An official website of the United States government
Abstract Studying how genetic variation is structured across space, and how it relates to divergence in phenotypic traits relevant to reproductive isolation, is important for our overall understanding of the speciation process. We used reduced-representation genomic data (ddRAD-seq) to examine patterns of genetic variation across the full distribution of an Andean warbler species complex (Myioborus ornatus–melanocephalus), which includes a known hybrid zone between two strikingly different plumage forms. Genetic structure largely reflects geographic variation in head plumage, some of which corresponds to major topographic barriers in the Andes. We also found evidence of isolation by distance shaping genetic patterns across the group’s broad latitudinal range. We found thatchrysopsandbairdi, two taxa with marked plumage differences that have a known hybrid zone, were characterized by low overall genetic divergence. Based on our cline analyses of both plumage and genomic hybrid indices, this hybrid zone extends for approximately 250 km, where advanced generation hybrids are likely most common. We also identified a slight difference in the centers of the plumage and genomic clines, potentially suggesting the asymmetric introgression ofchrysops-like plumage traits. By studying genetic variation in a phenotypically complex group distributed across a topographically complex area, which includes a hybrid zone, we were able to show how both geographic features and potentially sexually selected plumage traits may play a role in species formation in tropical mountains
more »
« less
Geographic barriers but not life history traits shape the phylogeography of North American mammals
Abstract AimSynthesize literature on genetic structure within species to understand how geographic features and species traits influence past responses to climate change. LocationNorth America. Time PeriodWe synthesized phylogeographic studies from 1978 to 2023, which describe genetic lineages that diverged during the Pleistocene (≥11,700 years ago). Major Taxa StudiedMammals. MethodsWe conducted a literature review to map genetic breaks in species distributions, then tested a set of geographic hypotheses (e.g., mountains, rivers) to explain their position by comparing break locations to a grid within each species' sampled range using logistic regression. We then conducted a meta‐analysis using species‐specific model estimates to ask if life‐history traits explained variation in which barriers were most important in species' past response to climate change. ResultsOur findings reveal heterogeneity in both where North American mammal phylogeography has been studied and the density of genetic breaks across 229 species. We found relatively high concordance among carnivores, ungulates and lagomorphs, where breaks were associated with mountains, major water bodies and relatively even terrain. In contrast, we found high variability within rodents and shrews, and no evidence that intrinsic factors related to dispersal ability explained the importance of hypothesized barriers across all species. Main ConclusionsSouthern Mexico is a hotspot for genetic breaks that has yet to be integrated into the broader story of North American phylogeography. We show that mountains and major water bodies play particularly important roles as barriers, but substantial variation across species within orders suggests that there is more to the story besides shared climatic or phylogenetic histories. Thus, understanding the phylogeography of individual species will continue to be important given that our results suggest high variability in how species may respond to future global change.
more »
« less
- PAR ID:
- 10530430
- Editor(s):
- NA
- Publisher / Repository:
- Wiley
- Date Published:
- Journal Name:
- Global Ecology and Biogeography
- Volume:
- 33
- Issue:
- 8
- ISSN:
- 1466-822X
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract BackgroundCapturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations. ResultsHere we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which are phased and scaffolded at chromosome scale. We generate a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the extent of the genomic diversity among wild grape species from sequence to gene level. The pangenome graph captures genomic variation between haplotypes within a species and across the different species, and it accurately assesses the similarity of hybrids to their parents. The species selected to build the pangenome are a great representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierce’s disease resistance loci. Using pangenome-wide association analysis, we demonstrate the utility of the super-pangenome by effectively mapping short reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes. ConclusionsThis study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of adaptive traits from wild relatives and accelerate crop breeding research.more » « less
-
Abstract AimWe reconstructed the genetic patterns and identified the main genetic breaks of several taxa across California and Baja California coast. Additionally, we evaluated the contribution of different variables to the level of structure. LocationCalifornia and Baja California coast. TaxonFish, invertebrates, algae, seagrass and mammals. MethodsWe generated a map to reconstruct the genetic patterns using genetic information (Fst index and phylogenetic clades distribution) from a literature review of population genetics publications from 2000 to 2023. For the analysis of genetic connectivity drivers, we explored the effect of different variables representing life history traits, reproductive strategies and biogeographic variables and generated five working hypotheses which were evaluated with generalized linear models (GLMs). ResultsWe identified 42 genetic breaks from 63 species across our study area. The largest number of breaks occurs from 27° N to 29° N and from 31° N to 35° N. This range includes transition zones between ecoregions such as Punta Eugenia, Baja California, Mexico and Point Conception, California, USA. We also identified Ensenada, Baja California region as a barrier to gene flow. From a transboundary perspective, we found 40 species with connectivity between California and Baja California, including 14 commercial and or recreational species. We found none of the variables explored had a clear effect on the level of genetic differentiation of the species assessed in the region. Main ConclusionGenetic breaks among different taxa do not distribute randomly across the latitudinal range from California and Baja California coastal area, rather they are mainly located in transition zones between marine ecoregions. The challenge to identify specific variables that explain general genetic patterns highlights the complexity that drives population connectivity processes in marine species.more » « less
-
Abstract AimIntraspecific genetic variation is key for adaptation and survival in changing environments and is known to be influenced by many factors, including population size, dispersal and life‐history traits. We investigated genetic variation within Neotropical amphibian species to provide insights into how natural history traits, phylogenetic relatedness, climatic and geographic characteristics can explain intraspecific genetic diversity. LocationNeotropics. TaxonAmphibians. MethodsWe assembled data sets using open‐access databases for natural history traits, genetic sequences, phylogenetic trees, climatic and geographic data. For each species, we calculated overall nucleotide diversity (π) and tested for isolation by distance (IBD) and isolation by environment (IBE). We then identified predictors ofπ, IBD and IBE using random forest (RF) regression or RF classification. We also fitted phylogenetic generalized linear mixed models (PGLMMs) to predictπ, IBD and IBE. ResultsWe compiled 4052 mitochondrial DNA sequences from 256 amphibian species (230 frogs and 26 salamanders), georeferencing 2477 sequences from 176 species that were not linked to occurrence data. RF regressions and PGLMMs were congruent in identifying range size and precipitation (σ) as the most important predictors ofπ, influencing it positively. RF classification and PGLMMs identified minimum elevation as an important predictor of IBD; most species without IBD tended to occur at higher elevations. Maximum latitude and precipitation (σ) were the best predictors of IBE, and most species without IBE occur at lower latitudes and in areas with more variable precipitation. Main ConclusionsThis study identified predictors of genetic variation in Neotropical amphibians using both machine learning and phylogenetic methods. This approach was valuable to determine which predictors were congruent between methods. We found that species with small ranges or living in zones with less variable precipitation tended to have low genetic diversity. We also showed that Western Mesoamerica, Andes and Atlantic Forest biogeographic units harbour high diversity across many species that should be prioritized for protection. These results could play a key role in the development of conservation strategies for Neotropical amphibians.more » « less
-
The existence of patterns in population dynamics across species geographic ranges and climatic niches is a pervasive idea in ecology. Population variability (i.e. temporal variability in population density) should hypothetically increase near range edges or niche limits because of less suitable environments in these areas, but the occurrence of such patterns remains largely unexplored. Further, fluctuations in temperature could pose demographic constraints on populations and also influence their variability. We used Breeding Bird Survey data to show that the population variability of 97 resident North American birds consistently increases towards their niche limits and in areas with more variable temperatures, but not towards their geographic range edges. However, our model has limited explanatory power, and phylogenetic history and species traits could not explain these results. These findings suggest that other factors, such as biotic interactions and resource availability, might be more important drivers of population variability in resident North American birds.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript
- Journal Article:
- https://doi.org/10.1111/geb.13875
