More Like this

1. Genomic Architecture Predicts Tree Topology, Population Structuring, and Demographic History in Amazonian Birds

   https://doi.org/10.1093/gbe/evae002  

   Thom, Gregory; Moreira, Lucas Rocha; Batista, Romina; Gehara, Marcelo; Aleixo, Alexandre; Smith, Brian Tilston (January 2024, Genome Biology and Evolution)

   Hancock, Angela (Ed.)

   Abstract Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on the spatial and temporal origins of population variation have been largely limited to evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known as genomic architecture in producing heterogeneity in differentiation across the genome. To test how variation in genomic characteristics (e.g. recombination rate) impacts our ability to reconstruct general patterns of differentiation between species that cooccur across geographic barriers, we sequenced the whole genomes of multiple bird populations that are distributed across rivers in southeastern Amazonia. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with species tree support. Gene flow was less pervasive in genomic regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection, skewing genome-wide estimates of effective population sizes and gene flow between populations toward lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from neutral processes to elucidate spatial patterns of population differentiation. 

   more » « less
2. Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation

   https://doi.org/10.1093/gbe/evab098  

   Tigano, Anna; Jacobs, Arne; Wilder, Aryn P; Nand, Ankita; Zhan, Ye; Dekker, Job; Therkildsen, Nina Overgaard (June 2021, Genome Biology and Evolution)

   Lohmueller, Kirk (Ed.)

   Abstract The levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10x Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside (Menidia menidia)—an established ecological model for studying the phenotypic effects of natural and artificial selection—and examined patterns of genomic variation across two individuals sampled from different populations with divergent local adaptations. Levels of diversity varied substantially across each chromosome, consistently being highly elevated near the ends (presumably near telomeric regions) and dipping to near zero around putative centromeres. Overall, our estimate of the genome-wide average heterozygosity in the Atlantic silverside is among the highest reported for a fish, or any vertebrate (1.32–1.76% depending on inference method and sample). Furthermore, we also found extreme levels of structural variation, affecting ∼23% of the total genome sequence, including multiple large inversions (> 1 Mb and up to 12.6 Mb) associated with previously identified haploblocks showing strong differentiation between locally adapted populations. These extreme levels of standing genetic variation are likely associated with large effective population sizes and may help explain the remarkable adaptive divergence among populations of the Atlantic silverside. 

   more » « less
3. Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome

   https://doi.org/10.1002/evl3.189  

   Wilder, Aryn P.; Palumbi, Stephen R.; Conover, David O.; Therkildsen, Nina Overgaard (October 2020, Evolution Letters)

   Abstract The study of local adaptation in the presence of ongoing gene flow is the study of natural selection in action, revealing the functional genetic diversity most relevant to contemporary pressures. In addition to individual genes, genome-wide architecture can itself evolve to enable adaptation. Distributed across a steep thermal gradient along the east coast of North America, Atlantic silversides (Menidia menidia) exhibit an extraordinary degree of local adaptation in a suite of traits, and the capacity for rapid adaptation from standing genetic variation, but we know little about the patterns of genomic variation across the species range that enable this remarkable adaptability. Here, we use low-coverage, whole-transcriptome sequencing of Atlantic silversides sampled along an environmental cline to show marked signatures of divergent selection across a gradient of neutral differentiation. Atlantic silversides sampled across 1371 km of the southern section of its distribution have very low genome-wide differentiation (median FST = 0.006 across 1.9 million variants), consistent with historical connectivity and observations of recent migrants. Yet almost 14,000 single nucleotide polymorphisms (SNPs) are nearly fixed (FST > 0.95) for alternate alleles. Highly differentiated SNPs cluster into four tight linkage disequilibrium (LD) blocks that span hundreds of genes and several megabases. Variants in these LD blocks are disproportionately nonsynonymous and concentrated in genes enriched for multiple functions related to known adaptations in silversides, including variation in lipid storage, metabolic rate, and spawning behavior. Elevated levels of absolute divergence and demographic modeling suggest selection maintaining divergence across these blocks under gene flow. These findings represent an extreme case of heterogeneity in levels of differentiation across the genome, and highlight how gene flow shapes genomic architecture in continuous populations. Locally adapted alleles may be common features of populations distributed along environmental gradients, and will likely be key to conserving variation to enable future responses to environmental change. 

   more » « less
4. Comparative Population Genomic Diversity and Differentiation in Trapdoor Spiders and Relatives (Araneae, Mygalomorphae)

   https://doi.org/10.1111/mec.17540  

   Monjaraz‐Ruedas, Rodrigo; Starrett, James; Newton, Lacie; Bond, Jason E; Hedin, Marshal (November 2024, Molecular Ecology)

   ABSTRACT Although patterns of population genomic variation are well‐studied in animals, there remains room for studies that focus on non‐model taxa with unique biologies. Here we characterise and attempt to explain such patterns in mygalomorph spiders, which are generally sedentary, often occur as spatially clustered demes and show remarkable longevity. Genome‐wide single nucleotide polymorphism (SNP) data were collected for 500 individuals across a phylogenetically representative sample of taxa. We inferred genetic populations within focal taxa using a phylogenetically informed clustering approach, and characterised patterns of diversity and differentiation within‐ and among these genetic populations, respectively. Using phylogenetic comparative methods we asked whether geographical range sizes and ecomorphological variables (behavioural niche and body size) significantly explain patterns of diversity and differentiation. Specifically, we predicted higher genetic diversity in genetic populations with larger geographical ranges, and in small‐bodied taxa. We also predicted greater genetic differentiation in small‐bodied taxa, and in burrowing taxa. We recovered several significant predictors of genetic diversity, but not genetic differentiation. However, we found generally high differentiation across genetic populations for all focal taxa, and a consistent signal for isolation‐by‐distance irrespective of behavioural niche or body size. We hypothesise that high population genetic structuring, likely reflecting combined dispersal limitation and microhabitat specificity, is a shared trait for all mygalomorphs. Few studies have found ubiquitous genetic structuring for an entire ancient and species‐rich animal clade. 

   more » « less
5. Adaptive divergence despite low effective population size in a peripherally isolated population of the pygmy rabbit, Brachylagus idahoensis

   https://doi.org/10.1111/mec.16040  

   Byer, Nathan W.; Holding, Matthew L.; Crowell, Miranda M.; Pierson, Todd W.; Dilts, Thomas E.; Larrucea, Eveline S.; Shoemaker, Kevin T.; Matocq, Marjorie D. (July 2021, Molecular Ecology)

   Abstract Local adaptation can occur when spatially separated populations are subjected to contrasting environmental conditions. Historically, understanding the genetic basis of adaptation has been difficult, but increased availability of genome‐wide markers facilitates studies of local adaptation in non‐model organisms of conservation concern. The pygmy rabbit (Brachylagus idahoensis) is an imperiled lagomorph that relies on sagebrush for forage and cover. This reliance has led to widespread population declines following reductions in the distribution of sagebrush, leading to geographic separation between populations. In this study, we used >20,000 single nucleotide polymorphisms, genotype‐environment association methods, and demographic modeling to examine neutral genetic variation and local adaptation in the pygmy rabbit in Nevada and California. We identified 308 loci as outliers, many of which had functional annotations related to metabolism of plant secondary compounds. Likewise, patterns of spatial variation in outlier loci were correlated with landscape and climatic variables including proximity to streams, sagebrush cover, and precipitation. We found that populations in the Mono Basin of California probably diverged from other Great Basin populations during late Pleistocene climate oscillations, and that this region is adaptively differentiated from other regions in the southern Great Basin despite limited gene flow and low effective population size. Our results demonstrate that peripherally isolated populations can maintain adaptive divergence. 

   more » « less