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

Biological Reviews (Impact Factor: 9.79). 04/1999; 74(2):143 - 175. DOI: 10.1111/j.1469-185X.1999.tb00184.x

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 Garnivora 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.

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Available from: Andy Purvis, Dec 16, 2013
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    • "Providing some idea of divergence times can improve many comparative analyses by allowing information on branch lengths to be incorporated. To do this for our musteloid tree we used 42 calibration points for nodes consistent with our tree from the literature (Bininda-Emonds et al. 1999; Marmi et al. 2004; Eizirik et al. 2010; Nyakatura and Bininda-Emonds 2012), shown in Appendix 1, ESM. These were then used to date the tree using the BLADJ function in Phylocom v4.1 (Webb et al. 2008). "
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    ABSTRACT: Avoidance of predation can impose opportunity costs on prey species that use behavioural avoidance strategies to evade detection. An animal that spends much time hiding or remaining immobile, for example, may have less time for other important activities such as foraging or finding mates. Here we examine the idea that the evolution of chemical defence may act to release prey from these constraints, freeing defended prey to exploit their habitats more effectively, and increasing their niche space. We tested this hypothesis using comparative methods on a mammal group containing both chemically defended and non-defended species: Musteloidea. We found that defended species had a more omnivorous diet and were more likely to be active during both day and night than non-defended species. We also found that chemically defended species were less likely to be strictly diurnal or to show sexual size dimorphism, and had earlier maturing females and a shorter lifespan than non-defended species. Taken together, our results support the hypothesis that chemical defence increases the niche space available to a species. More generally, this also supports recent suggestions that strategies taken to avoid natural enemies can have important effects on diverse components of life history.
    Evolutionary Ecology 09/2013; 27(5). DOI:10.1007/s10682-013-9629-z · 2.37 Impact Factor
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    • "Though the hypothesis of pinniped diphyly is still advocated by some workers (e.g., Koretsky and Barnes 2006), extensive morphological (Wyss 1989, Wyss and Flynn 1993, Berta and Wyss 1994) and molecular (Sarich 1969, ´ Arnason and Widegren 1986, ´ Arnason et al. 1995, Lento et al. 1995, Flynn and Nedbal 1998, Bininda-Emonds et al. 1999, Flynn et al. 2000, Davis et al. 2004, Flynn et al. 2005, ´ Arnason et al. 2006, Fulton and Strobeck 2006, Higdon et al. 2007, Dasmahapatra et al. 2009) analyses nearly unanimously support pinniped monophyly. Morphological analyses have suggested Ursidae as sister to pinnipeds (Wyss and Flynn 1993; Fig. 1C), whereas different molecular analyses have identified either Ursidae (Vrana et al. 1994) or Musteloidea ( ´ Arnason and Widegren 1986, Flynn and Nedbal 1998, Bininda-Emonds et al. 1999, Yu et al. 2004, Flynn et al. 2005, Fulton and Strobeck 2006, Yu and Zhang 2006; Fig. 1D) as sister taxa. Yet another hypothesis posits that Ursidae and Musteloidea form a clade that is sister to Pinnipedia, based on molecular evidence (Bininda- Emonds et al. 2007; Fig. 1E). "
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    ABSTRACT: Marine tetrapods have evolved different sensory solutions to meet the eco-logical challenges of foraging at depth. It has been proposed that pinnipeds, like ichthyosaurs, evolved large eyeballs for such demands. Here, we test this hypothesis using morphological and diving data from a comprehensive data set (n = 54 species; 435 individual specimens), including living and extinct pinnipeds and other select carnivorans as outgroup taxa. We used bony orbit size as a proxy for eyeball size, and recorded associated skull measurements to control for relative changes in orbit size; for diving depth, we used the deepest dive depth reported in the literature. Our analyses included both standard regressions and those corrected for phylogeny (i.e., independent contrasts). Standard regression statistics showed orbit size was a significantly good predictor of diving depth for phocids and for pinnipeds overall, although there was no correlation for otariids. In contrast, independent contrasts showed little support for a relationship between orbit size and diving depth for any group broader than family level, although this approach did demonstrate deep diving has evolved multiple times in crown Pinnipedia. Lastly, using select fossil taxa, we highlight the need to test adaptive hypotheses using comparative data in an evolutionary context.
    Marine Mammal Science 01/2013; 29(1):48-83. DOI:10.1111/j.1748-7692.2011.00545.x · 1.82 Impact Factor
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    • "The method is widely used and has been shown to be relatively robust for testing hypotheses of correlated evolution when good estimates of the topology and branch lengths of the phylogeny are available (Purvis et al., 1994; DõÂ az-Uriarte and Garland, 1996, 1998). A phylogeny of the mammal species used here was reconstructed from the information provided by Garland and Janis (1993), de Jong (1998), Morand and Poulin (1998), Simmons (1998), Randi et al. (1998), and Bininda-Emonds et al. (1999). The avian phylogeny used here was that proposed by Sibley and Ahlquist (1991), supplemented by information on relationships among Anatidae from Livezey (1991, 1995). "
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    ABSTRACT: The evolutionary diversification of living organisms is a central research theme in evolutionary ecology, and yet it remains difficult to infer the action of evolutionary processes from patterns in the distribution of rates of diversification among related taxa. Using data from helminth parasite communities in 76 species of birds and 114 species of mammals, the influence of four factors that may either be associated with or modulate rates of parasite speciation were examined in a comparative analysis. Two measures of the relative number of congeneric parasite species per host species were used as indices of parasite diversification, and related to host body mass, host density, latitude, and whether the host is aquatic or terrestrial. The occurrence of congeneric parasites was not distributed randomly with respect to these factors. Aquatic bird species tended to harbour more congeneric parasites than terrestrial birds. Large-bodied mammal species, or those living at low latitudes, harboured more congeneric parasites than small-bodied mammals, or than those from higher latitudes. Host density had no apparent association with either measures of parasite diversification. These patterns, however, reflect only the present-day distribution of parasite diversification among host taxa, and not the evolutionary processes responsible for diversification, because the apparent effects of the factors investigated disappeared once corrections were made for host phylogeny. This indicates that features other than host body size, host density, latitude, and whether the habitat is terrestrial or aquatic, have been the key driving forces in the diversification of parasitic helminth lineages.
    Evolutionary Ecology 04/2012; 13(5):455-467. DOI:10.1023/A:1006703927711 · 2.37 Impact Factor
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