Competition may explain the fine-scale spatial patterns and genetic structure of two co-occurring plant congeners

1. The spatial distribution of individual plants within a population and the population’s genetic structure are determined by several factors, like dispersal, reproduction mode or biotic interactions. The role of interspecific interactions in shaping the spatial genetic structure of plant populations remains largely unknown. 2. Species with a common evolutionary history are known to interact more closely with each other than unrelated species due to the greater number of traits they share. We hypothesize that plant interactions may shape the fine genetic structure of closely related congeners. 3. We used spatial statistics (georeferenced design) and molecular techniques (ISSR markers) to understand how two closely related congeners, Thymus vulgaris (widespread species) and T. loscosii (narrow endemic) interact at the local scale. Specific cover, number of individuals of both study species and several community attributes were measured in a 10 × 10 m plot. 4. Both species showed similar levels of genetic variation, but differed in their spatial genetic structure. Thymus vulgaris showed spatial aggregation but no spatial genetic structure, while T. loscosii showed spatial genetic structure (positive genetic autocorrelation) at short distances. The spatial pattern of T. vulgaris’ cover showed significant dissociation with that of T. loscosii. The same was true between the spatial patterns of the cover of T. vulgaris and the abundance of T. loscosii and between the abundance of each species. Most importantly, we found a correlation between the genetic structure of T. loscosii and the abundance of T. vulgaris: T. loscosii plants were genetically more similar when they were surrounded by a similar number of T. vulgaris plants. 5. Synthesis. Our results reveal spatially complex genetic structures of both congeners at small spatial scales. The negative association among the spatial patterns of the two species and the genetic structure found for T. loscosii in relation to the abundance of T. vulgaris indicate that competition between the two species may account for the presence of adapted ecotypes of T. loscosii to the abundance of a competing congeneric species. This suggests that the presence and abundance of close congeners can influence the genetic spatial structure of plant species at fine scales.

Quantifying pursuit-diving seabirds’ associations with fine-scale physical features in tidal streamenvironments

Acknowledgements James J. Waggitt was funded by a NERC Case studentship supported by OpenHydro Ltd and Marine Scotland Science (NE/J500148/1). Vessel-based transects were funded by a NERC (NE/J004340/1) and a Scottish National Heritage (SNH) grant. FVCOM modelling was funded by a NERC grant (NE/J004316/1). Marine Scotland Science provided time on the FRV Alba-na-Mara as part as the Marine Collaboration Research Forum (MarCRF). The bathymetry data used in hydrodynamic models (HI 1122 Sanday Sound to Westray Firth) was collected by the Maritime & Coastguard Agency (MCA) as part of the UK Civil Hydrography Programme. We wish to thank Christina Bristow, Matthew Finn and Jennifer Norris at the European Marine Energy Centre (EMEC); Marianna Chimienti, Ciaran Cronin, Tim Sykes and Stuart Thomas for performing vessel-based transects; Marine Scotland Science staff Eric Armstrong, Ian Davies, Mike Robertson, Robert Watret and Michael Stewart for their assistance; Shaun Fraser, Pauline Goulet, Alex Robbins, Helen Wade and Jared Wilson for invaluable discussions; Thomas Cornulier, Alex Douglas, James Grecian and Samantha Patrick for their help with statistical analysis; and Gavin Siriwardena, Leigh Torres, Mark Whittingham and Russell Wynn for their constructive comments on earlier versions of this manuscript.

Fine-scale spatial genetic correlation analyses reveal strong female philopatry within a brush-tailed rock-wallaby colony in southeast Queensland

We combine spatial data on home ranges of individuals and microsatellite markers to examine patterns of fine-scale spatial genetic structure and dispersal within a brush-tailed rock-wallaby (Petrogale penicillata) colony at Hurdle Creek Valley, Queensland. Brush-tailed rock-wallabies were once abundant and widespread throughout the rocky terrain of southeastern Australia; however, populations are nearly extinct in the south of their range and in decline elsewhere. We use pairwise relatedness measures and a recent multilocus spatial autocorrelation analysis to test the hypotheses that in this species, within-colony dispersal is male-biased and that female philopatry results in spatial clusters of related females within the colony. We provide clear evidence for strong female philopatry and male-biased dispersal within this rock-wallaby colony. There was a strong, significant negative correlation between pairwise relatedness and geographical distance of individual females along only 800 m of cliff line. Spatial genetic autocorrelation analyses showed significant positive correlation for females in close proximity to each other and revealed a genetic neighbourhood size of only 600 m for females. Our study is the first to report on the fine-scale spatial genetic structure within a rock-wallaby colony and we provide the first robust evidence for strong female philopatry and spatial clustering of related females within this taxon. We discuss the ecological and conservation implications of our findings for rock-wallabies, as well as the importance of fine-scale spatial genetic patterns in studies of dispersal behaviour.

Using JERS-1 and a DEM for regional scale mapping of the wet tropics world heritage area, Australia

Proceedings of the 11th Australasian Remote Sensing and Photogrammetry Conference

Turning Passive Detection Systems into Field Experiments: An Application Using Wetland Fishes and Enclosures to Track Fine-Scale Movement and Habitat Choice

Understanding habitat selection and movement remains a key question in behavioral ecology. Yet, obtaining a sufficiently high spatiotemporal resolution of the movement paths of organisms remains a major challenge, despite recent technological advances. Observing fine-scale movement and habitat choice decisions in the field can prove to be difficult and expensive, particularly in expansive habitats such as wetlands. We describe the application of passive integrated transponder (PIT) systems to field enclosures for tracking detailed fish behaviors in an experimental setting. PIT systems have been applied to habitats with clear passageways, at fixed locations or in controlled laboratory and mesocosm settings, but their use in unconfined habitats and field-based experimental setups remains limited. In an Everglades enclosure, we continuously tracked the movement and habitat use of PIT-tagged centrarchids across three habitats of varying depth and complexity using multiple flatbed antennas for 14 days. Fish used all three habitats, with marked species-specific diel movement patterns across habitats, and short-lived movements that would be likely missed by other tracking techniques. Findings suggest that the application of PIT systems to field enclosures can be an insightful approach for gaining continuous, undisturbed and detailed movement data in unconfined habitats, and for experimentally manipulating both internal and external drivers of these behaviors.

An evaluation of home range models for marine fish tracking and fine scale habitat use and movement patterns of age 1 Greenland cod (Gadus macrocephalus ogac)

My thesis examines fine-scale habitat use and movement patterns of age 1 Greenland cod (Gadus macrocephalus ogac) tracked using acoustic telemetry. Recent advances in tracking technologies such as GPS and acoustic telemetry have led to increasingly large and detailed datasets that present new opportunities for researchers to address fine-scale ecological questions regarding animal movement and spatial distribution. There is a growing demand for home range models that will not only work with massive quantities of autocorrelated data, but that can also exploit the added detail inherent in these high-resolution datasets. Most published home range studies use radio-telemetry or satellite data from terrestrial mammals or avian species, and most studies that evaluate the relative performance of home range models use simulated data. In Chapter 2, I used actual field-collected data from age-1 Greenland cod tracked with acoustic telemetry to evaluate the accuracy and precision of six home range models: minimum convex polygons, kernel densities with plug-in bandwidth selection and the reference bandwidth, adaptive local convex hulls, Brownian bridges, and dynamic Brownian bridges. I then applied the most appropriate model to two years (2010-2012) of tracking data collected from 82 tagged Greenland cod tracked in Newman Sound, Newfoundland, Canada, to determine diel and seasonal differences in habitat use and movement patterns (Chapter 3). Little is known of juvenile cod ecology, so resolving these relationships will provide valuable insight into activity patterns, habitat use, and predator-prey dynamics, while filling a knowledge gap regarding the use of space by age 1 Greenland cod in a coastal nursery habitat. By doing so, my thesis demonstrates an appropriate technique for modelling the spatial use of fish from acoustic telemetry data that can be applied to high-resolution, high-frequency tracking datasets collected from mobile organisms in any environment.

Direct and indirect genetic and fine-scale location effects on breeding date in song sparrows

Peer reviewed

Molecular genetics of primary open angle glaucoma and exfoliation syndrome

Glaucoma is the second leading cause of blindness worldwide. It is a group of optic neuropathies, characterized by progressive optic nerve degeneration, excavation of the optic disc due to apoptosis of retinal ganglion cells and corresponding visual field defects. Open angle glaucoma (OAG) is a subtype of glaucoma, classified according to the age of onset into juvenile and adult- forms with a cut-off point of 40 years of age. The prevalence of OAG is 1-2% of the population over 40 years and increases with age. During the last decade several candidate loci and three candidate genes, myocilin (MYOC), optineurin (OPTN) and WD40-repeat 36 (WDR36), for OAG have been identified. Exfoliation syndrome (XFS), age, elevated intraocular pressure and genetic predisposition are known risk factors for OAG. XFS is characterized by accumulation of grayish scales of fibrillogranular extracellular material in the anterior segment of the eye. XFS is overall the most common identifiable cause of glaucoma (exfoliation glaucoma, XFG). In the past year, three single nucleotide polymorphisms (SNPs) on the lysyl oxidase like 1 (LOXL1) gene have been associated with XFS and XFG in several populations. This thesis describes the first molecular genetic studies of OAG and XFS/XFG in the Finnish population. The role of the MYOC and OPTN genes and fourteen candidate loci was investigated in eight Finnish glaucoma families. Both candidate genes and loci were excluded in families, further confirming the heterogeneous nature of OAG. To investigate the genetic basis of glaucoma in a large Finnish family with juvenile and adult onset OAG, we analysed the MYOC gene in family members. Glaucoma associated mutation (Thr377Met) was identified in the MYOC gene segregating with the disease in the family. This finding has great significance for the family and encourages investigating the MYOC gene also in other Finnish OAG families. In order to identify the genetic susceptibility loci for XFS, we carried out a genome-wide scan in the extended Finnish XFS family. This scan produced promising candidate locus on chromosomal region 18q12.1-21.33 and several additional putative susceptibility loci for XFS. This locus on chromosome 18 provides a solid starting point for the fine-scale mapping studies, which are needed to identify variants conferring susceptibility to XFS in the region. A case-control and family-based association study and family-based linkage study was performed to evaluate whether SNPs in the LOXL1 gene contain a risk for XFS, XFG or POAG in the Finnish patients. A significant association between the LOXL1 gene SNPs and XFS and XFG was confirmed in the Finnish population. However, no association was detected with POAG. Probably also other genetic and environmental factors are involved in the pathogenesis of XFS and XFG.

Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the α subunit of protein kinase CK2

Hd6 is a quantitative trait locus involved in rice photoperiod sensitivity. It was detected in backcross progeny derived from a cross between the japonica variety Nipponbare and the indica variety Kasalath. To isolate a gene at Hd6, we used a large segregating population for the high-resolution and fine-scale mapping of Hd6 and constructed genomic clone contigs around the Hd6 region. Linkage analysis with P1-derived artificial chromosome clone-derived DNA markers delimited Hd6 to a 26.4-kb genomic region. We identified a gene encoding the α subunit of protein kinase CK2 (CK2α) in this region. The Nipponbare allele of CK2α contains a premature stop codon, and the resulting truncated product is undoubtedly nonfunctional. Genetic complementation analysis revealed that the Kasalath allele of CK2α increases days-to-heading. Map-based cloning with advanced backcross progeny enabled us to identify a gene underlying a quantitative trait locus even though it exhibited a relatively small effect on the phenotype.

Fragmentação florestal e prioridades para a conservação da biodiversidade

Um modelo dedicado ao planejamento da conservação e restauração de habitats deve incluir informações estratégicas para assegurar a eficácia e de fácil obtenção, para assegurar a agilidade necessária. Planos e estratégias para conservação usualmente são complexos e demandam informações detalhadas, difíceis de se obter, como inventários biológicos e certos tipos de mapeamento, o que traz limitações em termos de disponibilidade, qualidade e custo das informações. Assim, procurou-se testar a eficiência de métodos simples para a seleção, em escala local, de áreas prioritárias para conservação de habitats fortemente fragmentados e reduzidos, uma situação comum no sul do Brasil, usando dados de imagens LANDSAT e planos de informações disponíveis em mapeamentos comuns, e trabalho de campo. Inicialmente analisou-se a estrutura da paisagem e o padrão de fragmentação em parte da região norte do estado do Paraná, e testar se tamanho e forma são adequados para selecionar os fragmentos florestais mais importantes para a conservação, ou seja, as que contribuem para manter maior quantidade e melhor qualidade de habitats, bem como tenham maior impacto (positivo) na conectividade e em outras variáveis da paisagem. Os resultados mostram que a floresta madura cobre cerca de 3% da paisagem, e a cobertura florestal total atinge perto de 8%, consistindo principalmente de pequenos fragmentos (82% tem entre 1 e 10 ha). Fragmentos grandes (>100 ha) são apenas 1,4% dos remanescentes, mas somam 34% da área de floresta. Apesar de estarem sujeitos a efeitos de borda em toda ou quase toda a sua área, fragmentos pequenos mostraram ter um papel importante na conectividade da paisagem. Numa área maior, foi feita uma pré-seleção de áreas com potencial para estabelecimento de redes de conservação. A pré-seleção procurou responder às seguintes perguntas: 1-Quais são os sítios com maior potencial para a conservação da biodiversidade? 2-Quais são os sítios sob maior risco para objetivos de conservação? e 3-Quais sítios têm melhores oportunidades para o estabelecimento de zonas de conservação de uso múltiplo? Foi identificado um conjunto de 11 fragmentos pertencendo a 5 sub-regiões, sofrendo variados graus de pressão antrópica. Adicionalmente, usando medidas simples de estrutura da paisagem, relacionadas com tamanho, forma e conectividade dos fragmentos, procurou-se identificar tipos estruturais de fragmentos, como uma forma alternativa para auxiliar o estabelecimento de prioridades para conservação a partir do seu papel, efetivo ou potencial, na paisagem. Foram identificados 5 tipos de fragmentos, pequenos (ilhotas isoladas, trampolins), médios (núcleos auxiliares e corredores) e grandes (núcleos principais), que podem ser usados para subsidiar estratégias de conservação. Utilizando informações sobre a estrutura da paisagem, hidrografia e legislação ambiental, propõe-se aqui uma estratégia de conservação para o complexo das bacias dos ribeirões Apertados-Três Bocas (CATB), ordenando atividades de restauração e conservação de fragmentos florestais, criação e expansão de unidades de conservação, além da proposição de formas de uso do solo compatíveis com o entorno de unidades de conservação.

Fine-mapping the HOXB region detects common variants tagging a rare coding allele : evidence for synthetic association in prostate cancer

The HOXB13 gene has been implicated in prostate cancer (PrCa) susceptibility. We performed a high resolution fine-mapping analysis to comprehensively evaluate the association between common genetic variation across the HOXB genetic locus at 17q21 and PrCa risk. This involved genotyping 700 SNPs using a custom Illumina iSelect array (iCOGS) followed by imputation of 3195 SNPs in 20,440 PrCa cases and 21,469 controls in The PRACTICAL consortium. We identified a cluster of highly correlated common variants situated within or closely upstream of HOXB13 that were significantly associated with PrCa risk, described by rs117576373 (OR 1.30, P = 2.62×10(-14)). Additional genotyping, conditional regression and haplotype analyses indicated that the newly identified common variants tag a rare, partially correlated coding variant in the HOXB13 gene (G84E, rs138213197), which has been identified recently as a moderate penetrance PrCa susceptibility allele. The potential for GWAS associations detected through common SNPs to be driven by rare causal variants with higher relative risks has long been proposed; however, to our knowledge this is the first experimental evidence for this phenomenon of synthetic association contributing to cancer susceptibility.

Cartographic veracity in medieval mapping: analyzing geographical variation in the Gough Map of Great Britain

This article explores statistical approaches for assessing the relative accuracy of medieval mapping. It focuses on one particular map, the Gough Map of Great Britain. This is an early and remarkable example of a medieval “national” map covering Plantagenet Britain. Conventionally dated to c. 1360, the map shows the position of places in and coastal outline of Great Britain to a considerable degree of spatial accuracy. In this article, aspects of the map's content are subjected to a systematic analysis to identify geographical variations in the map's veracity, or truthfulness. It thus contributes to debates among historical geographers and cartographic historians on the nature of medieval maps and mapping and, in particular, questions of their distortion of geographic space. Based on a newly developed digital version of the Gough Map, several regression-based approaches are used here to explore the degree and nature of spatial distortion in the Gough Map. This demonstrates that not only are there marked variations in the positional accuracy of places shown on the map between regions (i.e., England, Scotland, and Wales), but there are also fine-scale geographical variations in the spatial accuracy of the map within these regions. The article concludes by suggesting that the map was constructed using a range of sources, and that the Gough Map is a composite of multiscale representations of places in Great Britain. The article details a set of approaches that could be transferred to other contexts and add value to historic maps by enhancing understanding of their contents.

Trans-Ancestral Studies Fine Map the SLE-Susceptibility Locus TNFSF4

We previously established an 80 kb haplotype upstream of TNFSF4 as a susceptibility locus in the autoimmune disease SLE. SLE-associated alleles at this locus are associated with inflammatory disorders, including atherosclerosis and ischaemic stroke. In Europeans, the TNFSF4 causal variants have remained elusive due to strong linkage disequilibrium exhibited by alleles spanning the region. Using a trans-ancestral approach to fine-map the locus, utilising 17,900 SLE and control subjects including Amerindian/Hispanics (1348 cases, 717 controls), African-Americans (AA) (1529, 2048) and better powered cohorts of Europeans and East Asians, we find strong association of risk alleles in all ethnicities; the AA association replicates in African-American Gullah (152,122). The best evidence of association comes from two adjacent markers: rs2205960-T (P = 1.71×10-34, OR = 1.43[1.26-1.60]) and rs1234317-T (P = 1.16×10-28, OR = 1.38[1.24-1.54]). Inference of fine-scale recombination rates for all populations tested finds the 80 kb risk and non-risk haplotypes in all except African-Americans. In this population the decay of recombination equates to an 11 kb risk haplotype, anchored in the 5′ region proximal to TNFSF4 and tagged by rs2205960-T after 1000 Genomes phase 1 (v3) imputation. Conditional regression analyses delineate the 5′ risk signal to rs2205960-T and the independent non-risk signal to rs1234314-C. Our case-only and SLE-control cohorts demonstrate robust association of rs2205960-T with autoantibody production. The rs2205960-T is predicted to form part of a decameric motif which binds NF-κBp65 with increased affinity compared to rs2205960-G. ChIP-seq data also indicate NF-κB interaction with the DNA sequence at this position in LCL cells. Our research suggests association of rs2205960-T with SLE across multiple groups and an independent non-risk signal at rs1234314-C. rs2205960-T is associated with autoantibody production and lymphopenia. Our data confirm a global signal at TNFSF4 and a role for the expressed product at multiple stages of lymphocyte dysregulation during SLE pathogenesis. We confirm the validity of trans-ancestral mapping in a complex trait. © 2013 Manku et al.

Towards the identification of a tumor suppressor gene on chromosome 3p12: Physical mapping and candidate gene screening

Renal cell carcinoma (RCC) is the most common malignant tumor of the kidney. Characterization of RCC tumors indicates that the most frequent genetic event associated with the initiation of tumor formation involves a loss of heterozygosity or cytogenetic aberration on the short arm of human chromosome 3. A tumor suppressor locus Nonpapillary Renal Carcinoma-1 (NRC-1, OMIM ID 604442) has been previously mapped to a 5–7 cM region on chromosome 3p12 and shown to induce rapid tumor cell death in vivo, as demonstrated by functional complementation experiments. ^ To identify the gene that accounts for the tumor suppressor activities of NRC-1, fine-scale physical mapping was conducted with a novel real-time quantitative PCR based method developed in this study. As a result, NRC-1 was mapped within a 4.6-Mb region defined by two unique sequences within UniGene clusters Hs.41407 and Hs.371835 (78,545Kb–83,172Kb in the NCBI build 31 physical map). The involvement of a putative tumor suppressor gene Robo1/Dutt1 was excluded as a candidate for NRC-1. Furthermore, a transcript map containing eleven candidate genes was established for the 4.6-Mb region. Analyses of gene expression patterns with real-time quantitative RT-PCR assays showed that one of the eleven candidate genes in the interval (TSGc28) is down-regulated in 15 out of 20 tumor samples compared with matched normal samples. Three exons of this gene have been identified by RACE experiments, although additional exon(s) seem to exist. Further gene characterization and functional studies are required to confirm the gene as a true tumor suppressor gene. ^ To study the cellular functions of NRC-1, gene expression profiles of three tumor suppressive microcell hybrids, each containing a functional copy of NRC-1, were compared with those of the corresponding parental tumor cell lines using 16K oligonucleotide microarrays. Differentially expressed genes were identified. Analyses based on the Gene Ontology showed that introduction of NRC-1 into tumor cell lines activates genes in multiple cellular pathways, including cell cycle, signal transduction, cytokines and stress response. NRC-1 is likely to induce cell growth arrest indirectly through WEE1. ^

Exploring the spatial variation of tides for seafloor mapping data corrections

Senior thesis written for Oceanography 445