cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5683/sp2/ibywnl
title: Data from: Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head-starting in a Galapagos giant tortoise

description: AbstractPopulation genetic theory related to the consequences of rapid population decline is well-developed, but there are very few empirical studies where sampling was conducted before and after a known bottleneck event. Such knowledge is of particular importance for species restoration, given links between genetic diversity and the probability of long-term persistence. To directly evaluate the relationship between current genetic diversity and past demographic events, we collected genome-wide single nucleotide polymorphism data from pre-bottleneck historical (c.1906) and post-bottleneck contemporary (c.2014) samples of Pinzón giant tortoises (Chelonoidis duncanensis; n=25 and 149 individuals, respectively) endemic to a single island in the Galapagos. Pinzón giant tortoises had a historically large population size that was reduced to just 150-200 individuals in the mid 20th century. Since then, Pinzón’s tortoise population has recovered through an ex situ head-start program in which eggs or pre-emergent individuals were collected from natural nests on the island, reared ex situ in captivity until they were 4-5 years old, and subsequently repatriated. We found that the extent and distribution of genetic variation in the historical and contemporary samples was very similar, with the latter group not exhibiting the characteristic genetic patterns of recent population decline. No population structure was detected either spatially or temporally. We estimated an effective population size (Ne) of 58 (95% CI = 50-69) for the post-bottleneck population; no pre-bottleneck Ne point estimate was attainable (95% CI = 39-infinity) likely due to the sample size being lower than the true Ne. Overall, the historical sample provided a valuable benchmark for evaluating the head-start captive breeding program, revealing high retention of genetic variation and no skew in representation despite the documented bottleneck event. Moreover, this work demonstrates the effectiveness of head-starting in rescuing the Pinzón giant tortoise from almost certain extinction.
DOI: 10.5683/sp2/gvwmki
title: Data from: Population structure and migration pattern of a conifer pathogen, Grosmannia clavigera, as influenced by its symbiont the mountain pine beetle

description: AbstractWe investigated the population structure of Grosmannia clavigera (Gc), a fungal symbiont of the mountain pine beetle (MPB) that plays a crucial role in the establishment and reproductive success of this pathogen. This insect–fungal complex has destroyed over 16 million ha of lodgepole pine forests in Canada, the largest MPB epidemic in recorded history. During this current epidemic, MPB has expanded its range beyond historically recorded boundaries, both northward and eastward, and has now reached the jack pine of Alberta, potentially threatening the Canadian boreal forest. To better understand the dynamics between the beetle and its fungal symbiont, we sampled 19 populations in western North America and genotyped individuals from these populations with eight microsatellite markers. The fungus displayed high haplotype diversity, with over 250 unique haplotypes observed in 335 single spore isolates. Linkage equilibria in 13 of the 19 populations suggested that the fungus reproduces sexually. Bayesian clustering and distance analyses identified four genetic clusters that corresponded to four major geographical regions, which suggested that the epidemic arose from multiple geographical sources. A genetic cluster north of the Rocky Mountains, where the MPB has recently become established, experienced a population bottleneck, probably as a result of the recent range expansion. The two genetic clusters located north and west of the Rocky Mountains contained many fungal isolates admixed from all populations, possibly due to the massive movement of MPB during the epidemic. The general agreement in north–south differentiation of MPB and G. clavigera populations points to the fungal pathogen’s dependence on the movement of its insect vector. In addition, the patterns of diversity and the individual assignment tests of the fungal associate suggest that migration across the Rocky Mountains occurred via a northeastern corridor, in accordance with meteorological patterns and observation of MPB movement data. Our results highlight the potential of this pathogen for both expansion and sexual reproduction, and also identify some possible barriers to gene flow. Understanding the ecological and evolutionary dynamics of this fungus–beetle association is important for the modelling and prediction of MPB epidemics.
DOI: 10.5683/sp2/zvu7lr
title: Data from: Population structure of mountain pine beetle symbiont Leptographium longiclavatum and the implication on the multipartite beetle-fungi relationships

description: AbstractOver 18 million ha of forests have been destroyed in the past decade in Canada by the mountain pine beetle (MPB) and its fungal symbionts. Understanding their population dynamics is critical to improving modeling of beetle epidemics and providing potential clues to predict population expansion. Leptographium longiclavatum and Grosmannia clavigera are fungal symbionts of MPB that aid the beetle to colonize and kill their pine hosts. We investigated the genetic structure and demographic expansion of L. longiclavatum in populations established within the historic distribution range and in the newly colonized regions. We identified three genetic clusters/populations that coincide with independent geographic locations. The genetic profiles of the recently established populations in northern British Columbia (BC) and Alberta suggest that they originated from central and southern BC. Approximate Bayesian Computation supports the scenario that this recent expansion represents an admixture of individuals originating from BC and the Rocky Mountains. Highly significant correlations were found among genetic distance matrices of L. longiclavatum, G. clavigera, and MPB. This highlights the concordance of demographic processes in these interacting organisms sharing a highly specialized niche and supports the hypothesis of long-term multipartite beetle-fungus co-evolutionary history and mutualistic relationships.
DOI: 10.5683/sp2/n30pgd
title: Data from: Portable device for the detection of colorimetric assays

description: AbstractIn this work, a low-cost, portable device is developed to detect colorimetric assays for in-field and point-of-care (POC) analysis. The device can rapidly detect both pH values and nitrite concentrations of 5 different samples, simultaneously. After mixing samples with specific reagents, a Hi-resolution digital camera collects a picture of the sample, and a single-board computer processes the image in real time to identify the hue-saturation-value (HSV) coordinates of the image. An internal light source reduces the effect of any ambient light so the device can accurately determine the corresponding pH values or nitrite concentrations. The device was purposefully designed to be low-cost, yet versatile and the accuracy of the results have been compared to those from a conventional method. The results obtained for pH values have a mean standard deviation of 0.03 and a correlation coefficient (R) of 0.998. The detection of nitrites is between concentrations of 0.4 to 1.6mg/L with a low detection limit of 0.2mg/L and has a mean standard deviation of 0.073 and an R-value of 0.999. The results represent the great potential of the proposed portable device as an excellent analytical tool for POC colorimetric analysis and offer broad accessibility in resource-limited settings.
DOI: 10.5683/sp2/yfpqlo
title: Data from: Positive relationship between genetic- and species diversity on limestone outcrops in the Carpathian Mountains

description: AbstractWe asked if the genetic diversity of Saponaria bellidifolia (a habitat specialist plant) and the species diversity of its habitat are driven by parallel landscape-level processes in an island-like system of limestone outcrops in the Carpathian Mountains. We tested the relationship of these two diversity levels at local and regional geographic scales. Local genetic and species diversity showed parallel patterns influenced by the number of plant communities. Likewise, at regional level there was strong evidence for parallel equilibrial dynamics of genotypes and species. However, a superimposed matrix effect enhanced the regional species diversity only. Genetic diversity of habitat specialist organisms and species diversity of these limestone outcrop islands on mainland are modulated by parallel landscape-level processes at different geographic scales, and mechanisms may be identified at very high spatial resolutions.
DOI: 10.5683/sp2/tavmnd
title: Data from: Post-glacial recolonization of the North American Arctic by Arctic char (Salvelinus alpinus): genetic evidence of multiple northern refugia and hybridization between glacial lineages

description: AbstractAims: We investigated post-glacial recolonization of the North American Arctic by Arctic char (Salvelinus alpinus) and examined potential hybridization between different glacial lineages upon secondary contact. Location: North American Arctic and adjacent areas. Methods: We collected mtDNA sequence data from 1355 individuals from 110 sampling locations and data from nine microsatellite loci from 931 individuals from 37 locations. We assessed the phylogenetic relationships and geographical distribution of mtDNA haplotypes and conducted historical demographic analyses. We used a Bayesian clustering analysis method to detect potential hybridization between glacial lineages. Results: Two highly divergent mtDNA lineages were identified in the Arctic region with distinct but overlapping geographic distributions: one in Beringia and the other over the entire Arctic Archipelago and coastal mainland east of Alaska. The microsatellite data also implied the existence of these two lineages. Evidence of hybridization was detected between the Arctic lineage and an Atlantic lineage in eastern North America. Main conclusions: Our data suggested survival and recolonization from two northern glacial refugia: one in Beringia and another in a smaller refugium, perhaps in the Arctic Archipelago itself or a separate refugium within Beringia. Patterns of hybridization detected supported the presence of a secondary contact zone between glacial lineages in the eastern Canadian Arctic.
DOI: 10.5683/sp2/xk8mhg
title: Data from: Predation risk and resource abundance mediate foraging behaviour and intraspecific resource partitioning among consumers in dominance hierarchies

description: AbstractDominance hierarchies and the resulting unequal resource partitioning among individuals are key mechanisms of population regulation. The strength of dominance hierarchies can be influenced by size-dependent trade-offs between foraging and predator avoidance whereby competitively inferior subdominants can access a larger proportion of limiting resources by accepting higher predation risk. Foraging-predation risk trade-offs also depend on resource abundance. Yet, few studies have manipulated predation risk and resource abundance simultaneously; consequently, their joint effect on resource partitioning within dominance hierarchies are not well understood. We addressed this gap by measuring behavioural responses of masu salmon (Oncorhynchus masou ishikawae) to experimental manipulations of predation risk and resource abundance in a natural temperate forest stream. Responses to predation risk depended on body size and social status such that larger fish (often social dominants) exhibited more risk-averse behaviour (e.g., lower foraging and appearance rates) than smaller subdominants after exposure to a simulated predator. The magnitude of this effect was lower when resources were elevated, indicating that dominant fish accepted a higher predation risk to forage on abundant resources. However, the influence of resource abundance did not extend to the population level, where predation risk altered the distribution of foraging attempts (a proxy for energy intake) from being skewed towards large individuals to being skewed towards small individuals after predator exposure. Our results imply that size-dependent foraging-predation risk trade-offs can weaken the strength of dominance hierarchies by allowing competitively inferior subdominants to access resources that would otherwise be monopolized.
DOI: 10.5683/sp2/bs6yvp
title: Data from: Predator kairomones change food web structure and function, regardless of cues from consumed prey

description: AbstractPredation risk in aquatic systems is often assessed by prey through chemical cues, either those released by prey or by the predator itself. Many studies on predation risk focus on simple pairwise interactions, with only a few studies examining community-level and ecosystem responses to predation risk in species-rich food webs. Further, of these few community-level studies, most assume that prey primarily assess predation risk through chemical cues from consumed prey, even heterospecific prey, rather than just those released by the predator. Here, we compared the effects of different predation cues (predator presence with or without consumed prey) on the structure and functioning of a speciose aquatic food web housed in tropical bromeliads. We found that the mere presence of the top predator (a damselfly) had a strong cascading effect on the food web, propagating down to nutrient cycling. This predation risk cue had no effect on the identity of colonizing species, but strongly reduced the abundance and biomass of the macroinvertebrate colonists. As a result, bacterial biomass and nitrogen cycling doubled, with a concomitant decrease in bacterial production, but CO2 flux was unaffected. These community and ecosystem effects of predator presence cues were not amplified by the addition of chemical cues from consumed prey. Our results show that some of the consequences of predation risk observed in controlled experiments with simplified food webs may be observed in a natural, species-rich food web.
DOI: 10.5683/sp2/lfvhvx
title: Data from: Predators, energetics and fitness drive neonatal reproductive failure in red squirrels

description: AbstractNeonatal reproductive failure should occur when energetic costs of parental investment outweigh fitness benefits. However, little is known about the drivers of neonatal reproductive failure in free ranging species experiencing continuous natural variation in predator abundance and in the energetic and fitness costs and benefits associated with parental investment. Long-term comprehensive studies are required to better understand how biotic, abiotic, and life history conditions interact to drive occurrences of reproductive failure in the wild. Using 24 years (1987-2011) of reproductive data from a northern boreal population of North American red squirrels in southwestern Yukon, we examined the effects of predator abundance, energetics (resource availability, ambient temperature and litter size), and fitness benefits (probability of overwinter juvenile survival and maternal age) on occurrences of neonatal reproductive failure (494/2670 reproductive attempts; 18.5%). Neonatal reproductive failure was driven by a combination of predator abundance, and the energetic and fitness costs and benefits of parental investment. The abundance of mustelids and maternal age were positively related to the occurrence of neonatal reproductive failure. High energy costs associated with a combination of low resource availability and cold ambient temperatures or large litters, corresponded to increased occurrences of neonatal reproductive failure. However, the strength of these relationships was influenced by variation in juvenile overwinter survival (i.e. fitness benefits). We provide evidence that predation pressure is an important driver of neonatal reproductive failure. In addition, we found a trade-off occurs between resource-dependent energetic and fitness costs and benefits of raising the current litter to independence
DOI: 10.5683/sp2/rflyvh
title: Data from: Predators modify the evolutionary response of prey to temperature change

description: AbstractAs climate regimes shift in many ecosystems worldwide, evolution may be a critical process allowing persistence in rapidly changing environments. Organisms regularly interact with other species, yet whether climate-mediated evolution can occur in the context of species interactions is not well understood. We tested whether a species interaction could modify evolutionary responses to temperature. We demonstrate that predation pressure by Dipteran larvae (Chaoborus americanus) modified the evolutionary response of a freshwater crustacean (Daphnia pulex) to its thermal environment over approximately seven generations in laboratory conditions. Daphnia kept at 21°C evolved higher population growth rates than those kept at 18°C, but only in those populations that were also reared with predators. Furthermore, predator-mediated selection resulted in the evolution of elevated Daphnia thermal plasticity. This laboratory natural selection experiment demonstrates that biotic interactions can modify evolutionary adaptation to temperature. Understanding the interplay between multiple selective forces can improve predictions of ecological and evolutionary responses of organisms to rapid environmental change.
DOI: 10.5683/sp2/nl4qxq
title: Data from: Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing

description: AbstractBackground: Genomic selection (GS) in forestry can substantially reduce the length of breeding cycle and increase gain per unit time through early selection and greater selection intensity, particularly for traits of low heritability and late expression. Affordable next-generation sequencing technologies made it possible to genotype large numbers of trees at a reasonable cost. Results: Genotyping-by-sequencing was used to genotype 1,126 Interior spruce trees representing 25 open-pollinated families planted over three sites in British Columbia, Canada. Four imputation algorithms were compared (mean value (MI), singular value decomposition (SVD), expectation maximization (EM), and a newly derived, family-based k-nearest neighbor (kNN-Fam)). Trees were phenotyped for several yield and wood attributes. Single- and multi-site GS prediction models were developed using the Ridge Regression Best Linear Unbiased Predictor (RR-BLUP) and the Generalized Ridge Regression (GRR) to test different assumption about trait architecture. Finally, using PCA, multi-trait GS prediction models were developed. The EM and kNN-Fam imputation methods were superior for 30 and 60% missing data, respectively. The RR-BLUP GS prediction model produced better accuracies than the GRR indicating that the genetic architecture for these traits is complex. GS prediction accuracies for multi-site were high and better than those of single-sites while multi-site predictability produced the lowest accuracies reflecting type-b genetic correlations and deemed unreliable. The incorporation of genomic information in quantitative genetics analyses produced more realistic heritability estimates as half-sib pedigree tended to inflate the additive genetic variance and subsequently both heritability and gain estimates. Principle component scores as representatives of multi-trait GS prediction models produced surprising results where negatively correlated traits could be concurrently selected for using PCA2 and PCA3. Conclusions: The application of GS to open-pollinated family testing, the simplest form of tree improvement evaluation methods, was proven to be effective. Prediction accuracies obtained for all traits greatly support the integration of GS in tree breeding. While the within-site GS prediction accuracies were high, the results clearly indicate that single-site GS models ability to predict other sites are unreliable supporting the utilization of multi-site approach. Principle component scores provided an opportunity for the concurrent selection of traits with different phenotypic optima.
DOI: 10.5683/sp2/wcdsv0
title: Data from: Predictive mapping to identify refuges for plant communities threatened by earthworm invasion

description: Abstract1. Biological invasions by cryptic ecosystem engineers can alter the ecological and socio-economic values of ecosystems in ways that may take decades to detect. The invasion of North American glacial refuges by non-native earthworms offers a prominent but understudied example of a cryptic invasion. Non-native earthworms are known to alter carbon sequestration, disrupt mycorrhizal networks, and homogenize plant communities, but natural resource managers still lack robust protocols to identify and safeguard high conservation value communities (HCVCs) from such invasions. In the absence of such protocols, or reliable methods to eradicate non-native earthworm populations once established, there is an urgent need for methods to identify HCVCs at risk of or potentially shielded from earthworm invasion by the existence of abiotic barriers to their dispersal or persistence in such sites. 2. We developed species distribution models (SDMs) using in-situ field surveys and remotely sensed data to (1) identify factors limiting the occurrence of non-native Lumbricus earthworms in imperiled coastal Douglas-fir (Pseudotsuga menziesii) forest and Garry oak (Quercus garryana) and maritime meadow ecosystems endemic to glacial refugia of the Pacific Northwest of North America to (2) evaluate their influence on plant species diversity and identify abiotic factors capable of preventing their dispersal or persistence at a site. 3. As predicted, shallow, drier soils, and steeper terrain limited earthworm occurrence and abundance in our highly heterogeneous study area, and earthworm presence appeared to reduce plant species richness. Our results indicated that HCVCs endemic to shallow-soil (&lt;12 ± 3 cm) sites that experience regular summer drought appear to act as refuges from invasion by non-native earthworms. Our results also elevate concerns for the conservation of deep-soil habitats not isolated from earthworm invasions by shallow soil, saltwater, or other barriers to earthworm dispersal. 4. The SDMs developed here offer guidance to the identification of potential refuges for the conservation of imperiled native species and communities from the detrimental effects non-native earthworms in glacial refugia of western North America, and should thereby facilitate proactive planning by conservation practitioners.