Ecological parasitology in the molecular genetics era

El estudio de la ecología de las relaciones entre parásitos y hospedadores se ha beneficiado recientemente de la aplicación de técnicas moleculares de diagnóstico e identificación de los parásitos. Dichas técnicas, basadas en la amplificación y secuenciación de un fragmento del ADN de los parásitos, no sólo facilitan enormemente la detección de infecciones, sino que han abierto un nuevo campo de investigación acerca de la diversidad –a menudo críptica– de estos parásitos, sus patrones de divergencia evolutiva, o sus singularidades ecológicas. Este tipo de aproximaciones han dado pujanza a la parasitología ecológica, que gracias a las técnicas moleculares ha experimentado un crecimiento exponencial durante la última década.The use of molecular techniques for diagnosing and identifying parasites has recently been incorporated into research on the ecology of host-parasite interactions. Molecular techniques based on the amplification by means of PCR of a fragment of parasite DNA have greatly helped to increase the rate of detection of parasite infections. In addition, these techniques have opened a new research field about the diversity of these parasites –which is often cryptic to the eye–, the patterns of evolutionary divergence of parasite lineages, or the ecological singularities exhibited by different parasites. These kinds of approaches have boosted up research on ecological parasitology, as shown by the exponetial growth of the field during the last decade

Migración y sedentarismo en los paseriformes forestales ibéricos : perspectivas ecológicas y evolutivas

Esta Tesis analiza la variación en el comportamiento migrador de los paseriformes forestales asociada a los cambios de estacionalidad en la península Ibérica, y las consecuencias de dicha variación sobre la demografia, ciclo vital y morfología de las aves. El comportamiento migrador se acentúa en las regiones más estacionales (las mesetas y montañas de la mitad norte ibérica), y desaparece en las zonas menos estacionales del sur peninsular. Así, la abundancia de estas especies disminuye durante el invierno en la meseta, donde las aves muestran además una menor constancia en sus áreas de cría. Las aves más migradoras muestran mayor fecundidad pero menor supervivencia, y sus integrantes tienen alas más largas y apuntadas y cola más corta. Esta covariación entre estacionalidad, migratoriedad, fecundidad, mortalidad y morfología de las aves, nunca antes ilustrada a nivel intraespecífico, plantea la conveniencia de revisar los criterios de conservación de especies ampliamente distribuidas, que deberían tener en cuenta la posible diferenciación local de sus poblaciones. Desde una perspectiva evolutiva, la invernada en simpatría de migradores y sedentarios plantea un dilema, dado que el desequilibrio numérico entre ambas poblaciones y la mayor fecundidad de las poblaciones migradoras deberia conducir a la extinción de los sedentarios. Sin embargo, estudios realizados en el Campo de Gibraltar con petirrojos (Erithacus rubecula) y currucas capirotadas (Sylvia atricapilla) muestran que los sedentarios cuentan con ventajas competitivas sobre los migradores durante el invierno. Esto permite responder preguntas centrales en la teoría de la evolución de la migración, como de qué modo los procesos dependientes de la densidad de población pudieron estar implicados en la dispersión de los primeros migradores fuera de sus áreas de cría, qué importancia tiene la competencia invernal como coste de la migración, o cómo han conseguido subsistir los sedentarios en las áreas de invernada de las poblaciones migradoras

Conservación de poblaciones singulares ante el cambio climático: el caso de las currucas capirotadas ibéricas

Depto. de Biodiversidad, Ecología y EvoluciónFac. de Ciencias BiológicasTRUEpu

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

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

Habitat distribution of migratory and sedentary blackcaps Sylvia atricapilla wintering in southern Iberia: a morphological and biogeochemical approach

In migratory species, the way in which conspecifics from different breeding populations 3 are distributed during the non-breeding period is important from and ecological, 4 evolutionary and conservation perspective, but such knowledge is still limited for most 5 species. Migratory and sedentary blackcaps Sylvia atricapilla wintering in southern Spain 6 can occupy two habitat types: forests and shrublands. According to earlier studies, 7 blackcaps prefer forests over shrublands, and residents remain nearly restricted to forests. 8 However, whether migrants with different breeding origin occupy the two habitats 9 differently is unknown. We used morphological and biogeochemical data (hydrogen isotope ratios measured on feathers: δ2 10 Hf), which show variation along the breeding range 11 of the species, to answer this question. Isotope analyses supported the reliability of 12 morphology as a method for distinguishing between migratory and sedentary blackcaps in 13 sympatry, showing that sedentary individuals are rare in shrublands while migratory ones are abundant in both habitat types. However, migratory blackcaps scored similar δ2 14 Hf 15 values in forests and shrublands, and neither did vary in structural size or flight 16 morphology between habitats. Our study suggests that migrants from a wide range of 17 breeding origins end up mixing between forests and shrublands, which may explain the 18 patterns of variation in space and time in the abundance of blackcaps in this area, and 19 supports the view that inequalities may arise among migrants with the same origin but 20 wintering in different habitats. Such inequalities might carry over into other stages of 21 blackcaps’ life cycle contributing to the regulation of its migratory population

Maternal Genetic Structure Reveals an Incipient Differentiation in the Canary Islands Chiffchaff Phylloscopus canariensis

The Canary Islands are characterised by an outstanding level of biodiversity with a high number of endemic taxa. The Canarian avifauna is no exception and six extant avian species are recognised as endemic. However, we have a limited understanding of the genetic structure of these taxa, which makes it difficult to identify conservation priorities based on the existence of unique lineages. we analysed the diversification process and demography of the Canary Islands Chiffchaff Phylloscopus canariensis using two mitochondrial genes (cytochrome b and cytochrome oxidase subunit I). Although the species colonised the Canary Islands during the early Pleistocene, our results suggest a recent process of differentiation, which ran in parallel to the Last Glacial Maximum. Chiffchaffs from Gran Canaria emerge as a unique lineage since none of the haplotypes found on this island were recorded anywhere else in the archipelago. Our findings suggest a process of divergence according to the gradual colonisation and subsequent isolation of nearby islands. Demographic results show a stable trend of Chiffchaff populations until the colonisation of Gran Canaria (ca. 15,000 years ago), where the species significantly increased its effective population size. Nowadays, the effective population size of the Canary Islands Chiffchaff is stable, which highlights the ability of Chiffchaffs to adapt to local disturbances related to human activities. Overall, our results provide a scenario of incipient differentiation of the Canary Islands Chiffchaff and, importantly, underscore once more the role of Gran Canaria in driving speciation processes in this archipelago

The evolutionary history and genomics of European blackcap migration

Seasonal migration is a taxonomically widespread behaviour that integrates across many traits. The European blackcap exhibits enormous variation in migration and is renowned for research on its evolution and genetic basis. We assembled a reference genome for blackcaps and obtained whole genome resequencing data from individuals across its breeding range. Analyses of population structure and demography suggested divergence began ~30,000 ya, with evidence for one admixture event between migrant and resident continent birds ~5000 ya. The propensity to migrate, orientation and distance of migration all map to a small number of genomic regions that do not overlap with results from other species, suggesting that there are multiple ways to generate variation in migration. Strongly associated single nucleotide polymorphisms (SNPs) were located in regulatory regions of candidate genes that may serve as major regulators of the migratory syndrome. Evidence for selection on shared variation was documented, providing a mechanism by which rapid changes may evolve