Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia)

Abstract

One way to build larger, more comprehensive phylogenies is to combine the vast amount of phylogenetic information already available. We review the two main strategies for accomplishing this (combining raw data versus combining trees), but employ a relatively new variant of the latter : supertree construction. The utility of one supertree technique, matrix representation using parsimony analysis (MRP), is demonstrated by deriving a complete phylogeny for all 271 extant species of the Carnivora from 177 literature sources. Beyond providing a ' consensus ' estimate of carnivore phylogeny, the tree also indicates taxa for which the relationships remain controversial (e.g. the red panda ; within canids, felids, and hyaenids) or have not been studied in any great detail (e.g. herpestids, viverrids, and intrageneric relationships in the procyonids). Times of divergence throughout the tree were also estimated from 74 literature sources based on both fossil and molecular data. We use the phylogeny to show that some lineages within the Mustelinae and Canidae contain significantly more species than expected for their age, illustrating the tree's utility for studies of macroevolution. It will also provide a useful foundation for comparative and conservational studies involving the carnivores.

Evolutionary and biogeographic history of weasel-like carnivorans (Musteloidea)

“…The monophyly of the mustelines, ictonychines, and lutrines was also strongly supported, corroborating results obtained in other molecular studies (Dragoo and Honeycutt, 1997;Flynn et al, 2005;Fulton and Strobeck, 2006;Rozhnov et al, 2006;Koepfli 22 et al, 2008;Harding and Smith, 2009;Agnarsson et al, 2010;Eizirik et al, 2010;Wolsan and Sato, 2010), which conflict with competing (largely morphology-based) hypotheses (e.g., Bryant et al, 1993;Baryshnikov and Abramov, 1998;Bininda-Emonds et al, 1999). Previous molecular investigations have suggested that ictonychines are most closely related to either mustelines (Fulton and Strobeck, 2006;Rozhnov et al, 2006;Harding and Smith, 2009;Agnarsson et al, 2010) or lutrines (Dragoo and Honeycutt, 1997;Fulton and Strobeck, 2006;Eizirik et al, 2010;Wolsan and Sato, 2010), or are sister to a hypothesized clade composed of mustelines and lutrines (Dragoo and Honeycutt, 1997;Flynn et al, 2005;Koepfli et al, 2008).…”

“…Alternative hypotheses about the relationships of ictonychines (e.g., Bryant et al, 1993;Baryshnikov and Abramov, 1998;Bininda-Emonds et al, 1999;Agnarsson et al, 2010) are thus rejected.…”

Non-invasive measurement of fecal estrogens in the spotted hyena (Crocuta crocuta)

“…Although E 2 was not run as a radiolabeled standard in our HPLC analysis, HPLC results from several felids, the taxonomic group closest to the hyenids (Bininda-Emonds et al, 1999) from which we have HPLC data from feces, reveal that elution of E 2 often overlaps with that of E 1 (Brown et al, 1994), the largest immunoreactive peak in fecal samples from both pregnant and non-pregnant hyenas seen here. Additionally, radiolabeled estrogens in the domestic cat are predominantly excreted as unconjugated E 2 and E 1 (Brown et al, 1994;Shille et al, 1984), and we presume because of their close taxonomic relationship to hyenas, these particular estrogens may also be important immunoreactive metabolites in hyena feces.…”

Ecological correlates of extra-group paternity in mammals

“…Phylogenetic relationships at the level of the family were based on Liu et al (2001). Smaller-scale phylogenies were used for the relationships among genera and species within families (Purvis 1995;Bininda-Emonds et al 1999;Michaux et al 2001). As comparable branch lengths across the whole tree were not available, branch lengths were set to 1 in our analyses (Garland & Ives 2000;Freckleton et al 2002).…”