Molecular gut content analysis of different spider body parts

Molecular gut-content analysis has revolutionized the study of food webs and feeding interactions, allowing the detection of prey DNA within the gut of many organisms. However, successful prey detection is a challenging procedure in which many factors affect every step, starting from the DNA extraction process. Spiders are liquid feeders with branched gut diverticula extending into their legs and throughout the prosoma, thus digestion takes places in different parts of the body and simple gut dissection is not possible. In this study, we investigated differences in prey detectability in DNA extracts from different parts of the spider's body: legs, prosoma and opisthosoma, using prey-specific PCR and metabarcoding approaches. We performed feeding trials with the woodlouse hunter spider Dysdera verneaui Simon, 1883 (Dysderidae) to estimate the time at which prey DNA is detectable within the predator after feeding. Although we found that all parts of the spider body are suitable for gut-content analysis when using prey-specific PCR approach, results based on metabarcoding suggested the opisthosoma is optimal for detection of predation in spiders because it contained the highest concentration of prey DNA for longer post feeding periods. Other spiders may show different results compared to D. verneaui, but given similarities in the physiology and digestion in different families, it is reasonable to assume this to be common across species and this approach having broad utility across spiders.Peer reviewe

A DNA barcode-assisted annotated checklist of the spider (Arachnida, Araneae) communities associated to white oak woodlands in Spanish National Parks

Background: A large scale semi-quantitative biodiversity assessment was conducted in white oak woodlands in areas included in the Spanish Network of National Parks, as part of a project aimed at revealing biogeographic patterns and identify biodiversity drivers. The semiquantitative COBRA sampling protocol was conducted in sixteen 1-ha plots across six national parks using a nested design. All adult specimens were identified to species level based on morphology. Uncertain delimitations and identifications due to either limited information of diagnostic characters or conflicting taxonomy were further investigated using DNA barcode information. New information: We identified 376 species belonging to 190 genera in 39 families, from the 8,521 adults found amongst the 20,539 collected specimens. Faunistic results include the discovery of 7 new species to the Iberian Peninsula, 3 new species to Spain and 11 putative new species to science. As largely expected by environmental features, the southern parks showed a higher proportion of Iberian and Mediterranean species than the northern parks, where the Palearctic elements were largely dominant. The analysis of approximately 3,200 DNA barcodes generated in the present study, corroborated and provided finer resolution to the morphologically based delimitation and identification of specimens in some taxonomically challenging families. Specifically, molecular data confirmed putative new species with diagnosable morphology, identified overlooked lineages that may constitute new species, confirmed assignment of specimens of unknown sexes to species and identified cases of misidentifications and phenotypic polymorphisms

Genomic divergence along the continuum of speciation in a recent evolutionary radiation of montane grasshoppers

[eng] Unraveling the proximate processes that have shaped genetic variation of populations and led to lineage diversification and speciation is fundamental to understand the origin of present-day biodiversity patterns at both local and global scales. Cyclical Pleistocene glaciations played a pivotal role in the evolution of mid-latitude montane biotas, leading to distributional shifts that generated multiple opportunities for both allopatric speciation and secondary contact. In this thesis, we integrate genomic, morphological and environmental data and combine a diverse array of analytical procedures to investigate processes of genomic and phenotypic divergence acting at different stages along the speciation continuum. Specifically, this thesis focuses on the subgenus Dreuxius (genus Omocestus), an lbero-Maghrebian complex of montane grasshoppers distributed across the main mountain ranges of the region. Phylogenomic and geometric morphometric analyses supported the recent Pleistocene origin (< 1 Ma) of the complex, two reticulation events involving lineages at different stages ·of the· diversification continuum and the phenotypic distinctiveness of most sister taxa (Chapter 1). Moreover, phylogenetic reconstructions did not recover the reciprocal monophyly of taxa from Iberia and northwestern Africa, supporting two overseas Pleistocene migration events between the two continents (Chapter 1). lntegrative species delimitation analyses focusing on the Pyrenean endemics O. navasi and O. antigai did not support their current taxonomic status, pointing to the presence of a single species with little phenotypic variation, a wide climatic niche, and a marked genetic structure explained by limited population connectivity across the abrupt landscapes of the region (Chapter 2). Analyses of interspecific gene flow in the partially sympatric O. minutissimus and O. uhagonii rejected the hypothesis of contemporary hybridization but revealed past introgression in the area where the distributions of the two species overlap (Chapters 1 and 3). This supports a scenario of historical gene flow after secondary contact followed by the evolution of reproductive isolation that currently prevents hybridization among sympatric populations (Chapter 3). Demographic inference and testing of alternative models of intraspecific gene flow within each of the narrow-endemics O. bolivari and O. femoralis supported population genetic admixture during glacial periods and postglacial colonization of sky islands, rather than long-term isolation, as the scenario best explaining the contemporary distribution of genomic variation in the two taxa. The results of this thesis emphasize the key role of range-shifts driven by Pleistocene glacial cycles in promoting not only allopatric divergence but also secondary contact and genetic admixture among previously isolated gene pools. Overall, this thesis highlights the importance of combining population and phylogenomic approaches to improve our understanding about the processes governing the diversification of montane biotas across evolutionary scales spanning the continuum of speciation, from populations to species

Glacial connectivity and current population fragmentation in sky islands explain the contemporary distribution of genomic variation in two narrow-endemic montane grasshoppers from a biodiversity hotspot

Aim: Cold-adapted biotas from mid-latitudes often show small population sizes, harbour low levels of local genetic diversity and are highly vulnerable to extinction due to ongoing climate warming and the progressive shrinking of montane and alpine ecosystems. In this study, we use a suite of analytical approaches to infer the demographic processes that have shaped contemporary patterns of genomic variation in Omocestus bolivari and Omocestus femoralis, two narrow-endemic and red-listed Iberian grasshoppers forming highly fragmented populations in the sky island archipelago of the Baetic System. Location: South-eastern Iberia. Methods: We quantified genomic variation in the two focal taxa and coupled ecological niche models and a spatiotemporally explicit simulation approach based on coalescent theory to determine the relative statistical support of a suite of competing demographic scenarios representing contemporary population isolation (i.e. a predominant role of genetic drift) versus historical connectivity and post-glacial colonization of sky islands (i.e. pulses of gene flow and genetic drift linked to Pleistocene glacial cycles). Results: Inference of spatial patterns of genetic structure, environmental niche modelling and statistical evaluation of alternative species-specific demographic models within an approximate Bayesian computation framework collectively supported genetic admixture during glacial periods and post-glacial colonization of sky islands, rather than long-term population isolation, as the scenario best explaining the current distribution of genomic variation in the two focal taxa. Moreover, our analyses revealed that isolation in sky islands has also led to extraordinary genetic fragmentation and contributed to reduce local levels of genetic diversity. Main conclusions: This study exemplifies the potential of integrating genomic and environmental niche modelling data across biological and spatial replicates to determine whether organisms with similar habitat requirements have experienced concerted/idiosyncratic responses to Quaternary climatic oscillations, which can ultimately help to reach more general conclusions about the vulnerability of mountain biodiversity hotspots to ongoing climate warmingPeer reviewe

Genomic footprints of an old affair: Single nucleotide polymorphism data reveal historical hybridization and the subsequent evolution of reproductive barriers in two recently diverged grasshoppers with partly overlapping distributions

Secondary contact in close relatives can result in hybridization and the admixture of previously isolated gene pools. However, after an initial period of hybridization, reproductive isolation can evolve through different processes and lead to the interruption of gene flow and the completion of the speciation process. Omocestus minutissimus and O. uhagonii are two closely related grasshoppers with partially overlapping distributions in the Central System mountains of the Iberian Peninsula. To analyse spatial patterns of historical and/or contemporary hybridization between these two taxa and understand how species boundaries are maintained in the region of secondary contact, we sampled sympatric and allopatric populations of the two species and obtained genome-wide single nucleotide polymorphism data using a restriction site-associated DNA sequencing approach. We used Bayesian clustering analyses to test the hypothesis of contemporary hybridization in sympatric populations and employed a suite of phylogenomic approaches and a coalescent-based simulation framework to evaluate alternative hypothetical scenarios of interspecific gene flow. Our analyses rejected the hypothesis of contemporary hybridization but revealed past introgression in the area where the distributions of the two species overlap. Overall, these results point to a scenario of historical gene flow after secondary contact followed by the evolution of reproductive isolation that currently prevents hybridization among sympatric populations

Principal component scores of morphological traits

Principal component scores (PC1 and PC2) summarizing shape variation of the different morphological traits (head, pronotum, forewing and ovopositor valve) analyzed in males and female

Raw landmark coordinates of morphological traits

This ZIP folder contains raw coordinates of landmarks used to characterize shape variation of the different morphological traits (head, pronotum, forewing and ovopositor valve) analyzed in males and females. Landmarks are stored in TPS format

CONSTRUCT input files

This ZIP folder contains the input files (genetic and geographic data) used for spatial analyses of genetic structure in CONSTRUC