Ongoing and predicted range loss of kelp forests in response to climatic stressors is pressing marine managers to look into the adaptive capacity of populations to inform conservation strategies. Characterising how adaptive genetic diversity and structure relate to present and future environmental variation represents an emerging approach to quantifying kelp vulnerability to environmental change and identifying populations with genotypes that potentially confer an adaptive advantage in future ocean conditions. The dominant Australian kelp, Ecklonia radiata, was genotyped from 10 locations spanning 2000 km of coastline and a 9.5°C average temperature gradient along the east coast of Australia, a global warming hotspot. ddRAD sequencing generated 10,700 high-quality single nucleotide polymorphisms (SNPs) and characterized levels of neutral and adaptive genomic diversity and structure. The adaptive dataset, reflecting portions of the genome putatively under selection, was used to infer genomic vulnerability by 2050 under the RCP 8.5 scenario. There was strong neutral genetic differentiation between Australia mainland and Tasmanian populations, but only weak genetic structure among mainland populations within the main path of the East Australian Current. Genetic diversity was highest in the center of the range and lowest in the warm-edge population. The adaptive SNP candidates revealed similar genetic structure patterns, with a spread of adaptive alleles across most warm (northern) populations. The lowest, but most unique, adaptive genetic diversity values were found in both warm and cool population edges, suggesting local adaptation but low evolutionary potential. Critically, genomic vulnerability modeling identified high levels of vulnerability to future environmental conditions in Tasmanian populations. Populations of kelp at range edges are unlikely to adapt and keep pace with predicted climate change. Ensuring the persistence of these kelp forests, by boosting resilience to climate change, may require active management strategies with assisted adaptation in warm-edge (northern) populations and assisted gene flow in cool-edge (Tasmania) populations.

Soybean domestication has been essential for crop evolution, adaptation, and modern breeding. Despite advancements in understanding soybean genetics, the genetic basis of DRTs has yet to be fully explored, particularly in the context of genome-wide association studies (GWASs) and gene interaction analyses (epistasis). This study evaluated 198 diverse soybean accessions using 23,574 high-quality SNPs obtained via ddRAD-seq. Nine key DRTs-including those related to seed size (length, width, and thickness), seed coat color, cotyledon color, hypocotyl color, stem growth habit, flower color, pod color, pubescence, and pod-shattering-were phenotyped in two environments. A GWASs conducted via the FarmCPU and BLINK models identified 78 significant SNPs, 14 consistently detected across both environments and models, demonstrating stability. Notably, the SNP rs.Gm16.29778273 linked to pod-shattering resistance. The functional annotation linked three known quantitative trait loci /genes and revealed 11 novel candidate genes associated with DRTs, providing insights into their roles via Gene Ontology (GO) terms. The main effect SNP × SNP interaction analysis revealed that the significant SNP rs.Gm13.16695800 exhibits a pleiotropic effect, controlling both hypocotyl and flower color. Furthermore, 324 epistatic interactions were identified, influencing the expression of DRTs, thereby highlighting the complex genetic architecture underlying these traits. These findings offer valuable insights into domestication and the traits linked to higher yield. They provide a solid foundation for developing marker-assisted selection (MAS) strategies and functional studies to improve soybean breeding for resilient, high-yielding varieties.

Tree species are often locally adapted to their environments, but the extent to which environmental adaptation contributes to incipient speciation is unclear. One of the rarest pines in the world, Torrey pine (Pinus torreyana Parry), persists naturally across one island and one mainland population in southern California. The two populations are morphologically and genetically differentiated but experience some connectivity, making it an ideal system for assessing the evolution of reproductive isolation. Previous work has found evidence of heterosis in F1 mainland-island hybrids, suggesting genetic rescue could be beneficial in the absence of reproductive barriers. Using ddRADseq and GWAS for a common garden experiment of island, mainland, and F1 individuals, we identified candidate loci for environmentally driven reproductive isolation, their function, and their relationship to fitness proxies. By simulating neutral evolution and admixture between the two populations, we identified loci that exhibited reduced heterozygosity in the F1s, evidence of selection against admixture. SNPs with reduced F1 heterozygosity were enriched for growth and pollination functions, suggesting genetic variants that could be involved in the evolution of reproductive barriers between populations. One locus with reduced F1 heterozygosity exhibited strong associations with growth and reproductive fitness proxies in the common garden, with the mainland allele conferring increased fitness. If this locus experiences divergent selection in the two natural populations, it could promote their reproductive isolation. Finally, although hybridization largely reduced allele fixation in the F1s initially, indicating heterosis is likely due to the masking of deleterious alleles, the emergence of reproductive isolation between populations may diminish the longer-term benefits of genetic rescue in F2 or advanced-generation hybrids. As Torrey pine is a candidate for interpopulation genetic rescue, caution is warranted where longer-term gene flow between diverged populations may result in reduced fitness if barriers have evolved.

Enhanced pea cultivation, which can increase the sustainability of European agriculture, requires better-performing cultivars. This study investigated the genomic selection (GS) ability to predict grain yield, protein content, and protein yield on the same or a different genetic base (target/non-target GB) relative to that employed for model training. GS models were developed on 276 lines from three Recombinant Inbred Line (RIL) populations evaluated in three Italian autumn-sown environments using 5537 SNPs from genotyping by sequencing. Validation in two cropping years concerned 108 independent lines from five RIL populations, of which two belonged to the GS training set, and three shared one parent each with training populations. A genome-wide association study performed on the GS training set using 18,674 SNPs highlighted the polygenic control of protein content and grain yield, with several environment-dependent QTLs for yield. Intermediate/high predictive ability within or across populations emerged for all traits in the target GB (0.359-0.675), with some variation depending on the population. Predictive ability in the non-target GB was modest/intermediate for protein content, and null/poor for the other traits. No inverse correlation emerged between grain yield and protein content. GS proved useful for all traits in the target GB and for protein content in a non-target GB.

Understanding population structure within species provides information on connections among different populations and how they evolve over time. This knowledge is important for studies ranging from evolutionary biology to large-scale variant-trait association studies. Current approaches to determining population structure include model-based approaches, statistical approaches, and distance-based ancestry inference approaches.

In this work, we identify population structure from DNA sequence data using an alignment-free approach. We use the frequencies of short DNA substrings from across the genome (k-mers) with principal component analysis (PCA). K-mer frequencies can be viewed as a summary statistic of a genome and have the advantage of being easily derived from a genome by counting the number of times a k-mer occurred in a sequence. In contrast, most population structure work employing PCA uses multi-locus genotype data (SNPs, microsatellites, or haplotypes). No genetic assumptions must be met to generate k-mers, whereas current population structure approaches often depend on several genetic assumptions and can require careful selection of ancestry informative markers to identify populations. We compare our k-mer based approach to population structure estimated using SNPs with both empirical and simulated data.

In this work, we show that PCA is able to determine population structure just from the frequency of k-mers found in the genome. The application of PCA and a clustering algorithm to k-mer profiles of genomes provides an easy approach to detecting the number and composition of populations (clusters) present in the dataset. Using simulations, we show that results are at least comparable to population structure estimates using SNPs. When using human genomes from populations identified by the 1000 Genomes Project, the results are better than population structure estimates using SNPs from the same samples, and comparable to those found by a model-based approach using genetic markers from larger numbers of samples.

This study shows that PCA, together with the clustering algorithm, is able to detect population structure from k-mer frequencies and can separate samples of admixed and non-admixed origin. Using k-mer frequencies to determine population structure has the potential to avoid some challenges of existing methods and may even improve on estimates from small samples.

The presence of cryptic species can hinder effective conservation planning and implementation, as has been the case for speciose groups of freshwater fishes that are difficult to differentiate due to conserved morphologies. The West Texas shiner Notropis megalops and the Texas shiner Notropis amabilis are a cryptic pair of leuciscids (minnows) that co-occur in spring-fed tributaries of the Rio Grande in Texas and Mexico. Both N. megalops and N. amabilis are listed as Species of Greatest Conservation Need by the Texas Parks and Wildlife Department. Notropis amabilis is widespread and listed as apparently secure by Texas Parks and Wildlife Department whereas N. megalops has a very limited distribution and has not been ranked by Texas Parks and Wildlife Department because of data deficiency. Morphological differences between these species have been described; however, proper identification in situ remains problematic. Furthermore, given their range of overlap there is potential for hybridization, and limited genetic data have been collected comparing the species. Therefore, reduced representation genomic and mitochondrial sequencing data were used to reassess the distinctness of the species, screen for hybridization, and characterize their relative frequencies throughout their range of overlap. Genomic analyses recovered two distinct genetic groups corresponding to the species (F'CT = 0.89) with no evidence of admixture or introgression. The species were found to co-occur at three sampling locations, two in the Devils River and one in the Pecos, but not in equal frequencies. Overall, these results provide data and tools for further research on N. megalops needed for accurate conservation policies and management practices.

Tropical reef fishes exhibit a large disparity of organismal morphologies contributing to their astonishing biodiversity. Morphological disparity, scaling from differences among individuals within populations to differences among species, is governed by ecological and evolutionary processes. Here, we examined the relationship between intra- and interspecific disparity in 1111 individuals from 17 tropical reef fish species, representing 10 families with different dispersal abilities, across four Indian Ocean regions. We compared intraspecific measurements with species-level measures from a database of 1061 reef fish species. Species with high morphological disparity among individuals from distinct regions are found to be nested in families that display a high disparity among their genera. We show an association between the morphological disparity at the intra- and interspecific levels for several morphological ratios such as the caudal peduncle elongation. We evaluated the link between morphological disparity and genetic diversity with species dispersal ability. A structural equation model indicates that dispersal ability correlates positively with species genetic diversity, which is associated with morphological disparity. Our results suggest that traits associated with dispersal may foster gene flow and morphological evolution. Future works combining genomic, morphological and environmental data across more species is necessary to generalize these findings to other regions.

The resilience of populations to extreme climatic events comprises the resistance to withstand and the ability to recover, which depends on factors such as remaining genetic diversity and population connectivity. In 2011, a MHW caused a 100 km range contraction of kelp (Ecklonia radiata) off Western Australia, but recently recovering kelp forests were discovered. To understand mechanisms of recovery and determine if recovering populations are survivors or immigrants, we used genotyping-by-sequencing to assess patterns of genetic diversity and connectivity. We found that two of the three recovering kelp forests (PG1 and 2) were likely survivors whereas a third smaller population (PGCr 1) was likely produced through re-colonisation from nearby surviving forests. Connectivity was high among populations and migration analysis identified one population (Horrocks) as the most important source for the recovering kelps. All recovering populations had higher neutral genetic diversity, and similar putative adaptive diversity to surrounding surviving populations, suggesting local adaptation. Our results elucidate how mixed processes can contribute to kelp forest resilience following MHWs but cryptic survival and maintenance of population connectivity is key to recovery.

Diversifying animal cultivation demands efficient genotyping for enabling genomic selection, but non-model species lack efficient genotyping solutions. The aim of this study was to optimize a genotyping-by-sequencing (GBS) double-digest RAD-sequencing (ddRAD) pipeline. Bovine data was used to automate the bioinformatic analysis. The application of the optimization was demonstrated on non-model European whitefish data.

DdRAD data generation was designed for a reliable estimation of relatedness and is scalable to up to 384 samples. The GBS sequencing yielded approximately one million reads for each of the around 100 assessed samples. Optimizing various strategies to create a de-novo reference genome for variant calling (mock reference) showed that using three samples outperformed other building strategies with single or very large number of samples. Adjustments to most pipeline tuning parameters had limited impact on high-quality data, except for the identity criterion for merging mock reference genome clusters. For each species, over 15k GBS variants based on the mock reference were obtained and showed comparable results with the ones called using an existing reference genome. Repeatability analysis showed high concordance over replicates, particularly in bovine while in European whitefish data repeatability did not exceed earlier observations.

The proposed cost-effective ddRAD strategy, coupled with an efficient bioinformatics workflow, enables broad adoption of ddRAD GBS across diverse farmed species. While beneficial, a reference genome is not obligatory. The integration of Snakemake streamlines the pipeline usage on computer clusters and supports customization. This user-friendly solution facilitates genotyping for both model and non-model species.

Revealing the spatial distribution of adaptive genetic variation is both a challenging and crucial task in evolutionary ecology, essential for understanding local adaptation within species, and in management, for predicting species responses to future climate change. This understanding is particularly important for long-lived tree species, which may not be able to migrate quickly enough to adapt to rapid climate changes and may need to rely on their standing genetic variation. In this study, we focused on Cryptomeria japonica, a major component of Japan's temperate forests and an important forestry species adapted to the humid environment of monsoon Asia. We extracted climate-associated genetic variation from the entire genome and evaluated its distribution and vulnerability under future climate scenarios using spatial modeling techniques. We analyzed 31,676 high-quality SNPs from 249 individuals across 22 natural populations of C. japonica, covering its entire distribution range. We identified 239 candidate climate-associated SNPs and found winter temperature, summer precipitation, and winter precipitation as the most significant factors explaining the genetic variation in these SNPs. The climate-associated genetic variation deviated from non-associated (neutral) genetic variation in the opposite (the Sea of Japan and Pacific Ocean) sides of Japanese archipelago, suggesting natural selection of different climate conditions in these regions. Difference in estimated allele frequency at the climate-associated loci (genetic offset) between the present and future (2090 in the SSP5-8.5 scenario) climate conditions was predicted to be larger in three areas (not only southwestern Japan but also coastal area on the Sea of Japan side and inland area on the Pacific Ocean side in northeastern Japan). This prediction implies the discrepancy between standing genetic variation at the present and that adaptive to the future climate in these areas, which underscores the necessity for proactive management to adjust the adaptive genetic variation.

Porites corals are vital components of tropical reef ecosystems worldwide, serving as ecosystem engineers and hubs of biodiversity in shallow water coral reefs. Despite their ecological significance and the widespread use of Porites spp. as models for research, the richness and evolutionary relationships of species within the genus remain elusive. In this study, we analyzed genomic data from 330 colonies of Porites from 17 localities across the Indo-Pacific region based on the reduced representation genomic approach ezRAD. We retrieved 25,163 SNPs and provided a phylogenomic hypothesis for 29 nominal species and 10 unknown morphologies, recovering 15 deeply rooted molecular clades. Among these, 12 clades included samples corresponding to single distinct morphospecies. One did not match any nominal species. The remaining two clades comprised species complexes, which included various massive and encrusting morphologies commonly used in experimental biology. Within these complexes, we observed additional geographic or morphological structure, indicating complex evolutionary dynamics, possibly reflecting distinct species, isolated populations or hybridization. Additionally, a series of divergent samples underscored the importance of more sampling to define species boundaries and refine phylogenomic relationships. We also integrated our findings with previous phylogenetic datasets and their respective sampling localities, challenging traditional notions about Porites species geographic distributions. Overall, our findings indicate a need to revise past synonymies and to formally establish new species. A precise understanding of Porites species and their diversity and distributions is necessary for effective reef conservation and management.

Genetic diversity and competitive ability, though extensively studied in the context of biological invasions, are still poorly understood in their relative importance, especially when shifting the perspective from an individual plant's phenotype to overall population performance. Most approaches addressing the role of genetic diversity involve the comparison of standing genetic variation in field populations combined with experimental treatments on individual plants. Composing predefined mixtures of populations to manipulate genetic diversity would be an experimental approach to test for direct effects on population performance. We determined pairwise genetic distances among 16 invasive and 22 native populations of Jacobaea vulgaris GAERTN. using single nucleotide polymorphisms (SNP). Based on this information, we created each 15 de-novo populations with different levels of genetic diversity for both origins. These de-novo populations were subjected to three levels of decreasing microsite availability by using a matrix of either 0, 5, or 10 individuals of Festuca rubra. We monitored population performance continuously throughout two growing seasons to study effects of interactions between origin, microsite availability, and genetic diversity with (generalized) linear effects models. This allowed us to uncover whether the relative importance of those factors varies with the life-stage of this biennial species. We found no ambiguous patterns on the hypothesized beneficial effect of genetic diversity for J. vulgaris populations. Native populations tended to respond negatively to increasing genetic diversity, especially under more favorable site conditions, but this was not a persistent pattern and was only evident through continuous monitoring. Invasive populations could benefit from increasing genetic diversity during early establishment, but not in interaction with restricted microsite availability. Our results do suggest that genetic variation supports population establishment and performance under certain environmental conditions. Therefore, for recommendations in nature conservation, efforts should still aim at limiting propagule addition in already invaded areas, even in well-established invasive species.

Sponges are key ecosystem engineers that shape, structure and enhance the biodiversity of marine benthic communities globally. Sponge aggregations and reefs are recognized as vulnerable marine ecosystems (or VMEs) due to their susceptibility to damage from bottom-contact fishing gears. Ensuring their long-term sustainability, preservation, and ecosystem functions requires the implementation of sound scientific conservation tools. Here, the genetic diversity, structure, and connectivity of the deep-sea glass sponge, Vazella pourtalesii (Schmidt, 1870), was investigated using 1,102 neutral SNPs obtained in RADseq. This species is distributed across the northwest Atlantic from Florida, USA to Nova Scotia, Canada and we sequenced samples covering this full distribution and provided evidence of strong genetic structure with two distinct clusters: Florida together with the Carolina Shelves and the Scotian Shelf. We estimated moderate levels of diversity with low migration across large distances (> 1000 kms) and high connectivity at smaller scales (< 300 kms). Further, fishing pressure on genetic diversity was evaluated, within two Sponge Conservation Areas (SCAs) on the Scotian Shelf. Those areas have different disturbance histories, and cumulative fishing pressure. Slightly lower levels of genetic diversity were found inside the SCAs, and yet they encompassed a high proportion of the diversity observed within the Scotian Shelf. We provide baseline data for future monitoring of the SCAs, discussing our findings in the light of existing area-based management tools.

Understanding the evolutionary processes underlying range-wide genomic variation is critical to designing effective conservation and restoration strategies. Evaluating the influence of connectivity, demographic change and environmental adaptation for threatened species can be invaluable to proactive conservation of evolutionary potential. In this study, we assessed genomic variation across the range of Fraxinus latifolia, a foundational riparian tree native to western North America recently exposed to the invasive emerald ash borer (Agrilus planipennis; EAB). Over 1000 individuals from 61 populations were sequenced using reduced representation (ddRAD-seq) across the species' range. Strong population structure was evident along a latitudinal gradient, with population connectivity largely maintained along central valley river systems, and a centre of genetic diversity coinciding with major river systems central to the species' range. Despite evidence of connectivity, estimates of nucleotide diversity and effective population size were low across all populations, suggesting the patchy distribution of F. latifolia populations may impact its long-term evolutionary potential. Range-wide estimates of genomic offset, which indicate genomic change required to adjust to future climate projections, were greatest in the eastern and lowest in the southern portions of the species' range, suggesting the regional distribution of genomic variation may impact evolutionary potential longer-term. To preserve evolutionary capacity across populations needed for the development of breeding and restoration programmes, prioritising conservation of range-wide genomic diversity will provide a foundation for long-term species management.

Karst ecosystems often contain extraordinary biodiversity, but the complex underground aquifers of karst regions present challenges for assessing and conserving stygobiont diversity and investigating their evolutionary history. We examined the karst-obligate salamanders of the Eurycea neotenes species complex in the Edwards Plateau region of central Texas using population genomics data to address questions about population connectivity and the potential for gene exchange within the underlying aquifer system. The E. neotenes species complex has historically been divided into three nominal species, but their status, and spatial extent of species ranges, have remained uncertain. We discovered evidence of extensive admixture among species within the complex and with adjacent lineages. We observed relatively low levels of differentiation among all sampling localities which supports the hypothesis of recent divergence. Nominal taxonomy, aquifer region and geography each accounted for a modest amount of the overall population genomic variation; however, these predictors were largely confounded and difficult to disentangle. Importantly, current taxonomy of the three nominal species does not reflect the admixture apparent in clustering analyses. Inference of migration events revealed a complex pattern of gene exchange, suggesting that Eurycea salamanders have a dynamic history of dispersal through the aquifer system. These results highlight the need for greater understanding of how stygobiont populations are connected via dispersal and gene exchange through karst aquifers. These results also highlight the applicability of population genomics data as a powerful lever for investigating connectivity among populations in systems where direct detection of dispersal paths is difficult, as in underground, aquatic systems.

In the marine realm, unidirectional ocean currents often lead to high migration rates of marine organisms and, therefore, inhibit the formation of their latitudinal genetic structure. In contrast, cryptic latitudinal structures associated with local adaptation may frequently exist in widespread species generally exposed to a strong environmental heterogeneity. However, our understanding of the evolvability of locally adapted populations in open marine environments still needs to be completed. The coastal area along the Sea of Japan, where the Tsushima Warm Current flows from south to north in the Japanese Archipelago, provides a good model system for exploring this question. This study explored evidence for latitudinal local adaptation along with the prevailing ocean current in the ice goby Leucopsarion petersii at the phenotypic and genomic levels. Common garden experiments clearly showed genetically based clinal variation in growth rate, strongly suggesting local adaptation through conutergradient selection of this fitness-related trait. Analyses based on reduced-representation sequencing revealed a slight signal of genetic differentiation between the southern and northern populations, although continuous historical gene flow between them was supported by demographic modelling. Also, whole-genome resequencing showed their independent demographic history during the last glacial period. Thus, these results suggest that gene flow along with the prevailing ocean current is somewhat limited, and the populations are not completely panmictic. Furthermore, the selection scan based on low-coverage genome-wide sequencing detected putative genomic signatures of latitudinal adaptation of growth-related genes. Thus, our integrative study provided a novel example of marine local adaptation under a large ocean current.

Eastern oysters, Crassostrea virginica, are historically a keystone species in many of the estuaries in which they reside, providing critical ecosystem services. Because oyster populations have been on the decline for the past century, restoration initiatives currently are underway in many estuarine systems, including Great Bay Estuary (GBE), New Hampshire. Results of prior studies of eastern oyster population genomics cannot be applied directly to GBE, as it is a well-mixed estuarine system that is relatively contained, and the sources of recruits are split among cultivated and native. This study aimed to identify the population genomic structure of eastern oysters in GBE to facilitate determination of effective population size and estimation of genetic differentiation among subpopulations. Results showed moderate genomic differentiation among native, cultivated, and restoration C. virginica subpopulations in the Bay. A small number of breeders (Ne=163-276) was found in all subpopulations except the Lamprey River site (Ne=995). This research provides a contemporary snapshot of eastern oyster subpopulation structure at the genomic level in GBE that will facilitate restoration and enhanced management.

The processes that restrict gene flow between populations are fundamental to speciation. Here, we develop a simple framework for studying whether divergence in morphology, climatic niche, time and space contribute to reduced gene flow among populations and species. We apply this framework to a model system involving a clade of spiny lizards (Sceloporus) occurring mostly in northeastern Mexico, which show striking variation in morphology and habitat among closely related species and populations. We developed a new time-calibrated phylogeny for the group using RADseq data from 152 individuals. This phylogeny identified 12 putative species-level clades, including at least two undescribed species. We then estimated levels of gene flow among 21 geographically adjacent pairs of species and populations. We also estimated divergence in morphological and climatic niche variables among these same pairs, along with divergence times and geographic distances. Using Bayesian generalised linear models, we found that gene flow between pairs of lineages is negatively related to divergence time and morphological divergence among them (which are uncorrelated), and not to geographic distance or climatic divergence. The framework used here can be applied to study speciation in many other organisms having genomic data but lacking direct data on reproductive isolation. We also found several other intriguing patterns in this system, including the parallel evolution of a strikingly similar montane blue-red morph from more dull-coloured desert ancestors within two different, nonsister species.

-Gene flow between diverging lineages challenges the resolution of species boundaries and the understanding of evolutionary history in recent radiations. Here, we integrate phylogenetic and coalescent tools to resolve reticulate patterns of diversification and use a perspective focused on evolutionary mechanisms to distinguish interspecific and intraspecific taxonomic variation. We use this approach to resolve the systematics for one of the most intensively studied but difficult to understand groups of reptiles: the spotted whiptail lizards of the genus Aspidoscelis (A. gularis complex). Whiptails contain the largest number of unisexual species known within any vertebrate group and the spotted whiptail complex has played a key role in the generation of this diversity through hybrid speciation. Understanding lineage boundaries and the evolutionary history of divergence and reticulation within this group is therefore key to understanding the generation of unisexual diversity in whiptails. Despite this importance, long-standing confusion about their systematics has impeded understanding of which gonochoristic species have contributed to the formation of unisexual lineages. Using reduced representation genomic data, we resolve patterns of divergence and gene flow within the spotted whiptails and clarify patterns of hybrid speciation. We find evidence that biogeographically structured ecological and environmental variation has been important in morphological and genetic diversification, as well as the maintenance of species boundaries in this system. Our study elucidates how gene flow among lineages and the continuous nature of speciation can bias the practice of species delimitation and lead taxonomists operating under different frameworks to different conclusions (here we propose that a 2 species arrangement best reflects our current understanding). In doing so, this study provides conceptual and methodological insights into approaches to resolving diversification patterns and species boundaries in rapid radiations with complex histories, as well as long-standing taxonomic challenges in the field of systematic biology.

Products from stingless bees are rich reservoirs of microbial diversity, including yeasts with fermentative potential. Previously, two Saccharomyces cerevisiae strains, JP14 and IP9, were isolated from Jataí (Tetragonisca angustula) and Iraí (Nannotrigona testaceicornis) bees, respectively, aiming at mead production. Both strains presented great osmotic and sulfite tolerance, and ethanol production, although they have a high free amino nitrogen demand. Herein, their genomes were sequenced, assembled, and annotated, and the variants were compared to the S. cerevisiae S288c reference strain. The final assembly of IP9 and JP14 presented high N50 and BUSCO scores, and more than 6430 protein-coding genes. Additionally, nQuire predicted the ploidy of IP9 as diploid, but the results were not enough to determine the ploidy of JP14. The mitochondrial genomes of IP9 and JP14 presented the same gene content as S288c but the genes were rearranged and fragmented in different patterns. Meanwhile, the genes with mutations of high impact (e.g., indels, gain of stop codon) for both yeasts were enriched for transmembrane transport, electron transfer, oxidoreductase, heme binding, fructose, mannose, and glucose transport, activities related to the respiratory chain and sugar metabolism. The IP9 strain presented copy number gains in genes related to sugar transport and cell morphogenesis; in JP14, genes were enriched for disaccharide metabolism and transport, response to reactive oxygen species, and polyamine transport. On the other hand, IP9 presented copy number losses related to disaccharide, thiamine, and aldehyde metabolism, while JP14 presented depletions related to disaccharide, oligosaccharide, asparagine, and aspartate metabolism. Notably, both strains presented a killer toxin gene, annotated from the assembling of unmapped reads, representing a potential mechanism for the control of other microorganisms population in the environment. Therefore, the annotated genomes of JP14 and IP9 presented a high selective pressure for sugar and nitrogen metabolism and stress response, consistent with their isolation source and fermentative properties.

Age data are essential for estimating life history parameters and are thus critical for population assessment, management, and conservation. Traditional vertebrae-based age estimation in elasmobranchs can be costly, time intensive, of low accuracy, and is by necessity lethal. Herein, epigenetic clocks were developed for an elasmobranch, the cownose ray (Rhinoptera bonasus), using aquarium-born individuals (n = 42) with known dates of birth (age range: 7-7,878 days or 0-21 years) and two tissue types (fin clips and whole blood) that can be sampled in a relatively non-invasive manner. Enzymatically-converted restriction site-associated DNA sequencing (ECrad-seq) was used to identify CpG sites that exhibited age-correlated DNA methylation. The epigenetic clocks developed were highly accurate (mean absolute error, MAE, < 0.75 years) and precise (R2 > 0.98). Age-associated CpG sites were identified across tissues, and a multi-tissue clock was also highly accurate (MAE < 1 year) and precise (R2 = 0.97). Using the developed fin clip clock, three wild-caught individuals of unknown age but managed in aquariums for > 22 years were predicted to be 22.10-23.49 years old. Overall, the results have important implications for future epigenetic clock development and noninvasive age estimation in elasmobranchs.

Unusually for oceanic islands, the granitic Seychelles host multiple lineages of endemic amphibians. This includes an ancient (likely ca. 60 million years) radiation of eight caecilian species, most of which occur on multiple islands.These caecilians have a complicated taxonomic history and their phylogenetic inter-species relationships have been difficult to resolve. Double-digest RAD sequencing (ddRADseq) has been applied extensively to phylogeography and increasingly to phylogenetics but its utility for resolving ancient divergences is less well established. To address this, we applied ddRADseq to generate a genome-wide SNP panel for phylogenomic analyses of the Seychelles caecilians, whose phylogeny has so far not been satisfactorily resolved with traditional DNA markers. Based on 129,154 SNPs, we resolved deep and shallow splits, with strong support. Our findings demonstrate the capability of genome-wide SNPs for evolutionary inference at multiple taxonomic levels and support the recently proposed synonymy of Grandisonia Taylor, 1968 with Hypogeophis Peters, 1879. We revealed three clades of Hypogeophis (large-, medium- and short-bodied) and identify a single origin of the diminutive, stocky-bodied and pointy-snouted phenotype.

Populations of marine top predators have been sharply declining during the past decades, and one-third of chondrichthyans are currently threatened with extinction. Sustainable management measures and conservation plans of large pelagic sharks require knowledge on population genetic differentiation and demographic connectivity. Here, we present the case of the Mediterranean blue shark (Prionace glauca, L. 1758), commonly found as bycatch in longline fisheries and classified by the IUCN as critically endangered. The management of this species suffers from a scarcity of data about population structure and connectivity within the Mediterranean Sea and between this basin and the adjacent Northeast Atlantic. Here, we assessed the genetic diversity and spatial structure of blue shark from different areas of the Mediterranean Sea and the Northeast Atlantic through genome scan analyses. Pairwise genetic differentiation estimates (F ST) on 203 specimens genotyped at 14,713 ddRAD-derived SNPs revealed subtle, yet significant, genetic differences within the Mediterranean sampling locations, and between the Mediterranean Sea and the Northeast Atlantic Ocean. Genetic differentiation suggests some degree of demographic independence between the Western and Eastern Mediterranean blue shark populations. Furthermore, results show limited genetic connectivity between the Mediterranean and the Atlantic basins, supporting the hypothesis of two distinct populations of blue shark separated by the Strait of Gibraltar. Although reproductive interactions may be limited, the faint genetic signal of differentiation suggests a recent common history between these units. Therefore, Mediterranean blue sharks may function akin to a metapopulation relying upon local demographic processes and connectivity dynamics, whereby the limited contemporary gene flow replenishment from the Atlantic may interplay with currently poorly regulated commercial catches and large-scale ecosystem changes. Altogether, these results emphasise the need for revising management delineations applied to these critically endangered sharks.

The Bonin Islands, comprised of the Mukojima, Chichijima, and Hahajima Islands, are known for their isolated and distinctive habitats, hosting a diverse array of endemic flora and fauna. In these islands, adaptive radiation has played a remarkable role in speciation, particularly evident in the Callicarpa genus that is represented by three species: Callicarpa parvifolia and C. glabra exclusive to the Chichijima Islands, and Callicarpa subpubescens, distributed across the entire Bonin Islands. Notably, C. subpubescens exhibits multiple ecotypes, differing in leaf hair density, flowering time, and tree size. In this study, we aimed to investigate species and ecotype diversification patterns, estimate divergence times, and explore cryptic species within Callicarpa in the Bonin Islands using phenotypic and genetic data (double-digest restriction site-associated DNA sequencing). Genetic analysis revealed that C. parvifolia and C. glabra both formed single, distinct genetic groups. Conversely, C. subpubescens consisted of six genetic groups corresponding to different ecotypes and regions, and a hybrid group resulting from the hybridization between two of these genetic groups. Population demography analysis focusing on six Chichijima and Hahajima Islands-based species/ecotypes indicated that all species and ecotypes except one ecotype diverged simultaneously around 73-77 kya. The star-shaped neighbor-net tree also suggests the simultaneous divergence of species and ecotypes. The species and ecotypes that simultaneously diverged adapted to dry environments and understory forests, suggesting that aridification may have contributed to this process of adaptive radiation. Moreover, leaf morphology, flowering time, and genetic analyses suggested the presence of two cryptic species and one hybrid species within C. subpubescens.

Genetic drift, gene flow, and natural selection commonly influence population genetic diversity. In populations of self-compatible hermaphrodites, the mating system (e.g., self-fertilization) further reduces individual heterozygosity. Furthermore, selfing, as a form of inbreeding, significantly impacts genetic drift by reducing effective population size (N e). This can potentially accelerate genetic drift, particularly in small populations where self-fertilization is likely during founder events. To investigate the roles of genetic drift and contemporary mating system in populations of the freshwater snail Lymnaea stagnalis, we examined their effective population sizes (N e) and Tajima's D values, which reflect genetic drift over extended time periods, as well as estimates of within-population selfing rates and pairwise relatedness reflecting contemporary mating system. We used 4054 SNP markers obtained using restriction site associated DNA (RAD) sequencing from individuals in five snail populations originating from geographically closely located ponds. We found strong population genetic structure and differences in genetic diversity among populations. Covariation between genetic diversity and N e estimates and Tajima's D values suggested drift being an important determinant of genetic diversity and structure in these populations. However, this effect was independent of the contemporary mating system, as indicated by the similarity of selfing rates and relatedness estimates among populations. Thus, founder events (possibly including historical inbreeding) and/or drift due to small sizes of L. stagnalis populations are likely to explain their genetic structure and limit within-population genetic diversity.

The Andes mountains of western South America are a globally important biodiversity hotspot, yet there is a paucity of resolved phylogenies for plant clades from this region. Filling an important gap in our understanding of the World's richest flora, we present the first phylogeny of Freziera (Pentaphylacaceae), an Andean-centered, cloud forest radiation. Our dataset was obtained via hybrid-enriched target sequence capture of Angiosperms353 universal loci for 50 of the ca. 75 spp., obtained almost entirely from herbarium specimens. We identify high phylogenomic complexity in Freziera, including the presence of data artifacts. Via by-eye observation of gene trees, detailed examination of warnings from recently improved assembly pipelines, and gene tree filtering, we identified that artifactual orthologs (i.e., the presence of only one copy of a multicopy gene due to differential assembly) were an important source of gene tree heterogeneity that had a negative impact on phylogenetic inference and support. These artifactual orthologs may be common in plant phylogenomic datasets, where multiple instances of genome duplication are common. After accounting for artifactual orthologs as source of gene tree error, we identified a significant, but nonspecific signal of introgression using Patterson's D and f4 statistics. Despite phylogenomic complexity, we were able to resolve Freziera into 9 well-supported subclades whose evolution has been shaped by multiple evolutionary processes, including incomplete lineage sorting, historical gene flow, and gene duplication. Our results highlight the complexities of plant phylogenomics, which are heightened in Andean radiations, and show the impact of filtering data processing artifacts and standard filtering approaches on phylogenetic inference.

Advancements in genome assembly and sequencing technology have made whole genome sequence (WGS) data and reference genomes accessible to study polyploid species. Compared to popular reduced-representation sequencing approaches, the genome-wide coverage and greater marker density provided by WGS data can greatly improve our understanding of polyploid species and polyploid biology. However, biological features that make polyploid species interesting also pose challenges in read mapping, variant identification, and genotype estimation. Accounting for characteristics in variant calling like allelic dosage uncertainty, homology between subgenomes, and variance in chromosome inheritance mode can reduce errors. Here, I discuss the challenges of variant calling in polyploid WGS data and discuss where potential solutions can be integrated into a standard variant calling pipeline.

The impact of climate change on populations will be contingent upon their contemporary adaptive evolution. In this study, we investigated the contemporary evolution of 4 populations of the cold-water kelp Laminaria digitata by analyzing their spatial and temporal genomic variations using ddRAD-sequencing. These populations were sampled from the center to the southern margin of its north-eastern Atlantic distribution at 2 time points, spanning at least 2 generations. Through genome scans for local adaptation at a single time point, we identified candidate loci that showed clinal variation correlated with changes in sea surface temperature (SST) along latitudinal gradients. This finding suggests that SST may drive the adaptive response of these kelp populations, although factors such as species' demographic history should also be considered. Additionally, we performed a simulation approach to distinguish the effect of selection from genetic drift in allele frequency changes over time. This enabled the detection of loci in the southernmost population that exhibited temporal differentiation beyond what would be expected from genetic drift alone: these are candidate loci which could have evolved under selection over time. In contrast, we did not detect any outlier locus based on temporal differentiation in the population from the North Sea, which also displayed low and decreasing levels of genetic diversity. The diverse evolutionary scenarios observed among populations can be attributed to variations in the prevalence of selection relative to genetic drift across different environments. Therefore, our study highlights the potential of temporal genomics to offer valuable insights into the contemporary evolution of marine foundation species facing climate change.

Selective breeding for production traits has yielded relatively rapid successes with high-fecundity aquaculture species. Discovering the genetic changes associated with selection is an important goal for understanding adaptation and can also facilitate better predictions about the likely fitness of selected strains if they escape aquaculture farms. Here, we hypothesize domestication as a genetic change induced by inadvertent selection in culture. Our premise is that standardized culture protocols generate parallel domestication effects across independent strains. Using eastern oyster as a model and a newly developed 600K SNP array, this study tested for parallel domestication effects in multiple independent selection lines compared with their progenitor wild populations. A single contrast was made between pooled selected strains (1-17 generations in culture) and all wild progenitor samples combined. Population structure analysis indicated rank order levels of differentiation as [wild - wild] < [wild - cultured] < [cultured - cultured]. A genome scan for parallel adaptation to the captive environment applied two methodologically distinct outlier tests to the wild versus selected strain contrast and identified a total of 1174 candidate SNPs. Contrasting wild versus selected strains revealed the early evolutionary consequences of domestication in terms of genomic differentiation, standing genetic diversity, effective population size, relatedness, runs of homozygosity profiles, and genome-wide linkage disequilibrium patterns. Random Forest was used to identify 37 outlier SNPs that had the greatest discriminatory power between bulked wild and selected oysters. The outlier SNPs were in genes enriched for cytoskeletal functions, hinting at possible traits under inadvertent selection during larval culture or pediveliger setting at high density. This study documents rapid genomic changes stemming from hatchery-based cultivation of eastern oysters, identifies candidate loci responding to domestication in parallel among independent aquaculture strains, and provides potentially useful genomic resources for monitoring interbreeding between farm and wild oysters.

Assessing direct fitness effects of individual genetic diversity is challenging due to the intensive and long-term data needed to quantify survival and reproduction in the wild. But resolving these effects is necessary to determine how inbreeding and outbreeding influence eco-evolutionary processes. We used 8 years of capture-recapture data and single nucleotide polymorphism genotypes for 1906 individuals to test for effects of individual heterozygosity on stage-specific survival probabilities in the salamander Gyrinophilus porphyriticus. The life cycle of G. porphyriticus includes an aquatic larval stage followed by metamorphosis into a semi-aquatic adult stage. In our study populations, the larval stage lasts 6-10 years, metamorphosis takes several months, and lifespan can reach 20 years. Previous studies showed that metamorphosis is a sensitive life stage, leading us to predict that fitness effects of individual heterozygosity would occur during metamorphosis. Consistent with this prediction, monthly probability of survival during metamorphosis declined with multi-locus heterozygosity (MLH), from 0.38 at the lowest MLH (0.10) to 0.06 at the highest MLH (0.38), a reduction of 84%. Body condition of larvae also declined significantly with increasing MLH. These relationships were consistent in the three study streams. With evidence of localised inbreeding within streams, these results suggest that outbreeding disrupts adaptations in pre-metamorphic and metamorphic individuals to environmental gradients along streams, adding to evidence that headwater streams are hotspots of microgeographic adaptation. Our results also underscore the importance of incorporating life history in analyses of the fitness effects of individual genetic diversity and suggest that metamorphosis and similar discrete life stage transitions may be critical periods of viability selection.

Patterns of genetic variation reflect interactions among microevolutionary forces that vary in strength with changing demography. Here, patterns of variation within and among samples of the mouthbrooding gafftopsail catfish (Bagre marinus, Family Ariidae) captured in the U.S. Atlantic and throughout the Gulf of Mexico were analyzed using genomics to generate neutral and non-neutral SNP data sets. Because genomic resources are lacking for ariids, linkage disequilibrium network analysis was used to examine patterns of putatively adaptive variation. Finally, historical demographic parameters were estimated from site frequency spectra. The results show four differentiated groups, corresponding to the (1) U.S. Atlantic, and the (2) northeastern, (3) northwestern, and (4) southern Gulf of Mexico. The non-neutral data presented two contrasting signals of structure, one due to increases in diversity moving west to east and north to south, and another to increased heterozygosity in the Atlantic. Demographic analysis suggested that recently reduced long-term effective population size in the Atlantic is likely an important driver of patterns of genetic variation and is consistent with a known reduction in population size potentially due to an epizootic. Overall, patterns of genetic variation resemble that of other fishes that use the same estuarine habitats as nurseries, regardless of the presence/absence of a larval phase, supporting the idea that adult/juvenile behavior and habitat are important predictors of contemporary patterns of genetic structure.

Research conducted during the past two decades has demonstrated that biological invasions are excellent models of rapid evolution. Even so, characteristics of invasive populations such as a short time for recombination to assemble optimal combinations of alleles may occasionally limit adaptation to new environments. Here, we investigated such genetic constraints to adaptation in the invasive brown anole (Anolis sagrei)-a tropical ectotherm that was introduced to the southeastern United States, a region with a much colder climate than in its native Caribbean range. We examined thermal physiology for 30 invasive populations and tested for a climatic cline in cold tolerance. Also, we used genomics to identify mechanisms that may limit adaptation. We found no support for a climatic cline, indicating that thermal tolerance did not shift adaptively. Concomitantly, population genomic results were consistent with the occurrence of recombination cold spots that comprise more than half of the genome and maintain long-range associations among alleles in invasive populations. These genomic regions overlap with both candidate thermal tolerance loci that we identified using a standard genome-wide association test. Moreover, we found that recombination cold spots do not have a large contribution to population differentiation in the invasive range, contrary to observations in the native range. We suggest that limited recombination is constraining the contribution of large swaths of the genome to adaptation in invasive brown anoles. Our study provides an example of evolutionary stasis during invasion and highlights the possibility that reduced recombination occasionally slows down adaptation in invasive populations.

Alfalfa, the most economically important forage legume worldwide, features modest genetic progress due to long selection cycles and the extent of the non-additive genetic variance associated with its autotetraploid genome.

To improve the efficiency of genomic selection in alfalfa, we explored the effects of genome parametrization (as tetraploid and diploid dosages, plus allele ratios) and SNP marker subsetting (all available SNPs, only genic regions, and only non-genic regions) on genomic regressions, together with various levels of filtering on reading depth and missing rates. We used genotyping by sequencing-generated data and focused on traits of different genetic complexity, i.e., dry biomass yield in moisture-favorable (FE) and drought stress (SE) environments, leaf size, and the onset of flowering, which were assessed in 143 genotyped plants from a genetically broad European reference population and their phenotyped half-sib progenies.

On average, the allele ratio improved the predictive ability compared with other genome parametrizations (+7.9% vs. tetraploid dosage, +12.6% vs. diploid dosage), while using all the SNPs offered an advantage compared with any specific SNP subsetting (+3.7% vs. genic regions, +7.6% vs. non-genic regions). However, when focusing on specific traits, different combinations of genome parametrization and subsetting achieved better performances. We also released Legpipe2, an SNP calling pipeline tailored for reduced representation (GBS, RAD) in medium-sized genotyping experiments.

The host genetic makeup plays a significant role in causing the within-breed variation among individuals after vaccination. The present study was undertaken to elucidate the genetic basis of differential immune response between high and low responder Landlly (Landrace X Ghurrah) piglets vis-à-vis CSF vaccination. For the purpose, E2 antibody response against CSF vaccination was estimated in sampled animals on the day of vaccination and 21-day post-vaccination as a measure of humoral immune response. Double-digestion restriction associated DNA (ddRAD) sequencing was undertaken on 96 randomly chosen Landlly piglets using Illumina HiSeq platform. SNP markers were called using standard methodology. Genome-wide association study (GWAS) was undertaken in PLINK program to identify the informative SNP markers significantly associated with differential immune response. The results revealed significant SNPs associated with E2 antibody response against CSF vaccination. The genome-wide informative SNPs for the humoral immune response against CSF vaccination were located on SSC10, SSC17, SSC9, SSC2, SSC3 and SSC6. The overlapping and flanking genes (500Kb upstream and downstream) of significant SNPs were CYB5R1, PCMTD2, WT1, IL9R, CD101, TMEM64, TLR6, PIGG, ADIPOR1, PRSS37, EIF3M, and DNAJC24. Functional enrichment and annotation analysis were undertaken for these genes in order to gain maximum insights into the association of these genes with immune system functionality in pigs. The genetic makeup was associated with differential immune response against CSF vaccination in Landlly piglets while the identified informative SNPs may be used as suitable markers for determining variation in host immune response against CSF vaccination in pigs.

Masting (synchronous and interannually variable seed production) is frequently called a reproductive strategy; yet it is unclear whether the reproductive behaviour of individuals has a heritable component. To address this, we used 22 years of annual fruit production data from 110 Sorbus aucuparia L. trees to examine the contributions of genetic factors to the reproductive phenotype of individuals, while controlling for environmental variation. Trees sharing close genetic relationships and experiencing similar habitat conditions exhibited similar levels of reproductive synchrony. Trees of comparable sizes displayed similar levels of year-to-year variation in fruiting, with relatedness contributing to this variation. External factors, such as shading, influenced the time intervals between years with abundant fruit production. The effects of genetic relatedness on the synchrony of reproduction among trees and on interannual variation provide long-awaited evidence that the masting phenotype is heritable, and can respond to natural selection.

Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. However, more training, appropriate use of novel genomic methods and communication with managers are needed. Here, we review practical guidance to improve applied conservation genomics. We share insights aimed at ensuring effectiveness of conservation actions around three themes: (1) improving pedagogy and training in conservation genomics including for online global audiences, (2) conducting rigorous population genomic analyses properly considering theory, marker types and data interpretation and (3) facilitating communication and collaboration between managers and researchers. We aim to update students and professionals and expand their conservation toolkit with genomic principles and recent approaches for conserving and managing biodiversity. The biodiversity crisis is a global problem and, as such, requires international involvement, training, collaboration and frequent reviews of the literature and workshops as we do here.

The Yellowfin tuna (Thunnus albacares) is a large tuna exploited by major fisheries in tropical and subtropical waters of all oceans except the Mediterranean Sea. Genomic studies of population structure, adaptive variation or of the genetic basis of phenotypic traits are needed to inform fisheries management but are currently limited by the lack of a reference genome for this species. Here we report a draft genome assembly and a linkage map for use in genomic studies of T. albacares.

Illumina and PacBio SMRT sequencing were used in combination to generate a hybrid assembly that comprises 743,073,847 base pairs contained in 2,661 scaffolds. The assembly has a N50 of 351,587 and complete and partial BUSCO scores of 86.47% and 3.63%, respectively. Double-digest restriction associated DNA (ddRAD) was used to genotype the 2 parents and 164 of their F1 offspring resulting from a controlled breeding cross, retaining 19,469 biallelic single nucleotide polymorphism (SNP) loci. The SNP loci were used to construct a linkage map that features 24 linkage groups that represent the 24 chromosomes of yellowfin tuna. The male and female maps span 1,243.8 cM and 1,222.9 cM, respectively. The map was used to anchor the assembly in 24 super-scaffolds that contain 79% of the yellowfin tuna genome. Gene prediction identified 46,992 putative genes 20,203 of which could be annotated via gene ontology.

The draft reference will be valuable to interpret studies of genome wide variation in T. albacares and other Scombroid species.

Genome assembly can be challenging for species that are characterized by high amounts of polymorphism, heterozygosity, and large effective population sizes. High levels of heterozygosity can result in genome mis-assemblies and a larger than expected genome size due to the haplotig versions of a single locus being assembled as separate loci. Here, we describe the first chromosome-level genome for the eastern oyster, Crassostrea virginica. Publicly released and annotated in 2017, the assembly has a scaffold N50 of 54 mb and is over 97.3% complete based on BUSCO analysis. The genome assembly for the eastern oyster is a critical resource for foundational research into molluscan adaptation to a changing environment and for selective breeding for the aquaculture industry. Subsequent resequencing data suggested the presence of haplotigs in the original assembly, and we developed a post hoc method to break up chimeric contigs and mask haplotigs in published heterozygous genomes and evaluated improvements to the accuracy of downstream analysis. Masking haplotigs had a large impact on SNP discovery and estimates of nucleotide diversity and had more subtle and nuanced effects on estimates of heterozygosity, population structure analysis, and outlier detection. We show that haplotig masking can be a powerful tool for improving genomic inference, and we present an open, reproducible resource for the masking of haplotigs in any published genome.