Characterizing the physical and genetic structure of the lodgepole pine × jack pine hybrid zone: mosaic structure and differential introgression.
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ABSTRACT:
SUBMITTER: Cullingham CI
PROVIDER: S-EPMC3552405 | biostudies-literature | 2012 Dec
REPOSITORIES: biostudies-literature
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Project description:Genome-wide scans of genetic differentiation between hybridizing taxa can identify genome regions with unusual rates of introgression. Regions of high differentiation might represent barriers to gene flow, while regions of low differentiation might indicate adaptive introgression-the spread of selectively beneficial alleles between reproductively isolated genetic backgrounds. Here we conduct a scan for unusual patterns of differentiation in a mosaic hybrid zone between two mussel species, Mytilus edulis and M. galloprovincialis. One outlying locus, mac-1, showed a characteristic footprint of local introgression, with abnormally high frequency of edulis-derived alleles in a patch of M. galloprovincialis enclosed within the mosaic zone, but low frequencies outside of the zone. Further analysis of DNA sequences showed that almost all of the edulis allelic diversity had introgressed into the M. galloprovincialis background in this patch. We then used a variety of approaches to test the hypothesis that there had been adaptive introgression at mac-1. Simulations and model fitting with maximum-likelihood and approximate Bayesian computation approaches suggested that adaptive introgression could generate a "soft sweep," which was qualitatively consistent with our data. Although the migration rate required was high, it was compatible with the functioning of an effective barrier to gene flow as revealed by demographic inferences. As such, adaptive introgression could explain both the reduced intraspecific differentiation around mac-1 and the high diversity of introgressed alleles, although a localized change in barrier strength may also be invoked. Together, our results emphasize the need to account for the complex history of secondary contacts in interpreting outlier loci.
| S-EPMC4096372 | biostudies-literature
Project description:BackgroundThe mountain pine beetle (MPB, Dendroctonus ponderosae) epidemic has affected lodgepole pine (Pinus contorta) across an area of more than 18 million hectares of pine forests in western Canada, and is a threat to the boreal jack pine (Pinus banksiana) forest. Defence of pines against MPB and associated fungal pathogens, as well as other pests, involves oleoresin monoterpenes, which are biosynthesized by families of terpene synthases (TPSs). Volatile monoterpenes also serve as host recognition cues for MPB and as precursors for MPB pheromones. The genes responsible for terpene biosynthesis in jack pine and lodgepole pine were previously unknown.ResultsWe report the generation and quality assessment of assembled transcriptome resources for lodgepole pine and jack pine using Sanger, Roche 454, and Illumina sequencing technologies. Assemblies revealed transcripts for approximately 20,000 - 30,000 genes from each species and assembly analyses led to the identification of candidate full-length prenyl transferase, TPS, and P450 genes of oleoresin biosynthesis. We cloned and functionally characterized, via expression of recombinant proteins in E. coli, nine different jack pine and eight different lodgepole pine mono-TPSs. The newly identified lodgepole pine and jack pine mono-TPSs include (+)-α-pinene synthases, (-)-α-pinene synthases, (-)-β-pinene synthases, (+)-3-carene synthases, and (-)-β-phellandrene synthases from each of the two species.ConclusionIn the absence of genome sequences, transcriptome assemblies are important for defence gene discovery in lodgepole pine and jack pine, as demonstrated here for the terpenoid pathway genes. The product profiles of the functionally annotated mono-TPSs described here can account for the major monoterpene metabolites identified in lodgepole pine and jack pine.
| S-EPMC3668260 | biostudies-literature
Project description:BACKGROUND:Hybrid zones formed by the secondary contact of divergent lineages represent natural laboratories for studying the genetic basis of speciation. Here we tested for patterns of differential introgression among three X-linked and 11 autosomal regions to identify candidate loci related to either reproductive isolation or adaptive introgression across a hybrid zone between two Chinese mainland subspecies of the intermediate horseshoe bat Rhinolophus affinis: R. a. himalayanus and R. a. macrurus. RESULTS:Our results support the previous suggestion that macrurus formed when a third subspecies (R. a. hainanus) recolonized the mainland from Hainan Island, and that himalayanus is the ancestral taxon. However, this overall evolutionary history was not reflected in all loci examined, with considerable locus-wise heterogeneity seen in gene tree topologies, levels of polymorphism, genetic differentiation and rates of introgression. Coalescent simulations suggested levels of lineage mixing seen at some nuclear loci might result from incomplete lineage sorting. Isolation with migration models supported evidence of gene flow across the hybrid zone at one intronic marker of the hearing gene Prestin. CONCLUSIONS:We suggest that phylogenetic discordance with respect to the species tree seen here is likely to arise via a combination of incomplete lineage sorting and a low incidence of introgression although we cannot rule out other explanations such as selection and recombination. Two X-linked loci and one autosomal locus were identified as candidate regions related to reproductive isolation across the hybrid zone. Our work highlights the importance of including multiple genomic regions in characterizing patterns of divergence and gene flow across a hybrid zone.
| S-EPMC4105523 | biostudies-literature
Project description:BackgroundExploring hybrid zone dynamics at different spatial scales allows for better understanding of local factors that influence hybrid zone structure. In this study, we tested hypotheses about drivers of introgression at two spatial scales within the Saltmarsh Sparrow (Ammospiza caudacuta) and Nelson's Sparrow (A. nelsoni) hybrid zone. Specifically, we evaluated the influence of neutral demographic processes (relative species abundance), natural selection (exogenous environmental factors and genetic incompatibilities), and sexual selection (assortative mating) in this mosaic hybrid zone. By intensively sampling adults (n = 218) and chicks (n = 326) at two geographically proximate locations in the center of the hybrid zone, we determined patterns of introgression on a fine scale across sites of differing habitat. We made broadscale comparisons of patterns from the center with those of prior studies in the southern edge of the hybrid zone.ResultsA panel of fixed SNPs (135) identified from ddRAD sequencing was used to calculate a hybrid index and determine genotypic composition/admixture level of the populations. Another panel of polymorphic SNPs (589) was used to assign paternity and reconstruct mating pairs to test for sexual selection. On a broad-scale, patterns of introgression were not explained by random mating within marshes. We found high rates of back-crossing and similarly low rates of recent-generation (F1/F2) hybrids in the center and south of the zone. Offspring genotypic proportions did not meet those expected from random mating within the parental genotypic distribution. Additionally, we observed half as many F1/F2 hybrid female adults than nestlings, while respective male groups showed no difference, in support of Haldane's Rule. The observed proportion of interspecific mating was lower than expected when accounting for mate availability, indicating assortative mating was limiting widespread hybridization. On a fine spatial scale, we found variation in the relative influence of neutral and selective forces between inland and coastal habitats, with the smaller, inland marsh influenced primarily by neutral demographic processes, and the expansive, coastal marsh experiencing higher selective pressures in the form of natural (exogenous and endogenous) and sexual selection.ConclusionsMultiple drivers of introgression, including neutral and selective pressures (exogenous, endogenous, and sexual selection), are structuring this hybrid zone, and their relative influence is site and context-dependent.
| S-EPMC7853311 | biostudies-literature
Project description:Hybrid zones have yielded considerable insight into many evolutionary processes, including speciation and the maintenance of species boundaries. Presented here are analyses from a hybrid zone that occurs among three salamanders -Plethodon jordani, Plethodon metcalfi and Plethodon teyahalee- from the southern Appalachian Mountains. Using a novel statistical approach for analysis of non-clinal, multispecies hybrid zones, we examined spatial patterns of variation at four markers: single-nucleotide polymorphisms (SNPs) located in the mtDNA ND2 gene and the nuclear DNA ILF3 gene, and the morphological markers of red cheek pigmentation and white flecks. Concordance of the ILF3 marker and both morphological markers across four transects is observed. In three of the four transects, however, the pattern of mtDNA is discordant from all other markers, with a higher representation of P. metcalfi mtDNA in the northern and lower elevation localities than is expected given the ILF3 marker and morphology. To explore whether climate plays a role in the position of the hybrid zone, we created ecological niche models for P. jordani and P. metcalfi. Modelling results suggest that hybrid zone position is not determined by steep gradients in climatic suitability for either species. Instead, the hybrid zone lies in a climatically homogenous region that is broadly suitable for both P. jordani and P. metcalfi. We discuss various selective (natural selection associated with climate) and behavioural processes (sex-biased dispersal, asymmetric reproductive isolation) that might explain the discordance in the extent to which mtDNA and nuclear DNA and colour-pattern traits have moved across this hybrid zone.
| S-EPMC5478279 | biostudies-literature
Project description:Hybrid zones provide insight into the nature of species boundaries and the evolution of barriers to gene exchange. Characterizing multiple regions within hybrid zones is essential for understanding both their history and current dynamics. Here, we describe a previously uncharacterized region of a well-studied hybrid zone between two species of field crickets, Gryllus pennsylvanicus and G. firmus. We use a combination of mitochondrial DNA sequencing, morphological data, and modeling of environmental variables to identify the ecological factors structuring the hybrid zone and define patterns of hybridization and introgression. We find an association between species distribution and natural habitat; Gryllus pennsylvanicus occupies natural habitat along forest edges and natural clearings, whereas G. firmus occupies more disturbed areas in agricultural and suburban environments. Hybridization and introgression occur across patch boundaries; there is evidence of substantial admixture both in morphological characters and mtDNA, over a broad geographic area. Nonetheless, the distribution of morphological types is bimodal. Given that F1 hybrids are viable and fertile in the lab, this suggests that strong pre-zygotic barriers are operating in this portion of the hybrid zone.
| S-EPMC3631409 | biostudies-literature
Project description:Sustainability of Climate and Pest Resilient Forests (RES-FOR) for Pinus contorta.
| PRJNA715165 | ENA
Project description:Hybridization in nature offers unique insights into the process of natural selection in incipient species and their hybrids. In order to evaluate the patterns and targets of selection, we examine a recently discovered baboon hybrid zone in the Kafue River Valley of Zambia, where Kinda baboons (Papio kindae) and grey-footed chacma baboons (P. ursinus griseipes) coexist with hybridization. We genotyped baboons at 14,962 variable genome-wide autosomal markers using double-digest RADseq. We compared ancestry patterns from this genome-wide data set to previously reported ancestry from mitochondrial-DNA and Y-chromosome sources. We also fit a Bayesian genomic cline model to scan for genes with extreme patterns of introgression. We show that the Kinda baboon Y chromosome has penetrated the species boundary to a greater extent than either mitochondrial DNA or the autosomal chromosomes. We also find evidence for overall restricted introgression in the JAK/STAT signalling pathway. Echoing results in other species including humans, we find evidence for enhanced and/or directional introgression of immune-related genes or pathways including the toll-like receptor pathway, the blood coagulation pathway, and the LY96 gene. Finally we show enhanced introgression and excess chacma baboon ancestry in the sperm tail gene ODF2. Together, our results elucidate the dynamics of introgressive hybridization in a primate system while identifying genes and pathways possibly under selection.
| S-EPMC8043982 | biostudies-literature
Project description:Lodgepole pine (Pinus contorta) forests are widely distributed throughout North America and are subject to mountain pine beetle (Dendroctonus ponderosae) epidemics, which have caused mortality over millions of hectares of mature trees in recent decades. Mountain pine beetle is known to influence stand structure, and has the ability to impact many forest processes. Dwarf mistletoe (Arceuthobium americanum) also influences stand structure and occurs frequently in post-mountain pine beetle epidemic lodgepole pine forests. Few studies have incorporated both disturbances simultaneously although they co-occur frequently on the landscape. The aim of this study is to investigate the stand structure of lodgepole pine forests 21-28 years after a mountain pine beetle epidemic with varying levels of dwarf mistletoe infection in the Deschutes National Forest in central Oregon. We compared stand density, stand basal area, canopy volume, proportion of the stand in dominant/codominant, intermediate, and suppressed cohorts, average height and average diameter of each cohort, across the range of dwarf mistletoe ratings to address differences in stand structure. We found strong evidence of a decrease in canopy volume, suppressed cohort height, and dominant/codominant cohort diameter with increasing stand-level dwarf mistletoe rating. There was strong evidence that as dwarf mistletoe rating increases, proportion of the stand in the dominant/codominant cohort decreases while proportion of the stand in the suppressed cohort increases. Structural differences associated with variable dwarf mistletoe severity create heterogeneity in this forest type and may have a significant influence on stand productivity and the resistance and resilience of these stands to future biotic and abiotic disturbances. Our findings show that it is imperative to incorporate dwarf mistletoe when studying stand productivity and ecosystem recovery processes in lodgepole pine forests because of its potential to influence stand structure.
| S-EPMC4164639 | biostudies-literature
Project description:The recent mountain pine beetle outbreak in western Canada provides an opportunity to study the selection and heritability of tree defenses. We examined terpenoid-based defenses of seedling lodgepole pines which were offspring of mature trees subjected to high levels of mountain pine beetle selective pressure. Seedlings were grown from one of three types of cones: old cones on live trees; young cones on live trees; and cones on trees killed by beetles. Offspring thus represented crosses of non-surviving (NS) x surviving (S), S x S, and NS x NS parents, respectively. Methyl jasmonate was used to induce a defensive reaction in the seedlings. Seed source had a significant effect on levels of ten different terpenes, but not on total terpene concentrations. When the seedlings were grouped by location and treatment type, the seedlings of different cone types could be almost entirely distinguished by terpene profiles.
| S-EPMC5951554 | biostudies-literature