Novel insights into adaptive evolution based on the unusual AT-skew in Acheilognathus gracilis mitogenome and phylogenetic relationships of bitterling

Acheilognathus gracilis, a bitterling species, distribute in lower reaches of Yangtze River. They are identified as the top-priority bitterling species for conservation as having high evolutionary distinctiveness and are at risk of extinction. In present study, we first sequenced the complete mitogenome of A. gracilis and analyzed its phylogenetic position using 13 PCGs. The A. gracilis mitogenome is 16,774 bp in length, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, a control region and the origin of the light strand replication. The overall base composition of A. gracilis in descending order is T 27.9 %, A 27.7 %, C 26.1 % and G 18.3 %, shows a unusual AT-skew with slightly negative. Further investigation revealed A. gracilis uses excess T over A in NADH dehydrogenase 5 (nd5), whereas the most of other bitterlings are biased toward to use A not T, implying there is likely to be unique strategy of adaptive evolution in A. gracilis. We also compared 13 PCGs of 30 bitterling mitogenomes and the results exhibit highly conservative. Phylogenetic trees constructed by 13 PCGs strongly support the monophyly of Acheilognathus and the paraphyly of Rhodeus and Tanakia. Current results will provide valuable information for follow-up research on conservation of species facing with serious population decline and can provide novel insights into the phylogenetic analysis and evolutionary biology research.

Description of three new species of Gyrodactylus von Nordmann, 1832 (Monogenea: Gyrodactylidae) on bitterling fishes (Acheilognathinae) from China

Three new species of Gyrodactylus are described from three species of bitterling in Donghu Lake, China: Gyrodactylus ocellorhodei n. sp. from Rhodeus ocellatus; G. sinenorhodei n. sp. from Rhodeus sinensis; and G. acheilorhodei n. sp. from Acheilognathus macropterus. All the three new species showed similar opisthaptor morphology, especially the marginal hooks: all had a slender and perpendicular sickle shaft, and flat sickle base with distinct heel and inner arch which was different from the G. rhodei-group species parasitic on bitterling. Multivariate analyses based on hamulus and marginal hooks suggested that these three new species cannot be completely distinguished, despite some morphology divergence observed in certain less reliable morphometric features, such as hamulus root length, ventral bar total length and process shape. These three new species shared an identical 18S ribosomal RNA gene sequence, while the variation in the Internal Transcribed Spacers (ITS1-ITS2) sequence among them (8.4-11.2%, K2P) far exceeded the 1% ITS sequence difference that had been suggested as a threshold for species delimitation of Gyrodactylus. Phylogenetic analysis based on ITS1-ITS2 showed that all these sequenced Gyrodactylus spp. parasitic on the subfamily Acheilognathinae host formed a monophyletic group. However, a clear differentiation (18.9-20.9%, K2P of ITS1-ITS2) could be found between the subgroup from China (G. ocellorhodei n. sp., G. sinenorhodei n. sp. and G. acheilorhodei n. sp.) and that from Europe (G. rhodei).

The complete mitogenome of Paratanakia chii (Cypriniformes; Cyprinidae)

Paratanakia chii is a bitterling fish of the genus Paratanakia, subfamily Acheilognathinae and family Cyprinidae. The mitochondrial DNA sequence of P. chii is reported in this paper. The complete mitochondrial genome of P. chii is 16,575 bp in length, including 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and 1 displacement loop (D-loop). The genome sequence is consistent with those of most other carp. The majority of PCGs have AT- (Met) start codons and TA- end codons. The A + T contents of the genome, PCGs, transfer RNAs (tRNAs), and ribosomal RNAs (rRNAs) are 56.92%, 58.07%, 56.34%, and 54.21%, respectively. Phylogenetic analysis showed that P. chii is most closely related to Tanankia himantegus. These data will benefit relative ecological and phylogenetic studies.

Reproductive ecology and adaptive host choice correlated with body size in an autumn-spawning bitterling Acheilognathus typus

The life history and reproductive ecology of an autumn-spawning bitterling Acheilognathus typus were studied under natural and experimental conditions. In the study pond, the embryos of A. typus emerged from mussels in May and grew rapidly until August, whereas overwintered age-1 fish grew slowly. Adult A. typus in the pond was smaller (32-47 mm in standard length) than they were in other habitats and mainly spawned in smaller mussels. The number of A. typus embryos in mussels was negatively correlated with the shell length of the mussel, and a lower number of embryos were observed in larger mussels (over 110 mm in shell length). In the mussel size-choice experiment conducted in an enclosure, smaller A. typus selected smaller mussels, and larger A. typus selected larger mussels for spawning. In some cases, smaller A. typus spawned in larger mussels and the number of spawned eggs ejected increased by over four times compared with other cases. These results of the enclosure experiment explained the lower number of embryos in larger mussels in the study pond. In addition, reproductive traits such as ovipositor length and the number of ovulated eggs of female A. typus, which are considered to contribute to their size-dependent host utilization, were positively correlated with their standard length. Because A. typus is geologically or seasonally isolated from other bitterling species, this size-dependent host utilization contributes to a reduction in intraspecies rather than interspecies competition.

Intensity-dependent energetic costs in a reciprocal parasitic relationship

Parasitic infections elicit host defences that pose energetic trade-offs with other fitness-related traits. Bitterling fishes and unionid mussels are involved in a two-way parasitic interaction. Bitterling exploit mussels by ovipositing into their gills. In turn, mussel larvae (glochidia) develop on the epidermis and gills of fish. Hosts have evolved behavioural responses to reduce parasite load, suggesting that glochidia and bitterling parasitism are costly. We examined the energetic cost of parasitism on both sides of this relationship. We used intermittent flow-through respirometry to measure (1) standard metabolic rate (SMR) of individual duck mussels Anodonta anatina (a common bitterling host) before and during infection by embryos of the European bitterling Rhodeus amarus, and (2) SMR and maximum oxygen uptake (MO₂max) of individual R. amarus before and during infection with glochidia of the Chinese pond mussel Sinanodonta woodiana (a mussel species that successfully infects bitterling). As predicted, we observed an increase in mussel SMR when infected by bitterling embryos and an increased SMR in glochidia-infected bitterling, though this was significantly mediated by the time post-infection. Contrary to our predictions, glochidia infection did not impair MO₂max and the number of glochidia attached to gills positively (rather than negatively) correlated with MO₂max. The results suggest that tolerance is the prevailing coping mechanism for both fish and mussels when infected, while resistance mechanisms appear to be confined to the behavioural level.

Infection Status with Clonorchis sinensis Metacercariae in Fish from Yangcheon (Stream) in Sancheong-gun, Gyeongsangnam-do, Korea

The infection status with Clonorchis sinensis metacercariae (CsMc) was examined in freshwater fishes from Yangcheon (a branch of Gyeongho-gang), which is located in Sancheong-gun, Gyeongsangnam-do, the Republic of Korea. Total 2,201 fishes in 26 species were examined by the artificial digestion method through 7 years. CsMc were detected in 1,171 (53.2%) fishes in 21 spp. (80.8%) and their density was 85 per fish infected. Total 532 (99.6%) out of 534 Pungtungia herzi (index fish) examined were infected with 147 CsMc per fish infected. Metacercarial densities in this fish were highest in 2015 (179 CsMc), followed by 2012 (168), 2013 (152), 2016 (145), 2014 (114), and 2017 (89) respectively. In the gobioninid fish group, i.e., P. herzi, Sarcocheilichthys spp., Squalidus spp., Pseudogobio esocinus, Hemibarbus longirostris, and Hemibarbus labeo, 841 (92.7%) fishes were infected with 117 CsMc per fish infected. Total 250 (54.7%) acheilognathinid fish (bitterlings), Acheilognathus spp. and Acanthorhodeus spp. were infected with 5.8 CsMc. In the rasborinid fish (chubs) group, i.e., Zacco platypus, Zacco temminckii, and Zacco koreanus, 77 (13.7%) out of 563 fish examined were infected with 2.4 CsMc in average. The susceptibility indices of CsMc were 49.09 in the overall positive fish group, 104.15 in the gobioninid group, 3.17 in the acheilognathinid group and 0.35 in the rasborinid fish group respectively. Only 1 CsMc was detected in 3 fish species, Coreoperca herzi, Channa argus, and Lepomis macrochirus, respectively. Conclusively, it was confirmed that CsMc are moderately prevalent in fishes from Yangcheon in Sancheon-gun, Gyeongsangnam-do, Korea.

Unusual AT-skew of Sinorhodeus microlepis mitogenome provides new insights into mitogenome features and phylogenetic implications of bitterling fishes

Sinorhodeus microlepis (S. microlepis) is recently described as a new species and represents a new genus Sinorhodeu of the subfamily Acheilognathinae. In this study, we first sequenced the complete mitogenome of S. microlepis and compared with the other 29 bitterling mitogenomes. The S. microlepis mitogenome is 16,591 bp in length and contains 37 genes. Gene distribution pattern is identical among 30 bitterling mitogenomes. A significant linear correlation between A+T% and AT-skew were found among 29 bitterling mitogenomes, except S. microlepis shows unusual AT-skew with slightly negative in tRNAs and PCGs. Bitterling mitogenomes exhibit highly conserved usage bias of start codon, relative synonymous codons and amino acids, overlaps and non-coding intergenic spacers. Phylogenetic trees constructed by 13 PCGs strongly support the polyphyly of the genus Acheilognathus and the paraphyly of Rhodeus and Tanakia. Together with the unusual characters of S. microlepis mitogenomes and phylogenetic trees, S. microlepis should be a sister species to the genus Rhodeu that might diverge about 13.69 Ma (95% HPD: 12.96-14.48 Ma).

Phylogeography of Endangered Bitterling Acheilognathus melanogaster Endemic to Eastern Japan

The bitterling Acheilognathus melanogaster is a critically endangered primary freshwater fish endemic to the Pacific side of eastern Japan. To elucidate A. melanogaster genetic structure, we investigated phylogeography in nine populations, using gene sequences of mitochondrial Cytochrome b (Cytb), as well as nuclear Rhodopsin (Rho) and glycosyltransferase (Glyt). We found four Cytb-based geographical clusters unevenly divided between the northern and southern regions, with smaller groups in the south. Of the nuclear genes, Glyt did not show geographical differentiation, whereas Rho formed two clusters: one widely occurring and another restricted to central regions. Genetic diversity was generally higher in southern than in northern populations. Our results suggest that conservation of southern local populations is particularly important in maintaining the genetic diversity of this endangered fish.

Complete mitochondrial genome of endangered Rhodeus pseudosericeus and its implications for the reconstruction of phylogenetic relationship among Acheilognathinae species

Rhodeus pseudosericeus is a native bitterling to the Korean Peninsula and found in very limited areas with small census size. Here, its complete mitochondrial genome was analyzed to provide novel data for the reconstruction of phylogenetic relationship among Acheilognathinae species. The genome was a 16,574 bp long consisting of 1 putative control region, 2 rRNA genes, 22 tRNA and 13 protein-coding genes. The gene arrangement was completely identical to those observed in other Acheilognathinae species as well as in other cyprinid species. In our phylogenetic analyses, three major genera of Acheilognathinae indepedently formed monophyletic groups in the tree reconstructed based on the whole genome sequences, whereas Rhodeus was not recovered as a single monophyly when solely considering protein-coding genes, indicating that the taxonomic reevaluation is still required in this subfamily.

Mitochondrial genome of Paracheilognathus imberbis (Cypriniformes: Cyprinidae: Acheilognathinae)

In this study, the complete mitochondrial genome (mitogenome) sequence of Paracheilognathus imberbis (Cypriniformes: Cyprinidae: Acheilognathinae) was determined by long PCR and primer-walking methods. The complete mitochondrial genome is 16,819 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes as well as a displacement loop (D-loop). The overall base composition of the genome is A(29.73%), T(27.25%), C(26.63%) and G(17.40%), respectively. The mitogenome of P. imberbis displayed novel gene order arrangement compared with published Rhodeus sinensis to date. The mitogenome would contribute to resolving phylogenetic position and interrelationships of Acheilognathinae.

Phylogenetic relationships of Acheilognathidae (Cypriniformes: Cyprinoidea) as revealed from evidence of both nuclear and mitochondrial gene sequence variation: evidence for necessary taxonomic revision in the family and the identification of cryptic species

Bitterlings are relatively small cypriniform species and extremely interesting evolutionarily due to their unusual reproductive behaviors and their coevolutionary relationships with freshwater mussels. As a group, they have attracted a great deal of attention in biological studies. Understanding the origin and evolution of their mating system demands a well-corroborated hypothesis of their evolutionary relationships. In this study, we provide the most comprehensive phylogenetic reconstruction of species relationships of the group based on partitioned maximum likelihood and Bayesian methods using DNA sequence variation of nuclear and mitochondrial genes on 41 species, several subspecies and three undescribed species. Our findings support the monophyly of the Acheilognathidae. Two of the three currently recognized genera are not monophyletic and the family can be subdivided into six clades. These clades are further regarded as genera based on both their phylogenetic relationships and a reappraisal of morphological characters. We present a revised classification for the Acheilognathidae with five genera/lineages: Rhodeus, Acheilognathus (new constitution), Tanakia (new constitution), Paratanakia gen. nov., and Pseudorhodeus gen. nov. and an unnamed clade containing five species currently referred to as "Acheilognathus". Gene trees of several bitterling species indicate that the taxa are not monophyletic. This result highlights a potentially dramatic underestimation of species diversity in this family. Using our new phylogenetic framework, we discuss the evolution of the Acheilognathidae relative to classification, taxonomy and biogeography.

Complete mitochondrial genome of Rhodeus lighti (Cypriniformes: Cyprinidae)

In this study, the complete mitochondrial genome (mitogenome) sequence of Rhodeus lighti (Cypriniformes: Cyprinidae) was determined by long PCR and primer walking methods. The complete mitochondrial genome is 16,677 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes as well as a displacement loop (D-loop). The overall base composition of the genome is A (28.87%), T (27.22%), C (26.53%) and G (17.38%). The mitogenome of R. lighti displayed novel gene order arrangement compared with published Rhodeus sinensis to date. The mitogenome would contribute to resolving phylogenetic position and interrelationships of Acheilognathinae.

Phylogenetic relationships of bitterling fishes (Teleostei: Cypriniformes: Acheilognathinae), inferred from mitochondrial cytochrome B sequences

Bitterling (Teleostei: Acheilognathinae) are small cyprinid fishes with a discrete distribution in East Asia and Europe. We used a complete mitochondrial cytochrome b sequence (1141 bp) from 49 species or subspecies in three genera (Tanakia, Rhodeus, and Acheilognathus), sampled across the major part of their distribution, to elucidate their phylogeny and biogeography, focusing particularly on their origin and dispersal. Based on high support value, the monophyletic Acheilognathinae separated into two major clades, Acheilognathus and Tanakia-Rhodeus. In the latter clade, the monophyly of Rhodeus was poorly supported, though it was topologically nested in Tanakia. On the basis of molecular-clock calibration, both clades diverged in the middle Miocene, with Tanakia-Rhodeus diverging slightly earlier than Acheilognathus. The Tanakia-Rhodeus clade expanded its distribution westward from the Far East, eventually reaching Europe, while Acheilognathus dispersed in the temperate regions of East Asia. A feature common to both clades is that most extant species, including Japanese endemics, appeared by the end of the Pliocene, corresponding with the present delineation of the Japanese archipelago. Autumn-spawning species with an embryonic diapause, unique to bitterling among cyprinid fishes, formed two distinct lineages (barbatulusrhombeus and longipinnis-typus) within Acheilognathus. The estimated time of divergence of the two lineages was approximately from the late Pliocene, a period characterized by glaciations. The timing of divergence suggests that the shift of spawning from spring to autumn, coupled with embryonic diapause, convergently emerged twice in the evolution of bitterling, possibly as an adaptation to the climate of the late Pliocene.

Complete mitochondrial genome of the Chinese bitterling Rhodeus sinensis (Cypriniformes: Cyprinidae)

The mitochondrial genome of the Chinese bitterling Rhodeus sinesis is a circular molecule of 16,677 bp in length, containing 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two main non-coding regions (the control region and the origin of the light strand replication). The gene composition and order of which were similar to most other vertebrates. All protein-coding genes are initiated with ATG except for COX 1, which begin with GTG instead. However, the termination codons of 13 protein-coding genes are varied with TAA, TA, T or TAG. The molecular data we presented here could provide useful information for the studies on species identification, evolutionary relationships and population genetics of the Acheilognathinae.