1981. They are exclusively distributed in undisturbed habitats, and some have high ornamental value. The species are morphologically diverse, but face a problem of taxonomic delineation, which is further complicated by the presence of putative hybrids. Sri Lanka and Indian Peninsula, represent the Deccan plate of the ancient Gondwanan supercontinent. The presence of a relict flora may indicate the significance of the geological history of the Deccan plate for the evolution of angiosperms. The high degree of endemism here, along with their affinities to the global angiosperm flora paints a complex picture, but its biogeographic history is still unclear. The pantropical family Gesneriaceae distributed in Sri Lanka and South India is therefore an appropriate study group in this context. Besides, the family itself has a complex but largely unresolved biogeographical history especially concerning the origin and diversification of Old World Gesneriaceae. Modern approaches for the taxonomic studies were applied, integrating morphological and molecular data. Multiple samples were collected for each species across their geographical distribution. Nuclear ITS and chloroplast trnL-F sequences for the taxa from Sri Lanka were used to generate regional genus phylogenies of all six genera, using maximum parsimony. The rate of evolution of the nuclear ITS region versus chloroplast trnL-F was varied greatly across the six genera studied. Molecular delimitations were mostly congruent with the classical taxonomy. Over 65 taxonomic characters were studied in detail to recognize synapomorphies for clades and taxa. A complete taxonomic revision of Gesneriaceae in Sri Lanka, including lectotypification, was conducted based on both, the molecular and morphological data. This resulted in the recognition of 14 species in the six genera, including one newly described species H. wijesundarae Ranasinghe and Mich. Möller. Henckelia communis and H. angusta were not supported molecularly as two separate entities but are recognized as two species because of consistent morphological differences between them. Henckelia humboldtiana is proposed to represent a species complex due to its highly variable and inconsistent molecular and morphological diversity and overlap with H. incana and H. floccosa; more research is needed here. National conservation assessments were conducted, and all 14 species were recognized as threatened. Biogeographic affinities of Sri Lankan Gesneriaceae were elucidated, generating a dated phylogeny using an existing matrix of four plastid gene regions; trnL-F, matK, rps16 and ndhF, amended by sequences generated in this study. The final combined matrix included 175 taxa including newly generated sequences for the 13 Sri Lankan taxa. Phylogenetic trees were generated using parsimony, maximum likelihood and Bayesian inference. Molecular dating was carried out using BEAST and ancestral area reconstruction using BioGeoBears. These analyses indicated that the six genera of Gesneriaceae arrived in Sri Lanka separately and sometimes different time periods. One lineage dated back to the early diversification of the subfamily Didymocarpoideae (generally regarded as the Old World Gesneriaceae), which occurred around the KT boundary, before the Deccan plate was connected to Asia.

Les écosystèmes des eaux souterraines sont de plus en plus reconnus pour leur faune endémique, phylogénétiquement ancienne et écologiquement spécialisée. Avec plus de 425 espèces décrites, les amphipodes niphargidés constituent la famille des eaux souterraines la plus riche en espèces au monde et un système modèle intéressant pour la biologie de l'évolution. Cependant, les scientifiques doivent faire face à des données incomplètes et biaisées en raison de trois déficits majeurs: le déficit Linnéen pour la taxonomie, le déficit Darwinien pour la phylogénie, et le déficit Wallacien pour la biogéographie. La présente thèse vise à évaluer l'importance de ces déficits chez les niphargidés, ouvrant ainsi la voie pour y remédier. Le premier chapitre est une évaluation des effets de la découverte d'espèces cryptiques (une des causes du déficit Linnéen) sur notre compréhension des modèles de distribution à grande échelle de la diversité des niphargidés. Contrairement à ce que l'on attendait, les espèces cryptiques putatives sont réparties de manière homogène le long des gradients environnementaux, et leur découverte ne modifie donc pas notre compréhension des modèles de distribution. Le deuxième chapitre analyse l'importance de l'application des techniques moléculaires à la taxonomie des niphargidés. En étudiant le genre Microniphargus, la morphologie seule s'est avérée peu informative en raison de la pédomorphose et de l'homoplasie. L'utilisation de marqueurs ADN a permis d'attribuer le genre à une famille différente (Pseudoniphargidae), venant éclaircir les relations phylogénétiques au sein des Niphargidae (et contribuant ainsi à remédier au déficit Darwinien). Le troisième chapitre traite du rôle des régressions et transgressions marines sur la distribution des niphargidés en utilisant la biogéographie moléculaire et une modélisation biogéographique innovante (afin de remédier au déficit Wallacien). Les résultats soutiennent l'idée que la dispersion a joué un rôle essentiel dans la biogéographie historique des niphargidés, en montrant que leurs voies de dispersion sont corrélées à des événements paléogéographiques anciens. Enfin, le quatrième chapitre traite de la taxonomie, de la phylogénie et de la biogéographie d'un clade de niphargidés distribué dans la région des Alpes et des Carpates, et illustre un cas de discordance mitonucléaire dans la délimitation d'espèces vivant dans des zones affectées par les glaciations quaternaires. Une histoire complexe de divergence de lignées évolutives et de contacts secondaires pendant les fluctuations climatiques du Pléistocène explique la plus grande variabilité de l'ADN mitochondrial par rapport aux marqueurs nucléaires. Dans une telle situation, la description formelle d'espèces cryptiques basée sur le seul barcodage de l'ADN mitochondrial, comme dans certains articles récents sur les niphargidés, n'est pas recommandée. Cette thèse ouvre plusieurs perspectives pour des recherches futures basées sur la taxonomie intégrative et la modélisation biogéographique, permettant aux niphargidés très diversifiés de jouer un rôle majeur dans la surveillance des écosystèmes des eaux souterraines.
Doctorat en Sciences
info:eu-repo/semantics/nonPublished

Accurate species delimitation has critical implications for ecological and conservation studies; and for understanding factors driving diversification. However, a growing body of evidence indicates that morphology-based species circumspection in lichenized ascomycetes often fails to accurately represent the number of fungal species. The use of molecular data in lichen systematics provides an important alternative to traditional morphological characters for identifying natural groups and assessing evolutionary histories in challenging lichen taxa. In this work, I examined two common lichen-forming genera in western North America, Rhizoplaca and Xanthoparmelia, as models for investigating character evolution, species delimitation in morphologically and chemically diverse species, and identification of lineages in the early stages of divergence. Phylogenetic hypotheses were reconstructed to assess character evolution using sequence data from four nuclear ribosomal markers and fragments from two nuclear loci. I applied a multifaceted approach to delimit species in Rhizoplaca and Xanthoparmelia by assembling multiple lines of evidence using DNA sequence data, and genealogical and population genetic analyses. I have found that traditionally circumscribed species are not supported by molecular data. For example, in Rhizoplaca previously unrecognized lineages were identified within what has thus far been considered a single species. In contrast, morphologically and chemically distinct species within Xanthoparmelia were not supported by molecular data. Distinct medullary chemistries, growth forms, and the production of vegetative diaspores appear to have evolved independently multiple times in Xanthoparmelia. This work clearly indicates that morphological and chemical characters do not always accurately reflect lichen species diversity within even the best known and studied genera. My study of the Rhizoplaca melanophthalma species complex demonstrates that the genus Rhizoplaca, as presently circumscribed, is more diverse in western North American than previously thought. I present these analyses as a working example of species delimitation in morphologically cryptic lichenized fungi. In Xanthoparmelia diagnostic morphological and chemical characters have evolved in a highly homoplasious manner. In contrast to other studies documenting previously undiscovered fungal lineages masked within lichen species circumscribed by traditional morphological and chemical characters, my work suggests that species diversity has been overestimated in the lichen genus Xanthoparmelia.

China harbors 10% of the world's salamander species. Studying their evolutionary history provides critical insights into the evolution of the fauna of the Far East. The stout newts (Pachytriton, also known as paddle-tailed newts) are a genus of aquatic montane salamanders that are widely distributed in southeastern China. Despite their longstanding popularity among the global pet trade, little is known of their biology beyond external morphology. My thesis presents the first systematic study to elucidate phylogenetic relationships, character evolution, biogeographic patterns, species delimitation, and speciation mechanisms in this genus.

Molecular taxonomy is the science that classifies and identifies organism basing on molecular information. Its application to species-rich groups of organisms, as insects, could improve and accelerate taxa identification and delimitation. The efficiency and the limits of the methods for molecular taxonomy have to be properly evaluated for achieving unbiased results with this taxonomic approach. The main aims of this thesis are: i) to develop COI barcode libraries for Euro-Mediterranean Chrysomelidae identification and test DNA-barcoding efficiency in the identification of the species of the family; ii) to estimate group-specific nucleotide distance thresholds for the molecular identification of Chrysomelidae taxa and compare the error related to their use with the error related to the use of a general threshold value estimated for the whole family; iii) to apply molecular species delimitation methods to other insects taxa with the aim of resolving their taxonomic status in an integrative taxonomy framework; vi) to test the influence of factors intrinsic to the analysed data on molecular species delimitation efficiency. The results obtained confirmed the high efficiency of DNA-Barcoding as tool for Chrysomelidae molecular identification (94-99% efficiency) and the usefulness of molecular delimitation methods in integrative taxonomy for resolving taxonomic debated issues. The use of groups specific thresholds resulted to be related to a significantly lower identification error than the use of a general threshold for the whole Chrysomelidae, suggesting how the use of fixed thresholds for taxa identification is unwise. Finally, some factors, i.e. the species delimitation methods used, the geographic intraspecific distance among individuals collection localities and the difficulties in morphological identification of species, resulted to affect the efficiency of molecular species delimitation.

Orientador: Antonia Cecilia Zacagnini Amaral
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: Espécies são unidades fundamentais da biologia e sua identificação é essencial para a pesquisa nos mais diversos campos. Esta tarefa, no entanto, é dificultada por limites interespecíficos naturalmente mal definidos, especialmente em ambientes marinhos, onde complexos de espécies crípticas são comuns. Assim, a delimitação de espécies tem recebido grande atenção nos últimos anos e técnicas moleculares têm se mostrado de grande importância para a questão. Corbula (Bivalvia: Corbulidae) é um gênero frequente e ecologicamente importante em comunidades bentônicas marinhas de sublitoral. A taxonomia do grupo é bastante confusa, em parte devido à plasticidade fenotípica das conchas que dificulta o estabelecimento de limites morfológicos entre as espécies. O presente estudo teve como objetivo estudar, com base em sequências de dois marcadores moleculares (COI e 16S), os limites entre seis espécies de Corbula morfologicamente identificadas da costa sudeste e sul do Brasil, de forma a testar a delimitação morfológica. Como se trata de espécies predominantemente de sublitoral, o material analisado encontrava-se preservado em álcool, havendo sido fixado em formol. Dessa forma, fez-se necessário o desenvolvimento de protocolos específicos de extração e amplificação. Uma combinação de extração orgânica com adsorção em sílica mostrou-se o melhor método de extração de DNA total. Para as reações de amplificação, a utilização de nested PCR produziu resultados superiores à PCR direta. As análises de delimitação utilizaram quatro métodos diferentes, dois baseados em árvores (GMYC e Brownie) e dois não (regra das 4x e ABGD). Os resultados divergiram entre métodos e marcadores, mas a combinação das diferentes linhas de evidência permitiu corroborar a delimitação morfológica de três espécies (Corbula caribaea, Corbula tryoni e Corbula lyoni). Os indivíduos identificados como Corbula patagonica dividiram-se em duas espécies distintas. O único indivíduo de Corbula aequivalvis foi considerado distinto das outras espécies e um indivíduo atribuído a Corbula sp1 não pôde ser distinguido de C. caribaea
Abstract: Species are fundamental unities in many biological studies and, being so, their identification is essential for researches in many different fields. This task, however, is complicated by badly defined interspecies boundaries, especially in the sea, where cryptic species are quite common. Species delimitation has been receiving much attention, and molecular techniques have been proved of great value to the matter. Corbula (Bivalvia, Corbulidae) is frequent and ecologically important genus in benthic marine communities. Nevertheless, its taxonomy is confusing, in part due to a plastic shell, which makes it difficult to establish species boundaries. This study aimed to analyze the COI and 16S sequences of six morphologically identified Corbula species occurring off the South-Southeastern Brazilian coast. Being a mainly sublittoral genus, most of the analyzed material had been previously sampled, fixed in formalin and preserved in alcohol. Hence, initially specific protocols for DNA extraction and PCR were developed. Better results were obtained with an extraction protocol combining organic extraction and silica adsorption. The nested PCR yielded more product than the direct PCR. Delimitation analyses were conducted with four different methods: two tree based (GMYC and Brownie) and two non-tree based (4x rule and ABGD). Different methods and markers produced different delimitations, but the combined evidence supports the morphological delimitation of three species: Corbula caribaea, Corbula tryoni and Corbula lyoni. Individuals assigned to Corbula patagonica were separated into two molecular species. Only one individual of Corbula aequivalvis was analyzed and it was distinguished from other species. One individual assigned to Corbula sp1 could not be distinguish from C. caribaea
Doutorado
Ecologia
Doutora em Ecologia

Understanding the processes that generate diversity is key to interpreting the patterns we see in the present. New developments in modelling these processes have promised unprecedented prospects for unravelling the evolutionary past. However, the empirical behaviour of these models in many of their practical applications is not well understood. This thesis investigates the influence of diversification models in a variety of contexts. First, I consider the Generalised Mixed Yule-Coalescent (GMYC) method for molecular species delimitation. This method identifies transition points between species- and population-level diversification processes on a time-resolved evolutionary tree. I show that this method is sensitive to the choice of mitochondrial marker used, and that the best marker can vary widely across study groups. Next, I investigate the influence of diversification models used to place prior distributions on time-resolved trees in molecular dating. Specifically, I look at the influence of the tree prior in analysing data sets with multiple individuals per species. These data sets can arise by accident where species boundaries are not well understood, and violate the assumptions of both population- and species-level tree priors. I use simulation to show that molecular date estimates can be seriously affected by the choice of tree prior in some circumstances, but are remarkably robust in general. Finally, I extend the analysis of tree prior sensitivity to new methods for dating the origins of human language families. I show that these methods are also robust to the choice of tree prior, and that speciation priors are preferred for language data sets regardless of taxonomic scale. My work will contribute to an improved understanding of the role of diversification models in empirical studies and will increase confidence in these methods across multiple realms of enquiry.

Orientadores: Karina Lucas da Silva Brandão, André Victor Lucci Freitas
Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: O gênero Hermeuptychia Forster (Nymphalidae, Satyrinae, Euptychiina) está amplamente distribuído no continente Americano, desde a Argentina até o sul dos Estados Unidos. O gênero foi anteriormente considerado um complexo de espécies, e atualmente são reconhecidas oito espécies . Todas as espécies possuem um padrão alar muito parecido, o que compromete a identificação taxonômica correta. Em adição, a posição filogenética do gênero dentro da subtribo Euptychiina permanece incerta. Para o presente estudo foram obtidos espécimens de 45 localidades de cinco países, com maior ênfase em uma amostragem no Brasil. Três marcadores moleculares, dois do DNA mitocondrial (cox1 5' e nad6) e um do DNA nuclear (RpS5) foram utilizados para gerar hipóteses filogenéticas (Máxima Parcimônia e Inferência Bayesiana), para delimitar espécies, e para gerar estimativas de tempo de divergência e distribuição ancestral. Adicionalmente, o desempenho da região anterior da cox1 como 'barcode - código de barras' para delimitar as espécies de Hermeuptychia foi testado. Além disso, análise morfológica da genitália masculina foi empregada para a delimitação e identificação de espécies. Os indivíduos amostrados agruparam-se em dez clados nas análises moleculares, correspondendo a sete espécies reconhecidas mais H. gisella, que havia sido anteriormente sinonimizada com H. cucullina. A análise morfológica dos indivíduos possibilitou o estabelecimento de caracteres diagnósticos para todas as espécies de Hermeuptychia - incluindo H. cucullina, que não está presente nas análises moleculares - e concordou com os agrupamentos obtidos através das análises moleculares. As relações filogenéticas entre as espécies de Hermeuptychia permanecem incertas, possivelmente devido a um padrão de evolução rápida, descrito anteriormente para outros Satyrini. Entretanto, dois grupos de espécies-irmãs podem ser identificados, H. pimpla + H. harmonia, e H. gisella + H. fallax, ambos sustentados por ocorrência simpátrica. Em adição, H. gisella e H. fallax parecem apresentar um isolamento reprodutivo incompleto, com formação de híbridos. Algumas espécies de Hermeuptychia estão distribuídas amplamente, como H. atalanta, H. hermes e H. gisella, sendo que H. atalanta é a espécie mais comum encontrada no Brasil. H. fallax é uma espécie restrita a Mata Atlântica; H. pimpla e H. harmonia são espécies restritas à região andina, encontradas em altitudes moderadas; H. maimoune pode ser encontrada na região andina e no sul da Amazônia brasileira, correspondendo a duas espécies crípticas; H. cucullina foi encontrada no centro-oeste brasileiro e na região andina, e é a espécie mais rara de Hermeuptychia; e H. sosybius pode ser encontrada do sul dos Estados Unidos até a região norte da Colômbia. O gênero diversificou-se de seu grupo-irmão a cerca de 8,2 milhões de anos (mya), a diversificação das espécies ocorreu entre 3,5 e 1,4 mya, e a distribuição ancestral estimada é a cordilheira dos Andes. Apenas com a região 'barcode' e análise de distância usando Neighbor-Joining, foi possível separar as espécies de Hermeuptychia com uma taxa de 2% de erro. O limite entre as distâncias intra e interespecíficas estimado fica em torno de 2% de divergência genética
Abstract: The Hermeuptychia genus Forster (Nymphalidae: Satyrinae: Euptychiina) is widely distributed in the American continent, from Argentina to South United States. Previously considered a species complex, the genus presents eight valid species taxa at the moment. Wing pattern is very similar in all Hermeuptychia species resulting in difficult and prone to error taxonomic identification. Additionally its position within the subtribe Euptichiina remains uncertain. Samples from 45 locations in five countries, with major emphasis in Brazilian territory sampling, were obtained for the present study. Three molecular markers, two from mitochondrial DNA (cox1 5' and nad6) and one from nuclear DNA (RpS5), were used to generate phylogenetic hypothesis (Maximum Parsimony and Bayesian Inference), to delimit species, and to estimate divergence time and ancestral distributions. The 'barcode' region performance (cox1 5') was tested for Hermeuptychia species. Male genitalia morphology was also used to identify and delimitate species. Sampled individuals are grouped in ten molecular clusters, corresponding to seven valid species and H. gisella, previously synonymized to H. cucullina. Morphological analysis of individuals revealed morphological diagnose traits to identify all Hermeuptychia species, including H. cucullina, which is not present in the molecular analysis, and was congruent with molecular analysis. Phylogenetic relationships among Hermeuptychia species remain unresolved due to a possible rapid evolutionary pattern common to Satyrini. However, two pairs of sister species could be identified: H. pimpla + H. harmonia and H. gisella + H. fallax, both sympatric. Additionally, H. gisella + H. fallax present incomplete reproductive isolation, with hybrids. Some Hermeuptychia are widely distributed as H. atalanta, H. hermes, and H. gisella, and H. atalanta is the most common species found in Brazil. H. fallax is restricted to Atlantic Forest; H. pimpla and H. harmonia are restricted to Andes region, at moderately high altitudes; H. maimoune is found in the Andine and in the Amazonian regions, corresponding to two cryptic species; H. cucullina is the rarest Hermeuptychia and was found in Central Brazil and in Andes; and H. sosybius is the only Hermeuptychia found in North America, been present from South United States to north Colombia. The genus diverged from its sister group around 8.2 my, species diversification occurred between 3.5 and 1.4 my and the ancestral estimate distribution is Andine region. Only the 'barcode' region was able to identify each Hermeuptychia species, with an 2% error rate and the molecular threshold for intra and interspecific distance was around 2% of genetic divergence
Mestrado
Ecologia
Mestre em Ecologia

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The family Threskiornithidae includes 13 genera and 32 species, but the relationships among genera, species or subspecies have been little studied. This family is traditionally divided into two subfamilies: Plataleinae and Threskiornithinae. One of the more interesting taxonomical questions within this group is the case of the species Eudocimus ruber and Eudocimus albus. They are usually considered as separate species, but they show similar behavior and there are also records of hybridization in nature. This study aims to reconstruct the phylogenetic relationships within the family Threskiornithidae as well as assess the level of genetic differentiation between Eudocimus albus and E. rubber, using mitochondrial and nuclear gene sequences. DNA was extracted from blood and tissue samples from 13 species of Threskiornithidae (seven genera) and two outgroups. For the Eudocimus study were extracted 10 individuals of each species. We sequenced the 16S rRNA and the intron 7 of β- Fibrinogen for all species. For Eudocimus Cytochrome B, Cytochrome Oxidase I, intron 11 of Glyceraldehyde-3-Phosphate Desidrogenase, intron 4 of the Myelin Proteolipid Protein and intron 2 of Myoglobin were also sequenced. Sequences for other five species of the family were obtained from GenBank. Phylogenetic trees were constructed using Neighbor-Joining, Maximum Parsimony, Maximum Likelihood, Bayesian inference and Bayesian inference of species tree. Networks and genetic distances were determined for Eudocimus haplotypes. Several approaches for species delimitation using multilocus data were applied. All analyses strongly supported the family Threskiornithidae (18 species) as a monophyletic group. However, the current classification of two subfamilies was not supported by our data: Plataleinae formed a monophyletic group, but nested within Threskiornithinae (a paraphyletic group). Tests of monophyly rejected the hypothesis of monophyly of Threskiornithinae. The family Threskiornithidae also showed a division into two groups: one with only genera endemic to the American continent (Theristicus and Eudocimus) and another with the remaining species. Within the latter clade, species of genus Plegadis are observed in a basal position, while subfamily Plataleinae was grouped with the remaining species. This pattern of species distribution suggests an initial Gondwana division and subsequent colonization by species from the Old to the New World. The divergence within the family was estimated at 35-40 million years, which is before the separation between America and Antarctica. Mitochondrial genetic analysis showed Eudocimus species as two different lineages. Multilocus analysis based on nuclear genes revealed a strong signal of speciation despite the polyphyly found in three of the four markers.
A família Threskiornithidae inclui 13 gêneros e 32 espécies e suas relações interespecíficas, assim como as designações dos gêneros, espécies ou subespécies foram pouco estudadas. A família tem sido dividida em duas subfamílias: Plataleinae e Threskiornithinae. O caso de Eudocimus ruber e Eudocimus albus é uma das questões interessantes da taxonomia do grupo, pois têm sido consideradas como espécies, mas mostram similaridades no comportamento e há registros de hibridização na natureza. Os objetivos do presente estudo foram reconstruir as relações filogenéticas dentro da família Threskiornithidae e avaliar o nível de diferenciação genética entre Eudocimus albus e E. ruber, baseando-se nos dados de sequências de genes mitocondriais e nucleares. DNA foi extraído de amostras de sangue e de tecidos de 13 espécies de Threskiornithidae, representantes de sete gêneros da família e de dois grupos externos. Para o estudo do caso de Eudocimus foram analisadas amostras de 10 indivíduos de cada espécie. Foram sequenciados os genes 16S rRNA e o íntron 7 do β-fibrinogênio para todas as espécies. Nos indivíduos de Eudocimus foram sequenciados também os genes Citocromo B, Citocromo Oxidase I, o íntron 11 da Gliceraldeído-3-Fosfato Desidrogenase, o íntron 4 da Proteína Proteolipídica da Mielina e o íntron 2 da Mioglobina. Sequências para outras cinco espécies da família foram obtidas do GenBank. Árvores filogenéticas foram construídas pelos métodos de inferência de Neighbor-Joining, Máxima Parcimônia, Máxima Verossimilhança, Análise Bayesiana e Estimativa Bayesiana de árvore de espécies. Redes de haplótipos e distâncias genéticas foram determinadas para as sequências de Eudocimus. Diversas abordagens de delimitação de espécies usando informação multilocus foram realizadas. A família Threskiornithidae com 18 espécies se apresentou como grupo monofilético fortemente sustentado em todas as análises. A classificação atual das duas subfamílias não foi corroborada: Plataleinae se apresentou como grupo monofilético, mas agrupada dentro dos Threskiornithinae, sendo este último um grupo parafilético. Os testes de monofilia rejeitaram a hipótese de Threskiornithinae ser um grupo monofilético. A família Threskiornithidae pode ser dividida em dois grupos: o primeiro agrupando somente gêneros endêmicos do continente americano (Theristicus e Eudocimus) e o outro com as demais espécies. Dentro deste ultimo clado, observa-se em posição basal as espécies do gênero Plegadis e a subfamília Plataleinae agrupada com o restante das espécies. Este padrão de distribuição de espécies concorda com uma divisão inicial Gondwânica e uma posterior colonização por espécies do velho ao novo mundo. A divergência da família foi estimada em 35 40 milhões de anos, data anterior à separação do continente Americano da Antártica. As análises genéticas mitocondriais mostraram as espécies de Eudocimus como duas linhagens diferentes. Nas análises multilocus baseadas nos genes nucleares foi possível recuperar um forte sinal de especiação apesar da polifilia encontrada em três dos quatro marcadores.

Rice is the staple food crop in Sri Lanka, which occupies 34% (0.77/million ha) of the total cultivated area. Sri Lanka currently produces 2.7 million tonnes of rough rice annually and satisfies around 95% of the domestic requirement. In Sri Lanka, genus Oryza consists of two species complexes, O. sativa (AA) and O. officinalis (CC). These two complexes are both pan tropical and have very similar overall distribution. Five wild rice species are reported in Sri Lanka, (O. nivara [AA], O. rufipogan (AA) O. eichengeri [CC], O. rhizomatis (CC) and O. granulate (GG). O. rhizomatis has been reported only in Sri Lanka and considered endemic to Sri Lanka. Recent studies demonstrated, the reliance on single source of information could mislead results in the phylogenetic inferences due to analytical inconsistency and biological processes. Therefore, exact number of wild rice species in Sri Lanka becomes uncertain and the necessity arises to assess Oryza species complexes in Sri Lanka using morphological, anatomical, and molecular information to enumerate number of species within each Oryza complex and characterization of species and species complexes. The study revealed, characterization of wild rice species, to a certain extent, can be made through morphological and anatomical characters, specially lamina anatomical characters. Molecular information is more reliable in delimitation of wild rice species complexes in Sri Lanka. O. rhizomatis and O. eichingeri (CC) are well separated from the rest of wild rice species (AA). Molecular data revealed, O. nivara and O. rufipogon have undergone independent evolution within Sri Lanka. Well separated five wild rice species are existing in Sri Lanka. Studies on ecological resilience of morphological, anatomical, and molecular studies are very useful for species enumeration of wild rice complexes in Sri Lanka. The findings led to conclude that wild rice species in Sri Lanka are “ecological swarms” and represents allopatric or sympatric populations. A comprehensive knowledge on genetic diversity and population structure of wild rice germplasm in Sri Lanka provides useful information to include these locally adapted and evolved wild rice species in rice crop improvement/breeding.