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1. 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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2. Genomic evidence for population‐specific responses to co‐evolving parasites in a New Zealand freshwater snail

   https://doi.org/10.1111/mec.14146  

   Bankers, Laura ; Fields, Peter ; McElroy, Kyle E. ; Boore, Jeffrey L. ; Logsdon, Jr., John M. ; Neiman, Maurine ( May 2017 , Molecular Ecology)

   Reciprocal co‐evolving interactions between hosts and parasites are a primary source of strong selection that can promote rapid and often population‐ or genotype‐specific evolutionary change. These host–parasite interactions are also a major source of disease. Despite their importance, very little is known about the genomic basis of co‐evolving host–parasite interactions in natural populations, especially in animals. Here, we use gene expression and sequence evolution approaches to take critical steps towards characterizing the genomic basis of interactions between the freshwater snailPotamopyrgus antipodarumand its co‐evolving sterilizing trematode parasite,Microphallussp., a textbook example of natural coevolution. We found thatMicrophallus‐infectedP. antipodarumexhibit systematic downregulation of genes relative to uninfectedP. antipodarum. The specific genes involved in parasite response differ markedly across lakes, consistent with a scenario where population‐level co‐evolution is leading to population‐specific host–parasite interactions and evolutionary trajectories. We also used anF_ST‐based approach to identify a set of loci that represent promising candidates for targets of parasite‐mediated selection across lakes as well as within each lake population. These results constitute the first genomic evidence for population‐specific responses to co‐evolving infection in theP. antipodarum‐Microphallusinteraction and provide new insights into the genomic basis of co‐evolutionary interactions in nature.

    

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3. Ecological genomics of local adaptation in Cornus florida L. by genotyping by sequencing

   https://doi.org/10.1002/ece3.2623  

   Pais, Andrew L. ; Whetten, Ross W. ; Xiang, Qiu‐Yun ( December 2016 , Ecology and Evolution)

   Discovering local adaptation, its genetic underpinnings, and environmental drivers is important for conserving forest species. Ecological genomic approaches coupled with next‐generation sequencing are useful means to detect local adaptation and uncover its underlying genetic basis in nonmodel species. We report results from a study on flowering dogwood trees (Cornus florida L.) using genotyping by sequencing (GBS). This species is ecologically important to easternUSforests but is severely threatened by fungal diseases. We analyzed subpopulations in divergent ecological habitats within North Carolina to uncover loci under local selection and associated with environmental–functional traits or disease infection. At this scale, we tested the effect of incorporating additional sequencing before scaling for a broader examination of the entire range. To test for biases ofGBS, we sequenced two similarly sampled libraries independently from six populations of three ecological habitats. We obtained environmental–functional traits for each subpopulation to identify associations with genotypes via latent factor mixed modeling (LFMM) and gradient forests analysis. To test whether heterogeneity of abiotic pressures resulted in genetic differentiation indicative of local adaptation, we evaluatedF_stper locus while accounting for genetic differentiation between coastal subpopulations and Piedmont‐Mountain subpopulations. Of the 54 candidate loci with sufficient evidence of being under selection among both libraries, 28–39 were Arlequin–BayeScanF_stoutliers. ForLFMM, 45 candidates were associated with climate (of 54), 30 were associated with soil properties, and four were associated with plant health. Reanalysis of combined libraries showed that 42 candidate loci still showed evidence of being under selection. We conclude environment‐driven selection on specific loci has resulted in local adaptation in response to potassium deficiencies, temperature, precipitation, and (to a marginal extent) disease. High allele turnover along ecological gradients further supports the adaptive significance of loci speculated to be under selection.

    

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4. Population genomics of the eastern cottonwood ( Populus deltoides )

   https://doi.org/10.1002/ece3.3466  

   Fahrenkrog, Annette M. ; Neves, Leandro G. ; Resende, Jr, Márcio F. R. ; Dervinis, Christopher ; Davenport, Ruth ; Barbazuk, W. Brad ; Kirst, Matias ( October 2017 , Ecology and Evolution)

   Despite its economic importance as a bioenergy crop and key role in riparian ecosystems, little is known about genetic diversity and adaptation of the eastern cottonwood (Populus deltoides). Here, we report the first population genomics study for this species, conducted on a sample of 425 unrelated individuals collected in 13 states of the southeastern United States. The trees were genotyped by targeted resequencing of 18,153 genes and 23,835 intergenic regions, followed by the identification of single nucleotide polymorphisms (SNPs). This naturalP. deltoidespopulation showed low levels of subpopulation differentiation (F_ST = 0.022–0.106), high genetic diversity (θ_W = 0.00100, π = 0.00170), a large effective population size (N_e ≈ 32,900), and low to moderate levels of linkage disequilibrium. Additionally, genomewide scans for selection (Tajima'sD), subpopulation differentiation (X^TX), and environmental association analyses with eleven climate variables carried out with two different methods (LFMMandBAYENV2) identified genes putatively involved in local adaptation. Interestingly, many of these genes were also identified as adaptation candidates in another poplar species,Populus trichocarpa, indicating possible convergent evolution. This study constitutes the first assessment of genetic diversity and local adaptation inP. deltoidesthroughout the southern part of its range, information we expect to be of use to guide management and breeding strategies for this species in future, especially in the face of climate change.

    

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5. Host plant‐related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi

   https://doi.org/10.1111/mec.15239  

   Bakovic, Vid ; Schuler, Hannes ; Schebeck, Martin ; Feder, Jeffrey L. ; Stauffer, Christian ; Ragland, Gregory J. ( October 2019 , Molecular Ecology)

   Elucidating the mechanisms and conditions facilitating the formation of biodiversity are central topics in evolutionary biology. A growing number of studies imply that divergent ecological selection may often play a critical role in speciation by counteracting the homogenising effects of gene flow. Several examples involve phytophagous insects, where divergent selection pressures associated with host plant shifts may generate reproductive isolation, promoting speciation. Here, we use ddRADseq to assess the population structure and to test for host‐related genomic differentiation in the European cherry fruit fly,Rhagoletis cerasi(L., 1758) (Diptera: Tephritidae). This tephritid is distributed throughout Europe and western Asia, and has adapted to two different genera of host plants,Prunusspp. (cherries) andLoniceraspp. (honeysuckle). Our data imply that geographic distance and geomorphic barriers serve as the primary factors shaping genetic population structure across the species range. Locally, however, flies genetically cluster according to host plant, with consistent allele frequency differences displayed by a subset of loci betweenPrunusandLoniceraflies across four sites surveyed in Germany and Norway. These 17 loci display significantly higher F_STvalues between host plants than others. They also showed high levels of linkage disequilibrium within and betweenPrunusandLoniceraflies, supporting host‐related selection and reduced gene flow. Our findings support the existence of sympatric host races inR. cerasiembedded within broader patterns of geographic variation in the fly, similar to the related apple maggot,Rhagoletis pomonella, in North America.

    

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