Emmanuel J. P. Douzery

Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules

Forty-nine complete 12S ribosomal RNA (rRNA) gene sequences from a diverse assortment of mammals (one monotreme, 11 marsupials, 37 placentals), including 11 new sequences, were employed to establish a “core” secondary structure model for mammalian 12S rRNA. Base-pairing interactions were assessed according to the criteria of potential base-pairing as well as evidence for base-pairing in the form of compensatory mutations. In cases where compensatory evidence was not available among mammalian sequences, we evaluated evidence among other vertebrate 12S rRNAs. Our results suggest a core model for secondary structure in mammalian 12S rRNAs with deletions as well as additions to the Gutell (1994:Nucleic Acids Res. 22) models forBos andHomo. In all, we recognize 40 stems, 34 of which are supported by at least some compensatory evidence within Mammalia. We also investigated the occurrence and conservation in mammalian 12S rRNAs of nucleotide positions that are known to participate in the decoding site inE. coli. Twenty-four nucleotide positions known to participate in the decoding site inE. coli also occur among mammalian 12S rRNAs and 17 are invariant for the same base as inE. coli. Patterns of nucleotide substitution were assessed based on our secondary structure model. Transitions in loops become saturated by approximately 10–20 million years. Transitions in stems, in turn, show partial saturation at 20 million years but divergence continues to increase beyond 100 million years. Transversions accumulate lin early beyond 100 million years in both stems and loops although the rate of accumulation of transversions is three- to fourfold higher in loops. Presumably, this difference results from constraints to maintain pairing in stems.

Molecular and Morphological Phylogenies of Ruminantia and the Alternative Position of the Moschidae

The ruminants constitute the largest group of ungulates, with >190 species, and its distribution is widespread throughout all continents except Australia and Antarctica. Six families are traditionally recognized within the suborder Ruminantia: Antilocapridae (pronghorns), Bovidae (cattle, sheep, and antelopes), Cervidae (deer), Giraffidae (giraffes and okapis), Moschidae (musk deer), and Tragulidae (chevrotains). The interrelationships of the families have been an area of controversy among morphology, palaeontology, and molecular studies, and almost all possible evolutionary scenarios have been proposed in the literature. We analyzed a large DNA data set (5,322 nucleotides) for 23 species including both mitochondrial (cytochrome b, 12S ribosomal RNA (rRNA), and 16S rRNA) and nuclear (kappa-casein, cytochrome P-450, lactoferrin, and alpha-lactalbumin) markers. Our results show that the family Tragulidae occupies a basal position with respect to all other ruminant families, confirming the traditional view that separates Tragulina and Pecora. Within the pecorans, Antilocapridae and Giraffidae emerge first, and the families Bovidae, Moschidae, and Cervidae are allied, with the unexpected placement of Moschus close to bovids rather than to cervids. We used these molecular results to assess the homoplastic evolution of morphological characters within the Ruminantia. A Bayesian relaxed molecular clock approach based on the continuous autocorrelation of evolutionary rates along branches was applied to estimate the divergence ages between the major clades of ruminants. The evolutionary radiation of Pecora occurred at the Early/Late Oligocene transition, and Pecoran families diversified and dispersed rapidly during the Early and Middle Miocene. We propose a biogeographic scenario to explain the extraordinary expansion of this group during the Cenozoic era.

A glimpse on the pattern of rodent diversification: a phylogenetic approach

BackgroundDevelopment of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the field of evolutionary biology and resulted in an unprecedented expansion of our knowledge about the tree of life. These methods have helped to shed light on the macroevolution of many taxonomic groups such as the placentals (Mammalia). However, despite the increase of studies addressing the diversification patterns of organisms, no synthesis has addressed the case of the most diversified mammalian clade: the Rodentia.ResultsHere we present a rodent maximum likelihood phylogeny inferred from a molecular supermatrix. It is based on 11 mitochondrial and nuclear genes that covers 1,265 species, i.e., respectively 56% and 81% of the known specific and generic rodent diversity. The inferred topology recovered all Rodentia clades proposed by recent molecular works. A relaxed molecular clock dating approach provided a time framework for speciation events. We found that the Myomorpha clade shows a greater degree of variation in diversification rates than Sciuroidea, Caviomorpha, Castorimorpha and Anomaluromorpha. We identified a number of shifts in diversification rates within the major clades: two in Castorimorpha, three in Ctenohystrica, 6 within the squirrel-related clade and 24 in the Myomorpha clade. The majority of these shifts occurred within the most recent familial rodent radiations: the Cricetidae and Muridae clades. Using the topological imbalances and the time line we discuss the potential role of different diversification factors that might have shaped the rodents radiation.ConclusionsThe present glimpse on the diversification pattern of rodents can be used for further comparative meta-analyses. Muroid lineages have a greater degree of variation in their diversification rates than any other rodent group. Different topological signatures suggest distinct diversification processes among rodent lineages. In particular, Muroidea and Sciuroidea display widespread distribution and have undergone evolutionary and adaptive radiation on most of the continents. Our results show that rodents experienced shifts in diversification rate regularly through the Tertiary, but at different periods for each clade. A comparison between the rodent fossil record and our results suggest that extinction led to the loss of diversification signal for most of the Paleogene nodes.

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

Until now the most efficient solution to align nucleotide sequences containing open reading frames was to use indirect procedures that align amino acid translation before reporting the inferred gap positions at the codon level. There are two important pitfalls with this approach. Firstly, any premature stop codon impedes using such a strategy. Secondly, each sequence is translated with the same reading frame from beginning to end, so that the presence of a single additional nucleotide leads to both aberrant translation and alignment. We present an algorithm that has the same space and time complexity as the classical Needleman-Wunsch algorithm while accommodating sequencing errors and other biological deviations from the coding frame. The resulting pairwise coding sequence alignment method was extended to a multiple sequence alignment (MSA) algorithm implemented in a program called MACSE (Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons). MACSE is the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence. MACSE is distributed as an open-source java file executable with freely available source code and can be used via a web interface at: http://mbb.univ-montp2.fr/macse.

Molecular phylogenetics of Diseae (Orchidaceae): a contribution from nuclear ribosomal ITS sequences

We present here the first molecular phylogeny of tribe Diseae (Orchidoideae: Orchidaceae). Nuclear ribosomal ITS1, 5.8S rDNA, and ITS2 sequences were compared for 30 Diseae, 20 Orchideae, and four Cranichideae and Diurideae outgroups. ITS - rDNA sequences exhibited a transition:transversion ratio of 1.3 and extensive ITS length polymorphism. Phylogenetic analyses using maximum parsimony identified seven major core orchidoid groups. The branching order of the five Diseae and two Orchideae clades was weakly supported but indicated paraphyly of Diseae, with Disperis sister to the rest, followed by successive divergence of Brownleea, Disinae, Coryciinae sensu stricto (s.s.), Satyriinae, and terminated by Orchidinae plus Habenariinae. Within the monophyletic Disinae, Herschelia and Monadenia were nested within a paraphyletic Disa and clustered with D. sect. Micranthae. Within monophyletic Satyriinae, Satyridium rostratum plus Satyrium bicallosum was sister to the rest of Satyrium, and then Satyrium nepalense plus S. odorum was distinct from a cluster of six species. Coryciinae are paraphyletic because Disperis is sister to all other core orchidoids. Coryciinae s.s. are sister to Satyriinae plus Orchideae, with Pterygodium nested within Corycium. Maximum likelihood analysis supported possible affinities among Disinae, Brownleeinae, and Coryciinae but did not support monophyly of Diseae or an affinity between Disinae and Satyriinae. Morphological characters are fully congruent with the well-supported groups identified in the ITS phylogeny.

Arrival and diversification of caviomorph rodents and platyrrhine primates in South America.

Platyrrhine primates and caviomorph rodents are clades of mammals that colonized South America during its period of isolation from the other continents, between 100 and 3 million years ago (Mya). Until now, no molecular study investigated the timing of the South American colonization by these two lineages with the same molecular data set. Using sequences from three nuclear genes (ADRA2B, vWF, and IRBP, both separate and combined) from 60 species, and eight fossil calibration constraints, we estimated the times of origin and diversification of platyrrhines and caviomorphs via a Bayesian relaxed molecular clock approach. To account for the possible effect of an accelerated rate of evolution of the IRBP gene along the branch leading to the anthropoids, we performed the datings with and without IRBP (3768 sites and 2469 sites, respectively). The time window for the colonization of South America by primates and by rodents is demarcated by the dates of origin (upper bound) and radiation (lower bound) of platyrrhines and caviomorphs. According to this approach, platyrrhine primates colonized South America between 37.0 +/- 3.0 Mya (or 38.9 +/- 4.0 Mya without IRBP) and 16.8 +/- 2.3 (or 20.1 +/- 3.3) Mya, and caviomorph rodents between 45.4 +/- 4.1 (or 43.7 +/- 4.8) Mya and 36.7 +/- 3.7 (or 35.8 +/- 4.3) Mya. Considering both the fossil record and these molecular datings, the favored scenarios are a trans-Atlantic migration of primates from Africa at the end of the Eocene or beginning of the Oligocene, and a colonization of South America by rodents during the Middle or Late Eocene. Based on our nuclear DNA data, we cannot rule out the possibility of a concomitant arrival of primates and rodents in South America. The caviomorphs radiated soon after their arrival, before the Oligocene glaciations, and these early caviomorph lineages persisted until the present. By contrast, few platyrrhine fossils are known in the Oligocene, and the present-day taxa are the result of a quite recent, Early Miocene diversification.

Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans

BackgroundComparative genomic data among organisms allow the reconstruction of their phylogenies and evolutionary time scales. Molecular timings have been recently used to suggest that environmental global change have shaped the evolutionary history of diverse terrestrial organisms. Living xenarthrans (armadillos, anteaters and sloths) constitute an ideal model for studying the influence of past environmental changes on species diversification. Indeed, extant xenarthran species are relicts from an evolutionary radiation enhanced by their isolation in South America during the Tertiary era, a period for which major climate variations and tectonic events are relatively well documented.ResultsWe applied a Bayesian approach to three nuclear genes in order to relax the molecular clock assumption while accounting for differences in evolutionary dynamics among genes and incorporating paleontological uncertainties. We obtained a molecular time scale for the evolution of extant xenarthrans and other placental mammals. Divergence time estimates provide substantial evidence for contemporaneous diversification events among independent xenarthran lineages. This correlated pattern of diversification might possibly relate to major environmental changes that occurred in South America during the Cenozoic.ConclusionsThe observed synchronicity between planetary and biological events suggests that global change played a crucial role in shaping the evolutionary history of extant xenarthrans. Our findings open ways to test this hypothesis further in other South American mammalian endemics like hystricognath rodents, platyrrhine primates, and didelphid marsupials.

Evidence for genetic exchange and hybridization in Trypanosoma cruzi based on nucleotide sequences and molecular karyotype.

Trypanosoma cruzi is thought to undergo predominant clonal evolution, as determined by population genetics studies. However, this model does not exclude occasional recombination, which existence is strongly suggested by several recent studies. We sequenced a portion of the maxicircle cytochrome b (CYb) gene and of the nuclear rRNA promoter region from representative strains of six T. cruzi genetic lineages isolated from anthroponotic environments and man (lineages IIb, IId and IIe), sylvatic environments (lineages IIa and IIc) or both (lineage I). Phylogenetic analyses based on the two genes were incongruent. Remarkably, in lineage IIe, CYb and rRNA sequences were very closely related to those of lineages IIc and IIb, respectively. One stock of lineage IId showed rRNA sequence heterogeneity, with both IIb-like and IIc-like copies. Analysis of the size variation of six distinct pairs of putative homologous chromosomes revealed a bimodal distribution of chromosomal sizes across T. cruzi. Notably, stocks of lineages IId and IIe had several chromosomal pairs distributed in distinct modes, with the corresponding modes individually found in lineages IIb and IIc. Together, these data indicate the origin of lineages IId and IIe by hybridization between representatives of lineages IIb and IIc. CYb and rRNA sequences clustered into three and four major lineages, respectively. Data were in agreement with the distinction of six genetic lineages, but not with their proposed grouping into two primary lineages, as lineage II was not monophyletic. Based on a CYb substitution rate of 1% per million years (Myr), the major lineages are estimated to have diverged around 10 million years ago.

Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA.

Here, we present a new primate phylogeny inferred from molecular supermatrix analyses of size 42 kb containing 70% of missing data, and representing 75% of primate species diversity. The supermatrix was analysed using a gene-partitioned maximum likelihood approach to obtain an exhaustive molecular phylogenetic framework. All clades recovered from recent molecular works were upheld in our analyses demonstrating that the presence of missing data did not bias our supermatrix inference. The resulting phylogenetic tree was subsequently dated with a molecular dating method to provide a timescale for speciation events. Results obtained from our relaxed molecular clock analyses concurred with previous works based on the same fossil constraints. The resulting dated tree allowed to infer of macroevolutionary processes among the primates. Shifts in diversification rate and speciation rates were determined using the SymmeTREE method and a birthdeath process. No significant asymmetry was detected for the primate clade, but significant shifts in diversification rate were identified for seven clades: Anthropoidea, Lemuriformes, Lemuridae, Galagidae, Callithrix genus, the Cercopithecinae and Asian Macaca. Comparisons with previous primate supertree results reveal that (i) there was a diversification event at the root of the Lemuriformes, (ii) a higher diversification rate is detected for Cercopithecidae and Anthropoidea and (iii) a shift in diversification is always recovered for Macaca genus. Macroevolutionary inferences and primate divergence dates show that major primate diversification events occurred after the Paleogene, suggesting the extinction of ancient primate lineages.

Contrasting GC-content dynamics across 33 mammalian genomes: Relationship with life-history traits and chromosome sizes

The origin, evolution, and functional relevance of genomic variations in GC content are a long-debated topic, especially in mammals. Most of the existing literature, however, has focused on a small number of model species and/or limited sequence data sets. We analyzed more than 1000 orthologous genes in 33 fully sequenced mammalian genomes, reconstructed their ancestral isochore organization in the maximum likelihood framework, and explored the evolution of third-codon position GC content in representatives of 16 orders and 27 families. We showed that the previously reported erosion of GC-rich isochores is not a general trend. Several species (e.g., shrew, microbat, tenrec, rabbit) have independently undergone a marked increase in GC content, with a widening gap between the GC-poorest and GC-richest classes of genes. The intensively studied apes and (especially) murids do not reflect the general placental pattern. We correlated GC-content evolution with species life-history traits and cytology. Significant effects of body mass and genome size were detected, with each being consistent with the GC-biased gene conversion model.