SDM: a fast distance-based approach for (super) tree building in phylogenomics

Phylogenomic studies aim to build phylogenies from large sets of homologous genes. Such "genome-sized" data require fast methods, because of the typically large numbers of taxa examined. In this framework, distance-based methods are useful for exploratory studies and building a starting tree to be refined by a more powerful maximum likelihood (ML) approach. However, estimating evolutionary distances directly from concatenated genes gives poor topological signal as genes evolve at different rates. We propose a novel method, named super distance matrix (SDM), which follows the same line as average consensus supertree (ACS; Lapointe and Cucumel, 1997) and combines the evolutionary distances obtained from each gene into a single distance supermatrix to be analyzed using a standard distance-based algorithm. SDM deforms the source matrices, without modifying their topological message, to bring them as close as possible to each other; these deformed matrices are then averaged to obtain the distance supermatrix. We show that this problem is equivalent to the minimization of a least-squares criterion subject to linear constraints. This problem has a unique solution which is obtained by resolving a linear system. As this system is sparse, its practical resolution requires O(naka) time, where n is the number of taxa, k the number of matrices, and a < 2, which allows the distance supermatrix to be quickly obtained. Several uses of SDM are proposed, from fast exploratory studies to more accurate approaches requiring heavier computing time. Using simulations, we show that SDM is a relevant alternative to the standard matrix representation with parsimony (MRP) method, notably when the taxa sets of the different genes have low overlap. We also show that SDM can be used to build an excellent starting tree for an ML approach, which both reduces the computing time and increases the topogical accuracy. We use SDM to analyze the data set of Gatesy et al. (2002, Syst. Biol. 51: 652-664) that involves 48 genes of 75 placental mammals. The results indicate that these genes have strong rate heterogeneity and confirm the simulation conclusions.     

Jumping and gliding rodents: Mitogenomic affinities of Pedetidae and Anomaluridae deduced from an RNA-Seq approach

An RNA-Seq strategy was used to obtain the complete set of protein-coding mitochondrial genes from two rodent taxa. Thanks to the next generation sequencing (NGS) 454 approach, we determined the complete mitochondrial DNA genome from Graphiurus kelleni (Mammalia: Rodentia: Gliridae) and partial mitogenome from Pedetes capensis (Pedetidae), and compared them with published rodent and outgroup mitogenomes. We finished the mitogenome sequencing by a series of amplicons using conserved PCR primers to fill the gaps corresponding to tRNA, rRNA and control regions. Phylogenetic analyses of the mitogenomes suggest a well-supported rodent phylogeny in agreement with nuclear gene trees. Pedetes groups with Anomalurus into the clade Anomaluromorpha, while Graphiurus branches within the squirrel-related clade. Moreover, Pedetes + Anomalurus branch with Castor into the mouse-related clade. Our study demonstrates the utility of NGS for obtaining new mitochondrial genomes as well as the importance of choosing adequate models of sequence evolution to infer the phylogeny of rodents.     

Phylogenetic relationships of artiodactyls and cetaceans as deduced from the comparison of cytochrome b and 12S rRNA mitochondrial sequences

A data set of complete mitochondrial cytochrome b and 12S rDNA sequences is presented here for 17 representatives of Artiodactyla and Cetacea, together with potential outgroups (two Perissodactyla, two Carnivora, two Tethytheria, four Rodentia, and two Marsupialia). We include seven sequences not previously published from Hippopotamidae (Ancodonta) and Camelidae (Tylopoda), yielding a total of nearly 2.1 kb for both genes combined. Distance and parsimony analyses of each gene indicate that 11 clades are well supported, including the artiodactyl taxa Pecora, Ruminantia (with low 12S rRNA support), Tylopoda, Suina, and Ancodonta, as well as Cetacea, Perissodactyla, Carnivora, Tethytheria, Muridae, and Caviomorpha. Neither the cytochrome b nor the 12S rDNA genes resolve the relationships between these major clades. The combined analysis of the two genes suggests a monophyletic Cetacea +Artiodactyla clade (defined as "Cetartiodactyla"), whereas Perissodactyla, Carnivora, and Tethytheria fall outside this clade. Perissodactyla could represent the sister taxon of Cetartiodactyla, as deduced from resampling studies among outgroup lineages. Cetartiodactyla includes five major lineages: Ruminantia, Tylopoda, Suina, Ancodonta, and Cetacea, among which the phylogenetic relationships are not resolved. Thus, Suiformes do not appear to be monophyletic, justifying their split into the Suina and Ancodonta infraorders. An association between Cetacea and Hippopotamidae is supported by the cytochrome b gene but not by the 12S rRNA gene. Calculation of divergence dates suggests that the Cetartiodactyla could have diverged from other Ferungulata about 60 MYA.      

New DNA data from a transthyretin nuclear intron suggest an Oligocene to Miocene diversification of living South America opossums (Marsupialia: Didelphidae)

Phylogenetic relationships of 19 species of didelphid marsupials were studied using two nuclear markers, the non-coding transthyretin intron 1 (TTR) and the coding interphotoreceptor retinoid binding protein exon 1 (IRBP), and two mitochondrial genes, the protein-coding cytochrome b (cyt-b) and the structural 12S ribosomal DNA (12S rDNA). Evolutionary dynamics of these four markers were compared to each other, revealing the appropriate properties presented by TTR intron 1 together with its well supported and resolved phylogenetic signal. Nuclear markers supported the monophyly of medium and large-sized opossums Metachirus+(Chironectes, Lutreolina, Didelphis, Philander), and the paraphyly of mouse-sized opossums, with the genera Gracilinanus, Thylamys, and Marmosops as a sister group to medium and large-sized didelphids. Conflicting branching patterns between mitochondrial and nuclear data involved the phylogenetic position of Marmosa-Micoureus-Monodelphis relative to other mouse-sized opossums. Nuclear phylogenetic inferences among genera were confirmed by the presence of synapomorphic indels observed in TTR intron 1. A Bayesian relaxed molecular clock dating of didelphid evolution using nuclear markers estimated their origin in the Middle Eocene (39.8 million years ago), with subsequent diversification during the Oligocene (Deseadan) and Miocene.     

Molecular systematics of armadillos (Xenarthra,Dasypodidae): contribution of maximum likelihood and Bayesian analyses of mitochondrial and nuclear genes

The 30 living species of armadillos, anteaters, and sloths (Mammalia: Xenarthra) represent one of the three major clades of placentals. Armadillos (Cingulata: Dasypodidae) are the earliest and most speciose xenarthran lineage with 21 described species. The question of their tricky phylogeny was here studied by adding two mitochondrial genes (NADH dehydrogenase subunit 1 [ND1] and 12S ribosomal RNA [12S rRNA]) to the three protein-coding nuclear genes (alpha2B adrenergic receptor [ADRA2B], breast cancer susceptibility exon 11 [BRCA1], and von Willebrand factor exon 28 [VWF]) yielding a total of 6869 aligned nucleotide sites for thirteen xenarthran species. The two mitochondrial genes were characterized by marked excesses of transitions over transversions-with a strong bias toward CT transitions for the 12S rRNA-and exhibited two- to fivefold faster evolutionary rates than the fastest nuclear gene (ADRA2B). Maximum likelihood and Bayesian phylogenetic analyses supported the monophyly of Dasypodinae, Tolypeutinae, and Euphractinae, with the latter two armadillo subfamilies strongly clustering together. Conflicting branching points between individual genes involved relationships within the subfamilies Tolypeutinae and Euphractinae. Owing to a greater number of informative sites, the overall concatenation favored the mitochondrial topology with the classical grouping of Cabassous and Priodontes within Tolypeutinae, and a close relationship between Euphractus and Chaetophractus within Euphractinae. However, low statistical support values associated with almost equal distributions of apomorphies among alternatives suggested that two parallel events of rapid speciation occurred within these two armadillo subfamilies.     

Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations

Reconstructing the chronology of mammalian evolution is a debated issue between molecule- and fossil-based inferences. A methodological limitation of molecules is the evolutionary rate variation among lineages, precluding the application of the global molecular clock. We considered 2422 first and second codon positions of the combined ADRA2B, IRBP, and vWF nuclear genes for a well-documented set of placentals including an extensive sampling of rodents. Using seven independent calibration points and a maximum-likelihood framework, we evaluated whether molecular and paleontological estimates of mammalian divergence dates may be reconciled by the local molecular clocks approach, allowing local constancy of substitution rates with variations at larger phylogenetic scales. To handle the difficulty of choosing among all possible rate assignments for various lineages, local molecular clocks were based on the results of branch-length and two-cluster tests. Extensive lineage-specific variation of evolutionary rates was detected, even among rodents. Cross-calibrations indicated some incompatibilities between divergence dates based on different paleontological references. To decrease the impact of a single calibration point, estimates derived from independent calibrations displaying only slight reciprocal incompatibility were averaged. The divergence dates inferred for the split between mice and rats (approximately 13-19 Myr) was younger than previously published molecular estimates. The most recent common ancestors of rodents, primates and rodents, boreoeutherians, and placentals were estimated to be, respectively, approximately 60, 70, 75, and 78 Myr old. Global clocks, local clocks, and quartet dating analyses suggested a Late Cretaceous origin of the crown placental clades followed by a Tertiary radiation of some placental orders like rodents.     

Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting

Extant xenarthrans (armadillos, anteaters and sloths) are among the most derived placental mammals ever evolved. South America was the cradle of their evolutionary history. During the Tertiary, xenarthrans experienced an extraordinary radiation, whereas South America remained isolated from other continents. The 13 living genera are relics of this earlier diversification and represent one of the four major clades of placental mammals. Sequences of the three independent protein-coding nuclear markers alpha2B adrenergic receptor (ADRA2B), breast cancer susceptibility (BRCA1), and von Willebrand Factor (VWF) were determined for 12 of the 13 living xenarthran genera. Comparative evolutionary dynamics of these nuclear exons using a likelihood framework revealed contrasting patterns of molecular evolution. All codon positions of BRCA1 were shown to evolve in a strikingly similar manner, and third codon positions appeared less saturated within placentals than those of ADRA2B and VWF. Maximum likelihood and Bayesian phylogenetic analyses of a 47 placental taxa data set rooted by three marsupial outgroups resolved the phylogeny of Xenarthra with some evidence for two radiation events in armadillos and provided a strongly supported picture of placental interordinal relationships. This topology was fully compatible with recent studies, dividing placentals into the Southern Hemisphere clades Afrotheria and Xenarthra and a monophyletic Northern Hemisphere clade (Boreoeutheria) composed of Laurasiatheria and Euarchontoglires. Partitioned likelihood statistical tests of the position of the root, under different character partition schemes, identified three almost equally likely hypotheses for early placental divergences: a basal Afrotheria, an Afrotheria + Xenarthra clade, or a basal Xenarthra (Epitheria hypothesis). We took advantage of the extensive sampling realized within Xenarthra to assess its impact on the location of the root on the placental tree. By resampling taxa within Xenarthra, the conservative Shimodaira-Hasegawa likelihood-based test of alternative topologies was shown to be sensitive to both character and taxon sampling.     

Variance of molecular datings, evolution of rodents and the phylogenetic affinities between Ctenodactylidae and Hystricognathi

The von Willebrand factor (vWF) gene has been used to understand the origin and timing of Rodentia evolution in the context of placental phylogeny vWF exon 28 sequences of 15 rodent families and eight non-rodent eutherian clades are analysed with two different molecular dating methods (uniform clock on a linearized tree; quartet dating). Three main conclusions are drawn from the study of this nuclear exon. First, Ctenodactylidae (gundis) and Hystricognathi (e.g. porcupines, guinea-pigs, chinchillas) robustly cluster together in a newly recognized clade, named 'Ctenohystrica'. The Sciurognathi monophyly is subsequently rejected. Pedetidae (springhares) is an independent and early diverging rodent lineage, suggesting a convergent evolution of the multiserial enamel of rodent incisors. Second, molecular date estimates are here more influenced by accuracy and choice of the palaeontological temporal references used to calibrate the molecular clock than by either characters analysed (nucleotides versus amino acids) or species sampling. The caviomorph radiation at 31 million years (Myr) and the pig porpoise split at 63 Myr appear to be reciprocally compatible dates. Third, during the radiation of Rodentia, at least three lineages (Gliridae, Sciuroidea and Ctenohystrica) emerged close to the Cretaceous-Tertiary boundary, and their common ancestor separated from other placental orders in the Late Cretaceous.     

CONVERGENT AND CORRELATED EVOLUTION OF MAJOR LIFE‐HISTORY TRAITS IN THE ANGIOSPERM GENUS LEUCADENDRON (PROTEACEAE)

Natural selection is expected to cause convergence of life histories among taxa as well as correlated evolution of different life‐history traits. Here, we quantify the extent of convergence of five key life‐history traits (adult fire survival, seed storage, degree of sexual dimorphism, pollination mode, and seed‐dispersal mode) and test hypotheses about their correlated evolution in the genus Leucadendron (Proteaceae) from the fire‐prone South African fynbos. We reconstructed a new molecular phylogeny of this highly diverse genus that involves more taxa and molecular markers than previously. This reconstruction identifies new clades that were not detected by previous molecular study and morphological classifications. Using this new phylogeny and robust methods that account for phylogenetic uncertainty, we show that the five life‐history traits studied were labile during the evolutionary history of the genus. This diversity allowed us to tackle major questions about the correlated evolution of life‐history strategies. We found that species with longer seed‐dispersal distances tended to evolve lower pollen‐dispersal distance, that insect‐pollinated species evolved decreased sexual dimorphism, and that species with a persistent soil seed‐bank evolved toward reduced fire‐survival ability of adults.