Background

Phylogenetic 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.

Results

The 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 grypuswas nested within a paraphyleticPusa, 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.

Conclusion

Our 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 inArctocephalus, 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.

Table 1.

General structure of the supertree

Our preferred hypothesis of pinniped evolution is that derived from the molecular supertree with all genes analyzed individually (Fig.1; see Methods). It agrees broadly with other recent studies (e.g., [10-15,23,24,26,32]). In particular, the monophyly of each of Pinnipedia, Otarioidea, Phocidae, Otariidae, and the two phocid subfamilies was supported. Many of these nodes are among the most strongly supported in the supertree. The high level of congruence across numerous studies using different data sources and methodologies would suggest that higher-level pinniped relationships are well resolved. However, many relationships closer to the tips of the tree, particularly those within each ofArctocephalusand Phocina, remain contentious.

Support values within the supertree (Table2) were generally much higher than values typically reported for the supertree-specific support measure rQS (see [51,52]), with an average rQS value (± SD) across the tree of 0.234 ± 0.214. As such, most nodes are directly supported by a majority of the 50 source trees containing all the relevant taxa. The only exception is the node comprisingHalichoerus grypus,Pusa caspicaandPusa sibirica, which has a slightly negative rQS value (-0.040). Even so, all more inclusive nodes possess positive rQS values, indicating that the conflict has more to do with the exact placement ofHalichoeruswithinPusarather than the placement of it within this genusper se.

Alternative analyses of the molecular data set (supertree analysis with all mtDNA forming a single source tree or ML or BI analyses of the combined supermatrix; Figures2 and3, respectively) yield topologies that agree broadly with that in Figure1. The rQs support measure across the supertree (0.18 ± 0.11) again showed that most nodes are directly supported by a majority of the 12 source trees containing all the relevant taxa. In all cases, the changes occur in parts of the tree with noticeably weaker support and/or branch lengths, indicating general regions of uncertainty: 1)Neophoca cinereanests deeper within otariids, either as the sister taxon toPhocarctos hookeri(ML) or to the clade comprising the generaArctocephalus,Otaria, andPhocarctos(BI), or forms the sister taxon toCallorhinus ursinus(supertree); 2) the formation of a sister-group relationship betweenOtaria byroniaandArctocephalus pusillus, which were previously adjacent to one another (all analyses); 3) the clades (Arctocephalus townsendii+A.phillippi) and (A.gazella+A.tropicalis) trade places (all analyses); and 4) changes to the internal relationships of Phocina, either withHalichoerus grypusandPusa caspicabeing pulled basally with respect to the remainder of the group, withHalichoerusforming the sister group to the remaining species (ML), or withPusa hispidaand the clade ofHistriophoca fasciataandPagophilus groenlandicusnesting deeper within the group (BI), or withPusa hispidamoving insideP.sibiricaand with a polytomy at the base of Phocini (supertree).

In the supertree, nodes 1 and 2 (see Fig.1) represent the divergences of the canid and ursid lineages, respectively, and nodes 3 to 35 represent the various pinniped divergences. The total sample size (molecular and fossil date estimates) underlying the divergence times for each node ranged from 0 (node 35 – the split betweenMonachus schauinslandiandM. tropicalis, where the date was interpolated using a constant birth model) to 27 (Table2). Over half (19) of the pinniped nodes were dated using at least 12 separate estimates. The remaining 14 nodes were dated by five or fewer estimates. Ten of these 14 nodes relate to otariid relationships, and seven concernArctocephalusspecies. Divergences within thePusa+Halichoerusclade were also dated by a comparatively small number of estimates. However, no obvious relationship existed between the variability in a date estimate (given by the coefficient of variation, CV) and the number of estimates it was derived from (R²= 0.02,P= 0.4849,df= 26).

Our inferred relDate dates for the supertree topology (see Methods) are also significantly correlated with those for comparable nodes (which are restricted largely to Phocidae) in the two major studies to estimate divergence times within pinnipeds, those of Bininda-Emonds et al. [23] (R²= 0.52,P= 0.004) and Arnason et al. [14] (R²= 0.958,P< 0.0001) (df= 12 in both cases using ln-transformed values). However, whereas our dates did not differ significantly from those of Bininda-Emonds et al. [23] (paired-tof ln-transformed values = -1.36,P= 0.197;df= 13), they were significantly more recent than those of Arnason et al. [14] (paired-tof ln-transformed values = -9.82,P< 0.0001;df= 13), probably reflecting their use of a only single and more distant calibration point (the caniform-feliform split at 52 mya) as well as topological differences between the trees and different methodologies used to derive the dates.

Both sets of multidivtime divergence dates (Table3) are significantly different from the relDate divergence dates (paired-tof ln-transformed values = -11.39,P< 0.0001;df= 32, for relDate versus multidivtime all genes; paired-tof ln-transformed values = -4.53,P< 0.0001;df= 32, for relDate versus multidivtime mtDNA only). The supertree (relDate) divergence dates underestimate the multidivtime dates from all genes and mtDNA genes by 88% and 51% on average, respectively. With respect to confidence intervals (CIs), only 9 and 7 (of 33) of the relDate dates fall into the range provided by the multidivtime CIs for mtDNA or all genes, respectively. Conversely, only 3 and 4 (of 33) dates for all genes and mtDNA only, respectively, fall within the CIs of the relDate dates. However, it is important to note that the two sets of multidivtime dates themselves are also significantly different from one another (paired-tof ln-transformed values = 2.36,P= 0.02;df= 32). In the following sections, we compare both sets of divergence dates (i.e., the relDate and multidivtime dates) with those from the fossil record and other studies.

Origins of major pinniped groups

The split between ursids and pinnipeds is estimated to be 35.7 ± 2.63 (= mean ± SE) mya (relDate, Table2; the multidivtime dates for this node were similar (Table3)), although this should not be taken to imply that ursids are the closest living relatives of pinnipeds among arctoid carnivores. Early pinnipeds (pinnipedimorphs) are held to have originated in the North Pacific during the late Oligocene (34-24 mya) ([2,22,45,53], but see [14], who speculate on an origin on the southern shores of North America), which is consistent with our estimate. Thereafter, a substantial lag is apparent, with the basal pinniped split between Phocidae and Otarioidea occurring some 12 million years later at 23.0 ± 1.36 mya (Table2) (ca. 26 mya with multidivtime, Table3). Both values are more recent than the 28.1 mya and 33.0 mya estimates obtained by Bininda-Emonds et al. [23] and Arnason et al. [14], respectively.

Odobenidae includes a single extant species and at least 20 fossil species in 14 genera [2], with the most basal taxa known from the late early Miocene (ca. 21-16 mya). Deméré et al. [2] suggest that odobenoids first evolved in the North Pacific region sometime before 18 mya (late early Miocene), and our data indicate the upper bound to be 20.8 mya. The multidivtime dates were similar at ca. 21 mya. Both values are substantially older than the 14.2 mya estimate obtained by Bininda-Emonds et al. [23], but younger than the 26.0 mya estimate of Arnason et al. [14].

Modern fur seals and sea lions are thought to have evolved from the ancestral family Enaliarctidae ca. 11 mya [54-56], with our data showing that the diversification of the crown group occurred shortly thereafter at 8.2 ± 2.09 mya (the dates estimated using multidivtime were again older, ca. 11 mya). Arnason et al. [14] consider the late Oligocene Enaliarctinae [57] to be the oldest otarioid lineage so far described (25–27 mya; [58]). However, Deméré et al. [2] consider this group to be early pinnipedimorphs that originated before the evolution of the modern crown-group pinnipeds.

The first phocid fossils date from the middle Miocene (ca. 16-14 mya) (but see [59,60]) in the North Atlantic [61], although some authors (e.g., [2,4,62]) have speculated over a North Pacific origin. Koretsky and Sanders [59,60] recently described the "Oligocene seal" from the late Oligocene (ca. 28 mya) in South Carolina as the oldest known true seal, a fossil that predates our estimate for the basal-most split in all pinnipeds. However, because this new description was based on a very small sample (two partial femora), and because Deméré et al. [2] noted that its stratigraphic provenience may be in question, we instead used 23 mya as a conservative fossil calibration point for the split between Phocidae and Otarioidea. Obviously, acceptance of the "Oligocene seal" as the oldest known phocid (and therefore crown-group pinniped) would cause all divergence times within the pinnipeds to be older than the ones that we report.

Otariidae

Phocidae

DNA sequence data

The use of large, multigene data sets provides the numerous informative changes required for correct inferences, and may also help to raise weak phylogenetic signals above the noise level [90]. In addition, the best topologies are often resolved when estimates are based on a combination of mitochondrial and nuclear DNA. With these points in mind, we mined GenBank for all available pinniped DNA sequence data to infer a phylogeny based on the largest data set possible. All sequence data were downloaded on January 30, 2006 and mined using the Perl script GenBankStrip v2.0 [91] to retain only those genes that had been sequenced for at least three pinniped species and were longer than 200 bp (except for tRNA genes, which had to be longer than 50 bp). For the 52 genes meeting these criteria (see Table4), matching sequences for exemplars from Canidae (eitherCanis lupusor, on one occasion,C. latrans) and/or Ursidae (usuallyUrsus arctos, but alsoU. americanusorU. maritimusas needed) were downloaded for outgroup analysis.

Sequences in each data set were aligned using ClustalW [92] or with transAlign [93] in combination with ClustalW for the protein-coding sequences, and improved manually where needed. Thereafter, each aligned data set was passed through the Perl script seqCleaner v1.0.2 [91] to standardize the species names, to eliminate inferior sequences (i.e., those with > 5% Ns), and to ensure that all sequences overlapped pairwise by at least 100 bps (or 25 bps for the tRNA genes). Note that although species names were standardized according to Wilson and Reeder [94] for the analyses, those used in the text for Phocini follow the currently accepted International Commission of Zoological Nomenclature (ICZN) taxonomy, which recognizes the five generaHalichoerus,Histriophoca,Pagophilus,Phoca, andPusa.

The final data set of 52 genes (Table4) comprises 26818 bps in total, or an average of 515.7 bp per gene (range = 68–1980 bps). On average, each gene was sampled for 11.2 species (range = 3–35); however, only an average of 5.5 species per nuclear gene were available for study. Two genes,LYZand exon 29 ofAPOB, contained fewer than three pinniped species and, as such, were uninformative for resolving pinniped interrelationships. However, they were still retained to determine times of divergence. Accession numbers for all sequences used in the final data set are provided as supplementary material (Additional file1).

The final data set is dominated by mitochondrial genes, which forms a single locus due to its common inheritance and general lack of recombination. As such, it must be kept in mind that all the resulting topologies (be they derived in a supertree or supermatrix framework) and divergence times could be biased by any peculiarities related to mitochondrial sequence data (e.g., introgression or linkage) or simply the disproportionately large amount of mitochondrial data. However, the data set represents the "current systematic database" for pinnipeds and so the best possible current data source for which to infer their phylogenetic relationships. However, to assess the impact of this potential source of bias, we performed a second supertree analysis where all mtDNA genes were combined to form a single source tree (yielding 12 source trees in total). Nevertheless, the collection of additional nuclear markers is desperately needed for this group.

The final data set used for the phylogenetic analyses, together with the supertree and supermatrix trees is freely available from TreeBASE [95] (study accession number S1911, matrix accession numbers M3516-M3518).

Phylogeny reconstruction and supertree analysis

Our general approach to infer the phylogeny of the pinnipeds involved a divide-and-conquer strategy in which individual genes trees were determined using the best possible methodology for each and then combined as a supertree. Compared to a simultaneous analysis of the multigene "supermatrix", this procedure has been argued to potentially account better for the differential models of evolution that might be present [96] and, for extremely large matrices, looks to be a faster analytical method without any appreciable loss of accuracy [97]. Although the use of mixed models is possible in both maximum likelihood (ML, [98]) and Bayesian frameworks, the accuracy of the resulting tree, at least in a Bayesian framework, has recently been called into question [99], especially when reasonable levels of conflict exist between the different data partitions [100]. Furthermore, Jeffroy et al. [101] have also recently argued that trees derived from multigene, phylogenomic data sets should be treated more cautiously than those from single-gene analyses given that the systematic biases inherent to phylogeny reconstruction become more apparent with larger data sets. Nevertheless, in light of the fierce criticism that the supertree approach has attracted (e.g., [102,103], but see [104,105]), we also conduct ML and Bayesian inference (BI) analyses of the concatenated supermatrix to help identify especially problematic regions of the pinniped tree as part of a global congruence framework [50] and to add to the growing body of studies comparing phylogenetic inference under these two frameworks (e.g., [15,106]).

For the supertree analyses, we used PHYML [106] to determine the ML tree for each of the 50 phylogenetically informative genes after determining their optimal model of evolution according to either AIC or AICc (as appropriate, the latter being a version of the AIC corrected for small sample sizes) using MrAIC [107] and PHYML [106] (Table4). The 50 gene trees were then used to build a weighted supertree of the group using matrix representation with parsimony (MRP, [48,49]). In so doing, we have assumed that each gene tree forms an independent unit in our preferred supertree, something that is admittedly debatable for the mitochondrial genes and especially the very small tRNA genes. However, in the absence of any robust linkage information, this assumption seemed more justifiable and objective than the defining of gene partitions based on assumed linkage or for purely practical considerations (e.g., concatenating all the tRNA genes because of their small size). Nonetheless, the sensitivity of these assumptions was assessed using the second supertree in which all mtDNA genes formed a single source tree.

All gene trees were encoded for the MRP analysis using semi-rooted coding [108], whereby only those trees with either a canid and/or ursid outgroup taxon and where the pinnipeds were reconstructed as being monophyletic were held to be rooted. Furthermore, the individual MRP characters, which correspond to a particular node on a gene tree, were weighted according to the bootstrap frequency [109] of that node, as determined using PHYML and based on 1000 replicates. This procedure has been demonstrated to increase the accuracy of MRP supertree construction in simulation [110]. The weighted parsimony analysis of the resulting MRP matrix was accomplished using a branch-and-bound search in PAUP* v4.0b10 [111], with Canidae and Ursidae being specified as a paraphyletic outgroup.Monachus tropicalis, for which no molecular data exist, was added to the supertree manually as the sister species ofM. schauinslandii(following [4,23]).

Support for both supertrees and the relationships in them were quantified with the supertree-specific rQS index [51,52], which compares the topology of the supertree to that of each of the source trees contributing to it. As such, it is preferable to such conventional, character-based support measures such as Bremer support [112] and the bootstrap, which are invalid in this context given that MRP characters for a given source tree are non-independent. Values for rQS range from + 1 to -1, with the two values indicating that a given node is directly supported or directly contradicted by all source trees, respectively. The rQS value for the entire tree is simply the average of all the nodal rQS values. Previous applications of the rQS index show that it often tends to negative values [51,52,113], indicating that more conflict than agreement generally exists among a set of source trees for a given node. As such, positive values of rQS can be taken to indicate good support in the sense that more source trees support the relationship than contradict it.

The individual gene data sets were also concatenated to form a single supermatrix that was analyzed using both partitioned ML and BI methods. ML analyses used RAxML VI-HPC v2.2.3 [114]. A GTR + G model was assumed for the data using the CAT approximation of the gamma distribution, with the model parameters being allowed to vary independently for each gene. CAT is both a fast approximation of the gamma model (due to its lower computational and memory costs) and one that appears to yield better log likelihood scores even when calculated under a real gamma model [115], and therefore is ideally suited to large, computationally intensive data matrices such as ours. The ML tree was taken to be the optimal tree over 100 replicates, for which nodal support was estimated using the bootstrap with 1000 replicates and search parameters matching those for the optimality search.

BI used MrBayes v3.1.2 [116], with the individual models specified for each individual gene matching the optimal model determined in the gene-tree analyses as closely as possible. Otherwise, flat priors were used in all cases. Searches employed a MCMC algorithm of two separate runs, each with four chains that were run for 10000000 generations and with the first 5000000 generations being discarded as burn-in. Trees were sampled every 5000 generations to derive the final BI tree and estimates of the posterior probabilities.

Divergence date estimations

Following Bininda-Emonds et al. [117], divergence times on the supertree only were determined using a combination of fossil calibration points and molecular dates under the assumption of a local molecular clock (see [118]). As a first step, the optimal model of evolution for all 52 genes was (re)determined using an AIC in ModelTEST v3.6 [119] in combination with PAUP*, with the appropriately pruned supertree topology being used as the reference tree in place of the default NJ tree. This combination was used here in place of the previous MrAIC/PHYML combination largely because it can be used to test for the applicability of a molecular clock (through PAUP*) using a likelihood-ratio test. The small taxonomic distribution meant that all but six genes (CYP1A1, MT-ND4, MT-ND5, MT-RNR2, OB, andMT-TQ) evolved according to a molecular clock.

Thereafter, we used PAUP* to fit the sequence data for each gene to the (pruned) supertree topology under the optimal model in a ML framework. In line with Purvis' [118] local-clock model, the relative branch lengths for each gene tree relative to the topology of the supertree were determined using the Perl script relDate v2.2.1 [91]. Only the gene trees for the clock-like genes were considered to be rooted and relative branch lengths were calculated with respect to ancestral nodes only (and not also with respect to daughter nodes).

Divergence times were then determined by calibrating the relative branch lengths for each gene tree using a set of fossil dates (Table5). For a given node, the initial divergence date was taken to be the maximum of 1) the median of all fossil plus molecular estimates and 2) the fossil estimate. In this way, the fossil estimate acts as a minimum age constraint that can overrule the molecular estimates. Upper and lower bounds on any given date estimates took the form of the 95% confidence interval derived from all individual gene and/or fossil estimates for that node. Although error in the branch-length estimation for the individual gene trees can also contribute to uncertainty in the final date estimates [120], it is likely to be less important than the variation present between the different genes themselves. However, together with uncertainties in the fossil dates, it cannot be excluded that our confidence intervals are underestimates of the true values.

Finally, the Perl script chronoGrapher v1.3.3 [91] was used to correct for any negative branch lengths and simultaneously to derive a divergence-time estimate for the single node lacking an initial estimate (that linkingMonachus schauinslandiandM. tropicalis). The date for this latter node was interpolated from the dates of up to five of its ancestral nodes based on the relative number of species descended from each node, assuming a constant birth model (see [117]).

More details regarding this dating procedure, including its strengths and weaknesses with respect to other relaxed molecular clock methods (recently reviewed in [121]) can be found in Bininda-Emonds et al. [117].

The Bayesian relaxed molecular clock method implemented by multidivtime [122,123] was also used to calculate divergence dates from the supermatrix data fitted to the preferred supertree topology. General methodology followed Rutschman [124], with maximum likelihood parameters estimated using PAML version 3.15 [125]. Incomplete overlap of sequences between taxa (in particular the outgroup sequence(s) not being represented in every partition) meant that model partitioning by gene was impossible; instead, a single F84 + gamma model was applied to the entire supermatrix. The root prior rttm (the mean of the prior distribution for the time from the ingroup root to the tips; in other words, the age of the ursid-pinniped split) was specified as 19.5 mya, with the remaining constraints the same as in the supertree dating analysis (Table5). Other multidivtime parameters were calculated following the recommendations of Rutschmann [124]: rtrate (mean of prior distribution for the rate at the root node) = X/rttm, where X is the median amount of evolution from the root to tips; rtratesd (standard deviation of rtrtate) = 0.5 × rtrate; brownmean (mean of the prior distribution for the autocorrelation parameter,v) = 1/rttm; brownsd (standard deviation of brownmean) = brownmean. Three independent multidivtime analyses were run for 1 × 10⁶cycles, with samples taken every 100 cycles after a burn-in period of 1 × 10⁵cycles. The dates presented here are mean values for the three runs. The multidivtime analyses were then repeated using only the mitochondrial genes to investigate whether the inclusion of nuclear genes greatly altered the estimated divergence dates.

Acknowledgements

This research was supported by ArcticNet, NSERC, Fisheries and Oceans Canada (JH and SF), a Heisenberg Scholarship of the DFG (Germany) and the BMBF (Germany) through the "Bioinformatics for the Functional Analysis of Mammalian Genomes" project (OB-E). A review by L. Postma and three anonymous reviewers greatly improved this manuscript.

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