cnfishbase: A cyber Chinese fish database

A review of age estimation methods in non-avian reptiles by growth marks in hard tissues

Age and growth-related data are basic biological parameters, essential in population ecology, evolution, and conservation biology. There is a growing body of published information on reptile demography derived from sclerochronology, a technique based on counting the growth layers deposited in bones (skeletochronology) and other hard body structures. Since the data are not always easily available, we compiled the existing published data, described the current status of knowledge, synthetized the conclusions of disparate studies, and identified patterns of research and information gaps, prioritizing the needs for future research. Our database includes the results of 468 published studies covering 236 reptile species from 41 families. These represent less than 2% of the total number of known extant species. Turtles and crocodiles are proportionally better studied, while snakes are the least examined group. The distribution of the research does not reflect conservation needs; we found an important geographic bias, with an overrepresentation of Northern temperate species. Only 23% of the studies checked the assumption of periodicity of growth marks deposition, and the method was found to be reliable or adequate in 79% of the cases. Overall, the data obtained through sclerochronology can be considered robust, especially if validation methods are employed, since the general goal is to characterize population parameters, trends, and dynamics, rather than determining the exact age of any specimen in particular.

Mitogenomic phylogeny, biogeography, and cryptic divergence of the genus Silurus (Siluriformes: Siluridae)

The genus Silurus, an important group of catfish, exhibits heterogeneous distribution in Eurasian freshwater systems. This group includes economically important and endangered species, thereby attracting considerable scientific interest. Despite this interest, the lack of a comprehensive phylogenetic framework impedes our understanding of the mechanisms underlying the extensive diversity found within this genus. Herein, we analyzed 89 newly sequenced and 20 previously published mitochondrial genomes (mitogenomes) from 13 morphological species to reconstruct the phylogenetic relationships, biogeographic history, and species diversity of Silurus. Our phylogenetic reconstructions identified eight clades, supported by both maximum-likelihood and Bayesian inference. Sequence-based species delimitation analyses yielded multiple molecular operational taxonomic units (MOTUs) in several taxa, including the Silurus asotus complex (four MOTUs) and Silurus microdorsalis (two MOTUs), suggesting that species diversity is underestimated in the genus. A reconstructed time-calibrated tree of Silurus species provided an age estimate of the most recent common ancestor of approximately 37.61 million years ago (Ma), with divergences among clades within the genus occurring between 11.56 Ma and 29.44 Ma, and divergences among MOTUs within species occurring between 3.71 Ma and 11.56 Ma. Biogeographic reconstructions suggested that the ancestral area for the genus likely encompassed China and the Korean Peninsula, with multiple inferred dispersal events to Europe and Central and Western Asia between 21.78 Ma and 26.67 Ma and to Japan between 2.51 Ma and 18.42 Ma. Key factors such as the Eocene-Oligocene extinction event, onset and intensification of the monsoon system, and glacial cycles associated with sea-level fluctuations have likely played significant roles in shaping the evolutionary history of the genus Silurus.

CoSFISH: a comprehensive reference database of COI and 18S rRNA barcodes for fish

Fish, being a crucial component of aquatic ecosystems, holds significant importance from both economic and ecological perspectives. However, the identification of fish at the species level remains challenging, and there is a lack of a taxonomically complete and comprehensive reference sequence database for fish. Therefore, we developed CoSFISH, an online fish database. Currently, the database contains 21 535 cytochrome oxidase I sequences and 1074 18S rRNA sequences of 21 589 species, belonging to 8 classes and 90 orders. We additionally incorporate online analysis tools to aid users in comparing, aligning and analyzing sequences, as well as designing primers. Users can upload their own data for analysis, in addition to using the data stored in the database directly. CoSFISH offers an extensive fish database and incorporates online analysis tools, making it a valuable resource for the study of fish diversity, phylogenetics and biological evolution. Database URL:  http://210.22.121.250:8888/CoSFISH/home/indexPage.