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1. Contemporary range position predicts the range‐wide pattern of genetic diversity in balsam poplar ( Populus balsamifera L.)

   https://doi.org/10.1111/jbi.13811  

   Gougherty, Andrew V.; Chhatre, Vikram E.; Keller, Stephen R.; Fitzpatrick, Matthew C.; Comes, ed., Hans‐Peter (February 2020, Journal of Biogeography)

   Abstract AimPatterns of genetic diversity within species’ ranges can reveal important insights into effects of past climate on species’ biogeography and current population dynamics. While numerous biogeographic hypotheses have been proposed to explain patterns of genetic diversity within species’ ranges, formal comparisons and rigorous statistical tests of these hypotheses remain rare. Here, we compared seven hypotheses for their abilities to describe the geographic pattern of two metrics of genetic diversity in balsam poplar (Populus balsamifera), a northern North American tree species. LocationNorth America. TaxonBalsam poplar (Populus balsamiferaL.). MethodsWe compared seven hypotheses, representing effects of past climate and current range position, for their ability to describe the geographic pattern of expected heterozygosity and per cent polymorphic loci across 85 populations of balsam poplar. We tested each hypothesis using spatial and non‐spatial least‐squares regression to assess the importance of spatial autocorrelation on model performance. ResultsWe found that both expected heterozygosity and per cent polymorphic loci could best be explained by the current range position and genetic structure of populations within the contemporary range. Genetic diversity showed a clear gradient of being highest near the geographic and climatic range centre and lowest near range edges. Hypotheses accounting for the effects of past climate (e.g. past climatic suitability, distance from the southern edge), in contrast, had comparatively little support. Model ranks were similar among spatial and non‐spatial models, but residuals of all non‐spatial models were significantly autocorrelated, violating the assumption of independence in least‐squares regression. Main conclusionsOur work adds strong support for the “Central‐Periphery Hypothesis” as providing a predictive framework for understanding the forces structuring genetic diversity across species’ ranges, and illustrates the value of applying a robust comparative model selection framework and accounting for spatial autocorrelation when comparing biogeographic models of genetic diversity. 

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2. The role of multiple Pleistocene refugia in promoting diversification in the Pacific Northwest

   https://doi.org/10.1111/mec.16595  

   Smith, Megan L.; Wallace, Jessica; Tank, David C.; Sullivan, Jack; Carstens, Bryan C. (July 2022, Molecular Ecology)

   Abstract Pleistocene glacial cycles drastically changed the distributions of taxa endemic to temperate rainforests in the Pacific Northwest, with many experiencing reduced habitat suitability during glacial periods. In this study, we investigate whether glacial cycles promoted intraspecific divergence and whether subsequent range changes led to secondary contact and gene flow. For seven invertebrate species endemic to the PNW, we estimated species distribution models (SDMs) and projected them onto current and historical climate conditions to assess how habitat suitability changed during glacial cycles. Using single nucleotide polymorphism (SNP) data from these species, we assessed population genetic structure and used a machine‐learning approach to compare models with and without gene flow between populations upon secondary contact after the last glacial maximum (LGM). Finally, we estimated divergence times and rates of gene flow between populations. SDMs suggest that there was less suitable habitat in the North Cascades and Northern Rocky Mountains during glacial compared to interglacial periods, resulting in reduced habitat suitability and increased habitat fragmentation during the LGM. Our genomic data identify population structure in all taxa, and support gene flow upon secondary contact in five of the seven taxa. Parameter estimates suggest that population divergences date to the later Pleistocene for most populations. Our results support a role of refugial dynamics in driving intraspecific divergence in the Cascades Range. In these invertebrates, population structure often does not correspond to current biogeographic or environmental barriers. Rather, population structure may reflect refugial lineages that have since expanded their ranges, often leading to secondary contact between once isolated lineages. 

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3. RAD‐tag and mitochondrial DNA sequencing reveal the genetic structure of a widespread and regionally imperiled freshwater mussel, Obovaria olivaria (Bivalvia: Unionidae)

   https://doi.org/10.1002/ece3.8560  

   Bucholz, Jamie R.; Sard, Nicholas M.; VanTassel, Nichelle M.; Lozier, Jeffrey D.; Morris, Todd J.; Paquet, Annie; Zanatta, David T. (January 2022, Ecology and Evolution)

   Abstract Obovaria olivariais a species of freshwater mussel native to the Mississippi River and Laurentian Great Lakes‐St. Lawrence River drainages of North America. This mussel has experienced population declines across large parts of its distribution and is imperiled in many jurisdictions.Obovaria olivariauses the similarly imperiledAcipenser fulvescens(Lake Sturgeon) as a host for its glochidia. We employed mitochondrial DNA sequencing and restriction site‐associated DNA sequencing (RAD‐seq) to assess patterns of genetic diversity and population structure ofO. olivariafrom 19 collection locations including the St. Lawrence River drainage, the Great Lakes drainage, the Upper Mississippi River drainage, the Ohioan River drainage, and the Mississippi Embayment. Heterozygosity was highest in Upper Mississippi and Great Lakes populations, followed by a reduction in diversity and relative effective population size in the St. Lawrence populations. PairwiseF_STranged from 0.00 to 0.20, and analyses of genetic structure revealed two major ancestral populations, one including all St. Lawrence River/Ottawa River sites and the other including remaining sites; however, significant admixture and isolation by river distance across the range were evident. The genetic diversity and structure ofO. olivariais consistent with the existing literature onAcipenser fulvescensand suggests that, although northern and southernO. olivariapopulations are genetically distinct, genetic structure inO. olivariais largely clinal rather than discrete across its range. Conservation and restoration efforts ofO. olivariashould prioritize the maintenance and restoration of locations whereO. olivariaremain, especially in northern rivers, and to ensure connectivity that will facilitate dispersal ofAcipenser fulvescensand movement of encysted glochidia. 

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4. Transcriptomic signatures of temperature adaptation in the eastern oyster Crassostrea virginica

   https://doi.org/10.1111/jeb.13789  

   Johnson, Kevin M.; Jones, Hollis R.; Casas, Sandra M.; La Peyre, Jerome F.; Kelly, Morgan W. (July 2021, Journal of Evolutionary Biology)

   Abstract The large geographic distribution of the eastern oyster,Crassostrea virginica,makes it an ideal species to test how populations have adapted to latitudinal gradients in temperature. Despite inhabiting distinct thermal regimes, populations ofC. virginicanear the species’ southern and northern geographic range show no population differences in their physiological response to temperature. In this study, we used comparative transcriptomics to understand how oysters from either end of the species’ range maintain enantiostasis across three acclimation temperatures (10, 20, and 30°C). With this approach, we identified genes that were differentially expressed in response to temperature between individuals ofC. virginicacollected from New Brunswick, Canada and Louisiana, USA. We observed a core set of genes whose expression responded to temperature in both populations, but also an even larger set of genes with expression patterns that were unique to each population. Intriguingly, the genes with population‐specific responses to temperature had elevatedF_STand Ka/Ks ratios compared to the genome‐wide average. In contrast, genes showing only a response to temperature were found to only have elevatedF_STvalues suggesting that divergentF_STmay be due to selection on linked regulatory regions rather than positive selection on protein coding regions. Taken together, our results suggest that, despite coarse‐scale physiological similarities, natural selection has shaped divergent gene expression responses to temperature in geographically separated populations of this broadly eurythermal marine invertebrate. 

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5. Limited genomic signatures of population collapse in the critically endangered black abalone ( Haliotis cracherodii )

   https://doi.org/10.1111/mec.17362  

   Wooldridge, Brock; Orland, Chloé; Enbody, Erik; Escalona, Merly; Mirchandani, Cade; Corbett‐Detig, Russell; Kapp, Joshua D.; Fletcher, Nathaniel; Cox‐Ammann, Karah; Raimondi, Peter; et al (April 2024, Molecular Ecology)

   Abstract The black abalone,Haliotis cracherodii, is a large, long‐lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by a bacterial disease known as withering syndrome (WS) that wiped out >90% of individuals, leading to the closure of all U.S. black abalone fisheries since 1993. Current conservation strategies include restoring diminished populations by translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity and strengthened geographic differentiation, making translocation‐based recovery contentious. Additionally, the current prevalence of WS remains unknown. To address these uncertainties, we sequenced and analysed the genomes of 133 black abalone individuals from across their present range. We observed no spatial genetic structure among black abalone, with the exception of a single chromosomal inversion that increases in frequency with latitude. Outside the inversion, genetic differentiation between sites is minimal and does not scale with either geographic distance or environmental dissimilarity. Genetic diversity appears uniformly high across the range. Demographic inference does indicate a severe population bottleneck beginning just 15 generations in the past, but this decline is short lived, with present‐day size far exceeding the pre‐bottleneck status quo. Finally, we find the bacterial agent of WS is equally present across the sampled range, but only in 10% of individuals. The lack of population genetic structure, uniform diversity and prevalence of WS bacteria indicates that translocation could be a valid and low‐risk means of population restoration for black abalone species' recovery. 

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