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1. Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

   https://doi.org/10.1186/s12862-020-01739-9  

   Klingler, Kelly B. ; Jahner, Joshua P. ; Parchman, Thomas L. ; Ray, Chris ; Peacock, Mary M. ( January 2021 , BMC Ecology and Evolution)

   Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada.

   Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θ_W = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θ_W = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θ_W = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’sDwas positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide.

   Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

    

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2. Urbanization reduces gene flow but not genetic diversity of stream salamander populations in the New York City metropolitan area

   https://doi.org/10.1111/eva.13025  

   Fusco, Nicole A. ; Pehek, Ellen ; Munshi‐South, Jason ( June 2020 , Evolutionary Applications)

   Natural landscape heterogeneity and barriers resulting from urbanization can reduce genetic connectivity between populations. The evolutionary, demographic, and ecological effects of reduced connectivity may lead to population isolation and ultimately extinction. Alteration to the terrestrial and aquatic environment caused by urban influence can affect gene flow, specifically for stream salamanders who depend on both landscapes for survival and reproduction. To examine how urbanization affects a relatively common stream salamander species, we compared genetic connectivity ofEurycea bislineata(northern two‐lined salamander) populations within and between streams in an urban, suburban, and rural habitat around the New York City (NYC) metropolitan area. We report reduced genetic connectivity between streams within the urban landscape found to correspond with potential barriers to gene flow, that is, areas with more dense urbanization (roadways, industrial buildings, and residential housing). The suburban populations also exhibited areas of reduced connectivity correlated with areas of greater human land use and greater connectivity within a preserve protected from development. Connectivity was relatively high among neighboring rural streams, but a major roadway corresponded with genetic breaks even though the habitat contained more connected green space overall. Despite greater human disturbance across the landscape, urban and suburban salamander populations maintained comparable levels of genetic diversity to their rural counterparts. Yet small effective population size in the urban habitats yielded a high probability of loss of heterozygosity due to genetic drift in the future. In conclusion, urbanization impacted connectivity among stream salamander populations where its continual influence may eventually hinder population persistence for this native species in urban habitats.

    

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3. Life history and socioecology of infancy

   https://doi.org/10.1002/ajpa.24145  

   Helfrecht, Courtney ; Roulette, Jennifer W. ; Lane, Avery ; Sintayehu, Birhanu ; Meehan, Courtney L. ( September 2020 , American Journal of Physical Anthropology)

   Evolution of human maternal investment strategies is hypothesized to be tied to biological constraints and environmental cues. It is likely, however, that the socioecological context in which mothers' decisions are made is equally important. Yet, a lack of studies examining maternal investment from a cross‐cultural, holistic approach has hindered our ability to investigate the evolution of maternal investment strategies. Here, we take a systems‐level approach to study how human life history characteristics, environments, and socioecology influence maternal investment in their children.

   We test how infant age and sex, maternal age, parity, and child loss, and the composition of a child's cooperative breeding network are associated with maternal investment across three small‐scale (hunter‐gatherer, horticultural, and agropastoral), sub‐Saharan populations (N= 212). Naturalistic behavioral observations also enable us to illustrate the breadth and depth of the human cooperative breeding system.

   Results indicate that infant age, maternal age and parity, and an infant's cooperative childcare network are significantly associated with maternal investment, controlling for population. We also find that human allomaternal care is conducted by a range of caregivers, occupying different relational, sex, and age categories. Moreover, investment by allomothers is widely distributed.

   Our findings illustrate the social context in which children are reared in contemporary small‐scale populations, and in which they were likely reared throughout our evolutionary history. The diversity of the caregiving network, coupled with life history characteristics, is predictive of maternal investment strategies, demonstrating the importance of cooperation in the evolution of human ontogeny.

    

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4. Drift, selection and adaptive variation in small populations of a threatened rattlesnake

   https://doi.org/10.1111/mec.15517  

   Ochoa, Alexander ; Broe, Michael ; Moriarty Lemmon, Emily ; Lemmon, Alan R. ; Rokyta, Darin R. ; Gibbs, H. Lisle ( July 2020 , Molecular Ecology)

   An important goal of conservation genetics is to determine if the viability of small populations is reduced by a loss of adaptive variation due to genetic drift. Here, we assessed the impact of drift and selection on direct measures of adaptive variation (toxin loci encoding venom proteins) in the eastern massasauga rattlesnake (Sistrurus catenatus), a threatened reptile that exists in small isolated populations. We estimated levels of individual polymorphism in 46 toxin loci and 1,467 control loci across 12 populations of this species, and compared the results with patterns of selection on the same loci following speciation ofS. catenatusand its closest relative, the western massasauga (S. tergeminus). Multiple lines of evidence suggest that both drift and selection have had observable impacts on standing adaptive variation. In support of drift effects, we found little evidence for selection on toxin variation within populations and a significant positive relationship between current levels of adaptive variation and long‐ and short‐term estimates of effective population size. However, we also observed levels of directional selection on toxin loci among populations that are broadly similar to patterns predicted from interspecific selection analyses that pre‐date the effects of recent drift, and that functional variation in these loci persists despite small short‐term effective sizes. This suggests that much of the adaptive variation present in populations may represent an example of “drift debt,” a nonequilibrium state where present‐day levels of variation overestimate the amount of functional genetic diversity present in future populations.

    

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5. Drift happens: Molecular genetic diversity and differentiation among populations of jewelweed ( Impatiens capensis Meerb.) reflect fragmentation of floodplain forests

   https://doi.org/10.1111/mec.15072  

   Toczydlowski, Rachel H. ; Waller, Donald M. ( May 2019 , Molecular Ecology)

   Landscape features often shape patterns of gene flow and genetic differentiation in plant species. Populations that are small and isolated enough also become subject to genetic drift. We examined patterns of gene flow and differentiation among 12 floodplain populations of the selfing annual jewelweed (Impatiens capensisMeerb.) nested within four river systems and two major watersheds in Wisconsin, USA. Floodplain forests and marshes provide a model system for assessing the effects of habitat fragmentation within agricultural/urban landscapes and for testing whether rivers act to genetically connect dispersed populations. We generated a panel of 12,856 single nucleotide polymorphisms and assessed genetic diversity, differentiation, gene flow, and drift. Clustering methods revealed strong population genetic structure with limited admixture and highly differentiated populations (mean multilocusF_ST = 0.32,F_ST’ = 0.33). No signals of isolation by geographic distance or environment emerged, but alleles may flow along rivers given that genetic differentiation increased with river distance. Differentiation also increased in populations with fewer private alleles (R² = 0.51) and higher local inbreeding (R² = 0.22). Populations varied greatly in levels of local inbreeding (F_IS = 0.2–0.9) andF_ISincreased in more isolated populations. These results suggest that genetic drift dominates other forces in structuring theseImpatienspopulations. In rapidly changing environments, species must migrate or genetically adapt. Habitat fragmentation limits both processes, potentially compromising the ability of species to persist in fragmented landscapes.

    

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