TdIF1 recognizes a specific DNA sequence through its Helix-Turn-Helix and AT-hook motifs to regulate gene transcription

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Geographic variation in the damselfish-red alga cultivation mutualism in the Indo-West Pacific

<p>Abstract</p> <p>Background</p> <p>On coral reefs, damselfish defend their territories from invading herbivores and maintain algal turfs, from which they harvest filamentous algae. In southern Japan, intensive weeding of indigestible algae by <it>Stegastes nigricans </it>results in overgrowth by one filamentous alga, <it>Polysiphonia </it>sp. 1. Because this alga is highly susceptible to grazing and is competitively inferior to other algae, it survives only within the protective territories of this fish species, suggesting an obligate mutualism between damselfish and their cultivated alga. The wide distribution of damselfish species through the Indo-Central Pacific raises the question of whether this species-specific mutualism is maintained throughout the geographic range of the fish. To address this question, from all 18 damselfish species we conducted comprehensive surveys of algal flora within their territories throughout the Indo-West Pacific, and identified species of <it>Polysiphonia </it>using morphological examination and gene sequencing data.</p> <p>Results</p> <p>Several species of the genus <it>Polysiphonia </it>were observed as a major crop in territories throughout the geographic range of <it>S. nigricans</it>. <it>Polysiphonia </it>sp. 1 occurred only in territories of <it>S. nigricans </it>in central areas of the Indo-Pacific. However, its occurrence was low from the Great Barrier Reef and Mauritius. In contrast, other indigenous <it>Polysiphonia </it>species, which formed a clade with <it>Polysiphonia </it>sp. 1, occurred in the territories of fishes from Egypt, Kenya, and the Maldives. The other <it>Polysiphonia </it>species in the clade only inhabited damselfish territories and were never found elsewhere.</p> <p>Conclusions</p> <p>Cultivation mutualism between the damselfish <it>S. nigricans </it>and algae of <it>Polysiphonia </it>was maintained throughout the Indo-West Pacific, although algal crop species and the mode of cultivation (<it>e.g.</it>, presence/absence of selective weeding, the species composition of algal turfs) varied among localities. This finding implies that damselfish utilize indigenous <it>Polysiphonia </it>species in newly colonized habitats in different ways, and therefore the algal composition and means of cultivation have diverged.</p

Differences in the genetic structure between and within two landlocked Ayu groups with different migration patterns in Lake Biwa revealed by environmental DNA analysis

Ayu (Plecoglossus altivelis) is largely an annual amphidromous fish, although a landlocked population lives in Lake Biwa, the largest lake in Japan. The landlocked population comprises two migrant groups, spring migrants and autumn migrants, which run to inlet rivers from the lake at different seasons. We used environmental DNA (eDNA) analysis, which is reported to be more sensitive and cost-effective than capture surveys, to clarify the genetic structure of this landlocked Ayu population with different migration patterns in Lake Biwa. We took water samples in 11 inlet rivers in the spring and autumn for 2 years in a row and quantitatively detected a total of 265 haplotypes of the mitochondrial D-loop region. The pairwise fixation index (FST) value and haplotype diversity indicated that there were genetic differences between the two migrant groups in their respective rivers, and the FST values were negatively related to latitude and the presence of artificial fish stocking. Additionally, isolation by distance within spring migrant group was observed when the lake was divided into the east and west sides. These findings show that the landlocked Ayu population in Lake Biwa has genetic structure associated with migration patterns and geographical distance. This study demonstrates that the eDNA approach will be effective for conducting a large-scale investigation of genetic structure beyond simple presence/absence tests

Evolution of feeding specialization in Tanganyikan scale-eating cichlids: a molecular phylogenetic approach

<p>Abstract</p> <p>Background</p> <p>Cichlid fishes in Lake Tanganyika exhibit remarkable diversity in their feeding habits. Among them, seven species in the genus <it>Perissodus </it>are known for their unique feeding habit of scale eating with specialized feeding morphology and behaviour. Although the origin of the scale-eating habit has long been questioned, its evolutionary process is still unknown. In the present study, we conducted interspecific phylogenetic analyses for all nine known species in the tribe Perissodini (seven <it>Perissodus </it>and two <it>Haplotaxodon </it>species) using amplified fragment length polymorphism (AFLP) analyses of the nuclear DNA. On the basis of the resultant phylogenetic frameworks, the evolution of their feeding habits was traced using data from analyses of stomach contents, habitat depths, and observations of oral jaw tooth morphology.</p> <p>Results</p> <p>AFLP analyses resolved the phylogenetic relationships of the Perissodini, strongly supporting monophyly for each species. The character reconstruction of feeding ecology based on the AFLP tree suggested that scale eating evolved from general carnivorous feeding to highly specialized scale eating. Furthermore, scale eating is suggested to have evolved in deepwater habitats in the lake. Oral jaw tooth shape was also estimated to have diverged in step with specialization for scale eating.</p> <p>Conclusion</p> <p>The present evolutionary analyses of feeding ecology and morphology based on the obtained phylogenetic tree demonstrate for the first time the evolutionary process leading from generalised to highly specialized scale eating, with diversification in feeding morphology and behaviour among species.</p

Origin of scarlet gynogenetic triploid Carassius fish: Implications for conservation of the sexual–gynogenetic complex

天然記念物ヒブナの起源を解明 --クローン繁殖のはずなのにキンギョと交雑--. 京都大学プレスリリース. 2022-10-21.Conservation of sperm-dependent asexual (gynogenetic) species is challenging due to their complicated ecological dynamics, which requires the stable coexistence with their sperm-providing sexual relatives, who often share similar niches. A symbolic but vulnerable gynogenetic animal is the scarlet Carassius fish, or Hibuna, which is mainly found in Lake Harutori on Hokkaido, Japan. Although Hibuna in Lake Harutori has been protected as a symbol of the Natural Monument of Japan, it has recently suffered population decline. To establish an effective conservation strategy for Hibuna, we investigated its origin, reproductive mode, and genetic diversity, with reference to the surrounding wild populations, using nuclear microsatellites and mitochondrial gene sequences. Our genetic analyses revealed that the main ploidy of Hibuna was triploid or tetraploid, and it reproduces gynogenetically. However, no co-existing sexual diploid Carassius was detected among our samples, suggesting that the sexual diploids and the gynogenetic population including Hibuna would be at risk of co-extirpation. In addition, Hibuna showed high genetic/clonal diversity and most Hibuna had nonindigenous mitochondrial haplotypes that are mostly identical to those reported from goldfish. These results indicate that Hibuna most probably originated from hybridization between indigenous gynogenetic triploids and goldfish introduced about 100 years ago, involving rare sexual reproduction. This spontaneous long-term field experiment exemplifies the recently documented diversification process of gynogenetic Carassius via complex interploidy gene flow. Although the priority to be placed on the conservation of Hibuna is controversial, the maintenance of gynogenetic Carassius, including Hibuna, requires strategic conservation of sexual populations

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

Phylogeny, hybridization, and life history evolution of Rhinogobius gobies in Japan, inferred from multiple nuclear gene sequences.

最も多様な淡水性ハゼ科魚類、ヨシノボリ類の進化史を解明 -回遊魚の淡水域への適応進化と大規模な種間交雑-. 京都大学プレスリリース. 2015-05-26.Rhinogobius fishes (Gobiidae) are distributed widely in East and Southeast Asia, and represent the most species-rich group of freshwater gobies with diversified life histories (i.e., amphidromous, fluvial, and lentic). To reveal their phylogenetic relationships and life history evolution patterns, we sequenced six nuclear and three mitochondrial DNA (mtDNA) loci from 18 species, mainly from the mainland of Japan and the Ryukyu Archipelago. Our phylogenetic tree based on nuclear genes resolved three major clades, including several distinct subclades. The mtDNA and nuclear DNA phylogenies showed large discordance, which strongly suggested mitochondrial introgression through large-scale interspecific hybridization in these regions. On the basis of the molecular dating using geological data as calibration points, the hybridization occurred in the early to middle Pleistocene. Reconstruction of the ancestral states of life history traits based on nuclear DNA phylogeny suggests that the evolutionary change from amphidromous to freshwater life, accompanied by egg size change, occurred independently in at least three lineages. One of these lineages showed two life history alterations, i.e., from amphidromous (small egg) to fluvial (large egg) to lentic (small egg). Although more inclusive analysis using species outside Japan should be further conducted, the present results suggest the importance of the life history evolution associated with high adaptability to freshwater environments in the remarkable species diversification in this group. Such life history divergences may have contributed to the development of reproductive isolation

A dataset of fishes in and around Inle Lake, an ancient lake of Myanmar, with DNA barcoding, photo images and CT/3D models

ミャンマーの古代湖インレー湖で一世紀ぶりに魚類相調査, 約四割が外来魚。標本の3Dモデルもオンライン公開. 京都大学プレスリリース. 2016-12-02.Background: Inle (Inlay) Lake, an ancient lake of Southeast Asia, is located at the eastern part of Myanmar, surrounded by the Shan Mountains. Detailed information on fish fauna in and around the lake has long been unknown, although its outstanding endemism was reported a century ago

平常時の災害時用非常食の準備状態と防災意識との関連性の検討

本研究ではA大学看護学部の1、2 年生137 名を対象とし学生の災害への備えの「非常食」現状、および防災意識の関連を明らかにして平常時の非常食備蓄に対する影響要因を検討した。この結果、非常食の備蓄に対する影響要因として「他者( 専門職・大学)から受ける支援」、「非常用のリュックや袋の準備」、「食器や棚が倒れてこないように工夫している」の3 要因が示された。また、学生は非常食の準備の必要性を感じていたことから、他者からの支援に関する情報提供や具体的な防災手段の紹介は、「防災意識」と「防災行動」を高め、非常食の準備を促す動機づけになることが示唆された