An official website of the United States government
ABSTRACT Hybridization and interspecific gene flow play a substantial role in the evolution of plant taxa. The eastern North American white oak syngameon, a group of approximately 15 ecologically, morphologically and genomically distinguishable species, has long been recognised as a model system for studying introgressive hybridization in temperate trees. However, the prevalence, genomic context and environmental correlates of introgression in this system remain largely unknown. To assess introgression in the eastern North American white oak syngameon and population structure within the widespreadQuercus macrocarpa, we conducted a rangewide survey ofQ. macrocarpaand four sympatric eastern North American white oak species. Using a Hyb‐Seq approach, we assembled a dataset of 3412 thinned single‐nucleotide polymorphisms (SNPs) in 445 enriched target loci including 62 genes putatively associated with various ecological functions, as well as associated intronic regions and some off‐target intergenic regions (not associated with the exons). Admixture analysis and hybrid class inference demonstrated species coherence despite hybridization and introgressive gene flow (due to backcrossing of F1s to one or both parents). Additionally, we recovered a genetic structure withinQ. macrocarpaassociated with latitude. Generalised linear mixed models (GLMMs) indicate that proximity to range edge predicts interspecific admixture, but rates of genetic differentiation do not appear to vary between putative functional gene classes. Our study suggests that gene flow between eastern North American white oak species may not be as rampant as previously assumed and that hybridization is most strongly predicted by proximity to a species' range margin.
more »
« less
This content will become publicly available on February 1, 2026
Trans‐Specific Polymorphisms Between Cryptic Daphnia Species Affect Fitness and Behavior
ABSTRACT Shared polymorphisms, loci with identical alleles across species, are of unique interest in evolutionary biology as they may represent cases of selection maintaining ancient genetic variation post‐speciation, or contemporary selection promoting convergent evolution. In this study, we investigate the abundance of shared polymorphism between two members of theDaphnia pulexspecies complex. We test whether the presence of shared mutations is consistent with the action of balancing selection or alternative hypotheses such as hybridization, incomplete lineage sorting or convergent evolution. We analyzed over 2,000 genomes from six taxa in theD. pulexspecies group and examined the prevalence and distribution of shared alleles between the focal species pair, North American and EuropeanD. pulex. We show that North American and EuropeanD. pulexdiverged over 10 million years ago, yet retained tens of thousands of shared polymorphisms. We suggest that the number of shared polymorphisms between North American and EuropeanD. pulexcannot be fully explained by hybridization or incomplete lineage sorting alone. We show that most shared polymorphisms could be the product of convergent evolution, that a limited number appear to be old trans‐specific polymorphisms, and that balancing selection is affecting convergent and ancient mutations alike. Finally, we provide evidence that a blue wavelength opsin gene with trans‐specific polymorphisms has functional effects on behavior and fitness in the wild.
more »
« less
- Award ID(s):
- 2021791
- PAR ID:
- 10628497
- Publisher / Repository:
- Wiley
- Date Published:
- Journal Name:
- Molecular Ecology
- Volume:
- 34
- Issue:
- 3
- ISSN:
- 0962-1083
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
ABSTRACT Many coastal marine species experienced Pleistocene gene flow between the North Pacific and Atlantic. Understanding historical connectivity between ocean basins should aid in predicting how regional faunas will respond to recent warming that has intensified trans‐Arctic dispersal. Wetland fauna of the Northwestern Atlantic may have survived in estuarine refugia throughout glacial cycles, or recolonised from the southern coast, North Pacific or Northeastern Atlantic. Here, we used multilocus genetic markers and historical climate data to investigate lineage distribution and connectivity among populations of the nominally cosmopolitan sea slugAlderia modesta, sampled from mudflats on both coasts of the North Pacific and North Atlantic. Mitochondrial DNA clades from European and North American populations were deeply divergent and reciprocally monophyletic; differences at seven polymorphic nuclear loci indicated prolonged absence of trans‐Atlantic gene flow. A Pacific ancestor likely first colonised the Atlantic during the marine biotic interchange of the middle Pliocene ~3.5 Ma. Both mtDNA phylogenetics and nuclear genotype assignments support repeated trans‐Arctic colonisation of the Northwestern Atlantic from the Pacific during inter‐glacial cycles; no gene flow was evident since the last glacial maximum, however. Time‐calibrated coalescent phylogenies, Bayesian skyline plots and haplotype networks all indicated recent population expansions in the Pacific and Europe, but not Northwestern Atlantic. In both the Pacific and Northwestern Atlantic, older lineages persisted in patchy refugia north of glacial margins, while a derived clade of Pacific haplotypes indicates northward post‐LGM expansion. The biogeographical history ofAlderiacontrasts with rocky‐shore taxa that were largely extirpated by glacial advance and recolonised from refugia following the last glacial maximum. Based on molecular differences and distinctions in radular and penial stylet morphology, we resurrect the nameAlderia harvardiensisGould 1870 forAlderiafrom the Northwestern Atlantic and North Pacific;A. modestarefers exclusively to European slugs.more » « less
-
Abstract Pleistocene diversity was much higher than today, for example there were three distinct wolf morphotypes (dire, gray, Beringian) in North America versus one today (gray). Previous fossil evidence suggested that these three groups overlapped ecologically, but split the landscape geographically. The Natural Trap Cave (NTC) fossil site in Wyoming,USAis an ideally placed late Pleistocene site to study the geographical movement of species from northern to middle North America before, during, and after the last glacial maximum. Until now, it has been unclear what type of wolf was present atNTC. We analyzed morphometrics of three wolf groups (dire, extant North American gray, Alaskan Beringian) to determine which wolves were present atNTCand what this indicates about wolf diversity and migration in Pleistocene North America. Results showNTCwolves group with Alaskan Beringian wolves. This provides the first morphological evidence for Beringian wolves in mid‐continental North America. Their location atNTCand their radiocarbon ages suggest that they followed a temporary channel through the glaciers. Results suggest high levels of competition and diversity in Pleistocene North American wolves. The presence of mid‐continental Beringian morphotypes adds important data for untangling the history of immigration and evolution ofCanisin North America.more » « less
-
Abstract Next‐generation sequencing technologies now allow researchers of non‐model systems to perform genome‐based studies without the requirement of a (often unavailable) closely related genomic reference. We evaluated the role of restriction endonuclease (RE) selection in double‐digest restriction‐site‐associatedDNAsequencing (ddRADseq) by generating reduced representation genome‐wide data using four differentREcombinations. Our expectation was thatREselections targeting longer, more complex restriction sites would recover fewer loci thanREwith shorter, less complex sites. We sequenced a diverse sample of non‐model arachnids, including five congeneric pairs of harvestmen (Opiliones) and four pairs of spiders (Araneae). Sample pairs consisted of either conspecifics or closely related congeneric taxa, and in total 26 sample pair analyses were tested. Sequence demultiplexing, read clustering and variant calling were performed in thepyRADprogram. The 6‐base pair cutterEcoRIcombined with methylated site‐specific 4‐base pair cutterMspIproduced, on average, the greatest numbers of intra‐individual loci and shared loci per sample pair. As expected, the number of shared loci recovered for a sample pair covaried with the degree of genetic divergence, estimated with cytochrome oxidase I sequences, although this relationship was non‐linear. Our comparative results will prove useful in guiding protocol selection for ddRADseq experiments on many arachnid taxa where reference genomes, even from closely related species, are unavailable.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
