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1. Elevational Range Impacts Connectivity and Predicted Deme Sizes From Models of Habitat Suitability

   https://doi.org/10.1111/mec.17593  

   French, Connor_M ; Damasceno, Roberta_P ; Vasconcellos, Mariana_M ; Rodrigues, Miguel_T ; Carnaval, Ana_C ; Hickerson, Michael_J ( November 2024 , Molecular Ecology)

   In integrative distributional, demographic and coalescent (iDDC) modelling, a critical component is the statistical relationship between habitat suitability and local population sizes. This study explores this relationship in twoEnyaliuslizard species from the Brazilian Atlantic Forest: the high‐elevationE. iheringiiand low‐elevationE. catenatusand how this transformation affects spatiotemporal demographic inference. Most previous iDDC studies assumed a linear relationship, but this study hypothesises that the relationship may be nonlinear, especially for high‐elevation species with broader environmental tolerances. We test two key hypotheses: (1) The habitat suitability to population size relationship is nonlinear forE. iheringii(high‐elevation) and linear forE. catenatus(low‐elevation); and (2)E. iheringiiexhibits higher effective migration across populations thanE. catenatus. Our findings provide clear support for hypothesis (2), but mixed support for hypothesis (1), with strong model support for a nonlinear transformation in the high‐elevationE. iheringiiand some (albeit weak) support for a nonlinear transformation also inE. catenatus. The iDDC models allow us to generate landscape‐wide maps of predicted genetic diversity for both species, revealing that genetic diversity predictions for the high‐elevationE. iheringiialign with estimated patterns of historical range stability, whereas predictions for low‐elevationE. catenatusare distinct from range‐wide stability predictions. This research highlights the importance of accurately modelling the habitat suitability to population size relationship in iDDC studies, contributing to our understanding of species' demographic responses to environmental changes.

    

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2. 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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3. Population genomics of divergence among extreme and intermediate color forms in a polymorphic insect

   https://doi.org/10.1002/ece3.1928  

   Lozier, Jeffrey D. ; Jackson, Jason M. ; Dillon, Michael E. ; Strange, James P. ( January 2016 , Ecology and Evolution)

   Geographic variation in insect coloration is among the most intriguing examples of rapid phenotypic evolution and provides opportunities to study mechanisms of phenotypic change and diversification in closely related lineages. The bumble beeBombus bifariuscomprises two geographically disparate color groups characterized by red‐banded and black‐banded abdominal pigmentation, but with a range of spatially and phenotypically intermediate populations across western North America. Microsatellite analyses have revealed thatB. bifariusin the USA are structured into two major groups concordant with geography and color pattern, but also suggest ongoing gene flow among regional populations. In this study, we better resolve the relationships among major color groups to better understand evolutionary mechanisms promoting and maintaining such polymorphism. We analyze >90,000 and >25,000 single‐nucleotide polymorphisms derived from transcriptome (RNAseq) and double digest restriction site associatedDNAsequencing (ddRAD), respectively, in representative samples from spatial and color pattern extremes inB. bifariusas well as phenotypic and geographic intermediates. Both ddRADandRNAseq data illustrate substantial genome‐wide differentiation of the red‐banded (eastern) color form from both black‐banded (western) and intermediate (central) phenotypes and negligible differentiation among the latter populations, with no obvious admixture among bees from the two major lineages. Results thus indicate much stronger background differentiation amongB. bifariuslineages than expected, highlighting potential challenges for revealing loci underlying color polymorphism from population genetic data alone. These findings will have significance for resolving taxonomic confusion in this species and in future efforts to investigate color‐pattern evolution inB. bifariusand other polymorphic bumble bee species.

    

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4. Seascape genetics of the stalked kelp Pterygophora californica and comparative population genetics in the Santa Barbara Channel

   https://doi.org/10.1111/jpy.12918  

   Hargarten, Heidi L. ; Johansson, Mattias L. ; Reed, Daniel C. ; Coelho, Nelson C. ; Siegel, David A. ; Alberto, Filipe ( November 2019 , Journal of Phycology)

   We conducted a population genetic analysis of the stalked kelp,Pterygophora californica, in the Santa Barbara Channel, California,USA. The results were compared with previous work on the genetic differentiation of giant kelp,Macrocystis pyrifera,in the same region. These two sympatric kelps not only share many life history and dispersal characteristics but also differ in that dislodgedP. californicadoes not produce floating rafts with buoyant fertile sporophytes, commonly observed forM. pyrifera. We used a comparative population genetic approach with these two species to test the hypothesis that the ability to produce floating rafts increases the genetic connectivity among kelp patches in the Santa Barbara Channel. We quantified the association of habitat continuity and oceanographic distance with the genetic differentiation observed in stalked kelp, like previously conducted for giant kelp. We compared both overall (across all patches) and pairwise (between patches) genetic differentiation. We found that oceanographic transit time, habitat continuity, and geographic distance were all associated with genetic connectivity inP. californica, supporting similar previous findings forM. pyrifera. Controlling for differences in heterozygosity between kelp species using Jost'sD_EST, we showed that global differentiation and pairwise differentiation were similar among patches between the two kelp species, indicating that they have similar dispersal capabilities despite their differences in rafting ability. These results suggest that rafting sporophytes do not play a significant role in effective dispersal ofM. pyriferaat ecologically relevant spatial and temporal scales.

    

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5. Spatial population genomics of the brown rat ( Rattus norvegicus ) in New York City

   https://doi.org/10.1111/mec.14437  

   Combs, Matthew ; Puckett, Emily E. ; Richardson, Jonathan ; Mims, Destiny ; Munshi‐South, Jason ( December 2017 , Molecular Ecology)

   Human commensal species such as rodent pests are often widely distributed across cities and threaten both infrastructure and public health. Spatially explicit population genomic methods provide insights into movements for cryptic pests that drive evolutionary connectivity across multiple spatial scales. We examined spatial patterns of neutral genomewide variation in brown rats (Rattus norvegicus) across Manhattan, New York City (NYC), using 262 samples and 61,401SNPs to understand (i) relatedness among nearby individuals and the extent of spatial genetic structure in a discrete urban landscape; (ii) the geographic origin ofNYCrats, using a large, previously published data set of global rat genotypes; and (iii) heterogeneity in gene flow across the city, particularly deviations from isolation by distance. We found that rats separated by ≤200 m exhibit strong spatial autocorrelation (r = .3,p = .001) and the effects of localized genetic drift extend to a range of 1,400 m. Across Manhattan, rats exhibited a homogeneous population origin from rats that likely invaded from Great Britain. While traditional approaches identified a single evolutionary cluster with clinal structure across Manhattan, recently developed methods (e.g., fineSTRUCTURE,sPCA,EEMS) provided evidence of reduced dispersal across the island's less residential Midtown region resulting in fine‐scale genetic structuring (F_ST = 0.01) and two evolutionary clusters (Uptown and Downtown Manhattan). Thus, while some urban populations of human commensals may appear to be continuously distributed, landscape heterogeneity within cities can drive differences in habitat quality and dispersal, with implications for the spatial distribution of genomic variation, population management and the study of widely distributed pests.

    

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