Advances in phylogenetic methods and high-throughput sequencing have allowed the reconstruction of deep phylogenetic relationships in the evolutionary history of eukaryotes. Yet, the root of the eukaryotic tree of life remains elusive. The most ‘popular’ (i.e. in textbooks and reviews) hypothesis for the root is between Unikonta (Opisthokonta + Amoebozoa) and Bikonta (all other eukaryotes), which emerged from analyses of a single gene fusion and a limited sampling of eukaryotic lineages. Subsequent highly-cited studies based on concatenation of genes supported this hypothesis with some variations or proposed a root within the Excavata. However, concatenation of genes neither considers phylogenetically-informative events (i.e. gene duplications and losses) nor provides an estimate of the root. A more recent study using gene tree-species tree reconciliation methods suggested the root lies between Opisthokonta and all other eukaryotes, but only including 59 taxa and 20 genes. Here we apply a gene tree – species tree reconciliation approach to a gene-rich and taxon-rich dataset (i.e. 2,786 gene families from two sets of ~158 diverse eukaryotic lineages) to assess the root, and we iterate each analysis 100 times to quantify tree space uncertainty. Our results estimate a root between Fungi and all other eukaryotes, or between Opisthokonta and all other eukaryotes, and reject alternative popular roots from the literature. Based on further analysis of genome size, we propose Opisthokonta + others as the most likely root. Finding the root of the eukaryotic tree of life is critical for the field of comparative biology as it allows us to understand the timing and mode of evolution of characters across the evolutionary history of eukaryotes.

Clonally transmissible cancers are tumour lineages that are transmitted between individuals via the transfer of living cancer cells. In marine bivalves, leukemia-like transmissible cancers, called hemic neoplasias, have demonstrated the ability to infect individuals from different species. We performed whole-genome sequencing in eight V. verrucosa clams that were diagnosed with hemic neoplasia, from two sampling points located more than 1,000 nautical miles away in the Atlantic Ocean and the Mediterranean Sea Coasts of Spain. Mitochondrial genome sequencing of tumour tissues from neoplastic animals revealed the coexistence of haplotypes from two different clam species. Phylogenies estimated from mitochondrial and nuclear markers confirmed this leukemia originated in C. gallina (or a closely related taxa) and was later transmitted to V. verrucosa, in which it survived as a contagious cancer. The analysis of mitochondrial and nuclear gene sequences supports all the studied tumours belonging to a single neoplastic C. gallina lineage that spread in the Seas of Southern Europe.

Thirty years after the discovery of HIV-1, the early transmission, dissemination and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M and non-pandemic group O were similar until ~1960, after which group M underwent an epidemiological transition and outpaced regional population growth. Our results reconstruct the early dynamics of HIV-1 and emphasize the role of social changes and transport networks in the establishment of this virus in human populations.

Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting or horizontal gene transfer. In this manuscript we address for the first time the problem of species tree inference from multilocus, genome-wide data sets in the presence of gene duplication and loss and incomplete lineage sorting, therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose input are with posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations under complex phylogenomic models in order to evaluate the performance ouf our approach in comparison with other species tree approaches able to deal with multilabeled trees. Our method ranked best, under both simulated and empirical data sets, in spite of ignoring branch lengths. Our results show in addition that under complex simulation scenarios , gene tree parsimony is also a competitive approach once we consider its speed in contrast to more sophisticated models.

The concept of homology lies at the root of evolutionary biology. Since the seminal work of Fitch (1970) three main categories of homology relationships have been defined at the molecular level: orthology, paralogy and xenology. In brief, if two gene copies arose by duplication they are paralogs, while if they arose via speciation they are orthologs. If one of them was transferred from a contemporaneous species, we call them xenologs (Fig. S1 in doi: ; see Gray and Fitch 1983; Fitch 2000). Indeed, these terms were coined under a phylogenetic framework in which species were represented by single individuals, and as such they have remained very much intact during the last four decades –although particular cases within these categories have received specific names (Mindell and Meyer 2001). However, advances in sequencing technology have changed the field, and it is now very common to collect data sets containing multiple gene loci and/or multiple individuals per species. In general, genome-wide data sets not only have unveiled extensive phylogenomic incongruence (Jeffroy, Brinkmann, et al. 2006; Salichos and Rokas 2013) but have brought back to the spotlight the consideration of how ancestral polymorphisms sort within populations (Edwards 2009). Altogether, phylogenomic data makes imperative the explicit distinction between organismal and gene histories.

A phylogenetic model selection test to quantify the evidence for the Universal Common Ancestry (UCA) of life forms was proposed recently (Theobald 2010a), based on the comparison of the statistical support, using likelihoods, the Akaike Information Criterion (AIC), or Bayes factors, for two different phylogenetic models representing the UCA and the independent origins (IOs) hypotheses (Sober and Steel 2002). In this test, the former is represented by a single phylogeny connecting all sequences, whereas the latter is depicted by several, independent phylogenetic trees (Fig. 1). Importantly, in the original UCA test, the same alignment was used to represent both hypotheses. When applied to a particular data set of 23 universally conserved proteins, the test strongly favored a UCA scenario.

Deciphering the process of genetic differentiation of species with insular distributions is relevant for biogeographic and conservation reasons. Despite its importance as old gondwanic islands and part of the Western Indian Ocean biodiversity hotspot, little is known concerning the genetic structure of taxa from the Seychelles islands. We have examined patterns of structure and isolation within Urocotyledon inexpectata (Reptilia: Geckkonidae), an endemic species from this archipelago. Genetic diversity was screened from populations across the archipelago for both mitochondrial and nuclear genes. Gene genealogies and model-based inference were used to explore patterns and timings of isolation between the main lineages. High levels of genetic diversity were found for the mitochondrial and some of the nuclear markers. This species harbours at least two highly differentiated lineages, exclusively distributed across the northern and southern groups of islands. The main split between these was dated back to the Miocene/Late Pliocene, but isolation events throughout the Pliocene and Pleistocene were also inferred. Migration between groups of islands was apparently non-existent, except for one case. The low dispersal capabilities of this species, together with the intrinsic fragmented nature of its geographic distribution seem to have resulted into highly structured populations, despite the cyclic periods of contact between the different island groups. These populations may currently represent more than one species, making U. inexpectata another example of morphologically cryptic lineages with deep genetic divergence within gekkonids. The observed patterns suggest a hypothetical biogeographic scenario (of a main north – south phylogeographic break) for the Seychelles that can be further tested with the exploration of the phylogeographic structure of other Seychellois taxa.