Biology subjects

Luisi, P.

Publications and source records attributed to Luisi, P..

5 recordsLinked to original sources

bioRxiv2026

Region-specific patterns of sexual shape variation in the human bony labyrinth: 3D geometric morphometric analysis of a sample with known genomic sex

The human bony labyrinth has attracted increasing interest because of its taxonomic, evolutionary, and functional significance. Although sexual dimorphism has been reported in several aspects of the temporal bone, the extent to which sex, age, size, and allometry contribute to labyrinth shape variation remains poorly understood. Here, we investigated patterns of sexual shape variation in the human bony labyrinth using three-dimensional geometric morphometrics in a sample of 98 archaeological individuals from South America with known genomic sex. Centroid size and allometric effects were assessed in a subset of 90 individuals with comparable metric scaling. In addition to analysing the complete labyrinth, the cochlea and semicircular canals were examined separately to evaluate region-specific patterns of sexual shape variation. Principal Component Analysis showed extensive overlap between females and males, and overall labyrinth shape did not differ significantly between sexes. Males exhibited significantly larger labyrinths than females, and centroid size explained a small but significant proportion of overall shape variation. Regional analyses showed no evidence of significant sexual shape differences in the cochlea or in any individual semicircular canal when analysed separately. In contrast, the combined semicircular canal system exhibited subtle but significant sexual shape variation independent of centroid size, whereas morphological disparity did not differ between sexes. The geometric comparison of the female and male consensus configurations further showed that sexual shape variation was regionally heterogeneous. Whereas the cochlea exhibited a pattern of localized changes with low directional coherence, the semicircular canals displayed more coordinated regional shape changes. The male consensus also exhibited slightly higher canal circularity across all three semicircular canals, particularly the posterior canal, while differences in canal-plane orientation remained minimal. These findings demonstrate that sexual shape variation in the human bony labyrinth is subtle and anatomically partitioned among its components. Although significant sex differences in centroid size were detected across most anatomical regions, overall labyrinth shape and cochlear morphology were primarily influenced by allometry, whereas significant sex-related shape differences were detected only when the semicircular canals were considered as an integrated anatomical system. These findings demonstrate that sexual dimorphism in the human bony labyrinth is subtle but regionally heterogeneous, with the cochlea and semicircular canals exhibiting distinct patterns of shape variation, suggesting that these structures are influenced by different developmental, functional, and evolutionary processes.

evolutionary biology↗

bioRxiv2025

{micro}CT Scanning Effects on DNA and a Multi-Step Workflow for Archaeological Petrous Bones

The petrous portion of the temporal bone is a key element in human evolutionary studies due to its exceptional preservation of biomolecules and morphological information. However, intensive and often redundant sampling has raised concerns about sustainability and long-term conservation. Here we present the first systematic evaluation of whether micro-Computed Tomography ({micro}CT)--a widely used tool for digital preservation--affects ancient DNA (aDNA) integrity in human petrous bones. We analyzed 93 archaeological samples from Argentina, of which 50 had been scanned using {micro}CT and 43 had not. We compared six molecular parameters, including endogenous content, read length, cytosine deamination patterns and contamination estimates. No statistically significant differences were observed between scanned and unscanned samples across any parameter (Mann-Whitney/Wilcoxon tests, p <0.05). Although mitochondrial contamination was marginally higher in scanned samples (p = 0.051), this was not driven by contamination estimates above the widely accepted 5% threshold for genomic analysis, Moreover, this pattern was not observed when considering nuclear contamination. These results indicate that, under appropriate scanning conditions, {micro}CT imaging does not compromise DNA preservation. Building on this evidence, we propose a sustainable, multi-step workflow that integrates biological profiling, osteobiography, imaging, and compositional pre-screening prior to molecular sampling. This interdisciplinary approach maximizes the scientific information obtained from skeletal collections while minimizing destructive practices, thereby promoting ethical and sustainable research on irreplaceable anthropological remains, and fosters collaboration across research fields.

paleontology↗

bioRxiv2020

Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina

Similarly to other populations across the Americas, Argentinean populations trace back their genetic ancestry into African, European and Native American ancestors, reflecting a complex demographic history with multiple migration and admixture events in pre- and post-colonial times. However, little is known about the sub-continental origins of these three main ancestries. We present new high-throughput genotyping data for 87 admixed individuals across Argentina. This data was combined to previously published data for admixed individuals in the region and then compared to different reference panels specifically built to perform population structure analyses at a sub-continental level. Concerning the Native American ancestry, we could identify four Native American components segregating in modern Argentinean populations. Three of them are also found in modern South American populations and are specifically represented in Central Andes, Central Chile/Patagonia, and Subtropical and Tropical Forests geographic areas. The fourth component might be specific to the Central Western region of Argentina, and it is not well represented in any genomic data from the literature. As for the European and African ancestries, we confirmed previous results about origins from Southern Europe, Western and Central Western Africa, and we provide evidences for the presence of Northern European and Eastern African ancestries. Author SummaryThe human genetic diversity in Argentina reflects demographic processes during which the European colonists invaded a territory where Native American populations were settled. During the colonial period, the slave trade also prompted many African people to move to Argentina. Little is known about the origins of these three continental ancestry components in Argentinean populations nowadays. Genotyping data for 87 admixed individuals throughout Argentina was generated and data from the literature was re-analyzed to shed light on this question. We confirmed that most of the European genetic ancestry comes from the South, although several individuals are related to Northern Europeans. We confirmed that the African origins in Argentina mainly trace back from Western and Central/Western regions, and we document some proportion of Eastern African origins poorly described before. As for the Native American ancestry, we identified that it can be divided into four main components that correspond to Central Chile/Patagonia, Subtropical and Tropical Forests, Central Andes and Central Western region of Argentina. In order to understand the specificity of the genetic diversity in Argentina, more effort is required to generate specific massive genomic knowledge at the local level.

genetics↗

bioRxiv2019

Population history and gene divergence in Native Mexicans inferred from 76 human exomes

Native American genetic variation remains underrepresented in most catalogs of human genome sequencing data. Previous genotyping efforts have revealed that Mexicos indigenous population is highly differentiated and substructured, thus potentially harboring higher proportions of private genetic variants of functional and biomedical relevance. Here we have targeted the coding fraction of the genome and characterized its full site frequency spectrum by sequencing 76 exomes from five indigenous populations across Mexico. Using diffusion approximations, we modeled the demographic history of indigenous populations from Mexico with northern and southern ethnic groups splitting 7.2 kya and subsequently diverging locally 6.5 kya and 5.7 kya, respectively. Selection scans for positive selection revealed BCL2L13 and KBTBD8 genes as potential candidates for adaptive evolution in Raramuris and Triquis, respectively. BCL2L13 is highly expressed in skeletal muscle and could be related to physical endurance, a well-known phenotype of the northern Mexico Raramuri. The KBTBD8 gene has been associated with idiopathic short stature and we found it to be highly differentiated in Triqui, a southern indigenous group from Oaxaca whose height is extremely low compared to other native populations.

genomics↗

bioRxiv2018

First genome-wide association study of non-severe malaria in two birth cohorts in Benin: hints towards the involvement of the STAT3 pathway.

Recent research efforts to identify genes involved in the susceptibility to P. falciparum malaria have focused on severe forms of malaria, with several genome-wide association studies (GWAS) and multi-center analyses published this past decade. Here we present the first GWAS performed on mild malaria susceptibility in young children, designed to identify genetic variants involved in innate immunity or innate resistance mechanisms. Two cohorts of infants from southern Benin (525 and 250 individuals respectively), used as discovery and replication cohorts, were closely followed from birth to 18-24 months of age, with an assessment of a space-and time-dependent risk of exposure to vector bites. GWAS was performed on 15.5 million genotyped and imputed variants, with the susceptibility of infants to mild malaria attacks and to malaria infections as a whole (both symptomatic and asymptomatic). Infant susceptibility to malaria was assessed by considering all malaria events occurring during the follow-up using a Cox-model for recurrent events. We found strong statistical support for a role of PTPRT, a tyrosine phosphatase receptors involved in STAT3 pathway, with the protection against both mild malaria attacks and malaria infections (p=9.70x10-8 and p=1.78x10-7 respectively in the discovery cohort, and both p < 0.05 in the replication cohort). Furthermore, our study highlights several other genes, among them, UROC1, ACER3 and the PLAG2 cluster, whose biological functions are relevant in malaria infection. Results show that despite the difficulty of setting up such longitudinal field studies, GWAS on non-severe malaria can successfully identify new candidate genes and inform physiological mechanisms underlying natural protection against malaria.\n\nAUTHOR SUMMARYMalaria remains a major worldwide public health problem with circa 219 million cases and 435,000 deaths per year. As for many infectious diseases, the genetics of the host plays a role in the disease course. So far, most studies on such genetic factors focused on severe malaria forms. Our study aimed to find factors associated with simple forms (asymptomatic forms and uncomplicated clinical forms). We used dense genome-wide data of two cohorts of infants closely followed during two years in Benin, and we incorporated an environmental risk of exposure estimated at individual level from entomological, climatic, and environmental data. This allowed us to unravel several genes that appear to play a role in the susceptibility to malaria infection, thus demonstrating the feasibility of a genome-wide approach on non-severe forms. Functional studies are needed to confirm the role of the genetic factors highlighted here. Some of these genes represent interesting targets for future prevention strategies and drug development.

genetics↗