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.

24The cyprinid species of the genus Gnathopogon, exhibiting flexible morphological and ecological 25 variation, include limnetic life forms. We examined the origin of the limnetic forms and the 26 population divergence of the Japanese Gnathopogon species, using molecular phylogenetic and 27 phylogeographic analyses. A Bayesian phylogenetic inference approach based on mtDNA 28 cytochrome b sequence data revealed three major lineages in G. elongatus. One of them formed a 29 monophyletic group with the limnetic species G. caerulescens, which is endemic to an ancient lake, 30 Lake Biwa. The divergence of the G. caerulescens lineage was estimated to date back to the early 31Pleistocene. This precedes the formation of the extensive pelagic environment in the present Lake 32Biwa. However, the recent genetic divergence of G. caerulescens was inferred to originate in the 33 present Lake Biwa in the late Pleistocene. Another lacustrine population in the Mikata Lakes was 34 shown to belong to a different lineage from G. caerulescens. The majority of the population 35 possessed unique, but non-monophyletic, haplotypes, suggesting a short evolutionary history. One 36 of the cryptic lineages of G. elongatus discovered in the Ina Valley, the lower area of Lake Suwa, 37 might be related to the extinct lacustrine subspecies G. elongatus suwae, which has been replaced 38 by introduced congeners. The previous and ongoing introductions of Gnathopogon fishes would 39 have produced genetic disturbance to the indigenous populations. 40 41 Keywords 42Lacustrine form · Lake Biwa · Mikata Lakes · Lake Suwa · divergence time · Bayesian random 43 local clock model 44 45 46 47 The family Cyprinidae is the most speciose group of freshwater fish. This group includes fishes 48 with a highly diverse morphology, ecology, and physiology that are adapted to the vast range of 49

Asexual vertebrates are rare and at risk of extinction due to their restricted adaptability through the loss of genetic recombination. We explore the mechanisms behind the generation and maintenance of genetic diversity in triploid asexual (gynogenetic) Carassius auratus fish, which is widespread in East Asian fresh waters and exhibits one of the most extensive distribution among asexual vertebrates despite its dependence on host sperm. Our analyses of genetic composition using dozens of genetic markers and genome-wide transcriptome sequencing uncover admixed genetic composition of Japanese asexual triploid Carassius consisting of both the diverged Japanese and Eurasian alleles, suggesting the involvement of Eurasian lineages in its origin. However, coexisting sexual diploid relatives and asexual triploids in Japan show regional genetic similarity in both mitochondrial and nuclear markers. These results are attributed to a unique unidirectional gene flow from diploids to sympatric triploids, with the involvement of occasional sexual reproduction. Additionally, the asexual triploid shows a weaker population structure than the sexual diploid, and multiple triploid lineages coexist in most Japanese rivers. The generated diversity via repeated interploidy gene flow as well as an increased establishment of immigrants is assumed to offset the cost of asexual reproduction and might contribute to the successful broad distribution of this asexual vertebrate.

No abstract

Hopong, a small town in the Salween (Thanlwin) River Basin, Myanmar, is located 35 km northeast of Inle Lake, a famous ancient lake with numerous endemic fish species. We surveyed the fish fauna of a spring pond in Hopong in 2016, 2019 and 2020 and identified 25 species. Of these, seven, including Inlecypris auropurpureus and Sawbwa resplendens, had been considered endemic to Inle Lake and at least three species were genetically unique. Eight were suspected or definite introduced species, including Oreochromis niloticus and Gambusia affinis. We were unable to identify a nemacheilid species of the genus Petruichthys, which would need a taxonomic examination. The Hopong area is being developed rapidly and, hence, it is crucial to conserve its native fish species and the freshwater ecosystems.

No abstract

Aphyocypris chinensis is a small cyprinid that is widely distributed in lowland areas of continental China, the Korean Peninsula, and the northwestern part of Kyushu, Japan. However, this species is severely threatened in Japan due to human impacts; thus, several facilities and citizen groups implemented captive breeding and reintroduction/reinforcement programs using several dozen founder fish collected from Tanushimaru, the location with the only known natural population, in the 1980s and 1990s. To determine the phylogenetic position and genetic authenticity of Japanese populations of A. chinensis, we conducted mtDNA and genome-wide SNP analyses using a total of 254 specimens from 31 wild and captive samples, including specimens of Chinese and Korean A. chinensis and the close relative A. kikuchii from Taiwan. The mtDNA divergence and phylogeny indicated that the haplotypes found exclusively in Japan were differentiated from the Chinese/Korean haplotypes (uncorrected p = 2.6% in the cytochrome b gene) to the same extent as they were from A. kikuchii haplotypes (p = 2.9%). Results from mtDNA sequences and 47-359 SNPs, obtained using the MIG-seq method with different parameter sets, revealed that the initial captive populations and an extinct wild population in Ukiha, adjacent to Tanushimaru, were genuine Japanese populations, whereas all extant captive and wild populations in Japan are hybrids between Japanese A. chinensis and A. kikuchii, or A. kikuchii itself. The details of the captive breeding and exchange programs, as well as evidence for the aquarium trade of A. kikuchii since the 1990s, strongly suggest that the mixture of A. kikuchii into Japanese populations occurred within the first several years of the establishment of captive populations in 1994. The present case of the highly probable extinction of genuine Japanese populations of A. chinensis emphasizes the importance of confirmation and management of the genetic authenticity of conservation-targeted species. Keywords Captive breeding • Endangered species • Ex situ conservation • Hybridization • MIG-seq • mtDNA cytochrome b JPN-1 (n=2) HFC16, KEE04 JPN-2 (4) LBM00,01, KEE04 JPN-3 (2) UK08 JPN-5 (1) UK07 JPN-4 (10) TNS08, CPR18, LBM09, KEE04 AB218688 TNS CK-1 (1) KOR07 CK-4 (2) KOR07 CK-6 (2) KOR07 CK-7 (1) KOR07 CK-8 (2) KOR07 CK-2 (2) CLN01 CK-3 (1) KOR07 CK-5 (1) KOR07 AF307452 CN KKC-1 (138) TNS08… JX184925 TW-Hualien KKC-2 (1) THL02 AP012123 Aquarium KKC-3 (1) THL02 CSC-2 (1) CSC02 CSC-1 (1) CSC02 AP011398 Yaoshanicus arcus AP011396 Nicholsicypris normalis JX311312 Pararasbora moltrechti 0.08

BackgroundInle (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.New informationBased on the fish specimens collected from markets, rivers, swamps, ponds and ditches around Inle Lake as well as from the lake itself from 2014 to 2016, we recorded a total of 948 occurrence data (2120 individuals), belonging to 10 orders, 19 families, 39 genera and 49 species. Amongst them, 13 species of 12 genera are endemic or nearly endemic to the lake system and 17 species of 16 genera are suggested as non-native. The data are all accessible from the document “A dataset of Inle Lake fish fauna and its distribution (http://ipt.pensoft.net/resource.do?r=inle_fish_2014-16)”, as well as DNA barcoding data (mitochondrial COI) for all species being available from the DDBJ/EMBL/GenBank (Accession numbers: LC189568–LC190411). Live photographs of almost all the individuals and CT/3D model data of several specimens are also available at the graphical fish biodiversity database (http://ffish.asia/INLE2016; http://ffish.asia/INLE2016-3D). The information can benefit the clarification, public concern and conservation of the fish biodiversity in the region.