Biology subjects

Rotger, A.

Publications and source records attributed to Rotger, A..

3 recordsLinked to original sources

bioRxiv2024

Population genetics and phylogeographic history of the insular lizard Podarcis lilfordi (Gunther, 1874) from the Balearic Islands based on genome-wide polymorphic data

Islands provide a great system to explore the processes that maintain genetic diversity and promote local adaptation. We explored the genomic diversity of the Balearic lizard Podarcis lilfordi, an endemic species characterized by numerous small insular populations with large phenotypic diversity. Using the newly available genome for this species, we characterized more than 300,000 SNPs, merging Genotype by Sequencing (GBS) data with previously published Restriction-site associated DNA sequencing (RADSeq) data, providing a dataset of 16 island populations (191 individuals) across the range of species distribution (Menorca, Mallorca, and Cabrera). Results indicate that each islet hosts a well-differentiated population (Fst=0.247{+/-}0.09), with no recent immigration/translocation events. Contrary to expectations, most populations harbor a considerable genetic diversity (mean nucleotide diversity, Pi=0.144{+/-}0.021), characterized by overall low inbreeding values (Fis<0.1). While the genetic diversity significantly decreased with decreasing islet surface, maintenance of substantial genetic diversity even in tiny islets suggests variable selection or other mechanisms that buffer genetic drift. Maximum-likelihood tree based on concatenated SNP data confirmed the existence of the two major independent lineages of Menorca and Mallorca/Cabrera. Multiple lines of evidence, including admixture and root testing, robustly placed the origin of the species in the Mallorca Island, rather than in Menorca. Outlier analysis mainly retrieved a strong signature of genome differentiation between the two major archipelagos, especially in the sexual chromosome Z. A set of proteins were target of multiple outliers and primarily associated with binding and catalytic activity, providing interesting candidates for future selection studies. This study provides the framework to explore crucial aspects of the genetic basis of phenotypic divergence and insular adaptation.

genomics↗

bioRxiv2023

Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Gunther, 1874) from the Balearic Islands (Spain)

The Mediterranean lizard Podarcis lilfordi is an emblematic species of the Balearic Islands. The extensive phenotypic diversity among extant isolated populations makes the species a great insular model system for eco-evolutionary studies, as well as a challenging target for conservation management plans. Here we report the first high quality chromosome-level assembly and annotation of the P. lilfordi genome, along with its mitogenome, based on a mixed sequencing strategy (10X Genomics linked reads, Oxford Nanopore Technologies long reads and Hi-C scaffolding) coupled with extensive transcriptomic data (Illumina and PacBio). The genome assembly (1.5 Gb) is highly contiguous (N50 = 90 Mb) and complete, with 99% of the sequence assigned to candidate chromosomal sequences and >97% gene completeness. We annotated a total of 25,663 protein-coding genes, assigning 72% to known functions. Comparison to the genome of the related species Podarcis muralis revealed substantial similarity in genome size, annotation metrics, repeat content, and strong collinearity, despite their evolutionary distance (~18-20 MYA). This genome expands the repertoire of available reptilian genomes and will facilitate the exploration of the molecular and evolutionary processes underlying the extraordinary phenotypic diversity of this insular species, while providing a critical resource for conservation genomics.

genomics↗

bioRxiv2022

Insular holobionts: persistence and seasonal plasticity of the Balearic wall lizard (Podarcis lilfordi) gut microbiota

Integrative studies of animals and associated microbial assemblages (i.e., the holobiont) are rapidly changing our perspectives on organismal ecology and evolution. Islands provide ideal natural systems to understand the biogeographic patterns that shape these symbiotic associations, their resilience and plasticity over temporal and spatial scales, and ultimately their role in the host ecological adaptation. Here we used the Balearic wall lizard Podarcis lilfordi to address the diversification of the holobiont in an insular context by dissecting the drivers of the gut microbiota diversity within and across host allopatric populations. By extensive fecal sampling of individually identified lizards from three closed populations/islets in the South of Mallorca (Na Moltona, Na Guardis and En Curt) along two years and two seasons (spring and autumn), we sorted out the effect of islet, year, season, sex and partly life stage on the microbiota composition. We further related microbiota distances to host genetics and trophic ecology. Overall, the three populations showed a remarkable conservation of the major microbial taxonomic profile, while carrying their unique microbial signature at finer level of taxonomic resolution (Amplicon Sequence Variants (ASVs)). Microbiota distances across populations were compatible with both host genetics (as inferred by microsatellites) and trophic niche distances (as inferred by stable isotopes and fecal content). Within populations, a large proportion of ASVs (30-50%) persisted along the four sampling dates. Microbial diversity was driven by life stage and season, with no annual or sex effect. Seasonal changes within islets were mainly associated with fluctuations in the relative abundances of few bacterial taxa (mostly families Lachnospiraceae and Ruminococcaceae), consistently in both sampled years and without any major compositional turnover. These results support a large resilience of the major compositional aspects of the P. lilfordi gut microbiota over the short-term evolutionary divergence of their host allopatric populations (<10,000 years), but also suggest an undergoing process of parallel diversification of the holobiont. The cyclic seasonal fluctuations in gut microbiota composition hint to an important plasticity of these bacterial communities in response to the host annual physiological/metabolic shifts. The importance of these microbial community dynamics in the host ecology and dietary flexibility remains to be investigated.

ecology↗