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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. Giant Tree Frog diversification in West and Central Africa: Isolation by physical barriers, climate, and reproductive traits

   https://doi.org/10.1111/mec.16169  

   Jaynes, Kyle E. ; Myers, Edward A. ; Gvoždík, Václav ; Blackburn, David C. ; Portik, Daniel M. ; Greenbaum, Eli ; Jongsma, Gregory F. M. ; Rödel, Mark‐Oliver ; Badjedjea, Gabriel ; Bamba‐Kaya, Abraham ; et al ( September 2021 , Molecular Ecology)

   Secondary sympatry amongst sister lineages is strongly associated with genetic and ecological divergence. This pattern suggests that for closely related species to coexist in secondary sympatry, they must accumulate differences in traits that mediate ecological and/or reproductive isolation. Here, we characterized inter‐ and intraspecific divergence in three giant tree frog species whose distributions stretch across West and Central Africa. Using genome‐wide single‐nucleotide polymorphism data, we demonstrated that species‐level divergence coincides temporally and geographically with a period of large‐scale forest fragmentation during the late Pliocene. Our environmental niche models further supported a dynamic history of climatic suitability and stability, and indicated that all three species occupy distinct environmental niches. We found modest morphological differentiation amongst the species with significant divergence in tympanum diameter and male advertisement call. In addition, we confirmed that two species occur in secondary sympatry in Central Africa but found no evidence of hybridization. These patterns support the hypothesis that cycles of genetic exchange and isolation across West and Central Africa have contributed to globally significant biodiversity. Furthermore, divergence in both ecology and reproductive traits appear to have played important roles in maintaining distinct lineages. At the intraspecific level, we found that climatic refugia, precipitation gradients, marine incursions, and potentially riverine barriers generated phylogeographic structure throughout the Pleistocene and into the Holocene. Further studies examining phenotypic divergence and secondary contact amongst these geographically structured populations may demonstrate how smaller scale and more recent biogeographic barriers contribute to regional diversification.

    

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3. Testing main Amazonian rivers as barriers across time and space within widespread taxa

   https://doi.org/10.1111/jbi.13676  

   Pirani, Renata M. ; Werneck, Fernanda P. ; Thomaz, Andréa T. ; Kenney, Mariah L. ; Sturaro, Marcelo J. ; Ávila‐Pires, Teresa C. S. ; Peloso, Pedro L. V. ; Rodrigues, Miguel T. ; Knowles, L. Lacey ( September 2019 , Journal of Biogeography)

   Present Amazonian diversity patterns can result from many different mechanisms and, consequently, the factors contributing to divergence across regions and/or taxa may differ. Nevertheless, the river‐barrier hypothesis is still widely invoked as a causal process in divergence of Amazonian species. Here we use model‐based phylogeographic analyses to test the extent to which major Amazonian rivers act similarly as barriers across time and space in two broadly distributed Amazonian taxa.

   Amazon rain forest.

   The lizardGonatodes humeralis(Sphaerodactylidae) and the tree frogDendropsophus leucophyllatus(Hylidae).

   We obtained RADseq data for samples distributed across main river barriers, representing main Areas of Endemism previously proposed for the region. We conduct model‐based phylogeographic and genetic differentiation analyses across each population pair.

   Measures of genetic differentiation (based onF_STcalculated from genomic data) show that all rivers are associated with significant genetic differentiation. Parameters estimated under investigated divergence models showed that divergence times for populations separated by each of the 11 bordering rivers were all fairly recent. The degree of differentiation consistently varied between taxa and among rivers, which is not an artifact of any corresponding difference in the genetic diversities of the respective taxa, or to amounts of migration based on analyses of the site‐frequency spectrum.

   Taken together, our results support a dispersal (rather than vicariance) history, without strong evidence of congruence between these species and rivers. However, once a species crossed a river, populations separated by each and every river have remained isolated—in this sense, rivers act similarly as barriers to any further gene flow. This result suggests differing degrees of persistence and gives rise to the seeming contradiction that the divergence process indeed varies across time, space and species, even though major Amazonian rivers have acted as secondary barriers to gene flow in the focal taxa.

    

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4. 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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5. Phylogeography of Solomon Islands blossom bats reflects oceanic divides and Pleistocene connections

   https://doi.org/10.1111/jbi.14585  

   Lavery, Tyrone H. ; DeCicco, Lucas H. ; Olson, Karen V. ; Holland, Piokera S. ; Moyle, Robert G. ( March 2023 , Journal of Biogeography)

   Periodic lowering of sea levels and formation of land bridges can reshape phylogeographic patterns of insular biotas. Using archipelago‐wide sampling, we aimed to test if phylogeography of an old‐endemic bat lineage reflected Pleistocene land bridges.

   Solomon Islands and Papua New Guinea.

   MelonycterisandNesonycterisbats (Pteropodidae).

   We sequenced genome‐wide RADseq data for 49 specimens from 15 islands. We assessed phylogenetic relationships using maximum likelihood inRAxMLand quartet‐based methods inSVDquartets, population structure usingStructure, and admixture using maximum likelihood methods inTreeMix. We tested for genetic and geographic distance correlations using distance‐based redundancy analyses (dbRDA), identifying best‐fit models using stepwise model selection.

   Phylogenetic analyses identified fiveNesonycterisclades corresponding to Greater Bukida, Guadalcanal, Makira, Malaita and New Georgia group. Makira samples were sister to remainingNesonycteris.Structureidentified four populations: New IrelandMelonycteris melanops; andNesonycterisfrom Greater Bukida (including Guadalcanal); Malaita and Makira; and New Georgia group. Genetic backgrounds of Mono, Ngella and Guadalcanal separated from remaining Greater Bukida islands. Makira and Malaita separated into two populations. New Georgia group lacked structure, and genetic and geographic distances were not correlated. The best‐fit geographic distance models forNesonycterisand a Greater Bukida subset were least shore‐to‐shore distance; and Euclidean and least‐cost distances respectively.

   Influences of modern and Pleistocene island isolation and connectivity were evident in the overall Phylogeography ofNesonycteris. The lack of structure or geographic distance correlations within the New Georgia group indicated all islands were interconnected during the Last Glacial Maximum or contemporary oceanic divides are ineffective barriers. Conversely, genetic divergence across Greater Bukida islands reflected land‐bridge constrained dispersal. A Makira clade sister to allNesonycterispossibly indicates an origin on Makira. Alternately it reflects Makira's long‐isolated geographic status, as similar results exist for a range of taxa.

    

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