Evolution of the structure and composition of house mouse satellite DNA sequences in the subgenus Mus (Rodentia: Muridea): a cytogenomic approach

International audienc

Evolution of the structure and composition of house mouse satellite DNA sequences in the subgenus Mus (Rodentia: Muridea): a cytogenomic approach

International audienc

Ascidian mitogenomics: comparison of evolutionary rates in closely related taxa provides evidence of ongoing speciation events.

Ascidians are a fascinating group of filter-feeding marine chordates characterized by rapid evolution of both sequences and structure of their nuclear and mitochondrial genomes. Moreover, they include several model organisms used to investigate complex biological processes in chordates. To study the evolutionary dynamics of ascidians at short phylogenetic distances, we sequenced 13 new mitogenomes and analyzed them, together with 15 other available mitogenomes, using a novel approach involving detailed whole-mitogenome comparisons of conspecific and congeneric pairs. The evolutionary rate was quite homogeneous at both intra-specific and congeneric level, and the lowest congeneric rates were found in cryptic (morphologically undistinguishable) and in morphologically very similar species pairs. Moreover, congeneric nonsynonymous rates (dN) were up to two orders of magnitude higher than in intra-species pairs. Overall, a clear-cut gap sets apart conspecific from congeneric pairs. These evolutionary peculiarities allowed easily identifying an extraordinary intra-specific variability in the model ascidian Botryllus schlosseri, where most pairs show a dN value between those observed at intra-species and congeneric level, yet consistently lower than that of the C. intestinalis cryptic species pair. These data suggest ongoing speciation events producing genetically distinct B. schlosseri entities. Remarkably, these ongoing speciation events were undetectable by the cox1 barcode fragment, demonstrating that, at low phylogenetic distances, the whole mitogenome has a higher resolving power than cox1. Our study shows that whole-mitogenome comparative analyses, performed on a suitable sample of congeneric and intra-species pairs, may allow detecting not only cryptic species but also ongoing speciation events

Population genetics of the African wolf (Canis lupaster) across its range : first evidence of hybridization with domestic dogs in Africa

Despite the known genetic permeability among wolf-like canids, there is currently no evidence of gene flow between the recently acknowledged African wolf (Canis lupaster) and domestic dogs (C. lupus familiaris). We genotyped African wolves across their range, together with African domestic dogs and 'reference' grey wolves (C. l. lupus; not occurring in Africa). Northwestern African wolves showed (1) the greatest genetic diversity as observed from microsatellite loci and mitochondrial + Y-chromosome markers, and (2) possible signs of past admixture with grey wolves. We detected two zones of hybridization between domestic dogs and African wolves, in northwestern Senegal and central Ethiopia. Hybrids were intermediary in the nuclear genetic space separating African wolves from domestic dogs (and grey wolves), and were in majority assigned to domestic dogs in STRUCTURE. Hybrids showed mitochondrial DNA haplotypes of African wolves, suggesting gene flow directionality between male African dogs and female African wolves. The roaming of feral and shepherds' dogs in degraded habitats occupied by African wolves may have promoted hybridization. Our results provide evidence that, subsequent to the possible hybrid origin ofC. lupaster, the genome of the African wolf is still subject to admixture withC. lupusdescendants. This could lead to the genetic dilution of endemic African wolf lineages, such as in eastern Africa, but may also imply disease prevalence and competition for resources with domestic dogs. Our study also is the first to show a significant level of differentiation (phi(ST)andF(ST)) between North African and West African wolves. Wider genetic screening of African wolves across their range should depict more accurately their population dynamics and the potential stakes related to gene flow with domestic dogs

Pockmark development in the Petrel Sub-basin, Timor Sea, Northern Australia: Seabed habitat mapping in support of CO2 storage assessments

The extent to which fluids may leak from sedimentary basins to the seabed is a critical issue for assessing the potential of a basin for carbon capture and storage. The Petrel Sub-basin, located beneath central and eastern Joseph Bonaparte Gulf in tropical northern Australia, was identified as potentially suitable for the geological storage of CO2 because of its geological characteristics and proximity to offshore gas and petroleum resources. In May 2012, a multidisciplinary marine survey (SOL5463) was undertaken to collect data in two targeted areas of the Petrel Sub-basin to facilitate an assessment of its CO2 storage potential. This paper focuses on Area 1 of that survey, a 471km2 area of sediment-starved shelf (water depths of 78 to 102m), characterised by low-gradient plains, low-lying ridges, palaeo-channels and shallow pockmarks. Three pockmark types are recognised: small shallow unit pockmarks 10-20m in diameter (generally <1m, rarely to 2m deep), composite pockmarks of 150-300m diameter formed from the co-location of several cross-cutting pockmarks forming a broad shallow depression (<1m deep), and pockmark clusters comprised of shallow unit pockmarks co-located side by side (150-300m width overall, <1m deep). Pockmark distribution is non-random, focused within and adjacent to palaeo-channels, with pockmark clusters also located adjacent to ridges. Pockmark formation is constrained by AMS 14C dating of in situ mangrove deposits and shells to have begun after 15.5calkaBP when a rapid marine transgression of Bonaparte Shelf associated with meltwater pulse 1A drowned coastal mangrove environments. Pockmark development is likely an ongoing process driven by fluid seepage at the seabed, and sourced from CO2 produced in the shallow sub-surface (<2m) sediment. No evidence for direct connection to deeper features was observed. © 2014

Conservation genetics and population history of the threatened European mink Mustela lutreola, with an emphasis on the west European population

In species of great conservation concern, special attention must be paid to their phylogeography, in particular the origin of animals for captive breeding and reintroduction. The endangered European mink lives now in at least three well-separated populations in northeast, southeast and west Europe. Our aim is to assess the genetic structure of these populations to identify `distinct population segments' (DPS) and advise captive breeding programmes. First, the mtDNA control region was completely sequenced in 176 minks and 10 polecats. The analysis revealed that the western population is characterized by a single mtDNA haplotype that is closely related to those in eastern regions but nevertheless, not found there to date. The northeast European animals are much more variable (piFLWINinfo:eu-repo/semantics/publishe

Evolution and phylogeography of Culex pipiens densovirus

Viruses of the Parvoviridae family infect a wide range of animals including vertebrates and invertebrates. So far, our understanding of parvovirus diversity is biased towards medically or economically important viruses mainly infecting vertebrate hosts, while invertebrate infecting parvoviruses-namely densoviruses-have been largely neglected. Here, we investigated the prevalence and the evolution of the only mosquito-infecting ambidensovirus, Culex pipiens densovirus (CpDV), from laboratory mosquito lines and natural populations collected worldwide. CpDV diversity generally grouped in two clades, here named CpDV-1 and -2. The incongruence of the different gene trees for some samples suggested the possibility of recombination events between strains from different clades. We further investigated the role of selection on the evolution of CpDV genome and detected many individual sites under purifying selection both in non-structural and structural genes. However, some sites in structural genes were under diversifying selection, especially during the divergence of CpDV-1 and -2 clades. These substitutions between CpDV-1 and -2 clades were mostly located in the capsid protein encoding region and might cause changes in host specificity or pathogenicity of CpDV strains from the two clades. However, additional functional and experimental studies are necessary to fully understand the protein conformations and the resulting phenotype of these substitutions between clades of CpDV