Utility of parentage-based tagging for monitoring Coho salmon (Oncorhynchus kisutch) in the interior Columbia River basin.

By the 1980s, after decades of declining numbers in the mid-1900s, Coho salmon (Oncorhynchus kisutch) were considered extirpated from the interior Columbia River. In the mid-1990s, the Confederated Tribes of the Umatilla Indian Reservation, the Confederated Tribes and Bands of the Yakama Nation, and the Nez Perce Tribe began successful reintroduction programs of Coho salmon upstream of Bonneville Dam, but which were initially sourced from lower Columbia River hatcheries. Here we present the first Coho salmon parentage-based tagging (PBT) baseline from seven hatchery programs located in the interior Columbia River basin, and two sites at or downstream of Bonneville Dam, composed of over 32,000 broodstock samples. Analyses of baseline collections revealed that genetic structure followed a temporal pattern based on 3-year broodlines rather than geographic location or stocking history. Across hatchery programs, similar levels of genetic diversity was present. The PBT baseline provided multiple direct applications such as identification of origin for Coho salmon collected in a mixed stock at Priest Rapids Dam and the detection of the proportion and distribution of hatchery-origin fish on the spawning grounds in the Methow River basin. The PBT baseline for Coho salmon is freely available for use and can be downloaded from FishGen.net.

Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure.

The distribution of ecotypic variation in natural populations is influenced by neutral and adaptive evolutionary forces that are challenging to disentangle. This study provides a high-resolution portrait of genomic variation in Chinook salmon (Oncorhynchus tshawytscha) with emphasis on a region of major effect for ecotypic variation in migration timing. With a filtered data set of ~13 million single nucleotide polymorphisms (SNPs) from low-coverage whole genome resequencing of 53 populations (3566 barcoded individuals), we contrasted patterns of genomic structure within and among major lineages and examined the extent of a selective sweep at a major effect region underlying migration timing (GREB1L/ROCK1). Neutral variation provided support for fine-scale structure of populations, while allele frequency variation in GREB1L/ROCK1 was highly correlated with mean return timing for early and late migrating populations within each of the lineages (r2  = .58-.95; p < .001). However, the extent of selection within the genomic region controlling migration timing was much narrower in one lineage (interior stream-type) compared to the other two major lineages, which corresponded to the breadth of phenotypic variation in migration timing observed among lineages. Evidence of a duplicated block within GREB1L/ROCK1 may be responsible for reduced recombination in this portion of the genome and contributes to phenotypic variation within and across lineages. Lastly, SNP positions across GREB1L/ROCK1 were assessed for their utility in discriminating migration timing among lineages, and we recommend multiple markers nearest the duplication to provide highest accuracy in conservation applications such as those that aim to protect early migrating Chinook salmon. These results highlight the need to investigate variation throughout the genome and the effects of structural variants on ecologically relevant phenotypic variation in natural species.

Going the distance to test local adaptation in Coho salmon.

The mechanisms underlying local adaptation, where populations evolve traits that confer advantages to the local environment, is a central topic for understanding evolution in natural systems. Conservation goals for species at risk often include defining population boundaries by identifying gene diversity, genetic differentiation, and adaptation to local environments. In this issue of Molecular Ecology, Rougemont et al. (2022) combine genome-wide SNP data with an extensive set of landscape variables to study the genomic mechanisms of local adaptation in the entire North American range of Coho salmon (Oncorhynchus kisutch), representing one of the largest studies of its kind. Migration distance, defined as the distance adult Coho salmon migrate from the ocean to their freshwater spawning ground, was found to be the primary factor driving local adaptation in this species. With climatic changes altering flow regimes and therefore the success of Coho salmon to return to spawning grounds, understanding environmental drivers and the genomic basis for migration is essential in the conservation of anadromous salmonids.

Influence of environmental conditions at spawning sites and migration routes on adaptive variation and population connectivity in Chinook salmon.

Many species that undergo long breeding migrations, such as anadromous fishes, face highly heterogeneous environments along their migration corridors and at their spawning sites. These environmental challenges encountered at different life stages may act as strong selective pressures and drive local adaptation. However, the relative influence of environmental conditions along the migration corridor compared with the conditions at spawning sites on driving selection is still unknown. In this study, we performed genome-environment associations (GEA) to understand the relationship between landscape and environmental conditions driving selection in seven populations of the anadromous Chinook salmon (Oncorhynchus tshawytscha)-a species of important economic, social, cultural, and ecological value-in the Columbia River basin. We extracted environmental variables for the shared migration corridors and at distinct spawning sites for each population, and used a Pool-seq approach to perform whole genome resequencing. Bayesian and univariate GEA tests with migration-specific and spawning site-specific environmental variables indicated many more candidate SNPs associated with environmental conditions at the migration corridor compared with spawning sites. Specifically, temperature, precipitation, terrain roughness, and elevation variables of the migration corridor were the most significant drivers of environmental selection. Additional analyses of neutral loci revealed two distinct clusters representing populations from different geographic regions of the drainage that also exhibit differences in adult migration timing (summer vs. fall). Tests for genomic regions under selection revealed a strong peak on chromosome 28, corresponding to the GREB1L/ROCK1 region that has been identified previously in salmonids as a region associated with adult migration timing. Our results show that environmental variation experienced throughout migration corridors imposed a greater selective pressure on Chinook salmon than environmental conditions at spawning sites.

The role of introgression and ecotypic parallelism in delineating intraspecific conservation units.

Parallel evolution can occur through selection on novel mutations, standing genetic variation or adaptive introgression. Uncovering parallelism and introgressed populations can complicate management of threatened species as parallelism may have influenced conservation unit designations and admixed populations are not generally considered under legislations. We examined high coverage whole-genome sequences of 30 caribou (Rangifer tarandus) from across North America and Greenland, representing divergent intraspecific lineages, to investigate parallelism and levels of introgression contributing to the formation of ecotypes. Caribou are split into four subspecies and 11 extant conservation units, known as designatable units (DUs), in Canada. Using genomes from all four subspecies and six DUs, we undertake demographic reconstruction and confirm two previously inferred instances of parallel evolution in the woodland subspecies and uncover an additional instance of parallelism of the eastern migratory ecotype. Detailed investigations reveal introgression in the woodland subspecies, with introgressed regions found spread throughout the genomes encompassing both neutral and functional sites. Our investigations using whole genomes highlight the difficulties in unequivocally demonstrating parallelism through adaptive introgression in nonmodel species with complex demographic histories, with standing variation and introgression both potentially involved. Additionally, the impact of parallelism and introgression on conservation policy for management units needs to be considered in general, and the caribou designations will need amending in light of our results. Uncovering and decoupling parallelism and differential patterns of introgression will become prevalent with the availability of comprehensive genomic data from nonmodel species, and we highlight the need to incorporate this into conservation unit designations.

The Caribou (Rangifer tarandus) Genome.

Rangifer tarandus, known as caribou or reindeer, is a widespread circumpolar species which presents significant variability in their morphology, ecology, and genetics. A genome was sequenced from a male boreal caribou (R. t. caribou) from Manitoba, Canada. Both paired end and Chicago libraries were constructed and sequenced on Illumina platforms. The final assembly consists of approximately 2.205 Gb, and has a scaffold N50 of 11.765 Mb. BUSCO (Benchmarking Universal Single-Copy Orthologs) reconstructed 3820 (93.1%) complete mammalian genes, and genome annotation identified the locations of 33,177 protein-coding genes. An alignment to the bovine genome was carried out, indicating sequence coverage on all bovine chromosomes. A high-quality reference genome will be invaluable for evolutionary research and for conservation efforts for the species. Further information about the genome, including a FASTA file of the assembly and the annotation files, is available on our caribou genome website. Raw sequence data is available at the National Centre for Biotechnology Information (NCBI), under the BioProject accession number PRJNA549927.

Parallel evolution of site-specific changes in divergent caribou lineages.

The parallel evolution of phenotypes or traits within or between species provides important insight into the basic mechanisms of evolution. Genetic and genomic advances have allowed investigations into the genetic underpinnings of parallel evolution and the independent evolution of similar traits in sympatric species. Parallel evolution may best be exemplified among species where multiple genetic lineages, descended from a common ancestor, colonized analogous environmental niches, and converged on a genotypic or phenotypic trait. Modern North American caribou (Rangifer tarandus) originated from three ancestral sources separated during the Last Glacial Maximum (LGM): the Beringian-Eurasian lineage (BEL), the North American lineage (NAL), and the High Arctic lineage (HAL). Historical introgression between the NAL and the BEL has been found throughout Ontario and eastern Manitoba. In this study, we first characterized the functional differentiation in the cytochrome-b (cytB) gene by identifying nonsynonymous changes. Second, the caribou lineages were used as a direct means to assess site-specific parallel changes among lineages. There was greater functional diversity within the NAL despite the BEL having greater neutral diversity. The patterns of amino acid substitutions occurring within different lineages supported the parallel evolution of cytB amino acid substitutions suggesting different selective pressures among lineages. This study highlights the independent evolution of identical amino acid substitutions within a wide-ranging mammal species that have diversified from different ancestral haplogroups and where ecological niches can invoke parallel evolution.

DNA analysis of traded shark fins and mobulid gill plates reveals a high proportion of species of conservation concern.

Continuously increasing demand for plant and animal products causes unsustainable depletion of biological resources. It is estimated that one-quarter of sharks and rays are threatened worldwide and although the global fin trade is widely recognized as a major driver, demand for meat, liver oil, and gill plates also represents a significant threat. This study used DNA barcoding and 16 S rRNA sequencing as a method to identify shark and ray species from dried fins and gill plates, obtained in Canada, China, and Sri Lanka. 129 fins and gill plates were analysed and searches on BOLD produced matches to 20 species of sharks and five species of rays or - in two cases - to a species pair. Twelve of the species found are listed or have been approved for listing in 2017 in the appendices of the Convention on International Trade in Endangered Species of Fauna and Flora (CITES), including the whale shark (Rhincodon typus), which was surprisingly found among both shark fin and gill plate samples. More than half of identified species fall under the IUCN Red List categories 'Endangered' and 'Vulnerable', raising further concerns about the impacts of this trade on the sustainability of these low productivity species.

De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis.

Next-generation sequencing techniques, such as RNA sequencing, have provided a wealth of genomic information for nonmodel species. Transcriptomic information can be used to quantify the patterns of gene expression, which can identify how environmental differences invoke organismal stress responses and provide a gauge in predicting species adaptability. In our study, we used RNA sequencing to characterize the first transcriptome from a naupliar tadpole shrimp (Triops newberryi) to identify the genes expressed during the early life history stages and which could be important for future genomic studies. RNA was extracted from naupliar T. newberryi that were reared in a laboratory-controlled setting and in two different water types, a native and a non-native condition. A total of six replicates, three per condition, were sequenced with the Illumina Hi-Seq 2000 achieving 365 M 50-nt reads. High-quality reads were produced and de novo assembly was used to construct a T. newberryi transcriptome that was approximately 24.8 M base pairs. More than 10 000 peptides were predicted from the assembly, and genes were sorted into gene ontology categories. The use of different water conditions allowed for a preliminary differential gene expression analysis in order to compare the changes in gene expression between conditions. There were 299 differentially expressed genes between water conditions that might serve as a focal point for future genomic studies of Triops acclimation to different environments. The Triops transcriptome could serve as vital genomic information for additional studies on Branchiopod crustaceans.

Self-Fertilization and the Role of Males in Populations of Tadpole Shrimp (Branchiopoda: Notostraca: Triops).

Self-fertilization has both negative and positive fitness effects on species evolution. Selfing can increase inbreeding depression, thereby decreasing genetic diversity. In contrast, self-fertilization can preserve beneficial gene combinations and facilitate colonization success. Within the class of crustaceans Branchiopoda, selfing is a primary reproductive mode. Some species of Triops, in the family Notostraca, are a few of the animal species thought to have a mixed mating system between hermaphrodites and males termed androdioecy. The objective of this study is to validate the reproductive mode utilized by Triops newberryi in southern New Mexico by the use of progeny arrays and population simulations. Individuals were reared in the lab from dried soil collected from temporary ponds inhabited by T. newberryi The adults reared and the encysted embryos contained within their brood pouches were genotyped using 7 T. newberryi specific microsatellite markers to determine the relatedness between parent and offspring. Overall microsatellite diversity was low with few heterozygous individuals and limited polymorphisms. Simulated populations and allele segregation analysis suggest hermaphroditism is the primary reproductive mode for T. newberryi In addition, based on the offspring's alleles, there was no direct evidence that a male (ovisacless) T. newberryi outcrossed with a female. Population simulations further suggest that the rate of successful outcrossing events must be low and could explain why outcrossing was not observed in the laboratory rearing trials.

Discriminating between the effects of founding events and reproductive mode on the genetic structure of Triops populations (Branchiopoda: Notostraca).

Crustaceans that initially colonize a freshwater temporary pond can strongly bias the subsequent genetic composition of the population, causing nearby populations to be genetically distinct. In addition, these crustaceans have various reproductive modes that can influence genetic differentiation and diversity within and between populations. We report on two species of tadpole shrimp, Triops newberryi and Triops longicaudatus "short", with different reproductive modes. Reproduction in the tadpole shrimp can occur clonally (parthenogenesis), with self fertilization (hermaphroditism), or through outcrossing of hermaphrodites with males (androdioecy). For all these reproductive modes, population genetic theory predicts decreased genetic diversity and increased population differentiation. Here we use mitochondrial control region (mtCR) sequences and nuclear microsatellite loci to determine if the difference in reproductive mode affects the high genetic structure typical of persistent founder effects. Previous authors indicated that T. newberryi is androdioecious because populations are composed of hermaphrodites and males, and T. longicaudatus "short" is hermaphroditic or parthenogenetic because males are absent. In our data, T. newberryi and T. longicaudatus "short" populations were highly structured genetically over short geographic distances for mtCR sequences and microsatellite loci (T. newberryi: ΦST = 0.644, FST = 0.252, respectively; T. l. "short": invariant mtCR sequences, FST = 0.600). Differences between the two Triops species in a number of diversity measures were generally consistent with expectations from population genetic theory regarding reproductive mode; however, three of four comparisons were not statistically significant. We conclude the high genetic differentiation between populations is likely due to founder effects and results suggest both species are composed of selfing hermaphrodites with some level of outcrossing; the presence of males in T. newberryi does not appreciably reduce inbreeding. We cannot exclude the possibility that males in T. newberryi are non-reproductive individuals and the two species have the same mating system.