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Exploring taxonomic diversity and biogeography of the family Nemacheilinae (Cypriniformes).

ABSTRACT: Nemacheilidae, in the superfamily Cobitoidea, is comprised of many of morphologically similar fish species that occur in Eurasian water bodies. This large group shows inconsistencies between traditional morphological taxonomy and molecular phylogenetic data. We used mitochondrial genomes, recombinase-activating gene proteins 1 (RAG1) and the mitochondrial cytochrome c oxidase I gene (COI) to study the phylogenetic relationships among Nemacheilidae species using Bayesian inference and maximum likelihood approaches. Phylogenetic analyses based on mitogenomes provided support for two clades (I and II). The mitogenomes, RAG1, and COI results indicated that several species and genera were not consistent with the traditional morphological subdivisions. The two clades inferred from mitogenomes showed clear geographical patterns. The Tibetan Plateau, Hengduan Mountains, and the Iran Plateau may act as a barrier dividing the clades. The estimated timing of clades separation (36.05 million years ago) coincides with the first uplift of the Tibetan Plateau. We conclude that the geological history of the Tibetan Plateau played a role in the diversification and distribution of the Nemacheilidae taxa. These results provided a phylogenetic framework for future studies of this complex group.

SUBMITTER: Chen W

PROVIDER: S-EPMC6787813 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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Exploring taxonomic diversity and biogeography of the family Nemacheilinae (Cypriniformes).

Chen Weitao W Yang Jiping J Li Yuefei Y Li Xinhui X

Ecology and evolution 20190828 18

Nemacheilidae, in the superfamily Cobitoidea, is comprised of many of morphologically similar fish species that occur in Eurasian water bodies. This large group shows inconsistencies between traditional morphological taxonomy and molecular phylogenetic data. We used mitochondrial genomes, recombinase-activating gene proteins 1 (RAG1) and the mitochondrial cytochrome <i>c</i> oxidase I gene (COI) to study the phylogenetic relationships among Nemacheilidae species using Bayesian inference and maxi ...[more]

PMID: 31624553

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Project description:BACKGROUND:Endophytes are microbes that colonize plant internal tissues without causing disease. In particular, seed-associated endophytes may be vectors for founder microbes that establish the plant microbiome, which may subsequently contribute beneficial functions to their host plants including nutrient acquisition and promotion of plant growth. The Cucurbitaceae family of gourds (e.g., cucumbers, melons, pumpkin, squash), including its fruits and seeds, is widely consumed by humans. However, there is limited data concerning the taxonomy and functions of seed-associated endophytes across the Cucurbitaceae family. Here, bacteria from surface-sterilized seeds of 21 curcurbit varieties belonging to seven economically important species were cultured, classified using 16S rRNA gene sequencing, and subjected to eight in vitro functional tests. RESULTS:In total, 169 unique seed-associated bacterial strains were cultured from selected cucurbit seeds. Interestingly, nearly all strains belonged to only two phyla (Firmicutes, Proteobacteria) and only one class within each phyla (Bacilli, ?-proteobacteria, respectively). Bacillus constituted 50 % of all strains and spanned all tested cucurbit species. Paenibacillus was the next most common genus, while strains of Enterobacteriaceae and lactic acid bacteria were also cultured. Phylogenetic trees showed limited taxonomic clustering of strains by host species. Surprisingly, 33 % of strains produced the plant hormone, indole-3-acetic acid (auxin), known to stimulate the growth of fruits/gourds and nutrient-acquiring roots. The next most common nutrient acquisition traits in vitro were (in rank order): nitrogen fixation/N-scavenging, phosphate solubilisation, siderophore secretion, and production of ACC deaminase. Secretion of extracellular enzymes required for nutrient acquisition, endophyte colonization and/or community establishment were observed. Bacillus strains had the potential to contribute all tested functional traits to their hosts. CONCLUSION:The seeds of economically important cucurbits tested in this study have a culturable core microbiota consisting of Bacillus species with potential to contribute diverse nutrient acquisition and growth promotion activities to their hosts. These microbes may lead to novel seed inoculants to assist sustainable food production. Given that cucurbit seeds are consumed by traditional societies as a source of tryptophan, the precursor for auxin, we discuss the possibility that human selection inadvertently facilitated auxin-mediated increases in gourd size.

Project description:BackgroundThe genus Algansea is one of the most representative freshwater fish groups in central Mexico due to its wide geographic distribution and unusual level of endemicity. Despite the small number of species, this genus has had an unsettled taxonomic history due to high levels of intraspecific morphological variation. Moreover, several phylogenetic hypotheses among congeners have been proposed but have had the following shortcomings: the use of homoplasious morphological characters, the use of character codification and polarisation methods that lacked objectivity, and incomplete taxonomic sampling. In this study, a phylogenetic analysis among species of Algansea is presented. This analysis is based upon two molecular markers, the mitochondrial gene cytochrome b and the first intron of the ribosomal protein S7 gene.ResultsBayesian analysis based on a combined matrix (cytochrome b and first intron S7) showed that Algansea is a monophyletic group and that Agosia chrysogaster is the sister group. Divergence times dated the origin of the genus around 16.6 MYA, with subsequent cladogenetic events occurring between 6.4 and 2.8 MYA. When mapped onto the molecular phylogenetic hypothesis, the character states of three morphological characters did not support previous hypotheses on the evolution of morphological traits in the genus Algansea, whereas the character states of the remaining six characters partially corroborated those hypotheses.ConclusionMonophyly of the genus Algansea was corroborated in this study. Tree topology shows the genus consists of three main lineages: Central-Eastern, Western, and Southern clades. However, the relationships among these clades remained unresolved. Congruence found between the available geological and climatic history and the divergence times made it possible to infer the biogeographical history of Algansea, which suggested that vicariance events were responsible for the evolutionary history of the genus. Interestingly, this pattern was shared with other members of the freshwater fish fauna of central Mexico. In addition, molecular data also show that some morphological traits alleged to represent synapomorphies in previous studies were actually homoplasies. Others traits were corroborated as synapomorphies, particularly in those species of a subgroup corresponding with the Central-Eastern clade within Algansea; this corroboration is interpreted as a result of evolutionary adaptations.

Dataset Information

Exploring taxonomic diversity and biogeography of the family Nemacheilinae (Cypriniformes).

Publications

Exploring taxonomic diversity and biogeography of the family Nemacheilinae (Cypriniformes).

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