Phylogeny and historical demography of endemic fishes in Lake Biwa: the ancient lake as a promoter of evolution and diversification of freshwater fishes in western Japan

To elucidate the origins of the endemic fish of Lake Biwa, an ancient lake in Japan, and the role of the lake in the diversification of freshwater fish in western Japan, we established a molecular phylogenetic framework with an absolute time scale and inferred the historical demography of a large set of fish species in and around the lake. We used mtDNA sequences obtained from a total of 190 specimens, including 11 endemic species of Lake Biwa and their related species, for phylogenetic analyses with divergence time estimations and from a total of 2319 specimens of 42 species (including 14 endemics) occurring in the lake for population genetic analyses. Phylogenetic analysis suggested that some of the endemic species diverged from their closest relatives earlier (1.3-13.0 Ma) than the period in which the present environmental characteristics of the lake started to develop (ca. 0.4 Ma), whereas others diverged more recently (after 0.4 Ma). In contrast, historical demographic parameters suggested that almost all species, including endemic and nonendemic ones, expanded their populations after the development of the present lake environment. In phylogeographic analyses, common or very close haplotypes of some species were obtained from Lake Biwa and other regions of western Japan. The phylogenetic and historical demographic evidence suggests that there was a time lag between phylogenetic divergence and population establishment and that phenotypic adaptation of some endemic species to the limnetic environment occurred much later than the divergences of those endemic lineages. Population structure and phylogeographic patterns suggest that Lake Biwa has functioned not only as the center of adaptive evolution but also as a reservoir for fish diversity in western Japan

Local adaptation and the evolution of genome architecture in threespine stickleback.

Theory predicts that local adaptation should favour the evolution of a concentrated genetic architecture, where the alleles driving adaptive divergence are tightly clustered on chromosomes. Adaptation to marine vs. freshwater environments in threespine stickleback has resulted in an architecture that seems consistent with this prediction: divergence among populations is mainly driven by a few genomic regions harbouring multiple quantitative trait loci (QTL) for environmentally adapted traits, as well as candidate genes with well-established phenotypic effects. One theory for the evolution of these "genomic islands" is that rearrangements remodel the genome to bring causal loci into tight proximity, but this has not been studied explicitly. We tested this theory using synteny analysis to identify micro- and macro-rearrangements in the stickleback genome and assess their potential involvement in the evolution of genomic islands. To identify rearrangements, we conducted a de novo assembly of the closely-related tubesnout (Aulorhyncus flavidus) genome and compared this to the genomes of threespine stickleback and two other closely related species. We found that small rearrangements, within-chromosome duplications, and Lineage-Specific Genes (LSGs) were enriched around genomic islands, and that all three chromosomes harbouring large genomic islands have experienced macro-rearrangements. We also found that duplicates and micro-rearrangements are 9.9x and 2.9x more likely to involve genes differentially expressed between marine and freshwater genotypes. While not conclusive, these results are consistent with the explanation that strong divergent selection on candidate genes drove the recruitment of rearrangements to yield clusters of locally adaptive loci

Genetic population structure of Hemigrammocypris rasborella (Cyprinidae) inferred from mtDNA sequences

The genetic population structure of the small cyprinid Hemigrammocypris rasborella, distributed widely in lowlands of western Japan, was examined using partial sequence data of mitochondrial DNA (mtDNA). Molecular phylogenetic analysis revealed that the populations of the western Kyushu region were markedly differentiated from all eastern populations, such that the groups would be comparable to different species; their divergence was inferred to have occurred in the Late Miocene–Pliocene. Also, a largely divergent mtDNA group (with divergence in the early Pleistocene) was found in the Sanyo and northeastern Shikoku regions, forming a secondary contact zone in the western Kinki with the eastern mtDNA group. To date, these aspects of the population structure of H. rasborella appear to be unique among lowland fishes in western Japan. Deeper understanding of the formation processes of freshwater faunas in western Japan will require further comparisons of the phylogeographic patterns and ecological traits of constituent species

Mesozoic origin and ‘out-of-India’ radiation of ricefishes (Adrianichthyidae)

The Indian subcontinent has an origin geologically different from Eurasia, but many terrestrial animal and plant species on it have congeneric or sister species in other parts of Asia, especially in the Southeast. This faunal and floral similarity between India and Southeast Asia is explained by either of the two biogeographic scenarios, ‘into-India’ or ‘out-of-India’. Phylogenies based on complete mitochondrial genomes and five nuclear genes were undertaken for ricefishes (Adrianichthyidae) to examine which of these two biogeographic scenarios fits better. We found that Oryzias setnai, the only adrianichthyid distributed in and endemic to the Western Ghats, a mountain range running parallel to the western coast of the Indian subcontinent, is sister to all other adrianichthyids from eastern India and Southeast–East Asia. Divergence time estimates and ancestral area reconstructions reveal that this western Indian species diverged in the late Mesozoic during the northward drift of the Indian subcontinent. These findings indicate that adrianichthyids dispersed eastward ‘out-of-India’ after the collision of the Indian subcontinent with Eurasia, and subsequently diversified in Southeast–East Asia. A review of geographic distributions of ‘out-of-India’ taxa reveals that they may have largely fuelled or modified the biodiversity of Eurasia.journal articl

異なった生息場所の利用に関連したコイ科魚類の適応的分化

京都大学0048新制・課程博士博士(理学)甲第17386号理博第3883号新制||理||1560(附属図書館)30152京都大学大学院理学研究科生物科学専攻(主査)准教授 渡辺 勝敏, 教授 曽田 貞滋, 教授 中務 真人学位規則第4条第1項該当Doctor of ScienceKyoto UniversityDA

The origins of limnetic forms and cryptic divergence in Gnathopogon fishes (Cyprinidae) in Japan

The cyprinid species of the genus Gnathopogon, exhibiting flexible morphological and ecological variation, include limnetic life forms. We examined the origin of the limnetic forms and the population divergence of the Japanese Gnathopogon species, using molecular phylogenetic and phylogeographic analyses. A Bayesian phylogenetic inference approach based on mtDNA cytochrome b sequence data revealed three major lineages in G. elongatus. One of them formed a monophyletic group with the limnetic species G. caerulescens, which is endemic to an ancient lake, Lake Biwa. The divergence of the G. caerulescens lineage was estimated to date back to the early Pleistocene. This precedes the formation of the extensive pelagic environment in the present Lake Biwa. However, the recent genetic divergence of G. caerulescens was inferred to originate in the present Lake Biwa in the late Pleistocene. Another lacustrine population in the Mikata Lakes was shown to belong to a different lineage from G. caerulescens. The majority of the population possessed unique, but non-monophyletic, haplotypes, suggesting a short evolutionary history. One of the cryptic lineages of G. elongatus discovered in the Ina Valley, the lower area of Lake Suwa, might be related to the extinct lacustrine subspecies G. elongatus suwae, which has been replaced by introduced congeners. The previous and ongoing introductions of Gnathopogon fishes would have produced genetic disturbance to the indigenous populations

Development and validation of novel SNP markers for the rapid identification of natural hybrids of the 11 closely related pufferfish species (Takifugu spp.) distributed in Japan

Accurate identification of interspecific hybrids is vital for breeding programs in hybridizing taxa, as well as for the use of hybrids in aquaculture and fisheries. The use of species-specific single nucleotide polymorphisms (SNPs) has become the standard for the molecular identification of hybrids. However, it remains challenging to use these SNPs to identify hybrids involving multiple candidate parental species. Here, we developed and validated SNP markers for the identification of hybrids of the 11 closely related pufferfish species (genus Takifugu) distributed in Japan; these species have different aquacultural characteristics, such as growth rate, physiology, behavior, and toxicity. In total, 1232 species-specific SNPs were identified through double-digest restriction-site-associated DNA sequencing. The species had 11 (T. flavipterus) to 295 (T. chrysops) species-specific SNPs. We validated 33 genome-wide species-specific SNPs using TaqMan® genotyping assays for the 11 species and their hybrids, which were identified using amplified fragment length polymorphism analyses. No false negative or positive assignments were observed in 77 and 30 specimens of pure species and F1 hybrids, respectively. This marker combination allows rapid and reliable identification of natural hybrids, which will be useful for pufferfish aquaculture and will enhance our understanding of the natural hybridization between various Takifugu species

Data from: Genomic architecture of habitat-related divergence and signature of directional selection in the body shapes of Gnathopogon fishes

Evolution of ecomorphologically relevant traits such as body shapes is important to colonize and persist in a novel environment. Habitat-related adaptive divergence of these traits is therefore common among animals. We studied the genomic architecture of habitat-related divergence in the body shape of Gnathopogon fishes, a novel example of lake–stream ecomorphological divergence, and tested for the action of directional selection on body shape differentiation. Compared to stream-dwelling Gnathopogon elongatus, the sister species Gnathopogon caerulescens, exclusively inhabiting a large ancient lake, had an elongated body, increased proportion of the caudal region and small head, which would be advantageous in the limnetic environment. Using an F2 interspecific cross between the two Gnathopogon species (195 individuals), quantitative trait locus (QTL) analysis with geometric morphometric quantification of body shape and restriction-site associated DNA sequencing-derived markers (1622 loci) identified 26 significant QTLs associated with the interspecific differences of body shape-related traits. These QTLs had small to moderate effects, supporting polygenic inheritance of the body shape-related traits. Each QTL was mostly located on different genomic regions, while colocalized QTLs were detected for some ecomorphologically relevant traits that are proxy of body and caudal peduncle depths, suggesting different degree of modularity among traits. The directions of the body shape QTLs were mostly consistent with the interspecific difference, and QTL sign test suggested a genetic signature of directional selection in the body shape divergence. Thus, we successfully elucidated the genomic architecture underlying the adaptive changes of the quantitative and complex morphological trait in a novel system

Centroid sizes of the samples from natural populations

Centroid sizes of the samples from the natural populations in NTS format. The numbers and the population codes (see supplementary Table S1) of the analysed populations are: 11 E1T, 20 E1S, 34 E1D, 32 E1M, 8 E2H, 18 E2R, 10 E2K, 6 E2I, 14 E3K, 10 E3I, 3 S, 28 CM, and 12 CN, in this order

A RAD-based linkage map and comparative genomics in the gudgeons (genus <it>Gnathopogon</it>, Cyprinidae)

<p>Abstract</p> <p>Background</p> <p>The construction of linkage maps is a first step in exploring the genetic basis for adaptive phenotypic divergence in closely related species by quantitative trait locus (QTL) analysis. Linkage maps are also useful for comparative genomics in non-model organisms. Advances in genomics technologies make it more feasible than ever to study the genetics of adaptation in natural populations. Restriction-site associated DNA (RAD) sequencing in next-generation sequencers facilitates the development of many genetic markers and genotyping. We aimed to construct a linkage map of the gudgeons of the genus <it>Gnathopogon</it> (Cyprinidae) for comparative genomics with the zebrafish <it>Danio rerio</it> (a member of the same family as gudgeons) and for the future QTL analysis of the genetic architecture underlying adaptive phenotypic evolution of <it>Gnathopogon</it>.</p> <p>Results</p> <p>We constructed the first genetic linkage map of <it>Gnathopogon</it> using a 198 F₂ interspecific cross between two closely related species in Japan: river-dwelling <it>Gnathopogon elongatus</it> and lake-dwelling <it>Gnathopogon caerulescens</it>. Based on 1,622 RAD-tag markers, a linkage map spanning 1,390.9 cM with 25 linkage groups and an average marker interval of 0.87 cM was constructed. We also identified a region involving female-specific transmission ratio distortion (TRD). Synteny and collinearity were extensively conserved between <it>Gnathopogon</it> and zebrafish.</p> <p>Conclusions</p> <p>The dense SNP-based linkage map presented here provides a basis for future QTL analysis. It will also be useful for transferring genomic information from a “traditional” model fish species, zebrafish, to screen candidate genes underlying ecologically important traits of the gudgeons.</p