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1. Sky, sea, and forest islands: Diversification in the African leaf‐folding frog Afrixalus paradorsalis (Anura: Hyperoliidae) of the Lower Guineo‐Congolian rain forest

   https://doi.org/10.1111/jbi.13365  

   Charles, Kristin L. ; Bell, Rayna C. ; Blackburn, David C. ; Burger, Marius ; Fujita, Matthew K. ; Gvoždík, Václav ; Jongsma, Gregory F. M. ; Kouete, Marcel Talla ; Leaché, Adam D. ; Portik, Daniel M. ( June 2018 , Journal of Biogeography)

   To investigate how putative barriers, forest refugia, and ecological gradients across the lower Guineo‐Congolian rain forest shape genetic and phenotypic divergence in the leaf‐folding frogAfrixalus paradorsalis, and examine the role of adjacent land bridge and sky‐islands in diversification.

   The Lower Guineo‐Congolian Forest, the Cameroonian Volcanic Line (CVL), and Bioko Island, Central Africa.

   Afrixalus paradorsalis(Family: Hyperoliidae), an African leaf‐folding frog.

   We used molecular and phenotypic data to investigate diversity and divergence among theA. paradorsalisspecies complex distributed across lowland rain forests, a land bridge island, and mountains in Central Africa. We examined the coincidence of population boundaries, landscape features, divergence times, and spatial patterns of connectivity and diversity, and subsequently performed demographic modelling using genome‐wide SNP variation to distinguish among divergence mechanisms in mainland (riverine barriers, forest refugia, ecological gradients) and land bridge island populations (vicariance, overwater dispersal).

   We detected four genetically distinct allopatric populations corresponding to Bioko Island, the CVL, and two lowland rain forest populations split by the Sanaga River. Although lowland populations are phenotypically indistinguishable, pronounced body size evolution occurs at high elevation, and the timing of the formation of the high elevation population coincides with mountain uplift in the CVL. Spatial analyses and demographic modelling revealed population divergence across mainland Lower Guinea is best explained by forest refugia rather than riverine barriers or ecological gradients, and that the Bioko Island population divergence is best explained by vicariance (marine incursion) rather than overseas dispersal.

   We provide growing support for the important role of forest refugia in driving intraspecific divergences in the Guineo‐Congolian rain forest. InA. paradorsalis, sky‐islands in the CVL have resulted in greater genetic and phenotypic divergences than marine incursions of the land bridge Bioko Island, highlighting important differences in patterns of island‐driven diversification in Lower Guinea.

    

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2. 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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3. Paleotemperatures and recurrent habitat shifts drive diversification of treefrogs across distinct biodiversity hotspots in sub‐Amazonian South America

   https://doi.org/10.1111/jbi.13997  

   Vasconcellos, Mariana M. ; Colli, Guarino R. ; Cannatella, David C. ( November 2020 , Journal of Biogeography)

   We investigate the biogeographical history and diversification in a treefrog lineage distributed in contrasting (open and forested) ecoregions of South America, including three biodiversity hotspots. We evaluate the role of dispersal and whether other factors such as diversity‐dependence or paleotemperatures could explain the diversification pattern for this group. Especially focusing on the savanna endemics, we illuminate the processes governing the species assembly and evolution of the Cerrado savanna.

   South American ecoregions south of the Amazon (i.e. Atlantic Forest, Cerrado, Araucaria Forest, Pampas, Central and Southern Andes).

   Boana pulchellagroup.

   We built the most complete time‐calibrated phylogeny for the group to date. We then reconstructed ancestral ranges using the dispersal‐extinction‐cladogenesis (DEC) model comparing different dispersal scenarios considering distance, adjacency and ecological similarity among regions. Centre‐of‐origin hypotheses in forest and open ecoregions were also tested. Using biogeographical stochastic mapping, we additionally estimated the contribution of range shifts across different biomes. Lastly, we evaluated several diversification models, including the effect of time, diversity‐dependence and temperature‐dependence on speciation and extinction rates.

   TheBoana pulchellagroup originated during the Early Miocene (~17.5 MYA) and underwent high speciation rates during the Middle Miocene Climatic Optimum, with a decreasing trend following the Miocene Climatic Transition. We found no support for a single ecoregion acting as a centre of origin and diversification; instead, we inferred recurrent range shifts with dispersal among dissimilar adjacent ecoregions. Speciation linearly dependent on paleotemperatures, with either no or very low constant extinction rates, best explained the slowdown diversification pattern.

   Our results support a species assembly of Cerrado savanna in South America during the Miocene with intermittent interchange with rain forest habitats. Past climate changes impacted the rate new species originated with apparently no impact on extinction. Finally, the repeated habitat shifts among open/dry and forested/humid ecoregions, rather than long‐term in‐situ diversification in single areas, highlights the very dynamic historical interchange between contrasting habitats in South America, possibly contributing to its high species diversity.

    

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4. Parallel evolution and cryptic diversification in a common and widespread Amazonian tree, Protium subserratum

   https://doi.org/10.1111/mec.16889  

   Misiewicz, Tracy M. ; Simmons, Tracey ; Carter, Benjamin E. ; Fine, Paul V. A. ; Moore, Abigail J. ( March 2023 , Molecular Ecology)

   The lowland Amazon rainforest houses some of the greatest tree diversity on Earth. While the vast majority of these species are rare, a small number are common and widespread and thus considered to play a disproportionate role in many of the global ecosystem services provided by the Amazon. However, the extent to which dominant Amazonian tree species actually include multiple clades, each on their own unique evolutionary trajectory, is unknown. Here we investigate the extent to which lineage divergence may be occurring withinProtium subserratum(Burseraceae), a common and widespread tree species that is monophyletic with populations exhibiting genotypic and phenotypic differences associated with soil and geography. Utilizing a combination of phylogenomic and population genomic methods with sampling from across the range, we found thatP. subserratumcontains at least eight distinct clades. Specialization onto white‐sand soils has evolved independently at least twice within the species; however, phenotype is not correlated with soil type. Finally, cryptic diversity at the base of the Andes is associated with elevational shifts. Together these results lend support to the hypothesis that common and widespread Amazon tree species may not represent evolutionary cohesive units. Instead, these dominant species may more commonly represent species complexes, undergoing evolutionary transitions on a trajectory to become multiple range‐restricted, specialist species.

    

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5. A few essential genetic loci distinguish Penstemon species with flowers adapted to pollination by bees or hummingbirds

   https://doi.org/10.1371/journal.pbio.3002294  

   Wessinger, Carolyn A. ; Katzer, Amanda M. ; Hime, Paul M. ; Rausher, Mark D. ; Kelly, John K. ; Hileman, Lena C. ( September 2023 , PLOS Biology)

   Barton, Nick H. (Ed.)

   In the formation of species, adaptation by natural selection generates distinct combinations of traits that function well together. The maintenance of adaptive trait combinations in the face of gene flow depends on the strength and nature of selection acting on the underlying genetic loci. Floral pollination syndromes exemplify the evolution of trait combinations adaptive for particular pollinators. The North American wildflower genusPenstemondisplays remarkable floral syndrome convergence, with at least 20 separate lineages that have evolved from ancestral bee pollination syndrome (wide blue-purple flowers that present a landing platform for bees and small amounts of nectar) to hummingbird pollination syndrome (bright red narrowly tubular flowers offering copious nectar). Related taxa that differ in floral syndrome offer an attractive opportunity to examine the genomic basis of complex trait divergence. In this study, we characterized genomic divergence among 229 individuals from aPenstemonspecies complex that includes both bee and hummingbird floral syndromes. Field plants are easily classified into species based on phenotypic differences and hybrids displaying intermediate floral syndromes are rare. Despite unambiguous phenotypic differences, genome-wide differentiation between species is minimal. Hummingbird-adapted populations are more genetically similar to nearby bee-adapted populations than to geographically distant hummingbird-adapted populations, in terms of genome-wided_XY. However, a small number of genetic loci are strongly differentiated between species. These approximately 20 “species-diagnostic loci,” which appear to have nearly fixed differences between pollination syndromes, are sprinkled throughout the genome in high recombination regions. Several map closely to previously established floral trait quantitative trait loci (QTLs). The striking difference between the diagnostic loci and the genome as whole suggests strong selection to maintain distinct combinations of traits, but with sufficient gene flow to homogenize the genomic background. A surprisingly small number of alleles confer phenotypic differences that form the basis of species identity in this species complex.

    

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