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opencc-zeroNov 2020View details →

R code, spatial and tabular data to fully reproduce STEPS simulations of population change for common brushtail possum, grassland melomys and northern brown bandicoot in northern Australia

<ol> <li> The development of effective fire management for biodiversity conservation is a global challenge. The highly dynamic nature of fire, the difficulty in replicating 'real-world' fire experiments, and the need to understand population changes at large spatiotemporal scales make computer simulations particularly useful for identifying optimal fire management regimes for biodiversity conservation. </li> <li> We aimed to develop a flexible modelling approach with which to investigate how the spatiotemporal application of fire (i.e. management scenarios) influences savanna biodiversity. We used existing data from a landscape-scale fire experiment to develop population simulations for the common brushtail possum (Trichosurus vulpecula), grassland melomys (Melomys burtoni) and northern brown bandicoot (Isoodon macrourus) across the Kapalga area of Kakadu National Park in northern Australia. We simulated how populations were expected to change between 1995 and 2015 in response to the fire patterns observed at Kapalga over this period, and under a hypothetical management scenario of extensive prescribed burning. </li> <li> Our models predicted a substantial decline in all three species in response to the observed fire regime at Kapalga, suggesting that the fire patterns observed at Kapalga, with the associated mechanisms and interactions with other ecological processes, were not conducive with the persistence of native mammal populations. </li> <li> Our prescribed burning scenario had little effect on the predicted population trajectory of the common brushtail possum and grassland melomys, but markedly improved the population trajectory of the northern brown bandicoot. These inconsistencies highlight the need for a nuanced approach to fire management across northern Australian savannas, that is tailored to local conditions and management objectives. </li> <li> Synthesis and applications. The modelling approach outlined here, provides a basis for identifying fire patterns that are beneficial for conserving biodiversity, thereby increasing our capacity to establish clear targets for prescribed fire management. Importantly, this approach is flexible and can be easily adapted to other taxa and fire-prone ecosystems. </li> </ol>

Data from: Impact of a recolonizing, cross-border carnivore population on ungulate harvest in Scandinavia

Predation from large carnivores and human harvest are the two main mortality factors affecting the dynamics of many ungulate populations. We examined long-term moose (Alces alces) harvest data from two countries that share cross-border populations of wolves (Canis lupus) and their main prey moose. We tested how a spatial gradient of increasing wolf territory density affected moose harvest density and age and sex composition of the harvested animals (n = 549,310), along a latitudinal gradient during 1995-2017. In areas containing average-sized wolf territories, harvest density was on average 37% (Norway) and 51% (Sweden) lower than in areas without wolves. In Sweden, calves made up a higher proportion of the moose harvest than in Norway, and this proportion was reduced with increased wolf territory density, while it increased in Norway. The proportion of females in the adult harvest was more strongly reduced in Sweden than in Norway as a response to increased wolf territory density. Moose management in both countries performed actions aimed to increase productivity in the moose population, in order to compensate for the increased mortality caused by wolves. These management actions are empirical examples of an adaptive management in response to the return of large carnivores.

Data from: Infection dynamics, dispersal, and adaptation: understanding the lack of recovery in a remnant frog population following a disease outbreak

Emerging infectious diseases can cause dramatic declines in wildlife populations. Sometimes these declines are followed by recovery, but many populations do not recover. Studying differential recovery patterns may yield important information for managing disease-afflicted populations and facilitating population recoveries. In the late1980s, a chytridiomycosis outbreak caused multiple frog species in Australia's Wet Tropics to decline. Populations of some species (e.g., Litoria nannotis) subsequently recovered, while others (e.g., Litoria dayi) did not. We examined the population genetics and current infection status of L. dayi, to test several hypotheses regarding the failure of its populations to recover: 1) a lack of individual dispersal abilities has prevented recolonization of previously occupied locations, 2) a loss of genetic variation has resulted in limited adaptive potential, and 3) L. dayi is currently adapting to chytridiomycosis. We found moderate to hig h levels of gene flow and diversity (Fst range: <0.01–0.15; minor allele frequency: 0.192–0.245), which were similar to previously published levels for recovered L. nannotis populations. This suggests that dispersal ability and genetic diversity do not limit the ability of L dayi to recolonize upland sites. Further, infection intensity and prevalence increased with elevation, suggesting that chytridiomycosis is still limiting the elevational range of L. dayi. Outlier tests comparing infected and uninfected individuals consistently identified 18 markers as putatively under selection, and several of those markers matched genes that were previously implicated in infection. This suggests that L. dayi has genetic variation for genes that affect infection dynamics and may be undergoing adaptation.

Data from: Continent-wide population genomic structure and phylogeography of North America's most destructive conifer defoliator, the spruce budworm (Choristoneura fumiferana)

The spruce budworm, Choristoneura fumiferana, is presumed to be panmictic across vast regions of North America. We examined the extent of panmixia by genotyping 3650 single nucleotide polymorphism (SNP) loci in 1975 individuals from 128 collections across the continent. We found three spatially structured subpopulations: Western (Alaska, Yukon), Central (southeastern Yukon to the Manitoba-Ontario border) and Eastern (Manitoba-Ontario border and Atlantic). Additionally, the most diagnostic genetic differentiation between the Central and Eastern subpopulations was chromosomally restricted to a single block of SNPs that may constitute an island of differentiation within the species. Geographic differentiation in the spruce budworm parallels that of its principal larval host, white spruce, Picea glauca, providing evidence that spruce trees survived in the Beringian refugium through the Last Glacial Maximum and that at least two isolated populations diverged with spruce/fir south of the ice sheets. Gene flow in the spruce budworm may also be affected by mountains in western North America, habitat isolation in West Virginia, regional adaptations, factors related to dispersal, and proximity of other species in the spruce budworm species complex. The central and eastern geographic regions contain individuals that assign to Eastern and Central subpopulations, respectively, indicating that these barriers are not complete. Our discovery of previously undetected geographic and genomic structure in the spruce budworm suggests that further population modelling of this ecologically important insect should consider regional differentiation, potentially co-adapted blocks of genes, and gene flow between subpopulations.

opencc-by-4.0Dec 2020View details →

zenodo32/100

Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data

This upload contains data and all the scripts required to reproduce the results of the artice entitled "Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data". Code is located within Code.zip . It contains scripts in R and Bash and launchers. Some of the scripts require data files contained within Data.zip. Data is located within Data.zip , such as the sequences, the inferred phylogeny and the Beast XML file.

Data used in: "Impacts of predator-mediated interactions along a climatic gradient on the population dynamics of an alpine bird"

Data for: Impacts of predator-mediated interactions along a climatic gradient on the population dynamics of an alpine bird doi: 10.1098/rspb.2020.2653 Diana E. Bowler, Mikkel A. J. Kvasnes, Hans C. Pedersen, Brett K. Sandercock, Erlend B. Nilsen Questions to: diana.e.bowler@gmail.com or erlend.nilsen@nina.no

Data from: Designing monitoring protocols to measure population trends of threatened insects: a case study of the cryptic, flightless grasshopper Brachaspis robustus

Statistically robust monitoring of threatened populations is essential for effective conservation management because the population trend data that monitoring generates is often used to make decisions about when and how to take action. Despite representing the highest proportion of threatened animals globally, the development of best practice methods for monitoring populations of threatened insects is relatively uncommon. Traditionally, population trend data for the Nationally Endangered New Zealand grasshopper Brachaspis robustus has been determined by counting all adults and nymphs seen on a single ~1.5 km transect searched once annually. This method lacks spatial and temporal replication, both of which are essential to overcome detection errors in highly cryptic species like B. robustus. It also provides no information about changes in the grasshopper's distribution throughout its range. Here, we design and test new population density and site occupancy monitoring protocols by comparing a) comprehensive plot and transect searches at one site and b) transect searches at two sites representing two different habitats (gravel road and natural riverbed) occupied by the species across its remaining range. Using power analyses, we determined a) the number of transects, b) the number of repeated visits and c) the grasshopper demographic to count to accurately detect long term change in relative population density. To inform a monitoring protocol design to track trends in grasshopper distribution, we estimated the probability of detecting an individual with respect to a) search area, b) weather and c) the grasshopper demographic counted at each of the two sites. Density estimates from plots and transects did not differ significantly. Population density monitoring was found to be most informative when large adult females present in early summer were used to index population size. To detect a significant change in relative density with power > 0.8 at the gravel road habitat, at least seventeen spatial replicates (transects) and four temporal replicates (visits) were required. Density estimates at the natural braided river site performed poorly and likely require a much higher survey effort. Detection of grasshopper presence was highest (pg > 0.6) using a 100 m x 1 m transect at both sites in February under optimal (no cloud) conditions. At least three visits to a transect should be conducted per season for distribution monitoring. Monitoring protocols that inform the management of threatened species are crucial for better understanding and mitigation of the current global trends of insect decline. This study provides an exemplar of how appropriate monitoring protocols can be developed for threatened insect species.

opencc-zeroJul 2021View details →

Data from: Large-scale connectivity, cryptic population structure, and relatedness in Eastern Pacific olive ridley sea turtles (Lepidochelys olivacea)

Endangered species are grouped into genetically discrete populations to direct conservation efforts. Mitochondrial Control Region (mtCR) haplotypes are used to elucidate deep divergences between populations, as compared to nuclear microsatellites that can detect recent structuring. When prior populations are unknown, it is useful to subject microsatellite data to clustering and/or ordination population inference. Olive ridley sea turtles (Lepidochelys olivacea) are the most abundant sea turtle, yet few studies have characterized olive ridley population structure. Recently, clustering results of olive ridleys in the Eastern Tropical Pacific Ocean suggested weak structuring (FST=0.02) between Mexico and Central America. We analyzed mtCR haplotypes, new microsatellite genotypes from Costa Rica, and pre-existing microsatellite genotypes from olive ridleys across the Eastern Tropical Pacific, to further explore population structuring in this region. We subjected inferred populations to multiple analyses to explore the mechanisms behind their structuring. We found 10 mtCR haplotypes from 60 turtles nesting at three sites in Costa Rica, but did not detect divergence between Costa Rican sites, or between Central America and Mexico. In Costa Rica, clustering suggested one population with no structuring, but ordination suggested four cryptic clusters with moderate structuring (FST=0.08, p<0.001). Across the Eastern Tropical Pacific, ordination suggested nine cryptic clusters with moderate structuring (FST=0.103, p<0.001) that largely corresponded to Mexican and Central American populations. All ordination clusters displayed significant internal relatedness relative to global relatedness (p<0.001) and contained numerous sibling pairs. This suggests that broadly dispersed family lineages have proliferated in Eastern Tropical Pacific olive ridleys and corroborates previous work showing basin-wide connectivity and shallow population structure in this region. The existence of broadly dispersed kin in Eastern Tropical Pacific olive ridleys has implications for management of olive ridleys in this region, and adds to our understanding of sea turtle ecology and life-history, particularly in light of the natal-homing paradigm.

opencc-zeroJan 2021View details →

Data from: DNA methylation changes associated with type 2 diabetes and diabetic kidney disease in an East Asian population

Objective: There is growing body of evidence that epigenetic changes including DNA methylation influence the risk of type 2 diabetes and its microvascular complications. We conducted a methylome-wide association study (MWAS) to identify differentially methylated regions (DMRs) of type 2 diabetes and diabetic kidney disease (DKD) in Korean population. Methods: We performed an initial MWAS in 232 participants in a case-control study design with type 2 diabetes and 197 non-diabetic controls with Illumina EPIC bead chip using peripheral blood leukocytes. Type 2 diabetes group was subdivided to 87 DKD cases and 80 non-DKD controls. Additional 819 individuals from two population-based cohorts were used to investigate the association of the identified DMRs with quantitative metabolic traits. We developed a DNA methylation score using identified DMRs to predict the occurrence of type 2 diabetes. To examine the causal relationship between the metabolic traits and differentially methylated status, we performed Mendelian randomization (MR) analyses. Results: We identified eight DMRs (each at BMP8A, NBPF20, STX18, ZNF365, CPT1A, and TRIM37, and two at TXNIP) which were significantly associated with risk of type 2 diabetes (P < 9.0×10-8), including three that were previously known (DMRs in TXNIP and CPT1A), in 429 type 2 diabetes cases and controls. DNA methylation score consisted of these DMRs differentiated the risk of developing type 2 diabetes in an independent prospective cohort with a relative risk of 2.44 (95% confidence interval 1.39–4.28) between the lowest and highest deciles of DNA methylation score. DMRs in CPT1A and TXNIP were associated with quantitative metabolic traits, including fasting glucose, HbA1c, and body mass index. We also identified three DMRs (on COMMD1, TMOD1, and FHOD1) associated with DKD in 167 DKD cases and controls. The DMRs of DKD did not show meaningful overlap with those of type 2 diabetes. In MR analysis, the estimated glomerular filtration rate was causally associated with DNA methylation of these three DMRs. Conclusions: In an East Asian population, we identified eight DMRs, including five novel ones, associated with type 2 diabetes and three DMRs associated with DKD at methylome-wide statistical significance. Our findings suggest that epigenetics of DKD may share little with those responsible for the development of type 2 diabetes.

opencc-zeroJan 2021View details →

Data from: Short-term effects of controlled mating and selection on the genetic variance of honeybee populations

Directional selection in a population yields reduced genetic variance due to the Bulmer effect. While this effect has been thoroughly investigated in mammals, it is poorly studied in social insects with biological peculiarities such as haplo-diploidy or the collective expression of traits. In addition to natural adaptation to climate change, parasites, and pesticides, honeybees increasingly experience artificial selection pressure through modern breeding programs. Besides selection, many honeybee breeding schemes introduce controlled mating. We investigated which individual effects selection and controlled mating have on genetic variance. We derived formulas to describe short-term changes of genetic variance in honeybee populations and conducted computer simulations to confirm them. Thereby, we found that the changes in genetic variance depend on whether variance is measured between queens (inheritance criterion), worker groups (selection criterion) or both (performance criterion). All three criteria showed reduced genetic variance under selection. In the selection and performance criteria, our formulas and simulations showed an increased genetic variance through controlled mating. This newly described effect counterbalanced and occasionally outweighed the Bulmer effect. It could not be observed in the inheritance criterion. A good understanding of the different notions of genetic variance in honeybees therefore appears crucial to interpret population parameters correctly.

zenodo32/100

Synthetic population data for Belgium for STRIDE

This repository contains population files with 11 million individuals for Belgium we used to explore the impact of contact tracing and household bubbles on Belgian deconfinement strategies after the COVID-19 related lockdown in 2020 (Willem et al 2021) and universal testing strategies for COVID-19 mitigation (Libin et al 2021). We created census-based synthetic populations for Belgium consisting of individuals that are part of “contact pools”, representing a household, school-class, workplace, or community. References: Willem L, Abrams S, Libin JK P, Petrof O, Coletti P, Kuylen E,  Møgelmose S, Wambua J, Herzog S A, Faes C, SIMID COVID19 team, Beutels P, Hens N: The impact of contact tracing and household bubbles on deconfinement strategies for COVID-19. Nature Communications 12, 1524 (2021) (<a href="https://doi.org/10.1038/s41467-021-21747-7">https://doi.org/10.1038/s41467-021-21747-7</a>). Libin JK P, Willem L, Verstraeten T, Torneri A, Vanderlocht J, Hens N. Assessing the feasibility and effectiveness of household-pooled universal testing to control COVID-19 epidemics. PLoS Computational Biology 17(3): e1008688 (2021) (<a href="https://doi.org/10.1371/journal.pcbi.1008688">https://doi.org/10.1371/journal.pcbi.1008688</a>)

opencc-by-4.0Dec 2020View details →

opencc-zeroDec 2017View details →

Data from: Pollen limitation as a main driver of fruiting dynamics in oak populations

In many perennial wind-pollinated plants, the dynamics of seed production is commonly known to be highly fluctuating from year to year and synchronized among individuals within populations. The proximate causes of such seeding dynamics, called masting, are still poorly understood in oak species that are widespread in the northern hemisphere, and whose fruiting dynamics dramatically impacts forest regeneration and biodiversity. Combining long-term surveys of oak airborne pollen amount and acorn production over large-scale field networks in temperate areas, and a mechanistic modeling approach, we found that the pollen dynamics is the key driver of oak masting. Mechanisms at play involved both internal resource allocation to pollen production synchronized among trees and spring weather conditions affecting the amount of airborne pollen available for reproduction. The sensitivity of airborne pollen to weather conditions might make oak masting and its ecological consequences highly sensitive to climate change.

opencc-zeroDec 2017View details →

Data from: Herbivore control in connected seascapes: habitat determines when population regulation occurs in the life history of a key herbivore

Herbivore outbreaks often trigger catastrophic overgrazing events in marine macrophyte ecosystems. The sea urchin Paracentrotus lividus, the dominant herbivore of shallow Mediterranean seascapes, is capable of precipitating shifts to barrens when its populations explode. P. lividus is found ubiquitously in rocky macroalgal communities and in sandy seagrass meadows of Posidonia oceanica, two of the most important subtidal habitats in the Mediterranean. We explored if habitat-specific regulation across the principal stages of the urchin life cycle could help explain the persistence of these populations in connected mosaics. We measured each of three relevant ecological process (i.e. settlement, post-settlement survival and predation) across a wide stretch of the Mediterranean coast (ca. 600km). Our results show that habitat-specific regulation is critical in determining urchin populations: each habitat limited urchin sub-populations at different life stages. Settlement was never limiting; urchins settled at similar rates in both habitats across the coast. Post-settlement survival was a clear bottleneck, particularly in seagrass meadows where no juvenile urchins were recorded. Despite this bottleneck in seagrasses, adult urchin populations were very similar in both seagrass and macroalgal habitats indicating that other processes (potentially migration) could be key in determining adult distributions across the mosaic. The fact that population regulation is clearly habitat-specific suggests that sea urchin populations may be significantly buffered from bottlenecks in mixed seascapes where both habitats co-occur. Sea urchin populations can therefore persist across the seascape despite strong habitat-specific regulation either by maintaining reproductive output in one habitat or by migrating between them. By affording these regulatory escapes to habitat-modifying species, patchy mosaics may be much more prone to herbivore outbreaks and a host of cascading effects that come in their wake.

Data from: Saguaro (Carnegiea gigantea) mortality and population regeneration in the cactus forest of Saguaro National Park: seventy-five years and counting

Annual census data spanning seventy-five years document mortality and regeneration in a population of saguaro cactus (Carnegiea gigantea) in the Cactus Forest of the Rincon Mountain District of Saguaro National Park near Tucson, AZ. On 6 four-hectare plots, each saguaro was censused and a methodical search for new saguaros was conducted annually each year from 1942 through 2016, with the exception of 1955. Regeneration has been episodic with 828 plants established from 1959 through 1993 compared with 34 plants established between 1942 and 1958 and only three plants established after 1993. The years preceding 1959 and following 1993, include some of the driest decades in centuries in southern Arizona. While woodcutting and cattle grazing are believed to be among the causes of decades of failed regeneration prior to 1958, neither of these factors contributed to the failed regeneration following 1993. The height structure of the population from 1942 to 2016 shifted dramatically from a population dominated by large saguaros (> 5.4 m tall) in the first three decades of the study to a population dominated by small saguaros (< 1.8 m tall) in the most recent two decades. Mortality is shown to be strongly age dependent. In the year following the 2011 catastrophic freeze, 21 of 59 plants older than 80 years died compared with zero deaths in 270 plants between the ages of 29 and 80 years. Saguaros under 40 years old, growing under small shrubs or in the open, have a lower probability of survival than better protected saguaros. Long-term population monitoring is essential to understanding the complex impacts of human and environmental factors on the population dynamics of long-lived species.

opencc-zeroDec 2010View details →

Data from: Mitochondrial gene diversity associated with the atp9 stop codon in natural populations of wild carrot (Daucus carota ssp. carota)

Mitochondrial genomes extracted from wild populations of Daucus carota have been used as a genetic resource by breeders of cultivated carrot, yet little is known concerning the extent of their diversity in nature. Of special interest is a SNP in the putative stop codon of the mitochondrial gene atp9 that has been associated previously with male-sterile and male-fertile phenotypic variants. In this study either sequence or PCR/RFLP genotypes were obtained from the mitochondrial genes atp1, atp9 and cox1 found in D. carota individuals collected from 24 populations in the eastern U.S. More than half of the 128 individuals surveyed had a CAA or AAA, rather than TAA, genotype at the position usually thought to function as an atp9 stop codon in this species. We also found no evidence for mitochondrial RNA editing (Cytosine to Uridine) of the CAA stop codon in either floral or leaf tissue. Evidence for intra-genic recombination, as opposed the more common inter-genic recombination in plant mitochondrial genomes, in our data set is presented. Indel and SNP variants elsewhere in atp9, and in the other two genes surveyed, were non-randomly associated with the three atp9 stop codon variants, though further analysis suggested that multi-locus genotypic diversity had been enhanced by recombination. Overall the mitochondrial genetic diversity was only modestly structured among populations with an Fst of 0.34.

Data from: Comparative spatial genetics and epigenetics of plant populations: heuristic value and a proof of concept

Despite the recent upsurge of interest on natural epigenetic variation of nonmodel organisms, factors conditioning the spatial structure of epigenetic diversity in wild plant populations remain virtually unexplored. We propose that information on processes shaping natural epigenetic variation can be gained using the spatial structure of genetic diversity as null model. Departures of epigenetic isolation-by-distance (IBD) patterns from genetic IBD patterns for the same sample, particularly differences in slope of similarity-distance regressions, will reflect the action of factors that operate specifically on epigenetic variation, including imperfect transgenerational inheritance and responsiveness to environmental factors of epigenetic marks. As a proof of concept, we provide a comparative analysis of spatial genetic and epigenetic structure of 200 mapped individuals of the perennial herb Helleborus foetidus. Plants were fingerprinted using nuclear microsatellites, amplified fragment length polymorphisms (AFLP) and methylation-sensitive AFLP markers. Expectations from individual-level IBD patterns were tested by means of kinship-distance regressions. Both genetic and epigenetic similarity between H. foetidus individuals conformed to theoretical expectations under individual-level IBD models. Irrespective of marker type, there were significant negative linear relationships between the kinship coefficient for plant pairs and their spatial separation. Regression slopes were significantly steeper for epigenetic markers. Epigenetic similarity between individuals was much greater than genetic similarity at shortest distances, such epigenetic 'kinship excess' tending to decrease as plant separation increased. Results suggest that moderate-to-high heritability and responsiveness to local environments are major drivers of epigenetic spatial structure in H. foetidus, and illustrate the heuristic value of comparing genetic and epigenetic spatial structure for formulating and testing hypotheses on forces shaping epigenetic diversity in wild plant populations.

opencc-zeroDec 2014View details →

Data from: Polyandry and postcopulatory sexual selection in a wild population

When females mate multiply, postcopulatory sexual selection can occur via sperm competition and cryptic female choice. Although postcopulatory selection has the potential to be a major force in driving evolution, few studies have estimated its strength in natural populations. Likewise, though polyandry is widespread across taxa and is the focus of a growing body of research, estimates of natural female mating rates are still limited in number. Microsatellites can be used to estimate the number of mates represented in females' sperm stores and the number of sires contributing to their offspring, enabling comparisons both of polyandry and of two components of postcopulatory selection: the proportion of males that mate but fail to sire offspring, and the degree of paternity skew among the males that do sire offspring. Here we estimate the number of mates and sires among wild females in the Hawaiian swordtail cricket Laupala cerasina. We compare these estimates to the actual mating rates and paternity shares we observed in a semi-natural population. Our results show that postcopulatory sexual selection operates strongly in this species: wild females mated with an average minimum of 3.6 males but used the sperm from only 58% of them. Furthermore, among the males that did sire offspring, paternity was significantly skewed. These patterns were similar to those observed in the field enclosure, where females mated with an average of 5.7 males and used the sperm from 62% of their mates, with paternity significantly skewed among the sires.

Data from: Population structure and persistence of Pacific herring following the Great Tohoku earthquake

We evaluated the effect of the Great Tohoku earthquake, which occurred on March 11, 2011 in Japan, on the genetic diversity and population structure of Pacific herring (Clupea pallasii). Pacific herring (n = 4466) were collected between 2003 and 2014 through more than 20 sampling events during spawning periods at nine spawning sites throughout the Pacific herring distribution range in Japan. We measured them and genotyped 3784 fish at five microsatellite loci. Following the tsunami, the sea-spawning population at the center of the affected area was almost extirpated and was replaced by a genetically distinct lagoon-spawning population from an adjacent brackish lake. However, the pattern of gene flow was stable for populations, with unique admixture proportions in local populations despite the high gene flow (FST = 0.0184). Our results indicate that Pacific herring in Japan spawn in a range of salinities and exchange genes between local populations regardless of the spawning ecotypes. We hypothesize that the combination of constant gene flow between local populations from straying of spawners and spawning fidelity creates weak but significantly differentiated stable population structure. This process can allow restoration of the genetic characteristics of damaged populations over many generations and can thereby promote the long-term viability of marine fishes that have high gene flow.

Data from: Negative relationships between population density and metabolic rates are not general

Population density has recently been suggested to be an important factor influencing metabolic rates, and to represent an important 'third axis' explaining variation beyond that explained by body mass and temperature. In situations where population density influences food consumption, the immediate effect on metabolism acting through specific dynamic action (SDA), and downregulation due to fasting over longer periods, is well understood. However, according to a recent review, previous studies suggest a more general effect of population density per se, even in the absence of such effects. It has been hypothesised that this results from animals performing anticipatory responses (i.e. reduced activity) to expected declines in food availability. Here we test the generality of this finding by measuring density effects on metabolic rates in 10 clones from two different species of the zooplankton Daphnia (Daphnia pulex Leydig and D. magna Straus). Using fluorescence-based respirometry we obtain high-precision measures of metabolism. We also identify additional studies on this topic that were not included in the previous review, compare the results, and evaluate the potential for measurement bias in all previous studies. We demonstrate significant variation in mass-specific metabolism among clones within both species. However, we find no evidence for a negative relationship between population density and mass-specific metabolism. The previously reported pattern also disappeared when we extended the set of studies analysed. We discuss potential reasons for the discrepancy among studies, including two main sources of potential bias (microbial respiration and declining oxygen consumption due to reduced oxygen availability). Only one of the previous studies gives sufficient information to conclude absence of such biases, and consistent with our results no effect of density on metabolism was found. We conclude that population density per se does not have a general effect on mass-specific metabolic rate.

Data from: Population genomic evidence for multiple Pliocene refugia in a montane-restricted harvestman (Arachnida, Opiliones, Sclerobunus robustus) from the southwestern United States

The integration of ecological niche modelling into phylogeographic analyses has allowed for the identification and testing of potential refugia under a hypothesis-based framework, where the expected patterns of higher genetic diversity in refugial populations and evidence of range expansion of nonrefugial populations are corroborated with empirical data. In this study, we focus on a montane-restricted cryophilic harvestman, Sclerobunus robustus, distributed throughout the heterogeneous Southern Rocky Mountains and Intermontane Plateau of southwestern North America. We identified hypothetical refugia using ecological niche models (ENMs) across three time periods, corroborated these refugia with population genetic methods using double-digest RAD-seq data and conducted population-level phylogenetic and divergence dating analyses. ENMs identify two large temporally persistent regions in the mid-latitude highlands. Genetic patterns support these two hypothesized refugia with higher genetic diversity within refugial populations and evidence for range expansion in populations found outside hypothesized refugia. Phylogenetic analyses identify five to six genetically divergent, geographically cohesive clades of S. robustus. Divergence dating analyses suggest that these separate refugia date to the Pliocene and that divergence between clades pre-dates the late Pleistocene glacial cycles, while diversification within clades was likely driven by these cycles. Population genetic analyses reveal effects of both isolation by distance (IBD) and isolation by environment (IBE), with IBD more important in the continuous mountainous portion of the distribution, while IBE was stronger in the populations inhabiting the isolated sky islands of the south. Using model-based coalescent approaches, we find support for postdivergence migration between clades from separate refugia.