Signal set tissue systems and overlapping localities

Algorithms and the Foundations of Software technolog

Field methods for rodent studies in Asia and the Indo-Pacific

Farm Management,

Divergent evolutionary processes associated with colonization of offshore islands

Peer reviewedPublisher PD

Genetic alterations and cancer formation in a European flatfish at sites of different contamination burdens

Fish diseases are an indicator for marine ecosystem health since they provide a biological end-point of historical exposure to stressors. Liver cancer has been used to monitor the effects of exposure to anthropogenic pollution in flatfish for many years. The prevalence of liver cancer can exceed 20%. Despite the high prevalence and the opportunity of using flatfish to study environmentally induced cancer, the genetic and environmental factors driving tumor prevalence across sites are poorly understood. This study aims to define the link between genetic deterioration, liver disease progression, and anthropogenic contaminant exposures in the flatfish dab (Limanda limanda). We assessed genetic changes in a conserved cancer gene, Retinoblastoma (Rb), in association with histological diagnosis of normal, pretumor, and tumor pathologies in the livers of 165 fish from six sites in the North Sea and English Channel. The highest concentrations of metals (especially cadmium) and organic chemicals correlated with the presence of tumor pathology and with defined genetic profiles of the Rb gene, from these sites. Different Rb genetic profiles were found in liver tissue near each tumor phenotype, giving insight into the mechanistic molecular-level cause of the liver pathologies. Different Rb profiles were also found at sampling sites of differing contaminant burdens. Additionally, profiles indicated that histological “normal” fish from Dogger sampling locations possessed Rb profiles associated with pretumor disease. This study highlights an association between Rb and specific contaminants (especially cadmium) in the molecular etiology of dab liver tumorigenesis

Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation

Natural selection often produces parallel phenotypic changes in response to a similar adaptive challenge. However, the extent to which parallel gene expression differences and genomic divergence underlie parallel phenotypic traits and whether they are decoupled or not remains largely unexplored. We performed a population genomic study of parallel ecological adaptation among replicate ecotype pairs of the rough periwinkle (Littorina saxatilis) at a regional geographical scale (NW Spain). We show that genomic changes underlying parallel phenotypic divergence followed a complex pattern of both repeatable differences and of differences unique to specific ecotype pairs, in which parallel changes in expression or sequence are restricted to a limited set of genes. Yet, the majority of divergent genes were divergent either for gene expression or coding sequence, but not for both simultaneously. Overall, our findings suggest that divergent selection significantly contributed to the process of parallel molecular differentiation among ecotype pairs, and that changes in expression and gene sequence underlying phenotypic divergence could, at least to a certain extent, be considered decoupled processesMinisterio de Economía y Competitividad | Ref. BFU2013- 44635-PMinisterio de Economía y Competitividad | Ref. CGL2016-75482-PMinisterio de Economía y Competitividad | Ref. CGL2016-75904-C2-1Xunta de Galicia | Ref. ED431C 2016-037Xunta de Galicia | Ref. INCITE09 310 006 PRSwedish Research Councils VR | Ref. Linnaeus grant Formas 217-2008-171

ECOLOGICAL, PHENOTYPIC AND GENETIC DIVERSIFICATION IN Oophaga POISON FROGS

Despite the incredible diversity of lowland tropical rainforests; we still have limited understanding of the drivers of speciation in these ecoregions. In these difficult-to-access habitats that maintain a significant reservoir of the world’s biodiversity, it is widely accepted that a vast amount of species would remain undescribed and that some of them will likely go extinct before they have a chance to be properly described and studied. The present work studies the ecological, phenotypic and genetic diversification of Neotropical Harlequin poison frogs of the genus Oophaga, a group of organisms where a perplexing variation in colouration and patterns have led to taxonomic uncertainty. First, in order to investigate the relative contribution of geographical and environmental factors to the diversification of these frogs, I combined phylogenetic methods with detailed geographic data and environmental niche modelling (ENM) to test the role of geographic isolation, climatic niche divergence and altitudinal gradients. Overall, my results suggested that speciation along climatic gradients on a structured landscape has been a major evolutionary force behind the diversification of Oophaga poison frogs. Second, by using an integrative taxonomy framework and different lines of evidence derived from environmental data and intrinsic biological attributes (phenotypic variation, genetics), I statistically tested competing lineage-boundary hypothesis within the currently known Oophaga histrionica species. I found that diversity within the complex has been underestimated and proposed the existence of at least three independent evolutionary lineages of Oophaga poison frogs that should be further studied as they potentially represent new species to science. These results have important conservation implications as some of its members are considered amongst the most endangered species of all amphibians. Third, I hypothesized that the genes, pathways, and/ or gene networks potentially associated with colouration, alkaloid metabolism, transport and storage, should be highly expressed in skin tissue. Then, by taking advantage of the high coverage offered by Next Generation sequencing (NGS), I investigated the common transcriptional profiles of five Oophaga lineages. To my knowledge, this represent the first transcriptome dataset for Dendrobatid frogs where a functional annotation and comparative analyses allowed the identification of potential candidate genes in important adaptive traits. The identification of more than 250 orthologous contigs across lineages allowed testing the current phylogenetics hypothesis for this group. Overall, in this part of my work I provide an important molecular resource not only for the study of aposematism within Dendrobatids but for the future assembling and annotation of Dendrobatid genomes. Finally, Harlequin poison frogs represent an excellent group, yet underexplored, to study the ultracellular structural basis of colour variation and the role of candidate genes in colour variation. In this final part of my dissertation, I report the basis of histological-cellular components of colouration and provide initial hypothesis of the functional effect of mutations at the Melanocortin-1 receptor gene (MC1R) and the genetic mechanisms of colour variation in this frogs. One of the most interesting findings was the observation of similar phenotypes appearing independently in nature as a consequence of different mutations of the same gene, a classical example of convergent phenotypic evolution and genetic repeatability. Broadly, I provided evidence to suggest that variation at the MC1R receptor could potentially be a major factor responsible for the high phenotypic variation of aposematic signals of Harlequin poison frogs

Pheromones in Heliconius butterflies: Chemical ecology, genetics, and behaviour

Sex pheromones are chemical signals that mediate communication between males and females of a species and are important for mating. They have been well-studied in female moths, where females release volatile compounds to attract males over long distances. Butterflies fly during the day and were thought to rely more on vision. However, male pheromones in butterflies have also been described but have rarely been studied to the same detail as the female pheromones of night-flying moths. The Neotropical butterflies, Heliconius, have a long history of ecological and genetic studies. Mate choice trials have focused on male preference for female colour pattern. In addition, two types of pheromone have been described in Heliconius. The first is produced by a region of the wing known as the androconia, and the second is anti-aphrodisiac, transferred from male genitals to females during mating to prevent re-mating by the female. In this thesis I investigate the role of chemical signalling in mate choice of Heliconius. I describe sexual dimorphism in wing scale morphology and androconial chemical profile of H. melpomene. I demonstrate the importance of male chemical signalling for female choice in this and other Heliconius species. Male pheromones in other groups can convey information about mate quality. I show that larval but not adult diet affects the production of only minor components of the male pheromone. This suggests that male signalling cannot convey information about adult diet quality but could reflect larval diet. I survey variation in pheromone components across the broad geographic range of several species. I show that this provides a useful approach to identify biologically active components, which we expect to be species-specific over a large geographic range. There is also considerable interest in understanding the genetic basis for adaptive traits, and pheromones provide a tractable system for such studies. I uncover the genetic basis for anti-aphrodisiac production in H. melpomene through genetic mapping and use in-vitro assays for enzymatic activity to identify a novel terpene synthase activity in a gene family not previously known for this role. This finding suggests that terpene synthesis has evolved independently multiple times in insects. The work presented in this thesis is one of the first studies integrating both chemical ecology and genetics in butterflies. By combining behavioural, genetic and chemical studies, we can understand not only the composition of the chemical profile of individuals and species, but also their function and evolution

Taxonomy, Species Limits, and Phylogenetic Relationships of Anoura Gray 1838 (Chiroptera: Phyllostomidae)

This dissertation addresses several aspects of the diversity and species limits in the nectarivorous bat genus Anoura Gray 1838(Chiroptera: Glossophaginae). Based on morphometric approaches, the current taxonomic arrangement for Anoura includes 8 to 10 species; however, previous taxonomic revisions did not include all closely related species in the genus. In Chapter 1, I investigate the identity of Anoura carishina and its position in the morphospace of the large-bodied Anoura using craniodental and external variables. I analyze traits thought to be diagnostic for these species, including 1) an elliptical Fourier transformation analysis of the shape of the third upper premolar (P4); 2) a comparison of the area of the second (P3) and third (P4) upper premolars; and 3) a comparison of maxillary toothrow angles. I find that A. carishina is morphologically indistinguishable from A. latidens, and that there is broad overlap in morphology between A. latidens and the A. geoffroyi species complex. Overall, results suggest that a stable taxonomy for the group should consider A. carishina as a junior synonym of A. latidens, and that A. latidens is distinguishable from A. geoffroyi. In Chapter 2, I study the species limits of Anourafrom a statistical perspective, based on characters that were generally used to describe species in the genus. I use Gaussian Mixture Models in order to find groups among 581 individual specimens in the phenotypic space defined by 12 cranial and 11 external morphological characters. The morphometric analyses using Gaussian Mixture Models do not support a clear separation within either large-bodied or small-bodied Anoura species. In Chapter 3, I address the phylogenetic relationships within Anoura by sequencing ultraconserved elements (UCEs) and inferring species trees under quartet-based methods and multispecies coalescent models. Phylogenetic analyses obtained four main well-supported clades supporting the monophyly of the proposed large- and small-bodied species complexes within Anoura, the monotypic status of A. caudifer, and the invalidation of A. aequatoris and A. peruana as independent species. This dissertation presents a thorough taxonomic revision, providing a dichotomous key and the most complete phylogenetic hypothesis to date for Anoura

Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring

<p>Abstract</p> <p>Background</p> <p>The rapid and accurate identification of species is a critical component of large-scale biodiversity monitoring programs. DNA arrays (micro and macro) and DNA barcodes are two molecular approaches that have recently garnered much attention. Here, we compare these two platforms for identification of an important group, the mammals.</p> <p>Results</p> <p>Our analyses, based on the two commonly used mitochondrial genes cytochrome <it>c </it>oxidase I (the standard DNA barcode for animal species) and cytochrome b (a common species-level marker), suggest that both arrays and barcodes are capable of discriminating mammalian species with high accuracy. We used three different datasets of mammalian species, comprising different sampling strategies. For DNA arrays we designed three probes for each species to address intraspecific variation. As for DNA barcoding, our analyses show that both cytochrome <it>c </it>oxidase I and cytochrome b genes, and even smaller fragments of them (mini-barcodes) can successfully discriminate species in a wide variety of specimens.</p> <p>Conclusion</p> <p>This study showed that DNA arrays and DNA barcodes are valuable molecular methods for biodiversity monitoring programs. Both approaches were capable of discriminating among mammalian species in our test assemblages. However, because designing DNA arrays require advance knowledge of target sequences, the use of this approach could be limited in large scale monitoring programs where unknown haplotypes might be encountered. DNA barcodes, by contrast, are sequencing-based and therefore could provide more flexibility in large-scale studies.</p

Recurrent allopolyploidizations diversify ecophysiological traits in marsh orchids (Dactylorhiza majalis s.l.).

Whole-genome duplication has shaped the evolution of angiosperms and other organisms, and is important for many crops. Structural reorganization of chromosomes and repatterning of gene expression are frequently observed in allopolyploids, with physiological and ecological consequences. Recurrent origins from different parental populations are widespread among polyploids, resulting in an array of lineages that provide excellent models to uncover mechanisms of adaptation to divergent environments in early phases of polyploid evolution. We integrate here transcriptomic and ecophysiological comparative studies to show that sibling allopolyploid marsh orchid species (Dactylorhiza, Orchidaceae) occur in different habitats (low nutrient fens vs. meadows with mesic soils) and are characterized by a complex suite of intertwined, pronounced ecophysiological differences between them. We uncover distinct features in leaf elemental chemistry, light-harvesting, photoprotection, nutrient transport and stomata activity of the two sibling allopolyploids, which appear to match their specific ecologies, in particular soil chemistry differences at their native sites. We argue that the phenotypic divergence between the sibling allopolyploids has a clear genetic basis, generating ecological barriers that maintain distinct, independent lineages, despite pervasive interspecific gene flow. This suggests that recurrent origins of polyploids bring about a long-term potential to trigger and maintain functional and ecological diversity in marsh orchids and other groups