Pike and salmon as sister taxa: detailed intraclade resolution and divergence time estimation of Esociformes + Salmoniformes based on whole mitochondrial genome sequences

Characterization and distribution of a 14-Mb chromosomal inversion in native populations of rainbow trout (Oncorhynchus mykiss)

Multiple studies in a range of taxa have found links between structural variants and the development of ecologically important traits. Such variants are becoming easier to find due, in large part, to the increase in the amount of genome-wide sequence data in nonmodel organisms. The salmonids (salmon, trout, and charr) are a taxonomic group with abundant genome-wide datasets due to their importance in aquaculture, fisheries, and variation in multiple ecologically important life-history traits. Previous research on rainbow trout (Oncorhynchus mykiss) has documented a large pericentric (∼55 Mb) chromosomal inversion (CI) on chromosome 5 (Omy05) and a second smaller (∼14 Mb) chromosome inversion on Omy20. While the Omy05 inversion appears to be associated with multiple adaptive traits, the inversion on Omy20 has received far less attention. In this study, we re-analyze RAD-seq and amplicon data from several populations of rainbow trout (O. mykiss) to better document the structure and geographic distribution of variation in the Omy20 CI. Moreover, we utilize phylogenomic techniques to characterize both the age- and the protein-coding gene content of the Omy20 CI. We find that the age of the Omy20 inversion dates to the early stages of O. mykiss speciation and predates the Omy05 inversion by ∼450,000 years. The 2 CIs differ further in terms of the frequency of the homokaryotypes. While both forms of the Omy05 CI are found across the eastern Pacific, the ancestral version of the Omy20 CI is restricted to the southern portion of the species range in California. Furthermore, the Omy20 inverted haplotype is comparable in genetic diversity to the ancestral form, whereas derived CIs typically show substantially reduced genetic diversity. These data contribute to our understanding of the age and distribution of a large CI in rainbow trout and provide a framework for researchers looking to document CIs in other nonmodel species.

Parvalbumin Gene: A Valuable Marker for Pike Authentication and Allergen Risk Assessment

Fish from the pike (Esox) genus are valued in gastronomy for their superior meat quality. However, they can cause allergic reactions in sensitive consumers. This work aimed to fill the gap in the detection of pike allergens using molecular-biological techniques. New, fast, and accurate loop-mediated isothermal amplification (LAMP) and real-time PCR (qPCR) assays were designed to detect pike DNA using the parvalbumin gene as a marker. LAMP was assessed by electrophoresis, SYBR green optical detection, and real-time fluorescence detection. The latter was the most sensitive, detecting as little as 0.78 ng of pike DNA; the qPCR detection limit was 0.1 ng. The LAMP analysis took 20-70 min, which is significantly faster than qPCR. The study provides reliable detection and quantification of the parvalbumin gene in both fresh and processed samples and further highlights the versatility of the use of the parvalbumin gene for the authentication of food products and consumer protection via refined allergen risk assessment that is independent of the type of tissue or food processing method used.

Effect of Moringa leaf flavonoids on the production performance, immune system, and rumen fermentation of dairy cows

BACKGROUND

Unreasonable use of antibiotics in animals is a major concern and will remain so, thus affecting people's health. However, the application of plant extracts can better solve this problem.

OBJECTIVES

The purpose of this study was to study the effect of Moringa leaf flavonoids on the production performance, immunity, and rumen fermentation of dairy cows.

METHODS

Nine Holstein multiparous cows (average weight: 550 kg; days of lactation: 150 ± 6 days) were used in the experiment, using a 3 × 3 Latin square design. Cows were divided into three groups, each of which was supplemented with 0, 50, or 100 mg/body weight (BW) Moringa oleifera leaf flavonoids. Each experimental period consisted of three periods of 21 days, and the prefeeding period lasted 15 days.

RESULTS

Our results indicated that supplementation with Moringa leaf flavonoids increased the protein content and decreased the number of somatic cells in milk; had little effect on the biochemical indices of blood, the rumen fermentation, and serum biochemical indicators; and improved the activity of antioxidant enzymes, the antioxidant capacity, and immunity.

CONCLUSIONS

Addition of 50 mg/BW Moringa leaf flavonoids to cow enhanced the antioxidant and immunity capacity in dairy cows but did not affect physiological levels of common biochemical parameters in blood or fermentation parameters in rumen.

Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics

The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.

Molecular Phylogeny and Adaptive Mitochondrial DNA Evolution of Salmonids (Pisces: Salmonidae)

Salmonids are composed of anadromous and freshwater fishes, which is an important model for studying adaptive evolution. Herein, 49 salmonid complete mitochondrial genomes and those of two outgroups were used to infer a robust phylogeny for the family Salmonidae. The BI and RAxML phylogenetic trees based on 13 concatenated mitochondrial protein-coding genes showed well-supported nodes, and topologies were highly congruent. The concatenated 13 mitochondrial protein-coding genes, ND2, ND3, and ND5 genes were shown to have significantly larger dN/dS ratios in anadromous species than in freshwater species of Salmonidae, but the CYTB gene had significantly smaller dN/dS in anadromous species. The FEL analysis identified positively selected sites and negatively selected sites in each mitochondrial protein-coding gene separately. The RELAX program revealed that the ATP8 and CYTB genes supported intensified selection of the anadromous lineages. Our results demonstrated the phylogeny of Salmonidae and explored the mitochondrial DNA evolution pattern between anadromous and freshwater salmonids.

Genome-Wide Reconstruction of Rediploidization Following Autopolyploidization across One Hundred Million Years of Salmonid Evolution

The long-term evolutionary impacts of whole-genome duplication (WGD) are strongly influenced by the ensuing rediploidization process. Following autopolyploidization, rediploidization involves a transition from tetraploid to diploid meiotic pairing, allowing duplicated genes (ohnologs) to diverge genetically and functionally. Our understanding of autopolyploid rediploidization has been informed by a WGD event ancestral to salmonid fishes, where large genomic regions are characterized by temporally delayed rediploidization, allowing lineage-specific ohnolog sequence divergence in the major salmonid clades. Here, we investigate the long-term outcomes of autopolyploid rediploidization at genome-wide resolution, exploiting a recent "explosion" of salmonid genome assemblies, including a new genome sequence for the huchen (Hucho hucho). We developed a genome alignment approach to capture duplicated regions across multiple species, allowing us to create 121,864 phylogenetic trees describing genome-wide ohnolog divergence across salmonid evolution. Using molecular clock analysis, we show that 61% of the ancestral salmonid genome experienced an initial "wave" of rediploidization in the late Cretaceous (85-106 Ma). This was followed by a period of relative genomic stasis lasting 17-39 My, where much of the genome remained tetraploid. A second rediploidization wave began in the early Eocene and proceeded alongside species diversification, generating predictable patterns of lineage-specific ohnolog divergence, scaling in complexity with the number of speciation events. Using gene set enrichment, gene expression, and codon-based selection analyses, we provide insights into potential functional outcomes of delayed rediploidization. This study enhances our understanding of delayed autopolyploid rediploidization and has broad implications for future studies of WGD events.

The pink salmon genome: Uncovering the genomic consequences of a two-year life cycle

Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A two-year life history of pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of a centromere drive or a combination of reduced recombination and genetic drift, and they could influence speciation. Other regions of the genome influenced by odd-year and even-year temporal isolation and tentatively under selection were mostly associated with genes related to immune function, organ development/maintenance, and behaviour.

The rise and fall of the ancient northern pike master sex-determining gene

The understanding of the evolution of variable sex determination mechanisms across taxa requires comparative studies among closely related species. Following the fate of a known master sex-determining gene, we traced the evolution of sex determination in an entire teleost order (Esociformes). We discovered that the northern pike (Esox lucius) master sex-determining gene originated from a 65 to 90 million-year-old gene duplication event and that it remained sex linked on undifferentiated sex chromosomes for at least 56 million years in multiple species. We identified several independent species- or population-specific sex determination transitions, including a recent loss of a Y chromosome. These findings highlight the diversity of evolutionary fates of master sex-determining genes and the importance of population demographic history in sex determination studies. We hypothesize that occasional sex reversals and genetic bottlenecks provide a non-adaptive explanation for sex determination transitions.

Comparative Genomic Analyses and a Novel Linkage Map for Cisco (Coregonus artedi) Provide Insights into Chromosomal Evolution and Rediploidization Across Salmonids

Whole-genome duplication (WGD) is hypothesized to be an important evolutionary mechanism that can facilitate adaptation and speciation. Genomes that exist in states of both diploidy and residual tetraploidy are of particular interest, as mechanisms that maintain the ploidy mosaic after WGD may provide important insights into evolutionary processes. The Salmonidae family exhibits residual tetraploidy, and this, combined with the evolutionary diversity formed after an ancestral autotetraploidization event, makes this group a useful study system. In this study, we generate a novel linkage map for cisco (Coregonus artedi), an economically and culturally important fish in North America and a member of the subfamily Coregoninae, which previously lacked a high-density haploid linkage map. We also conduct comparative genomic analyses to refine our understanding of chromosomal fusion/fission history across salmonids. To facilitate this comparative approach, we use the naming strategy of protokaryotype identifiers (PKs) to associate duplicated chromosomes to their putative ancestral state. The female linkage map for cisco contains 20,292 loci, 3,225 of which are likely within residually tetraploid regions. Comparative genomic analyses revealed that patterns of residual tetrasomy are generally conserved across species, although interspecific variation persists. To determine the broad-scale retention of residual tetrasomy across the salmonids, we analyze sequence similarity of currently available genomes and find evidence of residual tetrasomy in seven of the eight chromosomes that have been previously hypothesized to show this pattern. This interspecific variation in extent of rediploidization may have important implications for understanding salmonid evolutionary histories and informing future conservation efforts.

Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships

Recent and continued progress in the scale and sophistication of phylogenetic research has yielded substantial advances in knowledge of the tree of life; however, segments of that tree remain unresolved and continue to produce contradicting or unstable results. These poorly resolved relationships may be the product of methodological shortcomings or of an evolutionary history that did not generate the signal traits needed for its eventual reconstruction. Relationships within the euteleost fish family Salmonidae have proven challenging to resolve in molecular phylogenetics studies in part due to ancestral autopolyploidy contributing to conflicting gene trees. We examine a sequence capture dataset from salmonids and use alternative strategies to accommodate the effects of gene tree conflict based on aspects of salmonid genome history and the multispecies coalescent. We investigate in detail three uncertain relationships: (1) subfamily branching, (2) monophyly of Coregonus and (3) placement of Parahucho. Coregoninae and Thymallinae are resolved as sister taxa, although conflicting topologies are found across analytical strategies. We find inconsistent and generally low support for the monophyly of Coregonus, including in results of analyses with the most extensive dataset and complex model. The most consistent placement of Parahucho is as sister lineage of Salmo.

The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly

Arctic charr have a circumpolar distribution, persevere under extreme environmental conditions, and reach ages unknown to most other salmonids. The Salvelinus genus is primarily composed of species with genomes that are structured more like the ancestral salmonid genome than most Oncorhynchus and Salmo species of sister genera. It is thought that this aspect of the genome may be important for local adaptation (due to increased recombination) and anadromy (the migration of fish from saltwater to freshwater). In this study, we describe the generation of a new genetic map, the sequencing and assembly of the Arctic charr genome (GenBank accession: GCF_002910315.2) using the newly created genetic map and a previous genetic map, and present several analyses of the Arctic charr genes and genome assembly. The newly generated genetic map consists of 8,574 unique genetic markers and is similar to previous genetic maps with the exception of three major structural differences. The N50, identified BUSCOs, repetitive DNA content, and total size of the Arctic charr assembled genome are all comparable to other assembled salmonid genomes. An analysis to identify orthologous genes revealed that a large number of orthologs could be identified between salmonids and many appear to have highly conserved gene expression profiles between species. Comparing orthologous gene expression profiles may give us a better insight into which genes are more likely to influence species specific phenotypes.

Phylogeography and taxonomic status of trout and salmon from the Ponto-Caspian drainages, with inferences on European Brown Trout evolution and taxonomy

Current taxonomy of western Eurasian trout leaves a number of questions open; it is not clear to what extent some species are distinct genetically and morphologically. The purpose of this paper was to explore phylogeography and species boundaries in freshwater and anadromous trout from the drainages of the Black and the Caspian Seas (Ponto-Caspian). We studied morphology and mitochondrial phylogeny, combining samples from the western Caucasus within the potential range of five nominal species of trout that are thought to inhabit this region, and using the sequences available from GenBank. Our results suggest that the genetic diversity of trout in the Ponto-Caspian region is best explained with the fragmentation of catchments. (1) All trout species from Ponto-Caspian belong to the same mitochondrial clade, separated from the other trout since the Pleistocene; (2) the southeastern Black Sea area is the most likely place of diversification of this clade, which is closely related to the clades from Anatolia; (3) The species from the Black Sea and the Caspian Sea drainages are monophyletic; (4) except for the basal lineage of the Ponto-Caspian clade, Salmo rizeensis, all the lineages produce anadromous forms; (5) genetic diversification within the Ponto-Caspian clade is related to Pleistocene glacial waves; (6) the described morphological differences between the species are not fully diagnostic, and some earlier described differences depend on body size; the differences between freshwater and marine forms exceed those between the different lineages. We suggest a conservative taxonomic approach, using the names S. rizeensis and Salmo labrax for trout from the Black Sea basin and Salmo caspius and Salmo ciscaucasicus for the fish from the Caspian basin.

Whole genome duplications have provided teleosts with many roads to peptide loaded MHC class I molecules

Background

In sharks, chickens, rats, frogs, medaka and zebrafish there is haplotypic variation in MHC class I and closely linked genes involved in antigen processing, peptide translocation and peptide loading. At least in chicken, such MHCIa haplotypes of MHCIa, TAP2 and Tapasin are shown to influence the repertoire of pathogen epitopes being presented to CD8+ T-cells with subsequent effect on cell-mediated immune responses.

Results

Examining MHCI haplotype variation in Atlantic salmon using transcriptome and genome resources we found little evidence for polymorphism in antigen processing genes closely linked to the classical MHCIa genes. Looking at other genes involved in MHCI assembly and antigen processing we found retention of functional gene duplicates originating from the second vertebrate genome duplication event providing cyprinids, salmonids, and neoteleosts with the potential of several different peptide-loading complexes. One of these gene duplications has also been retained in the tetrapod lineage with orthologs in frogs, birds and opossum.

Conclusion

We postulate that the unique salmonid whole genome duplication (SGD) is responsible for eliminating haplotypic content in the paralog MHCIa regions possibly due to frequent recombination and reorganization events at early stages after the SGD. In return, multiple rounds of whole genome duplications has provided Atlantic salmon, other teleosts and even lower vertebrates with alternative peptide loading complexes. How this affects antigen presentation remains to be established.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1138-9) contains supplementary material, which is available to authorized users.

Revisiting the mitogenomic phylogeny of Salmoninae: new insights thanks to recent sequencing advances

The phylogeny of the Salmonidae family, the only living one of the Order Salmoniformes, remains still unclear because of several reasons. Such reasons include insufficient taxon sampling and/or DNA information. The use of complete mitochondrial genomes (mitogenomics) could provide some light on it, but despite the high number of mitogenomes of species belonging to this family published during last years, an integrative work containing all this information has not been done. In this work, the phylogeny of 46 Salmonidae species was inferred from their mitogenomic sequences. Results include a Bayesian molecular-dated phylogenetic tree with very high statistical support showing Coregoninae and Salmoninae as sister subfamilies, as well as several new phylogenetic relationships among species and genus of the family. All these findings contribute to improve our understanding of the Salmonidae systematics and could have consequences on related evolutionary studies, as well as highlight the importance of revisiting phylogenies with integrative studies.

Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences

Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. Here, we re-examine phylogenetic relationships among early-branching euteleostean fish lineages classically grouped in the Protacanthopterygii using DNA sequence data surrounding ultraconserved elements. We report and examine a dataset of thirty-four OTUs with 17,957 aligned characters from fifty-three nuclear loci. Phylogenetic analysis is conducted in concatenated, joint gene trees and species tree estimation and summary coalescent frameworks. All analytical frameworks yield supporting evidence for existing hypotheses of relationship for the placement of Lepidogalaxias salamandroides, monophyly of the Stomiatii and the presence of an esociform + salmonid clade. Lepidogalaxias salamandroides and the Esociformes + Salmoniformes are successive sister lineages to all other euteleosts in the majority of analyses. The concatenated and joint gene trees and species tree analysis types produce high support values for this arrangement. However, inter-relationships of Argentiniformes, Stomiatii and Neoteleostei remain uncertain as they varied by analysis type while receiving strong and contradictory indices of support. Topological differences between analysis types are also apparent within the otomorph and the percomorph taxa in the data set. Our results identify concordant areas with strong support for relationships within and between early-branching euteleost lineages but they also reveal limitations in the ability of larger datasets to conclusively resolve other aspects of that phylogeny.

Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification

BACKGROUND

The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversification are often temporally separated from WGD. Salmonid fish, whose ancestor underwent WGD by autotetraploidization ~95 million years ago, fit such a 'time-lag' model of post-WGD radiation, which occurred alongside a major delay in the rediploidization process. Here we propose a model, 'lineage-specific ohnologue resolution' (LORe), to address the consequences of delayed rediploidization. Under LORe, speciation precedes rediploidization, allowing independent ohnologue divergence in sister lineages sharing an ancestral WGD event.

RESULTS

Using cross-species sequence capture, phylogenomics and genome-wide analyses of ohnologue expression divergence, we demonstrate the major impact of LORe on salmonid evolution. One-quarter of each salmonid genome, harbouring at least 4550 ohnologues, has evolved under LORe, with rediploidization and functional divergence occurring on multiple independent occasions >50 million years post-WGD. We demonstrate the existence and regulatory divergence of many LORe ohnologues with functions in lineage-specific physiological adaptations that potentially facilitated salmonid species radiation. We show that LORe ohnologues are enriched for different functions than 'older' ohnologues that began diverging in the salmonid ancestor.

CONCLUSIONS

LORe has unappreciated significance as a nested component of post-WGD divergence that impacts the functional properties of genes, whilst providing ohnologues available solely for lineage-specific adaptation. Under LORe, which is predicted following many WGD events, the functional outcomes of WGD need not appear 'explosively', but can arise gradually over tens of millions of years, promoting lineage-specific diversification regimes under prevailing ecological pressures.

No evidence for the radiation time lag model after whole genome duplications in Teleostei

The short and long term effects of polyploidization on the evolutionary fate of lineages is still unclear despite much interest. First recognized in land plants, it has become clear that polyploidization is widespread in eukaryotes, notably at the origin of vertebrates and teleost fishes. Many hypotheses have been proposed to link the species richness of lineages and whole genome duplications. For instance, the radiation time lag model suggests that paleopolyploidy would favour the apparition of new phenotypic traits, although the radiation of the lineage would not occur before a later dispersion event. Some results indicate that this model may be observed during land plant evolution. In this work, we test predictions of the radiation time lag model using both fossil data and molecular phylogenies in ancient and more recent teleost whole genome duplications. We fail to find any evidence of delayed increase of the species number after any of these events and conclude that paleopolyploidization still remains to be unambiguously linked to taxonomic diversity in teleosts.

Genetic characterization of esocid herpesvirus 1 (EsHV1)

Blue spot disease, believed to be caused by esocid herpesvirus 1 (EsHV1), has been observed in wild northern pike Esox lucius in a number of cold-water locations, including the northern USA, Canada, and Ireland. In the spring of 2014, a northern pike was caught in Wisconsin displaying the characteristic bluish-white circular plaques on the dorsum and fins. Microscopic examination of hematoxylin and eosin-stained sections of the proliferative cutaneous lesions revealed a focally extensive abundance of panepidermal, megalocytic keratinocytes with karyomegaly. Enlarged nuclei stained basophilic, and an abundance of coarse eosinophilic granules were observed in the expanded cytoplasm. Transmission electron microscopy revealed aggregates of enveloped virus particles with electron-dense, hexagonal nucleocapsids surrounded by a uniformly staining ellipsoidal tegument layer within cytoplasmic vacuoles of megalocytic epidermal cells. More than 7000 bp of the EsHV1 genome were sequenced from infected skin tissues. Phylogenetic and phenetic analyses, based on the partial DNA-dependent DNA polymerase and terminase gene sequences, revealed EsHV1 forms a novel branch within the family Alloherpesviridae as the sister group to the clade that includes members of the genera Ictalurivirus and Salmonivirus. The gross, microscopic, and ultrastructural lesions reported in our study were identical to previous reports of blue spot disease in northern pike; however, here we provide the first molecular evidence supporting EsHV1 as a new species in the family Alloherpesviridae.

Preservation Obscures Pelagic Deep-Sea Fish Diversity: Doubling the Number of Sole-Bearing Opisthoproctids and Resurrection of the Genus Monacoa (Opisthoproctidae, Argentiniformes)

The family Opisthoproctidae (barreleyes) constitutes one of the most peculiar looking and unknown deep-sea fish groups in terms of taxonomy and specialized adaptations. All the species in the family are united by the possession of tubular eyes, with one distinct lineage exhibiting also drastic shortening of the body. Two new species of the mesopelagic opisthoproctid mirrorbelly genus Monacoa are described based on pigmentation patterns of the "sole"-a unique vertebrate structure used in the reflection and control of bioluminescence in most short-bodied forms. Different pigmentation patterns of the soles, previously noted as intraspecific variations based on preserved specimens, are here shown species-specific and likely used for communication in addition to counter-illumination of down-welling sunlight. The genus Monacoa is resurrected from Opisthoproctus based on extensive morphological synaphomorphies pertaining to the anal fin and snout. Doubling the species diversity within sole-bearing opisthoproctids, including recognition of two genera, is unambiguously supported by mitogenomic DNA sequence data. Regular fixation with formalin and alcohol preservation is shown problematic concerning the retention of species-specific pigmentation patterns. Examination or photos of fresh material before formalin fixation is shown paramount for correct species recognition of sole-bearing opisthoproctids-a relatively unknown issue concerning species diversity in the deep-sea pelagic realm.

Targeted sequencing for high-resolution evolutionary analyses following genome duplication in salmonid fish: Proof of concept for key components of the insulin-like growth factor axis

High-throughput sequencing has revolutionised comparative and evolutionary genome biology. It has now become relatively commonplace to generate multiple genomes and/or transcriptomes to characterize the evolution of large taxonomic groups of interest. Nevertheless, such efforts may be unsuited to some research questions or remain beyond the scope of some research groups. Here we show that targeted high-throughput sequencing offers a viable alternative to study genome evolution across a vertebrate family of great scientific interest. Specifically, we exploited sequence capture and Illumina sequencing to characterize the evolution of key components from the insulin-like growth (IGF) signalling axis of salmonid fish at unprecedented phylogenetic resolution. The IGF axis represents a central governor of vertebrate growth and its core components were expanded by whole genome duplication in the salmonid ancestor ~95Ma. Using RNA baits synthesised to genes encoding the complete family of IGF binding proteins (IGFBP) and an IGF hormone (IGF2), we captured, sequenced and assembled orthologous and paralogous exons from species representing all ten salmonid genera. This approach generated 299 novel sequences, most as complete or near-complete protein-coding sequences. Phylogenetic analyses confirmed congruent evolutionary histories for all nineteen recognized salmonid IGFBP family members and identified novel salmonid-specific IGF2 paralogues. Moreover, we reconstructed the evolution of duplicated IGF axis paralogues across a replete salmonid phylogeny, revealing complex historic selection regimes - both ancestral to salmonids and lineage-restricted - that frequently involved asymmetric paralogue divergence under positive and/or relaxed purifying selection. Our findings add to an emerging literature highlighting diverse applications for targeted sequencing in comparative-evolutionary genomics. We also set out a viable approach to obtain large sets of nuclear genes for any member of the salmonid family, which should enable insights into the evolutionary role of whole genome duplication before additional nuclear genome sequences become available.

Comparative analysis of complete mitochondrial genomes suggests that relaxed purifying selection is driving high nonsynonymous evolutionary rate of the NADH2 gene in whitefish (Coregonus ssp.)

Several studies have recently reported evidence for positive selection acting on the mitochondrial genome (mitogenome), emphasizing its potential role in adaptive divergence and speciation. In this study we searched 107 full mitogenomes of recently diverged species and lineages of whitefish (Coregonus ssp.) for signals of positive selection. These salmonids show several distinct morphological and ecological differences that may be associated with energetics and therefore potentially positive selection at the mitogenome level. We found that purifying selection and genetic drift were the predominant evolutionary forces acting on the analyzed mitogenomes. However, the NADH dehydrogenase 2 gene (ND2) showed a highly elevated dN/dS ratio compared to the other mitochondrial genes, which was significantly higher in whitefish compared to other salmonids. We therefore further examined nonsynonymous evolution in ND2 by (i) mapping amino acid changes to a protein model structure which showed that they were located away from key functional residues of the protein, (ii) locating them in the sequences of other species of fish (Salmonidae, Anguillidae, Scombridae and Percidae) only to find pronounced overlap of nonsynonymous regions. We thus conclude that relaxed purifying selection is driving the evolution of ND2 by affecting mostly regions that have lower functional relevance.

Beringian sub-refugia revealed in blackfish (Dallia): implications for understanding the effects of Pleistocene glaciations on Beringian taxa and other Arctic aquatic fauna

Background

Pleistocene climatic instability had profound and diverse effects on the distribution and abundance of Arctic organisms revealed by variation in phylogeographic patterns documented in extant Arctic populations. To better understand the effects of geography and paleoclimate on Beringian freshwater fishes, we examined genetic variability in the genus Dallia (blackfish: Esociformes: Esocidae). The genus Dallia groups between one and three nominal species of small, cold- and hypoxia-tolerant freshwater fishes restricted entirely in distribution to Beringia from the Yukon River basin near Fairbanks, Alaska westward including the Kuskokwim River basin and low-lying areas of Western Alaska to the Amguema River on the north side of the Chukotka Peninsula and Mechigmen Bay on the south side of the Chukotka Peninsula. The genus has a non-continuous distribution divided by the Bering Strait and the Brooks Range. We examined the distribution of genetic variation across this range to determine the number and location of potential sub-refugia within the greater Beringian refugium as well as the roles of the Bering land bridge, Brooks Range, and large rivers within Beringia in shaping the current distribution of populations of Dallia. Our analyses were based on DNA sequence data from two nuclear gene introns (S7 and RAG1) and two mitochondrial genome fragments from nineteen sampling locations. These data were examined under genetic clustering and coalescent frameworks to identify sub-refugia within the greater Beringia refugium and to infer the demographic history of different populations of Dallia.

Results

We identified up to five distinct genetic clusters of Dallia. Four of these genetic clusters are present in Alaska: (1) Arctic Coastal Plain genetic cluster found north of the Brooks Range, (2) interior Alaska genetic cluster placed in upstream locations in the Kuskokwim and Yukon river basins, (3) a genetic cluster found on the Seward Peninsula, and (4) a coastal Alaska genetic cluster encompassing downstream Kuskokwim River and Yukon River basin sample locations and samples from Southwest Alaska not in either of these drainages. The Chukotka samples are assigned to their own genetic cluster (5) similar to the coastal Alaska genetic cluster. The clustering and ordination analyses implemented in Discriminant Analysis of Principal Components (DAPC) and STRUCTURE showed mostly concordant groupings and a high degree of differentiation among groups. The groups of sampling locations identified as genetic clusters correspond to geographic areas divided by likely biogeographic barriers including the Brooks Range and the Bering Strait. Estimates of sequence diversity (θ) are highest in the Yukon River and Kuskokwim River drainages near the Bering Sea. We also infer asymmetric migration rates between genetic clusters. The isolation of Dallia on the Arctic Coastal Plain of Alaska is associated with very low estimated migration rates between the coastal Alaska genetic cluster and the Arctic Coastal Plain genetic cluster.

Conclusions

Our results support a scenario with multiple aquatic sub-refugia in Beringia during the Pleistocene and the preservation of that structure in extant populations of Dallia. An inferred historical presence of Dallia across the Bering land bridge explains the similarities in the genetic composition of Dallia in West Beringia and western coastal Alaska. In contrast, historic and contemporary isolation across the Brooks Range shaped the distinctiveness of present day Arctic Coastal Plain Dallia. Overall this study uncovered a high degree of genetic structuring among populations of Dallia supporting the idea of multiple Beringian sub-refugia during the Pleistocene and which appears to be maintained to the present due to the strictly freshwater nature and low dispersal ability of this genus.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0413-2) contains supplementary material, which is available to authorized users.

Mitochondrial genomic investigation of flatfish monophyly

We present the first study to use whole mitochondrial genome sequences to examine phylogenetic affinities of the flatfishes (Pleuronectiformes). Flatfishes have attracted attention in evolutionary biology since the early history of the field because understanding the evolutionary history and patterns of diversification of the group will shed light on the evolution of novel body plans. Because recent molecular studies based primarily on DNA sequences from nuclear loci have yielded conflicting results, it is important to examine phylogenetic signal in different genomes and genome regions. We aligned and analyzed mitochondrial genome sequences from thirty-nine pleuronectiforms including nine that are newly reported here, and sixty-six non-pleuronectiforms (twenty additional clade L taxa [Carangimorpha or Carangimorpharia] and forty-six secondary outgroup taxa). The analyses yield strong support for clade L and weak support for the monophyly of Pleuronectiformes. The suborder Pleuronectoidei receives moderate support, and as with other molecular studies the putatively basal lineage of Pleuronectiformes, the Psettodoidei is frequently not most closely related to other pleuronectiforms. Within the Pleuronectoidei, the basal lineages in the group are poorly resolved, however several flatfish subclades receive consistent support. The affinities of Lepidoblepharon and Citharoides among pleuronectoids are particularly uncertain with these data.

The genome and linkage map of the northern pike (Esox lucius): conserved synteny revealed between the salmonid sister group and the Neoteleostei

The northern pike is the most frequently studied member of the Esociformes, the closest order to the diverse and economically important Salmoniformes. The ancestor of all salmonids purportedly experienced a whole-genome duplication (WGD) event, making salmonid species ideal for studying the early impacts of genome duplication while complicating their use in wider analyses of teleost evolution. Studies suggest that the Esociformes diverged from the salmonid lineage prior to the WGD, supporting the use of northern pike as a pre-duplication outgroup. Here we present the first genome assembly, reference transcriptome and linkage map for northern pike, and evaluate the suitability of this species to provide a representative pre-duplication genome for future studies of salmonid and teleost evolution. The northern pike genome sequence is composed of 94,267 contigs (N50 = 16,909 bp) contained in 5,688 scaffolds (N50 = 700,535 bp); the total scaffolded genome size is 878 million bases. Multiple lines of evidence suggest that over 96% of the protein-coding genome is present in the genome assembly. The reference transcriptome was constructed from 13 tissues and contains 38,696 transcripts, which are accompanied by normalized expression data in all tissues. Gene-prediction analysis produced a total of 19,601 northern pike-specific gene models. The first-generation linkage map identifies 25 linkage groups, in agreement with northern pike's diploid karyotype of 2N = 50, and facilitates the placement of 46% of assembled bases onto linkage groups. Analyses reveal a high degree of conserved synteny between northern pike and other model teleost genomes. While conservation of gene order is limited to smaller syntenic blocks, the wider conservation of genome organization implies the northern pike exhibits a suitable approximation of a non-duplicated Protacanthopterygiian genome. This dataset will facilitate future studies of esocid biology and empower ongoing examinations of the Atlantic salmon and rainbow trout genomes by facilitating their comparison with other major teleost groups.

A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification

Whole genome duplication (WGD) is often considered to be mechanistically associated with species diversification. Such ideas have been anecdotally attached to a WGD at the stem of the salmonid fish family, but remain untested. Here, we characterized an extensive set of gene paralogues retained from the salmonid WGD, in species covering the major lineages (subfamilies Salmoninae, Thymallinae and Coregoninae). By combining the data in calibrated relaxed molecular clock analyses, we provide the first well-constrained and direct estimate for the timing of the salmonid WGD. Our results suggest that the event occurred no later in time than 88 Ma and that 40-50 Myr passed subsequently until the subfamilies diverged. We also recovered a Thymallinae-Coregoninae sister relationship with maximal support. Comparative phylogenetic tests demonstrated that salmonid diversification patterns are closely allied in time with the continuous climatic cooling that followed the Eocene-Oligocene transition, with the highest diversification rates coinciding with recent ice ages. Further tests revealed considerably higher speciation rates in lineages that evolved anadromy--the physiological capacity to migrate between fresh and seawater--than in sister groups that retained the ancestral state of freshwater residency. Anadromy, which probably evolved in response to climatic cooling, is an established catalyst of genetic isolation, particularly during environmental perturbations (for example, glaciation cycles). We thus conclude that climate-linked ecophysiological factors, rather than WGD, were the primary drivers of salmonid diversification.