Experimental validation of in silico predicted RAD locus frequencies using genomic resources and short read data from a model marine mammal

Background Restriction site-associated DNA sequencing (RADseq) has revolutionized the study of wild organisms by allowing cost-effective genotyping of thousands of loci. However, for species lacking reference genomes, it can be challenging to select the restriction enzyme that offers the best balance between the number of obtained RAD loci and depth of coverage, which is crucial for a successful outcome. To address this issue, PredRAD was recently developed, which uses probabilistic models to predict restriction site frequencies from a transcriptome assembly or other sequence resource based on either GC content or mono-, di- or trinucleotide composition. This program generates predictions that are broadly consistent with estimates of the true number of restriction sites obtained through in silico digestion of available reference genome assemblies. However, in practice the actual number of loci obtained could potentially differ as incomplete enzymatic digestion or patchy sequence coverage across the genome might lead to some loci not being represented in a RAD dataset, while erroneous assembly could potentially inflate the number of loci. To investigate this, we used genome and transcriptome assemblies together with RADseq data from the Antarctic fur seal (Arctocephalus gazella) to compare PredRAD predictions with empirical estimates of the number of loci obtained via in silico digestion and from de novo assemblies. Results PredRAD yielded consistently higher predicted numbers of restriction sites for the transcriptome assembly relative to the genome assembly. The trinucleotide and dinucleotide models also predicted higher frequencies than the mononucleotide or GC content models. Overall, the dinucleotide and trinucleotide models applied to the transcriptome and the genome assemblies respectively generated predictions that were closest to the number of restriction sites estimated by in silico digestion. Furthermore, the number of de novo assembled RAD loci mapping to restriction sites was similar to the expectation based on in silico digestion. Conclusions Our study reveals generally high concordance between PredRAD predictions and empirical estimates of the number of RAD loci. This further supports the utility of PredRAD, while also suggesting that it may be feasible to sequence and assemble the majority of RAD loci present in an organism’s genome

Detailed insights into pan-European population structure and inbreeding in wild and hatchery Pacific oysters (Crassostrea gigas) revealed by genome-wide SNP data.

Cultivated bivalves are important not only because of their economic value, but also due to their impacts on natural ecosystems. The Pacific oyster (Crassostrea gigas) is the world's most heavily cultivated shellfish species and has been introduced to all continents except Antarctica for aquaculture. We therefore used a medium-density single nucleotide polymorphism (SNP) array to investigate the genetic structure of this species in Europe, where it was introduced during the 1960s and has since become a prolific invader of coastal ecosystems across the continent. We analyzed 21,499 polymorphic SNPs in 232 individuals from 23 localities spanning a latitudinal cline from Portugal to Norway and including the source populations of Japan and Canada. We confirmed the results of previous studies by finding clear support for a southern and a northern group, with the former being indistinguishable from the source populations indicating the absence of a pronounced founder effect. We furthermore conducted a large-scale comparison of oysters sampled from the wild and from hatcheries to reveal substantial genetic differences including significantly higher levels of inbreeding in some but not all of the sampled hatchery cohorts. These findings were confirmed by a smaller but representative SNP dataset generated using restriction site-associated DNA sequencing. We therefore conclude that genomic approaches can generate increasingly detailed insights into the genetics of wild and hatchery produced Pacific oysters

Genome‐wide insights into introgression and its consequences for genome‐wide heterozygosity in the Mytilus species complex across Europe

The three mussel species comprising the Mytilus complex are widespread across Europe and readily hybridize when they occur in sympatry, resulting in a mosaic of populations with varying genomic backgrounds. Two of these species, M. edulis and M. galloprovincialis, are extensively cultivated across Europe, with annual production exceeding 230,000 tonnes. The third species, M. trossulus, is considered commercially damaging as hybridization with this species results in weaker shells and poor meat quality. We therefore used restriction site associated DNA sequencing to generate high‐resolution insights into the structure of the Mytilus complex across Europe and to resolve patterns of introgression. Inferred species distributions were concordant with the results of previous studies based on smaller numbers of genetic markers, with M. edulis and M. galloprovincialis predominating in northern and southern Europe respectively, while introgression between these species was most pronounced in northern France and the Shetland Islands. We also detected traces of M. trossulus ancestry in several northern European populations, especially around the Baltic and in northern Scotland. Finally, genome‐wide heterozygosity, whether quantified at the population or individual level, was lowest in M. edulis, intermediate in M. galloprovincialis, and highest in M. trossulus, while introgression was positively associated with heterozygosity in M. edulis but negatively associated with heterozygosity in M. galloprovincialis. Our study will help to inform mussel aquaculture by providing baseline information on the genomic backgrounds of different Mytilus populations across Europe and by elucidating the effects of introgression on genome‐wide heterozygosity, which is known to influence commercially important traits such as growth, viability, and fecundity in mussels

Population Genetic Structure is Unrelated to Shell Shape, Thickness and Organic Content in European Populations of the Soft-Shell Clam Mya Arenaria.

The soft-shell clam Mya arenaria is one of the most ancient invaders of European coasts and is present in many coastal ecosystems, yet little is known about its genetic structure in Europe. We collected 266 samples spanning a latitudinal cline from the Mediterranean to the North Sea and genotyped them at 12 microsatellite loci. In parallel, geometric morphometric analysis of shell outlines was used to test for associations between shell shape, latitude and genotype, and for a selection of shells we measured the thickness and organic content of the granular prismatic (PR), the crossed-lamellar (CL) and the complex crossed-lamellar (CCL) layers. Strong population structure was detected, with Bayesian cluster analysis identifying four groups located in the Mediterranean, Celtic Sea, along the continental coast of the North Sea and in Scotland. Multivariate analysis of shell shape uncovered a significant effect of collection site but no associations with any other variables. Shell thickness did not vary significantly with either latitude or genotype, although PR thickness and calcification were positively associated with latitude, while CCL thickness showed a negative association. Our study provides new insights into the population structure of this species and sheds light on factors influencing shell shape, thickness and microstructure

Population Genetic Structure Is Unrelated to Shell Shape, Thickness and Organic Content in European Populations of the Soft-Shell Clam Mya Arenaria

The soft-shell clam Mya arenaria is one of the most ancient invaders of European coasts and is present in many coastal ecosystems, yet little is known about its genetic structure in Europe. We collected 266 samples spanning a latitudinal cline from the Mediterranean to the North Sea and genotyped them at 12 microsatellite loci. In parallel, geometric morphometric analysis of shell outlines was used to test for associations between shell shape, latitude and genotype, and for a selection of shells we measured the thickness and organic content of the granular prismatic (PR), the crossed-lamellar (CL) and the complex crossed-lamellar (CCL) layers. Strong population structure was detected, with Bayesian cluster analysis identifying four groups located in the Mediterranean, Celtic Sea, along the continental coast of the North Sea and in Scotland. Multivariate analysis of shell shape uncovered a significant effect of collection site but no associations with any other variables. Shell thickness did not vary significantly with either latitude or genotype, although PR thickness and calcification were positively associated with latitude, while CCL thickness showed a negative association. Our study provides new insights into the population structure of this species and sheds light on factors influencing shell shape, thickness and microstructure

Population connectivity predicts vulnerability to white-nose syndrome in the Chilean myotis (Myotis chiloensis) - A genomics approach

Despite its peculiar distribution, the biology of the southernmost bat species in the world, the Chilean myotis (Myotis chiloensis), has garnered little attention so far. The species has a north-south distribution of c. 2800 km, mostly on the eastern side of the Andes mountain range. Use of extended torpor occurs in the southernmost portion of the range, putting the species at risk of bat white-nose syndrome, a fungal disease responsible for massive population declines in North American bats. Here, we examined how geographic distance and topology would be reflected in the population structure of M. chiloensis along the majority of its range using a double digestion RAD-seq method. We sampled 66 individuals across the species range and discovered pronounced isolation-by-distance. Furthermore, and surprisingly, we found higher degrees of heterozygosity in the southernmost populations compared to the north. A coalescence analysis revealed that our populations may still not have reached secondary contact after the Last Glacial Maximum. As for the potential spread of pathogens, such as the fungus causing WNS, connectivity among populations was noticeably low, especially between the southern hibernatory populations in the Magallanes and Tierra del Fuego, and more northerly populations. This suggests the probability of geographic spread of the disease from the north through bat-to-bat contact to susceptible populations is low. The study presents a rare case of defined population structure in a bat species and warrants further research on the underlying factors contributing to this. See the graphical abstract here.Peer reviewe

RAD sequencing resolves fine-scale population structure in a benthic invertebrate: implications for understanding phenotypic plasticity

The field of molecular ecology is transitioning from the use of small panels of classical genetic markers such as microsatellites to much larger panels of single nucleotide polymorphisms (SNPs) generated by approaches like RAD sequencing. However, few empirical studies have directly compared the ability of these methods to resolve population structure. This could have implications for understanding phenotypic plasticity, as many previous studies of natural populations may have lacked the power to detect genetic differences, especially over micro-geographic scales. We therefore compared the ability of microsatellites and RAD sequencing to resolve fine-scale population structure in a commercially important benthic invertebrate by genotyping great scallops (Pecten maximus) from nine populations around Northern Ireland at 13 microsatellites and 10 539 SNPs. The shells were then subjected to morphometric and colour analysis in order to compare patterns of phenotypic and genetic variation. We found that RAD sequencing was superior at resolving population structure, yielding higher Fst values and support for two distinct genetic clusters, whereas only one cluster could be detected in a Bayesian analysis of the microsatellite dataset. Furthermore, appreciable phenotypic variation was observed in size-independent shell shape and coloration, including among localities that could not be distinguished from one another genetically, providing support for the notion that these traits are phenotypically plastic. Taken together, our results suggest that RAD sequencing is a powerful approach for studying population structure and phenotypic plasticity in natural populations

Population Connectivity Predicts Vulnerability to White-Nose Syndrome in the Chilean Myotis (Myotis chiloensis)-A Genomics Approach

Despite its peculiar distribution, the biology of the southernmost bat species in the world, the Chilean myotis (Myotis chiloensis), has garnered little attention so far. The species has a north-south distribution of c. 2800 km, mostly on the eastern side of the Andes mountain range. Use of extended torpor occurs in the southernmost portion of the range, putting the species at risk of bat white-nose syndrome, a fungal disease responsible for massive population declines in North American bats. Here, we examined how geographic distance and topology would be reflected in the population structure of M. chiloensis along the majority of its range using a double digestion RAD-seq method. We sampled 66 individuals across the species range and discovered pronounced isolation-by-distance. Furthermore, and surprisingly, we found higher degrees of heterozygosity in the southernmost populations compared to the north. A coalescence analysis revealed that our populations may still not have reached secondary contact after the Last Glacial Maximum. As for the potential spread of pathogens, such as the fungus causing WNS, connectivity among populations was noticeably low, especially between the southern hibernatory populations in the Magallanes and Tierra del Fuego, and more northerly populations. This suggests the probability of geographic spread of the disease from the north through bat-to-bat contact to susceptible populations is low. The study presents a rare case of defined population structure in a bat species and warrants further research on the underlying factors contributing to this. See the graphical abstract here

Genomic and fitness consequences of a near-extinction event in the northern elephant seal

Understanding the genetic and fitness consequences of anthropogenic bottlenecks is crucial for biodiversity conservation. However, studies of bottlenecked populations combining genomic approaches with fitness data are rare. Theory predicts that severe bottlenecks deplete genetic diversity, exacerbate inbreeding depression and decrease population viability. However, actual outcomes are complex and depend on how a species' unique demography affects its genetic load. We used population genetic and veterinary pathology data, demographic modelling, whole-genome resequencing and forward genetic simulations to investigate the genomic and fitness consequences of a near-extinction event in the northern elephant seal. We found no evidence of inbreeding depression within the contemporary population for key fitness components, including body mass, blubber thickness and susceptibility to parasites and disease. However, we detected a genomic signature of a recent extreme bottleneck (effective population size = 6; 95% confidence interval = 5.0-7.5) that will have purged much of the genetic load, potentially leading to the lack of observed inbreeding depression in our study. Our results further suggest that deleterious genetic variation strongly impacted the post-bottleneck population dynamics of the northern elephant seal. Our study provides comprehensive empirical insights into the intricate dynamics underlying species-specific responses to anthropogenic bottlenecks