59 research outputs found

    Population genomics of a critically endangered data-deficient elasmobranch, the blue skate Dipturus batis

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    Doctoral thesis (PhD) - Nord University, 2021publishedVersio

    Phylogenomic systematics, bioacoustics, and morphology of frogs from Madagascar reveals that background noise drives the evolution of high frequency acoustic signaling

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    Madagascar is considered a globally important biodiversity hotspot, having some of the highest rates of species endemism in the world and has been the focus of substantial effort from researchers to understand the evolution of its distinctive biota. This is especially true for frogs, where the microcontinent hosts an impressively diverse amphibian fauna totaling over 500 species, where a large amount of this diversity has only been described relatively recently. Much of this accelerated taxonomic progress can be attributed to the combination of DNA barcoding and the widespread application of bioacoustics enabling more efficient species identification and characterization of new lineages. The availability of bioacoustic data for the majority of species has revealed the incredible diversity of acoustic signals in Malagasy frogs; despite the incredible acoustic diversity in Madagascar, explanations for the evolution of distinct advertisement calls have been little explored. Acoustic signaling is important to frogs because it is the primary mechanism of communication and mate selection and therefore it is expected that acoustic communication and factors that drive variation in acoustic signals should be under strong selection. Frogs from the most species-rich genus Boophis from the family Mantellidae in Madagascar communicate acoustically during a rainy and short breeding season and aggregate around water bodies in high abundance making Boophis an ideal model system to address the evolution of advertisement calls. A potential explanation for signal diversity is the acoustic adaptation hypothesis, which predicts that natural and sexual selection drive optimization of signal transmission and perception across different habitats. In many organisms, the efficiency of acoustic signal transmission can be affected by habitat structure or background noise. One prediction of the acoustic adaptation hypothesis is that environmental ambient noise, which is the background level of sound in the environment, will drive signal evolution if the noise is sufficiently similar and lessens the receiver’s perception of the signal. Because Boophis reproduce near water bodies and most often in stream habitats that might be noisy from the sound of rushing water, they present an excellent system to address acoustic interference. In Chapter 1, I describe a new species of Boophis that is morphologically cryptic with its sister species but differs remarkably in advertisement call, which underlines the importance of call variation in the genus. To contribute to the taxonomic progress and integration of bioacoustic data, I describe a new species of Boophis by using these multiple lines of evidence and also suggesting future research to understand the evolution of advertisement calls in the genus. I also develop the acoustic analysis pipeline used for acquiring frequency traits from thousands of calls rapidly, where these methods will be used in Chapter 5. In this study, I also suggest that reproductive character displacement could be driving divergence in advertisement calls and that other important factors from the environment could lead to broad patterns in the evolution of advertisement calls. In Chapter 2, to understand signal evolution across a broad range of taxa, a strongly supported phylogenetic hypothesis is needed and I estimate a new multi-locus phylogeny using Sanger sequencing. The systematics of frogs from the family Mantellidae have had a long and turbulent history where Mantellidae was considered a family relatively recently. In Boophis tree frogs, early researchers considered them as belonging to the Asian genus Rhacophorus because of their strong similarities and breeding habitat in water bodies. Furthermore, despite the numerous works that contributed to understanding the molecular phylogeny of Boophis many aspects of their evolutionary relationships remain insufficiently supported and a complete Sanger multi-locus phylogeny had not been estimated. For understanding the relationships among Boophis frogs, I estimated a multi-locus phylogeny from eight Sanger markers that includes as much diversity as possible. Despite these efforts, I could not adequately support the phylogenetic relationships among Boophis taxa and adding additional Sanger markers would not be likely to resolve these relationships. In Chapter 3 I aim to expand upon this dataset and develop a new sequencing technology to obtain thousands of markers affordably. The widespread use of high-throughput sequencing technologies to sequence large portions of organisms’ genome has led to new and exciting challenges and questions that can be addressed with the massive increase in sequence data these new methods provide. The objective of sequence capture is to sequence genomic regions typically through hybridization-based capture from a previously designed set of known markers and benefits from the potential to acquire markers that are useful at all evolutionary time-scales. Therefore, I developed a sequence capture probe set called FrogCap to sequence ~15,000 genomic markers that can be used across the entire frog radiation. I compare the efficacy of the probe set on six phylogenetic scales and quantify the number of markers sequenced, depth of coverage, missing data, and parsimony informative sites, and I also compared differences between these measures across different types of data. The results from this chapter show that FrogCap is a very promising new sequence capture probe set that can be used across all frogs. In Chapter 4 I test the effectiveness of FrogCap by addressing the systematics of frogs from the family Mantellidae, by comparing the FrogCap sequence capture results to those from transcriptomes. The phylogeny of Mantellidae remains unresolved and contentious, where the phylogenetic relationships among subfamilies and genera are not well delimited. Prior to this it was thought the different groups in Madagascar were non-monophyletic and were thought to be from several different families. I address the weak phylogenetic support and also test the FrogCap probe set on Mantellidae frogs, comparing the probe set to transcriptomic sequencing of samples from the same groups. I find that both FrogCap and transcriptomes work similarly well for resolving these difficult and contentious relationships. FrogCap sequence capture also provided several advantages over the transcriptomic data; FrogCap sequences non-protein coding markers from across the genome, such that these other types of markers could be useful by providing sequence data from potentially neutrally evolving genomic regions and also can serve as another line of phylogenetic evidence when compared to other data types. Transcriptomes also provide advantages through a larger amount of sequence data and lesser gene discordance because the transcriptomes are much longer and thus providing more resolution than shorter markers. I find that the FrogCap probe set is an effective tool at disentangling difficult phylogenetic problems, and that transcriptomic sequencing is less effective for phylogenetics. In Chapter 5, I estimate a new phylogeny for Boophis tree frogs using the FrogCap probe set and address whether acoustic interference leads to the evolution of higher frequency advertisement calls in Boophis frogs. I integrate an unprecedented dataset incorporating data collected from all previous chapters which includes a massive dataset of 300+ acoustic recordings from nearly every species in the genus, a new Boophis time-calibrated phylogeny using a backbone of ~15,000 genomic markers acquired from the sequence capture data combined with the data from Chapter 2 for full species sampling and used soft tissue computed tomography on 28 species to acquire detailed morphological information from the larynges of males. After finding that the sequence capture dataset provides strong statistical support for nearly every node in the tree, I time-calibrate the phylogeny and test the acoustic adaptation hypothesis. I find that Boophis tree frogs are evolving higher frequency acoustic signals in loud stream habitats, which is supported after correcting for body size. These results are further evidenced by laryngeal measurements from the CT Scans, where I find that loud stream frog laryngeal morphology is decoupled from the predicted relationship to body size that is found in quiet stream frogs

    Microbiota & infertility: microorganisms and immune factors in the idiopathic infertility

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    In the present work, the possible relationship between the idiopathic infertility, the alteration of the vaginal microbiota and that of the local immune response is investigated. The next-generation Ion Torrent PGM sequencing platform allowed the survey of the vaginal microbial composition, while the Luminex assay permitted the dosage of the soluble local immune mediators. After the analysis, the women affected by idiopathic infertility showed a vaginal microbiota similar to that of women affected by bacterial vaginosis (Chapter 1) and, especially, to those women who belong to the Intermediate group (Chapter 2). Among Lactobacilli, L. iners, crispatus and gasseri have a peculiar pattern in women affected by idiopathic infertility. Furthermore, secondary players such as A. vaginae, P. bivia, U. parvum, and E. fergusonii contribute to the affected microbiome. Simultaneously, an altered immune response is detected in the vaginal niche of the Idiopathic group

    Population and seascape genomics of a critically endangered benthic elasmobranch, the blue skate Dipturus batis

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    The blue skate (Dipturus batis) has a patchy distribution across the North-East Atlantic Ocean, largely restricted to occidental seas around the British Isles following fisheries-induced population declines and extirpations. The viability of remnant populations remains uncertain, and could be impacted by continued fishing and bycatch pressure and the projected impacts of climate change. We genotyped 503 samples of D. batis, obtained opportunistically from the widest available geographic range, across 6,350 single nucleotide polymorphisms (SNPs) using a reduced-representation sequencing approach. Genotypes were used to assess the species’ contemporary population structure, estimate effective population sizes, and identify putative signals of selection in relation to environmental variables using a seascape genomics approach. We identified genetic discontinuities between inshore (British Isles) and offshore (Rockall and Faroe Island) populations, with differentiation most pronounced across the deep waters of the Rockall Trough. Effective population sizes were largest in the Celtic Sea and Rockall, but low enough to be of potential conservation concern among Scottish and Faroese sites. Among the 21 candidate SNPs under positive selection was one significantly correlated with environmental variables predicted to be affected by climate change, including bottom temperature, salinity, and pH. The paucity of well annotated elasmobranch genomes precluded us from identifying a putative function for this SNP. Nevertheless, our findings suggest that climate change could inflict a strong selective force upon remnant populations of D. batis, further constraining its already restricted habitat. Furthermore, the results provide fundamental insights on the distribution, behaviour, and evolutionary biology of D. batis in the North-East Atlantic that will be useful for the establishment of conservation actions for this and other critically endangered elasmobranchs

    Small business innovation research. Abstracts of 1988 phase 1 awards

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    Non-proprietary proposal abstracts of Phase 1 Small Business Innovation Research (SBIR) projects supported by NASA are presented. Projects in the fields of aeronautical propulsion, aerodynamics, acoustics, aircraft systems, materials and structures, teleoperators and robots, computer sciences, information systems, data processing, spacecraft propulsion, bioastronautics, satellite communication, and space processing are covered

    Distribution, social structure and habitat use of short-finned pilot whale, Globicephala macrorhynchus, in the Canary Islands

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    The Canary Archipelago is considered one of the planet’s biodiversity hotspots and the short-finned pilot whale is a key species in need of conservation measures. To address a lack of knowledge, almost 2,000 day-surveys were conducted (1999-2012) resulting in 1,094 short-finned pilot whale sightings. The species was recorded year-round and distributed non-uniformly around the archipelago, with greater densities concentrated in patchy areas mainly on the leeward side of the main islands. A total of 1,320 well-marked individuals were identified, which exhibited a large degree of variability in site fidelity (from core residents to transients). Evidence of an island-associated sub-population and a transient one was found. Longitudinal data were used to infer population structure and estimate abundance, while a spatial modelling approach was used to study spatio-temporal patterns in habitat use, distribution and abundance. Spatial modelling revealed habitat preferences in areas between depths of 1000m and 1500m, and higher densities in the south-west of Tenerife and La Gomera (117 short-finned pilot whales recaptured within the two islands). Abundance of 1,980 individuals (CV = 0.33, 95% CI=1,442 – 2,324) was estimated for the entire archipelago, with higher density predicted during the summer months. Mark-recapture analysis estimated 636 resident individuals (CV = 0.028, 95% CI=602 - 671) in the southwest waters of Tenerife between 2007 and 2009. The social and temporal analyses of the behavioural relationships between pairs of individuals revealed a well-differentiated society with long-lasting and non-random social structure built of constant companions. A hierarchical social system is proposed composed of a population encompassing several clans of pilot whales, each one containing several pods. Nine long-term units were identified with a high degree of association (0.62 - 0.83). This study, the first to provide combined results on distribution, habitat use, and social structure of the species, provides essential information towards the development of recommendations for much needed conservation measures

    Tephrochronology and its application: A review

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    Tephrochronology (from tephra, Gk ‘ashes’) is a unique stratigraphic method for linking, dating, and synchronizing geological, palaeoenvironmental, or archaeological sequences or events. As well as utilising the Law of Superposition, tephrochronology in practise requires tephra deposits to be characterized (or ‘fingerprinted’) using physical properties evident in the field together with those obtained from laboratory analyses. Such analyses include mineralogical examination (petrography) or geochemical analysis of glass shards or crystals using an electron microprobe or other analytical tools including laser-ablation-based mass spectrometry or the ion microprobe. The palaeoenvironmental or archaeological context in which a tephra occurs may also be useful for correlational purposes. Tephrochronology provides greatest utility when a numerical age obtained for a tephra or cryptotephra is transferrable from one site to another using stratigraphy and by comparing and matching inherent compositional features of the deposits with a high degree of likelihood. Used this way, tephrochronology is an age-equivalent dating method that provides an exceptionally precise volcanic-event stratigraphy. Such age transfers are valid because the primary tephra deposits from an eruption essentially have the same short-lived age everywhere they occur, forming isochrons very soon after the eruption (normally within a year). As well as providing isochrons for palaeoenvironmental and archaeological reconstructions, tephras through their geochemical analysis allow insight into volcanic and magmatic processes, and provide a comprehensive record of explosive volcanism and recurrence rates in the Quaternary (or earlier) that can be used to establish time-space relationships of relevance to volcanic hazard analysis. The basis and application of tephrochronology as a central stratigraphic and geochronological tool for Quaternary studies are presented and discussed in this review. Topics covered include principles of tephrochronology, defining isochrons, tephra nomenclature, mapping and correlating tephras from proximal to distal locations at metre- through to sub-millimetre-scale, cryptotephras, mineralogical and geochemical fingerprinting methods, numerical and statistical correlation techniques, and developments and applications in dating including the use of flexible depositional age-modelling techniques based on Bayesian statistics. Along with reference to wide-ranging examples and the identification of important recent advances in tephrochronology, such as the development of new geoanalytical approaches that enable individual small glass shards to be analysed near-routinely for major, trace, and rare-earth elements, potential problems such as miscorrelation, erroneous-age transfer, and tephra reworking and taphonomy (especially relating to cryptotephras) are also examined. Some of the challenges for future tephrochronological studies include refining geochemical analytical methods further, improving understanding of cryptotephra distribution and preservation patterns, improving age modelling including via new or enhanced radiometric or incremental techniques and Bayesian-derived models, evaluating and quantifying uncertainty in tephrochronology to a greater degree than at present, constructing comprehensive regional databases, and integrating tephrochronology with spatially referenced environmental and archaeometric data into 3-D reconstructions using GIS and geostatistics

    Spatial and temporal population genetics of Swiss red foxes (Vulpes vulpes) following a rabies epizootic

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    Infectious disease can affect the demography of natural populations and, as a consequence, can alter the genetic variation within and between those populations. This study investigated long-term effects of rabies-induced mortality on the demography and genetic variation in two Swiss red fox populations over ten to fourteen generations. In Switzerland, the last rabies epizootic persisted from 1967 to 1999 and was continuously monitored by collecting fox carcasses throughout the country. Alongside records of rabies tests and post-mortem data, tooth samples were systematically archived for ageing. In this study, DNA from 666 individual teeth was extracted. For 279 extracts, the concentration of nuclear DNA was estimated in a quantitative PCR and found to be negatively correlated with storage time. After excluding samples with insufficient DNA concentration for reliable genotyping, 382 samples were screened using between nine and seventeen canine and red fox specific microsatellites. Tooth samples were combined with 189 modern tissue samples. By assessing the age structure continuously throughout and after the rabies epizootic for the first population, population census size and age structure were found to be altered by the high rabies-induced mortality. In contrast, no long-term trends in genetic diversity were identified although a high variation of Ho, He, F s was discovered both in short-term and longer-term. A strong isolation-by-distance pattern was revealed for the second population by comparing individual pairwise genetic with spatial distances using modern samples. Furthermore, genetic data demonstrated that dispersal was sex-biased and diverted by the topography of the landscape. When investigating isolation-by-distance patterns within the same population in 1971-73 and 1982-84 at lower population densities, density-dependant dispersal was observed. In conclusion, this study revealed no loss of genetic diversity in red foxes following a rabies epizootic despite a population bottleneck, yet highlights population density as an important factor to determine local spatial genetic structure.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

    Spatial and temporal population genetics of Swiss red foxes (Vulpes vulpes) following a rabies epizootic

    Get PDF
    Infectious disease can affect the demography of natural populations and, as a consequence, can alter the genetic variation within and between those populations. This study investigated long-term effects of rabies-induced mortality on the demography and genetic variation in two Swiss red fox populations over ten to fourteen generations. In Switzerland, the last rabies epizootic persisted from 1967 to 1999 and was continuously monitored by collecting fox carcasses throughout the country. Alongside records of rabies tests and post-mortem data, tooth samples were systematically archived for ageing. In this study, DNA from 666 individual teeth was extracted. For 279 extracts, the concentration of nuclear DNA was estimated in a quantitative PCR and found to be negatively correlated with storage time. After excluding samples with insufficient DNA concentration for reliable genotyping, 382 samples were screened using between nine and seventeen canine and red fox specific microsatellites. Tooth samples were combined with 189 modern tissue samples. By assessing the age structure continuously throughout and after the rabies epizootic for the first population, population census size and age structure were found to be altered by the high rabies-induced mortality. In contrast, no long-term trends in genetic diversity were identified although a high variation of Ho, He, F s was discovered both in short-term and longer-term. A strong isolation-by-distance pattern was revealed for the second population by comparing individual pairwise genetic with spatial distances using modern samples. Furthermore, genetic data demonstrated that dispersal was sex-biased and diverted by the topography of the landscape. When investigating isolation-by-distance patterns within the same population in 1971-73 and 1982-84 at lower population densities, density-dependant dispersal was observed. In conclusion, this study revealed no loss of genetic diversity in red foxes following a rabies epizootic despite a population bottleneck, yet highlights population density as an important factor to determine local spatial genetic structure.EThOS - Electronic Theses Online ServiceGBUnited Kingdo
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