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1. 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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2. Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics

   https://doi.org/10.1111/mec.13517  

   Hand, Brian K. ; Muhlfeld, Clint C. ; Wade, Alisa A. ; Kovach, Ryan P. ; Whited, Diane C. ; Narum, Shawn R. ; Matala, Andrew P. ; Ackerman, Michael W. ; Garner, Brittany A. ; Kimball, John S. ; et al ( February 2016 , Molecular Ecology)

   Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population‐specific and pairwiseF_ST) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin,USA. Using 151 putatively neutral and 29 candidate adaptiveSNPloci, we found that climate‐related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables andF_STacross all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin‐wide to the metapopulation scale). Sensitivity analysis (leave‐one‐population‐out) revealed consistent relationships between climate variables andF_STwithinthree metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.

    

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3. Neither larval duration nor dispersal distance predict spatial genetic diversity in planktonic dispersing species

   https://doi.org/10.3354/meps14419  

   Esser, EA ; Pringle, JM ; Byers, JE ( October 2023 , Marine Ecology Progress Series)

   The increase in genetic distance between marine individuals or populations with increasing distance has often been assumed to be influenced by dispersal distance. In turn, dispersal distance has often been assumed to correlate strongly with pelagic larval duration (PLD). We examined the consistency of these assumptions in species with long planktonic durations. Reviewing multiple marine species, Selkoe & Toonen (2011; Mar Ecol Prog Ser 436:291-305) demonstrated significant fit of a species’ PLD with metrics of genetic distance between sampling sites. However, for long dispersers (PLD >10 d) whose dispersal is more influenced by ocean currents, the fit of PLD and genetic connectivity metrics was not significant. We tested if using realistic ocean currents to determine simulated dispersal distances would produce an improved proxy for larval dispersal that correlates more strongly with genetic connectivity metrics. We estimated the dispersal distance of propagules for locations in the genetic studies compiled by Selkoe and Toonen with a global ocean model (Mercator, 1/12° resolution). The model-derived estimates of dispersal distance did not correlate better than PLD against the genetic diversity metrics globalF_STkm^-1and isolation-by-distance (IBD) slope. We explored 2 explanations: (1) our ocean circulation-based dispersal distance estimates are too simple to produce biologically meaningful improvement over PLD, and (2) IBD slope is not a powerful predictor of variation in dispersal distance between species with long PLD. Exploring these explanations suggests directions for future research which will enable better quantitative understanding of genetic diversity and its spatial distribution in coastal marine organisms.

    

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4. Species‐level view of population structure and gene flow for a critically endangered primate ( Varecia variegata )

   https://doi.org/10.1002/ece3.1119  

   Baden, Andrea L. ; Holmes, Sheila M. ; Johnson, Steig E. ; Engberg, Shannon E. ; Louis, Jr, Edward E. ; Bradley, Brenda J. ( June 2014 , Ecology and Evolution)

   Lemurs are among the world's most threatened mammals. The critically endangered black‐and‐white ruffed lemur (Varecia variegata), in particular, has recently experienced rapid population declines due to habitat loss, ecological sensitivities to habitat degradation, and extensive human hunting pressure. Despite this, a recent study indicates that ruffed lemurs retain among the highest levels of genetic diversity for primates. Identifying how this diversity is apportioned and whether gene flow is maintained among remnant populations will help to diagnose and target conservation priorities. We sampled 209 individuals from 19 sites throughout the remainingV. variegatarange. We used 10 polymorphic microsatellite loci and ~550 bp of mtDNAsequence data to evaluate genetic structure and population dynamics, including dispersal patterns and recent population declines. Bayesian cluster analyses identified two distinct genetic clusters, which optimally partitioned data into populations occurring on either side of theMangoro River. Localities north of the Mangoro were characterized by greater genetic diversity, greater gene flow (lower genetic differentiation) and higher mtDNAhaplotype and nucleotide diversity than those in the south. Despite this, genetic differentiation across all sites was high, as indicated by high averageF_ST(0.247) and Φ_ST(0.544), and followed a pattern of isolation‐by‐distance. We use these results to suggest future conservation strategies that include an effort to maintain genetic diversity in the north and restore connectivity in the south. We also note the discordance between patterns of genetic differentiation and current subspecies taxonomy, and encourage a re‐evaluation of conservation management units moving forward.

    

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5. Divergence, gene flow, and speciation in eight lineages of trans‐Beringian birds

   https://doi.org/10.1111/mec.15574  

   McLaughlin, Jessica F. ; Faircloth, Brant C. ; Glenn, Travis C. ; Winker, Kevin ( September 2020 , Molecular Ecology)

   Determining how genetic diversity is structured between populations that span the divergence continuum from populations to biological species is key to understanding the generation and maintenance of biodiversity. We investigated genetic divergence and gene flow in eight lineages of birds with a trans‐Beringian distribution, where Asian and North American populations have likely been split and reunited through multiple Pleistocene glacial cycles. Our study transects the speciation process, including eight pairwise comparisons in three orders (ducks, shorebirds and passerines) at population, subspecies and species levels. Using ultraconserved elements (UCEs), we found that these lineages represent conditions from slightly differentiated populations to full biological species. Although allopatric speciation is considered the predominant mode of divergence in birds, all of our best divergence models included gene flow, supporting speciation with gene flow as the predominant mode in Beringia. In our eight lineages, three were best described by a split‐migration model (divergence with gene flow), three best fit a secondary contact scenario (isolation followed by gene flow), and two showed support for both models. The lineages were not evenly distributed across a divergence space defined by gene flow (M) and differentiation (F_ST), instead forming two discontinuous groups: one with relatively shallow divergence, no fixed single nucleotide polymorphisms (SNPs), and high rates of gene flow between populations; and the second with relatively deeply divergent lineages, multiple fixed SNPs, and low gene flow. Our results highlight the important role that gene flow plays in avian divergence in Beringia.

    

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