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1. Demography and linked selection interact to shape the genomic landscape of codistributed woodpeckers during the Ice Age

   https://doi.org/10.1111/mec.16841  

   Moreira, Lucas Rocha; Klicka, John; Smith, Brian Tilston (January 2023, Molecular ecology)

   The influence of genetic drift on population dynamics during Pleistocene glacial cycles is well understood, but the role of selection in shaping patterns of genomic variation during these events is less explored. We resequenced whole genomes to investigate how demography and natural selection interact to generate the genomic landscapes of Downy and Hairy Woodpecker, species codistributed in previously glaciated North America. First, we explored the spatial and temporal patterns of genomic diversity produced by neutral evolution. Next, we tested (i) whether levels of nucleotide diversity along the genome are correlated with intrinsic genomic properties, such as recombination rate and gene density, and (ii) whether different demographic trajectories impacted the efficacy of selection. Our results revealed cycles of bottleneck and expansion, and genetic structure associated with glacial refugia. Nucleotide diversity varied widely along the genome, but this variation was highly correlated between the species, suggesting the presence of conserved genomic features. In both taxa, nucleotide diversity was positively correlated with recombination rate and negatively correlated with gene density, suggesting that linked selection played a role in reducing diversity. Despite strong fluctuations in effective population size, the maintenance of relatively large populations during glaciations may have facilitated selection. Under these conditions, we found evidence that the individual demographic trajectory of populations modulated linked selection, with purifying selection being more efficient in removing deleterious alleles in large populations. These results highlight that while genome-wide variation reflects the expected signature of demographic change during climatic perturbations, the interaction of multiple processes produces a predictable and highly heterogeneous genomic landscape. 

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2. The Chemodynamics of the Stellar Populations in M31 from APOGEE Integrated-light Spectroscopy

   https://doi.org/10.3847/1538-4357/acd9a9  

   Gibson, Benjamin J.; Zasowski, Gail; Seth, Anil; Ashok, Aishwarya; Goold, Kameron; Wainer, Tobin; Hasselquist, Sten; Holtzman, Jon; Imig, Julie; Bizyaev, Dmitry; et al (July 2023, The Astrophysical Journal)

   Abstract We present an analysis of nearly 1000 near-infrared, integrated-light spectra from APOGEE in the inner ∼7 kpc of M31. We utilize full-spectrum fitting with A-LIST simple stellar population spectral templates that represent a population of stars with the same age, [M/H], and [α/M]. With this, we determine the mean kinematics, metallicities,αabundances, and ages of the stellar populations of M31's bar, bulge, and inner disk (∼4–7 kpc). We find a nonaxisymmetric velocity field in M31 resulting from the presence of a bar. The bulge of M31 is less metal-rich (mean [M/H] = $-{0.149}_{-0.081}^{+0.067}$dex) than the disk, features minima in metallicity on either side of the bar ([M/H] ∼ −0.2), and is enhanced inαabundance (mean [α/M] = ${0.281}_{-0.038}^{+0.035}$). The disk of M31 within ∼7 kpc is enhanced in both metallicity ([M/H] = $-{0.023}_{-0.052}^{+0.050}$) andαabundance ([α/M] = ${0.274}_{-0.025}^{+0.020}$). Both of these structural components are uniformly old at ≃12 Gyr. We find the mean metallicity increases with distance from the center of M31, with the steepest gradient along the disk major axis (0.043 ± 0.021 dex kpc⁻¹). This gradient is the result of changing light contributions from the bulge and disk. The chemodynamics of stellar populations encodes information about a galaxy’s chemical enrichment, star formation history, and merger history, allowing us to discuss new constraints on M31's formation. Our results provide a stepping stone between our understanding of the Milky Way and other external galaxies. 

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3. 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. 

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4. An integrative genomic and phenomic analysis to investigate the nature of plant species in Escallonia (Escalloniaceae)

   https://doi.org/10.1038/s41598-021-03419-0  

   Jacobs, Sarah J.; Grundler, Michael C.; Henriquez, Claudia L.; Zapata, Felipe (December 2021, Scientific Reports)

   Abstract What we mean by species and whether they have any biological reality has been debated since the early days of evolutionary biology. Some biologists even suggest that plant species are created by taxonomists as a subjective, artificial division of nature. However, the nature of plant species has been rarely tested critically with data while ignoring taxonomy. We integrate phenomic and genomic data collected across hundreds of individuals at a continental scale to investigate this question inEscallonia(Escalloniaceae), a group of plants which includes 40 taxonomic species (the species proposed by taxonomists). We first show that taxonomic species may be questionable as they match poorly to patterns of phenotypic and genetic variation displayed by individuals collected in nature. We then use explicit statistical methods for species delimitation designed for phenotypic and genomic data, and show that plant species do exist inEscalloniaas an objective, discrete property of nature independent of taxonomy. We show that such species correspond poorly to current taxonomic species ($$< 20\%$$ $<20\%$) and that phenomic and genomic data seldom delimit congruent entities ($$< 20\%$$ $<20\%$). These discrepancies suggest that evolutionary forces additional to gene flow can maintain the cohesion of species. We propose that phenomic and genomic data analyzed on an equal footing build a broader perspective on the nature of plant species by helping delineate different ‘types of species’. Our results caution studies which take the accuracy of taxonomic species for granted and challenge the notion of plant species without empirical evidence. Note: A version of the complete manuscript in Spanish is available in the Supplemental Materials. 

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5. 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. 

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