More Like this

1. Loss of genetic diversity, recovery and allele surfing in a colonizing parasite, Geomydoecus aurei

   https://doi.org/10.1111/mec.14997  

   Demastes, James W.; Hafner, David J.; Hafner, Mark S.; Light, Jessica E.; Spradling, Theresa A. (February 2019, Molecular Ecology)

   Abstract Understanding the genetic consequences of changes in species distributions has wide‐ranging implications for predicting future outcomes of climate change, for protecting threatened or endangered populations and for understanding the history that has led to current genetic patterns within species. Herein, we examine the genetic consequences of range expansion over a 25‐year period in a parasite (Geomydoecus aurei) that is in the process of expanding its geographic range via invasion of a novel host. By sampling the genetics of 1,935G. aureilice taken from 64 host individuals collected over this time period using 12 microsatellite markers, we test hypotheses concerning linear spatial expansion, genetic recovery time and allele surfing. We find evidence of decreasing allelic richness (AR) with increasing distance from the source population, supporting a linear, stepping stone model of spatial expansion that emphasizes the effects of repeated bottleneck events during colonization. We provide evidence of post‐bottleneck genetic recovery, with average AR of infrapopulations increasing about 30% over the 225‐generation span of time observed directly in this study. Our estimates of recovery rate suggest, however, that recovery has plateaued and that this population may not reach genetic diversity levels of the source population without further immigration from the source population. Finally, we employ a grid‐based sampling scheme in the region of ongoing population expansion and provide empirical evidence for the power of allele surfing to impart genetic structure on a population, even under conditions of selective neutrality and in a place that lacks strong barriers to gene flow. 

   more » « less
2. Clustering multivariate time series using energy distance

   https://doi.org/10.1111/jtsa.12688  

   Davis, Richard A.; Fernandes, Leon; Fokianos, Konstantinos (April 2023, Journal of Time Series Analysis)

   A novel methodology is proposed for clustering multivariate time series data using energy distance defined in Székely and Rizzo (2013). Specifically, a dissimilarity matrix is formed using the energy distance statistic to measure the separation between the finite‐dimensional distributions for the component time series. Once the pairwise dissimilarity matrix is calculated, a hierarchical clustering method is then applied to obtain the dendrogram. This procedure is completely nonparametric as the dissimilarities between stationary distributions are directly calculated without making any model assumptions. In order to justify this procedure, asymptotic properties of the energy distance estimates are derived for general stationary and ergodic time series. The method is illustrated in a simulation study for various component time series that are either linear or nonlinear. Finally, the methodology is applied to two examples; one involves the GDP of selected countries and the other is the population size of various states in the U.S.A. in the years 1900–1999. 

   more » « less
3. Genomic time‐series data show that gene flow maintains high genetic diversity despite substantial genetic drift in a butterfly species

   https://doi.org/10.1111/mec.16111  

   Gompert, Zachariah; Springer, Amy; Brady, Megan; Chaturvedi, Samridhi; Lucas, Lauren K. (August 2021, Molecular Ecology)

   Abstract Effective population size affects the efficacy of selection, rate of evolution by drift and neutral diversity levels. When species are subdivided into multiple populations connected by gene flow, evolutionary processes can depend on global or local effective population sizes. Theory predicts that high levels of diversity might be maintained by gene flow, even very low levels of gene flow, consistent with species long‐term effective population size, but tests of this idea are mostly lacking. Here, we show thatLycaeidesbutterfly populations maintain low contemporary (variance) effective population sizes (e.g. ~200 individuals) and thus evolve rapidly by genetic drift. However, populations harboured high levels of genetic diversity consistent with an effective population size several orders of magnitude larger. We hypothesized that the differences in the magnitude and variability of contemporary versus long‐term effective population sizes were caused by gene flow of sufficient magnitude to maintain diversity but only subtly affect evolution on generational timescales. Consistent with this hypothesis, we detected low but nontrivial gene flow among populations. Furthermore, using short‐term population‐genomic time‐series data, we documented patterns consistent with predictions from this hypothesis, including a weak but detectable excess of evolutionary change in the direction of the mean (migrant gene pool) allele frequencies across populations and consistency in the direction of allele frequency change over time. The documented decoupling of diversity levels and short‐term change by drift inLycaeideshas implications for our understanding of contemporary evolution and the maintenance of genetic variation in the wild. 

   more » « less
4. Evidence for environmental filtering and limiting similarity depends on spatial scale and dissimilarity metrics

   https://doi.org/10.1002/ecy.70244  

   Perez‐Navarro, Maria A; Shepherd, Harry_E R; Brian, Joshua I; Clark, Adam T; Catford, Jane A (November 2025, Ecology)

   Abstract Darwin's theory of natural selection provides two seemingly contradictory hypotheses for explaining the success of biological invasions: (1) the pre‐adaptation hypothesis posits that introduced species that are closely related to native species will be more likely to succeed due to shared advantageous characteristics; (2) the limiting similarity hypothesis posits that invaders that are more similar to resident species will be less likely to succeed due to competitive exclusion. Previous studies assessing this conundrum show mixed results, possibly stemming from inconsistent study spatial scales and failure to integrate both functional and phylogenetic information. Here, we address these limitations using a 33‐year grassland successional survey at Cedar Creek Ecosystem Science Reserve (USA). We incorporate functional dissimilarities, phylogenetic distances, environmental covariates, and species origin data for 303 vascular plant taxa (256 native, 47 introduced), collected from 2700 plots. In contrast with other studies, we test both hypotheses at two fine spatial scales—neighborhood (0.5 m²) and site (~40 m²)—to better capture competition and environmental filtering, respectively. Findings related to Darwin's naturalization conundrum depended on spatial scale and dissimilarity metric. Our results agreed with the pre‐adaptation hypothesis at site scale (40 m²)—a much finer resolution than typically used to test the pre‐adaptation hypothesis—highlighting the role of environmental filtering. At the neighborhood scale (0.5 m²), support for the limiting similarity hypothesis emerged when using functional dissimilarity, while phylogenetic distance aligned with the pre‐adaptation hypothesis, demonstrating that different dissimilarity metrics can yield contrasting conclusions. In addition, native and introduced species showed different abundance patterns in relation to functional ranked dissimilarities, with introduced species reaching higher cover when they were taller than co‐occurring species, had higher leaf dry matter content (LDMC) and lower seed mass. Introduced species also reached high cover with higher soil N concentrations and a shorter time after colonization, relative to native species. Our results suggest that inconsistent findings related to Darwin's naturalization conundrum may arise from an overreliance on single dissimilarity metrics and the use of spatial scales failing to capture underlying ecological processes. This highlights the need for more nuanced methodologies when testing the pre‐adaptation and limiting similarity hypotheses. 

   more » « less
5. Polygenic Selection within a Single Generation Leads to Subtle Divergence among Ecological Niches

   https://doi.org/10.1093/gbe/evaa257  

   Ehrlich, Moritz A; Wagner, Dominique N; Oleksiak, Marjorie F; Crawford, Douglas L (February 2021, Genome Biology and Evolution)

   Fraser, Bonnie (Ed.)

   Abstract Selection on standing genetic variation may be effective enough to allow for adaptation to distinct niche environments within a single generation. Minor allele frequency changes at multiple, redundant loci of small effect can produce remarkable phenotypic shifts. Yet, demonstrating rapid adaptation via polygenic selection in the wild remains challenging. Here we harness natural replicate populations that experience similar selection pressures and harbor high within-, yet negligible among-population genetic variation. Such populations can be found among the teleost Fundulus heteroclitus that inhabits marine estuaries characterized by high environmental heterogeneity. We identify 10,861 single nucleotide polymorphisms in F. heteroclitus that belong to a single, panmictic population yet reside in environmentally distinct niches (one coastal basin and three replicate tidal ponds). By sampling at two time points within a single generation, we quantify both allele frequency change within as well as spatial divergence among niche subpopulations. We observe few individually significant allele frequency changes yet find that the “number” of moderate changes exceeds the neutral expectation by 10–100%. We find allele frequency changes to be significantly concordant in both direction and magnitude among all niche subpopulations, suggestive of parallel selection. In addition, within-generation allele frequency changes generate subtle but significant divergence among niches, indicative of local adaptation. Although we cannot distinguish between selection and genotype-dependent migration as drivers of within-generation allele frequency changes, the trait/s determining fitness and/or migration likelihood appear to be polygenic. In heterogeneous environments, polygenic selection and polygenic, genotype-dependent migration offer conceivable mechanisms for within-generation, local adaptation to distinct niches. 

   more » « less