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1. Exploring rain forest diversification using demographic model testing in the African foam‐nest treefrog Chiromantis rufescens

   https://doi.org/10.1111/jbi.13716  

   Leaché, Adam D. ; Portik, Daniel M. ; Rivera, Danielle ; Rödel, Mark‐Oliver ; Penner, Johannes ; Gvoždík, Václav ; Greenbaum, Eli ; Jongsma, Gregory F. M. ; Ofori‐Boateng, Caleb ; Burger, Marius ; et al ( October 2019 , Journal of Biogeography)

   Species with wide distributions spanning the African Guinean and Congolian rain forests are often composed of genetically distinct populations or cryptic species with geographic distributions that mirror the locations of the remaining forest habitats. We used phylogeographic inference and demographic model testing to evaluate diversification models in a widespread rain forest species, the African foam‐nest treefrogChiromantis rufescens.

   Guinean and Congolian rain forests, West and Central Africa.

   Chiromantis rufescens.

   We collected mitochondrial DNA (mtDNA) and single‐nucleotide polymorphism (SNP) data for 130 samples ofC. rufescens. After estimating population structure and inferring species trees using coalescent methods, we tested demographic models to evaluate alternative population divergence histories that varied with respect to gene flow, population size change and periods of isolation and secondary contact. Species distribution models were used to identify the regions of climatic stability that could have served as forest refugia since the last interglacial.

   Population structure withinC. rufescensresembles the major biogeographic regions of the Guinean and Congolian forests. Coalescent‐based phylogenetic analyses provide strong support for an early divergence between the western Upper Guinean forest and the remaining populations. Demographic inferences support diversification models with gene flow and population size changes even in cases where contemporary populations are currently allopatric, which provides support for forest refugia and barrier models. Species distribution models suggest that forest refugia were available for each of the populations throughout the Pleistocene.

   Considering historical demography is essential for understanding population diversification, especially in complex landscapes such as those found in the Guineo–Congolian forest. Population demographic inferences help connect the patterns of genetic variation to diversification model predictions. The diversification history ofC. rufescenswas shaped by a variety of processes, including vicariance from river barriers, forest fragmentation and adaptive evolution along environmental gradients.

    

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2. Repeated patterns of reptile diversification in Western North America supported by the Northern Alligator Lizard ( Elgaria coerulea )

   https://doi.org/10.1093/jhered/esad073  

   Leaché, Adam D. ; Davis, Hayden R. ; Feldman, Chris R. ; Fujita, Matthew K. ; Singhal, Sonal ; Blair, ed., Christopher ( November 2023 , Journal of Heredity)

   Understanding the processes that shape genetic diversity by either promoting or preventing population divergence can help identify geographic areas that either facilitate or limit gene flow. Furthermore, broadly distributed species allow us to understand how biogeographic and ecogeographic transitions affect gene flow. We investigated these processes using genomic data in the Northern Alligator Lizard (Elgaria coerulea), which is widely distributed in Western North America across diverse ecoregions (California Floristic Province and Pacific Northwest) and mountain ranges (Sierra Nevada, Coastal Ranges, and Cascades). We collected single-nucleotide polymorphism data from 120 samples of E. coerulea. Biogeographic analyses of squamate reptiles with similar distributions have identified several shared diversification patterns that provide testable predictions for E. coerulea, including deep genetic divisions in the Sierra Nevada, demographic stability of southern populations, and recent post-Pleistocene expansion into the Pacific Northwest. We use genomic data to test these predictions by estimating the structure, connectivity, and phylogenetic history of populations. At least 10 distinct populations are supported, with mixed-ancestry individuals situated at most population boundaries. A species tree analysis provides strong support for the early divergence of populations in the Sierra Nevada Mountains and recent diversification into the Pacific Northwest. Admixture and migration analyses detect gene flow among populations in the Lower Cascades and Northern California, and a spatial analysis of gene flow identified significant barriers to gene flow across both the Sierra Nevada and Coast Ranges. The distribution of genetic diversity in E. coerulea is uneven, patchy, and interconnected at population boundaries. The biogeographic patterns seen in E. coerulea are consistent with predictions from co-distributed species.

    

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3. The phylogeographic history of a range disjunction in eastern North America: the role of post‐glacial expansion into newly suitable habitat

   https://doi.org/10.1002/ajb2.1686  

   Mohn, Rebekah A. ; Oleas, Nora H. ; Smith, Adam B. ; Swift, Joel F. ; Yatskievych, George A. ; Edwards, Christine E. ( June 2021 , American Journal of Botany)

   A disjunct distribution, where a species’ geographic range is discontinuous, can occur through vicariance or long‐distance dispersal. Approximately 75 North American plant species exhibit a ~650 km disjunction between the Ozark and Appalachian regions. This disjunction is attributed to biogeographic forces including: (1) Eocene–Oligocene vicariance by the formation of the Mississippi embayment; (2) Pleistocene vicariance from interglacial flooding; (3) post‐Pleistocene northward colonization from separate glacial refugia; (4) Hypsithermal vicariance due to climate fluctuations; and (5) recent long‐distance dispersal. We investigated which of these pathways most likely gave rise to the Appalachian‐Ozark disjunction inDelphinium exaltatum.

   We genotyped populations ofD. exaltatumfrom five Ozark and seven Appalachian localities, analyzed genetic structure, tested the order and timing of divergences usingDIYABC, and conducted niche reconstructions up to 21,000 years before present (YBP).

   Populations fell into five main genetic clusters, i.e., a group in the central Appalachians, and four “lowland” groups. DIYABC analyses showed the central Appalachian and lowland lineages diverging 11,300 to17,000 YBP, and the lowland groups diverging 6800 to 10,900 YBP. Niche reconstructions showed that suitable climate for the central Appalachian lineage experienced large spatial discontinuity starting 14,000 YBP, such that divergence and persistence before this period is less plausible than divergence thereafter.

   Our results did not fully support any of the original hypotheses. Rather, the oldest divergence likely occurred after 13,500 YBP through expansion into newly opened habitat in the Appalachians. The Appalachian‐Ozark disjunction likely resulted from northward dispersal of the lowland lineage as climate warmed during the Holocene.

    

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4. Shifting ecosystem connectivity during the Pleistocene drove diversification and gene‐flow in a species complex of Neotropical birds (Tityridae: Pachyramphus)

   https://doi.org/10.1111/jbi.13862  

   Musher, Lukas J. ; Galante, Peter J. ; Thom, Gregory ; Huntley, Jerry W. ; Blair, Mary E. ( April 2020 , Journal of Biogeography)

   We aim to test the biogeographic drivers of diversification and gene‐flow at the Isthmus of Panama using a species complex of suboscine birds as a case study. We specifically evaluate whether diversification in these birds is better explained by continuous parapatry or a Refuge Model of periodic isolation and gene‐flow due glacial cycling.

   The Isthmus of Panama (Neotropics).

   Pachyramphus aglaiaeandPachyramphus homochrous(Aves: Tityridae).

   We develop an approach to distinguish among the two biogeographic hypotheses—parapatric ecological speciation versus climatically mediated speciation—by making explicit predictions for demographic history, niche evolution and change in geographic connectivity over time. We sequenced genome‐wide markers (ultraconserved elements) to estimate the evolutionary and demographic history of this group. We applied both phylogenomic network analyses and demographic modelling using a supervised machine learning approach. These genetic analyses were combined with a novel distribution modelling method that estimates the probability of interspecies contact as a function of climatic conditions through time.

   We found that both spatial and genetic analyses revealed concordant results. All speciation events occurred during the Pleistocene and were characterized by non‐continuous gene‐flow, supporting a scenario of climate‐mediated diversification. Spatial connectivity was highest at present, consistent with our best demographic model of secondary contact.

   This study exemplifies a mechanism by which speciation, dispersal and introgression unfold in an important region for Neotropical diversification—the Isthmus of Panama—where periods ofbothisolation and introgression probably drive diversification. Overall, our results are consistent with the Refuge Model of biotic diversification, but suggest that introgression may be a crucial yet underappreciated component of this classic paradigm.

    

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5. 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.

    

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