Biology subjects

Ibarra-Laclette, E.

Publications and source records attributed to Ibarra-Laclette, E..

3 recordsLinked to original sources

bioRxiv2026

From divergence to contact: demographic history and genomic context shape introgression across independent damselfly hybrid zones

Hybridisation outcomes often vary across space and time, yet the relative roles of demographic history and genomic architecture in shaping introgression remain unclear. Here, we investigate three replicated hybrid zones between the damselflies Ischnura elegans and Ischnura graellsii across Spain to test whether genomic introgression patterns are repeatable across independently formed zones. Using genome-wide data, we combined demographic modelling, genomic cline, and functional annotation of introgressed loci. Demographic inference supported three independent secondary contact events of different ages: The South-east zone forming first ([~]207 years ago), followed by the North-west ([~]73.5 years) and North-central ([~]33 years) hybrid zones. Despite similar cline steepness across autosomes, asymmetric gene flow from I. graellsii into I. elegans was observed, with a low overlap of introgressed loci between zones. These loci were mainly associated with broad regulatory and transport-related functions in both hybrid zones, indicating repeatability at the level of gene function rather than gene identity. In contrast, the X chromosome showed steeper clines, suggesting strong intrinsic genomic constraints. Together, demographic history explains geographic heterogeneity in introgression, whereas chromosome architecture imposes consistent constraints. These findings highlight how replicated hybrid zones can disentangle contingent versus repeatable genomic responses during early stages of speciation with gene flow.

evolutionary biology↗

bioRxiv2019

Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation.

BackgroundIn bacteria, pan-genomes are the result of the evolutionary \"tug of war\" between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size, resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT, resulting in closed pan-genomes and clonal lineages. In this study, we explored both hypotheses elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Cienegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes.\n\nResultsWe obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. Five of the lineages showed closed pan-genomes and were associated to either water or sediment environment; their high effective population size (Ne) estimates suggest that these lineages are not from a recent origin. The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low Ne, suggesting a recent origin. The recombination and mutation estimators (r/m) ranged from 0.0052 to 2.7249, which are similar to oceanic Vibrionaceae estimations; however, we identified 367 gene families with signals of positive selection, most of them found in the core genome; suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation purging the genomes and keeping closed pan-genome patterns. Moreover, we identify 598 SNPs associated with an unstructured environment; some of the genes under this SNPs were related to sodium transport.\n\nConclusionsDifferent lines of evidence suggest that the sampled Vibrionaceae, are part of the rare biosphere usually living under famine conditions. Two of these lineages were reported by the first time. Most Vibrionaceae lineages of CCB are adapted to their microhabitats rather than to the sampled environments. This pattern of adaptation agrees with the association of closed pan-genomes and local adaptation.

evolutionary biology↗

bioRxiv2019

The Avocado Genome Informs Deep Angiosperm Phylogeny, Highlights Introgressive Hybridization, and Reveals Pathogen Influenced Gene Space Adaptation

The avocado, Persea americana, is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently-diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. americana var. drymifolia, and the most commercially popular hybrid cultivar, Hass, and anchored the latter to chromosomes using a genetic map. Resequencing of Guatemalan and West Indian varieties revealed that [~]39% of the Hass genome represents Guatemalan source regions introgressed into a Mexican race background. Some introgressed blocks are extremely large, consistent with the recent origin of the cultivar. The avocado lineage experienced two lineage-specific polyploidy events during its evolutionary history. Although gene-tree/species-tree phylogenomic results are inconclusive, syntenic ortholog distances to other species place avocado as sister to the enormous monocot and eudicot lineages combined. Duplicate genes descending from polyploidy augmented the transcription factor diversity of avocado, while tandem duplicates enhanced the secondary metabolism of the species. Phenylpropanoid biosynthesis, known to be elicited by Colletotrichum (anthracnose) pathogen infection in avocado, is one enriched function among tandems. Furthermore, transcriptome data show that tandem duplicates are significantly up- and down-regulated in response to anthracnose infection, whereas polyploid duplicates are not, supporting the general view that collections of tandem duplicates contribute evolutionarily recent \"tuning knobs\" in the genome adaptive landscapes of given species.\n\nSIGNIFICANCE STATEMENTAvocado is a nutritious, economically important fruit species that occupies an unresolved position near the earliest evolutionary branchings of flowering plants. Our nuclear genome sequences of Mexican and Hass variety avocados inform ancient evolutionary relationships and genome doublings, the admixed nature of Hass, and provide a look at how pathogen interactions have shaped avocados more recent genomic evolutionary history.

genomics↗