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Lake water chemistry and population of origin interact to shape fecundity and growth in Daphnia ambigua

Freshwater environments vary widely in ion availability, owing to both natural and anthropogenic drivers. Field and laboratory work point to the importance of overall salinity as well as cation depletion, in shaping the physiology, behavior, and ecology of freshwater taxa. Yet, we currently have a poor understanding of the degree to which populations may vary in response to ion availability. Using Daphnia collected from three lakes that differ greatly in salinity and calcium availability, we conducted a laboratory reciprocal transplant experiment to assess how animals representing these populations vary in fecundity, body size, and survival when reared in lake water from each environment. The lake water environment and population of origin strongly interacted to shape Daphnia growth and reproduction. Surprisingly, we found only modest evidence that lake water with abundant calcium (5.5 mg/L vs. 1.2-2.3 mg/L) increased Daphnia growth or reproduction. In contrast, water from a relatively ion-rich lake (400 µS/cm specific conductance) strongly boosted Daphnia fecundity over lower-ion lake water (20-50 µS/cm), especially for the population originating from the high-ion environment. Our results suggest that ion-poor conditions common in regions around the world may exert stress on freshwater organisms, even for populations inhabiting these environments. Meanwhile, moderate salt enrichment may not prove harmful but could even benefit freshwater taxa in these ion-poor regions. The context dependence of how and when lake water chemistry affects Daphnia and other freshwater taxa deserves greater attention, in both ion-depleted and ion-rich conditions. Daphnia are key members of lake food webs and serve as an important model for ecology, evolution, and toxicology research. Consideration of how lake water chemistry may influence how Daphnia populations respond to abiotic and biotic stress may improve the ability to evaluate and predict ecological and evolutionary dynamics in lakes of varying chemical composition.

A Great Escape: resource availability and density-dependence shape population dynamics along trailing range edges

Populations along geographical range limits are often exposed to unsuitable climate and low resource availability relative to core populations. As such, there has been a renewed focus on understanding the factors that determine range limits to better predict how species will respond to global change. Using recent theory on range limits and classical understanding of density dependence, we evaluated the influence of resource availability on the snowshoe hare Lepus americanus along its trailing range edge. We estimated variation in population density, habitat use, survival, and parasite loads to test the Great Escape Hypothesis (GEH), i.e. that density dependence determines, in part, a species' persistence along trailing edges. We found that variability in resource availability affected density and population fluctuations and led to trade-offs in survival for snowshoe hare populations in the northeastern USA. Hares living in resource-limited environments had lower and less variable population density, yet higher survival and lower parasitism compared to populations living in resource-rich environments. We suggest that density-dependent dynamics, elicited by resource availability, provide hares a unique survival advantage and partly explain persistence along their trailing edge. We hypothesize that this low-density escape from predation and parasitism occurs for other prey species along trailing edges, but the extent to which it occurs is likely conditional on the quality of matrix habitat. Our work indicates that biotic factors play an important role in shaping species' trailing edges and more detailed examination of non-climatic factors is warranted to better inform conservation and management decisions.

Raw data for: Sex and population differences underlie variation in reproductive success in a warming environment

Current rising temperatures are threatening biodiversity. It is therefore crucial to understand how climate change impacts male and female fertility and whether evolutionary responses can help in coping with heat stress. We use experimental evolution to study male and female fertility during real-time evolution of two historically differentiated populations of Drosophila subobscura under different thermal selection regimes for 23 generations. We aim to (1) tease apart sex-specific differences in fertility after exposure to warming conditions during development, (2) test whether thermal selection can enhance fertility under thermal stress, and (3) address the role of historically distinct genetic backgrounds. Contrary to expectations, heat stress during development had a higher negative impact on female fertility than on male fertility. We did not find clear evidence for enhanced fertility in males or females evolving under warming conditions. Population history had a clear impact on fertility response under thermal stress, particularly in males with those from lower latitudes presenting better performance than their higher latitude counterparts. We show that the impact of thermal stress on fertility varies between traits, sexes and genetic backgrounds. Incorporating these several levels of variation is crucial for a deeper understanding of how fertility evolves under climate change.

Data from: Dynamics of reproductive isolation in stick insects at the transition between populations and species

Speciation is often viewed as a continuum along which populations diverge until they become reproductively-isolated species. However, such divergence may be heterogeneous, proceeding in `fits and bursts', rather than being uniform and gradual. We show in Timema stick insects that one form of reproductive isolation indeed evolves non-uniformly across this continuum, whereas another does not. Specifically, we use thousands of host-preference and mating trials to study habitat and sexual isolation among 42 pairs of taxa spanning a range of genomic differentiation and divergence time. We find that the evolution of habitat isolation is uncoupled from genomic differentiation within species, but accumulates linearly with it between species. In contrast, sexual isolation accumulates linearly across the speciation continuum. The results show different evolutionary dynamics for different components of reproductive isolation, indicate sudden transitions between phases of speciation, and highlight a special relevance for species status in the evolution of reproductive isolation.

Data from: Hidden demographic impacts of fishing and environmental drivers of fecundity in a sea turtle population

Fisheries bycatch is a critical threat to sea turtle populations worldwide, particularly because turtles are vulnerable to multiple gear types. The Canary Current is an intensely fished region, yet there has been no demographic assessment integrating bycatch and population management information of the globally significant Cabo Verde loggerhead turtle (Caretta caretta) population. Using Boa Vista island (Eastern Cabo Verde) subpopulation data from capture-recapture and nest monitoring (2013–2019), we evaluated population viability and estimated regional bycatch rates (2016–2020) in longline, trawl, purse-seine, and artisanal fisheries. We further evaluated current nesting trends in the context of bycatch estimates, existing hatchery conservation measures, and environmental (net primary productivity) variability in turtle foraging grounds. We projected that current bycatch mortality rates would lead to the near extinction of the Boa Vista subpopulation. Bycatch reduction in longline fisheries and all fisheries combined would increase finite population growth rate by 1.76% and 1.95%, respectively. Hatchery conservation increased hatchling production and reduced extinction risk, but alone it could not achieve population growth. Short-term increases in nest counts (2013–2021), putatively driven by temporary increases in net primary productivity, may be masking ongoing long-term population declines. When fecundity was linked to net primary productivity, our hindcast models simultaneously predicted these opposing long-term and short-term trends. Consequently, our results showed conservation management must diversify from land-based management. The masking effect we found has broad-reaching implications for monitoring sea turtle populations worldwide, demonstrating the importance of directly estimating adult survival and that nest counts might inadequately reflect underlying population trends.

opencc-by-4.0Jul 2020View details →

Figure 5 in The spatial structure of а snow leopard population (Panthera uncia, Felidae, Carnivora) in east Kyrgyzstan

Figure 5. Spatial distribution of snow leopards in the Sarychat–Ertash Reserve.

opencc-by-4.0Nov 2015View details →

Figure 5 in The population dynamics and reproduction of Streblospio gynobranchiata (Annelida, Spionidae), an alien polychaete worm, in the Sevastopol Bay (the Black Sea)

Figure 5. Adult worm (♂). Scale: 1 mm.

opencc-by-4.0Nov 2015View details →

Figure 6 in The population dynamics and reproduction of Streblospio gynobranchiata (Annelida, Spionidae), an alien polychaete worm, in the Sevastopol Bay (the Black Sea)

Figure 6. Average abundance of S. gynobranchiata in Sevastopol Bay in May and in October 2013.

Biophysical data for: Dispersive currents explain patterns of population connectivity in an ecologically and economically important fish

How to identify the drivers of population connectivity remains a fundamental question in ecology and evolution. Answering this question can be challenging in aquatic environments where dynamic lake and ocean currents coupled with high levels of dispersal and gene flow can decrease the utility of modern population genetic tools. To address this challenge, we used RAD-Seq to genotype 959 yellow perch (Perca flavescens), a species with an ~40-day pelagic larval duration (PLD), collected from 20 sites circumscribing Lake Michigan. We also developed a novel, integrative approach that couples detailed biophysical models with eco-genetic agent-based models to generate 'predictive' values of genetic differentiation. By comparing predictive and empirical values of genetic differentiation, we estimated the relative contributions for known drivers of population connectivity (e.g., currents, behavior, PLD). For the main basin populations (i.e., the largest contiguous portion of the lake), we found that high gene flow led to low overall levels of genetic differentiation among populations (FST = 0.003). By far the best predictors of genetic differentiation were connectivity matrices that were derived from periods of time when there were strong and highly dispersive currents. Thus, these highly dispersive currents are driving the patterns of population connectivity in the main basin. We also found that populations from the northern and southern main basin are slightly divergent from one another, while those from Green Bay and the main basin are highly divergent (FST = 0.11). By integrating biophysical and eco-genetic models with genome-wide data, we illustrate that the drivers of population connectivity can be identified in high gene flow systems.

Peak power and body mass as indices of bone loading in a healthy adult population

Objective: The purpose of this study was to examine whether a common, non-invasive, muscular fitness field test was a better predictor of bone strength compared to body mass. Methods: Hierarchical multiple regression analyses were used to determine the amount of variance that peak power explained for bone strength of the tibia compared to body mass. Peak power was estimated from maximal vertical jump height using Sayer's equation. Peripheral quantitative computed tomography scans were used to assess bone strength measures. Results: Peak power (ꞵ=0.541, p<0.001) contributed more to the unique variance in bone strength index for compression compared to body mass (ꞵ=-0.102, p=0.332). For polar strength strain index, the beta coefficient for body mass remained significant (ꞵ=0.257, p<0.006), however, peak power's contribution was similar (ꞵ=0.213, p= 0.051). Conclusion: Compared to body mass, peak power was a better predictor for trabecular bone strength but similar to body mass for cortical bone strength. These data provide additional support for the development of a vertical jump test as a simple, objective, valid and reliable measure to monitor bone strength among youth and adult populations.

Simulated population time series used to build and test a model of accuracy for population-based global biodiversity indicators

Global biodiversity is facing a crisis, which must be solved through effective policies and on-the-ground conservation. But governments, NGOs, and scientists need reliable indicators to guide research, conservation actions, and policy decisions. Developing reliable indicators is challenging because the data underlying those tools is incomplete and biased. For example, the Living Planet Index tracks the changing status of global vertebrate biodiversity, but taxonomic, geographic and temporal gaps and biases are present in the aggregated data used to calculate trends. But without a basis for real-world comparison, there is no way to directly assess an indicator's accuracy or reliability. Instead, a modelling approach can be used. We developed a model of trend reliability, using simulated datasets as stand-ins for the "real world", degraded samples as stand-ins for indicator datasets (e.g. the Living Planet Database), and a distance measure to quantify reliability by comparing sampled to unsampled trends. The model revealed that the proportion of species represented in the database is not always indicative of trend reliability. Important factors are the number and length of time series, as well as their mean growth rates and variance in their growth rates, both within and between time series. We found that many trends in the Living Planet Index need more data to be considered reliable, particularly trends across the global south. In general, bird trends are the most reliable, while reptile and amphibian trends are most in need of additional data. We simulated three different solutions for reducing data deficiency, and found that collating existing data (where available) is the most efficient way to improve trend reliability, and that revisiting previously-studied populations is a quick and efficient way to improve trend reliability until new long-term studies can be completed and made available.

opencc-by-4.0May 2023View details →

Individual multilocus genotypes of F1 seed progeny and recruits from two translocated populations of Campanula glomerata

Individual multilocus genotypes for 15 microsatellite loci and spatial coordinates of F1 seed progeny and recruits from two translocated populations of Campanula glomerata from southern Belgium. For more information, see Van Rossum et al.(2023), Assessing spatial mating patterns in translocated populations of Campanula glomerata, in Gobal Ecology and Conservation.

Landscape of Mast cell populations across organs in mice and humans

Mast cells (MCs) are tissue-resident immune cells which exhibit homeostatic and neuron-associated functions. Here we combined whole-tissue imaging and single-cell RNA sequencing datasets to generate a pan-organ analysis of MCs in mice and humans at steady state. In mice, we identify two mutually exclusive MC populations, MrgprB2+ connective tissue-type MCs and MrgprB2neg mucosal-type MCs, with specific transcriptomic core signatures. While MrgprB2+ MCs develop in-utero independently of the bone marrow, MrgprB2neg MCs develop after birth and are renewed by bone marrow progenitors. In humans, we unbiasedly identify 7 MC subsets (MC1 to 7) distributed across 12 organs with different transcriptomic core signatures. MC1 are preferentially enriched in the bladder, MC2 in the lungs, and MC4, MC6 and MC7 in the skin. Conversely, MC3 and MC5 are shared by most organs, but not skin. This comprehensive analysis offers valuable insights into the natural diversity of MC subtypes in both mice and humans.

Data for: Mechanisms that can cause population decline under heavily skewed male-biased adult sex ratios

<ol> <li>While adult sex ratio (ASR) is a crucial component for population management, there is still a limited understanding of how its fluctuation affects population dynamics. To demonstrate mechanisms that hinder population growth under a biased ASR, we examined changes in reproductive success with ASR using a decapod crustacean exposed to female-selective harvesting. </li> <li> We examined the effect of ASR on the spawning success of females. A laboratory experiment showed that the number of eggs carried by females decreased as the proportion of males in the mating groups increased. Although the same result was not observed in data collected over 25 years in the wild, the negative effect of ASR was suggested when success in carrying eggs was considered as a spawning success. These results indicate that a surplus of males results in females failing to carry eggs, probably due to sexual coercion, and the negative effect of ASR can be detected at the population level only when the bias increases because failure in spawning success occurs in part of population. </li> <li>We experimentally examined how male-biased sex ratios affected the maintenance of genetic diversity in a population. The diversity of paternity in a clutch increased with the number of candidate fathers. However, over 50% of a clutch was fertilised by a single male regardless of the sex ratio, and the degree of diversity was less than half of the highest diversity expected in each mating group. </li> <li>We also experimentally examined the mating ability of males during the breeding season. The experiment showed that multiple mating by males could not compensate for the risk that their genotypes would be lost when multiple males competed for one female. These results suggest that a male-biased ASR could trigger a decline of genetic diversity in a population.</li> <li>We show that ASR skewed by female-selective harvesting decreases reproductive success not only of males that have few mating opportunities but also of females. We discuss that we may still underestimate the significance of ASR on population persistence due to the difficulty of revealing the effect of ASR.</li> </ol>

opencc-by-4.0Feb 2023View details →

Data Release: "A parameter-free tour of the binary black hole population"

This dataset contains the results presented in "A parameter-free tour of the binary black hole population" (<a href="http://arxiv.org/abs/2302.07289">arXiv:2302.07289</a>). The code used to generate this data can be found in the repository <a href="https://github.com/tcallister/autoregressive-bbh-inference/">https://github.com/tcallister/autoregressive-bbh-inference/</a>. This repository includes <a href="https://github.com/tcallister/autoregressive-bbh-inference/tree/main/data">jupyter notebooks</a> that can be used to open, explore, and plot the files contained in this data set. Additional information about reproducing and/or using this dataset can be found in <a href="https://tcallister.github.io/autoregressive-bbh-inference/">our associated documentation</a>. Further notes: <ul> <li>The files sampleDict_FAR_1_in_1_yr.pickle and injectionDict_FAR_1_in_1.pickle, used as inputs to our analyses, are created via code in the repository <a href="https://github.com/tcallister/get-lvk-data">https://github.com/tcallister/get-lvk-data</a> (see also <a href="https://zenodo.org/record/6505409">https://zenodo.org/record/6505409</a>).</li> <li>The files posteriors_gaussian_spin_samples_FAR_1_in_1.json and o1o2o3_mass_c_iid_mag_iid_tilt_powerlaw_redshift_result.json, used for figure generation, were published by the LIGO Scientific Collaboration, Virgo Collaboration, and KAGRA Collaboration in support of the paper "<a href="https://arxiv.org/abs/2111.03634">The population of merging compact binaries inferred using gravitational waves through GWTC-3</a>" (see <a href="https://zenodo.org/record/5655785">https://zenodo.org/record/5655785</a>).</li> </ul> New in this version: This version (Version 3) contains the the newest results generated in the first round of journal referee review and reflected in v2 of the arXiv listing. Includes re-run of all analyses with updated priors, and new results from the injection study discussed in Appendix C.

Astyanax cavefish body shape coordinates from: Phylogeographic relationships and morphological evolution between cave and surface Astyanax mexicanus populations (De Fillipi 1853) (Actinopterygii, Characidae)

The Astyanax mexicanus complex includes two different morphs, a surface and a cave-adapted ecotype, found at three mountain ranges in Northeastern Mexico: Sierra de El Abra, Sierra de Guatemala, and Sierra de la Colmena (Micos). Since their discovery, multiple studies have attempted to characterize the timing and the number of events that gave rise to the evolution of these cave-adapted ecotypes. Here, using RAD-seq and genome-wide sequencing, we assessed the phylogenetic relationships, genetic structure, and gene flow events between the cave and surface Astyanax mexicanus populations, to estimate the time and mode of evolution of the cave-adapted ecotypes. We also evaluated the body shape evolution across different cave lineages using geometric morphometrics to examine the role of phylogenetic signal vs. environmental pressures. We found strong evidence of parallel evolution of cave-adapted ecotypes derived from two separate lineages of surface fish and hypothesize that there may be up to four independent invasions of caves from surface fish. Moreover, a strong congruence between the genetic structure and geographic distribution was observed across the cave populations, with the Sierra de Guatemala the region exhibiting most genetic drift among the cave populations analyzed. Interestingly, we found no evidence of phylogenetic signal in body shape evolution, but we found support for parallel evolution in body shape across independent cave lineages, with cavefish from the Sierra de El Abra reflecting the most divergent morphology relative to surface and other cavefish populations.

Population dynamics and social organization of sambar (Rusa unicolor unicolor) in Horton Plains National Park, Sri Lanka

We estimated the population density and investigated the social organization of sambar (Rusa unicolor unicolor) in Horton Plains National Park (HPNP), Sri Lanka. Distance sampling was conducted along six strip transects every month for a period over three years (2018–2020) to estimate the density of the sambar population in grasslands of HPNP (9.4 km2), while the antler stage of males and the behaviour of individuals were recorded to describe the population's reproductive stage and hence the social organization. Population density estimates showed relative stability over the three years and varied over the seasons but with consistent peaks from year to year with the highest population densities recorded in November-December (212.93 ± 25.38 animals/km2 in 2018, 187.91 ± 28.51 in 2019, and 179.76 ± 31.85 in 2020). The highest percentage of males in hard antlers was observed from November through January, while the percentage of antlers cast sambar peaked from March to April each year. Hinds were observed with newborn calves throughout the year, but the highest number of newborn calves were recorded from July to August each year, while the number of calves counted each year varied from 210–267 individuals. The mean group size was variable throughout each year with the largest groups recorded from September to December (up to 52), the period accompanied by the most observations of mating and sparring behaviour. Although on a tropical island, HPNP is situated on a rolling plateau landscape in the highlands, where sambar showed a degree of reproductive seasonality somewhat similar to temperate cervid species.

opencc-by-4.0Mar 2023View details →

A digital GIS update to the classic Ulbrich 1930 map of muskrat (Undatra zibethica) population range expansion in Central Europe

This dataset is a digital version of a seminal dispersal data set of muskrat spread in Central Europe. We obtained and scanned an original copy of Ulbrich (1930), creating a digital image file, which we then geo-referenced in Arc Gis 10.2. The data herein contains metadata explaining the conversion process, necessary images to geo-reference the map, reference points used to "fix" the dispersal map to a map of present-day Europe, intermediate files (points and polygons produced when tracing the population ranges), and the final spatial dataset.   Reference to the original data:  Ulbrich, Johannes.  1930.  Die Bisamratte; lebenweise, gang ihrer ausbreitung in Europa, wirtschaftliche bedeutung und bekampfung.  Heinrich, Dresden.

Ecosystem stability is determined by plant defense functional traits and population stability under mowing in a semi-arid temperate steppe

<ol> <li>As a common grassland management practice in many high-latitude regions worldwide, mowing has great impacts on grassland functioning and stability. Species richness, species asynchrony and species stability have been suggested as central in responses to environmental change. Mowing can evoke plant defense systems due to physical damages to plants. However, no studies have comprehensively evaluated the role of plant defense functional traits, species richness, species asynchrony and stability in ecosystem functioning under mowing regimes across time-scales. </li> <li> In the present study, we set up short-term (4-years) and long-term (16-years) mowing experiments with three stubble heights (control, 10 cm, 2 cm) in a temperate steppe of Inner Mongolia. We investigated the effects of mowing-induced changes in distribution metrics associated with plant defense traits, i.e. mean, variance, skewness and kurtosis of trait distribution, on ecosystem stability of grassland communities using structural equation modeling. </li> <li>We found that grassland ecosystem stability was enhanced by increasing mowing duration and decreasing stubble height. Mowing-induced increases in abundance and diversity of plant defense traits contributed to greater ecosystem stability by enhancing species asynchrony and population stability. Moreover, we found that mowing enhanced the abundance and diversity of plant defense traits of dominant species and contributed to population stability and species asynchrony, thus enhancing temporal stability of grassland ecosystems. </li> <li>These results demonstrate the important roles of plant defense traits in maintaining stability of grasslands under mowing, and highlight that, in addition to species richness, asynchrony and population stability, plant functional defense trait act in stabilizing ecosystem functions under human-induced environmental changes.</li> </ol>

Genotypes for yardstick population from the Nakai Plateau, Lao PDR at 25 loci

Conservation biologists often deal with species that have small, fragmented populations throughout their range, making it necessary to prioritize populations for management. Genetics provides tools to assist with prioritization according to the levels and distribution of genetic diversity and evolutionary distinctiveness. Many studies have used nuclear microsatellite loci to measure genetic diversity in disparate populations and mitochondrial DNA to assess genetic distinctiveness. However, comparing metrics based on microsatellite genotypes ascertained in different laboratories is complicated by the selection of different loci with distinct nucleotide repeat motifs. This issue may be resolved by comparing metrics to a well-characterized reference population with shared microsatellite markers. The Asian elephant, Elephas maximus, is an endangered species with 50–60% of populations in India and Sri Lanka, and small, fragmented populations throughout southeast and insular Asia. We assessed range-wide genetic diversity of the Asian elephant by directly comparing allelic diversity and heterozygosity estimates from 35 populations, overcoming marker selection bias by calibrating metrics to a large population on the Nakai Plateau, Lao PDR, genotyped at 25 loci. We coupled these results with mtDNA analysis to evaluate genetic distinctiveness and identify potential conservation management units. We found the greatest diversity in the populations of southeast Asia and the greatest genetic distinctiveness among the subspecies designations, particularly Borneo and Sumatra, and other southeast Asian populations. The populations of southeast Asia, albeit small, fragmented, and at high risk of extirpation, contain valuable diversity and distinctiveness and are thus of high priority for the preservation of the Asian elephant.