Phylogenomic reappraisal of the Neotropical catfish family Loricariidae using ultraconserved elements

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Phylogenomic reappraisal of the Neotropical catfish family Loricariidae using ultraconserved elements

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Fábio F.Roxo, Luz E.Ochoa, Mark H. Sabaj, Nathan K. Lujan, Raphaël Covaine, Gabriel S.C.Silva, Bruno F.Melo, James S.Albert, Jonathan Changh, Fausto Forestia, Michael E. Alfaro & Claudio Oliveira. 2019. Phylogenomic reappraisal of the Neotropical catfish family Loricariidae (Teleostei: Siluriformes) using ultraconserved elements. Molecular Phylogenetics and Evolution, In Press, Available online 22 February 2019.

Highlights:
Molecular dated phylogeny of Loricariidae based on 163 terminal taxa spanning 140 species (∼15%) and 75 genera (∼70%) distributed among all proposed subfamilies.

Loricariidae was found monophyletic.

Early diversification of Loricariidae occurred to Late Cretaceous at ∼65 mya.

Our results corroborate the monophyletic hypotheses and relationship among examined subfamilies.

Our results reinforce the established backbone of loricariid interrelationships.

Abstract:
Neotropical freshwaters host more than 6,000 fish species, of which 983 are suckermouth armored catfishes of the family Loricariidae – the most-diverse catfish family and fifth most species-rich vertebrate family on Earth. Given their diversity and ubiquitous distribution across many habitat types, loricariids are an excellent system in which to investigate factors that create and maintain Neotropical fish diversity, yet robust phylogenies needed to support such ecological and evolutionary studies are lacking. We sought to buttress the systematic understanding of loricariid catfishes by generating a genome-scale data set (1,041 loci, 328,330 bp) for 140 species spanning 75 genera and five of six previously proposed subfamilies. Both maximum likelihood and Bayesian analyses strongly supported the monophyly of Loricariidae. Our results also reinforced the established backbone of loricariid interrelationships: Delturinae as sister to all other analyzed loricariids, with subfamily Rhinelepinae diverging next, followed by Loricariinae sister to Hypostominae + Hypoptopomatinae. Previous DNA-based relationships within Hypostominae and Loricariinae were strongly supported. However, we evaluated for the first time DNA-based relationships among many Hypoptopomatinae genera and found significant differences with this subfamily’s current genus-level classification, prompting several taxonomic changes. Finally, we placed our topological results within a fossil-calibrated temporal context indicating that early Loricariidae diversification occurred across the Cretaceous-Paleogene boundary ∼65 million years ago (Ma). Our study lays a strong foundation for future research to focus on relationships among species and the macroevolutionary processes affecting loricariid diversification rates and patterns.

https://www.sciencedirect.com/science/a ... via%3Dihub
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Re: Phylogenomic reappraisal of the Neotropical catfish family Loricariidae using ultraconserved elements

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Figure from article
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Re: Phylogenomic reappraisal of the Neotropical catfish family Loricariidae using ultraconserved elements

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The final published citation is available:

Roxo, F.F., Ochoa, L.E., Sabaj, M.H., Lujan, N.K., Covaine, R., Silva, G.S.C., Melo, B.F., Albert, J.S., Chang, J., Foresti, F., Alfaro, M.E., & Oliveira, C. (2019). Phylogenomic reappraisal of the Neotropical catfish family Loricariidae (Teleostei: Siluriformes) using ultraconserved elements. Molecular Phylogenetics and Evolution, 135: 148-165.

https://doi.org/10.1016/j.ympev.2019.02.017
https://www.sciencedirect.com/science/a ... 0318307243
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Poor taxonomic sampling undermines nomenclatural stability: A reply to Roxo et al. (2019)

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Reis, RE, HA Britski, MR Britto, PA Buckup, BA Calegari, P Camelier, MLS Delapieve, F Langeani, P Lehmann A, PHF Lucinda, M Marinho, FO Martins, NA Menezes, CR Moreira, MCC de Pinna, CS Pavanelli, LHR Py-Daniel & LM Sousa, 2019. Poor taxonomic sampling undermines nomenclatural stability: A reply to Roxo et al. (2019). Zootaxa 4701: 497–500.

A recent study based on genomic data by Roxo et al. (2019) provided a phylogeny of the Loricariidae, the largest catfish family and second largest Neotropical fish family with approximately 1,000 species. The study represents a valuable and innovative contribution for understanding higher-level relationships within the family. The phylogenetic tree inferred by Roxo et al. (2019) thoroughly corroborates the monophyly and relationships of most currently accepted subfamilies of Loricariidae, based on a fair taxon sampling (nearly 14% of the species in the family) representing most genera of each but one of the subfamilies, the Lithogeninae, the sister-group of the remaining members of the family (Pereira & Reis, 2017; Reis et al., 2017). In addition to a hypothesis of relationships, Roxo et al. (2019) also proposed a series of lower-level taxonomic changes, which are deemed premature considering that the taxonomic sampling of the study targeted higher-level clades, and go against one of the pillars of biological classification: nomenclatural stability (e.g., Heterick & Majer, 2018; Beninger & Backeljau, 2019). Here we (1) discuss implications of inadequate taxonomic sampling as a basis for changes in classification of species; (2) explain why the taxonomic sampling design of Roxo et al. (2019) is inadequate for the proposed nomenclatural changes; and (3) advocate that changes to classifications must be grounded on phylogenies with dense sampling of taxa at the relevant level.
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Re: Phylogenomic reappraisal of the Neotropical catfish family Loricariidae using ultraconserved elements

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Re: Phylogenomic reappraisal of the Neotropical catfish family Loricariidae using ultraconserved elements

Post by lfinley58 »

The above paper noted by Silurus and Eric can be viewed in full at the following link:

https://www.researchgate.net/publicatio ... et_al_2019

Lee
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