More Like this

1. Regional drivers of diversification in the late Quaternary in a widely distributed generalist species, the common pheasant Phasianus colchicus

   https://doi.org/10.1111/jbi.13964  

   Liu, Simin ; Liu, Yang ; Jelen, Edouard ; Alibadian, Mansour ; Yao, Cheng‐Te ; Li, Xintong ; Kayvanfar, Nasrin ; Wang, Yutao ; Vahidi, Farhad S. M. ; Han, Jian‐Lin ; et al ( September 2020 , Journal of Biogeography)

   Pleistocene climate and associated environmental changes have influenced phylogeographic patterns of many species. These not only depend on a species’ life history but also vary regionally. Consequently, populations of widespread species that occur in several biomes might display different evolutionary trajectories. We aimed to identify regional drivers of diversification in the common pheasant, a widely distributed ecological generalist.

   Asia.

   Common pheasantPhasianus colchicus.

   Using a comprehensive geographical sampling of 204 individuals from the species’ entire range genotyped at seven nuclear and two mitochondrial loci, we reconstructed spatio‐temporal diversification and demographic history of the common pheasant. We applied Bayesian phylogenetic inference to describe phylogeographic structure, generated a species tree and inferred demographic history within and migration between lineages. Moreover, to establish a taxonomic framework, we conducted a species delimitation analysis.

   The common pheasant diversified during the Late Pleistocene into eight distinct lineages. It originated at the edge of the Qinghai–Tibetan plateau and spread to East and Central Asia. Only the widely distributed lowland lineage of East Asia displayed recent range expansion. Greater phylogeographic structure was identified elsewhere, with lineages showing no sign of recent demographic changes. One lineage in south‐central China is the result of long‐term isolation within a climatically stable but topographically complex region. In lineages from arid Central Asia and China, range expansions were impeded by repeated population fragmentation during dry glacial periods and by recent aridification.

   Spatio‐temporal phylogeographic frameworks of widespread taxa such as the common pheasant provide valuable opportunities to identify divergent drivers of regional diversification. Our results suggest that diversification and population histories in the eight distinct evolutionary lineages were shaped by regionally variable effects of past climate and associated environmental changes. The evolutionary history of the common pheasant is best reflected by its being split into three species.

    

   more » « less
2. Phylogenomics Resolves the Relationships within Antennaria (Asteraceae, Gnaphalieae) and Yields New Insights into its Morphological Character Evolution and Biogeography

   https://doi.org/10.1600/036364420X15862837791221  

   Thapa, Ramhari ; Bayer, Randall J. ; Mandel, Jennifer R. ( June 2020 , Systematic Botany)

   Abstract— Antennaria are dioecious perennial herbs distributed mainly in the Holarctic Region, with their major center of diversity in the Rocky Mountains of Western North America. The genus comprises 33 known sexual diploid/tetraploid species and at least five polyploid agamic complexes which mostly reproduce by forming asexual seeds. We performed a phylogenetic reconstruction of the 31 sexually-reproducing Antennaria species using a novel target enrichment method that employs custom capture probes designed to work across Asteraceae. Both concatenated and coalescent-based analyses of DNA sequence data from hundreds of nuclear loci recovered Antennaria as a monophyletic group except for the long-disputed species, Antennaria linearifolia , which was recovered outside of the genus. Antennaria was further resolved into three distinct, major lineages. Analysis of ancestral state reconstruction of 12 taxonomically important morphological characters elucidated patterns of character evolution throughout the genus. Estimations of ancestral geographic ranges and molecular dating analyses demonstrated the Rocky Mountain region, including the Vancouverian Province, as the center of origin for the genus Antennaria, around 5.8 MYA. Subsequent dispersals of Antennaria into the Arctic and Appalachian provinces, Canadian provinces, and Eurasia took place roughly 3.2 MYA, 2.4 MYA, and 1.6 MYA, respectively. Biogeographical stochastic mapping indicated that 51.4% of biogeographical events were based on within-area speciation. The remaining 48.6% of the events were divided into two types of dispersals: 1) range expansion dispersals (anagenic, 37%), and 2) founder/jump dispersals (cladogenic, 11.6%). Our results provide a framework for future evolutionary studies of Antennaria, including speciation, origin(s) of polyploidy, and agamospermy in the genus. 

   more » « less
3. Phylogenomics, biogeography, and evolution of morphology and ecological niche of the eastern Asian–eastern North American Nyssa (Nyssaceae)

   https://doi.org/10.1111/jse.12599  

   Zhou, Wenbin ; Xiang, Qiu‐Yun ; Wen, Jun ( June 2020 , Journal of Systematics and Evolution)

   Nyssa(Nyssaceae, Cornales) represents a classical example of the well‐known eastern Asian–eastern North American floristic disjunction. The genus consists of three species in eastern Asia, four species in eastern North America, and one species in Central America. Species of the genus are ecologically important trees in eastern North American and eastern Asian forests. The distribution of living species and a rich fossil record of the genus make it an excellent model for understanding the origin and evolution of the eastern Asian–eastern North American floristic disjunction. However, despite the small number of species, relationships within the genus have remained unclear and have not been elucidated using a molecular approach. Here, we integrate data from 48 nuclear genes, fossils, morphology, and ecological niche to resolve species relationships, elucidate its biogeographical history, and investigate the evolution of morphology and ecological niches, aiming at a better understanding of the well‐known EA–ENA floristic disjunction. Results showed that the Central American (CAM)Nyssa talamancanawas sister to the remaining species, which were divided among three, rapidly diversified subclades. Estimated divergence times and biogeographical history suggested thatNyssahad an ancestral range in Eurasia and western North America in the late Paleocene. The rapid diversification occurred in the early Eocene, followed by multiple dispersals between and within the Erasian and North American continents. The genus experienced two major episodes of extinction in the early Oligocene and end of Neogene, respectively. The Central AmericanN. talamancanarepresents a relic lineage of the boreotropical flora in the Paleocene/Eocene boundary that once diversified in western North America. The results supported the importance of both the North Atlantic land bridge and the Bering land bridge (BLB) for the Paleogene dispersals ofNyssaand the Neogene dispersals, respectively, as well as the role of Central America as refugia of the Paleogene flora. The total‐evidence‐based dated phylogeny suggested that the pattern of macroevolution ofNyssacoincided with paleoclimatic changes. We found a number of evolutionary changes in morphology (including wood anatomy and leaf traits) and ecological niches (precipitation and temperature) between the EA–ENA disjunct, supporting the ecological selection driving trait evolutions after geographic isolation. We also demonstrated challenges in phylogenomic studies of lineages with rapid diversification histories. The concatenation of gene data can lead to inference of strongly supported relationships incongruent with the species tree. However, conflicts in gene genealogies did not seem to impose a strong effect on divergence time dating in our case. Furthermore, we demonstrated that rapid diversification events may not be recovered in the divergence time dating analysis using BEAST if critical fossil constraints of the relevant nodes are not available. Our study provides an example of complex bidirectional exchanges of plants between Eurasia and North America in the Paleogene, but “out of Asia” migrations in the Neogene, to explain the present disjunct distribution ofNyssain EA and ENA.

    

   more » « less
4. Population genomics and geographical parthenogenesis in Japanese harvestmen (Opiliones, Sclerosomatidae, Leiobunum )

   https://doi.org/10.1002/ece3.3605  

   Burns, Mercedes ; Hedin, Marshal ; Tsurusaki, Nobuo ( November 2017 , Ecology and Evolution)

   Naturally occurring population variation in reproductive mode presents an opportunity for researchers to test hypotheses regarding the evolution of sex. Asexual reproduction frequently assumes a geographical pattern, in which parthenogenesis‐dominated populations are more broadly dispersed than their sexual conspecifics. We evaluate the geographical distribution of genomic signatures associated with parthenogenesis using nuclear and mitochondrialDNAsequence data from two Japanese harvestman sister taxa,Leiobunum manubriatumandLeiobunum globosum. Asexual reproduction is putatively facultative in these species, and female‐biased localities are common in habitat margins. Past karyotypic and current cytometric work indicatesL. globosumis entirely tetraploid, whileL. manubriatummay be either diploid or tetraploid. We estimated species phylogeny, genetic differentiation, diversity, and mitonuclear discordance in females collected across the species range in order to identify range expansion toward marginal habitat, potential for hybrid origin, and persistence of asexual lineages. Our results point to northward expansion of a tetraploid ancestor ofL. manubriatumandL. globosum, coupled with support for greater male gene flow in southernL. manubriatumlocalities. Specimens from localities in the Tohoku and Hokkaido regions were indistinct, particularly those ofL. globosum, potentially due to little mitochondrial differentiation or haplotypic variation. AlthoughL. manubriatumoverlaps withL. globosumacross its entire range,L. globosumwas reconstructed as monophyletic with strong support using mtDNA, and marginal support with nuclear loci. Ultimately, we find evidence for continued sexual reproduction in both species and describe opportunities to clarify the rate and mechanism of parthenogenesis.

    

   more » « less
5. Bayesian analyses detect a history of both vicariance and geodispersal in Neotropical freshwater fishes

   https://doi.org/10.1111/jbi.13207  

   Machado, Carolina Barros ; Galetti, Jr, Pedro Manoel ; Carnaval, Ana Carolina ( March 2018 , Journal of Biogeography)

   Among the main biogeographical hypotheses explaining the remarkable diversity of fishes in the Neotropics is the “palaeogeographical hypothesis”, focusing on vicariance, and the “hydrogeological hypothesis”, focusing on geodispersal. Yet while reflecting different processes, they may result in similar biogeographical patterns. We employed a model‐based Bayesian approach to test these alternative hypotheses and determine which shaped the phylogeographical patterns observed in a group of Neotropical fishes.

   South America.

   Salminus.

   We used mitochondrial and nuclear markers to infer phylogenetic relationships and estimate divergence times amongSalminusspecies, associating the results with known geological events. We then employed approximate Bayesian computation (ABC) to explore changes in population size over time, asking whether vicariance or geodispersal events best explain the phylogeographical signature observed in the data. Because geodispersal captures a few individuals from a parental population, which can then expand and lead to a new lineage, we expect to find genetic signatures of a founder event following population expansion under this scenario, but not under vicariance.

   The analyses suggest that the diversification process inSalminusbegan in Upper Miocene, andABCindicates that it involved both vicariance and geodispersal events: while a vicariance event better explains the phylogeographical structure withinS. brasiliensisand the genetic patterns of differentiation betweenS. sp. Amazon andS. sp. Araguaia, geodispersal appears to have been the most important event structuring lineages ofSalminus hilarii.

   Both vicariance and geodispersal signatures were detected in our biological model, inferring a complex yet realistic demographic history ofSalminuslineages. The correspondence between theABCresults and traditional phylogeographical interpretations provide further confidence in the models drawn and tested. This study reinforces the value of applying anABCframework in phylogeographical studies, particularly for those interested in testing alternative and biologically plausible processes underlying similar biogeographical patterns.

    

   more » « less