Multilocus phylogeny of a cryptic radiation of Afrotropical long-fingered bats (Chiroptera,Miniopteridae)

The Old World bat family Miniopteridae comprises only the genus Miniopterus, which includes 20 currently recognized species from the Afrotropical realm and 15 species from Eurasia and Australasia. Since 2003, the number of recognized Miniopterus species has grown from 19 to 35, with most newly described species endemic to Madagascar and the Comoros Archipelago. We investigated genetic variation, phylogenetic relationships and clade membership in Miniopterus focusing on Afrotropical taxa. We generated mitochondrial cytochrome-b (cyt-b) and nuclear intron data (five genes) from 352 vouchered individuals collected at 78 georeferenced localities. Including 99 additional mitochondrial sequences from GenBank, we analysed a total of 25 recognized species. Mitochondrial genetic distances among cyt-b-supported clades averaged 9.3%, representing as many as five undescribed species. Multilocus coalescent delimitation strongly supported the genetic isolation of eight of nine tested unnamed clades. A large number of sampled clades in sub-Saharan Africa are distributed wholly or partly in East Africa (nine of 13 clades), suggesting that Miniopterus diversity has been grossly underestimated. Although 25 of 27 cyt-b and 23 of 25 nuclear gene tree lineages from the Afrotropics were strongly supported as monophyletic, a majority of deep nodes were poorly resolved in phylogenetic analyses. Long terminal branches subtending short backbone internodes in the phylogenetic analyses suggest a rapid radiation model of diversification. This hypothesis needs to be tested using more phylogenetically informative data.     

Molecular phylogenetics of slit‐faced bats (Chiroptera: Nycteridae) reveal deeply divergent African lineages

The bat family Nycteridae contains only the genus Nycteris, which comprises 13 currently recognized species from Africa and the Arabian Peninsula, one species from Madagascar, and two species restricted to Malaysia and Indonesia in South‐East Asia. We investigated genetic variation, clade membership, and phylogenetic relationships in Nycteridae with broad sampling across Africa for most clades. We sequenced mitochondrial cytochrome b (cytb) and four independent nuclear introns (2,166 bp) from 253 individuals. Although our samples did not include all recognized species, we recovered at least 16 deeply divergent monophyletic lineages using independent mitochondrial and multilocus nuclear datasets in both gene tree and species tree analyses. Mean pairwise uncorrected genetic distances among species‐ranked Nycteris clades (17% for cytb and 4% for concatenated introns) suggest high levels of phylogenetic diversity in Nycteridae. We found a large number of designated clades whose members are distributed wholly or partly in East Africa (10 of 16 clades), indicating that Nycteris diversity has been historically underestimated and raising the possibility that additional unsampled and/or undescribed Nycteris species occur in more poorly sampled Central and West Africa. Well‐resolved mitochondrial, concatenated nuclear, and species trees strongly supported African ancestry for SE Asian species. Species tree analyses strongly support two deeply diverged subclades that have not previously been recognized, and these clades may warrant recognition as subgenera. Our analyses also strongly support four traditionally recognized species groups of Nycteris. Mitonuclear discordance regarding geographic population structure in Nycteris thebaica appears to result from male‐biased dispersal in this species. Our analyses, almost wholly based on museum voucher specimens, serve to identify species‐rank clades that can be tested with independent datasets, such as morphology, vocalizations, distributions, and ectoparasites. Our analyses highlight the need for a comprehensive revision of Nycteridae.     

Climate-influenced boreotropical survival and rampant introgressions explain the thriving of New World grapes in the north temperate zone

The north temperate region was characterized by a warm climate and a rich thermophilic flora before the Eocene, but early diversifications of the temperate biome under global climate change and biome shift remain uncertain. Moreover, it is becoming clear that hybridization/introgression is an important driving force of speciation in plant diversity. Here, we applied analyses from biogeography and phylogenetic networks to account for both introgression and incomplete lineage sorting based on geno...     

Phylogeny of Campanuloideae (Campanulaceae) with Emphasis on the Utility of Nuclear Pentatricopeptide Repeat (PPR) Genes

Background

The Campanuloideae (Campanulaceae) are a highly diverse clade of angiosperms found mostly in the Northern Hemisphere, with the highest diversity in temperate areas of the Old World. Chloroplast markers have greatly improved our understanding of this clade but many relationships remain unclear primarily due to low levels of molecular evolution and recent and rapid divergence. Furthermore, focusing solely on maternally inherited markers such as those from the chloroplast genome may obscure processes such as hybridization. In this study we explore the phylogenetic utility of two low-copy nuclear loci from the pentatricopeptide repeat gene family (PPR). Rapidly evolving nuclear loci may provide increased phylogenetic resolution in clades containing recently diverged or closely related taxa. We present results based on both chloroplast and low-copy nuclear loci and discuss the utility of such markers to resolve evolutionary relationships and infer hybridization events within the Campanuloideae clade.

Results

The inclusion of low-copy nuclear genes into the analyses provides increased phylogenetic resolution in two species-rich clades containing recently diverged taxa. We also obtain support for the placement of two early diverging lineages (Jasione and Musschia-Gadellia clades) that have previously been unresolved. Furthermore, phylogenetic analyses of PPR loci revealed potential hybridization events for a number of taxa (e.g., Campanula pelviformis and Legousia species). These loci offer greater overall topological support than obtained with plastid DNA alone.

Conclusion

This study represents the first inclusion of low-copy nuclear genes for phylogenetic reconstruction in Campanuloideae. The two PPR loci were easy to sequence, required no cloning, and the sequence alignments were straightforward across the entire Campanuloideae clade. Although potentially complicated by incomplete lineage sorting, these markers proved useful for understanding the processes of reticulate evolution and resolving relationships at a wide range of phylogenetic levels. Our results stress the importance of including multiple, independent loci in phylogenetic analyses.     

The timing and the mode of evolution of wild grapes (Vitis)

Wild grapes are woody climbers, found mostly in temperate regions of the northern hemisphere, comprising the genus Vitis. Despite its importance, the evolutionary history of Vitis is still contentious. Past studies have led to conflicting hypotheses about the phylogeny, speciation events, and biogeographic history of the genus. Here we investigate the evolutionary history of Vitis using data from four chloroplast spacers (trnH-psbA, trnK-rps16, trnF-nahJ, and rpl32-trnL) and the nuclear gene RPB2-I, and we explore mechanisms that could have shaped the observed distribution of current species. Maximum likelihood and Bayesian analyses provided similar results, strongly supporting the presence of two subgenera and suggesting a species clustering within subgenus Vitis that mainly mirrors the disjunction between the Old and New World. Vitis vinifera subsp. sylvestris was found to be sister to the Asian species while three major clades were found in the American species. A network approach confirmed the main geographic groups and highlighted different chloroplast haplotype patterns between Asian and American species. Molecular dating analysis provided the time boundaries to discuss our results. Our study shows wild grape diversification to be a continuous and complex process that concerned the Tertiary as well as the Quaternary, most likely involving both geographical and climatic forces. Local variations in extent and timing of these forces were discussed based on observed differences between groups. In the context of the Tertiary–Quaternary debate, we provide evidence in favor of the “continuous hypothesis” to explain present diversity. Finally, two directions for future research are highlighted: (i) was the earliest grape American or Asian? and (ii) are all modern grape species real?     

Cryptic species,taxonomic inflation,or a bit of both? New species phenomenon in Sri Lanka as suggested by a phylogeny of dwarf geckos (Reptilia,Squamata, Gekkonidae,Cnemaspis)

We evaluated the status of 16 of 22 recognized Sri Lankan Cnemaspis Strauch species, and flagged overlooked diversity with two mitochondrial (cyt b & ND2) and two nuclear markers (RAG1 & PDC) totalling 2829 base pairs. A fossil-calibrated timetree and sampling of other South Asian Cnemaspis provide insights into the diversification of the genus in peninsular India and Sri Lanka. Phylogenetic analyses consistently inferred two broad clades within South Asian Cnemaspis, with Sri Lankan species in two clades, which we call the podihuna and kandiana clades. Each Sri Lankan clade as a whole is sister to Indian taxa and nested within Indian lineages. Cnemaspis modigliani Das from Indonesia is a member of the kandiana clade. This suggests a minimum of two dispersal events between India and Sri Lanka and one between Sri Lanka/India and South-east Asia. South Asian Cnemaspis date back to at least the Eocene, in Sri Lanka to the early Miocene, with late Miocene diversification in the kandiana clade. All but one of the named species we sampled is likely to be valid, and 10 divergent unnamed lineages may warrant specific recognition. A resolution of Sri Lankan Cnemaspis taxonomy will require thorough sampling and the use of both morphological and molecular data.     

Origins and patterns of endemic diversity in two specialized lizard lineages from the Australian Monsoonal Tropics (Oedura spp.)

Aim

Savanna biomes cover around 20% of land surfaces, yet the origins and processes that have shaped their biodiversity remain understudied. Here, we assess the timing of diversification and how patterns of genetic diversity vary along an aridity gradient in specialized saxicoline gecko clades (Oedura spp.) from the tropical savannas of northern Australia.

Location

Australian Monsoonal Tropics (AMT), Kimberley region (Western Australia).

Methods

We compiled mitochondrial and nuclear data for two Kimberley endemic lizard clades (Oedura filicipoda/murrumanu and O. gracilis), and allied non‐Kimberley taxa (O. marmorata complex). Species delimitation methods were used to identify evolutionary lineages, Maximum‐likelihood and Bayesian phylogenetic methods were employed to assess relationships and diversification timeframes, and rainfall data and range sizes were tested for correlations.

Results

Phylogenetic analyses of cryptic or recently discovered lineage diversity revealed late‐Miocene to early‐Pliocene crown ages. Microendemism and diversity were highest in high‐rainfall regions, while the most widespread lineages occurred in the central and south‐east Kimberley, and showed evidence of introgression with parapatric lineages.

Main conclusions

The initial diversification in both clades was broadly concordant with global climatic events linked to the expansion of savanna biomes in the lateMiocene. Higher endemism in mesic and refugial areas suggests long histories of localized persistence, while wider distributions and evidence of introgression suggest a dynamic history at the arid‐monsoonal interface.     

A dated phylogeny of Lardizabalaceae reveals an unusual long-distance dispersal across the Pacific Ocean and the rapid rise of East Asian subtropical evergreen broadleaved forests in the late Miocene

Temperate South American–Asian disjunct distributions are the most unusual in organisms, and challenging to explain. Here, we address the origin of this unusual disjunction in Lardizabalaceae using explicit models and molecular data. The family (c.40 species distributed in ten genera) also provides an opportunity to explore the historical assembly of East Asian subtropical evergreen broadleaved forests, a typical and luxuriant vegetation in East Asia. DNA sequences of five plastid loci of 42 accessions representing 23 species of Lardizabalaceae (c. 57.5% of estimated species diversity), and 19 species from the six other families of Ranunculales, were used to perform phylogenetic analyses. By dating the branching events and reconstructing ancestral ranges, we infer that extant Lardizabalaceae dated to the Upper Cretaceous of East Asia and that the temperate South American lineage might have split from its East Asian sister group at c. 24.4 Ma. A trans-Pacific dispersal possibly by birds from East Asia to South America is plausible to explain the establishment of the temperate South American–East Asian disjunction in Lardizabalaceae. Diversification rate analyses indicate that net diversification rates of Lardizabalaceae experienced a significant increase around c. 7.5 Ma. Our findings suggest that the rapid rise of East Asian subtropical evergreen broadleaved forests occurred in the late Miocene, associated with the uplift of the Tibetan Plateau and the intensified East Asian monsoon, as well as the higher winter temperature and atmospheric CO₂ levels.     

Out of the forest: past and present range expansion of a parthenogenetic weevil pest,or how to colonize the world successfully

Previous research revealed complex diversification patterns in the parthenogenetic weevil Naupactus cervinus. To understand the origin of clonal diversity and successful spreading of this weevil, we investigated its geographic origin and possible dispersal routes and whether parthenogens can persist in habitats under unsuitable environmental conditions. This study is based on samples taken throughout a broad area of the species’ range. We used both mitochondrial and nuclear markers and applied phylogenetic and network analyses to infer possible relationships between haplotypes. Bayesian phylogeographic analyses and ecological niche modeling were used to investigate the processes that shaped genetic diversity and enabled the colonization of new geographic areas. Southeastern Brazil emerges as the original distribution area of N. cervinus. We detected two range expansions, one along natural corridors during the Pleistocene and the other in countries outside South America during recent times. Isolation due to climate shifts during the early Pleistocene led to diversification in two divergent clades, which probably survived in different refugia of the Paranaense Forest and the Paraná River delta. The origin of the clonal diversity was probably a complex process including mutational diversification, hybridization, and secondary colonization. The establishment of N. cervinus in areas outside its native range may indicate adaptation to drier and cooler conditions. Parthenogenesis would be advantageous for the colonization of new environments by preventing the breakup of successful gene combinations. As in other insect pests, the present distribution of N. cervinus results from both its evolutionary history and its recent history related to human activities.     

Nuclear and plastid phylogenomic analyses provide insights into the reticulate evolution,species delimitation,and biogeography of the Sino-Japanese disjunctive Diabelia (Caprifoliaceae)

Understanding biological diversity and the mechanisms of the Sino-Japanese disjunctions are major challenges in eastern Asia biogeography. The Sino-Japanese flora has been broadly studied as an ideal model for plant phylogeography. Diabelia Landrein (Caprifoliaceae) is an East Asian genus, with a disjunctive distribution across the Sino-Japanese region. However, relationships within Diabelia remain elusive. In this study, we reconstructed the phylogeny of Diabelia and inferred historical biogeography and evolutionary patterns based on nuclear and plastid sequences from target enrichment and genome skimming approaches, respectively. We found that the main clades within Diabelia were discordant between nuclear and plastid trees. Both nuclear and plastid phylogenetic analyses supported five main clades: Diabelia serrata (Siebold & Zucc.) Landrein, Diabelia tetrasepala (Koidz.) Landrein, Diabelia sanguinea (Makino) Landrein, Diabelia stenophylla (Honda) Landrein, and Diabelia spathulata (Siebold & Zucc.) Landrein. Species network analyses revealed that Diabelia tetrasepala is likely the result of a hybridization event. Divergence time estimation and ancestral area reconstructions showed that Diabelia originated in Japan during the early Miocene, with subsequent vicariance and dispersal events between Japan and Korea, and between Japan and China. Overall, our results support the division of Diabelia into five main clades and the recognition of five species in the genus. This research provides new insights into the species delimitation and speciation processes of taxonomically complex lineages such as Diabelia.     

Molecular phylogeny of the Herpestidae (Mammalia, Carnivora) with a special emphasis on the Asian Herpestes

Until now, phylogenetic studies of the mongooses (Carnivora, Herpestidae) have not included an exhaustive sampling of the Asian members of this family. In this study, we used mitochondrial (Cytochrome b and ND2), nuclear (β-fibrinogen intron 7 and Transthyretin intron 1) sequences from almost all of the recognized mongoose species to produce a well-resolved phylogeny of the Herpestidae. We also performed molecular dating analyses to infer divergence dates of the different lineages within the Herpestidae. Our results confirmed the paraphyly of the Herpestes genus and other phylogenetic relationships, which previously had only been moderately supported. The Asian herpestid species were found to form a monophyletic group within the Herpestidae. Within the Asian species, a cyto-nuclear conflict was discovered between the small Indian mongoose (Herpestes auropunctatus), the Indian gray mongoose (Herpestes edwardsii) and the Javan mongoose (Herpestes javanicus), which may have occurred through interspecific hybridization. This study inferred an Early Miocene origin for the Herpestidae and a Middle Miocene origin for the Asian mongooses.     

Phylogenetic relationships of toads of the Rhinella granulosa group (Anura: Bufonidae): a molecular perspective with comments on hybridization and introgression

The Rhinella granulosa group consists of 13 species of toads distributed throughout open areas of South America and Panama. In this paper we perform a phylogenetic analysis considering all but one species of the group, employing five nuclear and four mitochondrial genes, for up to 7910 bp per specimen. Separate phylogenetic analyses under direct optimization (DO) of nuclear and mitochondrial sequences recovered the R. granulosa group as monophyletic and revealed topological incongruence that can be explained mainly by multiple events of hybridization and introgression, both mitochondrial and nuclear. The DO combined analysis, after the exclusion of putatively introgressed or heterozygous genomes, resulted in a phylogenetic hypothesis for the R. granulosa group in which most of the species are recovered as monophyletic, but with interspecific relationships poorly supported. The optimization of morphological (adult and larval), chromosomal, and behavioural characters resulted in 12 putative phenotypic synapomorphies for this species group and some other synapomorphies for internal clades. Our results indicate the need for additional population genetic studies on R. dorbignyi and R. fernandezae to corroborate the taxonomic status of both taxa. Finally, we discuss biological and genetic characteristics of Bufonidae, as possible explanations for the common occurrence of hybridization and introgression observed in some lineages of this family.     

ELUCIDATION OF CRYPTIC DIVERSITY IN A WIDESPREAD NEARCTIC TREEFROG REVEALS EPISODES OF MITOCHONDRIAL GENE CAPTURE AS FROGS DIVERSIFIED ACROSS A DYNAMIC LANDSCAPE

We investigate the evolutionary history of the wide‐ranging Nearctic treefrog Hyla arenicolor through the integration of extensive range‐wide sampling, phylogenetic analyses of multilocus genetic data, and divergence dating. Previous phylogeographic studies of this frog documented a potential signature of introgressive hybridization from an ecologically and morphologically divergent sister species. Based on our Bayesian phylogenetic analyses of mitochondrial DNA, we inferred strong phylogeographic structure in H. arenicolor as indicated by seven well‐supported clades, five of which correspond to well‐defined biogeographic regions. Clades from the Balsas Basin and southwestern Central Mexican Plateau in Mexico, and the Grand Canyon of Arizona, group with the morphologically, behaviorally, and ecologically divergent mountain treefrogs in the H. eximia group, rendering H. arenicolor as paraphyletic. The phylogenetic position of at least two of these three H. arenicolor clades within the H. eximia group, however, is most likely the result of several episodes of introgressive hybridization and subsequent mitochondrial gene capture separated in time and space, as supported by evidence from the nuclear genes. Hyla arenicolor from the Balsas Basin appear to be deeply divergent from other H. arenicolor and represent a distinctly different species. Results suggests that introgressive hybridization events, both ancient and contemporary, coupled with late Neogene vicariance and Pleistocene climate‐driven range shifts, have all played a role in the historical diversification of H. arenicolor.     

西南地区6种魔芋属植物基于cpDNA序列的遗传多样性研究

研究野生作物资源的遗传变异及分化机制对种质资源的收集与改良具有重要意义。魔芋是我国西南地区的特色经济作物,但由于受到人为活动干扰,野生种群不断衰退。为评估西南地区魔芋属(Amorphophallus)野生群体的遗传多样性,探究代表性物种的系统发育地位,该研究利用3个叶绿体DNA(cpDNA)片段,分析了魔芋6个物种的遗传多样性,重建了种间系统发育关系。结果表明:(1)西南地区野生魔芋群体的遗传多样性普遍较低,虽然单倍型多样性(H_d)均值为0.428,但近一半群体只有1个单倍型,6个物种整体水平上的单倍型多样性在0.704到0.983之间。(2)在6个物种间检测到高水平的遗传分化,遗传分化系数(F_ST)值在0.481到0.967之间。(3)系统发育分析表明,选取的27个魔芋种主要聚成3个分支:非洲分支、东南亚分支和东亚大陆分支。疣柄魔芋(A. paeoniifolius)隶属于东南亚分支,而东亚大陆分支A包含花魔芋(A. konjac)和西盟魔芋(A. krausei),东亚大陆分支B由东亚魔芋(A. kiusianus)、滇魔芋(A. yunnanensis)和东京魔芋(A. tonkinensis)构成。生境隔离与人为干扰造成了西南地区野生魔芋群体较低的遗传多样性,魔芋属东亚大陆分支的分化可能与早期的快速扩张和生态适应有关。该研究为西南地区魔芋资源的合理保护、可持续利用和杂交育种提供了参考资料。     

Genomewide SNP data reveal cryptic phylogeographic structure and microallopatric divergence in a rapids‐adapted clade of cichlids from the Congo River

The lower Congo River is a freshwater biodiversity hot spot in Africa characterized by some of the world's largest rapids. However, little is known about the evolutionary forces shaping this diversity, which include numerous endemic fishes. We investigated phylogeographic relationships in Teleogramma, a small clade of rheophilic cichlids, in the context of regional geography and hydrology. Previous studies have been unable to resolve phylogenetic relationships within Teleogramma due to lack of variation in nuclear genes and discrete morphological characters among putative species. To sample more broadly across the genome, we analysed double‐digest restriction‐associated sequencing (ddRAD) data from 53 individuals across all described species in the genus. We also assessed body shape and mitochondrial variation within and between taxa. Phylogenetic analyses reveal previously unrecognized lineages and instances of microallopatric divergence across as little as ~1.5 km. Species ranges appear to correspond to geographic regions broadly separated by major hydrological and topographic barriers, indicating these features are likely important drivers of diversification. Mitonuclear discordance indicates one or more introgressive hybridization events, but no clear evidence of admixture is present in nuclear genomes, suggesting these events were likely ancient. A survey of female fin patterns hints that previously undetected lineage‐specific patterning may be acting to reinforce species cohesion. These analyses highlight the importance of hydrological complexity in generating diversity in certain freshwater systems, as well as the utility of ddRAD‐Seq data in understanding diversification processes operating both below and above the species level.     

Genetic variation and biogeography of the disjunct Vitis subg. Vitis (Vitaceae)

Aim Vitis subg. Vitis provides an example of a plant disjunction occurring in the Northern Hemisphere. It shows broad morphological variation but is assumed to be a species complex with limited genetic differentiation. Based on a comprehensive sampling of taxa and polymorphism in both chloroplast and nuclear DNA, we assessed genetic variation within this subgenus. Our aims were to clarify the relationships among species and to examine their historical biogeography. Location Asia, Europe, North America. Methods We analysed a total of 30 species and putative hybrids from subgenus Vitis and examined the infra‐specific variation in some species. Polymorphism in chloroplast DNA was assessed in trnL and trnH–psbA–trnK sequences (c. 2170 bp) and in 15 microsatellite loci. We also obtained nuclear data for size variation at 24 microsatellite loci. Phylogenetic inference was performed with Bayesian analyses. A maximum parsimony network was constructed to depict the evolutionary relationships among haplotypes, and microsatellite data were also subjected to hierarchical clustering analysis using the Ward distance. In addition, we assessed size homoplasy by sequencing both chloroplast and nuclear microsatellite loci. Results Chloroplast polymorphisms resolved subgenus Vitis as a monophyletic group with limited genetic variation. The ancestral haplotypes were found in Eurasia. American taxa all harboured derived haplotypes. Most of them formed a monophyletic group that did not include Vitis californica. The four main haplotypes in Vitis vinifera corresponded to two different origins. Nuclear microsatellites indicated that genetic variation was especially large in North America. Asian species exhibited a lower level of nuclear divergence and the European V. vinifera corresponded to a differentiated nuclear lineage. Main conclusions We obtained some evidence that subgenus Vitis has an Asian origin and then dispersed to Europe and North America. Geographic separation was followed by diversification, presumably during the Pleistocene, resulting in phylogeographic patterns similar to other biota. In contrast to chloroplast DNA, nuclear DNA shows a larger than expected genetic variation. Our molecular data also highlight the need to re‐examine certain aspects of the current subgeneric classification.     

The noncosmopolitanism paradigm of freshwater zooplankton: insights from the global phylogeography of the predatory cladoceran Polyphemus pediculus (Linnaeus, 1761) (Crustacea,Onychopoda)

A major question in our understanding of eukaryotic biodiversity is whether small bodied taxa have cosmopolitan distributions or consist of geographically localized cryptic taxa. Here, we explore the global phylogeography of the freshwater cladoceran Polyphemus pediculus (Linnaeus, 1761) (Crustacea, Onychopoda) using two mitochondrial genes, cytochrome c oxidase subunit I and 16s ribosomal RNA, and one nuclear marker, 18s ribosomal RNA. The results of neighbour‐joining and Bayesian phylogenetic analyses reveal an exceptionally pronounced genetic structure at both inter‐ and intra‐continental scales. The presence of well‐supported, deeply divergent phylogroups across the Holarctic suggests that P. pediculus represents an assemblage of at least nine, largely allopatric cryptic species. Interestingly, all phylogenetic analyses support the reciprocal paraphyly of Nearctic and Palaearctic clades. Bayesian inference of ancestral distributions suggests that P. pediculus originated in North America or East Asia and that European lineages of Polyphemus were established by subsequent intercontinental dispersal events from North America. Japan and the Russian Far East harbour exceptionally high levels of genetic diversity at both regional and local scales. In contrast, little genetic subdivision is apparent across the formerly glaciated regions of Europe and North America, areas that historical demographic analyses suggest that were recolonized just 5500–24 000 years ago.     

Phylogeny and biogeography of the Rhinella marina species complex (Amphibia,Bufonidae) revisited: implications for Neotropical diversification hypotheses

Vallinoto, M., Sequeira, F., Sodré, D., Bernardi, J. A. R., Sampaio, I. & Schneider, H. (2009). Phylogeny and biogeography of the Rhinella marina species complex (Amphibia, Bufonidae) revisited: implications for Neotropical diversification hypotheses. —Zoologica Scripta, 39, 128–140. A number of distinct hypotheses have been proposed to account for the origin of the considerable biological diversity found in the Neotropics, which is still a matter of intense debate. Here, we conducted a phylogenetic analysis of the Rhinella marina complex, a group of species widely distributed in Central and South America, combining published data with new sequences of three mtDNA genes (12S, 16S and cyt b) in order to clarify the evolutionary relationships and biogeographical history of the group. We included eight of the ten currently recognized R. marina group species and several outgroups. Maximum parsimony, maximum likelihood, and Bayesian inference analyses produced similar topologies, with two well‐supported main clades, each characterized by a deep subdivision. One of these major clades includes the samples of R. marina from Central America and Ecuador (west of the Andes), whereas the other comprises the remaining species of the group and samples of R. marina from the Amazon basin and other areas east of the Andes. A Bayesian coalescent‐based method (BEAST) dated the divergence between the two major clades, and between the Central American and Ecuadorian clades to the Miocene, matching the timing of other Central‐South American faunal divergences. Taken together, the results highlight the importance of Tertiary events such as the Pebas/marine incursions into the Amazon basin and Andean uplift for the diversification and historical biogeography of R. marina, making such taxa paraphyletic, and provide new perspectives on the debate on its species status.     

Rapid diversification of Tragopogon and ecological associates in Eurasia

Tragopogon comprises approximately 150 described species distributed throughout Eurasia from Ireland and the UK to India and China with a few species in North Africa. Most of the species diversity is found in Eastern Europe to Western Asia. Previous phylogenetic analyses identified several major clades, generally corresponding to recognized taxonomic sections, although relationships both among these clades and among species within clades remain largely unresolved. These patterns are consistent with rapid diversification following the origin of Tragopogon, and this study addresses the timing and rate of diversification in Tragopogon. Using BEAST to simultaneously estimate a phylogeny and divergence times, we estimate the age of a major split and subsequent rapid divergence within Tragopogon to be ~2.6 Ma (and 1.7–5.4 Ma using various clock estimates). Based on the age estimates obtained with BEAST (HPD 1.7–5.4 Ma) for the origin of crown group Tragopogon and 200 estimated species (to accommodate a large number of cryptic species), the diversification rate of Tragopogon is approximately 0.84–2.71 species/Myr for the crown group, assuming low levels of extinction. This estimate is comparable in rate to a rapid Eurasian radiation in Dianthus (0.66–3.89 species/Myr), which occurs in the same or similar habitats. Using available data, we show that subclades of various plant taxa that occur in the same semi‐arid habitats of Eurasia also represent rapid radiations occurring during roughly the same window of time (1.7–5.4 Ma), suggesting similar causal events. However, not all species‐rich plant genera from the same habitats diverged at the same time, or at the same tempo. Radiations of several other clades in this same habitat (e.g. Campanula, Knautia, Scabiosa) occurred at earlier dates (45–4.28 Ma). Existing phylogenetic data and diversification estimates therefore indicate that, although some elements of these semi‐arid communities radiated during the Plio‐Pleistocene period, other clades sharing the same habitat appear to have diversified earlier.