Variación genética y fenotípica en "Psammodromus algirus" (lagartija colilarga: implicaciones ecológicas y evolutivas

Esta tesis trata de, una vez explorados los rasgos fenotípicos que pueden interpretarse como adaptaciones locales, contestar a preguntas que tienen que ver con cómo responde el genoma a las presiones selectivas divergentes que subyacen a la diferenciación de dichos rasgos. En general, no se pretende descubrir la base genética de la adaptación a los gradientes ambientales que generan adaptación local; lo que se busca es desentrañar cómo la evolución provee la variación genética necesaria para afrontar diferentes retos ecológicos en una especie capaz de subsistir en una gran variedad de ambientes.Mediante escaneos genómicos a gran escala, conseguimos definir fracciones del genoma relacionadas con la adaptación a distintos ambientes, revelando patrones de convergencia y divergencia adaptativa gracias a procesos tanto de mantenimiento de diversidad genética ancestral como de innovación genética..

Lizard thermoregulation revisited after two decades of global warming

CRUE-CSIC (Acuerdos Transformativos 2022)1.Although the effects of global warming on thermoregulation are usually explored using predictions of climate envelop modelling, such effects should best be analysed empirically, studying the same population with the same methods after a long enough period of temperature rise. 2. We used a 30-year long database about body temperatures (Tbs) of field-active Psammodromus algirus lizards inhabiting a well-conserved temperate open forest, and we focused on the summers of 1997 and 2017 to compare Tbs, environmental operative temperatures (Tes), their proximity to the selected thermal range (Tsel), and the selection of sunlit and shaded patches all along the day. From these data, we estimated the precision (standard deviation of Tbs), accuracy (average distance between Tbs and Tsel) and effectiveness (extent to which Tbs are closer to Tsel than Tes) of thermoregulation. 3. Of the highest 5% of all Tbs in the database, 95% were recorded in 2017, when the adjustment to Tsel was much better for Tbs selected in a laboratory thermogradient than for field Tbs (percentages of Tbs above Tsel of 2% and 52% respectively). 4. In 2017, especially after 12:00 h, the selection of shaded patches (87% of lizards in full shade vs. <1% in full sun) was more intense than in 1997, contributed more to overall thermoregulation, and produced a larger difference between Tes and Tbs. In spite of this, Tbs were lower—and closer to Tsel—in 1997 (when most shaded patches offered favourable thermal opportunities, with Tes within or below Tsel) than in 2017 (when only 33% of full shade Tes, and 8% of all Tes, were within or below Tsel). As a consequence, estimates of the accuracy and effectiveness of thermoregulation decreased over the 20-year period examined. 5. We conclude that given the low availability of Tes within or below Tsel, lizards cannot longer prevent the rise of their Tbs above Tsel, at least in hot summer days. Thus, the effects of global warming are already hindering the ability of lizards to buffer environmental change by behavioural means, even in temperate forests with a fine-grained mosaic of sun and shade patches.Depto. de Biodiversidad, Ecología y EvoluciónFac. de Ciencias BiológicasTRUEMinisterio de Ciencia e Innovación (MICINN)pu

There is more to the picture than meets the eye: adaptation for crypsis blurs phylogeographical structure in a lizard

Aim: We examined dorsal coloration in and genetic relationships among Iberian populations of the lizard Psammodromus algirus to determine the extent to which the current distribution of phenotypic variation is correlated with phylogeographical history or local environmental conditions. Location: Iberian Peninsula, western Palaearctic.Methods: We sequenced mitochondrial DNA (ND4 and adjacent tRNAs genes) in 36 populations, and seven microsatellite loci in eight representative populations. In 23 populations, lizards were classified according to the presence and intensity of a dorsal striped pattern, the heritability of which was estimated by means of mother–offspring regressions. To determine whether colour pattern is an adaptation for crypsis, we compared the time taken by humans to detect striped and unstriped lizards in different environments.Results: The analysis of mtDNA revealed an ancient split between a western clade, subdivided into south- and north-western haplogroups, and an eastern clade with central, south-eastern and eastern haplogroups. In contrast, nuclear markers showed a post-glacial admixture of central and western haplogroups, with the central haplogroup apparently isolated from the rest of its clade. This was consistent with variation in the dorsal striped pattern, a heritable phenotypic trait: central and western lizards were unstriped, whereas eastern lizards were striped. We then suggest that dorsal coloration promotes crypsis: in eastern locations detection times were longer for striped than for unstriped lizards, whereas the opposite was true in western and central locations.Main conclusions: Our results indicate that natural selection for crypsis may promote not only divergence within clades, as suggested by the apparent isolation between unstriped central lizards and striped members of eastern haplogroups, but also admixture between them. We conclude that ecologically driven selection is crucial for understanding the phylogeographical background of phenotypic variation, because recent adaptation to the environment can blur the effects of ancestral isolation.This study is a contribution to projects CGL2010-17928/BOS and CGL2013-41642-P, funded by the Spanish Ministry of Education and SciencePeer reviewe

The combined use of raw and phylogenetically independent methods of outlier detection uncovers genome‐wide dynamics of local adaptation in a lizard

Local adaptation is a dynamic process by which different allele combinations are se-lected in different populations at different times, and whose genetic signature can be inferred by genome-wide outlier analyses. We combined gene flow estimates with two methods of outlier detection, one of them independent of population coances-try (CIOA) and the other one not (ROA), to identify genetic variants favored when ecology promotes phenotypic convergence. We analyzed genotyping-by-sequencing data from five populations of a lizard distributed over an environmentally heteroge-neous range that has been changing since the split of eastern and western lineages ca. 3 mya. Overall, western lizards inhabit forest habitat and are unstriped, whereas eastern ones inhabit shrublands and are striped. However, one population (Lerma) has unstriped phenotype despite its eastern ancestry. The analysis of 73,291 SNPs confirmed the east–west division and identified nonoverlapping sets of outliers (12 identified by ROA and 9 by CIOA). ROA revealed ancestral adaptive variation in the uncovered outliers that were subject to divergent selection and differently fixed for eastern and western populations at the extremes of the environmental gradient. Interestingly, such variation was maintained in Lerma, where we found high levels of heterozygosity for ROA outliers, whereas CIOA uncovered innovative variants that were selected only there. Overall, it seems that both the maintenance of ancestral variation and asymmetric migration have counterbalanced adaptive lineage split-ting in our model species. This scenario, which is likely promoted by a changing and heterogeneous environment, could hamper ecological speciation of locally adapted populations despite strong genetic structure between lineages

Adaptive divergence under gene flow along an environmental gradient in two coexisting stickleback species

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Low genome‐wide divergence between two lizard populations with high adaptive phenotypic differentiation

Usually, adaptive phenotypic differentiation is paralleled by genetic divergence between locally adapted populations. However, adaptation can also happen in a scenario of nonsignificant genetic divergence due to intense gene flow and/or recent differentiation. While this phenomenon is rarely published, findings on incipient ecologically driven divergence or isolation by adaptation are relatively common, which could confound our understanding about the frequency at which they actually occur in nature. Here, we explore genome-wide traces of divergence between two populations of the lacertid lizard Psammodromus algirus separated by a 600 m elevational gradient. These populations seem to be differentially adapted to their environments despite showing low levels of genetic differentiation (according to previously studies of mtDNA and microsatellite data). We performed a search for outliers (i.e., loci subject to selection) trying to identify specific loci with FST statistics significantly higher than those expected on the basis of overall, genome-wide estimates of genetic divergence. We find that local phenotypic adaptation (in terms of a wide diversity of characters) was not accompanied by genome-wide differentiation, even when we maximized the chances of unveiling such differentiation at particular loci with FSTbased outlier detection tests. Instead, our analyses confirmed the lack of genomewide differentiation on the basis of more than 70,000 SNPs, which is concordant with a scenario of local adaptation without isolation by environment. Our results add evidence to previous studies in which local adaptation does not lead to any kind of isolation (or early stages of ecological speciation), but maintains phenotypic divergence despite the lack of a differentiated genomic background

Environmental association modelling with loci under divergent selection predicts the distribution range of a lizard

During the historical building of a species range, individual colonizers have to confront different ecological challenges, and the capacity of the species to broaden its range may depend on the total amount of adaptive genetic variation supplied by evolution. We set out to increase our understanding of what defines a range and the role of underlying genetics by trying to predict an entire species’ range from the geographical distribution of its genetic diversity under selection. We sampled five populations of the western Mediterranean lizard Psammodromus algirus that inhabit a noticeable environmental gradient of temperature and precipitation. We correlated the genotypes of 95 individuals (18–20 individuals per population) for 21 SNPs putatively under selection with environmental scores on a bioclimatic gradient, using 1 × 1 km2 grid cells as sampling units. By extrapolating the resulting model to all possible combinations of alleles, we inferred all the geographic cells that were theoretically suitable for a given amount of genetic variance under selection. The inferred distribution range overlapped to a large extent with the realized range of the species (77.46% of overlap), including an accurate prediction of internal gaps and range borders. Our results suggest an adaptability threshold determined by the amount of genetic variation available that would be required to warrant adaptation beyond a certain limit of environmental variation. These results support the idea that the expansion of a species’ range can be ultimately linked to the arising of new variants under selection (either newly selected variants from standing genetic variation or innovative mutations under selection)

Increased individual homozygosity is correlated with low fitness in a fragmented lizard population

Isolation owing to anthropogenic habitat fragmentation is expected to increase the homozygosity of individuals, which might reduce their fitness as a result of inbreeding depression. Using samples from a fragmented population of the lizard Psammodromus algirus, for which we had data about two correlates of fitness, we genotyped individuals for six microsatellite loci that correctly capture genome-wide individual homozygosity of these lizards (as validated with an independent sample of lizards genotyped for both these microsatellites and > 70 000 single nucleotide polymorphisms). Our data revealed genetic structure at a very small geographical scale, which was compatible with restricted gene flow among populations disconnected in a matrix of inhospitable habitat. Lizards from the same fragment were genetically more related to one another than expected by chance, and individual homozygosity was greater in small than in large fragments. Within fragments, individual homozygosity was negatively associated with adult body size and clutch mass, revealing a link among reduced gene flow, increased homozygosity and lowered fitness that might reduce population viability deterministically. Our results contribute to mounting evidence of the impact of the loss of genetic diversity on fragmented wild populations

Clonal chromosomal mosaicism and loss of chromosome Y in elderly men increase vulnerability for SARS-CoV-2

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, individuals with clonal mosaic events (clonal mosaicism for chromosome alterations and/or loss of chromosome Y) showed an increased risk of COVID-19 lethality

Genome-wide raw data on local adaptation in a mediterranean lizard

Raw genomic data for 5 locally adapted populations of a mediterranean lizard. We used the restriction enzyme Pst1 for GBS library preparation. Sequencing was done in an Illumina HiSeq2500 sequencer. The pipeline used for SNPs discovery was UNEAK, implemented in TASSEL v.3.0. After quality and linkage disiquilibrium filtering steps, we obtained a dataset with > 73,000 SNPs. We also provide data on phenotypic variation