Interaction among morphological, trophic and genetic groups in the rapidly radiating Salvelinus fishes from Lake Kronotskoe

Phylogenomic analysis of the Lake Kronotskoe species flock of Dolly Varden charr reveals genetic and developmental signatures of sympatric radiation

Recent adaptive radiations provide evolutionary case studies, which provide the context to parse the relationship between genomic variation and the origins of distinct phenotypes. Sympatric radiations of the charr complex (genus Salvelinus) present a trove for phylogenetics as charrs have repeatedly diversified into multiple morphs with distinct feeding specializations. However, species flocks normally comprise only two to three lineages. Dolly Varden charr inhabiting Lake Kronotske represent the most extensive radiation described for the charr genus, containing at least seven lineages, each with defining morphological and ecological traits. Here, we perform the first genome-wide analysis of this species flock to parse the foundations of adaptive change. Our data support distinct, reproductively isolated lineages with little evidence of hybridization. We also find that specific selection on thyroid signaling and craniofacial genes forms a genomic basis for the radiation. Thyroid hormone is further implicated in subsequent lineage partitioning events. These results delineate a clear genetic basis for the diversification of specialized lineages, and highlight the role of developmental mechanisms in shaping the forms generated during adaptive radiation.

Life-history variation as a source of diversity for endemic white charr (Salmonidae) of the lower Kamchatka River

Sympatric fish morphs diversifying in their feeding pattern in fresh waters typically implement alternative migratory tactics so that omnivores become migrants and specialists-residents. Charrs of the genus Salvelinus populating the lower Kamchatka River (Northeast Asia) are a rare example wherein two related sympatric morphs both implement a variety of life-history tactics in parallel. Here the authors analyse the ecological diversity in the endemic piscivorous "white" morph that exploits resources of the Kamchatka River in sympatry with the partially anadromous invertivorous "Dolly Varden" (DV) morph. Eco-morphological criteria allowed the authors to validate the morph identification. The white charr (WC) was found to subdivide into the small-sized (up to 1.6 kg) fish inhabiting the lacustrine part of the ecosystem and the large-sized (up to 3.4 kg) fish inhabiting the main river channel. The persistent spatial segregation of the sub-groups was confirmed by significant differences in the life span, muscle δ¹³ С signature and parasite load. According to contrasting patterns of strontium accumulation in otoliths, the riverine WC is represented by resident and semi-anadromous individuals. At the same time, the lack of microsatellite DNA differentiation and allometric nature of the morphometric discrepancy point to the intra-population source of the WC polymorphism. The authors suggest that WC diverged from DV as a result of feeding specialization on the threespine stickleback numerous in the ecosystem since the temporary flooding by marine waters in the middle Holocene. The modern stickleback division into local stocks following the ecosystem differentiation into a river, side lake and estuary resulted in the WC life-history split and ecological radiation.

The gut microbiota of Cystidicola farionis parasitizing the swim bladder of the nosed charr morph Salvelinus malma complex in Lake Kronotskoe (Kamchatka, Russia)

Using the approach of sequencing the V3–V4 region of the 16S rRNA gene, we have analyzed the bacterial diversity associated with the gut and “body” (other parts of nematode after dissection: cuticle, epidermis and longitudinal muscles, etc) of Cystidicola farionis parasitizing the swim bladder of different morphotypes of the nosed charr. Comparisons of the gut microbiota of nematodes with their “body” has revealed that the associated microbiota are closely related to each other. Taxonomic analysis indicated that the relative abundances of the dominant nematode-associated bacteria varied with individual fish. The common dominant microbiota of the gut and “body” of nematodes were represented by Aeromonas, Pseudomonas, Shewanella, and Yersinia, while the associated microbiota of the swim bladder of the nosed charr was dominated by Acinetobacter, Cetobacterium, Pajaroellobacter, Paracoccus, Pseudomonas, Shewanella. By comparing the associated microbiota of nematode parasitizing the different morphotypes of the nosed charr the difference in richness estimates (number of OTU’s and Chao1) were revealed between the N1g and N2 morphs.

Genetic Causes and Consequences of Sympatric Morph Divergence in Salmonidae: A Search for Mechanisms

Repeatedly and recently evolved sympatric morphs exhibiting consistent phenotypic differences provide natural experimental replicates of speciation. Because such morphs are observed frequently in Salmonidae, this clade provides a rare opportunity to uncover the genomic mechanisms underpinning speciation. Such insight is also critical for conserving salmonid diversity, the loss of which could have significant ecological and economic consequences. Our review suggests that genetic differentiation among sympatric morphs is largely nonparallel apart from a few key genes that may be critical for consistently driving morph differentiation. We discuss alternative levels of parallelism likely underlying consistent morph differentiation and identify several factors that may temper this incipient speciation between sympatric morphs, including glacial history and contemporary selective pressures. Our synthesis demonstrates that salmonids are useful for studying speciation and poses additional research questions to be answered by future study of this family. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Caucasian treasure: Genomics sheds light on the evolution of half-extinct Sevan trout, Salmo ischchan, species flock

Five ecologically and phenotypically divergent ecomorphs of the genus Salmo are known from a landlocked alpine lake in the Caucasus, Lake Sevan. It is an example of sympatric diversification within a species-rich lineage with predominate mode of speciation being allopatric. The diversification of Sevan trouts was accompanied by spawning resource partitioning. Four lacustrine ecomorphs with different temporal-spatial spawning strategies and divergent morphology and coloration evolved along with a fifth ecomorph, brook trout, inhabiting the tributaries. Unfortunately, the Sevan trout diversity was almost destroyed by human activity, with two ecomorphs becoming extinct in the 1980s. We performed reconstruction of the evolutionary history of Sevan trouts based on high-throughput sequencing of both contemporary and historical DNA (∼ 50 y.o.) of all Sevan trout ecomorphs. Our study of complete mitogenomes along with genome-wide SNP data revealed the monophyly of four lacustrine ecomorphs and local brook trout, all derived from the anadromous form Caspian salmon, S. caspius. The species tree suggests a scenario of stepwise evolution from riverine to lacustrine spawning. Three genomic clusters were revealed, of which two refer to the riverine and lacustrine spawners within the flock of Sevan trouts (with F_ST value = 0.069). A few SNP outliers under selection were discovered that could be responsible for assortative mating based on visual recognition. The Holocene climatic oscillations and the desiccation of tributaries could have played an important role in the origin of lacustrine spawning. The relationships between lacustrine ecomorphs were not yet fully resolved. This radiation warrants further investigation.

Ambient temperature as a factor contributing to the developmental divergence in sympatric salmonids

Factors and mechanisms promoting resource-based radiation in animals still represent a main challenge to evolutionary biology. The modifications of phenotype tied with adaptive diversification may result from an environmentally related shift having occurred at the early stage of development. Here, we study the role of temperature dynamics on the reproductive sites in the early-life divergence and adaptive radiation of the salmonid fish Salvelinus malma dwelling in the Lake Kronotskoe basin (North-East Asia). Local sympatric charr ecomorphs demonstrate strict homing behaviour guiding the preordained distribution along tributaries and, hence, further development under different temperatures. We thoroughly assessed the annual temperature dynamics at the spawning grounds of each morph as compared to an ancestral anadromous morph. Then we carried out an experimental rearing of both under naturally diverging and uniformed temperatures. To compare the morphs' development under the dynamically changing temperatures, we have designed a method based on calculating the accumulated heat by the Arrhenius equation. The proposed equation shows a strong predictive power and, at the same time, is not bias-susceptible when the developmental temperature approximates 0°C. The temperature was found to significantly affect the charrs' early ontogeny, which underlies the divergence of developmental and growth rates between the morphs, as well as morph-specific ontogenetic adaptations to the spawning site's temperatures. As opposed to the endemic morphs from Lake Kronotskoe, the anadromous S. malma, being unexposed to selection оn highly specific reproduction conditions, showed a wide temperature tolerance, Our findings demonstrate that the hatch, onset timing of external feeding, and size dissimilarities between the sympatric morphs reveal themselves during the development under contrast temperatures. As a result of the observed developmental disparities, the morphs occupy specific definitive foraging niches in the lake.