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1. Population genetics of wild Macaca fascicularis with low‐coverage shotgun sequencing of museum specimens

   https://doi.org/10.1002/ajpa.24099  

   Yao, Lu ; Witt, Kelsey ; Li, Hongjie ; Rice, Jonathan ; Salinas, Nelson R. ; Martin, Robert D. ; Huerta‐Sánchez, Emilia ; Malhi, Ripan S. ( July 2020 , American Journal of Physical Anthropology)

   Long‐tailed macaques (Macaca fascicularis) are widely distributed throughout the mainland and islands of Southeast Asia, making them a useful model for understanding the complex biogeographical history resulting from drastic changes in sea levels throughout the Pleistocene. Past studies based on mitochondrial genomes (mitogenomes) of long‐tailed macaque museum specimens have traced their colonization patterns throughout the archipelago, but mitogenomes trace only the maternal history. Here, our objectives were to trace phylogeographic patterns of long‐tailed macaques using low‐coverage nuclear DNA (nDNA) data from museum specimens.

   We performed population genetic analyses and phylogenetic reconstruction on nuclear single nucleotide polymorphisms (SNPs) from shotgun sequencing of 75 long‐tailed macaque museum specimens from localities throughout Southeast Asia.

   We show that shotgun sequencing of museum specimens yields sufficient genome coverage (average ~1.7%) for reconstructing population relationships using SNP data. Contrary to expectations of divergent results between nuclear and mitochondrial genomes for a female philopatric species, phylogeographical patterns based on nuclear SNPs proved to be closely similar to those found using mitogenomes. In particular, population genetic analyses and phylogenetic reconstruction from the nDNA identify two major clades withinM. fascicularis: Clade A includes all individuals from the mainland along with individuals from northern Sumatra, while Clade B consists of the remaining island‐living individuals, including those from southern Sumatra.

   Overall, we demonstrate that low‐coverage sequencing of nDNA from museum specimens provides enough data for examining broad phylogeographic patterns, although greater genome coverage and sequencing depth would be needed to distinguish between very closely related populations, such as those throughout the Philippines.

    

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2. Genomic investigation of colour polymorphism and phylogeographic variation among populations of black‐headed bulbul ( Brachypodius atriceps ) in insular southeast Asia

   https://doi.org/10.1111/mec.16089  

   Shakya, Subir B. ; Haryoko, Tri ; Irham, Mohammad ; Suparno ; Prawiradilaga, Dewi M. ; Sheldon, Frederick H. ( August 2021 , Molecular Ecology)

   Intraspecific polymorphism in birds, especially plumage colour polymorphism, and the mechanisms that control it are an area of active research in evolutionary biology. The black‐headed bulbul (Brachypodius atriceps) is a polymorphic species with two distinct morphs, yellow and grey. This species inhabits the mainland and virtually all continental islands of Southeast Asia where yellow morphs predominate, but on two islands in the Sunda region, Bawean and Maratua, grey morphs are common or exclusive. Here, we generated a high‐quality reference genome of a yellow individual and resequenced genomes of multiple individuals of both yellow and grey morphs to study the genetic basis of coloration and population history of the species. Using PCA and STRUCTURE analysis, we found the Maratua Island population (which is exclusively grey) to be distinct from all otherB.atricepspopulations, having been isolated c. 1.9 million years ago (Ma). In contrast, Bawean grey individuals (a subset of yellow and grey individuals on that island) are embedded within an almost panmictic Sundaic clade of yellow birds. UsingF_STandd_xyto compare variable genomic segments between Maratua and yellow individuals, we located peaks of divergence and identified candidate loci involved in the colour polymorphism. Tests of selection among coding‐proteins in highF_STregions, however, did not indicate selection on the candidate genes. Overall, we report on some loci that are potentially responsible for the grey/yellow polymorphism in a species that otherwise shows little genetic diversification across most of its range.

    

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3. Founder effects shape linkage disequilibrium and genomic diversity of a partially clonal invader

   https://doi.org/10.1111/mec.15854  

   Flanagan, Ben A. ; Krueger‐Hadfield, Stacy A. ; Murren, Courtney J. ; Nice, Chris C. ; Strand, Allan E. ; Sotka, Erik E. ( April 2021 , Molecular Ecology)

   The genomic variation of an invasive species may be affected by complex demographic histories and evolutionary changes during the invasion. Here, we describe the relative influence of bottlenecks, clonality, and population expansion in determining genomic variability of the widespread red macroalgaAgarophyton vermiculophyllum. Its introduction from mainland Japan to the estuaries of North America and Europe coincided with shifts from predominantly sexual to partially clonal reproduction and rapid adaptive evolution. A survey of 62,285 SNPs for 351 individuals from 35 populations, aligned to 24 chromosome‐length scaffolds indicate that linkage disequilibrium (LD), observed heterozygosity (H_o), Tajima's D, and nucleotide diversity (Pi) were greater among non‐native than native populations. Evolutionary simulations indicate LD and Tajima's D were consistent with a severe population bottleneck. Also, the increased rate of clonal reproduction in the non‐native range could not have produced the observed patterns by itself but may have magnified the bottleneck effect on LD. Elevated marker diversity in the genetic source populations could have contributed to the increasedH_oand Pi observed in the non‐native range. We refined the previous invasion source region to a ~50 km section of northeastern Honshu Island. Outlier detection methods failed to reveal any consistently differentiated loci shared among invaded regions, probably because of the complexA. vermiculophyllumdemographic history. Our results reinforce the importance of demographic history, specifically founder effects, in driving genomic variation of invasive populations, even when localized adaptive evolution and reproductive system shifts are observed.

    

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4. Status, kinship, and place of burial at Early Bronze Age Bab adh‐Dhra': A biogeochemical comparison of charnel house human remains

   https://doi.org/10.1002/ajpa.23982  

   Gregoricka, Lesley A. ; Ullinger, Jaime ; Sheridan, Susan G. ( December 2019 , American Journal of Physical Anthropology)

   The Early Bronze Age (EBA; ca. 3,600–2000 BCE) of the southern Levant underwent considerable transformation as agro‐pastoral communities began to utilize their land more intensively, constructing larger, fortified towns prior to site abandonment at the end of the third millennium. At the site of Bab adh‐Dhra' in Jordan, the dead of the Early Bronze (EB) II–III (ca. 3,100–2,500 BCE) period were communally interred within charnel houses, but important disparities between these structures and their contents may be reflective of ownership and use by particular extended kin groups whose activity patterns, subsistence strategies, and even social status may have differed from one another. Subsequently, we hypothesized that differences in mobility and dietary intake may differentiate tomb groups from one another.

   Dental enamel from 31 individuals interred in three different Early Bronze Age charnel houses (A56, A22, A55) at Bab adh‐Dhra', Jordan were analyzed for strontium, oxygen, and carbon isotope values.

   Strontium isotope ratios (range: 0.70793–0.70842) possessed medians that did not differ statistically from one another, but had ranges that exhibited significant differences in variance. Carbon isotope values (= −13.2 ± 0.5‰, 1σ) were not significantly different.

   General similarities in human isotopic signatures between EB II–III charnel houses A22 and A55 suggest that their activities were likely similar to one another and agree with findings from excavated domestic spaces with little archaeological evidence for economic, social, or political differentiation. More variable strontium isotope ratios and lower carbon isotope values from A22 could reflect a greater involvement with pastoralist practices or regional trade, including the consumption of more¹³C‐depleted foods, while those in A55 may have led a more sedentary lifestyle with greater involvement in cultivating orchard crops. All charnel houses contained nonlocal individuals likely originating from other Dead Sea Plain sites with no EB II–III cemeteries of their own, supporting the idea that extended kin groups throughout the region returned to Bab adh‐Dhra' to bury their dead.

    

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5. Molecular signatures of long‐distance oceanic dispersal and the colonization of Pacific islands in Lycium carolinianum

   https://doi.org/10.1002/ajb2.1626  

   Levin, Rachel A. ; Miller, Jill S. ( April 2021 , American Journal of Botany)

   Long‐distance dispersal has been important in explaining the present distributions of many plant species. Despite being infrequent, such dispersal events have considerable evolutionary consequences, because bottlenecks during colonization can result in reduced genetic diversity. We examined the phylogeographic history ofLycium carolinianum, a widespread taxon that ranges from southeastern North America to several Pacific islands, with intraspecific diversity in sexual and mating systems.

   We used Bayesian, likelihood, and coalescent approaches with nuclear and plastid sequence data and genome‐wide single nucleotide polymorphisms to reconstruct the dispersal history of this species. We also compared patterns of genetic variation in mainland and island populations using single nucleotide polymorphisms and allelic diversity at theS‐RNasemating system gene.

   Lycium carolinianumis monophyletic and dispersed once from the North American mainland, colonizing the Pacific islands ca. 40,100 years ago. This dispersal was accompanied by a loss of genetic diversity in SNPs and theS‐RNaselocus due to a colonization bottleneck and the loss of self‐incompatibility. Additionally, we documented at least two independent transitions to gynodioecy: once following the colonization of the Hawaiian Islands and loss of self‐incompatibility, and a second time associated with polyploidy in the Yucatán region of Mexico.

   Long‐distance dispersal via fleshy, bird dispersed fruits best explains the unusually widespread distribution ofL. carolinianum. The collapse of diversity at theS‐RNaselocus in island populations suggests that self‐fertilization may have facilitated the subsequent colonization of Pacific islands following a single dispersal from mainland North America.

    

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