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1. Siberian genetic diversity reveals complex origins of the Samoyedic‐speaking populations

   https://doi.org/10.1002/ajhb.23194  

   Karafet, Tatiana M. ; Osipova, Ludmila P. ; Savina, Olga V. ; Hallmark, Brian ; Hammer, Michael F. ( November 2018 , American Journal of Human Biology)

   We examined autosomal genome‐wide SNPs and Y‐chromosome data from 15 Siberian and 12 reference populations to study the affinities of Siberian populations, and to address hypotheses about the origin of the Samoyed peoples.

   Samples were genotyped for 567 096 autosomal SNPs and 147 Y‐chromosome polymorphic sites. For several analyses, we used 281 093 SNPs from the intersection of our data with publicly available ancient Siberian samples. To examine genetic relatedness among populations, we applied PCA,F_ST, TreeMix, and ADMIXTURE analyses. To explore the potential effect of demography and evolutionary processes, the distribution of ROH and IBD sharing within population were studied.

   Analyses of autosomal and Y‐chromosome data reveal high differentiation of the Siberian groups. The Siberian populations have a large proportion of their genome in ROH and IBD segments. Several populations (ie, Nganasans, Evenks, Yukagirs, and Koryaks) do not appear to have experienced admixture with other Siberian populations (ie, producing only positive f3), while for the other tested populations the composition of mixing sources always included Nganasans or Evenks. The Nganasans from the Taymyr Peninsula demonstrate the greatest level of shared shorter ROH and IBD with nearly all other Siberian populations.

   Autosomal SNP and Y‐chromosome data demonstrate that Samoyedic populations differ significantly in their genetic composition. Genetic relationship is observed only between Forest and Tundra Nentsi. Selkups are affiliated with the Kets from the Yenisey River, while the Nganasans are separated from their linguistic neighbors, showing closer affinities with the Evenks and Yukagirs.

    

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2. Genomic signatures of inbreeding and mutation load in a threatened rattlesnake

   https://doi.org/10.1111/mec.16147  

   Ochoa, Alexander ; Gibbs, H. Lisle ( September 2021 , Molecular Ecology)

   Theory predicts that threatened species living in small populations will experience high levels of inbreeding that will increase their genetic load, but recent work suggests that the impact of load may be minimized by purging resulting from long‐term population bottlenecks. Empirical studies that examine this idea using genome‐wide estimates of inbreeding and genetic load in threatened species are limited. Here we use individual genome resequencing data to compare levels of inbreeding, levels of genetic load (estimated as mutation load) and population history in threatened Eastern massasauga rattlesnakes (Sistrurus catenatus), which exist in small isolated populations, and closely related yet outbred Western massasauga rattlesnakes (Sistrurus tergeminus). In terms of inbreeding,S. catenatusgenomes had a greater number of runs of homozygosity of varying sizes, indicating sustained inbreeding through repeated bottlenecks when compared toS. tergeminus. At the species level, outbredS. tergeminushad higher genome‐wide levels of mutation load in the form of greater numbers of derived deleterious mutations compared toS. catenatus, presumably due to long‐term purging of deleterious mutations inS. catenatus. In contrast, mutations that escaped species‐level drift effects withinS. catenatuspopulations were in general more frequent and more often found in homozygous genotypes than inS. tergeminus, suggesting a reduced efficiency of purifying selection in smallerS. catenatuspopulations for most mutations. Our results support an emerging idea that the historical demography of a threatened species has a significant impact on the type of genetic load present, which impacts implementation of conservation actions such as genetic rescue.

    

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3. A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population

   https://doi.org/10.1093/gbe/evac122  

   Wilder, Aryn P ; Dudchenko, Olga ; Curry, Caitlin ; Korody, Marisa ; Turbek, Sheela P ; Daly, Mark ; Misuraca, Ann ; Wang, Gaojianyong ; Khan, Ruqayya ; Weisz, David ; et al ( August 2022 , Genome Biology and Evolution)

   Enard, David (Ed.)

   Abstract High-quality reference genomes are fundamental tools for understanding population history, and can provide estimates of genetic and demographic parameters relevant to the conservation of biodiversity. The federally endangered Pacific pocket mouse (PPM), which persists in three small, isolated populations in southern California, is a promising model for studying how demographic history shapes genetic diversity, and how diversity in turn may influence extinction risk. To facilitate these studies in PPM, we combined PacBio HiFi long reads with Omni-C and Hi-C data to generate a de novo genome assembly, and annotated the genome using RNAseq. The assembly comprised 28 chromosome-length scaffolds (N50 = 72.6 MB) and the complete mitochondrial genome, and included a long heterochromatic region on chromosome 18 not represented in the previously available short-read assembly. Heterozygosity was highly variable across the genome of the reference individual, with 18% of windows falling in runs of homozygosity (ROH) >1 MB, and nearly 9% in tracts spanning >5 MB. Yet outside of ROH, heterozygosity was relatively high (0.0027), and historical Ne estimates were large. These patterns of genetic variation suggest recent inbreeding in a formerly large population. Currently the most contiguous assembly for a heteromyid rodent, this reference genome provides insight into the past and recent demographic history of the population, and will be a critical tool for management and future studies of outbreeding depression, inbreeding depression, and genetic load. 

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4. Dynamics of reduced genetic diversity in increasingly fragmented populations of Florida scrub jays , Aphelocoma coerulescens

   https://doi.org/10.1111/eva.13421  

   Nguyen, Tram N. ; Chen, Nancy ; Cosgrove, Elissa J. ; Bowman, Reed ; Fitzpatrick, John W. ; Clark, Andrew G. ( June 2022 , Evolutionary Applications)

   Understanding the genomic consequences of population decline is important for predicting species' vulnerability to intensifying global change. Empirical information about genomic changes in populations in the early stages of decline, especially for those still experiencing immigration, remains scarce. We used 7834 autosomal SNPs and demographic data for 288 Florida scrub jays (Aphelocoma coerulescens; FSJ) sampled in 2000 and 2008 to compare levels of genetic diversity, inbreeding, relatedness, and lengths of runs of homozygosity (ROH) between two subpopulations within dispersal distance of one another but have experienced contrasting demographic trajectories. At Archbold Biological Station (ABS), the FSJ population has been stable because of consistent habitat protection and management, while at nearby Placid Lakes Estates (PLE), the population declined precipitously due to suburban development. By the onset of our sampling in 2000, birds in PLE were already less heterozygous, more inbred, and on average more related than birds in ABS. No significant changes occurred in heterozygosity or inbreeding across the 8‐year sampling interval, but average relatedness among individuals decreased in PLE, thus by 2008 average relatedness did not differ between sites. PLE harbored a similar proportion of short ROH but a greater proportion of long ROH than ABS, suggesting one continuous population of shared demographic history in the past, which is now experiencing more recent inbreeding. These results broadly uphold the predictions of simple population genetic models based on inferred effective population sizes and rates of immigration. Our study highlights how, in just a few generations, formerly continuous populations can diverge in heterozygosity and levels of inbreeding with severe local population decline despite ongoing gene flow.

    

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5. Late Pleistocene range expansion of North American topminnows accompanied by admixture and introgression

   https://doi.org/10.1111/jbi.13597  

   Duvernell, David D. ; Westhafer, Eric ; Schaefer, Jacob F. ( June 2019 , Journal of Biogeography)

   We used genome‐scale sampling to assess the phylogeography of a group of topminnows in theFundulus notatusspecies complex. Two of the species have undergone extensive range expansions resulting in broadly overlapping distributions, and sympatry within drainages has provided opportunities for hybridization and introgression. We assessed the timing and pattern of range expansion in the context of late Pleistocene–Holocene drainage events and evaluated the evidence for introgressive hybridization between species.

   Central and southern United States including drainages of the Gulf of Mexico Coastal Plain and portions of the Mississippi River drainage in and around the Central Highlands.

   Topminnows, GenusFundulus, subgenusZygonectes—Fundulus notatus, Fundulus olivaceus, Fundulus euryzonus.

   We sampled members of theF. notatusspecies complex throughout their respective ranges, including numerous drainage systems where species co‐occur. We collected genome‐wide single nucleotide polymorphisms (SNPs) using the genotype‐by‐sequencing (GBS) method and subjected data to population genetic analyses to infer the population histories of both species, including explicit tests for admixture and introgression. The methods employed includedSTRUCTURE, principal coordinates analysis, TreeMix and approximate Bayesian computation.

   Genetic data are presented for 749 individuals sampled from 14F. notatus, 20F. olivaceusand 2F. euryzonuspopulations. Members of the species complex differed in phylogeographic structure, withF. notatusexhibiting geographic clusters corresponding to Pleistocene coastal drainages andF. olivaceuscomparatively lacking in phylogeographic structure. Evidence for interspecific introgression varied by drainage.

   Populations ofF. notatusandF. olivaceusexhibited contrasting patterns of lineage diversity among coastal drainages, indicating interspecific differences in their Pleistocene southern refugia. Phylogeographic patterns in both species indicated that range expansions into the northern limits of contemporary distributions coincided with and continued subsequent to the Last Glacial Maximum. There was evidence of introgression between species in some, but not all drainages where the species co‐occur, in a pattern that is correlated with previous estimates of hybridization rates.

    

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