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119 results for “ecological genomics”

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dryad36/100

Using genomics to guide seed-sourcing at the right taxonomical level for ecological restoration projects: the complex case of Carex bigelowii s.lat. in Norway

There is a growing demand for ecological restoration using suitable seeds following international standards or national legal demands for local seed-sourcing. However, before selecting the appropriate geographic origin of seeds, it is vital to explore taxonomic complexity related to the focal taxa. We used ddRAD-seq to screen genomic diversity within Carex bigelowii s.lat. focussing on Norway. This species complex is considered a candidate for seeding, but presents considerable morphological, ecological, and genetic variation. The genetic structure of 132 individuals of C. bigelowii s.lat., including C. nigra as an outgroup, was explored using ordinations, clustering analyses, and a genetic barrier algorithm. Two highly divergent clusters were evident, supporting the recognition of two taxonomic units 'C. dacica' and 'subsp. bigelowii'. Previously defined seed-sourcing regions for C. bigelowii s.lat. did not consider the known taxonomic complexity, and therefore interpreted the overall genetic structure as seed-sourcing regions, not taxa. We estimated genetic neighbourhood sizes within each taxon to be 100-150 km and 300 km, respectively, indicating species-specific delimitations of local seed-sourcing regions. Frequent hybrids, local genetic distinctiveness, and suggested ecotypes add complexity to the discussed seed-sourcing regions. Our results show how genomic screening of diversity and structure in a species complex can alleviate the taxonomic impediment, inform practical questions and legal requirements related to seed-sourcing, and together with traditional taxonomic work provide necessary information for a sound management of biodiversity.

opencc-zeroNov 2022View details →

dryad36/100

Genomic insights into diversification and ecological speciation of three Saccharina species

Aim: Saccharina is a genus within the brown algae that is of ecological and economic importance and shows rapid adaptive radiation, while the process and genetic mechanism of diversification and speciation remains unclear. In this study, we conducted genome resequencing of three typical Saccharina species, including the four varieties of S. japonica, and its two sister species (S. angustata and S. longissima) to investigate the genetic mechanism of ecological speciation. Location: coast of Japan Methods: We assess the genomic differentiation and genetic diversity of these Saccharina kelps based on whole-genome resequencing. We applied composite-likelihood approach to identify the ancestral species and reconstruct the evolutionary history. Selective sweep analysis was conducted to detect selective signatures when they adapted to diverse habitat. Results: The demography suggested that S. angustata, S. longissima and S. japonica var. japonica underwent adaptive speciation early, with S. japonica var. japonica as the oldest variant that diverged into three other varieties. The newly evolved variety SR has the highest genetic diversity, and the variety SD has the lowest genetic diversity. Interspecific hybridization among these congeneric species was low, indicating these species exist in genetic isolation in nature. We detected that some stress response genes (e.g. ubiquitin-like protein) and growth-related genes (e.g. imm upregulated 3) were under positive selection during the ecological speciation. Low linkage disequilibrium decay rate and extensive signals of selective sweeps are present in these Saccharina species, providing strong support for adaptive differentiation under natural selection as the driving force for its ecological speciation. Main conclusions: The main driving force of speciation in this genus appears to be not natural hybridization, but genetic isolation and adaptive differentiation by nature selection. The evolutionary history and ecological speciation of Saccharina species allow us to predict how common the species responds to environmental change, and whether they require different management strategies.

opencc-zeroSep 2023View details →

dryad36/100

Data from: Genomic and transcriptomic analyses reveal polygenic architecture for ecologically-important functional traits in aspen (Populus tremuloides Michx.)

Intraspecific genetic variation in foundation species such as aspen (Populus tremuloides Michx.) shapes their impact on forest structure and function. Identifying genes underlying ecologically important traits is key to understanding that impact. Previous studies, using single-locus genome-wide association (GWA) analyses to identify candidate genes, have identified fewer genes than anticipated for highly heritable quantitative traits. Mounting evidence suggests that polygenic control of quantitative traits is largely responsible for this "missing heritability" phenomenon. Our research characterized the genetic architecture of 30 ecologically important traits using a common garden of aspen through genomic and transcriptomic analyses. A multilocus association model revealed that most traits displayed a highly polygenic architecture, with most variation explained by loci with small effects (likely below the detection levels of single-locus GWA methods). Consistent with a polygenic architecture, our single-locus GWA analyses found only 38 significant SNPs in 22 genes across 15 traits. Next, we used differential expression analysis on a subset of aspen genets with divergent concentrations of salicinoid phenolic glycosides (key defense traits). This complementary method to traditional GWA discovered 1,243 differentially expressed genes for a polygenic trait. Soft clustering analysis revealed three gene clusters (241 candidate genes) involved in secondary metabolite biosynthesis and regulation. Our work reveals that ecologically important traits governing higher-order community- and ecosystem-level attributes of a foundation forest tree species have complex underlying genetic structures and will require methods beyond traditional GWA analyses to unravel.

opencc-zeroSep 2023View details →

dryad36/100

Gene prediction for: A reference genome for ecological restoration of the sunflower sea star, Pycnopodia helianthoides

<div> <div> <div> <div>Wildlife diseases, such as the sea star wasting (SSW) epizootic that outbroke in the mid-2010s, appear to be associated with acute and/or chronic abiotic environmental change; dissociating the effects of different drivers can be difficult. The sunflower sea star, Pycnopodia helianthoides, was the species most severely impacted during the SSW outbreak, which overlapped with periods of anomalous atmospheric and oceanographic conditions, and there is not yet a consensus on the cause(s). Genomic data may reveal underlying molecular signatures that implicate a subset of factors and, thus, clarify past events while also setting the scene for effective restoration efforts. To advance this goal, we used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to generate a highly contiguous genome assembly that was then annotated using RNA-seq-informed gene prediction. The genome assembly is 484 Mb long, with contig N50 of 1.9 Mb, scaffold N50 of 21.8 Mb, BUSCO completeness score 96.1%, and 22 major scaffolds consistent with prior evidence that sea star genomes comprise 22 autosomes. These statistics generally fall between those of other recently assembled chromosome-scale assemblies for two species in the distantly related asteroid genus Pisaster. These novel genomic resources for Pycnopodia helianthoides will underwrite population genomic, comparative genomic, and phylogenomic analyses — as well as their integration across scales — of SSW and environmental stressors. This data resource contains the files associated with gene prediction.</div> </div> </div> </div>

opencc-zeroOct 2023View details →

dryad36/100