Molekulare Analyse und Phylogeographie neotropischer Amphibien

In this thesis, I comprised molecular and phylogeographic studies of neotropical frogs, presented in three chapters. The first chapter is focused on the molecular and acoustic analysis of the direct developing frog, Ischcnocnema guentheri (Brachycephalidae). This species is thought to have a widespread distribution range in the Brazilian Atlantic Forest (AF). Here I show that I. guentheri actually is a species complex composed of a minimum of six species. Two of these species were assigned to available names: I. guentheri and I henselii. The other four were defined as candidate new species. Their phylogeographical pattern partially agrees with paleo-models for the Atlantic Forest, but also suggests the existence of micro-refugia in less stable areas. I. guentheri sensu stricto, previously considered to be widespread, was found only in its type locality, a reserve within the urban area of Rio de Janeiro city. Until now, neither I. guentheri nor I. henselii has ben considered threatened according to IUCN (International Union for Conservation of Nature). However, my findings suggest, that the status has to be carefully re-evaluated in the next comprehensive update of the Red List of Brazil's amphibians. The second study is about the molecular and biogeographic analysis of Dendropsophus minutus. Studies comprising the entire distribution of species that are assumed to occupy vast continental areas across political borders are rare, because data sampling is handicapped by financial, logistic and political factors. Consequently, taxonomic and phylogeographical studies are often focused on specific regions, whereas the entire range is studied rarely. Such is the case in Dendropsophus minutus, a putatively continentally distributed South American hylid. This species is still considered widespread despite regional morphological and biacustical differences. To analyze the molecular diversity and the phylogeographical pattern throughout the range of the species, I made a collaborative effort bringing together 416 tissue samples representing almost the entire distribution of the species. We found more than 19 largely allopatric deep mitochondrial lineages within D. minutus, most of them with high node support in the phylogenetic tree inference. Ten of these lineages form a monophyletic clade which I define as the D. minutus complex. The other lineages represent related species that together with the D. minutus complex form the D. minutus group. My results support an Amazonian origin of the D. minutus group with a subsequent dispersal to eastern Brazil and Atlantic Forest where the D. minutus complex originates. The phylogeographical pattern of the D. minutus complex largely agrees with previous molecular studies of the AF fauna. The third chapter presents a comparative analysis of nine AF species. The AF is a species-rich tropical region that contains a high level of endemism. In recent years, attention has been given to this tropical area and scientists have been proposing different diversification mechanism to explain its diversity pattern. One of the most debated hypotheses is the Refugia Model (RM). Molecular studies have shown evidence both for rejecting and supporting the hypothesis. One aspect that weakens the RM is the existence of high genetic diversity in some populations distributed in areas that were supposed to contain low genetic diversity according to the model. This evidence suggests the existence of additional stable areas in the AF besides the ones currently proposed. Comparative phylogeography has the potential to uncover the existence of a common biogeographic history among co-distributed taxa. In order to perform a comparative analysis of AF species, I included published mitochondrial sequences from six well-sampled AF species: five amphibians and one snake. Additionally I have generated sequence data for three other co-distributed frog species to be included in the analysis. For the comparative analysis, I used a method recently implemented in the software BEAST 1.7 that can estimate the geographical origin of nodes of a genealogy. The results show that deep mitochondrial sister lineages have originated apart from each other and away from contact zones. Furthermore, I found high overlapping frequency of center of origins of co-distributed lineages in two regions of the studied area. One region is located at the northern centre of the AF, which coincides with the recently proposed RM. The other center of origin is in the southeastern AF, which agrees with floristic studies proposing a refugium in this region.In dieser Dissertation habe ich in drei Kapiteln die molekularen und phylogeographischen Arbeiten an neotropischen Fröschen zusammengestellt. Das erste Kapitel befasst sich mit der molekularen und akustischen Untersuchung von der sich direkt entwickelnden Froschart Ischnocnema guentheri (Brachycephalidae). Bei dieser Art wurde davon ausgegangen, dass sie ein sehr grosses Verbreitungsgebiet im brasilianischem Atlantischem Regenwald (AR) hat. Ich habe herausgefunden, dass I. guentheri ein Artenkomplex ist, der aus mindestens sechs Arten besteht. Zwei dieser Gruppen habe ich bereits beschriebenen Arten zugeordnet, nämlich I. guentheri und I. henselii. Die anderen vier sind voraussichtlich neue Arten. Ihr phylogeographisches Muster stimmt zum Teil mit Paleoklimatischen Modellierungen für den AR überein, aber lässt auch vermuten, dass Mikrorefugien in weniger stabilen Gegenden existiert haben. Die Art I. guentheri (im engeren Sinne), von der bisher vermutet wurde, dass sie ein großes Verbreitungsgebiet hat, habe ich nur in ihrem Typusgebiet entdecken können, nämlich einem Schutzgebiet in einer urbanen Gegend der Stadt Rio de Janeiro. Obwohl bisher weder von I. guentheri noch von I. henselii vermutet wurde, dass sie vom Aussterben bedroht sind, empfehle ich, dass der Bedrohungszustand gemäß IUCN (Internationale Vereinigung für die Bewahrung der Natur und natürlicher Ressourcen) bei der nächsten Überarbeitung der Roten Liste von Brasiliens Amphibien noch einmal überprüft werden sollte. Der zweite Teil meiner Dissertation befasst sich mit der molekularen und bioakustischen Untersuchung von D. minutus. Bisher gibt es nur wenige Untersuchungen an Arten, die das gesamte Verbreitungsgebiet berücksichtigen, besonders wenn es sich über eine großes Areal und über politische Grenzen hinweg erstreckt, da die Probennahme durch finanzielle, logistische und politische Faktoren erschwert wird. Das hat zur Folge, dass sich taxonomische und phylogeographische Untersuchungen oft nur auf einen Teil eines Verbreitungsgebietes beziehen. Dieses ist beispielsweise der Fall bei D. minutus, einem vermeintlich sehr weit verbreiteten südamerikanischen Hyliden. Die Art ist sehr weit verbreitet, obwohl es regional morphologische und bioakustische Unterschiede gibt. Um die molekulare Diversität und phylogeographischen Muster aus dem gesamten Verbreitungsgebiet zu untersuchen, habe ich mit der Unterstützung anderer Wissenschaftler 416 Gewebeproben aus zumindest fast dem gesamten Verbreitungsgebiet zusammenstellen können. Ich habe mehr als 19 allopatrische sehr unterschiedliche mitochondriale Linien innerhalb von D. minutus gefunden, bei denen die Mehrheit der Knotenpunkte des phylogentischen Baums statistisch stark abgesichert ist. Zehn dieser Linien gehören zu einer monophyletischen Klade, die ich als den D. minutus Komplex bezeichne. Die anderen Linien gehören zu verwandten Arten, die zusammen mit dem D. minutus Komplex die D. minutus Gruppe ausmachen. Meine Ergebnisse unterstützen, dass der Ursprung der D. minutus Gruppe im Amazonasgebiet liegt, mit einer darauffolgenden Ausbreitung nach Ostbrasilien und in den AR, in dem wiederum der D. minutus Komplex seinen Ursprung hat. Das phylogeographische Muster des D. minutus Komplexes stimmt größtenteils mit dem anderer molekularen Untersuchungen der Fauna des Atlantischen Regenwaldes überein. Das dritte Kapitel beinhaltet eine vergleichende Untersuchung von insgesamt neun Arten aus dem AR. Dieser ist ein artenreiches tropisches Gebiet, das einen hohen Grad an Endemismus aufweist. Seit einigen Jahren wird diesem Gebiet viel Aufmerksamkeit erteilt und Wissenschaftler haben verschiedene Mechanismen vorgeschlagen, die die Diversitätsmuster erklären sollen. Eines der am meisten diskutierten Modelle ist das Refugialmodell (RM), das von den Ergebnissen einiger molekularer Arbeiten unterstützt wird aber von anderen wiederum nicht. Ein Aspekt der das RM schwächt ist der, dass in einigen Gebieten Populationen mit hoher genetischer Diversität gefunden wurden, die aber dem Modell nach nur wenig genetische Variabilität enthalten sollten. Dieses kann als Beweis dafür interpretiert werden, dass es zusätzlich zu den bekannten Gebieten auch noch weitere klimatisch stabile Gegenden gegeben hat. Vergleichende phylogeographische Untersuchungen ermöglichen es, bei Arten mit ähnlicher Verbreitung, eine eventuelle gemeinsame biogeographische Geschichte aufzudecken. Um eine solche vergleichende Untersuchung von Arten aus dem AR durchzuführen, habe ich bereits veröffentlichte mitochondriale Sequenzen von sechs gut untersuchten Arten aus dem AR verwendet, nämlich von fünf Froscharten und einer Schlange. Zusätzlich habe ich für diese Analyse Sequenzdaten für drei weitere Froscharten mit demselben Verbreitungsgebiet generiert. Für diese vergleichende Analyse habe ich eine kürzlich veröffentlichte Methode, integriert in der Software BEAST 1.7, verwendet, mit der man den geographischen Ursprung für Verzweigungsknoten einer Genealogie abschätzen kann. Die Ergebnisse zeigen, dass alte mitochondriale Schwestergruppen ihren Ursprung in unterschiedlichen Gebieten hatten, der auch nicht in der Nähe heutiger Kontaktzonen liegt. Des Weiteren habe ich eine große Übereinstimmung der ermittelten wahrscheinlichen Ursprunggebiete bei verschiedenen Linien mit heute ähnlichen Verbreitungsgebieten gefunden. Das eine Gebiet befindet sich im nördlichen Zentrum des AR, und stimmt mit dem kürzlich vorgeschlagenen RM überein. Das andere Ursprungsgebiet befindet sich im südöstlichen AR und stimmt mit dem Refugium überein, das bei floristischen Untersuchungen ermittelt wurde

Phylogeny and species delimitation of near Eastern Neurergus newts (Salamandridae) based on genome-wide RADseq data analysis

We reconstruct the molecular phylogeny of Near Eastern mountain brook newts of the genus Neurergus (family Salamandridae) based on newly determined RADseq data, and compare the outcomes of concatenation-based phylogenetic reconstruction with species-tree inference. Furthermore, we test the current taxonomy of Neurergus (with four species: Neurergus strauchii, N. crocatus, N. kaiseri, and N. derjugini) against coalescent-based species-delimitation approaches of our genome-wide genetic data set. While the position of N. strauchii as sister species to all other Neurergus species was consistent in all of our analyses, the phylogenetic relationships between the three remaining species changed depending on the applied method. The concatenation approach, as well as quartet-based species-tree inference, supported a topology with N. kaiseri as the closest relative to N. derjugini, while full-coalescent species-tree inference approaches supported N. crocatus as sister species of N. derjugini. Investigating the individual signal of gene trees highlighted an extensive variation among gene histories, most likely resulting from incomplete lineage sorting. Coalescent-based species-delimitation models suggest that the current taxonomy might underestimate the species richness within Neurergus and supports seven species. Based on the current sampling, our analysis suggests that N. strauchii, N. derjugini and N. kaiseri might each be subdivided into further species. However, as amphibian species are known to be composed of deep conspecific lineages that do not always warrant species status, these results need to be cautiously interpreted in an integrative taxonomic framework. We hypothesize that the rather shallow divergences detected within N. kaiseri and N. derjugini likely reflect an ongoing speciation process and thus require further investigation. On the contrary, the much deeper genetic divergence found between the two morphologically and geographically differentiated subspecies of N. strauchii leads us to propose that N. s. barani should be considered a distinct species, Neurergus barani Öz, 1994

Environmental heterogeneity and not vicariant biogeographic barriers generate community-wide population structure in desert-adapted snakes

Genetic structure can be influenced by local adaptation to environmental heterogeneity and biogeographic barriers, resulting in discrete population clusters. Geographic distance among populations, however, can result in continuous clines of genetic divergence that appear as structured populations. Here, we evaluate the relevant importance of these three factors over a landscape characterized by environmental heterogeneity and the presence of a hypothesized biogeographic barrier in producing population genetic structure within 13 codistributed snake species using a genomic data set. We demonstrate that geographic distance and environmental heterogeneity across western North America contribute to population genomic divergence. Surprisingly, landscape features long thought to contribute to biogeographic barriers play little role in divergence community wide. Our results suggest that isolation by environment is the most important contributor to genomic divergence. Furthermore, we show that models of population clustering that incorporate spatial information consistently outperform nonspatial models, demonstrating the importance of considering geographic distances in population clustering. We argue that environmental and geographic distances as drivers of community-wide divergence should be explored before assuming the role of biogeographic barriers.see also the Perspective by Alencar and QuentalPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/1/mec15182-sup-0004-AppendixS4.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/2/mec15182_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/3/mec15182-sup-0005-AppendixS5.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/4/mec15182-sup-0002-AppendixS2.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/5/mec15182-sup-0010-AppendixS10.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/6/mec15182.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/7/mec15182-sup-0003-AppendixS3.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/8/mec15182-sup-0006-AppendixS6.pd

Environmental heterogeneity and not vicariant biogeographic barriers generate community-wide population structure in desert-adapted snakes

Genetic structure can be influenced by local adaptation to environmental heterogeneity and biogeographic barriers, resulting in discrete population clusters. Geographic distance among populations, however, can result in continuous clines of genetic divergence that appear as structured populations. Here, we evaluate the relevant importance of these three factors over a landscape characterized by environmental heterogeneity and the presence of a hypothesized biogeographic barrier in producing population genetic structure within 13 codistributed snake species using a genomic data set. We demonstrate that geographic distance and environmental heterogeneity across western North America contribute to population genomic divergence. Surprisingly, landscape features long thought to contribute to biogeographic barriers play little role in divergence community wide. Our results suggest that isolation by environment is the most important contributor to genomic divergence. Furthermore, we show that models of population clustering that incorporate spatial information consistently outperform nonspatial models, demonstrating the importance of considering geographic distances in population clustering. We argue that environmental and geographic distances as drivers of community-wide divergence should be explored before assuming the role of biogeographic barriers.see also the Perspective by Alencar and QuentalPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/1/mec15182-sup-0004-AppendixS4.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/2/mec15182_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/3/mec15182-sup-0005-AppendixS5.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/4/mec15182-sup-0002-AppendixS2.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/5/mec15182-sup-0010-AppendixS10.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/6/mec15182.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/7/mec15182-sup-0003-AppendixS3.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/8/mec15182-sup-0006-AppendixS6.pd

Genomic Architecture Predicts Tree Topology, Population Structuring, and Demographic History in Amazonian Birds

Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on the spatial and temporal origins of population variation have been largely limited to evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known as genomic architecture in producing heterogeneity in differentiation across the genome. To test how variation in genomic characteristics (e.g. recombination rate) impacts our ability to reconstruct general patterns of differentiation between species that cooccur across geographic barriers, we sequenced the whole genomes of multiple bird populations that are distributed across rivers in southeastern Amazonia. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with species tree support. Gene flow was less pervasive in genomic regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection, skewing genome-wide estimates of effective population sizes and gene flow between populations toward lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from neutral processes to elucidate spatial patterns of population differentiation

Taxonomic Review of South American Butter Frogs: Phylogeny, Geographic Patterns, and Species Delimitation in the Leptodactylus latrans Species Group (Anura: Leptodactylidae)

The Leptodactylus latrans species group currently comprises eight medium- to large-sized frog species with a convoluted taxonomic history, particularly related to the specific limits of the L. latrans complex, and the species pair Leptodactylus chaquensis–Leptodactylus macrosternum. Their homogeneous external morphology and continental geographic distribution in South America have posed severe limitations to a comprehensive review, such that taxonomic consensus and species limits remain uncertain. This is further worsened by the presence of chromatic polymorphism among coexisting species that can hardly be distinguished by external morphology. Based on a large-scale geographic sampling including multilocus DNA analyses, and acoustic and morphological data, we provide a comprehensive evaluation of the taxonomic status and species limits of the L. latrans group, focusing on the resolution of the L. latranscomplex and the species pair L. chaquensis–L. macrosternum. We gathered 728 mitochondrial sequences from 429 localities, encompassing the entire geographic distribution of the group. Both generalized mixed Yule coalescent and automatic barcode gap discovery species delimitation methods recovered four major mitochondrial evolutionary lineages within the L. latrans complex, also supported by distribution patterns, multilocus molecular, morphological and/or bioacoustic data. One lineage is linked to nominal L. latrans,one revalidated as Leptodactylus luctator, and the other two are formally named and described. Another lineage encompasses all specimens previously assigned to the species pair L. chaquensis–L. macrosternum, clustered as a single evolutionary entity and is now regarded as L. macrosternum. We provide a revised diagnosis for these species based on acoustic data, morphological/chromatic variation, and phylogenetic relationships of all species currently included in the L. latrans group. Our findings reinforce the view that Neotropical diversity is highly underestimated and stress that appropriate geographic sampling in an integrative framework is crucial for the establishment of specific limits among broadly distributed and morphologically cryptic Neotropical frogs

High Levels of Diversity Uncovered in a Widespread Nominal Taxon: Continental Phylogeography of the Neotropical Tree Frog

Species distributed across vast continental areas and across major biomes provide unique model systems for studies of biotic diversification, yet also constitute daunting financial, logistic and political challenges for data collection across such regions. The tree frog Dendropsophus minutus (Anura: Hylidae) is a nominal species, continentally distributed in South America, that may represent a complex of multiple species, each with a more limited distribution. To understand the spatial pattern of molecular diversity throughout the range of this species complex, we obtained DNA sequence data from two mitochondrial genes, cytochrome oxidase I (COI) and the 16S rhibosomal gene (16S) for 407 samples of D. minutus and closely related species distributed across eleven countries, effectively comprising the entire range of the group. We performed phylogenetic and spatially explicit phylogeographic analyses to assess the genetic structure of lineages and infer ancestral areas. We found 43 statistically supported, deep mitochondrial lineages, several of which may represent currently unrecognized distinct species. One major clade, containing 25 divergent lineages, includes samples from the type locality of D. minutus. We defined that clade as the D. minutus complex. The remaining lineages together with the D. minutus complex constitute the D. minutus species group. Historical analyses support an Amazonian origin for the D. minutus species group with a subsequent dispersal to eastern Brazil where the D. minutus complex originated. According to our dataset, a total of eight mtDNA lineages have ranges >100,000 km2. One of them occupies an area of almost one million km2 encompassing multiple biomes. Our results, at a spatial scale and resolution unprecedented for a Neotropical vertebrate, confirm that widespread amphibian species occur in lowland South America, yet at the same time a large proportion of cryptic diversity still remains to be discovered

Filogeografia do le?o-marinho-do-sul, otaria flavescens shaw 1800

Made available in DSpace on 2015-04-14T13:09:13Z (GMT). No. of bitstreams: 1 419881.pdf: 1337852 bytes, checksum: be16275c921dc2e6fc5db0597763a47e (MD5) Previous issue date: 2009-03-10Neste estudo investigamos a estrutura populacional do le?o-marinho-do-sul (Otaria flavescens), um otarideo amplamente distribu?do ao longo das costas dos oceanos Atl?ntico e Pac?fico na Am?rica do Sul, e que foi extremamente ca?ado durante os dois ?ltimos s?culos. Apesar de sua ampla distribui??o e intera??es com atividades de pesca, ate o momento poucos trabalhos avaliaram as diferen?as gen?ticas e estrutura??o ao longo da distribui??o da esp?cie. No presente trabalho, utilizamos marcadores de microssat?lites (10 loci) e DNA mitocondrial para avaliar a estrutura populacional e hist?ria evolutiva da esp?cie. Encontramos estrutura??o significativa entre as popula??es dos oceanos Pac?fico e Atl?ntico, correspondendo a duas linhagens mitocondriais reciprocamente monofil?ticas, separadas desde o in?cio do Pleistoceno, indicando forte filopatria das f?meas. Tamb?m encontramos estrutura??o gen?tica significativa intra-oce?nica entre diferentes s?tios de reprodu??o. A an?lise dos microssat?lites tamb?m demonstrou que as popula??es dos dois oceanos s?o significativamente diferentes, possuindo diversos alelos exclusivos, apesar de que um pequeno fluxo g?nico inter-oce?nico atrav?s dos machos n?o pode ser descartado. Nossos dados mostram que a esp?cie n?o sofreu recentemente nenhuma redu??o significativa na sua diversidade gen?tica. Estes resultados indicam fortemente que as popula??es de O. flavescens do Pac?fico e do Atl?ntico s?o duas unidades evolutivas significativas (ESUs) e que as col?nias de reprodu??o em cada oceano devem ser manejadas separadamente

Data from: The biogeography of deep time phylogenetic reticulation

Most phylogenies are typically represented as purely bifurcating. However, as genomic data has become more common in phylogenetic studies, it is not unusual to find reticulation among terminal lineages or among internal nodes (deep time reticulation; DTR). In these situations, gene flow must have happened in the same or adjacent geographic areas for these DTRs to have occurred and therefore biogeographic reconstruction should provide similar area estimates for parental nodes, provided extinction or dispersal has not eroded these patterns. We examine the phylogeny of the widely distributed New World kingsnakes (Lampropeltis), determine if DTR is present in this group, and estimate the ancestral area for reticulation. Importantly, we develop a new method that uses coalescent simulations in a machine learning framework to show conclusively that this phylogeny is best represented as reticulating at deeper time. Using joint probabilities of ancestral area reconstructions on the bifurcating parental lineages from the reticulating node, we show that this reticulation likely occurred in northwestern Mexico/southwestern US and subsequently led to the diversification of the Mexican kingsnakes. This region has been previously identified as an area important for understanding speciation and secondary contact with gene flow in snakes and other squamates. This research shows that phylogenetic reticulation is common, even in well-studied groups, and that the geographic scope of ancient hybridization is recoverable

Data 3. BioGeoBEARS code for estimating ancestral area in Lampropeltis.

BioGeoBEARS code for estimating ancestral area in Lampropeltis