| The Gobioninae (gudgeons), a group of small or medium-sized primary freshwater fishes, is one of the most speciose subfamily in Cyprinide. Comprising more than 190 species and subspecies in about 30 genera and subgenera, Gobioninae are mainly distributed in east Asia with only several genera widespread in Eurasia. Because members within this subfamily exhibit a broad range morphological, ecological, and behavioral variation, the monophyly, systematic position, validities of some genera and intergeneric relationships of this group are still unresolved. In the present study, we investigated the possible monophyly of the Gobioninae and analysed the interrelationships within the group by using complete mitochondrial cytochrome b (cyt b) gene and the control region (d-loop) sequences from most genera within the gobionine group with other cyprinids as outgroups. Based on molecular clock established with cyt b gene sequences, we also analysed the evolutionary processes, as well as biogeography processes of some representative genera and species. Lastly, combined with the molecular phylogenetic results, we inferred the evolutionary processes of morphological characters of Gobioninae fishes. The following are the main conclusions: 1. We determined 70 complete mitochondrial cyt b gene sequences, which contain 61 individuals representing 55 species and 23 genera of the Gobioninae as well as 9 individuals representing 9 species and 9 genera of other cyprinid fishes. And we retrieved 4 cyt b sequences representing 4 species and 4 genera of the Gobioninae as well as 8 cyt b sequences representing 8 species and 8 genera of Leuciscinii from the Genbank. Totally 82 sequences were used to infer the phylogenetic relationships of the Gobioninae, with Barbus barbus, Cyprinus carpio and Discogobio tetrabarbatus as outgroups. Phylogenetic trees were estimated with maximum parsimony (MP), maximum likelihood (ML), neighbor joining (NJ) and Bayesian optimality criteria. Our results show when Gobiobotia and Gobiocypris included, the Gobioninae is a monophyletic group and belongs to Leuciscinii. We also identified four monophyletic groups within the subfamily: Hemibarbininii, Sarcocheilichthysinii, Gobioninii and Pseudogobioninii. Our results also suggested that genera Romanogobio, Huigobio, Rostrogobio, and Platysmacheilus should be treated as valid. However, genera Belligobio, Paraleucogobio were suggested as the synonyms of Hemibarbus and Gnthopogon, respectively. 2. Based on the control region and cyt b gene sequences of 37 specimens that represent 34 species and 20 genera of Gobioninae, we compared the evolutionary rates of these two genes and analyzed the structure of d-loop, and discussed the phylogenetic implications on the Gobioninae. The comparison of evolution rate between d-loop and cyt b gene sequences indicated that sequence divergences of the former were broadly higher than those of the latter. However, considering for the closely related species only, d-loop was evolving slower than cyt b gene. Similar to that of other reported fishes, structure of d-loop region in gobionine fishes can be identified as three blocks: Extended termination associated sequence (ETAS), Central conserved domain (CD) and Conserved sequence block (CSB). Some conserved sequences were identified and their general sequences were given. We also established the phylogenetic trees based on d-loop sequences using maximum parsimony (MP) and Bayesian methods. Molecular phylogenetic results showed that the Gobioninae is not monophyletic because someLeuciscinae species were mixed within it. Such results indicated that d-loop sequences might not be an appropriate molecular marker for study the Gobioninae phylogeny. However, the result still supported this subfamily grouped as Hemibarbininii, Sarcocheilichthysinii, Gobioninii and Pseudogobioninii four monophyletic groups when ignoring the Leuciscinae taxa. 3. Based on the molecular clock theory and using the earliest and the latest fossil records of the Gobioninae fishes as calibration points, we constructed a relaxed molecular clock tree with cyt b gene sequences to estimate divergent times of the Gobioninae fishes. The estimation results indicated that the Gobioninae most possibly originated in early Eocene. The four groups of the Gobioninae all diverged in Oligocene and most of genera had diverged before middle Miocene. The species divergence mostly concentrated in four periods, 16-15 MYA, 8-7 MYA, 4-3 MYA and 2-0.5 MYA. According to results of the estimation, we also analyzed the evolutionary rules of the Gobioninae fishes. The results show that the lineages of the Gobioninae increased with exponential function y = 1.9754×e0.176x. Although the numbers of lineages increased all the time, the increasing rate and net increasing rate of the numbers of lineages decreased, and the latter decreased more distinct. The life-span of the Gobioninae fishes above species level has a broadly range with some lineage survived older than 15 MYA, but most of them concentrated within 4 MYA. This phenomenon may be induced by difference of species birth rate and extinct rate which induced by natural selection. The life-span of the extant the Gobioninae fishes is similar with that of the above species taxa, which indicated that natural selection influenced the divergence of the Gobioninae fishes not only above species level, but also at species level. The fact that the extant species of Hemibarbinii are less than those of the other three groups might be explained by the reason that the species selection resulted in different random extinction among groups, or species equilibrium in niche. 4. Because the Gobioninae have lots of species and genera, and almost all the genera are widespread, it is nearly impossible to analyze the biogeography of the wholesubfamily. However, recent diverged species and populations usually comparted distinctive, and exhibit obvious vicariance events. Therefore, we selected Sarcocheilichthys, Saurogobio, Abbottina and Pseudorasbora parva as representative groups, of which specimens were also collected comprehensively, to analyze the biogeographical process of the Gobioninae fishes at species and population level. Our results indicated that under short time scale the biogeographical process of the Gobioninae fishes could be described as population differentiation in the south and north Eastern Asia. If magnifiing the time scale, the biogeographical process of the Gobioninae fishes exhibited species level differentiation from north to south Eastern Asia. Tectonic movements and changing environment, as well as different adaptive abilities of fishes might have worked together on these biogeographical processes. 5. Combined with the molecular phylogenetic result, we selected 8 characters, the row of teeth, body shape, anus position, swim bladder, mouth position, lower lips structure, barbels length, eye size, and habitat, to discuss the morphological character evolution of the Gobioninae fishes. The result showed that the morphological character evolution of the Gobioninae fishes could be divided into two dimensions: spatial and nutritional. Characters, such as body shape, anus position, swim bladder and lower lips structure, could be related to spacial niche; characters, such as row of teeth, mouth position, barbels length and eye size, might be induced by differentiation of diet and habitat, namely as nutritional niche. Comparing with the result of molecular phylogeny and characters of outgroup, we propose that the Hemibarbinii are a group of lower or medial dwellers living in large rivers and big lakes, and remain some ancestral characters, such as elongate and compressed body shape, anus close to the anal fin, developed and free swim bladder and simple lower lips; compared with the Hemibarbinii, the Sarcocheilichthysinii are medial dwellers which has some specialized characters, such as oblong and compressed body shape; the Gobioninii, lower dwellers, have some more specialized characters, such as body shape elongate and cylindrical, anus close to the pelvic fin, etc.; the Pseudogobioninii are the most specialized benthicdwellers, and their body shapes evolved as elongate and cylindrical, anus close to the pelvic fins, swim bladders reduced and the posterior chamber smaller than the anterior, the first chamber enclosed in a osseous or fibrous capsule, lower lip was divided into lobes with developed papillae on it. As for the nutritional related characters, such as row of teeth, mouth position, eye size and barbels length, and so on, they evolved in parallel among the different groups.
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