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1. Radiation with reticulation marks the origin of a major malaria vector

   https://doi.org/10.1073/pnas.2018142117  

   Small, Scott T. ; Labbé, Frédéric ; Lobo, Neil F. ; Koekemoer, Lizette L. ; Sikaala, Chadwick H. ; Neafsey, Daniel E. ; Hahn, Matthew W. ; Fontaine, Michael C. ; Besansky, Nora J. ( December 2020 , Proceedings of the National Academy of Sciences)

   null (Ed.)

   Advances in genomics have led to an appreciation that introgression is common, but its evolutionary consequences are poorly understood. In recent species radiations the sharing of genetic variation across porous species boundaries can facilitate adaptation to new environments and generate novel phenotypes, which may contribute to further diversification. Most Anopheles mosquito species that are of major importance as human malaria vectors have evolved within recent and rapid radiations of largely nonvector species. Here, we focus on one of the most medically important yet understudied anopheline radiations, the Afrotropical Anopheles funestus complex (AFC), to investigate the role of introgression in its diversification and the possible link between introgression and vector potential. The AFC comprises at least seven morphologically similar species, yet only An. funestus sensu stricto is a highly efficient malaria vector with a pan-African distribution. Based on de novo genome assemblies and additional whole-genome resequencing, we use phylogenomic and population genomic analyses to establish species relationships. We show that extensive interspecific gene flow involving multiple species pairs has shaped the evolutionary history of the AFC since its diversification. The most recent introgression event involved a massive and asymmetrical movement of genes from a distantly related AFC lineage into An. funestus , an event that predated and plausibly facilitated its subsequent dramatic geographic range expansion across most of tropical Africa. We propose that introgression may be a common mechanism facilitating adaptation to new environments and enhancing vectorial capacity in Anopheles mosquitoes. 

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2. Genomic and geographic diversification of a “great-speciator” ( Rhipidura rufifrons )

   https://doi.org/10.1093/ornithology/ukac049  

   Klicka, Lukas B ; Campillo, Luke C ; Manthey, Joseph D ; Andersen, Michael J ; Dumbacher, John P ; Filardi, Christopher E ; Joseph, Leo ; Uy, J Albert ; Weidemann, Douglas E ; Moyle, Robert G ( September 2022 , Ornithology)

   Abstract The radiation of so-called “great speciators” represents a paradox among the myriad of avian radiations endemic to the southwest Pacific. In such radiations, lineages otherwise capable of dispersing across vast distances of open ocean differentiate rapidly and frequently across relatively short geographic barriers. Here, we evaluate the phylogeography of the Rufous Fantail (Rhipidura rufifrons). Although a presumed “great-speciator”, no formal investigations across its range have been performed. Moreover, delimitation of lineages within R. rufifrons, and the biogeographic implications of those relationships, remain unresolved. To investigate whether R. rufifrons represents a great speciator we identified thousands of single nucleotide polymorphisms for 89 individuals, representing 19 described taxa. Analyses recovered 7 divergent lineages and evidence of gene flow between geographically isolated populations. We also found plumage differences to be a poor proxy for evolutionary relationships. Given the relatively recent divergence dates for the clade (1.35–2.31 mya), rapid phenotypic differentiation, and evidence for multiple independent lineages within the species complex, we determine that R. rufifrons possesses the characteristics of a great speciator. 

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3. The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages

   https://doi.org/10.7717/peerj.4409  

   Dudoit, ‘Ale‘alani ; Iacchei, Matthew ; Coleman, Richard R. ; Gaither, Michelle R. ; Browne, William E. ; Bowen, Brian W. ; Toonen, Robert J. ( January 2018 , PeerJ)

   The banded coral shrimp, Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) is a popular marine ornamental species with a circumtropical distribution. The planktonic larval stage lasts ∼120–253 days, indicating considerable dispersal potential, but few studies have investigated genetic connectivity on a global scale in marine invertebrates. To resolve patterns of divergence and phylogeography of S. hispidus , we surveyed 525 bp of mitochondrial cytochrome c oxidase subunit I (COI) from 198 individuals sampled at 10 locations across ∼27,000 km of the species range. Phylogenetic analyses reveal that S. hispidus has a Western Atlantic lineage and a widely distributed Indo-Pacific lineage, separated by sequence divergence of 2.1%. Genetic diversity is much higher in the Western Atlantic ( h = 0.929; π  = 0.004) relative to the Indo-Pacific ( h = 0.105; π  < 0.001), and coalescent analyses indicate that the Indo-Pacific population expanded more recently (95% HPD (highest posterior density) = 60,000–400,000 yr) than the Western Atlantic population (95% HPD = 300,000–760,000 yr). Divergence of the Western Atlantic and Pacific lineages is estimated at 710,000–1.8 million years ago, which does not readily align with commonly implicated colonization events between the ocean basins. The estimated age of populations contradicts the prevailing dispersal route for tropical marine biodiversity (Indo-Pacific to Atlantic) with the oldest and most diverse population in the Atlantic, and a recent population expansion with a single common haplotype shared throughout the vast Indian and Pacific oceans. In contrast to the circumtropical fishes, this diminutive reef shrimp challenges our understanding of conventional dispersal capabilities of marine species. 

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4. Phylogeographic and phenotypic outcomes of brown anole colonization across the Caribbean provide insight into the beginning stages of an adaptive radiation

   https://doi.org/10.1111/jeb.13581  

   Reynolds, Robert Graham ; Kolbe, Jason J. ; Glor, Richard E. ; López‐Darias, Marta ; Gómez Pourroy, C. Verónica ; Harrison, Alexis S. ; de Queiroz, Kevin ; Revell, Liam J. ; Losos, Jonathan B. ( January 2020 , Journal of Evolutionary Biology)

   Some of the most important insights into the ecological and evolutionary processes of diversification and speciation have come from studies of island adaptive radiations, yet relatively little research has examined how these radiations initiate. We suggest thatAnolis sagreiis a candidate for understanding the origins of the CaribbeanAnolisadaptive radiation and how a colonizing anole species begins to undergo allopatric diversification, phenotypic divergence and, potentially, speciation. We undertook a genomic and morphological analysis of representative populations across the entire native range ofA. sagrei, finding that the species originated in the early Pliocene, with the deepest divergence occurring between western and eastern Cuba. Lineages from these two regions subsequently colonized the northern Caribbean. We find that at the broadest scale, populations colonizing areas with fewer closely related competitors tend to evolve larger body size and more lamellae on their toepads. This trend follows expectations for post‐colonization divergence from progenitors and convergence in allopatry, whereby populations freed from competition with close relatives evolve towards common morphological and ecological optima. Taken together, our results show a complex history of ancient and recent Cuban diaspora with populations on competitor‐poor islands evolving away from their ancestral Cuban populations regardless of their phylogenetic relationships, thus providing insight into the original diversification of colonist anoles at the beginning of the radiation. Our research also supplies an evolutionary framework for the many studies of this increasingly important species in ecological and evolutionary research.

    

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5. The molecular biogeography of the Indo‐Pacific: Testing hypotheses with multispecies genetic patterns

   https://doi.org/10.1111/geb.12905  

   Crandall, Eric D. ; Riginos, Cynthia ; Bird, Chris E. ; Liggins, Libby ; Treml, Eric ; Beger, Maria ; Barber, Paul H. ; Connolly, Sean R. ; Cowman, Peter F. ; DiBattista, Joseph D. ; et al ( April 2019 , Global Ecology and Biogeography)

   To test hypothesized biogeographic partitions of the tropical Indo‐Pacific Ocean with phylogeographic data from 56 taxa, and to evaluate the strength and nature of barriers emerging from this test.

   The Indo‐Pacific Ocean.

   Pliocene through the Holocene.

   Fifty‐six marine species.

   We tested eight biogeographic hypotheses for partitioning of the Indo‐Pacific using a novel modification to analysis of molecular variance. Putative barriers to gene flow emerging from this analysis were evaluated for pairwise Φ_ST, and these Φ_STdistributions were compared to distributions from randomized datasets and simple coalescent simulations of vicariance arising from the Last Glacial Maximum. We then weighed the relative contribution of distance versus environmental or geographic barriers to pairwise Φ_STwith a distance‐based redundancy analysis (dbRDA).

   We observed a diversity of outcomes, although the majority of species fit a few broad biogeographic regions. Repeated coalescent simulation of a simple vicariance model yielded a wide distribution of pairwise Φ_STthat was very similar to empirical distributions observed across five putative barriers to gene flow. Three of these barriers had median Φ_STthat were significantly larger than random expectation. Only 21 of 52 species analysed with dbRDA rejected the null model. Among these, 15 had overwater distance as a significant predictor of pairwise Φ_ST, while 11 were significant for geographic or environmental barriers other than distance.

   Although there is support for three previously described barriers, phylogeographic discordance in the Indo‐Pacific Ocean indicates incongruity between processes shaping the distributions of diversity at the species and population levels. Among the many possible causes of this incongruity, genetic drift provides the most compelling explanation: given massive effective population sizes of Indo‐Pacific species, even hard vicariance for tens of thousands of years can yield Φ_STvalues that range from 0 to nearly 0.5.

    

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