An official website of the United States government
Abstract BackgroundDistributional 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. ResultsOur 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; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 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. ConclusionsSubstantial 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.
more »
« less
Phylogeography and population genetics reveal ring species patterns in a highly polymorphic California lily
Abstract AimNatural selection typically results in the homogenization of reproductive traits, reducing natural variation within populations; thus, highly polymorphic species present unresolved questions regarding the mechanisms that shape and maintain gene flow given a diversity of phenotypes. We used an integrative framework to characterize phenotypic diversity and assess how evolutionary history and population genetics affect the highly polymorphic nature of a California endemic lily. LocationCalifornia, United States. TaxonButterfly mariposa lily,Calochortus venustus(Liliaceae). MethodsWe summarized phenotypic diversity at both metapopulation and subpopulation scales to explore spatial phenotypic distributions. We sampled 174 individuals across the species range representing multiple samples for each population and each phenotype. We used restriction‐site‐associated DNA sequencing (RAD‐Seq) to detect population clusters, gene flow between phenotypes and between populations, infer haplotype networks, and reconstruct ancestral range evolution to infer historical migration and range expansion. ResultsPolymorphic floral traits within the species such as petal pigmentation and distal spots are geographically structured, and inferred evolutionary history is consistent with a ring species pattern involving a complex of populations having experienced sequential change in genetic and phenotypic variation from the founding population. Populations remain interconnected yet have differentiated from each other along a bifurcating south‐to‐north range expansion, consequently indicating parallel evolution towards the white morphotype in the northern range. Thus, our phylogeographical analyses reveal morphological convergence with population genetic cohesion irrespective of phenotypic diversity. Main conclusionsPhenotypic variation in the highly polymorphicCalochortus venustusis not due to genetic differentiation between phenotypes; rather there is genetic cohesion within six geographically defined populations, some of which maintain a high level of within‐population phenotypic diversity. Our results demonstrate that analyses of polymorphic taxa greatly benefit from disentangling phenotype from genotype at various spatial scales. We discuss results in light of ring species concepts and the need to determine the adaptive significance of the patterns we report.
more »
« less
- Award ID(s):
- 1929318
- PAR ID:
- 10362856
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Journal of Biogeography
- Volume:
- 49
- Issue:
- 2
- ISSN:
- 0305-0270
- Page Range / eLocation ID:
- p. 416-430
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
PremiseDivergence 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. MethodsUsing 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. ResultsWe 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. ConclusionsPatterns 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.more » « less
-
Abstract BackgroundInsecticide 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. MethodsMosquitoes 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. ResultsPhenotypic 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 FSTvalues were low for both anophelines (− 0.00457 to 0.04213), Nmvalues 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. ConclusionDespite 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.more » « less
-
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.more » « less
-
Abstract Uncovering whether convergent adaptations share a genetic basis is consequential for understanding the evolution of phenotypic diversity. This information can help us understand the extent to which shared ancestry or independent evolution shape adaptive phenotypes. In this study, we first ask whether the same genes underlie polymorphic mimicry inPapilioswallowtail butterflies. By comparing signatures of genetic variation between polymorphic and monomorphic species, we then investigate how ancestral variation, hybridization, and independent evolution contributed to wing pattern diversity in this group. We report that a single gene,doublesex (dsx), controls mimicry across multiple taxa, but with species-specific patterns of genetic differentiation and linkage disequilibrium. In contrast to widespread examples of phenotypic evolution driven by introgression, our analyses reveal distinct mimicry alleles. We conclude that mimicry evolution in this group was likely facilitated by ancestral polymorphism resulting from early co-option ofdsxas a mimicry locus, and that evolutionary turnover ofdsxalleles may underlie the wing pattern diversity of extant polymorphic and monomorphic lineages.more » « less
