Browsing by Author "Martinez, Felipe I."

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    Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes
    (2023) Mutti, Giacomo ; Oteo-Garcia, Gonzalo ; Caldon, Matteo ; Ferreira da Silva, Maria Joana; Minhós, Tânia ; Cowlishaw, Guy ; Gottelli, Dada ; Huchard, Elise ; Carter, Alecia ; Martinez, Felipe I. ; Raveane, Alessandro ; Capelli, Cristian
    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.
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    Postadmixture Selection on Chileans Targets Haplotype Involved in Pigmentation, Thermogenesis and Immune Defense against Pathogens
    (2020) Vicuña, Lucas ; Klimenkova, Olga ; Norambuena, Tomás; Martinez, Felipe I.; Fernandez, Mario I.; Shchur, Vladimir ; Eyheramendy, Susana ; Yi, Soojin
    Detection of positive selection signatures in populations around the world is helping to uncover recent human evolutionary history as well as the genetic basis of diseases. Most human evolutionary genomic studies have been performed in European, African, and Asian populations. However, populations with Native American ancestry have been largely underrepresented. Here, we used a genome-wide local ancestry enrichment approach complemented with neutral simulations to identify postadmixture adaptations underwent by admixed Chileans through gene flow from Europeans into local Native Americans. The top significant hits (P=2.4x10(-7)) are variants in a region on chromosome 12 comprising multiple regulatory elements. This region includes rs12821256, which regulates the expression of KITLG, a well-known gene involved in lighter hair and skin pigmentation in Europeans as well as in thermogenesis. Another variant from that region is associated with the long noncoding RNA RP11-13A1.1, which has been specifically involved in the innate immune response against infectious pathogens. Our results suggest that these genes were relevant for adaptation in Chileans following the Columbian exchange.
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    The first Miocene fossils from coastal woodlands in the southern East African Rift
    (2023) Bobe, Rene; Aldeias, Vera; Alemseged, Zeresenay; Anemone, Robert L.; Archer, Will; Aumaitre, Georges; Bamford, Marion K.; Biro, Dora; Bourles, Didier L.; Boyd, Melissa Doyle; Braun, David R.; Capelli, Cristian; Coelho, Joao d'Oliveira; Habermann, Joerg M.; Head, Jason J.; Keddadouche, Karim; Kupczik, Kornelius; Lebatard, Anne-Elisabeth; Luedecke, Tina; Macoa, Amelia; Martinez, Felipe I.; Mathe, Jacinto; Mendes, Clara; Paulo, Luis Meira; Pinto, Maria; Presnyakova, Darya; Pueschel, Thomas A.; Regala, Frederico Tata; Sier, Mark; da Silva, Maria Joana Ferreira; Stalmans, Marc; Carvalho, Susana
    The Miocene was a key time in the evolution of African ecosystems witnessing the origin of the African apes and the isolation of eastern coastal forests through an expanding arid corridor. Until recently, however, Miocene sites from the southeastern regions of the continent were unknown. Here, we report the first Miocene fossil teeth from the shoulders of the Urema Rift in Gorongosa National Park, Mozambique. We provide the first 1) radiometric ages of the Mazamba Formation, 2) reconstructions of paleovegetation in the region based on pedogenic carbonates and fossil wood, and 3) descriptions of fossil teeth. Gorongosa is unique in the East African Rift in combining marine invertebrates, marine vertebrates, reptiles, terrestrial mammals, and fossil woods in coastal paleoenvironments. The Gorongosa fossil sites offer the first evidence of woodlands and forests on the coastal margins of southeastern Africa during the Miocene, and an exceptional assemblage of fossils including new species.