Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset

Abstract

BackgroundPhylogenetic comparative methods are often improved by complete phylogenies with meaningful branch lengths (e.g., divergence dates). This study presents a dated molecular supertree for all 34 world pinniped species derived from a weighted matrix representation with parsimony (MRP) supertree analysis of 50 gene trees, each determined under a maximum likelihood (ML) framework. Divergence times were determined by mapping the same sequence data (plus two additional genes) on to the supertree topology and calibrating the ML branch lengths against a range of fossil calibrations. We assessed the sensitivity of our supertree topology in two ways: 1) a second supertree with all mtDNA genes combined into a single source tree, and 2) likelihood-based supermatrix analyses. Divergence dates were also calculated using a Bayesian relaxed molecular clock with rate autocorrelation to test the sensitivity of our supertree results further.ResultsThe resulting phylogenies all agreed broadly with recent molecular studies, in particular supporting the monophyly of Phocidae, Otariidae, and the two phocid subfamilies, as well as an Odobenidae + Otariidae sister relationship; areas of disagreement were limited to four more poorly supported regions. Neither the supertree nor supermatrix analyses supported the monophyly of the two traditional otariid subfamilies, supporting suggestions for the need for taxonomic revision in this group. Phocid relationships were similar to other recent studies and deeper branches were generally well-resolved. Halichoerus grypus was nested within a paraphyletic Pusa, although relationships within Phocina tend to be poorly supported. Divergence date estimates for the supertree were in good agreement with other studies and the available fossil record; however, the Bayesian relaxed molecular clock divergence date estimates were significantly older.ConclusionOur results join other recent studies and highlight the need for a re-evaluation of pinniped taxonomy, especially as regards the subfamilial classification of otariids and the generic nomenclature of Phocina. Even with the recent publication of new sequence data, the available genetic sequence information for several species, particularly those in Arctocephalus, remains very limited, especially for nuclear markers. However, resolution of parts of the tree will probably remain difficult, even with additional data, due to apparent rapid radiations. Our study addresses the lack of a recent pinniped phylogeny that includes all species and robust divergence dates for all nodes, and will therefore prove indispensable to comparative and macroevolutionary studies of this group of carnivores.

Pinniped phylogenetic relationships inferred using AFLP markers

“…These results suggest that AFLP markers should carry little or no phylogenetic signal when comparisons are carried out between taxa that have diverged more than a few million years ago. In contrast to this expectation we find sufficient phylogenetic signal even as far back as B15 MYA (Higdon et al, 2007) Phylogenetic reconstruction with AFLP markers KK Dasmahapatra et al fail to recover pinniped outgroup relationships, but this is not surprising given that fewer than 20% of bands are shared among the deepest pinniped lineages (Figure 3a), corresponding to 20-26 MYA (Higdon et al, 2007). Extrapolating the linear relationship in Figure 3a, one would expect very few shared homologous bands between the outgroup taxon and pinnipeds as this split is dated to 30-41 MYA (Higdon et al, 2007).…”

“…Pinnipeds, or seals, are a diverse group of aquatic mammals (Riedman, 1990) comprising 34 extant species spread across three distinct families: the Odobenidae, the Otariidae and the Phocidae (Rice, 1998). It is estimated that this group of mammals originated 23-26 million years ago (MYA), but much of the current species diversity is of relatively recent origin, having arisen during and after the Pleistocene (Arnason et al, 2006;Higdon et al, 2007). Pinnipeds have been intensively studied due to their ecological importance as top predators in marine ecosystems and conservation concerns facing many species.…”

“…On the other main pinniped branch, the Phocidae, relatively rapid speciation, especially within the Phocinae, has led to uncertainty about the exact relationships among several species. The analyses in Higdon et al (2007) are dominated by mitochondrial genes, and from a nuclear perspective the species coverage is low with an average of only 5.5 species' represented at each nuclear gene. A further limitation of this study is that where sequences were available, each species was represented by a single sequence.…”

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

“…The resolution to this problem depends to some degree on what should be done with Phoca ( sensu lato ), which varies regularly between being recognized as a single genus (for example, [13,57]), as four separate genera (for example, [14,53,58]) or some intermediate solution (for example, [54]). Given the relative divergence times inferred in this and other studies (for example, [49,50,59]), we would argue that Histriophoca and Pagophilus should remain as distinct genera, with both Halichoerus and Pusa being subsumed with Phoca . In the latter case, the designation of subgenera within Phoca is difficult due to the paraphyly of Pusa , unless one is willing to subsume Halichoerus within the subgenus Pusa .…”

Un lobo marino en controversia: Materialidad, taxonomía y disputa científica (segunda mitad del siglo xix)

“…En este sentido, el uso de un "robusto análisis estadístico" como de una "investigación molecular" aún no ha zanjado la cuestión 56 . Actualmente, usando métodos comparativos filogenéticos, la entonces llamada Otaria philipii es reconocida en dos sinonimias de especies: como Arctocephalus philippii (Peters, 1866) y como Arctophoca philippii (Peters, 1866) 57 . En este sentido se puede afirmar que los restos estudiados por los museos de Alemania y Chile y discutidos por los investigadores de Inglaterra y Argentina durante la segunda mitad del siglo xix han dado lugar a dos géneros: al Arctocephalus y al Arctophoca.…”