Biology subjects

Emiliano Trucchi

Publications and source records attributed to Emiliano Trucchi.

4 recordsLinked to original sources

bioRxiv2016

RADpainter and fineRADstructure: population inference from RADseq data

Powerful approaches to inferring recent or current population structure based on nearest neighbour haplotype coancestry have so far been inaccessible to users without high quality genome-wide haplotype data. With a boom in non-model organism genomics, there is a pressing need to bring these methods to communities without access to such data. Here we present RADpainter, a new program designed to infer the coancestry matrix from restriction-site-associated DNA sequencing (RADseq) data. We combine this program together with a previously published MCMC clustering algorithm into fineRADstructure - a complete, easy to use, and fast population inference package for RADseq data (https://github.com/millanek/fineRADstructure). Finally, with two example datasets, we illustrate its use, benefits, and robustness to missing RAD alleles in double digest RAD sequencing.

Evolutionary Biology↗

bioRxiv2016

Genomic and Metagenomic Analyses Reveal Parallel Ecological Divergence in Heliosperma pusillum (Caryophyllaceae)

Cases of parallel ecological divergence in closely related taxa offer an invaluable material to study the processes of ecological speciation. Applying a combination of population genetic and metagenomic tools on a high-coverage RAD sequencing dataset, we test for parallel evolution across six population pairs of Heliosperma pusillum and H. veselskyi (Caryophyllaceae), two plant species found in the south-eastern Alps and characterized by clear morphological (glabrous vs. hairy) and ecological (alpine vs. montane, wet vs. dry) differentiation. Our analyses support a scenario of multiple independent instances of divergence between these species during the last 10,000 years. Structure analyses and simulations show that interspecific gene flow in each population pair is very low. A single locus, annotated as E3 ubiquitin ligase, an enzyme involved in plant innate immunity, shows a pattern of non-random segregation across populations of both species. A metagenomic analysis revealed information about contaminant exogenous DNA present in RAD sequencing libraries obtained from leaf material. Results of this analysis show clearly divergent bacterial and fungal phyllosphere communities between the species, but consistent communities across populations within each species. A similar set of biotic interactions is involved, together with abiotic factors, in shaping common selective regimes at different growing sites of each species. Different occurrences of H. veselskyi appear now genetically isolated from H. pusillum and from each other, and may independently proceed along the speciation continuum. Our work supports the hypothesis that repeated ecological divergence, observed here at an early stage, may be a common process of species diversification.

Evolutionary Biology↗

bioRxiv2015

The African wolf is a missing link in the wolf-like canid phylogeny

Here we present the first genomic data for the African wolf (Canis aureus lupaster) and conclusively demonstrate that it is a unique taxon and not a hybrid between other canids. These animals are commonly misclassified as golden jackals (Canis aureus) and have never been included in any large-scale studies of canid diversity and biogeography, or in investigations of the early stages of dog domestication. Applying massive Restriction Site Associated DNA (RAD) sequencing, 110481 polymorphic sites across the genome of 7 individuals of African wolf were aligned and compared with other wolf-like canids (golden jackal, Holarctic grey wolf, Ethiopian wolf, side-striped jackal and domestic dog). Analyses of this extensive sequence dataset (ca. 8.5Mb) show conclusively that the African wolves represent a distinct taxon more closely related to the Holarctic grey wolf than to the golden jackal. Our results strongly indicate that the distribution of the golden jackal needs to be re-evaluated and point towards alternative hypotheses for the evolution of the rare and endemic Ethiopian wolf (Canis simensis). Furthermore, the extension of the grey wolf phylogeny and distribution opens new possible scenarios for the timing and location of dog domestication.

Evolutionary Biology↗

bioRxiv2015

Long live the alien: is high genetic diversity a pivotal aspect of crested porcupine (Hystrix cristata) long-lasting and successful invasion?

Studying the evolutionary dynamics of an alien species surviving and continuing to expand after several generations can provide fundamental information on the relevant features of clearly successful invasions. Here, we tackle this task by investigating the dynamics of the genetic diversity in invasive crested porcupine (Hystrix cristata) populations, introduced to Italy about 1500 years ago, which are still growing in size, distribution range and ecological niche. Using genome-wide RAD markers, we describe the structure of the genetic diversity and the demographic dynamics of the H. cristata invasive populations and compare their genetic diversity with that of native African populations of both H. cristata and its sister species, H. africaeaustralis. First, we demonstrate that genetic diversity is lower in both the invasive Italian and the North Africa source range relative to other native populations from Sub-Saharan and South Africa. Second, we find evidence of multiple introduction events in the invasive range followed by very limited gene flow. Through coalescence-based demographic reconstructions, we also show that the bottleneck at introduction was mild and did not affect the introduced genetic diversity. Finally, we reveal that the current spatial expansion at the northern boundary of the range is following a leading-edge model characterized by a general reduction of genetic diversity towards the edge of the expanding range. We conclude that the level of genome-wide diversity of H. cristata invasive populations is less important in explaining its successful invasion than species-specific life-history traits or the phylogeographic history in the native source range.

Evolutionary Biology↗