Speciation and genetic divergence of three species of charr from ancient Lake El'gygytgyn (Chukotka) and their phylogenetic relationships with other representatives of the genusSalvelinus

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.

Thyroid-Mediated Metabolic Differences Underlie Ecological Specialization of Extremophile Salmonids in the Arctic Lake El’gygytgyn

El’gygytgyn, the only “ancient lake” in the Arctic (3.6 MY), is a deep (176 m) and extremely cold (always ≤ 4°C) waterbody inhabited by unique salmonids, which colonized the ecosystem stepwise during the global fluctuations of the Quaternary climate. The descendant of the first-wave-invaders (long-finned charr) dwells in the deep waters and feeds on amphipods. The second-wave-invaders (smallmouth charr) consume copepods in the mid-waters. Recent third-wave-invaders (Boganida charr) are spread throughout the ecosystem and feed on insects when they are young shifting to piscivory at an older age. Here, we present the data on the charrs’ thyroid status and metabolic characteristics, confirming their ecological specialization. The long-finned charr exhibits an extremely low thyroid content, the substitution of carbohydrates for lipids in the cellular respiration, an increased hemoglobin level and a high antioxidant blood capacity. These traits are likely to be the legacy of anaerobic survival under perennial ice cover during several Quaternary glaciations. Moderate thyroid status and reduced metabolic rate of the smallmouth charr, along with an inactive lifestyle, could be regarded as a specialization to saving energy under the low food supply in the water column. The piscivorous Boganida charr could be sub-divided into shallow-water and deep-water groups. The former demonstrates a significantly elevated thyroid status and increased metabolism. The latter is characterized by a reduced thyroid level, metabolic rate, and lipid accumulation. Thus, the endemic El’gygytgyn charrs represent a wide spectrum of contrast physiological adaptation patterns essential to survive in sympatry under extremely cold conditions.

Comparing diversification rates in lakes, rivers, and the sea

The diversity of species inhabiting freshwater relative to marine habitats is striking, given that freshwater habitats encompass <1% of Earth's water. The most commonly proposed explanation for this pattern is that freshwater habitats are more fragmented than marine habitats, allowing more opportunities for allopatric speciation and thus increased diversification rates in freshwater. However, speciation may be generally faster in sympatry than in allopatry, as illustrated by lacustrine radiations such as African cichlids. Such differences between rivers and lakes may be important to consider when comparing diversification broadly among freshwater and marine groups. Here I compared diversification rates of teleost fishes in marine, riverine and lacustrine habitats. I found that lakes had faster speciation and net diversification rates than other aquatic habitats. However, most freshwater diversity arose in rivers. Surprisingly, riverine and marine habitats had similar rates of net diversification on average. Biogeographic models suggest that lacustrine habitats are evolutionarily unstable, explaining the dearth of lacustrine species in spite of their rapid diversification. Collectively, these results suggest that strong diversification rate differences are unlikely to explain the freshwater paradox. Instead, this pattern may be attributable to the comparable amount of time spent in riverine and marine habitats over the 200-million-year history of teleosts.

Complete mitochondrial genome and phylogenetic position of the Levanidov's charr Salvelinus levanidovi Chereshnev, Skopetz et Gudkov, 1989 (Salmoniformes, Salmonidae)

The complete mitochondrial genome was sequenced in Levanidov’s charr Salvelinus levanidovi. The genome sequences are 16,624 bp, and the gene arrangement, composition, and size are similar to the charr genomes. The level of divergence between S. levanidovi and charr belonging to the genus Salvelinus was in the range from 4.80% to 3.65%. Molecular phylogeny provides new evidence that S. levanidovi is closely related to the common ancestor of the genus Salvelinus. The present study confirms that S. fontinalis, S. levanidovi, S. leucomaensis, and S. namaycus form a basal group of taxa, each of them belongs to an independent evolutionary line.

First report of three complete mitochondrial genomes of the long-finned charr Salvethymus svetovidovi Chereshnev et Skopetz, 1990 (Salmoniformes: Salmonidae) with phylogenetic consideration

The complete mitochondrial genome was sequenced in three individuals of long-finned charr Salvethymus svetovidovi from Lake El'gygytgyn (Chukotka Peninsula, Russia). The genome sequences are 16,655 bp in size and the gene arrangement, composition, and size are similar to the charr genomes published previously. The difference between the three genomes studied is low, 0.07%. Our results support the phylogenetic closeness of Sl. svetovidovi with representatives of the genus Salvelinus and their origin from a common ancestor. A placement of Sl. svetovidovi in the phylogenetic tree is strictly defined and this taxon should be included in the genus Salvelinus.

Juvenile divergence in adaptive traits among seven sympatric fish ecomorphs arises before moving to different lacustrine habitats

Identifying the mechanisms initiating sympatric diversification in vertebrates has remained a conceptual challenge. Here, we analyse an assemblage of sympatric charr (Salvelinus malma) morphs from landlocked Lake Kronotskoe basin as a model to uncover the divergence pathways in freshwater fishes during the early life history stages. All morphs have distinct developmental biology, but a similar developmental rate retardation compared to the ancestor. Our study reveals that adult morphological differences, which acquire functionality at maturation, originate in the early juvenile stages due to heterochrony in skeletogenesis and allometric changes triggered by variation in metabolic activity. The craniofacial differences among the morphs result from asynchronous development of several skeletal modules. The accelerated ossification of teeth-armed bones occurs in predatory feeding morphs, whereas cranial cover ossification is promoted in benthivorous morphs. These contrasting growth patterns have led to seven phenotypes that span a range far beyond the ancestral variability. The most distinct morphs are a riverine spawning, epilimnetic predator and a lacustrine spawning, profundal benthic feeder. Taken together, we argue that the adaptive morphological differentiation in these sympatric freshwater fishes is driven by diverging patterns in ossification rate and metabolic activity against a background of uneven somatic growth. This divergence is primarily associated with basic environmental differences on the nursery grounds that might be unrelated to resource use. This nonheritable phenotype divergence is then exposed to natural selection that could result in further adaptive genetic changes.

A Narrowing of the Phenotypic Diversity Range after Large Rearrangements of the Karyotype in Salmonidae: The Relationship between Saltational Genome Rearrangements and Gradual Adaptive Evolution

The problem of how a gradual development of ecological and morphological adaptations combines with large genome rearrangements, which have been found to occur in the phylogeny of many groups of organisms, is a matter of discussion in the literature. The objective of this work was to study the problem with the example of salmonids, whose evolution included at least six events of multiple chromosome fusions. Large karyotype rearrangements are associated with a decrease in ecological and morphological diversity in salmonids. In the above example, genome rearrangements seem to distort the function of the genetic systems that are responsible for the occurrence of certain ecological forms in salmonids.

Occurrence of sympatric charr groups, Salvelinus, Salmonidae, in the lakes of Kamchatka: a legacy of the last glaciations

Six postglacial lakes were studied along both sides of the Kamchatka central mountain range, Russia. Pairs of local morphotypes of species of Arctic charrs, Salvelinus spp., have previously been described from the southernmost lakes while the fish fauna of the four northernmost lakes was studied here for the first time. Phenotypic data support the division of Kamchatkan lacustrine charrs into two groups according to the number of gill rakers and pyloric caeca, as well as snout-dorsal and snout-ventral distances (MANOVA, P < 0·001). These groups respectively correspond to phenotypes commonly referred to as Salvelinus malma and Salvelinus taranetzi. To clarify the identity of these groups, D-loop and cytochrome b (cytb) region sequences were analysed. Haplotype network analysis of mtDNA shows the salmonids inhabiting four lakes on the south and north are phylogenetically close to either Beringian S. malma or to S. taranetzi from the Chukotka and Kolyma River basins (the mean ± s.e. pairwise per cent sequence divergence is 0·006 ± 0·001). Phenotype-genotype discordance suggests that mitochondrial introgression between species has occurred in the two smallest lakes (<0·5 km² ) in the central part of the peninsula. Identical haplotypes of D-loop and cytb regions were found for the populations of S. taranetzi from the most distant southern and northern lakes, indicating all lakes were colonized by both species simultaneously after the last glacial maximum. Salvelinus taranetzi may have colonized the Kamchatka peninsula from one or both of two different source regions: the Arctic Beringia and the northern coast of the Okhotsk Sea.