Phylogenetic relationships of the family Tarumaniidae (Characiformes) based on nuclear and mitochondrial data

Arcila, Dahiana; Petry, Paulo; Ortı́, Guillermo

doi:10.1590/1982-0224-20180016

Cited by 8 publications

(10 citation statements)

References 15 publications

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“…; Arcila et al. ). Among the newly sequenced data, two species had to be excluded due to cross‐contamination detected by analyses of COI sequences (barcodes) obtained with the exon‐capture probe set.…”

Section: Methodsmentioning

confidence: 98%

“…This expanded taxonomic sampling consists of 321 individuals representing 318 distinct species-level taxa, of which 206 are characiforms (173 genera), 21 are cypriniforms (21 genera), 13 are gymnotiforms (10 genera), and 78 are siluriforms (77 genera). The order Characiformes is represented by 23 (out of 24) families; the only family not sampled here is the Neotropical and monotypic Tarumaniidae, hypothesized to be the sister group of Erythrinidae (de Pinna et al 2017;Arcila et al 2018). Among the newly sequenced data, two species had to be excluded due to cross-contamination detected by analyses of COI sequences (barcodes) obtained with the exon-capture probe set.…”

Section: Sequencingmentioning

confidence: 99%

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Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes*

et al. 2018

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Phylogenomic studies using genome‐wide datasets are quickly becoming the state of the art for systematics and comparative studies, but in many cases, they result in strongly supported incongruent results. The extent to which this conflict is real depends on different sources of error potentially affecting big datasets (assembly, stochastic, and systematic error). Here, we apply a recently developed methodology (GGI or gene genealogy interrogation) and data curation to new and published datasets with more than 1000 exons, 500 ultraconserved element (UCE) loci, and transcriptomic sequences that support incongruent hypotheses. The contentious non‐monophyly of the order Characiformes proposed by two studies is shown to be a spurious outcome induced by sample contamination in the transcriptomic dataset and an ambiguous result due to poor taxonomic sampling in the UCE dataset. By exploring the effects of number of taxa and loci used for analysis, we show that the power of GGI to discriminate among competing hypotheses is diminished by limited taxonomic sampling, but not equally sensitive to gene sampling. Taken together, our results reinforce the notion that merely increasing the number of genetic loci for a few representative taxa is not a robust strategy to advance phylogenetic knowledge of recalcitrant groups. We leverage the expanded exon capture dataset generated here for Characiformes (206 species in 23 out of 24 families) to produce a comprehensive phylogeny and a revised classification of the order.

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Section: Methodsmentioning

confidence: 98%

Section: Sequencingmentioning

confidence: 99%

Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes*

et al. 2018

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“…Lebiasinidae was formerly considered to be phylogenetically related to Erythrinidae, Ctenoluciidae, and Hepsetidae, due to sharing of some particular morphological similarities (Buckup, 1998). Nonetheless, more recent robust molecular phylogenetic analyses indicated that Erythrinidae and Hepsetidae are in fact not closely related to Lebiasinidae; instead, the close relationship between Lebiasinidae and Ctenoluciidae was demonstrated (Arcila et al, 2017; Arcila et al, 2018). However, while providing significant advances to this issue, these relationships still require complementary studies for the comprehensive understanding of the evolutionary history among its evolutionary lineages.…”

Section: Introductionmentioning

confidence: 99%

Comparative Cytogenetics and Neo-Y Formation in Small-Sized Fish Species of the Genus Pyrrhulina (Characiformes, Lebiasinidae)

et al. 2019

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Although fishes have traditionally been the subject of comparative evolutionary studies, few reports have concentrated on the application of multipronged modern molecular cytogenetic techniques (such as comparative genomic hybridization = CGH and whole chromosome painting = WCP) to analyze deeper the karyotype evolution of specific groups, especially the historically neglected small-sized ones. Representatives of the family Lebiasinidae (Characiformes) are a notable example, where only a few cytogenetic investigations have been conducted thus far. Here, we aim to elucidate the evolutionary processes behind the karyotype differentiation of Pyrrhulina species on a finer-scale cytogenetic level. To achieve this, we applied C-banding, repetitive DNA mapping, CGH and WCP in Pyrrhulina semifasciata and P. brevis . Our results showed 2n = 42 in both sexes of P. brevis , while the difference in 2n between male and female in P. semifasciata (♂41/♀42) stands out due to the presence of a multiple X 1 X 2 Y sex chromosome system, until now undetected in this family. As a remarkable common feature, multiple 18S and 5S rDNA sites are present, with an occasional synteny or tandem-repeat amplification. Male- vs .-female CGH experiments in P. semifasciata highlighted the accumulation of male-enriched repetitive sequences in the pericentromeric region of the Y chromosome. Inter-specific CGH experiments evidenced a divergence between both species’ genomes based on the presence of several species-specific signals, highlighting their inner genomic diversity. WCP with the P . semifasciata -derived Y (PSEMI-Y) probe painted not only the entire metacentric Y chromosome in males but also the X 1 and X 2 chromosomes in both male and female chromosomes of P. semifasciata. In the cross-species experiments, the PSEMI-Y probe painted four acrocentric chromosomes in both males and females of the other tested Pyrrhulina species. In summary, our results show that both intra- and interchromosomal rearrangements together with the dynamics of repetitive DNA significantly contributed to the karyotype divergence among Pyrrhulina species, possibly promoted by specific populational and ecological traits and accompanied in one species by the origin of neo-sex chromosomes. The present results suggest how particular evolutionary scenarios found in fish species can help to clarify several issues related to genome organization and the karyotype evolution of vertebrates in general.

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“…The following Datasets were prepared for downstream analyses ( 74 and concatenated in SequenceMatrix 75 to produce one sequence for each representative species. Concatenated sequences are useful to overcome sampling error and missing data, and can show accuracy in generating taxonomic topologies [76][77][78] .…”

Section: Selection Of Target Regionsmentioning

confidence: 99%

Genetic origins and diversity of bushpigs from Madagascar (Potamochoerus larvatus, family Suidae)

Lee

Day

Pedrono

et al. 2020

Sci Rep

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The island of Madagascar, situated off the southeast coast of Africa, shows the first evidence of human presence ~ 10,000 years ago; however, other archaeological data indicates a settlement of the modern peoples of the island distinctly more recent, perhaps > 1500 years ago. Bushpigs of the genus Potamochoerus (family Suidae), are today widely distributed in Madagascar and presumed to have been introduced from Africa at some stage by human immigrants to the island. However, disparities about their origins in Madagascar have been presented in the literature, including the possibility of endemic subspecies, and few empirical data are available. Furthermore, the separation of bushpigs in Madagascar from their mainland relatives may have favoured the evolution of a different repertoire of immune genes first due to a founder effect and then as a response to distinct pathogens compared to their ancestors. Molecular analysis confirmed the species status of the bushpig in Madagascar as P. larvatus, likely introduced from the central region of southern Africa, with no genetic evidence for the recognition of eastern and western subspecies as suggested from previous cranial morphology examination. Investigation of the immunologically important SLA-DQB1 peptide-binding region showed a different immune repertoire of bushpigs in Madagascar compared to those on the African mainland, with seventeen exon-2 haplotypes unique to bushpigs in Madagascar (2/28 haplotypes shared). This suggests that the MHC diversity of the Madagascar populations may have enabled Malagasy bushpigs to adapt to new environments.

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Phylogenetic relationships of the family Tarumaniidae (Characiformes) based on nuclear and mitochondrial data

Cited by 8 publications

References 15 publications

Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes*

Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes*

Comparative Cytogenetics and Neo-Y Formation in Small-Sized Fish Species of the Genus Pyrrhulina (Characiformes, Lebiasinidae)

Genetic origins and diversity of bushpigs from Madagascar (Potamochoerus larvatus, family Suidae)

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