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Phylogeny of the Bovidae (Artiodactyla, Mammalia), based on mitochondrial ribosomal DNA sequences.

Open access
John Gatesy, Deborah L. Yelon, Rob DeSalle, Elisabeth S. Vrba·1992·Molecular Biology and Evolution
DOI 10.1093/oxfordjournals.molbev.a040734
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Abstract

Portions of the 12S and 16S mitochondrial ribosomal genes for 16 species representing nine tribes in the mammal family Bovidae were compared with six previously published orthologous sequences. Phylogenetic analysis of variable nucleotide positions under different constraints and weighting schemes revealed no robust groupings among tribes. Consensus trees support previous hypotheses of monophyly for four clades, including the traditional subfamily Bovinae. However, the basal diversification of bovid tribes, which was largely unresolved by morphological, immunodiffusion, allozyme, and protein sequence data, remains unresolved with the addition of DNA sequence data. The intractability of this systematic problem is consistent with a rapid radiation of the major bovid groups. Several analyses of our data show that monophyly of the Bovidae, which was weakly supported by previous morphological and molecular work, is questionable.

AI snapshot

Written from the paper’s full text.

TL;DR

Mitochondrial 12S and 16S rDNA sequences from bovid tribes and pecoran outgroups fail to resolve basal bovid intertribal relationships, supporting a rapid radiation. The data recover four clades congruent with prior hypotheses but question bovid monophyly, since monophyly requires extra steps and is not robustly supported.

Key findings

  • No robust groupings among bovid tribes were found; consensus trees support monophyly for four clades, including the traditional subfamily Bovinae, but the basal diversification of bovid tribes remains unresolved.
  • Bovid monophyly is questionable: the complete data set required six additional steps to enforce it, approximately a 1% increase in tree length; in the transversion analysis, bovid monophyly was found 12 times among 84 shortest unconstrained trees.
  • Data partitions differed: 34% of 16S sites were varied versus 26% of 12S sites; loop regions were more varied (40%) than stem regions (20%); transversions characterized 37% of varied nucleotide positions.
  • Prior hypotheses were often at odds with the data: the allozyme-distance tree of Georgiadis et al. cost 29 additional steps (6% of total tree length), and their allozyme-parsimony tree required 20 additional steps. Four groupings were strictly congruent with past analyses: Tragelaphini+Bovini, Hippotragini+Alcelaphini, Bovini+Tragelaphini+Boselaphini, and Reduncini+Hippotragini+Antilopini+Cephalophini+Caprini+Alcelaphini.

Methods

  • Portions of the 12S and 16S mitochondrial ribosomal genes were compared for 16 species representing nine tribes in Bovidae, along with six previously published orthologous sequences; pecoran families Cervidae, Giraffidae, and Antilocapridae were included, and *Tragulus napu* was used to root the trees.
  • DNA was extracted from brain, kidney, and liver tissues; single-stranded segments were PCR-amplified with conserved primers, and approximately 250 bases of 12S and 350 bases of 16S were sequenced per sample; sequences were aligned by eye.
  • Phylogenetic analysis used PAUP 3.0 parsimony with heuristic searches, nearest-neighbor-interchange branch swapping, 100 random initial trees, and 100 bootstrap replications; data were partitioned by gene, stem/loop regions, and transversions, constrained for bovid monophyly and prior topologies, and compensatory stem pairs were down-weighted.

Limitations

  • Stated: the basal radiation of bovids remains unresolved; no robust intertribal relationships are obvious; rapid radiation and morphological convergence confound resolution; bovid monophyly is questionable, and rigorous outgroup analysis is problematic because higher-level pecoran relationships lack consensus.
  • Stated: the secondary-structure model for divergent mt-rRNA may be inaccurate, the timing and frequency of compensatory stem changes are unclear, and some stem nucleotide pairings may have limited functional importance.
  • Evident: inferences rest on short mt-rDNA segments (approximately 250 and 350 bases) from a limited taxon sample, without independent morphological or nuclear data; many clades are weakly supported, and clades unique to these shortest trees await future testing.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1093/oxfordjournals.molbev.a040734

Cites

49 of 49 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 52 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    The basal diversification of bovid tribes, which was largely unresolved by morphological, immunodiffusion, allozyme, and protein sequence data, remains unresolved with the addition of DNA sequence data.

    “However, the basal diversification of bovid tribes, which was largely unresolved by morphological, immunodiffusion, allozyme, and protein sequence data, remains unresolved with the addition of DNA sequence data.”
    Quote in the paperSubstantial claim
  • Findingown data

    Separate phylogenetic analyses of the 12s and 16s genes show a higher level of character support for the 16s gene, according to the retention index.

    “Separate phylogenetic analyses of these two genes show a higher level of character support for the 16s gene, according to the retention index of Farris ( 1989; also see table 2).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Farris 1989 source
  • Findingown data

    Genera are confidently placed within proper tribes.

    “However, genera are confidently placed within proper tribes.”
    Quote in the paperSubstantial claim
  • Findingown data

    When stem and loop data are analyzed separately, the retention index is higher for the stem data.

    “When the two groups of data are analyzed separately, the retention index is higher for the stem data (table 2).”
    Quote in the paperNot a substantial claim
  • Findingown data

    Consensus trees support previous hypotheses of monophyly for four clades, including the traditional subfamily Bovinae.

    “Consensus trees support previous hypotheses of monophyly for four clades, including the traditional subfamily Bovinae.”
    • Also stated in: § Discussion · plain
      “Strict-consensus trees from our work are characterized by four groupings strictly congruent with past analyses: Tragelaphini+Bovini (Beintema et al. 1986), Hippotragini+Alcelaphini (Georgiadis et al. 199 1 ), Bo-vini+Tragelaphini+Boselaphini (Simpson 1945;Beintema 1986;Lowenstein 1986b), and Reduncini+Hippotragini+Antilopini+Cephalophini+Caprini+Alcelaphini (Lowenstein 1986b).”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites Beintema et al. 1986 source
    • cites Georgiadis et al. 1991

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

    • cites Simpson 1945 source
  • May combine two claims. 18
  • Classified as probably not a substantial claim. 11

  • May combine two claims.

    Findingown data

    34% of the sites in the 16s gene are varied, while only 26% of the sites in the 12s gene are varied in the taxa sampled here.

    “Our comparisons indicate that 34% of the sites in the 16s gene are varied, while only 26% of the sites in the 12s gene are varied in the taxa sampled here.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The Bovidae do not fall out as a unified group in the equally weighted unconstrained analysis, as the cervids and Antilocapra cluster within the bovids.

    “The Bovidae do not fall out as a unified group in this analysis, as the cervids and Antilocupru cluster within the bovids.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Analyses constrained by bovid monophyly additionally supported the sister group Reduncini+Antilopini, while the unconstrained analyses supported Alcelaphini+Hippotragini.

    “For instance, the analyses constrained by bovid monophyly additionally supported the sister group Redun-cini+Antilopini while the unconstrained analyses supported Alcelaphini+Hippotragini.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingreasoning

    Compensation is delayed in T. angasi but not to the same extent that it is in B. taurus.

    “Compensation is delayed in T. angasibut not to the same extent that it is in B. taurus.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    In most analyses, extra evolutionary steps are invoked to satisfy the condition of bovid monophyly, although the additional number of steps is not great in comparison with overall tree length.

    “In most analyses, extra evolutionary steps are invoked to satisfy the condition of bovid monophyly, although the additional number of steps is not great in comparison with overall tree length (table 2).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Transversion parsimony analysis of these positions produced 84 equally parsimonious trees resulting in the strict-consensus tree of figure 3A.

    “Transversion parsimony analysis (Lake 1987) of these positions produced 84 equally parsimonious trees resulting in the strict-consensus tree of figure 3A.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Lake 1987 source

  • May combine two claims.

    Findingcitation

    A longer lag can be seen on the line leading to Bos taurus; compensation is delayed 3 11.5 Myr, the minimum estimate for the common node of B. taurus and Tragelaphus angasi.

    “A longer lag can be seen on the line leading to Bos taurus.Here, compensation is delayed 3 11.5 Myr, the minimum estimate for the common node of B. taurus and Tragelaphus angasi (Hill et al. 1985; E. S. Vrba, unpublished data).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Hill et al. 1985

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

    • cites E. S. Vrba, unpublished data

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Findingown data

    The complete data set required six additional steps to account for bovid monophyly, which is approximately a 1% increase in tree length.

    “The complete data set required six additional steps to account for bovid monophyly (fig.2B).This is approximately a 1% increase in tree length.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingcitation

    The lag in compensation for Damaliscus hunteri is ~2.5 Myr, the minimum estimate of the divergence time for D. hunteri and D. dorcas.

    “This lag in compensation is ~2.5 Myr, the minimum estimate of the divergence time for D. hunteri and D. dorcas (Vrba 1979(Vrba , 1985)).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Vrba 1979 source
    • cites Vrba 1985

  • May combine two claims.

    Findingown data

    Strict-consensus trees derived from the down-weighted data were more resolved but never inconsistent with the analysis of the equally weighted data, whether the complementary nucleotide pairs were down-weighted by the maximum, by one-half, or less severely.

    “The strict-consensus trees derived from these data were more resolved but never inconsistent with the analysis of the equally weighted data, whether the complementary nucleotide pairs were downweighted by the maximum, by one-half, or less severely.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Results were checked by sequencing each fragment at least two times.

    “Results were checked by sequencing each fragment at least two times.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Both strands were sequenced in the majority of samples.

    “Both strands were sequenced in the majority of samples.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Since its first appearance in the Miocene ~20 Mya, the Bovidae underwent a rapid radiation that is unparalleled in other mammals of large body size.

    “Since its first appearance in the Miocene -20 Mya (Savage and Russell 1983;Vrba 1985), the Bovidae underwent a rapid radiation that is unparalleled in other mammals of large body size.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Savage and Russell 1983
    • cites Vrba 1985

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    The remainder were sequenced multiple times in the same direction from different PCR amplifications.

    “The remainder were sequenced multiple times in the same direction from different PCR amplifications.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    Compensation is instantaneous at the level of resolution provided by the data, and homoplasy is compounded.

    “Compensation is instantaneous at the level of resolution provided by the data, and homoplasy is compounded.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based). May combine two claims.

    Premisenone given

    There are only 15 possible rooted cladograms relating the families Bovidae, Cervidae, Antilocapridae, and Giraffidae; 11 have been proposed in the literature.

    “There are only 15 possible rooted cladograms relating the families Bovidae, Cervidae, Antilocapridae, and Giraffidae; 11 have been proposed in the literature.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    In vertebrate mt-rDNA as well as in nuclear rDNA, transversions tend to occur much less frequently than transitions.

    “In vertebrate mt-rDNA (Hixson and Brown 1986) as well as in nuclear rDNA (Larson and Wilson 1989;Hedges et al. 1990), transversions tend to occur much less frequently than transitions.”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Hixson and Brown 1986 source
    • cites Larson and Wilson 1989 source
    • cites Hedges et al. 1990 source

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Simpson's (1945) classification based on morphology allocated the family into 13 tribes, most of which are thought to be monophyletic.

    “Simpson' s ( 1945) classification based on morphology (fig.5A) allocated the family into 13 tribes, most of which are thought to be monophyletic.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Simpson 1945 source

  • May combine two claims.

    Premisecitation

    Both molecular and morphological systematists have investigated the phylogenetic relationships within Pecora, yet there is no consensus on its evolutionary history.

    “Both molecular (Beintema et al. 1986;Lowenstein 1986a;Miyamoto and Goodman 1986;Irwin et al. 199 1;Kraus and Miyamoto 199 1) and morphological (Romer 1966;Hamilton 1978;Leinders and Heintz 1980;Webb and Taylor 1980;Janis and Scott 1987;Gentry and Hooker 1988) systematists have investigated the phylogenetic relationships within this group, yet there is no consensus on its evolutionary history.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    Once an initial change in a stem position occurs, the pairing nucleotide will be selected to change as well.

    “Once an initial change in a stem position occurs, the pairing nucleotide will be selected to change as well.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Wheeler and Honeycutt 1988

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    The Bovidae along with the families Antilocapridae, Giraffidae, Cervidae, and Moschidae form the extant components of the infraorder Pecora.

    “The Bovidae along with the families Antilocapridae (pronghorn antelope), Giraffidae (giraffes), Cervidae (antlered deer), and Moschidae (musk deer) form the extant components of the infraorder Pecora.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    A parsimony analysis of amino acid replacements in pancreatic-type ribonuclease sequences retained Simpson's subfamily Bovinae (Tragelaphini+Bovini+Boselaphini), in agreement with Lowenstein.

    “A parsimony analysis of amino acid replacements in pancreatic-type ribonuclease sequences (fig.5D; Beintema et al. 1986) retained Simpson' s subfamily Bovinae (Tra-gelaphini+Bovini+Boselaphini), in agreement with Lowenstein (fig.5B).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Beintema et al. 1986

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

    • cites Lowenstein 1986b

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Premisecitation

    Lowenstein (1986b) presented an immunodiffusion phenogram with some resolution, but many tribes were sunk into a large polytomy.

    “Lowenstein ( 1986b) presented an immunodifhtsion phenogram with some resolution, but many tribes were sunk into a large polytomy (fig.5C).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Lowenstein 1986b

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • Classified as probably not a substantial claim.

    Premisecitation

    In a reanalysis of arthropod nuclear rDNA sequences, Wheeler and Honeycutt (1988) found a statistically significant number of instances in which changes in one stem position were compensated by changes in the complementary stem position.

    “In a reanalysis of arthropod nuclear rDNA sequences, Wheeler and Honeycutt ( 1988) found a statistically significant number of instances in which changes in one stem position were compensated by changes in the complementary stem position.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Wheeler and Honeycutt 1988

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Georgiadis et al.'s (1991) distance and parsimony analyses of allozymes allow contrasting interpretations of bovid history.

    “Georgiadis et al.' s ( 199 1) distance and parsimony analyses of allozymes (fig.5E and F) allow contrasting interpretations of bovid history.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Georgiadis et al. 1991

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Premisereasoning

    All of the above contributions are marked by both a lack of resolution at the tribal level and a general incongruence with each other.

    “All of the above contributions are marked by both a lack of resolution at the tribal level and a general incongruence with each other.”
    Quote in the paperSubstantial claim
26 of 26

  • The authors state this as an assumption.

    Rates of molecular change are, on the average, constant through long time.

    “If rates of molecular change are assumed to be, on the average, constant through long time, then this is indicative of a rapid splitting of lineages.”

  • The paper relies on this without support.

    The compared mt-rDNA sequences are orthologous.

    “The orthologous DNA sequences, having a limited amount of length variability, were aligned by eye (fig, 1).”
2 of 2

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Lowenstein analysis is cited as the wrong figure panel

    Minor

    The text identifies Lowenstein's analysis as figure 5B, but the figure caption assigns Lowenstein to panel 5C. Panel 5B is the strict consensus of other hypotheses.

1 of 1

Cites

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Related

Authors
Gatesy, J., Yelon, D. L., DeSalle, R., & Vrba, E. S.
Affiliations
  • Yale University (US)
  • American Museum of Natural History (US)
ORCID
Venue
Molecular Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
1992-05
Volume
9
Issue
3
Pages
433-46
ISSN
  • 0737-4038 (ISSN-L)
  • 1537-1719
DOI
10.1093/oxfordjournals.molbev.a040734
OpenAlex
W2163051777
Cited by
80
References
49
Citations by year
2021: 1 · 2020: 4 · 2019: 2 · 2018: 1 · 2015: 1 · 2014: 2 · 2013: 2 · 2012: 2
FWCI
9.42
Type
journal article
Language
en
Open access
Locations
  • Molecular Biology and Evolution (publishedVersion)
  • PubMed (publishedVersion)
Funders
National Science Foundation (8907673)
Topics
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
Keywords
Bovidae, phylogeny, 12S rRNA, 16S rRNA, Bovinae, monophyly, molecular systematics, Artiodactyla
MeSH terms
Animals, Artiodactyla, Base Sequence, DNA, DNA, Ribosomal, Mitochondria, Molecular Sequence Data, Phylogeny, Sequence Homology, Nucleic Acid

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