On homology searches by protein Blast and the characterization of the age of genes

BACKGROUND: It has been shown in a variety of organisms, including mammals, that genes that appeared recently in evolution, for example orphan genes, evolve faster than older genes. Low functional constraints at the time of origin of novel genes may explain these results. However, this observation has been recently attributed to an artifact caused by the inability of Blast to detect the fastest genes in different eukaryotic genomes. Distinguishing between these two possible explanations would be of great importance for any studies dealing with the taxon distribution of proteins and the origin of novel genes. RESULTS: Here we used simulations of protein sequences to examine the capacity of Blast to detect proteins of diverse evolutionary rates in the different species of an eukaryotic phylogenetic tree that included metazoans, fungi and plants. We simulated the evolution of protein genes with the same evolutionary rates than those observed in functional mammalian genes and with among-site rate heterogeneity. Under these conditions, we found that only a very small percentage of simulated ancestral eukaryotic proteins was affected by the Blast artifact. We show that the good detectability of Blast is due to the heterogeneity of protein evolutionary rates at different sites, since only a small conserved motif in a sequence suffices to detect its homologues. Our results indicate that Blast, at least when applied within eukaryotes, only misses homologues of extremely fast-evolving sequences, which are rare in the mammalian genome, as well as sequences evolving homogeneously or pseudogenes. CONCLUSION: Although great care should be exercised in the recognition of remote homologues, most functional mammalian genes can be detected in eukaryotic genomes by Blast. That is, the majority of functional mammalian genes are not as fast as for not being detected in other metazoans, fungi or plants, if they had been present in these organisms. Thus, the correlation previously found between age and rate seems not to be due to a pure Blast artifact, at least for mammals. This may have important implications to understand the mechanisms by which novel genes originate

Novel intron markers to study the phylogeny of closely related mammalian species

BACKGROUND: Multilocus phylogenies can be used to infer the species tree of a group of closely related species. In species trees, the nodes represent the actual separation between species, thus providing essential information about their evolutionary history. In addition, multilocus phylogenies can help in analyses of species delimitation, gene flow and genetic differentiation within species. However, few adequate markers are available for such studies. RESULTS: In order to develop nuclear markers that can be useful in multilocus studies of mammals, we analyzed the mammalian genomes of human, chimpanzee, macaque, dog and cow. Rodents were excluded due to their unusual genomic features. Introns were extracted from the mammalian genomes because of their greater genetic variability and ease of amplification from the flanking exons. To an initial set of more than 10,000 one-to-one orthologous introns we applied several filters to select introns that belong to single-copy genes, show neutral evolutionary rates and have an adequate length for their amplification. This analysis led to a final list of 224 intron markers randomly distributed along the genome. To experimentally test their validity, we amplified twelve of these introns in a panel of six mammalian species. The result was that seven of these introns gave rise to a PCR band of the expected size in all species. In addition, we sequenced these bands and analyzed the accumulation of substitutions in these introns in five pairs of closely related species. The results showed that the estimated genetic distances in the five species pairs was quite variable among introns and that this divergence cannot be directly predicted from the overall intron divergence in mammals. CONCLUSIONS: We have designed a new set of 224 nuclear introns with optimal features for the phylogeny of closely related mammalian species. A large proportion of the introns tested experimentally showed a perfect amplification and enough variability in most species, indicating that this marker set can be very helpful in multilocus phylogenetics of mammals. Due to the lower variability and stronger stochasticity of nuclear markers with respect to mitochondrial genes, studies should be designed to make use of several markers like the ones designed here

Is mammalian chromosomal evolution driven by regions of genome fragility?

BACKGROUND: A fundamental question in comparative genomics concerns the identification of mechanisms that underpin chromosomal change. In an attempt to shed light on the dynamics of mammalian genome evolution, we analyzed the distribution of syntenic blocks, evolutionary breakpoint regions, and evolutionary breakpoints taken from public databases available for seven eutherian species (mouse, rat, cattle, dog, pig, cat, and horse) and the chicken, and examined these for correspondence with human fragile sites and tandem repeats. RESULTS: Our results confirm previous investigations that showed the presence of chromosomal regions in the human genome that have been repeatedly used as illustrated by a high breakpoint accumulation in certain chromosomes and chromosomal bands. We show, however, that there is a striking correspondence between fragile site location, the positions of evolutionary breakpoints, and the distribution of tandem repeats throughout the human genome, which similarly reflect a non-uniform pattern of occurrence. CONCLUSION: These observations provide further evidence that certain chromosomal regions in the human genome have been repeatedly used in the evolutionary process. As a consequence, the genome is a composite of fragile regions prone to reorganization that have been conserved in different lineages, and genomic tracts that do not exhibit the same levels of evolutionary plasticity

Spatial mixing of mitochondrial lineages and greater genetic diversity in some invasive populations of the American mink (Neovison vison) compared to native populations

The genetic characteristics of introduced populations have a relevant impact on their ability to establish and spread. The American mink (Neovison vison), native to North America, is an important invasive species in the Iberian Peninsula. Here, we used mitochondrial DNA sequences data to investigate the genetic diversity and phylogeographic structure of invasive versus native populations of this species. We also evaluated whether genetic diversity in invasive populations could be explained by the genetic characteristics of the native sources from which they derived. Phylogenetic analysis revealed two major lineages in the native range, which indicated a clear separation between western and eastern populations. On the contrary, we found no evidence of genetic structure in the invasive range. This was probably the result of the diverse origins of the released specimens and the rapid expansion and encounters of the introduced populations. We detected spatial mixing of both North American lineages in several sampling localities of the north central area of the Iberian Peninsula, giving rise to high levels of genetic diversity in some areas compared to North American populations. This could potentially lead to higher fitness of these individuals and thus increase the population viability and invasiveness of this species. These results point to the need to better study the populations in which lineages mix and, if necessary, intensify control efforts in them

FIRST INSIGHTS INTO THE MIGRATION PATTERN OF AN UPLAND GOOSE (CHLOEPHAGA PICTA) BASED ON SATELLITE TRACKING

Detailed knowledge of the migratory strategies is important to understand the ecology and evolution of migration and the conservation of migratory birds The Argentinean federal government declared sheldgeese (Chloephaga spp.) pests in 1930, claiming that they reduce crop yield. Currently sheldgeese have suffered severe reductions in their populations and are the focus of serious conservation concern. From September to April they breed in southern Patagonia (Argentina and Chile) while from May to September they winter mainly in the southern Pampas (central east Argentina). The precise knowledge of their migratory routes is essential to ensure protection of necessary resources and sites needed on their annual journeys. Here, by using a satellite transmitter for the first time we unravel the migration route of an Upland Goose (Chloephaga picta), a species endemic to southern South America with an unknown migration strategy. We received data for 121 days (from September 2014 to January 2015). During this time, the bird migrated 1485 km from the wintering grounds in Buenos Aires Province to the breeding area in Santa Cruz province, Patagonia. Part of the migration route was over the sea. The largest displacement was 817 km in 19 hours, representing a minimum mean speed of 43 km h-1

Topological variation in single-gene phylogenetic trees

A large-scale phylogenetic study of the human lineage dramatically points up the problems of using single genes to build phylogenetic trees

Impact of Deep Coalescence on the Reliability of Species Tree Inference from Different Types of DNA Markers in Mammals

An important challenge for phylogenetic studies of closely related species is the existence of deep coalescence and gene tree heterogeneity. However, their effects can vary between species and they are often neglected in phylogenetic analyses. In addition, a practical problem in the reconstruction of shallow phylogenies is to determine the most efficient set of DNA markers for a reliable estimation. To address these questions, we conducted a multilocus simulation study using empirical values of nucleotide diversity and substitution rates obtained from a wide range of mammals and evaluated the performance of both gene tree and species tree approaches to recover the known speciation times and topological relationships. We first show that deep coalescence can be a serious problem, more than usually assumed, for the estimation of speciation times in mammals using traditional gene trees. Furthermore, we tested the performance of different sets of DNA markers in the determination of species trees using a coalescent approach. Although the best estimates of speciation times were obtained, as expected, with the use of an increasing number of nuclear loci, our results show that similar estimations can be obtained with a much lower number of genes and the incorporation of a mitochondrial marker, with its high information content. Thus, the use of the combined information of both nuclear and mitochondrial markers in a species tree framework is the most efficient option to estimate recent speciation times and, consequently, the underlying species tree