Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes

Y chromosome markers can shed light on male-specific population dynamics but for many species no such markers have been discovered and are available yet, despite the potential for recovering Y-linked loci from available genome sequences. Here, we investigated how effective available bioinformatic tools are in recovering informative Y chromosome microsatellites from whole genome sequence data. In order to do so, we initially explored a large dataset of whole genome sequences comprising individuals at various coverages belonging to different species of baboons (genus: Papio) using Y chromosome references belonging to the same genus and more distantly related species (Macaca mulatta). We then further tested this approach by recovering Y-STRs from available Theropithecus gelada genomes using Papio and Macaca Y chromosome as reference sequences. Identified loci were validated in silico by a) comparing within-species relationships of Y chromosome lineages and b) genotyping male individuals in available pedigrees. Each STR was selected not to extend in its variable region beyond 100 base pairs, so that loci can be developed for PCR-based genotyping of non-invasive DNA samples. In addition to assembling a first set of Papio and Theropithecus Y-specific microsatellite markers, we released TYpeSTeR, an easy-to-use script to identify and genotype Y chromosome STRs using population genomic data which can be modulated according to available male reference genomes and genomic data, making it widely applicable across taxa

Genomic variation in baboons from central Mozambique unveils complex evolutionary relationships with other Papio species

Background Gorongosa National Park in Mozambique hosts a large population of baboons, numbering over 200 troops. Gorongosa baboons have been tentatively identified as part of Papio ursinus on the basis of previous limited morphological analysis and a handful of mitochondrial DNA sequences. However, a recent morphological and morphometric analysis of Gorongosa baboons pinpointed the occurrence of several traits intermediate between P. ursinus and P. cynocephalus, leaving open the possibility of past and/or ongoing gene flow in the baboon population of Gorongosa National Park. In order to investigate the evolutionary history of baboons in Gorongosa, we generated high and low coverage whole genome sequence data of Gorongosa baboons and compared it to available Papio genomes. Results We confirmed that P. ursinus is the species closest to Gorongosa baboons. However, the Gorongosa baboon genomes share more derived alleles with P. cynocephalus than P. ursinus does, but no recent gene flow between P. ursinus and P. cynocephalus was detected when available Papio genomes were analyzed. Our results, based on the analysis of autosomal, mitochondrial and Y chromosome data, suggest complex, possibly male-biased, gene flow between Gorongosa baboons and P. cynocephalus, hinting to direct or indirect contributions from baboons belonging to the “northern” Papio clade, and signal the presence of population structure within P. ursinus. Conclusions The analysis of genome data generated from baboon samples collected in central Mozambique highlighted a complex set of evolutionary relationships with other baboons. Our results provided new insights in the population dynamics that have shaped baboon diversity.info:eu-repo/semantics/publishedVersio

Through 40,000 years of human presence in Southern Europe: the Italian case study

none5noneAneli, Serena; Caldon, Matteo; Saupe, Tina; Montinaro, Francesco; Pagani, LucaAneli, Serena; Caldon, Matteo; Saupe, Tina; Montinaro, Francesco; Pagani, Luc

The dynamic behaviour of the mammoth in the Spanish fortress, L’Aquila, Italy

The fossil remains of a “Mammuthus Meridionalis” were found the 25th of march 1954 in a lime quarry close to the city of L’Aquila. The Mammoth skeleton was soon “reconstructed” on a forged iron frame, and it was located in one of the main halls of the Spanish fortress in L’Aquila. A comprehensive restoration was recently completed (2013-2015), also considering the study of the adequacy of the supporting frame, which demonstrated to survive the relevant 2009 l’Aquila earthquake. After a laser-scanner survey, allowing to build a very detailed Finite Element model, Operational Modal Analysis was employed in order to obtain the dynamic identification of the structure. Results of the experimental activities explained the capacity of the structure to bear the 2009 main shock, since the natural frequencies demonstrated to be quite reduced. The structure acted as a “natural” seismic device, avoiding to reach its Ultimate Limit State however paying the toll of relevant displacements. The seismic motion caused several cracks at the edge of the bones, indicating the non-fulfilment of the ALS (damage Limit State of Artistic contents). A proposal for seismic isolation and redesign of the supporting frame was then discussed. The paper illustrates the scientific activities assisting the restoration intervention, entailing a multidisciplinary approach, in the fields of restoration, palaeontology and seismic engineering

Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes

Abstract Y chromosome markers can shed light on male-specific population dynamics but for many species no such markers have been discovered and are available yet, despite the potential for recovering Y-linked loci from available genome sequences. Here, we investigated how effective available bioinformatic tools are in recovering informative Y chromosome microsatellites from whole genome sequence data. In order to do so, we initially explored a large dataset of whole genome sequences comprising individuals at various coverages belonging to different species of baboons (genus: Papio) using Y chromosome references belonging to the same genus and more distantly related species (Macaca mulatta). We then further tested this approach by recovering Y-STRs from available Theropithecus gelada genomes using Papio and Macaca Y chromosome as reference sequences. Identified loci were validated in silico by a) comparing within-species relationships of Y chromosome lineages and b) genotyping male individuals in available pedigrees. Each STR was selected not to extend in its variable region beyond 100 base pairs, so that loci can be developed for PCR-based genotyping of non-invasive DNA samples. In addition to assembling a first set of Papio and Theropithecus Y-specific microsatellite markers, we released TYpeSTeR, an easy-to-use script to identify and genotype Y chromosome STRs using population genomic data which can be modulated according to available male reference genomes and genomic data, making it widely applicable across taxa