Impacts of newly established non-indigenous green crab (Carcinus maenas) on native fauna in Placentia Bay, Newfoundland

The recent invasion of the European green crab (Carcinus maenas) populations in Placentia Bay, Newfoundland and Labrador (NL) raises great concern about potential impacts on local fisheries and native biodiversity. Green crab are highly adaptable and in both native and invaded areas, green crab are well established predators that can outcompete other similarly sized decapods. The main objectives of this thesis were to: 1) identify the native species that green crab compete with for resources; 2) determine the depths and substrate types in which these interactions likely occur; 3) assess the indirect effects of green crab on native crustaceans and their changes in behavior; 4) assess the impacts of green crab on benthic community structure; 5) compare the NL population with other Atlantic Canadian populations in terms of competitive abilities; and 6) compare morphological features of the NL population with other Atlantic Canadian populations. I found that green crab overlap in space and diet with both rock crab (Cancer irroratus) and American lobster (Homarus americanus), potentially leading to a shift in habitat. Laboratory studies on naïve juvenile lobster also suggested shifts in behavior related to green crab, in that lobster decreased foraging activity and increased shelter use in the presence of green crab. Benthic community analyses showed fewer species in mud, sand, and eelgrass sites heavily populated by green crab compared to sites without green crab, although results depended on the taxa involved and I could not eliminate environmental differences through a short term caging study. Foraging ability of green crab varied in intraspecific competition experiments, with populations from NL and Prince Edward Island dominating longer-established populations from Nova Scotia and New Brunswick. Additional studies excluded claw size as a factor driving these results and behavioral differences likely reflected differences in invasion time and population genetics. Overall, green crab in Placentia Bay appear to be altering community structure of benthic invertebrates through predation and they also appear to indirectly impact native crustaceans through competition.

Molecular analysis of evolutionary relationships of Phaseolus dumosus with the gene pool of common bean

Valuable genetic variation for bean breeding programs is held within the common bean secondary gene pool which consists of Phaseolus albescens, P. coccineus, P. costaricensis, and P. dumosus. However, the use of close relatives for bean improvement is limited due to the lack of knowledge about genetic variation and genetic plasticity of many of these species. Characterisation and analysis of the genetic diversity is necessary among beans' wild relatives; in addition, conflicting phylogenies and relationships need to be understood and a hypothesis of a hybrid origin of P. dumosus needs to be tested. This thesis research was orientated to generate information about the patterns of relationships among the common bean secondary gene pool, with particular focus on the species Phaseolus dumosus. This species displays a set of characteristics of agronomic interest, not only for the direct improvement of common bean but also as a source of valuable genes for adaptation to climate change. Here I undertake the first comprehensive study of the genetic diversity of P. dumosus as ascertained from both nuclear and chloroplast genome markers. A germplasm collection of the ancestral forms of P. dumosus together with wild, landrace and cultivar representatives of all other species of the common bean secondary gene pool, were used to analyse genetic diversity, phylogenetic relationships and structure of P. dumosus. Data on molecular variation was generated from sequences of cpDNA loci accD-psaI spacer, trnT-trnL spacer, trnL intron and rps14-psaB spacer and from the nrDNA the ITS region. A whole genome DArT array was developed and used for the genotyping of P. dumosus and its closes relatives. 4208 polymorphic markers were generated in the DArT array and from those, 742 markers presented a call rate >95% and zero discordance. DArT markers revealed a moderate genetic polymorphism among P. dumosus samples (13% of polymorphic loci), while P. coccineus presented the highest level of polymorphism (88% of polymorphic loci). At the cpDNA one ancestral haplotype was detected among all samples of all species in the secondary genepool. The ITS region of P. dumosus revealed high homogeneity and polymorphism bias to P. coccineus genome. Phylogenetic reconstructions made with Maximum likelihood and Bayesian methods confirmed previously reported discrepancies among the nuclear and chloroplast genomes of P. dumosus. The outline of relationships by hybridization networks displayed a considerable number of interactions within and between species. This research provides compelling evidence that P. dumosus arose from hybridisation between P. vulgaris and P. coccineus and confirms that P. costaricensis has likely been involved in the genesis or backcrossing events (or both) in the history of P. dumosus. The classification of the specie P. persistentus was analysed based on cpDNA and ITS sequences, the results found this species to be highly related to P. vulgaris but not too similar to P. leptostachyus as previously proposed. This research demonstrates that wild types of the secondary genepool carry a significant genetic variation which makes this a valuable genetic resource for common bean improvement. The DArT array generated in this research is a valuable resource for breeding programs since it has the potential to be used in several approaches including genotyping, discovery of novel traits, mapping and marker-trait associations. Efforts should be made to search for potential populations of P. persistentus and to increase the collection of new populations of P. dumosus, P. albescens and P. costaricensis that may provide valuable traits for introgression into common bean and other Phaseolus crops.

Scaling limits of a model for selection at two scales

The dynamics of a population undergoing selection is a central topic in evolutionary biology. This question is particularly intriguing in the case where selective forces act in opposing directions at two population scales. For example, a fast-replicating virus strain outcompetes slower-replicating strains at the within-host scale. However, if the fast-replicating strain causes host morbidity and is less frequently transmitted, it can be outcompeted by slower-replicating strains at the between-host scale. Here we consider a stochastic ball-and-urn process which models this type of phenomenon. We prove the weak convergence of this process under two natural scalings. The first scaling leads to a deterministic nonlinear integro-partial differential equation on the interval $[0,1]$ with dependence on a single parameter, $\lambda$. We show that the fixed points of this differential equation are Beta distributions and that their stability depends on $\lambda$ and the behavior of the initial data around $1$. The second scaling leads to a measure-valued Fleming-Viot process, an infinite dimensional stochastic process that is frequently associated with a population genetics.

Genetic Diversity and Conservation of Pseudophoenix (Arecaceae) in Hispaniola

The Caribbean genus Pseudophoenix (Arecaceae) has its center of taxonomic diversity in Hispaniola (Haiti and the Dominican Republic). Three species (P. ekmanii, P. lediniana, and P. vinifera) are restricted to this island. In this thesis I investigated the population genetic diversity and structure of Pseudophoenix using ten microsatellite loci. Results showed homozygote excess and high inbreeding coefficients in all populations across all polymorphic loci. Overall, there was high differentiation among populations. Results from the Bayesian and Neighbor Joining cluster analyses identified groups that were consistence with currently accepted species delimitation. We included the only known population of an undescribed morph from the Dominican Republic that has been suggested to represent a new species. Results from the cluster analyses suggested that this putative species is closely related to P. sargentii from Turk and Caicos. Our study provided insights pertinent to the conservation genetics and management of this genus in Hispaniola.

Genomic consequences of mating system evolution in the Pacific coastal dune endemic, Abronia umbellata (Nyctaginaceae)

The advent of next-generation sequencing has significantly reduced the cost of obtaining large-scale genetic resources, opening the door for genomic studies of non-model but ecologically interesting species. The shift in mating system, from outcrossing to selfing, has occurred thousands of times in angiosperms and is accompanied by profound changes in the population genetics and ecology of a species. A large body of work has been devoted to understanding why the shift occurs and the impact of the shift on the genetics of the resulting selfing populations, however, the causes and consequences of the transition to selfing involve a complicated interaction of genetic and demographic factors which are difficult to untangle. Abronia umbellata is a Pacific coastal dune endemic which displays a striking shift in mating system across its geographic range, with large-flowered outcrossing populations south of San Francisco and small-flowered selfing populations to the north. Abronia umbellata is an attractive model system for the study of mating system transitions because the shift appears to be recent and therefore less obscured by post-shift processes, it has a near one-dimensional geographic range which simplifies analysis and interpretation, and demographic data has been collected for many of the populations. In this study, we generated transcriptome-level data for 12 plants including individuals from both subspecies, along with a resequencing study of 48 individuals from populations across the range. The genetic analysis revealed a recent transition to selfing involving a drastic reduction in genetic diversity in the selfing lineage, potentially indicative of a recent population bottleneck and a transition to selfing due to reproductive assurance. Interestingly, the genetic structure of the populations was not coincident with the current subspecies demarcation, and two large-flowered populations were classified with the selfing subspecies, suggesting a potential need for re-evaluation of the current subspecies classification. Our finding of low diversity in selfing populations may also have implications for the conservation value of the threatened selfing subspecies.

Storytelling and story testing in domestication

The domestication of plants and animals marks one of the most significant transitions in human, and indeed global, history. Traditionally, study of the domestication process was the exclusive domain of archaeologists and agricultural scientists; today it is an increasingly multidisciplinary enterprise that has come to involve the skills of evolutionary biologists and geneticists. Although the application of new information sources and methodologies has dramatically transformed our ability to study and understand domestication, it has also generated increasingly large and complex datasets, the interpretation of which is not straightforward. In particular, challenges of equifinality, evolutionary variance, and emergence of unexpected or counter-intuitive patterns all face researchers attempting to infer past processes directly from patterns in data. We argue that explicit modeling approaches, drawing upon emerging methodologies in statistics and population genetics, provide a powerful means of addressing these limitations. Modeling also offers an approach to analyzing datasets that avoids conclusions steered by implicit biases, and makes possible the formal integration of different data types. Here we outline some of the modeling approaches most relevant to current problems in domestication research, and demonstrate the ways in which simulation modeling is beginning to reshape our understanding of the domestication process.

The onset of lactase persistence in Europe

The genomic region containing the lactase (LCT) gene shows one of the strongest signals of positive selection in Europeans, detectable using a range of approaches including haplotype length, linked microsatellite variation and population-differentiation-based tests. Lactase is the enzyme that carries out the digestion of the milk sugar lactose. Its expression decreases at some point after the weaning period is over in most mammals and in around 68% of all living adult humans. However, in some humans, particularly those from populations with a history of dairying, lactase is expressed throughout adulthood. This trait is called lactase persistence (LP), and in people of European ancestry, it is associated with a single mutation (-13910*T). Evidence from the detection of dairy fat residues in potsherds, and allele frequencies in ancient DNA samples suggest that LP arose after dairying practices had developed. However, the reasons why LP may have been advantageous are still debated, and the respective contribution of demography and natural selection remains to be disentangled. This paper discusses various studies, from archaeology to population genetics, that have shed some light on the subject by investigating the evolution of LP in Europe.

Historical comparisons reveal multiple drivers of decadal change of an ecosystem engineer at the range edge

Biogenic reefs are important for habitat provision and coastal protection. Long-term datasets on the distribution and abundance of Sabellaria alveolata (L.) are available from Britain. The aim of this study was to combine historical records and contemporary data to (1) describe spatiotemporal variation in winter temperatures, (2) document short-term and long-term changes in the distribution and abundance of S. alveolata and discuss these changes in relation to extreme weather events and recent warming, and (3) assess the potential for artificial coastal defense structures to function as habitat for S. alveolata. A semi-quantitative abundance scale (ACFOR) was used to compare broadscale, long-term and interannual abundance of S. alveolata near its range edge in NW Britain. S. alveolata disappeared from the North Wales and Wirral coastlines where it had been abundant prior to the cold winter of 1962/1963. Population declines were also observed following the recent cold winters of 2009/2010 and 2010/2011. Extensive surveys in 2004 and 2012 revealed that S. alveolata had recolonized locations from which it had previously disappeared. Furthermore, it had increased in abundance at many locations, possibly in response to recent warming. S. alveolata was recorded on the majority of artificial coastal defense structures surveyed, suggesting that the proliferation of artificial coastal defense structures along this stretch of coastline may have enabled S. alveolata to spread across stretches of unsuitable natural habitat. Long-term and broadscale contextual monitoring is essential for monitoring responses of organisms to climate change. Historical data and gray literature can be invaluable sources of information. Our results support the theory that Lusitanian species are responding positively to climate warming but also that short-term extreme weather events can have potentially devastating widespread and lasting effects on organisms. Furthermore, the proliferation of coastal defense structures has implications for phylogeography, population genetics, and connectivity of coastal populations.

Historical comparisons reveal multiple drivers of decadal change of an ecosystem engineer at the range edge

Biogenic reefs are important for habitat provision and coastal protection. Long-term datasets on the distribution and abundance of Sabellaria alveolata (L.) are available from Britain. The aim of this study was to combine historical records and contemporary data to (1) describe spatiotemporal variation in winter temperatures, (2) document short-term and long-term changes in the distribution and abundance of S. alveolata and discuss these changes in relation to extreme weather events and recent warming, and (3) assess the potential for artificial coastal defense structures to function as habitat for S. alveolata. A semi-quantitative abundance scale (ACFOR) was used to compare broadscale, long-term and interannual abundance of S. alveolata near its range edge in NW Britain. S. alveolata disappeared from the North Wales and Wirral coastlines where it had been abundant prior to the cold winter of 1962/1963. Population declines were also observed following the recent cold winters of 2009/2010 and 2010/2011. Extensive surveys in 2004 and 2012 revealed that S. alveolata had recolonized locations from which it had previously disappeared. Furthermore, it had increased in abundance at many locations, possibly in response to recent warming. S. alveolata was recorded on the majority of artificial coastal defense structures surveyed, suggesting that the proliferation of artificial coastal defense structures along this stretch of coastline may have enabled S. alveolata to spread across stretches of unsuitable natural habitat. Long-term and broadscale contextual monitoring is essential for monitoring responses of organisms to climate change. Historical data and gray literature can be invaluable sources of information. Our results support the theory that Lusitanian species are responding positively to climate warming but also that short-term extreme weather events can have potentially devastating widespread and lasting effects on organisms. Furthermore, the proliferation of coastal defense structures has implications for phylogeography, population genetics, and connectivity of coastal populations.

Morphological and molecular characterization of a new species of Atlantic stalked barnacle (Scalpelliformes: Pollicipedidae) from the Cape Verde Islands

[EN] The taxonomy of pedunculate cirripedes belonging to the genus Pollicipes has essentially remained unchanged since Charles Darwin described them in his exhaustive work on the Cirripedia. This genus includes three species of stalked barnacles: Pollicipes pollicipes in the north-eastern Atlantic, P. polymerus in the north-eastern Pacific and P. elegans in the central-eastern Pacific. However, a population genetics analysis of P. pollicipes suggested the presence of a putative cryptic species collected from the Cape Verde Islands in the central-eastern Atlantic. This study examines the morphology of these genetically divergent specimens and compares them with that of representative Atlantic samples of the biogeographically closely related P. pollicipes and with the poorly described P. elegans.

Apomixia determinando a estrutura genética de uma população de Plinia cauliflora no sudoeste do Paraná

CAPES

Caracterização de frutos, divergência genética e estrutura espacial de jaboticabeiras nativas de fragmento florestal em Clevelândia - PR

To design strategies for the conservation and use of genetic resources of tree species such as jaboticaba tree, it is essential to make the characterization. In southwestern Paraná region, there are several forest fragments containing native jaboticaba tree (Plinia cauliflora), whose materials have broad potential for commercial orchards or breeding programs. As is the potential genetic diversity of a population to produce different genotypes, it would be able to start in such a characterization one of these fragments. The aim was to characterize fruits of jaboticaba tree (P. caulifora) of forest fragment kept in Clevelândia - PR for the presence of phenotypic variability, seeking to identify those superiors named for future selection as farming or male parent, as well as estimate genetic divergence between them, as a complementary tool for this purpose. Also, verify the regeneration and spatial distribution of the species. For the study was defined portion of a hectare (10.000 m²), with all individuals identified, mapped, with local coordinate system, and measured height and diameter. Fruits were characterized by sensory and biochemical characteristics in two years, 70 genotypes at 2013 and 56 at 2014, and of these 33 genotypes in both years. As a pre-selection criteria was adopted the choice of 20% of the genotypes that showed the highest frequency of superiority in the evaluated characteristics of the fruit. Genetic divergence among 33 genotypes per year was analyzed. The distribution pattern and spatial association was evaluated by Ripley's K function. It was classified for the first time the following ontogenetic stages of jaboticaba tree, by plant height, seedling (from 0.01 to 0.99 m), juvenile (1.0 to 4.99 m), immature (> 5.0 m, non-reproductive), adult (reproductive). It was also have been describe for the first time the naturally occurring juxtaposed seedlings, indicating polyembryony. The number of regenerating identified in the population (seedlings: n = 2163; juveniles: n = 330; immature: n = 59) was much larger than the number of adults (n = 132). The species showed reverse J-shaped size structure standard, with high concentration of regenerating. The regeneration distribution occurs in aggregate pattern and there is seedling-adult dependence, due seed dispersal and seedling emergence closest to mothers. The jaboticaba tree regeneration is sufficient to maintain the species for long term in this population, which should serve as reference to regeneration success for other studies of this important fruiting species from Ombrofile Mixed Forests. Has been pre-selected the jaboticaba trees 7, 42, 43, 47, 54, 91, 97, 104, 105, 118, 134, 153, 154, 157, 163, 169, 177, 186, 212, J7-01 and J7- 02, and 16 and 194 the ones that can now be selected by the superior characteristics of both cycles. It was recommended to carry out hybridization between genotypes 79 and 119, and 96 to 148. The quality of fruit analyzed showed potential for use as a dual purpose serving both in natura market or processing.

Ecological drivers of a vector borne pathogen: distribution and abundance of Borrelia burgdorferi sensu lato and its vector Ixodes ricinus in Scotland

Vector-borne disease emergence in recent decades has been associated with different environmental drivers including changes in habitat, hosts and climate. Lyme borreliosis is among the most important vector-borne diseases in the Northern hemisphere and is an emerging disease in Scotland. Transmitted by Ixodid tick vectors between large numbers of wild vertebrate host species, Lyme borreliosis is caused by bacteria from the Borrelia burgdorferi sensu lato species group. Ecological studies can inform how environmental factors such as host abundance and community composition, habitat and landscape heterogeneity contribute to spatial and temporal variation in risk from B. burgdorferi s.l. In this thesis a range of approaches were used to investigate the effects of vertebrate host communities and individual host species as drivers of B. burgdorferi s.l. dynamics and its tick vector Ixodes ricinus. Host species differ in reservoir competence for B. burgdorferi s.l. and as hosts for ticks. Deer are incompetent transmission hosts for B. burgdorferi s.l. but are significant hosts of all life-stages of I. ricinus. Rodents and birds are important transmission hosts of B. burgdorferi s.l. and common hosts of immature life-stages of I. ricinus. In this thesis, surveys of woodland sites revealed variable effects of deer density on B. burgdorferi prevalence, from no effect (Chapter 2) to a possible ‘dilution’ effect resulting in lower prevalence at higher deer densities (Chapter 3). An invasive species in Scotland, the grey squirrel (Sciurus carolinensis), was found to host diverse genotypes of B. burgdorferi s.l. and may act as a spill-over host for strains maintained by native host species (Chapter 4). Habitat fragmentation may alter the dynamics of B. burgdorferi s.l. via effects on the host community and host movements. In this thesis, there was lack of persistence of the rodent associated genospecies of B. burgdorferi s.l. within a naturally fragmented landscape (Chapter 3). Rodent host biology, particularly population cycles and dispersal ability are likely to affect pathogen persistence and recolonization in fragmented habitats. Heterogeneity in disease dynamics can occur spatially and temporally due to differences in the host community, habitat and climatic factors. Higher numbers of I. ricinus nymphs, and a higher probability of detecting a nymph infected with B. burgdorferi s.l., were found in areas with warmer climates estimated by growing degree days (Chapter 2). The ground vegetation type associated with the highest number of I. ricinus nymphs varied between studies in this thesis (Chapter 2 & 3) and does not appear to be a reliable predictor across large areas. B. burgdorferi s.l. prevalence and genospecies composition was highly variable for the same sites sampled in subsequent years (Chapter 2). This suggests that dynamic variables such as reservoir host densities and deer should be measured as well as more static habitat and climatic factors to understand the drivers of B. burgdorferi s.l. infection in ticks. Heterogeneity in parasite loads amongst hosts is a common finding which has implications for disease ecology and management. Using a 17-year data set for tick infestations in a wild bird community in Scotland, different effects of age and sex on tick burdens were found among four species of passerine bird (Chapter 5). There were also different rates of decline in tick burdens among bird species in response to a long term decrease in questing tick pressure over the study. Species specific patterns may be driven by differences in behaviour and immunity and highlight the importance of comparative approaches. Combining whole genome sequencing (WGS) and population genetics approaches offers a novel approach to identify ecological drivers of pathogen populations. An initial analysis of WGS from B. burgdorferi s.s. isolates sampled 16 years apart suggests that there is a signal of measurable evolution (Chapter 6). This suggests demographic analyses may be applied to understand ecological and evolutionary processes of these bacteria. This work shows how host communities, habitat and climatic factors can affect the local transmission dynamics of B. burgdorferi s.l. and the potential risk of infection to humans. Spatial and temporal heterogeneity in pathogen dynamics poses challenges for the prediction of risk. New tools such as WGS of the pathogen (Chapter 6) and blood meal analysis techniques will add power to future studies on the ecology and evolution of B. burgdorferi s.l.

Random Mating Between Two Widely Divergent Mitochondrial Lineages of Cryptolestes ferrugineus (Coleoptera: Laemophloeidae): A Test of Species Limits in a Phosphine-Resistant Stored Product Pest

Effective pest management relies on accurate delimitation of species and, beyond this, on accurate species identification. Mitochondrial COI sequences are useful for providing initial indications in delimiting species but, despite acknowledged limitations in the method, many studies involving COI sequences and species problems remain unresolved. Here we illustrate how such impasses can be resolved with microsatellite and nuclear sequence data, to assess more directly the amount of gene flow between divergent lineages. We use a population genetics approach to test for random mating between two 8 ± 2% divergent COI lineages of the rusty grain beetle, Cryptolestes ferrugineus (Stephens). This species has become strongly resistant to phosphine, a fumigant used worldwide for disinfesting grain. The possibility of cryptic species would have significant consequences for resistance management, especially if resistance was confined to one mitochondrial lineage. We find no evidence of restricted gene flow or nonrandom mating across the two COI lineages of these beetles, rather we hypothesize that historic population structure associated with early Pleistocene climate changes likely contributed to divergent lineages within this species.

Development, characterization and use of genomic SSR markers for assessment of genetic diversity in some Saudi date palm ( Phoenix dactylifera L.) cultivars

Background: The present study was undertaken towards the development of SSR markers and assessing genetic relationships among 32 date palm ( Phoenix dactylifera L.) representing common cultivars grown in different geographical regions in Saudi Arabia. Results: Ninety-three novel simple sequence repeat markers were developed and screened for their ability to detect polymorphism in date palm. Around 71% of genomic SSRs were dinucleotide, 25% tri, 3% tetra and 1% penta nucleotide motives. Twenty-two primers generated a total of 91 alleles with a mean of 4.14 alleles per locus and 100% polymorphism percentage. A 0.595 average polymorphic information content and 0.662 primer discrimination power values were recorded. The expected and observed heterozygosities were 0.676 and 0.763 respectively. Pair-wise similarity values ranged from 0.06 to 0.89 and the overall cultivars averaged 0.41. The UPGMA cluster analysis recovered by principal coordinate analysis illustrated that cultivars tend to group according to their class of maturity, region of cultivation, and fruit color. Analysis of molecular variations (AMOVA) revealed that genetic variation among and within cultivars were 27% and 73%, respectively according to geographical distribution of cultivars. Conclusions: The developed microsatellite markers are additional values to date palm characterization tools that can be used by researchers in population genetics, cultivar identification as well as genetic resource exploration and management. The tested cultivars exhibited a significant amount of genetic diversity and could be suitable for successful breeding program. Genomic sequences generated from this study are available at the National Center for Biotechnology Information (NCBI), Sequence Read Archive (Accession numbers. LIBGSS_039019).