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opencc-zeroSep 2022View details →

Population genomics of a predatory mammal reveals patterns of decline and impacts of exposure to toxic toads

Mammal declines across northern Australia are one of the major biodiversity loss events occurring globally. There has been no regional assessment of the implications of these species declines for genomic diversity. To address this, we conducted a species-wide assessment of genomic diversity in the northern quoll (Dasyurus hallucatus), an Endangered marsupial carnivore. We used next-generation sequencing methods to genotype 10,191 SNPs in 352 individuals from across a 3220 km length of the continent, investigating patterns of population genomic structure and diversity, and identifying loci showing signals of putative selection. We found strong heterogeneity in the distribution of genomic diversity across the continent, characterised by (1) biogeographic barriers driving hierarchical population structure through long-term isolation, and (2) severe reductions in diversity resulting from population declines, exacerbated by the spread of introduced toxic cane toads (Rhinella marina). These results warn of a large ongoing loss of genomic diversity and associated adaptive capacity as mammals decline across northern Australia. Encouragingly, populations of the northern quoll established on toad-free islands by translocations appear to have maintained most of the initial genomic diversity after 16 years. By mapping patterns of genomic diversity within and among populations, and investigating these patterns in the context of population declines, we can provide conservation managers with data critical to informed decision-making. This includes the identification of populations that are candidates for genetic management, the importance of remnant island and insurance/translocated populations for the conservation of genetic diversity, and the characterisation of putative evolutionarily significant units.

opencc-zeroSep 2022View details →

Data from: Linking environmental stability with genetic diversity and population structure in two Atlantic Forest palm trees

Spatial patterns of biodiversity in the Atlantic Forest of Brazil are well characterized. However, there is no consensus on the biological processes underlying these patterns, and multiple competing hypotheses have been proposed, several of which center on climatic stability. Here, we ask if Late Quaternary climatic stability predicts contemporary population structure and genomic-level diversity in two palm species: Syagrus botryophora and S. pseudococos (Arecaceae) We first use species occurrence data to model the distribution of suitable environments in 62 time-slice climate projections over the last 120 thousand years, and summarize stability over that period. We then use >25,000 RADseq-generated SNPs to i) describe the spatial patterns of genomic variation in both species, ii) test how well genomic variation is explained by isolation by distance and by the environmental resistance imposed by historical instability (isolation by resistance) and iii) test for a correlation between genetic diversity and historical stability. The contemporary range of S. botryophora has been relatively stable over the last 30 thousand years and there are two isolated regions of high stability for S. pseudococos. The genomic data recovers a clear pattern of isolation by distance in S. botryophora and two structured populations in S. pseudococos. Consequently, the contribution of isolation by resistance to overall genetic structure is much higher in S. pseudococos. Genetic diversity is not significantly correlated with historical stability in either species. Based on the concordance between historical stability and genetic structure, Late Quaternary climate stability may have maintained population connectivity within S. botryophora and promoted intraspecific divergence in S. pseudococos. Conversely, historical stability does not seem to be driving spatial patterns of genetic diversity. This study supports the primary role of climatic stability in determining spatial population structure, but not genetic diversity, in the Atlantic Forest.

opencc-zeroSep 2022View details →

Population density does not affect seasonal regulation of reproductive physiology in male water voles

Most small rodent species display cyclic fluctuations in their population density. The mechanisms behind these cyclical variations are not yet clearly understood. Density-dependent effects on reproductive function could affect these population variations. The fossorial water vole ecotype, Arvicola terrestris, undergoes a multi-year cycle dynamic with outbreak peaks. Here, we monitored different water vole populations over three years, in spring and autumn, to evaluate whether population density be related to male reproductive physiology. Our results show an effect of season and inter-annual factors in testes mass, plasmatic testosterone level, and androgen-dependent seminal vesicles mass. By contrast, population density does not affect any of these parameters, thus suggesting a lack of modulation of population dynamics of population density.

opencc-by-4.0Oct 2022View details →

Multi-Modal Population Dataset for Sub-Saharan Africa

A multi-modal population dataset for three cities in Sub-Saharan Africa, namely Dakar (Senegal), Nairobi (Kenya) and Dar es Salaam (Tanzania). The dataset contains patches of rasterized building footprints (0.5 m), Sentinel-2 MSI data (10 m) and population labels at the patch level (100 m).

Compensatory recruitment unlikely in high elevation amphibian populations challenged with disease

Population-level variation in host responses to disease can be observed across a wide array of host-pathogen systems. Some host populations are extirpated, some persist at lower densities or abundances, and others rebound to pre-disease levels. Understanding the causes of this variation, and the mechanisms of successful persistence, can serve as vital information for species conservation. One such mechanism of population persistence that has gained support in the amphibian Batrachochytrium dendrobatidis (Bd) host-pathogen system is the demographic process of compensatory recruitment. Host populations may persist by increasing recruitment to compensate for reduced survival due to infection, thus limiting the negative effects of the disease on population trajectories. However, high-elevation amphibian populations are inherently vulnerable to stochastic processes and may be limited in their ability to exhibit compensatory recruitment relative to lower-elevation populations. We use long-term mark-recapture data from five populations of boreal toads (Anaxyrus boreas boreas), across an elevational gradient in Colorado, before and after pathogen arrival to assess whether populations can persist with Bd via compensatory recruitment. Prior to Bd arrival, we found a life history tradeoff between survival and recruitment across elevations, where high-elevation toads have high survival but lower recruitment and vice versa at lower elevations. Bd arrival had a strong negative effect on apparent annual survival and recruitment, and led to negative population growth rates and dramatically reduced host abundances. The data did not support the occurrence of compensatory recruitment. Synthesis and applications. Our unique dataset suggests that demographic responses to pathogens may be environmentally (i.e., elevationally) context-dependent and highlights the value of long-term monitoring. We recommend that practitioners verify that potential persistence mechanisms occur across multiple populations and relevant environmental gradients to counter any assumptions of the mechanism existing species-wide. Quantifying any variation in population responses to disease will aid in understanding the bounds of such persistence mechanisms, and identify particularly vulnerable populations where mechanisms are non-existent.

opencc-by-4.0Apr 2018View details →

Figure 2 in A population growth model of Tetranychus urticae Koch (Acari: Tetranychidae)

Figure 2. Growth of total population of T. urticae on two bean fitted to logistic curve.

opencc-by-4.0Apr 2018View details →

Figure 1 in A population growth model of Tetranychus urticae Koch (Acari: Tetranychidae)

Figure 1. Population fluctuation of total population of T. urticae on two bean fields in 2016.

opencc-by-nd-4.0Oct 2019View details →

Figure 4 in Phenology of an urban population of Lyssomanes jemineus Peckham & Wheeler (Araneae: Salticidae) with a list of other jumping spiders from the same Costa Rican site

Figure 4. Lyssomanes jemineus from study site in Costa Rica. A, Spiderling, 18 weeks old, feeding on Drosophila melanogaster. B, Spiderlings, 2 weeks old, with a mm scale at the left. C, Oviposition by adult female. D-E, Maternal care of hatching spiderlings by female during the month of May. F, Adult female feeding on a microhymenopteran. G.-I, Adult male. G, Dorsal view. H, Ventral view. I, Ventral view of right pedipalp. J-L, Adult female. J, Dorsal view. K, Ventral view. L, Ventral view of right pedipalp. Macrophotography with Reflex Camera 850, 20X microscope lenses and focus stacking of 180 images.

opencc-by-nd-4.0Oct 2019View details →

Figure 1 in Phenology of an urban population of Lyssomanes jemineus Peckham & Wheeler (Araneae: Salticidae) with a list of other jumping spiders from the same Costa Rican site

Figure 1. Study area at the University of Costa Rica in San Pedro de Montes de Oca, northwest of the

Data and scripts from: Microbiome composition is shaped by geography and population structure in the parasitic wasp Asobara japonica, but not in the presence of the endosymbiont Wolbachia

The microbial community composition is crucial for diverse life-history traits in many organisms. However, we still lack a sufficient understanding of how the host microbiome is acquired and maintained, a pressing issue in times of global environmental change. Here we investigated to what extent host genotype, environmental conditions, and the endosymbiont Wolbachia influence the bacterial communities in the parasitic wasp Asobara japonica. We sampled multiple wasp populations across ten locations in their natural distribution range in Japan and sequenced the host genome (whole genome sequencing) and microbiome (16S rRNA gene). We compared the host population structure and bacterial community composition of wasps that reproduce sexually and are uninfected with Wolbachia with wasps that reproduce asexually and carry Wolbachia. The bacterial communities in asexual wasps were highly similar due to a strong effect of Wolbachia rather than host genomic structure. In contrast, in sexual wasps, bacterial communities appear primarily shaped by a combination of population structure and environmental conditions. Our research highlights that multiple factors shape the bacterial communities of an organism and that the presence of a single endosymbiont can strongly alter their compositions. This information is crucial to understanding how organisms and their associated microbiome will react in the face of environmental change.

Temperature and land-use rates of change for populations of fast and slow species in the LPD

Human-induced environmental changes have a direct impact on species populations, with some species experiencing declines while others display population growth. Understanding why and how species populations respond differently to environmental changes is fundamental to mitigate and predict future biodiversity changes. Theoretically, species life-history strategies are key determinants shaping the response of populations to environmental impacts. Despite this, the association between species' life-histories and the response of populations to environmental changes has not been tested. In this study, we analysed the effects of recent land-cover and temperature changes on rates of population change of 1,072 populations recorded in the Living Planet Database. We selected populations with at least 5 yearly consecutive records (after imputation of missing population estimates) between 1992 and 2016, and for which we achieved high population imputation accuracy (in the cases where missing values had to be imputed). These populations were distributed across 553 different locations and included 461 terrestrial amniote vertebrate species (273 birds, 137 mammals, and 51 reptiles) with different life-history strategies. We showed that populations of fast-lived species inhabiting areas that have experienced recent expansion of cropland or bare soil present positive population trends on average, whereas slow-lived species display negative population trends. Although these findings support previous hypotheses that fast-lived species are better adapted to recover their populations after an environmental perturbation, the sensitivity analysis revealed that model outcomes are strongly influenced by the addition or exclusion of populations with extreme rates of change. Therefore, the results should be interpreted with caution. With climate and land-use changes likely to increase in the future, establishing clear links between species characteristics and responses to these threats is fundamental for designing and conducting conservation actions. The results of this study can aid in evaluating population sensitivity, assessing the likely conservation status of species with poor data coverage, and predicting future scenarios of biodiversity change.

opencc-by-4.0Dec 2021View details →

Dataset for "Genetic diversity and population structure of a wide Pisum spp. core collection."

Silico-DArT and SNP datasets of the IAS pea core collection. Each file contain key information of the molecular markers used to establish the population structure and genetic diversity of the IAs pea core collection.

opencc-by-4.0Oct 2022View details →

Africa map showing population and grid infrastructure.

Used for Wikipedia. Produced using <a href="https://github.com/pypsa-meets-earth/pypsa-earth">PyPSA-Earth</a> and the plotting scripts given in <a href="https://github.com/pypsa-meets-earth/documentation">https://github.com/pypsa-meets-earth/documentation</a>/ Credits to the PyPSA-Earth authors (previously PyPSA-Africa authors).

Population genetic structure of the gastropod species Bulinus truncatus

Background: Gastropod snails remain strongly understudied, despite their important role in transmitting parasitic diseases. Knowledge on their distribution and population dynamics increases our understanding of processes driving disease transmission. This is the first study using High Throughput Sequencing (HTS) to elucidate the population genetic structure of the hermaphroditic snail Bulinus truncatus (Gastropoda, Heterobranchia) on a regional (17 to 150 km) and an inter-regional (1,000 – 5,400 km) scale. This snail species acts as an intermediate host of Schistosoma haematobium and Schistosoma bovis, which cause human and animal schistosomiasis respectively. Methods: Bulinus truncatus snails were collected in Senegal, Cameroon, Egypt and France and identified through DNA barcoding. A single-end Genotyping by Sequencing (GBS) library, comprising of 87 snail specimens from the respective countries, was built and sequenced on an Illumina HiSeq 2000 platform. Reads were mapped against S. bovis and S. haematobium reference genomes to identify schistosome infections and Single Nucleotide Polymorphisms (SNPs) were scored using the Stacks pipeline. These SNPs were used to estimate genetic diversity, assess population structure and to construct phylogenetic trees of Bulinus truncatus. Results: A total of 10,750 SNPs were scored and used in downstream analyses. The phylogenetic analysis identified five clades, each consisting of snails from a single country but with two distinct clades within Senegal. Genetic diversity was low in all populations, reflecting high selfing rates, but varied between locations due to habitat variability. Significant genetic differentiation and isolation by distance patterns were observed at both spatial scales, indicating that gene flow is not strong enough to counteract the effects of population bottlenecks, high selfing rates and genetic drift. Remarkably, the population genetic differentiation on a regional scale (i.e. within Senegal) was as large as between populations on an inter-regional scale. The blind GBS technique was able to pick up parasite DNA in snail tissue, demonstrating the potential of HTS techniques to further elucidate the role of snail species in parasite transmission. Conclusions: HTS techniques offer a valuable toolbox to further investigate the population genetic patterns of schistosome intermediate host snails and the role of snail species in parasite transmission.

opencc-zeroDec 2021View details →

A novel SNP assay reveals increased genetic variability and abundance following translocations to a remnant Allegheny woodrat population

Background: Allegheny woodrats (Neotoma magister) are found in metapopulations distributed throughout the Interior Highlands and Appalachia. Historically these metapopulations persisted as relatively fluid networks, enabling gene flow between subpopulations and recolonization of formerly extirpated regions. However, over the past 45 years, Allegheny woodrat populations have experienced population declines throughout their range due to a combination of habitat destruction, declining hard mast availability, and roundworm parasitism. In an effort to initiate genetic rescue of a small, genetically depauperate subpopulation in New Jersey, woodrats were translocated from a genetically robust population in Pennsylvania (PA) in 2015, 2016, and 2017. Herein, we assess the efficacy of these translocations to restore genetic diversity within the recipient population. Results: We designed a novel 134 single nucleotide polymorphism panel, which was used to genotype the six woodrats translocated from PA and 82 individuals from the NJ population captured before and after the translocation events. These data indicated that a minimum of two translocated individuals successfully produced at least 16 offspring, who reproduced as well. Further, population-wide observed heterozygosity rose substantially following the first set of translocations, reached levels comparable to that of populations in Indiana and Ohio, and remained elevated throughout the following years. Abundance also increased during the monitoring period, suggesting Pennsylvania translocations initiated the genetic rescue of the New Jersey population. Conclusions: Our results indicate, encouragingly, that very small numbers of translocated individuals can successfully restore the genetic diversity of a threatened population. Our work also highlights the risks of managing very small populations, such as when translocated individuals have greater reproductive success relative to residents. Finally, we note that ongoing work with Allegheny woodrats may broadly shape our understanding of genetic rescue within metapopulations and across heterogeneous landscapes.

Reduced sexual size dimorphism in a pipefish population where males do not prefer larger females

Within a species' distribution, populations are often exposed to diverse environments and may thus experience different sources of both natural and sexual selection. These differences are likely to impact the balance between costs and benefits to individuals seeking reproduction, thus entailing evolutionary repercussions. Here, we look into an unusual population (Baltic Sea) of the broadnosed pipefish, Syngnathus typhle, where males do not seem to select females based on size and hypothesise that this pattern may derive from a reduction of direct benefits to the male. We further hypothesise that if larger females do not persistently secure a higher reproductive success, either through pre- or post-copulatory sexual selection, a decrease in sexual size dimorphism in the Baltic population should be apparent, especially when contrasted with a well-studied population, inhabiting similar latitudes (Swedish west coast), where males prefer larger females. We found that, in the Baltic population, variation in female quality is low. We were unable to find differences in abortion rates or protein concentration in oocytes produced by females of contrasting sizes. Direct benefits from mating with large partners seem, thus, reduced in the Baltic population. We also found no evidence of any post-copulatory mechanism that could favour larger mothers as embryo development was unrelated to female size. While female size can still be selected through intrasexual competition or fecundity selection, the pressure for large female body size seems to be lower in the Baltic. Accordingly, we found a noticeable decrease in sexual size dimorphism in the Baltic population. We conclude that, although far from negating the significance of other selective process, sexual selection seems to have a decisive role in supporting pipefish sexual size asymmetries.

Replication data for: Demographic declines and responses of breeding bird populations to human footprint in the Athabasca Oil Sands Region, Alberta, Canada

This data package includes data files and an R script to reproduce results reported in the paper "Demographic declines and responses of breeding bird populations to human footprint in the Athabasca Oil Sands Region, Alberta, Canada". Analyses include hierarchical multispecies models applied to data from 31 bird species at 38 Monitoring Avian Productivity and Survivorship (MAPS) stations to assess 10-year (2011–2020) demographic trends and responses to energy sector disturbance (human footprint proportion) in the Athabasca oil sands region of Alberta, Canada. Adult captures, productivity, and residency probability all declined over the study period, and adult apparent survival probability also tended to decline. Trends in adult captures, productivity, and survival were all more negative at stations with larger increases in disturbance over the study period. Species associated with early seral stages were more commonly captured at more disturbed stations, while species typical of mature forests were more commonly captured at less disturbed stations. Productivity was positively correlated with disturbance within 5 km of stations after controlling for disturbance within 1 km of stations. Adult apparent survival showed relatively little response to disturbance; stresses experienced beyond the breeding grounds likely play a larger role in influencing survival. Residency probability was negatively related to disturbance within 1-km scale of stations and could reflect processes affecting the ability of birds to establish or maintain territories in disturbed landscapes.

Phenotypic convergence in a natural Daphnia population acclimated to low temperature

Fluidity of a given membrane decreases at lower ambient temperatures, whereas it rises at increasing temperatures, which is achieved through changes in membrane lipid composition. In consistence with homeoviscous adaptation theory, lower temperatures result in increased tissue concentrations of polyunsaturated fatty acids (PUFAs) in D. magna, suggesting a higher PUFA requirement at lower temperatures. However, so far homeoviscous adaptation has been suggested for single or geographically separated Daphnia genotypes only. Here we investigated changes in relative fatty acid (FA) tissue concentrations in response to a lower temperature (15°C) within a D. magna population. We determined juvenile growth rates (JGR) and FA patterns of 14 genotypes, that were grown on Chlamydomonas klinobasis at 15°C and 20°C. We report significant differences of JGR and the relative body content of various FAs between genotypes at either temperature and between temperatures. Based on slopes of reaction norms, we found genotype-specific changes in FA profiles between temperatures suggesting that genotypes have different strategies to cope with changing temperatures. In a hierarchical clustering analysis we grouped genotypes according to differences in direction and magnitude of changes in relative FA content, which resulted in three clusters of genotypes following different patterns of changes in FA composition. These patterns suggest a lower importance of the PUFA eicosapentaenoic acid (EPA, C20:5ω3) than previously assumed. We calculated an unsaturation index (UI) as a proxy for membrane fluidity at 15°C, and we neither found significant differences for this UI nor for fitness, measured as JGR, between the three genotype clusters. We conclude that these three genotype clusters represent different physiological solutions to temperature changes by altering the relative share of different FAs, but that their phenotypes converge with respect to membrane fluidity and JGR. These clusters will be subjected to different degrees of PUFA-limitation when sharing the same diet.

Determining haploblocks and haplotypes in the MAGIC winter wheat population WM-800 based on the wheat 15k Infinium and the 135k Affymetrix SNP arrays

Haplotypes are derived from single nucleotide polymorphisms (SNPs). They are beneficial (i) to remove redundant sequence information in genetic populations and, more important, (ii) to distinguish more than two variants/alleles at a genomic locus. A haploblock locus, made of multiple haplotypes, is very useful in multiparent-advanced-generation-intercross (MAGIC) populations, where, ideally, multiple founder alleles need to be distinguished at each locus to subsequently carry out efficient genome-wide association analysis studies (GWAS). In this regard, the dataset contains genotype matrices (made of SNP, haploblock and haplotype data) for 800 lines of the MAGIC WHEAT population WM-800 (Sannemann et al. 2018). The datasets are based on genotyping the lines with both the already published wheat 15k Infinium SNP array (Sannemann et al. 2018) and the new wheat 135k Affymetrix SNP array.