An official website of the United States government
Populations of the non-migratory estuarine fish Fundulus heteroclitus inhabiting the heavily polluted New Bedford Harbour (NBH) estuary have shown inherited tolerance to local pollutants introduced to their habitats in the past 100 years. Here we examine two questions: (i) Is there pollution-driven selection on the mitochondrial genome across a fine geographical scale? and (ii) What is the pattern of migration among sites spanning a strong pollution gradient? Whole mitochondrial genomes were analysed for 133 F. heteroclitus from seven nearby collection sites: four sites along the NBH pollution cline (approx. 5 km distance), which had pollution-adapted fish, as well as one site adjacent to the pollution cline and two relatively unpolluted sites about 30 km away, which had pollution-sensitive fish. Additionally, we used microsatellite analyses to quantify genetic variation over three F. heteroclitus generations in both pollution-adapted and sensitive individuals collected from two sites at two different time points (1999/2000 and 2007/2008). Our results show no evidence for a selective sweep of mtDNA in the polluted sites. Moreover, mtDNA analyses revealed that both pollution-adapted and sensitive populations harbour similar levels of genetic diversity. We observed a high level of non-synonymous mutations in the most polluted site. This is probably associated with a reduction in N e and concomitant weakening of purifying selection, a demographic expansion following a pollution-related bottleneck or increased mutation rates. Our demographic analyses suggest that isolation by distance influences the distribution of mtDNA genetic variation between the pollution cline and the clean populations at broad spatial scales. At finer scales, population structure is patchy, and neither spatial distance, pollution concentration or pollution tolerance is a good predictor of mtDNA variation. Lastly, microsatellite analyses revealed stable population structure over the last decade.
more »
« less
Hybrid zone or hybrid lineage: a genomic reevaluation of Sibley’s classic species conundrum in Pipilo towhees
Abstract Hybrid zones can be studied by modeling clines of trait variation (e.g., morphology, genetics) over a linear transect. Yet, hybrid zones can also be spatially complex, can shift over time, and can even lead to the formation of hybrid lineages with the right combination of dispersal and vicariance. We reassessed Sibley’s (1950) gradient between Collared Towhee (Pipilo ocai) and Spotted Towhee (Pipilo maculatus) in Central Mexico to test whether it conformed to a typical tension-zone cline model. By comparing historical and modern data, we found that cline centers for genetic and phenotypic traits have not shifted over the course of 70 years. This equilibrium suggests that secondary contact between these species, which originally diverged over 2 million years ago, likely dates to the Pleistocene. Given the amount of mtDNA divergence, parental ends of the cline have very low autosomal nuclear differentiation (FST = 0.12). Dramatic and coincident cline shifts in mtDNA and throat color suggest the possibility of sexual selection as a factor in differential introgression, while a contrasting cline shift in green back color hints at a role for natural selection. Supporting the idea of a continuum between clinal variation and hybrid lineage formation, the towhee gradient can be analyzed as one population under isolation-by-distance, as a two-population cline, and as three lineages experiencing divergence with gene flow. In the middle of the gradient, a hybrid lineage has become partly isolated, likely due to forested habitat shrinking and fragmenting as it moved upslope after the last glacial maximum and a stark environmental transition. This towhee system offers a window into the potential outcomes of hybridization across a dynamic landscape including the creation of novel genomic and phenotypic combinations and incipient hybrid lineages.
more »
« less
- Award ID(s):
- 1652979
- PAR ID:
- 10406156
- Date Published:
- Journal Name:
- Evolution
- Volume:
- 77
- Issue:
- 3
- ISSN:
- 0014-3820
- Page Range / eLocation ID:
- 852 to 869
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract The North American racers (Coluber constrictor) are widely distributed across the Nearctic and numerous studies have demonstrated extensive variation in morphology, ecology, and population genetic structure. Here we take an integrative approach to understand lineage diversification within this taxon by combining genomic sequence capture data, mtDNA sequence data, morphometrics, and ecological niche models. Both the genomic data and mtDNA phylogeographic analyses support five lineages distributed across the range of this species. However, demographic model selection based on these two datasets strongly conflict in both the model of divergence and estimates of timing of lineage divergence. While mtDNA and concatenated genomic data suggest a Miocene origin of these distinct groups, coalescent-based demographic models with the sequence capture data suggest lineage diversification occurred at ~33 kya in allopatry without gene flow. Using linear morphological measurements of head shape we demonstrate that lineages distributed largely east and west of the Mississippi River are distinguishable. Furthermore, ecological niche models demonstrate that lineages distributed in subtropical habitats have environmental niche space that is significantly differentiated from lineages distributed across the continent. Taken together, these results suggest that ecology is an important axis of lineage divergence within this group and that more fine-scale analyses may find even greater differentiation between the populations identified here. This abstract translated to Spanish is avaliable in the Supporting Infromation section (Este resumen traducido al español está disponible en la sección, Supporting Infromation).more » « less
-
Abstract Phenotypic differences between urban and rural populations are well‐documented, but the evolutionary processes driving trait variation along urbanization gradients are often unclear. We combined spatial data on abundance, trait variation, and measurements of fitness to understand cline structure and test for natural selection on heritable coat color morphs (melanic, gray) of eastern gray squirrels (Sciurus carolinensis) along an urbanization gradient. Population surveys using remote cameras and visual counts at 76 sites along the urbanization gradient revealed a significant cline in melanism, decreasing from 48% in the city center to <5% in rural woodlands. Among 76 squirrels translocated to test for phenotypic selection, survival was lower for the melanic than gray morph in rural woodlands, whereas there was no difference in survival between color morphs in the city. These results suggest the urban–rural cline in melanism is explained by natural selection favoring the gray morph in rural woodlands combined with relaxed selection in the city. Our study illustrates how trait variation between urban and rural populations can emerge from selection primarily in rural populations rather than adaptation to novel features of the urban environment.more » « less
-
ABSTRACT Coalescent modelling of hybrid zones can provide novel insights into the historical demography of populations, including divergence times, population sizes, introgression proportions, migration rates and the timing of hybrid zone formation. We used coalescent analysis to determine whether the hybrid zone between phylogeographic lineages of the Plateau Fence Lizard (Sceloporus tristichus) in Arizona formed recently due to human‐induced landscape changes, or if it originated during Pleistocene climatic shifts. Given the presence of mitochondrial DNA from another species in the hybrid zone (Southwestern Fence Lizard,S. cowlesi), we tested for the presence ofS. cowlesinuclear DNA in the hybrid zone as well as reassessed the species boundary betweenS. tristichusandS. cowlesi. No evidence ofS. cowlesinuclear DNA is found in the hybrid zone, and the paraphyly of both species raises concerns about their taxonomic validity. Introgression analysis placed the divergence time between the parental hybrid zone populations at approximately 140 kya and their secondary contact and hybridization at approximately 11 kya at the end of the Pleistocene. Introgression proportions estimated for hybrid populations are correlated with their geographic distance from parental populations. The multispecies coalescent with migration provided significant support for unidirectional migration moving from south to north, which is consistent with spatial cline analyses that suggest a slow but steady northward shift of the centre of the hybrid zone over the last two decades. When analysing hybrid populations sampled along a linear transect, coalescent methods can provide novel insights into hybrid zone dynamics.more » « less
-
Abstract The outcomes of speciation across organismal dimensions (e.g., ecological, genetic, phenotypic) are often assessed using phylogeographic methods. At one extreme, reproductively isolated lineages represent easily delimitable species differing in many or all dimensions, and at the other, geographically distinct genetic segments introgress across broad environmental gradients with limited phenotypic disparity. In the ambiguous gray zone of speciation, where lineages are genetically delimitable but still interacting ecologically, it is expected that these lineages represent species in the context of ontology and the evolutionary species concept when they are maintained over time with geographically well‐defined hybrid zones, particularly at the intersection of distinct environments. As a result, genetic structure is correlated with environmental differences and not space alone, and a subset of genes fail to introgress across these zones as underlying genomic differences accumulate. We present a set of tests that synthesize species delimitation with the speciation process. We can thereby assess historical demographics and diversification processes while understanding how lineages are maintained through space and time by exploring spatial and genome clines, genotype‐environment interactions, and genome scans for selected loci. Employing these tests in eight lineage‐pairs of snakes in North America, we show that six pairs represent 12 “good” species and that two pairs represent local adaptation and regional population structure. The distinct species pairs all have the signature of divergence before or near the mid‐Pleistocene, often with low migration, stable hybrid zones of varying size, and a subset of loci showing selection on alleles at the hybrid zone corresponding to transitions between distinct ecoregions. Locally adapted populations are younger, exhibit higher migration, and less ecological differentiation. Our results demonstrate that interacting lineages can be delimited using phylogeographic and population genetic methods that properly integrate spatial, temporal, and environmental data.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript
- Journal Article:
- https://doi.org/10.1093/evolut/qpac068
