Dataset Information

Phylogenomic analysis of trichomycterid catfishes (Teleostei: Siluriformes) inferred from ultraconserved elements.

ABSTRACT: The family Trichomycteridae is one of the most diverse groups of freshwater catfishes in South and Central America with eight subfamilies, 41 genera and more than 300 valid species. Its members are widely distributed throughout South America, reaching Costa Rica in Central America and are recognized by extraordinary anatomical specializations and trophic diversity. In order to assess the phylogenetic relationships of Trichomycteridae, we collected sequence data from ultraconserved elements (UCEs) of the genome from 141 specimens of Trichomycteridae and 12 outgroup species. We used a concatenated matrix to assess the phylogenetic relationships by Bayesian inference (BI) and maximum likelihood (ML) searches and a coalescent analysis of species trees. The results show a highly resolved phylogeny with broad agreement among the three distinct analyses, providing overwhelming support for the monophyletic status of subfamily Trichomycterinae including Ituglanis and Scleronema. Previous relationship hypotheses among subfamilies are strongly corroborated, such as the sister relationship between Copionodontinae and Trichogeninae forming a sister clade to the remaining trichomycterids and the intrafamilial clade TSVSG (Tridentinae-Stegophilinae-Vandelliinae-Sarcoglanidinae-Glanapteryginae). Monophyly of Glanapteryginae and Sarcoglanidinae was not supported and the enigmatic Potamoglanis is placed outside Tridentinae.

SUBMITTER: Ochoa LE

PROVIDER: S-EPMC7021825 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Phylogenomic analysis of trichomycterid catfishes (Teleostei: Siluriformes) inferred from ultraconserved elements.

Ochoa Luz E LE Datovo Aléssio A DoNascimiento Carlos C Roxo Fabio F FF Sabaj Mark H MH Chang Jonathan J Melo Bruno F BF Silva Gabriel S C GSC Foresti Fausto F Alfaro Michael M Oliveira Claudio C

Scientific reports 20200214 1

The family Trichomycteridae is one of the most diverse groups of freshwater catfishes in South and Central America with eight subfamilies, 41 genera and more than 300 valid species. Its members are widely distributed throughout South America, reaching Costa Rica in Central America and are recognized by extraordinary anatomical specializations and trophic diversity. In order to assess the phylogenetic relationships of Trichomycteridae, we collected sequence data from ultraconserved elements (UCEs ...[more]

PMID: 32060350

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Project description:BackgroundAfrican catfishes of the families Bagridae and Clariidae are known to be parasitized with monogeneans of Quadriacanthus Paperna, 1961 (Dactylogyridae). The genus remains taxonomically challenging due to its speciose nature and relatively wide host range representing two fish orders, i.e. Siluriformes and Osteoglossiformes, in Africa and Asia. Here, we investigated diversity of Quadriacanthus spp. parasitizing Clarias gariepinus (Burchell), Heterobranchus bidorsalis Geoffroy Saint-Hilaire, and Bagrus docmak (Forsskål) collected in the Lake Turkana (Kenya) and Nile River Basin (Sudan). The interspecific relationships among Quadriacanthus spp. parasitizing catfishes inferred from ribosomal DNA sequences were investigated for the first time.MethodsA combined morphological and molecular approach was used for description of the new species and for a critical review of the previously described Quadriacanthus spp., by means of phase contrast microscopic examination of sclerotized structures, and assessing the genetic divergence among the species found using rDNA sequences.ResultsSeven species (including four new) of Quadriacanthus were identified. These were as follows: Quadriacanthus aegypticus El-Naggar & Serag, 1986, Quadriacanthus clariadis Paperna, 1961, Quadriacanthus fornicatus n. sp., Quadriacanthus pravus n. sp., and Quadriacanthus zuheiri n. sp. from Clarias gariepinus (Clariidae); Quadriacanthus mandibulatus n. sp. from Heterobranchus bidorsalis (Clariidae); and Quadriacanthus bagrae Paperna, 1979 from Bagrus docmak (Bagridae). For both 18S-ITS1 and 28S rDNA regions, Q. clariadis from a clariid fish was found to be most closely related to Q. bagrae from a bagrid host. Quadriacanthus mandibulatus n. sp. was observed to be the most distant species from the others. The separation of Q. mandibulatus n. sp. from the other species corresponds with the different morphology of its copulatory tube. The copulatory tube is terminally enlarged in Q. mandibulatus n. sp., while the tube in all other congeners studied is comparatively small and with an oblique tapering termination.ConclusionsThis study contributes to a better understanding of African dactylogyrid diversity and provides the first molecular characterization of Quadriacanthus spp. The observed interspecific genetic relationships among Quadriacanthus spp. from clariids and Q. bagrae from a bagrid host suggest a possible host-switching event in the evolutionary history of the genus. Our records extend the currently known geographical range for Quadriacanthus spp. to Kenya and Sudan.

Project description:The phylogenetic relationships of dactylogyrids (Monogenea: Dactylogyridae) parasitising catfishes (Siluriformes) from the Neotropical region were investigated for the first time.Partial sequences of the 28S rRNA gene of 40 specimens representing 25 dactylogyrid species were analysed together with sequences from GenBank using Bayesian inference, Maximum likelihood and Parsimony methods. Monophyly of dactylogyrids infecting catfishes and the Ancyrocephalinae was evaluated using the Approximately Unbiased test.The Ancyrocephalinae is a paraphyletic group of species clustering in three main clades as follows: (i) clade A comprising freshwater dactylogyrids from the Holarctic parasitising perciforms clustering together with species (Ameloblastella, Unibarra and Vancleaveus) parasitising Neotropical catfishes; (ii) clade B including species of Dactylogyrus (Dactylogyrinae) and Pseudodactylogyrus (Pseudodactylogyrinae) along with Ancyrocephalus mogurndae, and marine dactylogyrids with cosmopolitan distribution, parasites of scorpaeniforms and perciforms, along with the freshwater Cichlidogyrus and Scutogyrus (infecting African cichlids [Cichlidae]) and (iii) clade C containing exclusively dactylogyrids of siluriforms, freshwater and marine, with Palaearctic, Ethiopian, Oriental and Neotropical distributions; species of Aphanoblastella and Dactylogyridae gen. sp. 4 from the Neotropical region clustering together with species allocated in the Ancylodiscoidinae, along with species of Cosmetocleithrum, Demidospermus and Dactylogyridae gen. spp.The position of the Ancylodiscoidinae within a larger clade of dactylogyrids (ancyrocephalines) indicates that this subfamily does not represent a natural group. Instead, species allocated to this clade (dactylogyrids of siluriforms along with species of the Ancylodiscoidinae) should be considered as a separate subfamily within the Dactylogyridae. The erection of this taxon requires the search for morphological diagnostic characters in addition to phylogenetic information. A similar strategy should be considered for a new classification of the paraphyletic Ancyrocephalinae. Members of the three clades do not seem to share obvious morphological synapomorphies nor clear patterns in host-parasite associations, zoogeographical distribution or ecology. Clade A should be considered as the Ancyrocephalinae sensu stricto since it includes the type species Ancyrocephalus paradoxus Creplin, 1839. A new subfamily should be proposed to accommodate species currently allocated to Ancyrocephalinae clustering within clade B. Future attempts to propose a new classification of the subfamilies in the Dactylogyridae should include the phylogenetically diverse Neotropical dactylogyrids.

Project description:Choosing among types of genomic markers to be used in a phylogenomic study can have a major influence on the cost, design, and results of a study. Yet few attempts have been made to compare categories of next-generation sequence markers limiting our ability to compare the suitability of these different genomic fragment types. Here we explore properties of different genomic markers to find if they vary in the accuracy of component phylogenetic trees and to clarify the causes of conflict obtained from different datasets or inference methods. As a test case, we explore the causes of discordance between phylogenetic hypotheses obtained using a novel dataset of ultraconserved elements (UCEs) and a recently published exon dataset of the cichlid tribe Heroini. Resolving relationships among heroine cichlids has historically been difficult, and the processes of colonization and diversification in Middle America and the Greater Antilles are not yet well understood. Despite differences in informativeness and levels of gene tree discordance between UCEs and exons, the resulting phylogenomic hypotheses generally agree on most relationships. The independent datasets disagreed in areas with low phylogenetic signal that were overwhelmed by incomplete lineage sorting (ILS) and non-phylogenetic signals. For UCEs, high levels of ILS were found to be the major cause of gene tree discordance, whereas, for exons, non-phylogenetic signal is most likely caused by a reduced number of highly informative loci. This paucity of informative loci in exons might be due to heterogeneous substitution rates that are problematic to model (i.e., computationally restrictive) resulting in systematic errors that UCEs (being less informative individually but more uniform) are less prone to. These results generally demonstrate the robustness of phylogenomic methods to accommodate genomic markers with different biological and phylogenetic properties. However, we identify common and unique pitfalls of different categories of genomic fragments when inferring enigmatic phylogenetic relationships.

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Dataset Information

Phylogenomic analysis of trichomycterid catfishes (Teleostei: Siluriformes) inferred from ultraconserved elements.

Publications

Phylogenomic analysis of trichomycterid catfishes (Teleostei: Siluriformes) inferred from ultraconserved elements.

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