Biology subjects

Di Santo, L. N.

Publications and source records attributed to Di Santo, L. N..

6 recordsLinked to original sources

bioRxiv2026

Tracing the Neanderthal-Modern Human hybrid zone using paleogenomic data

Interbreeding between closely related lineages is a pervasive evolutionary feature across taxa1, including modern humans, who admixed with Neanderthals and other archaic hominins2,3. Identifying where gene flow between these lineages happened can shed light on ecological and adaptive contexts in which introgressed genes were acquired. However, mapping ancient hybrid zones is challenging because post-admixture population dynamics obscure their genetic signatures. Here, we determine the conditions under which spatial patterns of introgressed DNA in ancient genomes allow the inference of the geographic location of past hybridization events during population expansions. Using computational simulations, we identify the conditions under which introgression-based statistics provide informative signals about past hybridization events. We show that the mean genomic proportion of introgressed DNA, which can be readily calculated from low-coverage ancient genomes, reveals a cline that increases with distance from the population expansion source until reaching the hybrid zone boundary and persists over time. Comparison with empirical Neanderthal introgression distribution from an extended Eurasian paleogenomic dataset supports a prolonged admixture pulse extending far beyond the Levant in western Eurasia. Our findings highlight the power of paleogenomics to reconstruct the spatiotemporal dynamics of species interactions.

evolutionary biology↗

bioRxiv2024

Genomic signature of reproductive isolation between the last two remnant populations of Torrey pine (Pinus torreyana Parry)

Tree species are often locally adapted to their environments, but the extent to which environmental adaptation contributes to incipient speciation is unclear. One of the rarest pines in the world, Torrey Pine (Pinus torreyana Parry), persists naturally across one island and one mainland population in southern California. The two populations are morphologically and genetically differentiated, but experience some connectivity, making it an ideal system for assessing the evolution of reproductive isolation. Previous work has found evidence of heterosis in F1 mainland-island hybrids, suggesting genetic rescue could be beneficial in the absence of reproductive barriers. Using ddRADseq and GWAS for a common garden experiment of island, mainland, and F1 individuals, we identified candidate loci for environmentally-driven reproductive isolation, their function, and their relationship to fitness proxies. By simulating neutral evolution and admixture between the two populations, we identified loci that exhibited reduced heterozygosity in the F1s, evidence of selection against admixture. SNPs with reduced F1 heterozygosity were enriched for growth and pollination functions, suggesting genetic variants that could be involved in the evolution of reproductive barriers between populations. One locus with reduced F1 heterozygosity exhibited strong associations with growth and reproductive fitness proxies in the common garden, with the mainland allele conferring increased fitness. If this locus experiences divergent selection in the two natural populations, it could promote their reproductive isolation. Finally, although hybridization largely reduced allele fixation in the F1s initially, indicating heterosis is likely due to the masking of deleterious alleles, the emergence of reproductive isolation between populations may diminish the longer-term benefits of genetic rescue in F2 or advanced-generation hybrids. As Torrey pine is a candidate for interpopulation genetic rescue, caution is warranted where longer-term gene flow between diverged populations may result in reduced fitness if barriers have evolved.

genomics↗

bioRxiv2023

Temporal variation in introgressed segments' length statistics sheds light on past admixture pulses

AbstractHybridization is recognized as an important evolutionary force, but identifying and timing admixture events between divergent lineages remains a major aim of evolutionary biology. While this has traditionally been done using inferential tools on contemporary genomes, the latest advances in paleogenomics have provided a growing wealth of temporally distributed genomic data. Here, we used individual-based simulations to generate chromosome-level genomics data for a two-population system and described temporal neutral introgression patterns under a single- and two-pulse admixture model. We computed three summary statistics aiming to inform the timing and number of admixture pulses between interbreeding entities: lengths of introgressed sequences and their variance within-genomes, as well as genome-wide introgression proportions. The first two statistics can confidently be used to infer inter-lineage hybridization history, peaking at the beginning and shortly after an admixture pulse. Temporal variation in introgression proportions provided more limited insights. We then computed these statistics on Homo sapiens paleogenomes and successfully inferred the hybridization pulse with Neanderthal that occurred approximately 40 to 60 kya. The scarce number of genomes dating from this period prevented more precise inferences, but the accumulation of paleogenomic data opens promising perspectives as our approach only requires a limited number of genomes.

genomics↗

bioRxiv2021

Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana Parry) with implications for rare species conservation

Understanding the contribution of neutral and adaptive evolutionary processes to population differences is often necessary for better informed management and conservation of rare species. In this study, we focused on Pinus torreyana Parry (Torrey pine), one of the worlds rarest pines, endemic to one island and one mainland population in California. Small population size, low genetic diversity, and susceptibility to abiotic and biotic stresses suggest Torrey pine may benefit from inter-population genetic rescue to preserve the species evolutionary potential. We leveraged reduced representation sequencing to tease apart the respective contributions of stochastic and deterministic evolutionary processes to population differentiation. We applied these data to model spatial and temporal demographic changes in effective population sizes and genetic connectivity, to assess loci possibly under selection, and evaluate genetic rescue as a potential conservation strategy. Overall, we observed exceedingly low standing variation reflecting consistently low effective population sizes across time and limited genetic differentiation suggesting maintenance of gene flow following divergence. However, genome scans identified more than 2000 SNPs candidates for divergent selection. Combined with previous observations indicating population phenotypic differentiation, this indicates that natural selection has likely contributed to population genetic differences. Thus, while reduced genetic diversity, small effective population size, and genetic connectivity between populations suggest genetic rescue could mitigate the adverse effect of rarity, divergent selection between populations indicates that genetic mixing could disrupt adaptation. Further work evaluating the fitness consequences of inter-population admixture is necessary to empirically evaluate the trade-offs associated with genetic rescue in Torrey pine.

genomics↗

bioRxiv2020

Seed morphology and emergence variability in a conservation collection of Pinus torreyana

BackgroundUnderstanding the within- and among-population distribution of trait variation within seed collections may provide a means to approximate standing genetic variation and inform plant conservation. AimsThis study aimed to estimate population- and family-level seed trait variability for existing seed collections of Torrey pine (Pinus torreyana), and to use these data to guide sampling of future collections. MethodsWe quantified variation in 14 seed morphological traits and seedling emergence within and among Torrey pine populations. Using a simulation-based approach, we used estimates of within-population variance to assess the number of maternal families required to capture 95% of trait variation within each existing seed collection. ResultsSubstantial structure was observed both within and among Torrey pine populations, with island and mainland seeds varying in seed size and seed coat thickness. Despite morphological differences, seedling emergence was similar across populations. Simulations revealed that 83% and 71% of all maternal families within island and mainland seed collections respectively needed to be resampled to capture 95% of seed trait variation within existing collections. ConclusionsFrom a conservation perspective, our results indicate that to optimize genetic diversity captured in Torrey pine seed collections, maximizing the number of maternal families sampled within each population will be necessary.

plant biology↗

bioRxiv2020

Environmental and geographic data optimize ex situ collections and the preservation of adaptive evolutionary potential

Maintenance of biodiversity, through seed banks and botanical gardens where the wealth of species genetic variation may be preserved ex situ, is a major goal of conservation. However, challenges can persist in optimizing ex situ collections where trade-offs exist between expense, effort, and conserving species evolutionary potential, particularly when genetic data is not available. Within this context, we evaluate the genetic consequences of guiding population preservation using geographic (isolation-by-distance, IBD) and environmental (isolation-by-environment, IBE) data for ex situ collections where provenance data is available. We use 19 genetic and genomic datasets from 15 plant species to (i) assess the proportion of population genetic differentiation explained by geographic and environmental factors, and (ii) simulate ex situ collections prioritizing source populations based on pairwise geographic or environmental distances. Specifically, we test the impact prioritizing sampling based on environmental and geographic distances may have on capturing neutral, functional or putatively adaptive genetic diversity and differentiation. We find that collectively IBD and IBE explain a substantial proportion of genetic differences among functional (median 45%) and adaptive (median 71%) loci, but not for neutral loci (median 21.5%). Simulated ex situ collections reveal that inclusion of IBD and IBE increases both allelic diversity and genetic differentiation captured among populations, particularly for loci that may be important for adaptation. Thus, prioritizing population collections using environmental and geographic distance data can impact genetic variation captured ex situ. This provides value for the vast majority of plant species for which we have no genetic data, informing conservation of genetic variation needed to maintain evolutionary potential within collections.

genomics↗