Phylogenomic analysis of the Neotropical fish subfamily Characinae using ultraconserved elements (Teleostei: Characidae)

Souza, Camila Silveira; Melo, Bruno F.; Mattox, George M. T.; Oliveira, Cláudio

doi:10.1016/j.ympev.2022.107462

Cited by 5 publications

(3 citation statements)

References 69 publications

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“…Such investigations rely on the availability of robust phylogenetic hypotheses for clades of interest, but phylogenetic inference has often been challenged by the rapid diversification experienced by many of these lineages. While efforts to elucidate the evolutionary history of Neotropical freshwater fishes have vastly benefited from the application of phylogenomic methods [e.g., [3][4][5][6][7][8][9][10][11], there remains considerable uncertainty about phylogenetic relationships and species delimitations, particularly at recent time scales.…”

Section: Introductionmentioning

confidence: 99%

Phylogenomics of trans-Andean tetras of the genus Hyphessobrycon Durbin 1908 (Stethaprioninae: Characidae) and colonization patterns of Middle America

Elías

McMahan²,

Alda³

et al. 2023

PLoS ONE

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Hyphessobrycon is one of the most species rich and widely distributed genera in the family Characidae, with more than 160 species ranging from Veracruz, Mexico to Mar Chiquita Lagoon in Buenos Aires, Argentina. The majority of Hyphessobrycon diversity shows a cis-Andean distribution; only nine species are trans-Andean including H. compressus (Meek 1908). It is well established that Hyphessobrycon is not monophyletic but it has been suggested that natural groups can be identified within the larger Hyphessobrycon species group. In this study, we tested the monophyly of trans-Andean species of Hyphessobrycon and investigated the placement of H. compressus. We inferred the first phylogenomic hypothesis of trans-Andean Hyphessobrycon that includes nearly complete taxonomic sampling (eight of nine valid species) using ultraconserved elements (UCEs). We analyzed 75% (1682 UCEs), 90% (1258 UCEs), and 95% (838 UCEs) complete data matrices, and inferred phylogenomic hypotheses under concatenation and coalescent approaches. In all cases, we recovered the monophyly of trans-Andean Hyphessobrycon inclusive of H. compressus, strong support for three species groups, and evidence of cryptic diversity within the widespread H. compressus and H. condotensis. We used our phylogenomic hypothesis to investigate the biogeographic history of Hyphessobrycon in Middle America. Our ancestral range estimation analysis suggests a single event of cis- to trans-Andean colonization followed by stepwise colonization from the Pacific slope of northwestern South America (Chocó block) to northern Middle America (Maya block). Our work supports the recognition of the trans-Andean species as Hyphessobrycon sensu stricto and provides an evolutionary template to examine morphological characters that will allow us to better understand the diversity of Hyphessobrycon in Middle America.

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Section: Introductionmentioning

confidence: 99%

Phylogenomics of trans-Andean tetras of the genus Hyphessobrycon Durbin 1908 (Stethaprioninae: Characidae) and colonization patterns of Middle America

Elías

McMahan²,

Alda³

et al. 2023

PLoS ONE

View full text Add to dashboard Cite

show abstract

“…Such investigations rely on the availability of robust phylogenetic hypotheses for clades of interest, but phylogenetic inference has often been challenged by the rapid diversification experienced by many of these lineages. While efforts to elucidate the evolutionary history of Neotropical freshwater fishes have been vastly benefited from the application of phylogenomic methods [e.g., 3 – 11], there remains considerable uncertainty about phylogenetic relationships and species delimitations, particularly at recent time scales.…”

Section: Introductionmentioning

confidence: 99%

Phylogenomics oftrans-Andean tetras of the genusHyphessobryconDurbin 1908 and colonization patterns of Middle America

Elías

McMahan

Alda

et al. 2022

Preprint

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Hyphessobrycon is one of the most species rich and widely distributed genera in the family Characidae, with more than 160 species ranging from Veracruz, Mexico to Argentina. The majority of the diversity of Hyphessobrycon shows a cis-Andean distribution; only nine species are trans-Andean including H. compressus (Meek 1908). It is well established that Hyphessobrycon is not monophyletic but has been suggested that natural groups can be identified within the larger Hyphessobrycon species group. In this study, we test the monophyly of trans-Andean species of Hyphessobrycon and investigate the placement of H. compressus. We have inferred the first phylogenomic hypothesis of trans-Andean Hyphessobrycon that includes nearly complete taxonomic sampling (eight of nine valid species) using ultraconserved elements (UCEs). We analyzed 75% (1682 UCEs), 90% (1258 UCEs), and 95% (838 UCEs) complete data matrices, and inferred phylogenomic hypotheses under concatenation and coalescent approaches. In all cases, we recovered the monophyly of trans-Andean Hyphessobrycon inclusive of H. compressus, and strong support for three species groups and evidence of cryptic diversity within the widespread H. compressus and H. condotensis. We used our phylogenomic hypothesis to investigate the biogeographic history of Hyphessobrycon in Middle America. Our ancestral range estimation analysis suggests a single event of cis- to trans-Andean colonization followed by stepwise colonization from the Pacific slope of northwestern South America (Chocó block) to northern Middle America (Maya block). Our work supports the recognition of the trans-Andean species as Hyphessobrycon sensu stricto and provides a robust evolutionary template to examine morphological characters that will allow us to better understand the diversity of Hyphessobrycon in Middle America.

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“…Although recent studies have found difficulties in resolving early branches of Ostariophysi and other clades using exons or UCEs (Chakrabarty et al, 2017;Betancur-R et al, 2019;Alda et al, 2021), the implementation of a method that assembles more than a thousand loci is relevant to reconstruct molecular phylogenies in many situations. More recently, a new ultraconserved element (UCE) probe set was designed to capture 2,708 UCE loci for Ostariophysi (Faircloth et al, 2020) which has been used to construct molecular supermatrices and to time-calibrate the diversification of many ostariophysan clades (Alda et al, 2018(Alda et al, , 2021Roxo et al, 2019;Mateussi et al, 2020;Ochoa et al, 2020;Silva et al, 2021a,b;Melo et al, 2022;Souza et al, 2022). In this context, our study aims to test the phylogenetic position of the rare and uniquely fossorial Tarumania using genomic data and estimate its timing of diversification relative to Erythrinoidea s.s. and other Characiformes.…”

Section: Introductionmentioning

confidence: 99%

Paleogene emergence and evolutionary history of the Amazonian fossorial fish genus Tarumania (Teleostei: Tarumaniidae)

et al. 2022

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Tarumania walkerae is a rare fossorial freshwater fish species from the lower Rio Negro, Central Amazonia, composing the monotypic and recently described family Tarumaniidae. The family has been proposed as the sister group of Erythrinidae by both morphological and molecular studies despite distinct arrangements of the superfamily Erythrinoidea within Characiformes. Recent phylogenomic studies and time-calibrated analyses of characoid fishes have not included specimens of Tarumania in their analyses. We obtained genomic data for T. walkerae and constructed a phylogeny based on 1795 nuclear loci with 488,434 characters of ultraconserved elements (UCEs) for 108 terminals including specimens of all 22 characiform families. The phylogeny confirms the placement of Tarumaniidae as sister to Erythrinidae but differs from the morphological hypothesis in the placement of the two latter families as sister to the clade with Hemiodontidae, Cynodontidae, Serrasalmidae, Parodontidae, Anostomidae, Prochilodontidae, Chilodontidae, and Curimatidae. The phylogeny calibrated with five characoid fossils indicates that Erythrinoidea diverged from their relatives during the Late Cretaceous circa 90 Ma (108–72 Ma), and that Tarumania diverged from the most recent common ancestor of Erythrinidae during the Paleogene circa 48 Ma (66–32 Ma). The occurrence of the erythrinoid-like †Tiupampichthys in the Late Cretaceous–Paleogene formations of the El Molino Basin of Bolivia supports our hypothesis for the emergence of the modern Erythrinidae and Tarumaniidae during the Paleogene.

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Phylogenomic analysis of the Neotropical fish subfamily Characinae using ultraconserved elements (Teleostei: Characidae)

Cited by 5 publications

References 69 publications

Phylogenomics of trans-Andean tetras of the genus Hyphessobrycon Durbin 1908 (Stethaprioninae: Characidae) and colonization patterns of Middle America

Phylogenomics of trans-Andean tetras of the genus Hyphessobrycon Durbin 1908 (Stethaprioninae: Characidae) and colonization patterns of Middle America

Phylogenomics oftrans-Andean tetras of the genusHyphessobryconDurbin 1908 and colonization patterns of Middle America

Paleogene emergence and evolutionary history of the Amazonian fossorial fish genus Tarumania (Teleostei: Tarumaniidae)

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