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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. Incomplete reproductive isolation and low genetic differentiation despite floral divergence across varying geographic scales in Castilleja

   https://doi.org/10.1002/ajb2.1700  

   Wenzell, Katherine E. ; McDonnell, Angela J. ; Wickett, Norman J. ; Fant, Jeremie B. ; Skogen, Krissa A. ( July 2021 , American Journal of Botany)

   Divergence depends on the strength of selection and frequency of gene flow between taxa, while reproductive isolation relies on mating barriers and geographic distance. Less is known about how these processes interact at early stages of speciation. Here, we compared population‐level differentiation in floral phenotype and genetic sequence variation among recently divergedCastillejato explore patterns of diversification under different scenarios of reproductive isolation.

   Using target enrichment enabled by the Angiosperms353 probe set, we assessed genetic distance among 50 populations of fourCastillejaspecies. We investigated whether patterns of genetic divergence are explained by floral trait variation or geographic distance in two focal groups: the widespreadC. sessilifloraand the more restrictedC. purpureaspecies complex.

   We document thatC. sessilifloraand theC. purpureacomplex are characterized by high diversity in floral color across varying geographic scales. Despite phenotypic divergence, groups were not well supported in phylogenetic analyses, and little genetic differentiation was found across targeted Angiosperms353 loci. Nonetheless, a principal coordinate analysis of single nucleotide polymorphisms revealed differentiation withinC. sessilifloraacross floral morphs and geography and less differentiation among species of theC. purpureacomplex.

   Patterns of genetic distance inC. sessiliflorasuggest species cohesion maintained over long distances despite variation in floral traits. In theC. purpureacomplex, divergence in floral color across narrow geographic clines may be driven by recent selection on floral color. These contrasting patterns of floral and genetic differentiation reveal that divergence can arise via multiple eco‐evolutionary paths.

    

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3. Genetic and functional variation across regional and local scales is associated with climate in a foundational prairie grass

   https://doi.org/10.1111/nph.16547  

   Hoffman, Ava M. ; Bushey, Julie A. ; Ocheltree, Troy W. ; Smith, Melinda D. ( April 2020 , New Phytologist)

   Global change forecasts in ecosystems require knowledge of within‐species diversity, particularly of dominant species within communities. We assessed site‐level diversity and capacity for adaptation inBouteloua gracilis, the dominant species in the Central US shortgrass steppe biome.

   We quantified genetic diversity from 17 sites across regional scales, north to south from New Mexico to South Dakota, and local scales in northern Colorado. We also quantified phenotype and plasticity within and among sites and determined the extent to which phenotypic diversity inB. graciliswas correlated with climate.

   Genome sequencing indicated pronounced population structure at the regional scale, and local differences indicated that gene flow and/or dispersal may also be limited. Within a common environment, we found evidence of genetic divergence in biomass‐related phenotypes, plasticity, and phenotypic variance, indicating functional divergence and different adaptive potential. Phenotypes were differentiated according to climate, chiefly median Palmer Hydrological Drought Index and other aridity metrics.

   Our results indicate conclusive differences in genetic variation, phenotype, and plasticity in this species and suggest a mechanism explaining variation in shortgrass steppe community responses to global change. This analysis ofB. gracilisintraspecific diversity across spatial scales will improve conservation and management of the shortgrass steppe ecosystem in the future.

    

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4. Snakes on a plain: biotic and abiotic factors determine venom compositional variation in a wide-ranging generalist rattlesnake

   https://doi.org/10.1186/s12915-023-01626-x  

   Smith, Cara F. ; Nikolakis, Zachary L. ; Ivey, Kathleen ; Perry, Blair W. ; Schield, Drew R. ; Balchan, Neil R. ; Parker, Joshua ; Hansen, Kirk C. ; Saviola, Anthony J. ; Castoe, Todd A. ; et al ( June 2023 , BMC Biology)

   Snake venoms are trophic adaptations that represent an ideal model to examine the evolutionary factors that shape polymorphic traits under strong natural selection. Venom compositional variation is substantial within and among venomous snake species. However, the forces shaping this phenotypic complexity, as well as the potential integrated roles of biotic and abiotic factors, have received little attention. Here, we investigate geographic variation in venom composition in a wide-ranging rattlesnake (Crotalus viridis viridis) and contextualize this variation by investigating dietary, phylogenetic, and environmental variables that covary with venom.

   Using shotgun proteomics, venom biochemical profiling, and lethality assays, we identify 2 distinct divergent phenotypes that characterize major axes of venom variation in this species: a myotoxin-rich phenotype and a snake venom metalloprotease (SVMP)-rich phenotype. We find that dietary availability and temperature-related abiotic factors are correlated with geographic trends in venom composition.

   Our findings highlight the potential for snake venoms to vary extensively within species, for this variation to be driven by biotic and abiotic factors, and for the importance of integrating biotic and abiotic variation for understanding complex trait evolution. Links between venom variation and variation in biotic and abiotic factors indicate that venom variation likely results from substantial geographic variation in selection regimes that determine the efficacy of venom phenotypes across populations and snake species. Our results highlight the cascading influence of abiotic factors on biotic factors that ultimately shape venom phenotype, providing evidence for a central role of local selection as a key driver of venom variation.

    

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5. Fine-scale spatial distribution of deltamethrin resistance and population structure of Anopheles funestus and Anopheles arabiensis populations in Southern Mozambique

   https://doi.org/10.1186/s12936-023-04522-5  

   Das, Smita ; Máquina, Mara ; Phillips, Keeley ; Cuamba, Nelson ; Marrenjo, Dulcisaria ; Saúte, Francisco ; Paaijmans, Krijn P ; Huijben, Silvie ( December 2023 , Malaria Journal)

   Insecticide resistance in malaria vectors can be spatially highly heterogeneous, yet population structure analyses frequently find relatively high levels of gene flow among mosquito populations. Few studies have contemporaneously assessed phenotypic, genotypic and population structure analysis on mosquito populations and none at fine geographical scales. In this study, genetic diversity, population structure, and insecticide resistance profiles ofAnopheles funestusandAnopheles arabiensiswere examined across mosquito populations from and within neighbouring villages.

   Mosquitoes were collected from 11 towns in southern Mozambique, as well as from different neighbourhoods within the town of Palmeira, during the peak malaria transmission season in 2016. CDC bottle bioassay and PCR assays were performed withAnophelesmosquitoes at each site to determine phenotypic and molecular insecticide resistance profiles, respectively. Microsatellite analysis was conducted on a subsample of mosquitoes to estimate genetic diversity and population structure.

   Phenotypic insecticide resistance to deltamethrin was observed inAn. funestussensu stricto (s.s.) throughout the area, though a high level of mortality variation was seen. However, 98% ofAn. funestus s.s.wereCYP6P9ahomozygous resistant.An. arabiensiswas phenotypically susceptible to deltamethrin and 99% werekdrhomozygous susceptible. BothAnophelesspecies exhibited high allelic richness and heterozygosity. Significant deviations from Hardy–Weinberg equilibrium were observed, and high linkage disequilibrium was seen forAn. funestus s.s.,supporting population subdivision. However, the F_STvalues were low for both anophelines (− 0.00457 to 0.04213), N_mvalues were high (9.4–71.8 migrants per generation), AMOVA results showed almost 100% genetic variation among and within individuals, andStructureanalysis showed no clustering ofAn. funestus s.s.andAn. arabiensispopulations. These results suggest high gene flow among mosquito populations.

   Despite a relatively high level of phenotypic variation in theAn. funestuspopulation, molecular analysis shows the population is admixed. These data indicate thatCYP6P9aresistance markers do not capture all phenotypic variation in the area, but also that resistance genes of high impact are likely to easily spread in the area. Conversely, other strategies, such as transgenic mosquito release programmes will likely not face challenges in this locality.

    

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