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Cited by 36Evolution and Paleontology StudiesGenetic diversity and population structureGenomics and Phylogenetic Studies

A multi-locus species phylogeny of African forest duikers in the subfamily Cephalophinae: evidence for a recent radiation in the Pleistocene

Open access
Johnston, Anne R, Anthony, Nicola M·2012·BMC Evolutionary Biology
DOI 10.1186/1471-2148-12-120PMC PMC3523051
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Abstract

BACKGROUND: Duikers in the subfamily Cephalophinae are a group of tropical forest mammals believed to have first originated during the late Miocene. However, knowledge of phylogenetic relationships, pattern and timing of their subsequent radiation is poorly understood. Here we present the first multi-locus phylogeny of this threatened group of tropical artiodactyls and use a Bayesian uncorrelated molecular clock to estimate divergence times. RESULTS: A total of 4152 bp of sequence data was obtained from two mitochondrial genes and four nuclear introns. Phylogenies were estimated using maximum parsimony, maximum likelihood, and Bayesian analysis of concatenated mitochondrial, nuclear and combined datasets. A relaxed molecular clock with two fossil calibration points was used to estimate divergence times. The first was based on the age of the split between the two oldest subfamilies within the Bovidae whereas the second was based on the earliest known fossil appearance of the Cephalophinae and molecular divergence time estimates for the oldest lineages within this group. Findings indicate strong support for four major lineages within the subfamily, all of which date to the late Miocene/early Pliocene. The first of these to diverge was the dwarf duiker genus Philantomba, followed by the giant, eastern and western red duiker lineages, all within the genus Cephalophus. While these results uphold the recognition of Philantomba, they do not support the monotypic savanna-specialist genus Sylvicapra, which as sister to the giant duikers leaves Cephalophus paraphyletic. BEAST analyses indicate that most sister species pairs originated during the Pleistocene, suggesting that repeated glacial cycling may have played an important role in the recent diversification of this group. Furthermore, several red duiker sister species pairs appear to be either paraphyletic (C.callipygus/C. ogilbyi and C. harveyi/C. natalensis) or exhibit evidence of mitochondrial admixture (C. nigrifrons and C. rufilatus), consistent with their recent divergence and/or possible hybridization with each other. CONCLUSIONS: Molecular phylogenetic analyses suggest that Pleistocene-era climatic oscillations have played an important role in the speciation of this largely forest-dwelling group. Our results also reveal the most well supported species phylogeny for the subfamily to date, but also highlight several areas of inconsistency between our current understanding of duiker taxonomy and the evolutionary relationships depicted here. These findings may therefore prove particularly relevant to future conservation efforts, given that many species are presently regulated under the Convention for Trade in Endangered Species.

AI snapshot

Written from the paper’s full text.

TL;DR

This study presents the first multi-locus phylogeny of African forest duikers in Cephalophinae, using 4152 bp from two mitochondrial genes and four nuclear introns with a fossil-calibrated Bayesian relaxed clock. It finds four major lineages and estimates that most sister species pairs originated during the Pleistocene, with several red duiker pairs showing paraphyly or mitochondrial admixture.

Key findings

  • The aligned matrix contained 4152 characters: 1172 mitochondrial and 2980 nuclear. Mitochondrial data had 38% variable sites and 368 parsimony-informative characters (31%); nuclear data had 15% variable sites and 208 parsimony-informative characters (8% in text; 7% in Table 1).
  • Analyses supported four major lineages: Philantomba diverged first, followed by giant, eastern red, and western red duiker lineages. Philantomba was monophyletic, but Sylvicapra was sister to the giant duikers, leaving Cephalophus paraphyletic.
  • BEAST estimated the Philantomba split at 8.73 Ma (6.27–11.43 HPD), the giant/Sylvicapra versus red duiker split at 7.03 Ma (5.02–9.19 HPD), and the east/west red duiker split at 4.98 Ma (3.58–6.69 HPD). Most sister species pairs originated in the Pleistocene (<2.558 Ma), except P. monticola/P. maxwelli.
  • Several red duiker sister pairs showed paraphyly or admixture: C. callipygus/C. ogilbyi and C. harveyi/C. natalensis were paraphyletic, while C. nigrifrons and C. rufilatus showed evidence of mitochondrial admixture; C. callipygus and C. ogilbyi formed an unresolved polytomy in the nuclear tree.

Methods

  • Tissue was sampled from 24 Cephalophinae individuals representing all 18 IUCN-recognized species, plus GenBank sequences for P. walteri and C. rubidus. Outgroups included O. oreotragus, N. moschatus, M. kirkii, T. scriptus, and T. spekei.
  • Sequences comprised 514 bp of cytb, 658 bp of COX1, and four nuclear introns: MGF, PRKCl, SPTBN1, and THY. Phylogenies were estimated with maximum parsimony, maximum likelihood, and Bayesian analysis for mitochondrial, nuclear, and combined datasets; ILD and SH tests assessed incongruence, and jModelTest/BIC selected substitution models.
  • Divergence times were estimated in BEAST v1.6.1 using a relaxed uncorrelated lognormal clock and Yule tree prior, with two fossil calibration points: a lognormal prior on the Cephalophinae node offset at 5.3 Ma and a normal prior on the Bovinae/Antilopinae split with mean 20.1 Ma and SD 2.25 Ma. Two MCMC chains ran for 10 million generations, with 25% burn-in.

Limitations

  • Stated in the paper: the harmonic mean is not the best estimator of marginal likelihoods for Bayes Factor analysis, and alternative methods were computationally intensive or not readily implementable at the time.
  • Evident from the text: nuclear sequences were unavailable for C. weynsi, C. rubidus, and P. walteri; ILD tests rejected congruence among the four nuclear genes (p < 0.10), and mitochondrial and nuclear topologies were incongruent (p ≤ 0.006).
  • Evident from the text: individual nuclear gene trees recovered different topologies with generally weak node support, and the placement of C. adersi and C. zebra remained unresolved or weakly supported.

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

Integrity signals

Registry

Crossref · 10.1186/1471-2148-12-120

Cites

76 of 76 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 87 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    There is generally little support for most nodes within the individual nuclear gene trees.

    “Given that there was generally little support for most of the nodes within the individual nuclear gene trees, many of these differences between gene genealogies likely represent soft polytomies.”
    Quote in the paperSubstantial claim
  • Findingown data

    All four nuclear genealogies support the monophyly of Philantomba.

    “All four genealogies support the monophyly of Philantomba (MGF: MP = 95%, ML = 95%, BA =1.0; PRKCl: MP = 96%, ML = 100%, BA = 1.0; STBN1: MP = 97%, ML = 97%, BA = 1.0; THY: MP = 83%, ML = 87%, BA = 1.0).”
    Quote in the paperNot a substantial claim
  • Findingown data

    Within Cephalophus, support was generally weak or lacking for the giant, east and west African red duiker lineages described by van Vuuren and Robinson [22].

    “Within Cephalophus, support was generally weak or lacking for the giant, east and west African red duiker lineages described by van Vuuren and Robinson [22] although the STBN1 genealogy supported the monophyly of the west African red duiker lineage (MP = 85%, ML = 88%, BA = 1.0) and the THY genealogy recovered the giant duiker lineage (MP = 84%, ML = 85%, BA = 0.99).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [22]

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

  • Findingown data

    ILD and SH tests suggested that the mitochondrial and nuclear topologies are incongruent (p ≤ 0.006).

    “As results from ILD and SH tests suggested that the mitochondrial and nuclear topologies are incongruent (p ≤ 0.006), both datasets were first analysed separately and then combined.”
    Quote in the paperSubstantial claim
  • Findingown data

    Individual nuclear gene genealogies estimated using Maximum Parsimony, Maximum Likelihood and Bayesian Analysis recovered different topologies regardless of method.

    “Individual nuclear gene genealogies estimated using Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian Analysis (BA) methods recovered different topologies (Figures 1, 2, 3 and 4; Additional file 1 for node support values) and these differences were evident regardless of method.”
    Quote in the paperSubstantial claim
  • May combine two claims. 44
  • Classified as probably not a substantial claim. 31

  • May combine two claims.

    Findingown data

    The MGF genealogy supports two clades of giant duikers while the THY genealogy supports only one clade.

    “For example, the MGF genealogy supports two clades of giant duikers (MP bootstrap = 63% and 94%, ML bootstrap = 75% and 92%, BA posterior probability = 0.99 and 1.00) while the THY genealogy supports only one clade (MP = 84, ML = 85, BA = 0.99).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Nuclear analyses support a sister relationship between Sylvicapra and the C. silvicultor/C. spadix group, making both the genus Cephalophus and the giant duiker lineage paraphyletic.

    “Nuclear analyses also support a sister relationship between Sylvicapra and the C. silvicultor/C. spadix group (MP = 75%, ML = 66/75%, BA = 1.0/0.98), making both the genus Cephalophus and the giant duiker lineage paraphyletic.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In the nuclear tree, C. harveyi is paraphyletic with respect to C. natalensis, as is P. monticola to P. maxwelli.

    “However, C. harveyi is paraphyletic with respect to C. natalensis, as is P. monticola to P. maxwelli.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In the combined analysis, the east and west African red duiker lineages are monophyletic and are sister to one another.

    “The east and west African red duiker lineages are monophyletic and are sister to one another.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The mitochondrial tree shows weak support for the monophyly of Philantomba but strong support for the sister placement of these taxa relative to all other Cephalophinae.

    “The mitochondrial tree of all species within Cephalophinae (Figure 5) shows weak support for the monophyly of Philantomba (MP = 88%, ML = 53%, BA = 0.76), but has strong support for the sister placement of these taxa relative to all other Cephalophinae (MP = 68%, ML = 91%, BA = 1.0).”
    Quote in the paperNot a substantial claim

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

    Findingown data

    The mitochondrial partition contained 368 parsimony informative characters (31%) while the nuclear partition contained 208 parsimony informative characters (8%).

    “The mitochondrial partition contained 368 parsimony informative characters (31%) while the nuclear partition contained 208 parsimony informative characters (8%).”
    Quote in the paperNot a substantial claim

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

    Findingown data

    The mitochondrial partition contained a greater proportion of variable sites (38%) than the nuclear matrix (15%).

    “As expected, the mitochondrial partition contained a greater proportion of variable sites (38%) relative to the nuclear matrix (15%).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    There is weak support for the paraphyly of C. rufilatus relative to C. nigrifrons and strong support for the paraphyly of C. callipygus relative to C. ogilbyi and C. weynsi in the mitochondrial tree.

    “There is also weak support for the paraphyly of C. rufilatus relative to C. nigrifrons (MP = 59%, ML = 44%, BA = 0.87) and strong support for the paraphyly of C. callipygus relative to C. ogilbyi and C. weynsi (MP = 98%, ML = 97, BA = 1.0).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The position of C. adersi and C. zebra varied across nuclear genealogies and remained unresolved or weakly supported, except MGF supported C. zebra as sister to the C. jentinki/C. dorsalis clade and THY supported C. adersi as sister to the east and west African red duikers.

    “The position of C. adersi and C. zebra varied across genealogies and remained unresolved or weakly supported, with the exception of the MGF genealogy which supported C. zebra as sister to the C. jentinki/C. dorsalis clade (MP = 94%, ML = 92%, BA = 1.0) and the THY genealogy which supported C. adersi as sister to the east and west African red duikers (MP = 82%, ML = 80%, BA = 1.0).”
    Quote in the paperNot a substantial claim

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

    Findingown data

    Pair-wise ILD tests between the two mitochondrial partitions fail to reject the null hypothesis that both loci are congruent.

    “Results from the pair-wise ILD test between the two mitochondrial partitions fail to reject the null hypothesis that both loci are congruent.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    In the mitochondrial tree, Sylvicapra is sister to the giant duikers, although this node has weak support.

    “Sylvicapra is sister to the giant duikers, although this node has weak support (MP = 32%, ML = 58%, BA = 0.84).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Within Cephalophus, the mitochondrial tree has strong support for the monophyly of the giant duikers, the east African red duikers, and the west African red duikers, but weak support for their placement relative to one another.

    “Within Cephalophus, there is strong support for the monophyly of the giant duikers (MP = 98%, ML = 97%, BA = 1.0%), the east African red duikers (MP = 93%, ML = 98%, BA = 1.0), and the west African red duikers (MP = 87%, ML = 83%, BA = 0.99), but weak support for their placement relative to one another.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Sylvicapra was sister to some or all of the giant duikers in three of the four nuclear trees but this relationship lacked significant support.

    “Sylvicapra was sister to some or all of the giant duikers in three of the four nuclear trees (MGF: MP = 66%, BA = 0.52%; PRKCl: ML = 54%, BA = 0.61; STNB1: MP = 60%, ML = 56%, BA = 0.97) but this relationship lacked significant support.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The consistency index and retention index values in the mitochondrial partition are lower than those of the nuclear matrix, indicating higher levels of homoplasy in the mitochondrial dataset.

    “The consistency index (CI) and retention index (RI) values in the mitochondrial partition (CI: 0.417, RI: 0.621) are lower than those of the nuclear matrix (CI: 0.823, RI: 0.846), indicating higher levels of homoplasy in the mitochondrial dataset.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Nuclear analyses support the monophyly of the east African red duiker lineage, the west African red duiker lineage, and a sister relationship between these two red African duiker lineages.

    “There is also support for the monophyly of the east African red duiker lineage (MP = 91%, ML = 91/98%, BA = 0.99/1.0), the west African red duiker lineage (MP = 67%, ML = 75/86%, BA = 1.0/1.0), and a sister relationship between these two red African duiker lineages (MP = 95%, ML = 100%/100%, BA = 1.0/0.82).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In the combined analysis, Cephalophus was paraphyletic, with Sylvicapra as sister to the monophyletic giant duiker clade.

    “Cephalophus was paraphyletic, with Sylvicapra as sister to the monophyletic giant duiker clade.”
    Quote in the paperSubstantial claim

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

    Findingown data

    The final aligned data matrix contained four unlinked nuclear DNA regions and two mitochondrial DNA regions for a total of 4152 characters, of which 1172 were mitochondrial and 2980 were nuclear.

    “The final aligned data matrix contained four unlinked nuclear DNA regions and two mitochondrial DNA regions for a total of 4152 characters, of which 1172 were from mitochondrial and 2980 were from nuclear loci (Table 1).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The STBN1 genealogy supported the monophyly of the west African red duiker lineage and the THY genealogy recovered the giant duiker lineage.

    “Within Cephalophus, support was generally weak or lacking for the giant, east and west African red duiker lineages described by van Vuuren and Robinson [22] although the STBN1 genealogy supported the monophyly of the west African red duiker lineage (MP = 85%, ML = 88%, BA = 1.0) and the THY genealogy recovered the giant duiker lineage (MP = 84%, ML = 85%, BA = 0.99).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    In the combined analysis, Philantomba is both monophyletic and sister to the remainder of the Cephalophinae.

    “Philantomba is both monophyletic and sister to the remainder of the Cephalophinae.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Splits between taxa that occupy a west versus western central African distribution include C. jentinki from C. dorsalis, C. ogilbyi from C. callipygus, and P. maxwelli and P. monticola.

    “Similarly, we have also observed splits between taxa that occupy a west versus western central African distribution, notably: 1) C. jentinki (west African) from C. dorsalis (west and western central African) 2) C. ogilbyi (west and western central African) from C. callipygus (western central African) and 3) P. maxwelli (west Africa) and P. monticola (western central, eastern and South African).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    There is a pattern of north versus south speciation in the forest-dwelling C. nigrifrons and its savanna-dwelling sister species C. rufilatus, as well as an east versus south African species split between C. harveyi and C. natalensis.

    “Lastly, we also observed a pattern of north versus south speciation in the forest-dwelling C. nigrifrons and its savanna-dwelling sister species C. rufilatus, as well as an east versus south African species split between C. harveyi and C. natalensis.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    C. nigrifrons and C. rufilatus exhibit a paraphyletic relationship in mitochondrial analyses and a reciprocally monophyletic relationship in nuclear analyses.

    “However, C. nigrifrons and C. rufilatus do not follow either of these patterns, exhibiting a paraphyletic relationship in mitochondrial analyses and a reciprocally monophyletic relationship in nuclear analyses.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The Pleistocene sister species pairs comprise C. jentinki and C. dorsalis, C. nigrifrons and C. rufilatus, C. natalensis and C. harveyi, C. spadix and C. silvicultor, and C. callipygus and C. ogilbyi.

    “These sister species pairs comprise C. jentinki and C. dorsalis, C. nigrifrons and C. rufilatus, C. natalensis and C. harveyi, C. spadix and C. silvicultor, and C. callipygus and C. ogilbyi.”
    Quote in the paperSubstantial claim

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

    Findingown data

    BEAST analyses recovered the same topologies as those obtained by Bayesian Analysis methods.

    “Analyses in BEAST recovered the same topologies as those obtained by BA methods.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The tree estimated using both nuclear and mitochondrial data was better resolved with higher support and narrower confidence intervals than the tree estimated from nuclear analysis alone.

    “However, the tree estimated using both nuclear and mitochondrial data was better resolved with higher support and narrower confidence intervals than the tree estimated from nuclear analysis alone.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Phylogenetic analysis in this study finds significant support for the recognition of a distinct west African red duiker taxon C. rubidus, which is geographically restricted and was previously treated as a subspecies of C. nigrifrons within the east African red duiker clade.

    “Phylogenetic analysis in this study finds significant support for the recognition of a distinct west African red duiker taxon C. rubidus which is geographically-restricted and was previously treated as a subspecies of C. nigrifrons within the east African red duiker clade.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingreasoning

    Several sister species groups exhibit paraphyletic relationships and/or evidence of recent hybridization, consistent with their recent origin.

    “Consistent with their recent origin, several sister species groups exhibit paraphyletic relationships and/or evidence of recent hybridization.”
    Quote in the paperSubstantial claim

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

    Premisecitation

    Most species divergence times pre-date the Pleistocene.

    “However, the majority of studies to date suggest that these effects are most evident at the population level [8,11-16] but see [17] with most species divergence times pre-dating the Pleistocene [18-20].”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [18]

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    • cites [19]

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    • cites [20]

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  • Classified as probably not a substantial claim.

    Premisecitation

    Most studies to date suggest that Pleistocene effects on tropical forest taxa are most evident at the population level.

    “However, the majority of studies to date suggest that these effects are most evident at the population level [8,11-16] but see [17] with most species divergence times pre-dating the Pleistocene [18-20].”
    Quote in the paperSubstantial claim0 of 8 sources checked
    • cites [8]

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    • cites [11]

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    • cites [16]

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    • cites [17]

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  • Classified as probably not a substantial claim.

    Premisecitation

    Cephalophus comprises three major mitochondrial lineages: giant duikers, east African red duikers, and west African red duikers.

    “Jansen van Vuuren and Robinson [22] have further sub-divided Cephalophus into three major mitochondrial lineages comprising the giant duikers (C. silvicultor, C. spadix, C. dorsalis, and C. jentinki), east African red duikers (C. leucogaster, C. rufilatus, C. nigrifrons, C. natalensis, C. rubidus, and C. harveyi) and west African red duikers (C. callipygus, C. weynsi, C. ogilbyi, and C. niger).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [22]

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

  • May combine two claims.

    Premisecitation

    Cephalophinae originated in the Late Miocene and subsequently underwent rapid radiation.

    “Duikers in the subfamily Cephalophinae are a group of tropical forest mammals believed to have first originated during the late Miocene.”
    • Also stated in: § Background · plain
      “The duikers in the subfamily Cephalophinae (family Bovidae) constitute an ideal group for testing the role of Pleistocene refugia in tropical vertebrate speciation because of their recent origin in the Late Miocene and subsequent rapid radiation [21,22].”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [21]

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    • cites [22]

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  • May combine two claims.

    Premisecitation

    The position of C. adersi and C. zebra remains unresolved and appears highly labile between studies.

    “Furthermore, the position of the two remaining taxa, C. adersi and C. zebra, remains unresolved and appears to be highly labile between studies [22-24].”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [22]

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    • cites [23]

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    • cites [24]

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  • May combine two claims.

    Interpretationown data

    The present study provides convincing support for the position of Philantomba as sister to the remaining Cephalophinae and the recognition of the genus.

    “This study also provides convincing support for the position of Philantomba as sister to the remaining Cephalophinae and the recognition of the genus, as recommended by Jansen van Vuuren and Robinson [22].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [22]

      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

    Divergence times reported for many central African taxa support the claim that many species divergence times pre-date the Pleistocene.

    “Divergence times reported for many central African taxa support this claim [18-20,26,39]; but see [17], although there is ample evidence for intra-specific diversification within many groups including tropical forest mammals [3].”
    Quote in the paperNot a substantial claim0 of 7 sources checked
    • cites [18]

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    • cites [26]

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    • cites [39]

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    • cites [17]

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    • cites [3]

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  • May combine two claims.

    Interpretationcitation

    In recently diverged lineages, paraphyly observed in mitochondrial DNA should also be reflected in the nuclear data, as observed for C. natalensis/C. harveyi and C. ogilbyi/C. callipygus.

    “Thus, in recently diverged lineages it is expected that the paraphyly observed in mitochondrial DNA should would also be reflected in the nuclear data [30], as is observed for C. natalensis/C. harveyi and C. ogilbyi/C. callipygus.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [30]

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

  • May combine two claims.

    Interpretationreasoning

    Incomplete lineage sorting would explain the paraphyly observed in the nuclear DNA of species that exhibit reciprocally monophyletic relationships in mitochondrial analyses, as appears to be the case for C. sylvicapra/C. spadix and P. monticola/P. maxwelli.

    “Incomplete lineage sorting would also explain the paraphyly observed in the nuclear DNA of species that exhibit reciprocally monophyletic relationships in mitochondrial analyses, as appears to be the case for C. sylvicapra/C. spadix and P. monticola/P. maxwelli.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    Grassland expansion during glacial maxima would have confined forest adapted species to fragments of suitable habitat and broken up the formerly contiguous Equatorial African rainforest belt into several major refugia to the west, center and east of Africa.

    “Grassland expansion during glacial maxima would have confined forest adapted species to fragments of suitable habitat and broken up the formerly contiguous Equatorial African rainforest belt into several major refugia to the west, center and east of Africa [33-35].”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [33]

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    • cites [35]

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  • Classified as probably not a substantial claim.

    Premisecitation

    Such geographic isolation is postulated to have provided ideal opportunities for the allopatric fragmentation and speciation of tropical forest species.

    “Such geographic isolation is thus postulated to have provided ideal opportunities for the allopatric fragmentation and speciation of tropical forest species [36]; reviewed in [9].”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [36]

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    • cites [9]

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  • May combine two claims.

    Interpretationown data

    S. grimmia represents the sole savanna-dwelling member of the giant duiker lineage within Cephalophus and likely evolved from a forest-dwelling common ancestor.

    “Instead, our findings suggests that S. grimmia represents the sole savanna-dwelling member of the giant duiker lineage within Cephalophus and likely evolved from a forest-dwelling common ancestor, further reinforcing Grubb's [28] belief that habitat transitions occur primarily from forest to savannah.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [28]

      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

    The onset of drier, colder periods at the boundary between the Miocene and Pliocene and subsequent intensification of glacial cycles throughout the Pleistocene is thought to have provided important opportunities for the diversification and increased turnover of African vertebrate species, including many arid-adapted bovids.

    “The onset of much drier, colder periods at the boundary between these two epochs and subsequent intensification of glacial cycles throughout the Pleistocene is thought to have provided important opportunities for the diversification and increased turnover of African vertebrate species, including many arid-adapted bovids [21,32].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [21]

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

    • cites [32]

      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). May combine two claims.

    Premisecitation

    More recent studies of Tragelaphus scriptus point to a large sub-specific diversification within this taxon whose timing might also have been driven by Pleistocene climate change.

    “More recent studies of Tragelaphus scriptus also point to a large sub-specific diversification within this taxon whose timing might also have been driven by Pleistocene climate change [15].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [15]

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

  • May combine two claims.

    Interpretationown data

    The savannah duiker diverged early in the group's evolutionary history, but its return to the savannah does not predate the appearance of other forest-dwelling taxa.

    “While Jansen van Vuuren and Robinson [22] were correct in hypothesizing that the savannah duiker diverged early in the group’s evolutionary history, this study shows that its return to the savannah does not predate the appearance of other forest-dwelling taxa.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [22]

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

  • May combine two claims.

    Interpretationown data

    The present phylogeny provides much stronger support for the three main lineages of Cephalophus identified by Jansen van Vuuren and Robinson [22] and for the first time provides significant support for their placement relative to one another.

    “The present phylogeny also provides much stronger support for the three main lineages of Cephalophus identified by Jansen van Vuuren and Robinson [22] and for the first time provides significant support for their placement relative to one another.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [22]

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

  • Probably not a substantial claim: may not pass S1 (asserted), S3 (load-bearing). May combine two claims.

    Premisecitation

    Forest refugia simply acted as reservoirs of genetic variation but did not drive speciation per se.

    “Opponents of tropical Pleistocene refuge theory have argued that many species divergence times pre-date the Pleistocene [37] or that forest refugia simply acted as reservoirs of genetic variation but did not drive speciation per se[20,38].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [20]

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

    • cites [38]

      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).

    Interpretationcitation

    The divergence times observed in this study are consistent with earlier estimates for this group.

    “Although our results are surprising, the divergences times we observed here are also consistent with earlier estimates for this group [22].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [22]

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

  • Classified as probably not a substantial claim.

    Premisecitation

    From the mid-Miocene climatic optimum onwards, the earth has experienced a gradual cooling trend that continued through the Plio-Pleistocene.

    “From the mid-Miocene climatic optimum onwards, the earth has experienced a gradual cooling trend that continued through the Plio-Pleistocene [31].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [31]

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

  • May combine two claims.

    Premisecitation

    Because mitochondrial DNA has a quarter of the effective population size of nuclear DNA, mitochondrial haplotypes generally sort much more rapidly.

    “Because mitochondrial DNA has a quarter of the effective population size of nuclear DNA, mitochondrial haplotypes generally sort much more rapidly [29].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [29]

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

  • May combine two claims.

    Interpretationreasoning

    Mitochondrial introgression between C. nigrifrons and C. rufilatus, followed by extensive back-crossing to the original parental taxa, may have obscured mitochondrial relationships but maintained their monophyly at the nuclear level.

    “One explanation for these findings is that mitochondrial introgression between C. nigrifrons and C. rufilatus, followed by extensive back-crossing to the original parental taxa, may have obscured mitochondrial relationships but maintained their monophyly at the nuclear level.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: C. nigrifrons and C. rufilatus occupy parallel distributions across central Africa, providing ample opportunities for hybridization.

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

    Premisecitation

    There is ample genetic evidence to suggest that the split between eastern and western gorillas (Gorilla gorilla) arose during the Pleistocene as a result of climate-induced changes in forest cover.

    “Similarly, there is ample genetic evidence to suggest that the split between eastern and western gorillas (Gorilla gorilla) arose during the Pleistocene as a result of climate-induced changes in forest cover this period [13,42].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [13]

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

    • cites [42]

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

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    Convergence in BEAST analyses was determined when the combined independent chains yielded posterior probability effective sample sizes (ESS) greater than 200.

    “after which convergence was determined when the combined independent chains yielded posterior probability effective sample sizes (ESS) greater than 200.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S2 (checkable).

    Premisecitation

    An accurate estimation of a species tree is often a useful precursor for guiding conservation and management decisions.

    “An accurate estimation of a species tree is often a useful precursor for guiding conservation and management decisions [45].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [45]

      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).

    Study design and conductnone given

    A blank was included to control for DNA contamination during extraction of the C. jentinki fecal sample.

    “The C. jentinki fecal sample was extracted using the QIAamp DNA Stool Minikit (Qiagen) in a designated room and a blank was included to control for DNA contamination.”
    Quote in the paperNot a substantial claim

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

    Premisecitation

    Fluctuations in climate and increasing aridity over the past few million years are thought to have played an important role in shaping diversification of many African taxa.

    “Fluctuations in climate and increasing aridity over the past few million years are thought to have played an important role in shaping diversification of many African taxa [21,32,48].”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [21]

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

    • cites [32]

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

    • cites [48]

      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

    Many previous studies have shown that the majority of speciation events date to the Pliocene.

    “Although many previous studies have shown that the majority of speciation events date to the Pliocene (e.g. [18,20,49,50])”
    Quote in the paperNot a substantial claim0 of 4 sources checked
    • cites [18]

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

    • cites [20]

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

    • cites [49]

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

    • cites [50]

      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).

    Study design and conductown data

    Nuclear sequences were not available for C. weynsi, C. rubidus and P. walteri either because the sample failed to amplify or because no tissue was available.

    “Nuclear sequences were not available for C. weynsi, C. rubidus and P. walteri either because the sample failed to amplify or because no tissue was available for the present study.”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    Trace files were evaluated with Tracer and 10% of points collected prior to chain stationarity were discarded as burn-in.

    “Additionally, trace files were evaluated with the program Tracer vers. 1.5 [72] and 10% of points collected prior to chain stationarity were discarded as burn-in.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [72]

      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

    The split between the Bovinae and Antilopinae is believed to have occurred between 16.4 and 23.8 Ma.

    “This prior distribution encompasses the dates (16.4 – 23.8 Ma) within which the split between the Bovinae and Antilopinae is believed to have occurred [53].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [53]

      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

    Pleistocene-era climatic oscillations are also thought to have played an important role in shaping patterns of diversification, particularly at the population level.

    “Pleistocene-era climatic oscillations are also thought to have played an important role in shaping patterns of diversification, particularly at the population level (e.g. [11,13]).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [11]

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

    • cites [13]

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

  • May combine two claims.

    Study design and conductown data

    Mitochondrial gene sequences were translated to amino acids to test for non-functional nuclear translocated copies of mitochondrial DNA (Numts), and no evidence of frameshifts or stop codons was found.

    “To test for the potential presence of non-functional nuclear translocated copies of mitochondrial DNA (Numts), each of the mitochondrial gene sequences were translated to amino acids in the program MEGA v3. [60]. No evidence of frameshifts or stop codons were found.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [60]

      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).

    Study design and conductown data

    Heterozygous individuals at nuclear loci were verified by the presence of two similarly sized, overlapping peaks observed in both sequencing directions and were coded using standard IUPAC ambiguity codes.

    “For nuclear loci, heterozygous individuals were verified by the presence of two similarly sized, overlapping peaks observed in both sequencing directions, and were coded using standard IUPAC ambiguity codes.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductreasoning

    Convergence in Bayesian analyses was determined when the standard deviation of split frequencies between simultaneous runs was less than 0.01.

    “Therefore, convergence was determined when the standard deviation of split frequencies between simultaneous runs was less than 0.01, as calculated by MrBayes.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    The lack of clear genetic distinction between C. callipygus and C. ogilbyi is consistent with a history of either recent or on-going hybridization and/or incomplete lineage sorting.

    “Inclusion of nuclear data further substantiates the lack of any clear genetic distinction between these two taxa and is consistent with a history of either recent or on-going hybridization and/or incomplete lineage sorting.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    Nuclear markers and supertree analysis do not provide support for a sister relationship between Oreotragus oreotragus and Cephalophinae, or for any consistent sister group to the Cephalophinae.

    “However, nuclear markers [25] and supertree analysis [55] do not provide support for this relationship, or for any consistent sister group to the Cephalophinae.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [25]

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

    • cites [55]

      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). May combine two claims.

    Study design and conductcitation

    The harmonic mean is not the best estimator of the marginal likelihoods used to compute the Bayes Factor, but alternative methods are either computationally intensive or not readily implementable at this time.

    “Although the harmonic mean is not the best estimator of the marginal likelihoods used to compute the Bayes Factor, alternative methods [75-77] are either computationally intensive or not readily implementable at this time.”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [75]

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

    • cites [76]

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

    • cites [77]

      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

    Recent mitochondrial studies have suggested that the klipspringer (Oreotragus oreotragus) may be sister to the Cephalophinae.

    “recent mitochondrial studies have suggested that the klipspringer (Oreotragus oreotragus) may be sister to the Cephalophinae [53,54].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [53]

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

    • cites [54]

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

  • Classified as probably not a substantial claim. May combine two claims.

    Interpretationown data

    The apparent conflict between the phylogenetic placement of C. rubidus and its previous treatment lends strength to the recommendation that C. rubidus be managed as a distinct species, elevating its conservation status from threatened to endangered.

    “This apparent conflict lends strength to Jansen van Vuuren & Robinson's [22] recommendation that this taxon should be managed as a distinct species, elevating its conservation status from threatened to endangered [46].”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [22]

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

    • cites [46]

      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).

    Study design and conductnone given

    A photographic record was used to verify the species identity of all WCS collected bushmeat samples, except for the easily distinguishable P. monticola and T. spekei.

    “With the exception of the easily distinguishable P. monticola and T. spekei, a photographic record was used to verify the species identity of all WCS collected bushmeat samples.”
    Quote in the paperNot a substantial claim
67 of 67

  • The paper relies on this without support.

    Knowledge of phylogenetic relationships, pattern and timing of radiation of Cephalophinae is poorly understood.

    “However, knowledge of phylogenetic relationships, pattern and timing of their subsequent radiation is poorly understood.”

  • The paper relies on this without support.

    Support for the three Cephalophus lineages has been based solely on single mitochondrial gene genealogies.

    “To date, support for these lineages has been based solely on single mitochondrial gene genealogies that may not accurately reflect the evolutionary history of this group.”

  • The paper relies on this without support.

    Single mitochondrial gene genealogies may not accurately reflect the evolutionary history of this group.

    “To date, support for these lineages has been based solely on single mitochondrial gene genealogies that may not accurately reflect the evolutionary history of this group.”

  • The paper relies on this without support.

    C. nigrifrons and C. rufilatus occupy parallel distributions across central Africa, providing ample opportunities for hybridization.

    “These two taxa occupy parallel distributions across central African, providing ample opportunities for hybridization.”

  • The paper relies on this without support.

    The two fossil calibration points used in the molecular clock accurately date the relevant divergence events.

    “A relaxed molecular clock with two fossil calibration points was used to estimate divergence times. The first was based on the age of the split between the two oldest subfamilies within the Bovidae whereas the second was based on the earliest known fossil appearance of the Cephalophinae and molecular divergence time estimates for the oldest lineages within this group.”

  • The paper relies on this without support.

    Taxa within this group are tied to forest environments.

    “As is the case for other forest artiodactyls, taxa within this group are tied to forest environments”
6 of 6

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.

  • Combined-data Bayes factor has the opposite sign

    Major

    The stated formula gives 2 × [−15370.43 − (−15851.64)] = +962.42, not −962.42. The reported sign therefore reverses the stated model-selection conclusion.

  • Total-evidence node-21 median lies outside its reported interval

    Major

    The reported median of 0.30 Ma is below the lower bound of its stated 95% HPD interval, 0.74 Ma.

  • Nuclear-only Bayes factor has the opposite sign

    Major

    The stated formula gives 2 × [−8088.25 − (−7976.32)] = −223.86, not +223.86. By the paper's stated threshold, these values do not provide strong evidence for the partitioned model.

  • A listed sister-species divergence predates the stated Pleistocene cutoff

    Minor

    The text includes C. jentinki and C. dorsalis among pairs estimated to have originated during the Pleistocene (< 2.558 Ma), but Table 2 gives their divergence as 2.60 Ma.

  • Nuclear parsimony-informative percentage is misstated

    Minor

    The nuclear partition has 208 parsimony-informative characters out of 2980 characters, or about 7%, as Table 1 reports-not 8%.

    Reported 8 · recomputed 6.979866

  • Nuclear node-5 median lies outside its reported interval

    Minor

    Table 2 defines the first age as a median and the bracketed range as its 95% HPD interval. The nuclear median of 7.55 Ma is below that interval's lower bound of 8.49 Ma.

  • Table 2 points to the wrong figure for node labels

    Minor

    The species-tree caption says its numbered divergence-time nodes are given in Table 2, whereas the Table 2 note says its labels refer to Figure 4, which is captioned as a THY gene genealogy.

7 of 7

Cites

Flagged first, then by citations

Cited by

Still being checked.

Related

Authors
Johnston, A. R., & Anthony, N. M.
Affiliations
LSU New Orleans (US)
ORCID
Anthony, Nicola M
Venue
BMC Evolutionary Biology
Publisher
Springer Science and Business Media LLC
Published
2012
Volume
12
Issue
1
Pages
120
ISSN
1471-2148 (ISSN-L)
DOI
10.1186/1471-2148-12-120
PMC
PMC3523051
OpenAlex
W2154083713
Semantic Scholar
36c2e2fbeccb65384561880d72c706ece83063ef
Cited by
36
References
76
Citations by year
2025: 2 · 2024: 1 · 2023: 2 · 2022: 5 · 2021: 3 · 2020: 4 · 2019: 3 · 2018: 2 · 2017: 2 · 2016: 3 · 2015: 2 · 2014: 5 · 2013: 2
FWCI
2.17
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • BMC Evolutionary Biology (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (submittedVersion, cc-by)
  • PubMed Central (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • National Science Foundation (0516425)
  • Division of Environmental Biology
Topics
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology 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
duikers, Cephalophinae, species phylogeny, divergence time estimation, glacial-interglacial cycles, speciation, Cephalophus, hybridization, paraphyly, Bovidae, tropical forest mammals, taxonomy, mitochondrial genes, nuclear introns
MeSH terms
Animals, Cell Nucleus, Climate, Biological Evolution, Introns, Mitochondria, Phylogeny, Ruminants, Multilocus Sequence Typing

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-10.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-10.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

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