Biology subjects

Musiani, M.

Publications and source records attributed to Musiani, M..

4 recordsLinked to original sources

bioRxiv2026

Wolves in black: multiple introgressions and natural selection may explain melanism in Italian wolves

Hybridisation between wild and domestic taxa can favour the spread of domestic alleles into wild populations through backcrossing. The complex interplay of random genetic drift, recombination, and selection can shape the fate of introgressed alleles. Maladaptive domestic variants are likely to be purged by natural selection, but others may persist across generations. It has long been known that the Apennine Italian wolf population, exposed to large numbers of free-ranging dogs, has experienced extensive introgression. The unusually high frequency of black wolves observed in Italy, compared to other European populations, may parallel patterns documented in North American wolves, where the melanistic KB allele at the CBD103 gene, of domestic origin, has spread over thousands of years of introgression. We tested whether the KB mutation entered the peninsular Italian wolf population via hybridisation and spread through adaptive introgression. Genome-wide analyses of black and wild-type (grey-coated) Apennine wolves showed no clear signatures of recent dog ancestry in most melanistic animals. Our ancestry reconstruction approaches identified two distinct KB haplogroups of domestic origin, suggesting multiple introgression events. Notably, we found molecular evidence consistent with balancing selection on the KB haplotypes, whose functional role, nonetheless, warrants further research. Therefore, the microevolutionary genomic and ecological consequences of wolf-dog hybridisation in Italy should be carefully investigated to inform appropriate science-based conservation management strategies.

genomics↗

bioRxiv2026

Inbreeding and demographic history of caribou (Rangifer tarandus) in western Canada inferred from genome-wide SNP data

Assessing genetic diversity is essential for conserving endangered populations, yet comprehensive genomic evaluations remain limited for many declining species. Here, we investigated inbreeding levels and effective population sizes (Ne) of caribou (Rangifer tarandus) in western Canada, where populations have experienced pronounced declines over the past centuries due to anthropogenic pressures and climate change. We analyzed 33,346 Single Nucleotide Polymorphisms (SNPs) from 759 individuals representing 45 subpopulations within six metapopulations to: (1) assess inbreeding using runs of homozygosity (ROHs), (2) estimate contemporary and historical Ne, and (3) evaluate relationships between census size (Nc), inbreeding, and Ne. Small and endangered subpopulations, predominantly in southern regions, generally exhibited high inbreeding (FROH > 0.1), although some larger populations also showed elevated levels. Most subpopulations displayed a mixture of short and long ROHs, indicating both ancient shared ancestry and recent inbreeding. Twelve subpopulations had Ne <50, and 28 subpopulations and all metapopulations had Ne < 500, suggesting compromised short-term viability and long-term adaptive potential. Nc significantly predicted inbreeding (R{superscript 2} = 0.25), whereas contemporary Ne did not. Historical Ne reconstructions revealed a north-to-south gradient in bottleneck timing: northern populations declined in [~]1700-1780, central populations in [~]1780-1860, and southern populations in [~]1860-1940, likely driven by sequential impacts of climate shifts and anthropogenic disturbances. Our findings identify at-risk populations requiring urgent genetic intervention and demonstrate that integrating inbreeding and Ne estimates provides a robust framework for caribou recovery and the management of fragmented wildlife populations.

evolutionary biology↗

bioRxiv2025

Glacial history and landscape features shape the hierarchical population genetic structure of woodland caribou (Rangifer tarandus caribou) in western Canada

Caribou, listed as a species at risk across Canada, have experienced a wide range of evolutionary and selective pressures at multiple scales, from large-scale range shifts and recolonisations driven by glacial cycles to more localized contemporary habitat degradation and fragmentation. Given these multi-scale evolutionary forces, genetic variation and diversity are expected to be hierarchically structured. Characterising hierarchical population structure is crucial to understanding a species evolutionary history and informing effective conservation and management strategies. In this study, we analysed genomic diversity and variation in woodland caribou (Rangifer tarandus caribou) across western Canada using genotypes from [~]33,000 Single Nucleotide Polymorphism (SNP) loci from 759 geo-referenced individuals spanning 45 pre-defined subpopulations. We employed genetic clustering methods and measures of genetic differentiation to characterize hierarchical population structure in the region and tested for latitudinal changes in heterozygosity resulting from post-glacial recolonisation and hybridisation. Our results confirm that woodland caribou genetic diversity and differentiation occur at multiple hierarchical levels, reflecting post-glacial recolonisation patterns and landscape heterogeneity. Notably, the major genetic clusters identified in our study do not align with current conservation units for the species in this region. We also observe elevated heterozygosity in the mid-latitudes of the sampled range, indicative of hybridisation following secondary contact during post-glacial recolonisation. These findings underscore the need to consider and include genetic diversity at all hierarchical levels in conservation planning, as wide-ranging species often experience diverse and complex evolutionary histories and pressures.

evolutionary biology↗

bioRxiv2025

Jointly representing long-range genetic similarity and spatially heterogeneous isolation-by-distance

Isolation-by-distance patterns in genetic variation are a widespread feature of the geo-graphic structure of genetic variation in many species, and many methods have been developed to illuminate such patterns in genetic data. However, long-range genetic similarities also exist, often as a result of rare or episodic long-range gene flow. Jointly characterizing patterns of isolation-by-distance and long-range genetic similarity in genetic data is an open data analysis challenge that, if resolved, could help produce more complete representations of the geographic structure of genetic data in any given species. Here, we present a computationally tractable method that identifies long-range genetic similarities in a background of spatially heterogeneous isolation-by-distance variation. The method uses a coalescent-based framework, and models long-range genetic similarity in terms of directional events with source fractions describing the fraction of ancestry at a location tracing back to a remote source. The method produces geographic maps annotated with inferred long-range edges, as well as maps of uncertainty in the geographic location of each source of long-range gene flow. We have implemented the method in a package called FEEMSmix (an extension to FEEMS from Marcus et al., 2021), and validated its implementation using simulations representative of typical data applications. We also apply this method to two empirical data sets. In a data set of over 4,000 humans (Homo sapiens) across Afro-Eurasia, we recover many known signals of long-distance dispersal from recent centuries. Similarly, in a data set of over 100 gray wolves (Canis lupus) across North America, we identify several previously unknown long-range connections, some of which were attributable to recording errors in sampling locations. Therefore, beyond identifying genuine long-range dispersals, our approach also serves as a useful tool for quality control in spatial genetic studies. Author SummaryThe movement of individuals across landscapes shapes genetic diversity and has significant implications for both evolutionary studies and conservation efforts. Advances in sequencing now allow researchers to analyze thousands of samples from broad geographic areas, helping to estimate local gene flow. However, long-range genetic flow can occur due to a host of reasons (e.g. natural weather patterns, migration for resources, etc.), and existing methods struggle to represent these patterns. In this study, we developed a method to identify and model these long-range genetic similarities as dispersals from a source to a destination over a landscape. In applying this method to over 4,000 human samples from Afro-Eurasia, we detected signatures of known long-distance dispersals from recent centuries. In applying this method to 100 gray wolf samples from North America, we found many unexpected long-range genetic connections, some of which turned out to be recording errors in sample locations. Thus, beyond detecting real long-range dispersal, our approach also serves as a useful tool for quality control in spatial genetic studies.

evolutionary biology↗