Find research datasets worth reusing

Data from: Prediction limits of mobile phone activity modelling

Thanks to their widespread usage, mobile devices have become one of the main sensors of human behaviour and digital traces left behind can be used as a proxy to study urban environments. Exploring the nature of the spatio-temporal patterns of mobile phone activity could thus be a crucial step towards understanding the full spectrum of human activities. Using 10 months of mobile phone records from Greater London resolved in both space and time, we investigate the regularity of human telecommunication activity on urban scales. We evaluate several options for decomposing activity timelines into typical and residual patterns, accounting for the strong periodic and seasonal components. We carry out our analysis on various spatial scales, showing that regularity increases as we look at aggregated activity in larger spatial units with more activity in them. We examine the statistical properties of the residuals and show that it can be explained by noise and specific outliers. Also, we look at sources of deviations from the general trends, which we find to be explainable based on knowledge of the city structure and places of attractions. We show examples how some of the outliers can be related to external factors such as specific social events.

opencc-zeroDec 2011View details →

Data from: Limited oxygen availability in utero may constrain the evolution of live-birth in reptiles

Although viviparity (live birth) has evolved from oviparity (egg laying) at least 140 times in vertebrates, nearly 120 of these independent events occurred within a single reptile taxon. Surprisingly, only squamate reptiles (lizards and snakes) are capable of facilitating embryonic development to increasingly advanced stages inside the mother during extended periods of oviducal egg retention. Viviparity has never evolved in turtle lineages, presumably because embryos enter and remain in an arrested state until after eggs are laid, regardless of the duration of egg retention. Until now, the limiting factor that initiates and maintains developmental arrest has remained elusive. Here, we show that oviducal hypoxia arrests embryonic development. We demonstrate that hypoxia can maintain developmental arrest after oviposition and that subsequent exposure of arrested embryos to normoxia triggers resumption of their development. We discovered remarkably low oxygen partial pressure in the oviducts of gravid turtles and found that secretions produced by the oviduct retard oxygen diffusion. Our results suggest that an extremely hypoxic environment in the oviduct arrests embryonic development and may constrain the evolution of viviparity in turtles, with the reduced diffusive capacity of oviducal secretions possibly creating or contributing to this hypoxia. We anticipate that these findings will allow us to better understand the mechanisms underlying the evolutionary transition between reproductive modes.

Data from: Male zebra finches have limited ability to identify high-fecundity females

In species with biparental care and lifetime monogamy, the fecundity of a male's partner can be a major component of his fitness but it is unclear whether males can assess female fecundity before breeding. We carried out an experiment in which we measured variation in female fecundity (repeatability 39%, 213 females) in a captive zebra finch population and tested whether males preferred unfamiliar females of high fecundity (approximately top 10% of the population; 30 eggs laid on average) over those of low fecundity (bottom 10%; 6 eggs). We first tested whether naïve human observers could identify the high-fecundity female when confronted with duos of high and low fecundity. Humans guessed correctly in 58% of the cases (95% confidence interval [CI] 50–66%) indicating that differences in female condition were not highly obvious to humans. Zebra finch males preferred the high-fecundity female in 59% of choice tests that lasted 20 min (CI 52–66%). When extending such choice tests over several days, male "success" in associating with the high-fecundity female was still modest (61% correct choices, CI 44–76%). Overall, male zebra finches seem to have only limited abilities to identify the better mate when faced with a choice between extremes in terms of female fecundity. We found no male preference for heavier females. We speculate that such a preference may not have evolved because, in contrast to many ectothermic species, predicting fecundity from female weight is not sufficiently accurate (r2 = 0.04) for the benefits to outweigh the costs of increased male–male competition for heavy females.

Data from: Whole-genome sequencing approaches for conservation biology: advantages, limitations, and practical recommendations

Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved (huWGR) or resolved haplotypes (hrWGR), the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq), and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in non-model species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons, and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g. structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently though, no single WGR approach fulfills all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many non-model species and fields including conservation biology.

Data from: Quantifying how constraints limit the diversity of viable routes to adaptation

Convergent adaptation can occur at the genome scale when independently evolving lineages use the same genes to respond to similar selection pressures. These patterns provide insights into the factors that facilitate or constrain the diversity of genetic responses that contribute to adaptive evolution. A first step in studying such factors is to quantify the observed amount of repeatability relative to expectations under a null hypothesis. Here, we formulate a novel metric to quantify the constraints driving the observed amount of repeated adaptation in pairwise contrasts based on the hypergeometric distribution, and then generalize this for simultaneous analysis of multiple lineages. This metric is explicitly based on the probability of observing a given amount of repeatability by chance under an arbitrary null hypothesis, and is readily compared among different species and types of trait. We also formulate a metric to quantify the effective proportion of genes in the genome that have the potential to contribute to adaptation. As an example of how these metrics can be used to draw inferences, we assess the amount of repeatability observed in existing datasets on adaptation to antibiotics in yeast and climate in conifers. This approach provides a method to test a wide range of hypotheses about how different kinds of factors can facilitate or constrain the diversity of genetic responses observed during adaptive evolution.

Data from: Extent of adaptation is not limited by unpredictability of the environment in laboratory populations of Escherichia coli

Environmental variability is on the rise in different parts of the earth and the survival of many species depend on how well they cope with these fluctuations. Our current understanding of how organisms adapt to unpredictably fluctuating environments is almost entirely based on studies that investigate fluctuations among different values of a single environmental stressor like temperature or pH. How would unpredictability affect adaptation when the environment fluctuates between qualitatively very different kinds of stresses? To answer this question, we subjected laboratory populations of Escherichia coli to selection over ~260 generations. The populations faced predictable and unpredictable environmental fluctuations across qualitatively different selection environments, namely, salt and acidic pH. We show that predictability of environmental fluctuations does not play a role in determining the extent of adaptation, although the extent of ancestral adaptation to the chosen selection environments is of key importance. This is good news given that the unpredictability of environmental fluctuations all over the world is on the rise.

Data from: Ejaculate evolution in external fertilizers: influenced by sperm competition or sperm limitation?

The evolution of sperm quality and quantity is shaped by various selective processes, with sperm competition generally considered the primary selective agent. Particularly in external fertilizers, however, sperm limitation through gamete dispersal can also influence gamete investments, but empirical data examining this effect are limited. Here, we studied the relative importance of sperm competition and the spawning conditions in explaining the macroevolutionary patterns of sperm size and number within two taxa with external fertilization but differences in their reproductive biology. In frogs, sperm swim slowly but for up to hours as they penetrate the gelatinous egg coating, whereas fish sperm typically swim fast, are very short-lived (seconds to minutes), and often face a relatively higher risk of being moved away from the ova by currents. Our phylogenetic models and path analyses revealed different trajectories of ejaculate evolution in these two taxa. Sperm size and number responded primarily to variation in sperm competition in the anurans, but more strongly to egg number and water turbulence in the fishes. Whereas the results across anurans align with the general expectation that sexual selection is the main driver of ejaculate evolution, our findings across the fishes suggest that sperm limitation has been underappreciated.

opencc-zeroDec 2015View details →

Data from: Identifying homomorphic sex chromosomes from wild-caught adults with limited genomic resources

We demonstrate a genotyping-by-sequencing approach to identify homomorphic sex chromosomes and their homolog in a distantly related reference genome, based on noninvasive sampling of wild-caught individuals, in the moor frog Rana arvalis. Double-digest RADseq libraries were generated using buccal swabs from 30 males and 21 females from the same population. Search for sex-limited markers from the unfiltered data set (411 446 RAD tags) was more successful than searches from a filtered data set (33 073 RAD tags) for markers showing sex differences in heterozygosity or in allele frequencies. Altogether, we obtained 292 putatively sex-linked RAD loci, 98% of which point to male heterogamety. We could map 15 of them to the Xenopus tropicalis genome, all but one on chromosome pair 1, which seems regularly co-opted for sex determination among amphibians. The most efficient mapping strategy was a three-step hierarchical approach, where R. arvalis reads were first mapped to a low-coverage genome of Rana temporaria (17 My divergence), then the R. temporaria scaffolds to the Nanorana parkeri genome (90 My divergence), and finally the N. parkeri scaffolds to the X. tropicalis genome (210 My). We validated our conclusions with PCR primers amplifying part of Dmrt1, a candidate sex determination gene mapping to chromosome 1: a sex-diagnostic allele was present in all 30 males but in none of the 21 females. Our approach is likely to be productive in many situations where biological samples and/or genomic resources are limited.

Data from: Self-limiting population genetic control with sex-linked genome editors

In male heterogametic species the Y chromosome is transmitted solely from fathers to sons, and is selected for based only on its impacts on male fitness. This fact can be exploited to develop efficient pest control strategies that use Y-linked editors to disrupt the fitness of female descendants. With simple population genetic and dynamic models we show that Y-linked editors can be substantially more efficient than other self-limiting strategies and, while not as efficient as gene drive approaches, are expected to have less impact on non-target populations with which there is some gene flow. Efficiency can be further augmented by simultaneously releasing an autosomal X-shredder construct, in either the same or different males. Y-linked editors may be attractive option to consider when efficient control of a species is desired in some locales but not others.

Data from: Testing the heat dissipation limit theory in a breeding passerine

The maximum work rate of animals has recently been suggested to be determined by the rate at which excess metabolic heat generated during work can be dissipated (heat dissipation limitation theory; HDL). As a first step towards testing this theory in wild animals, we experimentally manipulated brood size in breeding marsh tits (Poecile palustris) to change their work rate. Parents feeding nestlings generally operated at above-normal body temperatures. Body temperature in both males and females increased with maximum ambient temperature and with manipulated work rate, sometimes even exceeding 45 °C, which is close to suggested lethal levels for birds. Such high body temperatures have previously only been described for birds living in hot and arid regions. Thus, reproductive effort in marsh tits may potentially be limited by the rate of heat dissipation. Females had lower body temperatures, a possible consequence of their brood patch serving as a thermal window facilitating heat dissipation. Because increasing body temperatures are connected to somatic costs, we suggest that the HDL theory may constitute a possible mediator of the trade-off between current and future reproduction. It follows that globally increasing, more stochastic, ambient temperatures may restrict the capacity for sustained work of animals in the future.

Data from: A large 28S rDNA-based phylogeny confirms the limitations of established morphological characters for classification of proteocephalidean tapeworms (Platyhelminthes, Cestoda)

Proteocephalidean tapeworms form a diverse group of parasites currently known from 315 valid species. Most of the diversity of adult proteocephalideans can be found in freshwater fishes (predominantly catfishes), a large proportion infects reptiles, but only a few infect amphibians, and a single species has been found to parasitize possums. Although they have a cosmopolitan distribution, a large proportion of taxa are exclusively found in South America. We analyzed the largest proteocephalidean cestode molecular dataset to date comprising more than 100 species (30 new), including representatives from 54 genera (80%) and all subfamilies, thus significantly improving upon previous works to develop a molecular phylogeny for the group. The Old World origin of proteocephalideans is confirmed, with their more recent expansion in South America. The earliest diverging lineages are composed of Acanthotaeniinae and Gangesiinae but most of the presently recognized subfamilies (and genera) appear not to be monophyletic; a deep systematic reorganization of the order is thus needed and the present subfamilial system should be abandoned. The main characters on which the classical systematics of the group has been built, such as scolex morphology or relative position of genital organs in relation to the longitudinal musculature, are of limited value, as demonstrated by the very weak support for morphologically-defined subfamilies. However, new characters, such as the pattern of uterus development, relative ovary size, and egg structure have been identified, which may be useful in defining phylogenetically well-supported subgroups. A strongly supported lineage infecting various snakes from a wide geographical distribution was found. Although several improvements over previous works regarding phylogenetic resolution and taxon coverage were achieved in this study, the major polytomy in our tree, composed largely of siluriform parasites from the Neotropics, remained unresolved and possibly reflects a rapid radiation. The genus Spasskyellina Freze, 1965 is resurrected for three species of Monticellia bearing spinitriches on the margins of their suckers.

opencc-zeroDec 2018View details →

Data from: Community-level economics spectrum of fine-roots driven by nutrient limitations in subalpine forests

1. Fine-root traits show remarkable variation with plant community structure and environmental shifts, but there is limited understanding of how trait covariation that exists among fine-root traits shifts among different communities, especially in forests. We explored links among the fine-root traits of forest communities to determine whether community root traits shift predictably according to an economics framework along environmental gradients. 2. Measurements of root morphology, nitrogen, phosphorus and carbon concentrations, and measures of standing root densities were collected on fine roots (diameter ≤ 2 mm) from 129 forest plots in five subalpine forests. 3. This study demonstrates an existence of a community-level fine-root economics spectrum (REScom) in the subalpine forests, in which specific root length was strongly and positively related to root nitrogen and phosphorusconcentrations, but negatively related to root diameter. Soil nutrient limitation was a major driver of the REScom as changes in soil [N], [P] and [C] contents were related to changes in SRL, root [N], root [P]. Variables related to standing fine-root length and mass were independent of the REScom and was primarily related to forest community structure, particularly in tree closure and herbaceous plant mass. 4. These results indicate two distinct functional dimensions of community fine-root trait variation: resource-use efficiency via changes in root structure and construction, and separately via changes in the standing root system. Identifying shifts in allocation to and investment in fine roots enhances our understanding of a root and whole-plant economics spectrum and community functioning.

opencc-zeroDec 2012View details →

Data from: Heritability of lifespan is largely sex-limited in Drosophila

Males and females differ with respect to lifespan and rate of aging in most animal species. Such sexual dimorphism can be associated with a complex genetic architecture, where only part of the genetic variation is shared between the sexes. To the extent this is true for lifespan and aging is not known, since studies of lifespan have given contradictory results and because aging has not been studied from this perspective. Here we investigate the additive genetic architecture of lifespan and aging in Drosophila melanogaster. We find substantial amounts of additive genetic variation for both traits, and that more than three quarters of this variation is available for sex-specific evolutionary change. This result shows that the sexes have a profoundly different additive genetic basis for these traits, which has several implications. First it translated into an, on average, three times higher heritability of lifespan within compared to between the sexes. Second, it implies that the sexes are relatively free to evolve with respect to these traits. And third, as lifespan and aging are traits that integrate over all genetic factors that contribute to mortal disease, it also implies that the genetics of heritable disease differs vastly between the sexes.

opencc-zeroDec 2015View details →

Data from: Food limitation constrains host immune responses to nematode infections

Trade-offs in the allocation of finite-energy resources among immunological defences and other physiological processes are believed to influence infection risk and disease severity in food-limited wildlife populations. However, this prediction has received little experimental investigation. Here we test the hypothesis that food limitation impairs the ability of wild field voles (Microtus agrestis) to mount an immune response against parasite infections. We conducted a replicated experiment on vole populations maintained in large outdoor enclosures during boreal winter, using food supplementation and anthelmintic treatment of intestinal nematodes. Innate immune responses against intestinal parasite infections were compared between food-supplemented and non-supplemented voles. Voles with high food availability mounted stronger immune responses against intestinal nematode infections than food-limited voles. No food effects were seen in immune responses to intracellular coccidian parasites, possibly owing to their ability to avoid activation of innate immune pathways. Our findings demonstrate that food availability constrains vole immune responses against nematode infections, and support the concept that spatio-temporal heterogeneity in food availability creates variation in infectious disease susceptibility.

opencc-zeroDec 2010View details →

Data from: Seed supply, recruitment, and assembly: quantifying relative seed and establishment limitation in a plant community context

There is growing consensus that the relative constraints of seed limitation and establishment limitation in recruitment strongly influence abundance patterns in plant communities. Although these constraints have direct relevance to coexistence, most investigations utilize a seed addition approach that offers limited insight into these dynamics. Here we report results of an assembly experiment with annual plant species of California grasslands to examine how propagule pool characteristics (dominant species abundance, functional diversity) influence establishment and seed limitation (density independence and density dependence across a gradient of seed supply) for each species, and how these constraints affect community diversity. Species were predominantly co-limited by seed and establishment constraints, exhibiting saturating recruitment functions with increased seed supply. Consistent with competition-colonization trade-off predictions, recruitment constraints often depended on the degree of seed limitation of the competitive dominant, Brassica nigra; diversity was greatest in communities where Brassica was seed limited. Functional similarity within the propagule pool did not affect recruitment across a range of seed supply; likewise, functional diversity of the propagule pool was not related to community diversity. We conclude that seed limitation of the dominant species rather than niche similarity influences interspecific competition for safe sites and scales up to affect community-level diversity.

Data from: Limiting opportunities for cheating stabilizes virulence in insect parasitic nematodes

Cooperative secretion of virulence factors by pathogens can lead to social conflict when cheating mutants exploit collective secretion, but do not contribute to it. If cheats outcompete cooperators within hosts, this can cause loss of virulence. Insect parasitic nematodes are important biocontrol tools that secrete a range of significant virulence factors. Critically, effective nematodes are hard to maintain without live passage, which can lead to virulence attenuation. Using experimental evolution we tested whether social cheating might explain unstable virulence in the nematode Heterorhabditis floridensis by manipulating relatedness via multiplicity of infection (MOI), and the scale of competition. Passage at high MOI, which should reduce relatedness, led to loss of fitness: virulence and reproductive rate declined together and all eight independent lines suffered premature extinction. As theory predicts, relatedness treatments had more impact under stronger global competition. In contrast, low MOI passage led to more stable virulence and increased reproduction. Moreover, low MOI lineages showed a trade-off between virulence and reproduction, particularly for lines under stronger between-host competition. Overall, this study indicates that evolution of virulence theory is valuable for the culture of biocontrol agents: effective nematodes can be improved and maintained if passage methods mitigate possible social conflicts.

Data from: Limits to future adaptation in the invasive plant Polygonum cespitosum: expression of functional and fitness traits at elevated CO2

For organisms to adapt to future environments, they must both evolve appropriate functional responses and phenotypically express those responses under future climatic and CO2 conditions. We examined these 2 components of future adaptation in an invasive annual plant (Polygonum cespitosum) by performing a "resurrection" experiment under field conditions simulating a future environment. Resurrection experiments reveal recent evolution by comparing genotypes from natural populations sampled across a multigeneration interval. We collected genotypes from the same 3 North American populations in 1994 and 2005 and raised inbred lines from these collections under free air CO2 enrichment to examine functional and fitness traits expressed in hot, dry conditions at both ambient and elevated CO2 (N = 295 plants). The species has rapidly evolved in its introduced range to increase photosynthetic rate (collection year effect P ≤ 0.011) and delay senescence (P = 0.017) under full-sun, dry field conditions, but these adaptive changes were not expressed when the field environment included elevated CO2 (within-treatment year effect P ≥ 0.20 for both traits). Populations showed different levels of reproductive output and its genetic variance in these novel, stressful conditions. These findings illustrate constraints on evolutionary adaptation to predicted future conditions at both the species and population levels.

Data from: Limited dispersal in an ectoparasitic mite, Laelaps giganteus, contributes to significant phylogeographic congruence with their rodent hosts, Rhabdomys

To explore how biogeography, parasite life history and host vagility influences evolutionary codivergences, we followed a comparative phylogeography approach using a host specific non-permanent mite, Laelaps giganteus that occurs on four rodent species within the genus Rhabdomys. A mtDNA COI haplotype network derived for 278 parasite specimens showed marked phylogeographic congruence with host distributions. Analysis of the less variable nuclear intron Tropomyosin was in part consistent with these results. Although distance-based cophylogenetic analyses in AXPARAFIT failed to support significant mtDNA codivergences (P ≥ 0.02), event-based analyses revealed significant cophylogeny between sampling localities of Rhabdomys and Laelaps using CORE-PA (P = 0.046) and JANE (P = 0.026; P = 0.00). These findings, in conjunction with the weak congruence previously reported among the permanent ectoparasitic lice Polyplax and Rhabdomys, suggest that host-parasite intimacy is not the most important driver of significant codivergence in our study system. Instead the more restricted dispersal ability of L. giganteus, when compared to Polyplax, resulted in stronger spatial structuring and this could have resulted in significant codivergence. Host switching occurred predominantly on the edges of host distributions and was probably facilitated by climate-induced range shifts. When host ranges shift, the phylogeographic structure of L. giganteus is not reflecting the host movements since most of the nest bound parasites do not disperse with the host (they miss the boat) and the genetic contribution of the few dispersing mite individuals is often overwhelmed by the large number of individuals already present in nests within the new environment (causing them to drown on arrival).

Data from: Fitness declines toward range limits and local adaptation to climate affect dispersal evolution during climate-induced range shifts

Dispersal ability will largely determine whether species track their climatic niches during climate change, a process especially important for populations at contracting (low-latitude/low-elevation) range limits that otherwise risk extinction. We investigate whether dispersal evolution at contracting range limits is facilitated by two processes that potentially enable edge populations to experience and adjust to the effects of climate deterioration before they cause extinction: (i) climate-induced fitness declines towards range limits and (ii) local adaptation to a shifting climate gradient. We simulate a species distributed continuously along a temperature gradient using a spatially explicit, individual-based model. We compare range-wide dispersal evolution during climate stability vs. directional climate change, with uniform fitness vs. fitness that declines towards range limits (RLs), and for a single climate genotype vs. multiple genotypes locally adapted to temperature. During climate stability, dispersal decreased towards RLs when fitness was uniform, but increased when fitness declined towards RLs, due to highly dispersive genotypes maintaining sink populations at RLs, increased kin selection in smaller populations, and an emergent fitness asymmetry that favoured dispersal in low-quality habitat. However, this initial dispersal advantage at low-fitness RLs did not facilitate climate tracking, as it was outweighed by an increased probability of extinction. Locally adapted genotypes benefited from staying close to their climate optima; this selected against dispersal under stable climates but for increased dispersal throughout shifting ranges, compared to cases without local adaptation. Dispersal increased at expanding RLs in most scenarios, but only increased at the range centre and contracting RLs given local adaptation to climate.

Data from: Resource allocation and seed size selection in perennial plants under pollen limitation

Pollen limitation may affect resource allocation patterns in plants, but its role in the selection of seed size is not known. Using an evolutionarily stable strategy model of resource allocation in perennial iteroparous plants, we show that under density-independent population growth, pollen limitation (i.e., a reduction in ovule fertilization rate) should increase the optimal seed size. At any level of pollen limitation (including none), the optimal seed size maximizes the ratio of juvenile survival rate to the resource investment needed to produce one seed (including both ovule production and seed provisioning); that is, the optimum maximizes the fitness effect per unit cost. Seed investment may affect allocation to postbreeding adult survival. In our model, pollen limitation increases individual seed size but decreases overall reproductive allocation, so that pollen limitation should also increase the optimal allocation to postbreeding adult survival. Under density-dependent population growth, the optimal seed size is inversely proportional to ovule fertilization rate. However, pollen limitation does not affect the optimal allocation to postbreeding adult survival and ovule production. These results highlight the importance of allocation trade-offs in the effect pollen limitation has on the ecology and evolution of seed size and postbreeding adult survival in perennial plants.