The phylogeny of Cetartiodactyla: The importance of dense taxon sampling, missing data, and the remarkable promise of cytochrome b to provide reliable species-level phylogenies

https://doi.org/10.1016/j.ympev.2008.05.046Get rights and content

Abstract

We perform Bayesian phylogenetic analyses on cytochrome b sequences from 264 of the 290 extant cetartiodactyl mammals (whales plus even-toed ungulates) and two recently extinct species, the ‘Mouse Goat’ and the ‘Irish Elk’. Previous primary analyses have included only a small portion of the species diversity within Cetartiodactyla, while a complete supertree analysis lacks resolution and branch lengths limiting its utility for comparative studies. The benefits of using a single-gene approach include rapid phylogenetic estimates for a large number of species. However, single-gene phylogenies often differ dramatically from studies involving multiple datasets suggesting that they often are unreliable. However, based on recovery of benchmark clades—clades supported in prior studies based on multiple independent datasets—and recovery of undisputed traditional taxonomic groups, Cytb performs extraordinarily well in resolving cetartiodactyl phylogeny when taxon sampling is dense. Missing data, however, (taxa with partial sequences) can compromise phylogenetic accuracy, suggesting a tradeoff between the benefits of adding taxa and introducing question marks. In the full data, a few species with a short sequences appear misplaced, however, sequence length alone seems a poor predictor of this phenomenon as other taxa with equally short sequences were not conspicuously misplaced. Although we recommend awaiting a better supported phylogeny based on more character data to reconsider classification and taxonomy within Cetartiodactyla, the new phylogenetic hypotheses provided here represent the currently best available tool for comparative species-level studies within this group. Cytb has been sequenced for a large percentage of mammals and appears to be a reliable phylogenetic marker as long as taxon sampling is dense. Therefore, an opportunity exists now to reconstruct detailed phylogenies of most of the major mammalian clades to rapidly provide much needed tools for species-level comparative studies.

Introduction

The mammalian superorder Cetartiodactyla (whales and even-toed ungulates) contains nearly 300 species including many of immense commercial importance (cow, pig, and sheep) and of conservation interest and aesthetic value (antelopes, deer, giraffe, dolphins, and whales) (MacDonald, 2006). Certain members of this superorder count among the best studied organisms on earth, whether speaking morphologically, behaviorally, physiologically or genetically. Understanding the interrelationships among cetartiodactyl species, therefore, is of obvious importance.

Much of the recent phylogenetic work has focused either on higher level questions such as the placement of Cetacea with respect to Artiodactyla, and the monophyly and relationships among Cetartiodactylan suborders and families (e.g., Gatesy et al., 1999, Nikaido et al., 1999, Lum et al., 2000, Matthee et al., 2001, Murphy et al., 2001, Naylor and Adams, 2001, Thewissen et al., 2001, Hassanin and Douzery, 2003, Arnason et al., 2004, Reyes et al., 2004, Gu et al., 2007, Wada et al., 2007, O’Leary and Gatesy, 2008), or on lower level questions of some smaller clades within the superorder (e.g., Pitra et al., 2004, Ropiquet and Hassanin, 2004, Ropiquet and Hassanin, 2005, Hassanin and Ropiquet, 2004, Willows-Munro et al., 2005, Gilbert et al., 2006, Guha et al., 2007). Hence, while a consensus seems to be emerging from a range of datasets (morphology, mitochondrial and nuclear DNA, SINEs) on many of the higher level relationships (for reviews see Price et al., 2005, Hernandez and Vrba, 2005, May-Collado and Agnarsson, 2006, O’Leary and Gatesy, 2008), understanding of species-level phylogenetics across the superorder is patchy.

Detailed species-level phylogenies are of paramount importance for comparative studies (Harvey and Pagel, 1991). In general, statistical power of comparative methods increases as taxon sampling approaches completion and as resolution increases (both adding to the number of possible sister-taxon comparisons). In addition, many methods in the toolkit of comparative biology perform best when branch length estimates are available (e.g., Felsenstein, 2004, Bollback, 2006).

To date, however, the most comprehensive primary-data-based phylogenetic study on cetartiodactylans included only 51 extant species (Gatesy et al., 2002; note that May-Collado and Agnarsson, 2006 and May-Collado et al., 2007 included 90 and 92 species, respectively, but focused on Cetacea and O’Leary and Gatesy, 2008 include 64 species but focus on extinct taxa). By combining multiple types of data for a strategically chosen set of taxa Gatesy et al. (2002) and O’Leary and Gatesy (2008) offered strong hypotheses of higher level relationships within Cetartiodactyla. However, lack of a more detailed phylogeny limits the types of questions that can be address using the comparative method. To remedy this Lalueza-Fox et al., 2002, Price et al., 2005, (see also Hernandez and Vrba, 2005) combined multiple phylogenetic studies, and non-quantitative taxonomies, to produce a complete phylogeny of Cetartiodactyla using a supertree approach (Bininda-Emonds and Bryant, 1998, Bininda-Emonds et al., 2002). While representing a significant advancement, the supertree has some shortcomings (for a general critique of supertree techniques see e.g. Gatesy et al., 2002). For example, large portions of the tree are simply reflecting taxonomy, rather than quantitatively addressing species interrelationships. Equally important for its use for comparative studies, the resolution of the supertree is relatively low (59.9%) and it does not provide estimates of branch lengths. A better resolved phylogeny with branch lengths, even though taxon-incomplete, may represent a more powerful tool for many comparative questions and methods.

Here, we present a near species-complete phylogeny of Cetartiodactyla based on cytochrome b sequence data. We evaluate the “reliability” of the phylogeny based on the recovery of numerous higher level benchmark clades and undisputed taxonomic groups. We argue that, at least for cytb within this group of mammals, dense taxon sampling may simultaneously overcome some of the commonly cited shortcomings of single-gene phylogenies and increase the value of the resulting phylogenies. We conclude that a profitable short-term research program will be the use of cytb data to rapidly provide species-level phylogenies for large clades across mammals providing valuable tools for comparative biology. Such phylogenies are not competing with character rich studies of relatively few taxa, nor with supertrees, but offer alternative tools, and ultimately will increase the power of supertree approaches to reconstruct even larger and better resolved “megatrees”.

Section snippets

Data and phylogenetic analyses

Cytochrome data was compiled from GenBank for 276 taxa representing 266 cetartiodactylans (including two recently extinct taxa, Myotragus balearicus, the ‘Mouse Goat’, and Megaloceros giganteus, the ‘Irish Elk’ or ‘Giant Deer’), and 10 outgroups (see Table 1 for Accession Nos.). We chose outgroup taxa representing two groups from Pegasoferae a recently proposed group hypothesized to be sister to Cetartiodactyla (Nishihara et al., 2006). Given that missing data can cause problems in phylogenetic

Benchmark clades

In the full dataset, all of the benchmark clades were recovered (Fig. 1, Fig. 2 and Table 2), except that one species Moschiola meminna, a member of Tragulidae grouped with Bovidae (Fig. 3), thereby rendering both families paraphyletic (according with current taxonomic classification). Moschiola has available sequence shorter than 30% (but slightly longer than 15%) of the full cytb sequence length is thus only included in the full matrix. In a subsequent analysis of the full matrix with this

Recovery of benchmark clades: the reliability of cytochrome b and importance of dense taxon sampling

Nearly all benchmark clades were recovered in all analyses (Fig. 1, Fig. 2, Fig. 3, Fig. 5 and Table 2). At the level of families the only real inconsistency surrounds a single species with a very short sequences available (Moschiola, Fig. 2). Otherwise, our results differ only from some traditional classifications in the placement of species whose phylogenetic position has been questioned by many previous studies (i.e. taxa that recent evidence suggests are misplaced in traditional

Conclusions

By analyzing a large number of cetartiodactylan species using a single mitochondrial gene our primary goal here is to provide a tool for species-level comparative studies. This approach offers rapid phylogenetic estimates for large clades, but may suffer by providing less reliable (less accurate) results than studies that include proportionally greater amount of character data. However, our results are, by and large, consistent with all major clades that can be treated as ‘known’ due to strong

Acknowledgments

Funding for this project came from a Slovenian Research Agency research fellowship (ARRS Z1-9799-0618-07) to Ingi Agnarsson, and Judith Parker Travel Grant, Lerner-Gray Fund for Marine Research of the American Museum of Natural History, Cetacean International Society, Latin American Student Field Research Award of the American Society of Mammalogists, Whale and Dolphin Conservation Society, the Russell E. Train Education Program-WWF, and FIU Dissertation Year Fellowship all to Laura

References (109)

  • A. Hassanin et al.

    Molecular phylogeny of the tribe Bovini (Bovidae, Bovinae) and the taxonomic status of the Kouprey, Bos sauveli Urbain 1937

    Mol. Phylogenet. Evol.

    (2004)
  • S. Hughes et al.

    Molecular phylogeny of the extinct giant deer Megaloceros giganteus

    Mol. Phylogenet. Evol.

    (2006)
  • C. Lalueza-Fox et al.

    Molecular phylogeny and evolution of the extinct bovid Myotragus balearicus

    Mol. Phylogenet. Evol.

    (2002)
  • C.J. Ludt et al.

    Mitochondrial DNA phylogeography of red deer (Cervus elaphus)

    Mol. Phylogenet. Evol.

    (2004)
  • L.J. May-Collado et al.

    Cytochrome b and Bayesian inference of whale phylogeny

    Mol. Phylogenet. Evol.

    (2006)
  • M. Nikaido et al.

    Toothed whale monophyly reassessed by SINE insertion analysis: the absence of lineage sorting effects suggests a small population of a common ancestral species

    Mol. Phylogenet. Evol.

    (2007)
  • C. Pitra et al.

    Evolution and phylogeny of old world deer

    Mol. Phylogenet. Evol.

    (2004)
  • F. Rodríguez et al.

    The general stochastic model of nucleotide substitution

    J. Theor. Biol.

    (1990)
  • P.F. Rosel et al.

    Phylogenetic relationships among the true porpoises (Cetacea: Phocoenidae)

    Mol. Phylogenet. Evol.

    (1995)
  • D.E. Soltis et al.

    Genomic-scale data, angiosperm relationships, and ‘ending incongruence’: a cautionary tale in phylogenetics

    Trends Plant Sci.

    (2004)
  • U. Arnason et al.

    Comparison between the complete mtDNA sequences of the blue and the fin whale, two species that can hybridize in nature

    J. Mol. Evol.

    (1993)
  • U. Arnason et al.

    The complete mitochondrial genome of the sperm whale and the establishment of a new molecular reference for estimating eutherian divergence dates

    J. Mol. Evol.

    (2000)
  • U. Arnason et al.

    Mammalian mitogenomic relationships and the root of the eutherian tree

    Proc. Natl. Acad. Sci. USA

    (2002)
  • O.R.P. Bininda-Emonds et al.

    Properties of matrix representation with parsimony analyses

    Syst. Biol.

    (1998)
  • O.R.P. Bininda-Emonds et al.

    The (super)tree of life: procedures, problems, and prospects

    Annu. Rev. Ecol. Systematics

    (2002)
  • J.R. Boisserie et al.

    The position of Hippopotamidae within Cetartiodactyla

    Proc. Natl. Acad. Sci. USA

    (2005)
  • J.P. Bollback

    SIMMAP: stochastic character mapping of discrete traits on phylogenies

    BMC Bioinformatics

    (2006)
  • H. Cap et al.

    The phylogeny and behavior of Cervidae (Ruminantia Pecora)

    Ethol. Ecol. Evol.

    (2002)
  • I. Cassens et al.

    Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages

    Proc. Natl. Acad. Sci. USA

    (2000)
  • P.S. Corneli

    Complete mitochondrial genomes and eutherian evolution

    J. Mammal. Evol.

    (2003)
  • M.L. Dalebout et al.

    A comprehensive and validated molecular taxonomy of beaked whales, Family Ziphiidae

    J. Hered.

    (2004)
  • C. De Muizon

    Les relations phylogogenetiques des Delphinida (Cetacea, Mammalia)

    Ann. Paleontol.

    (1988)
  • L. Fajardo-Mellor et al.

    The phylogenetic relationships and biogeography of true porpoises (Mammalia: Phocoenidae) based on morphological data

    Mar. Mammal. Sci.

    (2006)
  • J. Felsenstein

    Inferring Phylogenies

    (2004)
  • J. Gatesy

    More DNA support for a Cetacea/Hippopotamidae clade: the blood-clotting protein gene √-fibrinogen

    Mol. Biol. Evol.

    (1997)
  • J. Gatesy et al.

    Evidence from milk casein genes that cetaceans are close relatives of hippopotamid artiodactyls

    Mol. Biol. Evol.

    (1996)
  • J. Gatesy et al.

    Stability of cladistic relationships between Cetacea and higher-level Artiodactyl taxa

    Syst. Biol.

    (1999)
  • J. Gatesy et al.

    Resolution of a supertree/supermatrix paradox

    Syst. Biol.

    (2002)
  • J.H. Geisler et al.

    Morphological evidence for the phylogeny of Cetacea

    J. Mammal. Evol.

    (2003)
  • A.W. Gentry

    Caprinae and Hippotragini (Bovidae, Mammalia) in the upper Miocene

  • K. Geuten et al.

    Experimental design criteria in phylogenetics: where to add taxa

    Syst. Biol.

    (2007)
  • A. Graybeal

    Is it better to add taxa or characters to a difficult phylogenetic problem?

    Syst. Biol.

    (1998)
  • C.P. Groves et al.

    Taxonomy of musk deer, genus Moschus (Moschidae, Mammalia)

    Acta Theriol. Sin.

    (1995)
  • H. Hamilton et al.

    Evolution of river dolphins

    Proc. R. Soc. Lond. B

    (2001)
  • P.H. Harvey et al.

    The comparative method in evolutionary biology

    (1991)
  • A. Hassanin et al.

    Molecular and morphological phylogenies of Ruminantia and the alternative position of the Moschidae

    Syst. Biol.

    (2003)
  • S.M. Hedtke et al.

    Resolution of phylogenetic conflict in large data sets by increased taxon sampling

    Syst Biol.

    (2006)
  • M.F. Hernandez et al.

    A complete estimate of the phylogenetic relationships in Ruminantia: a dated species-level supertree of the extant ruminants

    Biol. Rev.

    (2005)
  • J.E. Heyning

    Comparative facial anatomy of beaked whales (Ziphidae) and a systematic revision among the families of extant Odontoceti

    Cont. Sci. Nat. Hist. Mus. Los Angeles

    (1989)
  • D.M. Hillis

    Inferring complex phylogenies

    Nature

    (1996)
  • Cited by (163)

    • Unraveling the phylogenetic relationships of the extinct bovid Myotragus balearicus Bate 1909 from the Balearic Islands

      2019, Quaternary Science Reviews
      Citation Excerpt :

      As some of our results contradict previous molecular phylogenetic analyses of Myotragus, we compared our new high-quality mitochondrial sequences to the previously published gene fragments. Most studies have used the cytb sequence published by Lalueza-Fox et al. (2005a) and found, variously: 1) a close relationship between Myotragus/Ovis (Lalueza-Fox et al., 2000, 2002, 2005a, 2005b; Ramírez et al., 2009) or 2) a largely unresolved position of Myotragus within Caprini (Agnarsson and May-Collado, 2008; Bibi et al., 2012). We observed up to 97 mismatches (8.5% divergence) between the Lalueza-Fox et al. (2005a) sequence (AY380560) and the corresponding positions (14,157–15,297) of our new mitochondrial sequence from sample ACAD13066.

    • Biology and Cultural Importance of the Narwhal

      2024, Annual Review of Animal Biosciences
    View all citing articles on Scopus
    1

    Present address: Department of Biology, University of Puerto Rico, P.O. Box 23360, San Juan PR 00931-3360, USA.

    View full text