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Cited by 32Fish Biology and Ecology StudiesGenetic diversity and population structureGenomics and Phylogenetic Studies

Unraveling historical introgression and resolving phylogenetic discord within Catostomus (Osteichthys: Catostomidae)

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Bangs, Max R., Douglas, Marlis R., Mussmann, Steven M., Douglas, Michael E.·2018·BMC Evolutionary Biology
DOI 10.1186/s12862-018-1197-yPMC PMC5992631
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Abstract

BACKGROUND: Porous species boundaries can be a source of conflicting hypotheses, particularly when coupled with variable data and/or methodological approaches. Their impacts can often be magnified when non-model organisms with complex histories of reticulation are investigated. One such example is the genus Catostomus (Osteichthys, Catostomidae), a freshwater fish clade with conflicting morphological and mitochondrial phylogenies. The former is hypothesized as reflecting the presence of admixed genotypes within morphologically distinct lineages, whereas the latter is interpreted as the presence of distinct morphologies that emerged multiple times through convergent evolution. We tested these hypotheses using multiple methods, to including multispecies coalescent and concatenated approaches. Patterson's D-statistic was applied to resolve potential discord, examine introgression, and test the putative hybrid origin of two species. We also applied naïve binning to explore potential effects of concatenation. RESULTS: We employed 14,007 loci generated from ddRAD sequencing of 184 individuals to derive the first highly supported nuclear phylogeny for Catostomus. Our phylogenomic analyses largely agreed with a morphological interpretation,with the exception of the placement of Xyrauchen texanus, which differs from both morphological and mitochondrial phylogenies. Additionally, our evaluation of the putative hybrid species C. columbianus revealed a lack introgression and instead matched the mitochondrial phylogeny. Furthermore, D-statistic tests clarified all discrepancies based solely on mitochondrial data, with agreement among topologies derived from concatenation and multispecies coalescent approaches. Extensive historic introgression was detected across six species-pairs. Potential endemism in the Virgin and Little Colorado Rivers was also apparent, and the former genus Pantosteus was derived as monophyletic, save for C. columbianus. CONCLUSIONS: Complex reticulated histories detected herein support the hypothesis that introgression was responsible for conflicts that occurred within the mitochondrial phylogeny, and explains discrepancies found between it and previous morphological phylogenies. Additionally, the hybrid origin of C. columbianus was refuted, but with the caveat that more fine-grain sampling is still needed. Our diverse phylogenomic approaches provided largely concordant results, with naïve binning useful in exploring the single conflict. Considerable diversity was found within Catostomus across southwestern North America, with two drainages [Virgin River (UT) and Little Colorado River (AZ)] reflecting unique composition.

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  • Xyrauchen is nested within Catostomus rather than as a distinct lineage.

    “For X. texanus, we used Catostomus commersoni as a phylogenetic proxy, justified by phylogenetic analyses placing Xyrauchen as nested within Catostomus rather than as a distinct lineage (99, 100).”

    From Convergent genome streamlining accompanies independent miniaturization in the world’s smallest fishes (2026) · cites this paper as [100]

    The Abstract (Results) says the nuclear phylogeny places Xyrauchen texanus differently from morphological and mitochondrial phylogenies, but does not specify where it falls. The Methods (Sampling) calls its placement questionable, and the Discussion (Tests for introgression that resolved phylogenetic discord) identifies a mitochondrial sister relationship with C. insignis as discordant. None of the retrieved text establishes that Xyrauchen is nested within Catostomus. (LLM, conf=0.70)

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Cited by

Sorted by citations

Authors
Bangs, M. R., Douglas, M. R., Mussmann, S. M., & Douglas, M. E.
Affiliations
University of Arkansas at Fayetteville (US)
Corresponding author
Bangs, Max R.
ORCID
Venue
BMC Evolutionary Biology
Publisher
Springer Science and Business Media LLC
Published
2018-06-07
Volume
18
Issue
1
Pages
86-86
ISSN
1471-2148 (ISSN-L)
DOI
10.1186/s12862-018-1197-y
PMC
PMC5992631
OpenAlex
W2805233664
Cited by
32
References
1
Citations by year
2026: 5 · 2025: 4 · 2024: 2 · 2023: 1 · 2022: 6 · 2021: 2 · 2020: 6 · 2019: 6
FWCI
3.31
Type
journal article
Language
en
Open access
Licence
Locations
  • BMC Evolutionary Biology (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • University of Arkansas
  • Utah Department of Natural Resources
  • Arkansas Economic Development Commission
  • Directorate for Biological Sciences
  • U.S. Geological Survey
  • National Park Service (H1200040001)
  • Arkansas High Performance Computing Center, University of Arkansas
Topics
  • Life Sciences › Agricultural and Biological Sciences › Aquatic Science › Fish Biology and Ecology Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
Catostomus, Catostomidae, introgression, hybrid origin, Xyrauchen texanus, mitochondrial phylogeny, morphological phylogeny, convergent evolution, multispecies coalescent, ddRAD sequencing, phylogenomics, endemism, Virgin River, Little Colorado River, freshwater fish
MeSH terms
Animals, Cypriniformes, DNA, Mitochondrial, Geography, Phylogeny, Species Specificity, United States, Evolution, Molecular

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