Find research datasets worth reusing

Data from: Resource availability and sexual size dimorphism: differential effects of prey abundance on the growth rates of tropical snakes

1. Broad phylogenetic patterns in sexual size dimorphism (SSD) are shaped by sex differences in net selection pressures (e.g., sexual selection, fecundity selection, survival selection), but environmental and ecological factors can also affect the expression of SSD. 2. Discussions of proximate ecological influences on SSD have focused on niche divergence; for example, increase in a prey type used by only one sex can elevate growth rates of that sex but not the other. Food limitation also can generate spatial and temporal variation in SSD. Under restricted prey abundance, curtailed growth may mask SSD even if the optimal size is greater for one sex than the other. Because an increase in food availability then elicits increased feeding and growth by the sex that benefits more from increased body size, variation in prey abundance can generate variation in SSD. 3. We used mark-recapture methods to study growth rates relative to prey (frog) abundance in two species of sexually dimorphic colubrid snake species in tropical Australia. 4. In Slatey-grey snakes (Stegonotus cucullatus), a species in which larger body size enhances reproductive output in both sexes (because larger males win combat bouts, and larger females produce more / heavier eggs), increased abundance of frogs caused equivalent increases in growth rates in both sexes, and hence did not affect SSD. In Keelbacks (Tropidonophis mairii), a species in which larger size enhances reproductive output in females more than males (reflecting a lack of male-male combat), increased abundance of frogs elicited higher growth rates of females only. Thus, SSD in Keelbacks was modified by prey abundance. 5. Our results show that the magnitude of sex differences in adult body size can be influenced by proximate environmental factors, and support the hypothesis of sex-specific targets for maximum feeding rates.

opencc-zeroDec 2014View details →

Data from: Evaluating noninvasive genetic sampling techniques to estimate large carnivore abundance

Monitoring large carnivores is difficult because of intrinsically low densities and can be dangerous if physical capture is required. Noninvasive genetic sampling (NGS) is a safe and cost-effective alternative to physical capture. We evaluated the utility of two NGS methods (scat detection dogs and hair sampling) to obtain genetic samples for abundance estimation of coyotes, black bears and Canada lynx in three areas of Newfoundland, Canada. We calculated abundance estimates using program capwire, compared sampling costs, and the cost/sample for each method relative to species and study site, and performed simulations to determine the sampling intensity necessary to achieve abundance estimates with coefficients of variation (CV) of <10%. Scat sampling was effective for both coyotes and bears and hair snags effectively sampled bears in two of three study sites. Rub pads were ineffective in sampling coyotes and lynx. The precision of abundance estimates was dependent upon the number of captures/individual. Our simulations suggested that ~3.4 captures/individual will result in a < 10% CV for abundance estimates when populations are small (23–39), but fewer captures/individual may be sufficient for larger populations. We found scat sampling was more cost-effective for sampling multiple species, but suggest that hair sampling may be less expensive at study sites with limited road access for bears. Given the dependence of sampling scheme on species and study site, the optimal sampling scheme is likely to be study-specific warranting pilot studies in most circumstances.

opencc-zeroDec 2017View details →

Data from: Spatiotemporal heterogeneity in prey abundance and vulnerability shapes the foraging tactics of an omnivore

1. Prey abundance and prey vulnerability vary across space and time, but we know little about how they mediate predator-prey interactions and predator foraging tactics. To evaluate the interplay between prey abundance, prey vulnerability, and predator space use, we examined patterns of black bear (Ursus americanus) predation of caribou (Rangifer tarandus) neonates in Newfoundland, Canada using data from 317 collared individuals (9 bears, 34 adult female caribou, 274 caribou calves). 2. During the caribou calving season, we predicted that landscape features would influence calf vulnerability to bear predation, and that bears would actively hunt calves by selecting areas associated with increased calf vulnerability. Further, we hypothesized that bears would dynamically adjust their foraging tactics in response to spatiotemporal changes in calf abundance and vulnerability (collectively, calf availability). Accordingly, we expected bears to actively hunt calves when they were most abundant and vulnerable, but switch to foraging on other resources as calf availability declined. 3. As predicted, landscape heterogeneity influenced risk of mortality, and bears displayed the strongest selection for areas where they were most likely to kill calves, which suggested they were actively hunting caribou. Initially, the per-capita rate at which bears killed calves followed a type-I functional response, but as the calving season progressed and calf vulnerability declined, kill rates dissociated from calf abundance. In support of our hypothesis, bears adjusted their foraging tactics when they were less efficient at catching calves, highlighting the influence that predation phenology may have on predator space use. Contrary to our expectations, however, bears appeared to continue to hunt caribou as calf availability declined, but switched from a tactic of selecting areas of increased calf vulnerability to a tactic that maximized encounter rates with calves. 4. Our results reveal that generalist predators can dynamically adjust their foraging tactics over short time scales in response to changing prey abundance and vulnerability. Further, they demonstrate the utility of integrating temporal dynamics of prey availability into investigations of predator-prey interactions, and move towards a mechanistic understanding of the dynamic foraging tactics of a large omnivore.

Data from: Body mass as a supertrait linked to abundance and behavioural dominance in hummingbirds: a phylogenetic approach

Body mass has been considered one of the most critical organismal traits, and its role in many ecological processes has been widely studied. In hummingbirds body mass has been linked to ecological features like foraging performance, metabolic rates, and cost of flying, among others. We used an evolutionary approach to test if body mass is a good predictor of two of the main ecological features of hummingbirds: their abundances and behavioural dominance. To determine whether a species was abundant and/or behaviourally dominant, we used information from the literature on 249 hummingbird species. For abundance we classified a species as "plentiful" if it was described as the most abundant species in at least part of its geographic distribution, while we deemed a species to be "behaviourally dominant" when it was described as pugnacious (notably aggressive). We found that plentiful hummingbird species had intermediate body masses and were more phylogenetically related to each other than expected by chance. Conversely, behaviourally dominant species tended to have larger body mass and showed a random pattern of distribution in the phylogeny. Additionally, small-bodied hummingbird species were not considered plentiful by our definition and did not exhibit behavioural dominance. These results suggest a link between body mass, abundance, and behavioural dominance in hummingbirds. Our findings indicate the existence of a body mass range associated with the capacity of hummingbird species to be plentiful, behaviourally dominant, or to show both traits. The mechanisms behind these relationships are still unclear; however, our results provide support for the hypothesis that body mass is a supertrait that explains abundance and behavioural dominance in hummingbirds.

opencc-zeroDec 2017View details →

Data from: Grazing and resource availability control soil nematode body size and abundance-mass relationship in semi-arid grassland

1. Body size is a central functional trait in ecological communities. Despite recognition of the importance of above-belowground interactions, effects of aboveground herbivores on size and abundance-size relationships in soil fauna are almost uncharted. Depending on climate and soil properties, herbivores may increase basal resources of soil food webs, or reduce pore space, mechanisms expected to have contrasting effects on soil animal body size. 2. We investigated how body size and shape of soil nematodes responded to mammalian grazers in three semi-arid grassland sites, along a gradient of soil texture and organic matter (OM) in a long-term herbivore removal study. We analysed nematode mass, length, diameter, body size distribution, and biomass distribution. We formulated two mechanistic hypotheses to assess whether resource availability or pore space was the dominant abiotic control and modulated the effects of grazing. 3. In ungrazed soils, average and maximum nematode size, as well as abundance and biomass of large nematodes, were greater in the high-OM than in the low-OM soil, and intermediate in the medium-OM soil. Grazing promoted larger sizes in the low-OM soil, where it had been shown to increase organic matter and microbial biomass, and led to more homogeneous average size and body size distribution across sites. The results support the hypothesis that nematode size was controlled by basal resource availability rather than by pore space. However, body shape might have been constrained by small pores in the fine-texture, high-OM soil, where nematodes were more elongated. 4. Grazing may facilitate larger sizes in soil nematode communities by boosting basal resources where these are limiting, with important implications for estimations of nematode biomass and contribution to carbon and nutrient cycling. These findings contribute to the insofar-limited mechanistic understanding of how herbivores can shape functional traits of soil fauna, and demonstrate that animals at one trophic level may control patterns in body size and abundance-size relationships in other trophic levels without a direct predator-prey or competitive linkage between them.

Data from: Abundance drives broad patterns of generalisation in plant-hummingbird pollination networks

Abundant pollinators are often more generalised than rare pollinators. This could be because abundant species have more chance encounters with potential interaction partners. On the other hand, generalised species could have a competitive advantage over specialists, leading to higher abundance. Determining the direction of the abundance-generalisation relationship is therefore a 'chicken-and-egg' dilemma. Here we determine the direction of the relationship between abundance and generalisation in plant-hummingbird pollination networks across the Americas. We find evidence that hummingbird pollinators are generalised because they are abundant, and little evidence that hummingbirds are abundant because they are generalised. Additionally, most patterns of species-level abundance and generalisation were well explained by a null model that assumed interaction neutrality (interaction probabilities defined by species relative abundances). These results suggest that neutral processes play a key role in driving broad patterns of generalisation in animal pollinators across large spatial scales.

Data from: Host plant phylogeny and abundance predict root-associated fungal community composition and diversity of mutualists and pathogens

• Interactions between plants and their root-associated fungi (RAF) may influence the relative abundance of tree species and determine forest community diversity. Such plant-soil feedbacks in turn depend on the degree to which spatial distance and phylogenetic relatedness of host trees structure pathogen and mutualist communities, but research detailing these aspects of RAF communities is lacking. Here, we characterize plant-RAF associations across a diverse plant community, focusing on the degree to which RAF communities are structured by spatial distance, host phylogenetic relatedness, and host abundance. We compare results for different functional groups, including both putative mutualists and pathogens, an aspect poorly examined hitherto. • We collected roots at regular intervals along ten 50 m by 2 m transects, then used DNA barcoding to identify host plants, and characterize the associated fungal community. Variance partitioning was used to measure the relative contributions of host phylogenetic relatedness and spatial distance to explaining RAF community composition. A weighted linear regression was used to measure the correlation between host abundance and RAF diversity. • Phylogenetic distance among hosts was a better predictor of RAF community composition than spatial distance, but this relationship was stronger for putative pathogens than for mutualists, suggesting that pathogens show stronger host preference than mutualists. Across all functional groups, RAF showed similar levels of spatial structure. Additionally, RAF communities of locally abundant plants were less diverse than RAF communities of rare plants. • Synthesis: We found that RAF communities are structured by the phylogenetic relatedness of hosts and, to a lesser extent, by spatial distance, with pathogens showing stronger host preference than mutualists. Abundant hosts had less diverse RAF communities than rare hosts, which is notable because abundant plants tend to experience weaker negative plant-soil feedback. Going forward, mechanisms underlying the host abundance-RAF diversity relationship warrant further investigation. Additionally, the survey approach presented here could be paired with experiments linking RAF community composition to plant recruitment.

Data from: Effects of early-season insect herbivory on subsequent pathogen infection and ant abundance on wild cotton (Gossypium hirsutum)

1. Plant induced defences play an important role in mediating interactions between insects and pathogens. Yet, the plant traits underlying these effects, the extended consequences for higher trophic levels (i.e. predators), and the implications for plant growth and reproduction have received little attention. 2. Here we asked whether simulated early insect leaf damage on wild cotton (Gossypium hirsutum) affected subsequent damage by insect leaf chewers and pathogenic fungi, as well as ant abundance. To address the mechanisms behind such effects, we measured plant defensive traits induced by early leaf damage to determine which inducible traits might determine the effects on plant-associates. We also evaluated whether early damage influenced plant growth and flower production, and if such effects were mediated by subsequent insect herbivory or pathogen infection. 3. We show that simulated early leaf damage reduced damage by subsequent leaf-chewing insects, increased plant fungal infections, but did not affect ant abundance. Leaf defensive traits (lignins and pubescence) were significantly induced by early damage and were negatively associated with insect herbivory and infection severity, but did not account for the effects of early leaf damage on either of these subsequent attackers. In addition, ant abundance was not associated with (or accounted for) subsequent herbivory or infection, suggesting they did not confer plant protection. Finally, early leaf damage negatively affected plant growth and flower production and analyses suggested that the effect on the latter was, at least partly, mediated by increased fungal infections. 4. Synthesis: Overall, these findings show that early herbivory determines the outcome of cotton interactions with subsequent attackers, and such effects have an impact on plant growth and flower output.

Data from: Predation risk and resource abundance mediate foraging behaviour and intraspecific resource partitioning among consumers in dominance hierarchies

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

opencc-zeroDec 2011View details →

Data from: The effects of contig length and depth on the estimation of SNP frequencies, and the relative abundance of SNPs in protein-coding and non-coding transcripts of tiger salamanders (Ambystoma tigrinum)

BACKGROUND: Next-generation sequencing methods have contributed to rapid progress in the fields of genomics and population genetics. Using this high-throughput and cost-effective technology, a number of studies have estimated single nucleotide polymorphism (SNP) frequency by calculating the mean number of SNPs per unit sequence length (e.g., mean SNPs/kb). However, both read length and contig depth are highly variable and thus raise doubt about simple methods of SNP frequency estimation. RESULTS: We used 454 pyrosequencing to identify 2,980 putative SNPs in the eastern tiger salamander (Ambystoma tigrinum tigrinum) transcriptome, then constructed analytical models to estimate SNP frequency. The model which considered only contig length (i.e., the method employed in most published papers) was evaluated with very poor likelihood. Our most robust model considered read depth as well as contig length, and was 7.5 × 1055 times more likely than the length-only model. Using this novel modeling approach, we estimated SNP frequency in protein-coding (mRNA) and non-coding transcripts (e.g., small RNAs). We found little difference in SNP frequency in the contigs, but we found a trend of a higher frequency of SNPs in long contigs representing non-coding transcripts relative to protein-coding transcripts. These results support the hypothesis that long non-coding transcripts are less conserved than long protein-coding transcripts. CONCLUSIONS: A modeling approach (i.e., using multiple model construction and model selection approaches) can be a powerful tool for identifying selection on specific functional sequence groups by comparing the frequency and distribution of polymorphisms.

Data from: Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows

The effects of sunflower oil (SO) (0 or 50 g/kg diet dry matter), supplemented to diets contrasting in the proportion of forage and concentrate (FC) (65:35 vs 35:65), were evaluated for their influence on rumen microbiome. Four multiparous Nordic Red dairy cows fitted with rumen cannulae were used in a 4 × 4 Latin square with a 2 × 2 factorial arrangement of treatments and four 35-d periods. Ruminal digesta samples were collected on d 22 and d 24 of each experimental period and DNA was extracted from a combined sample. Diet effect on rumen microbial community was explored by qPCR, T-RFLP and metabarcoding sequencing. QPCR analysis showed that the total amounts of bacteria, archaea or ciliate protozoa were not significantly altered either by FC ratio or addition of SO. Only fungi were reduced by half in high concentrate (H) compared to high forage (L) diets (P=0.03). Further significant reduction of fungi was observed due to SO in both HSO and LSO diets but the effect was stronger in HSO (H vs HSO by 10.5x, P=0.03; L vs LSO by 1.9x, P=0.04). Metabarcoding sequencing analysis showed that SO affected bacterial, archaeal, ciliate protozoa and fungal community structure and diversity and the effect was FC ratio dependent. As expected, Simpson's index of diversity was higher in diets containing higher proportion of forage. These diets were dominated by Firmicutes, while Bacteroidetes and Proteobacteria were more abundant in H diets. Methanobrevibacter ruminantium and Methanobrevibacter gottschalkii dominated archaea community but they were in negative relation to each other. Methanobrevibacter gottschalkii was more abundant in L, while Methanobrevibacter ruminantium in H diet. The strongest diet effect was observed on fungal community, represented by both well classified and novel fungal groups. Both, increase in concentrate and supplementation of SO significantly reduced fungal diversity. We explored microbial interactions by building taxa co-occurrence networks. Our results suggest that studying entire rumen microbiome simultaneously is needed aiming to better understand how diet induced changes within microbial community are associated with microbial function, subsequently leading to better understanding of rumen fermentation and methanogenesis.

Data from: Silicon-induced root nodulation and synthesis of essential amino acids in a legume is associated with higher herbivore abundance

Ecologists have become increasingly aware that silicon uptake by plants, especially the Poaceae, can have beneficial effects on both plant growth and herbivore defence. The effects of silicon on other plant functional groups, such as nitrogen-fixing legumes, have been less well studied. Silicon could, however, indirectly promote herbivore performance in this group if reported increases in N2-fixation caused improvements in host plant quality for herbivores. We tested how silicon supplementation in the legume Medico sativa affected plant growth rates, root nodulation and foliage quality (silicon content and amino acid profiles) for an insect herbivore (Acyrthosiphon pisum). Plants supplemented with silicon (Si+) grew three times as quickly as those without supplementation (Si-), almost entirely in shoot mass. While root growth was unaffected by silicon uptake, root nodules containing nitrogen-fixing bacteria were 44% more abundant on Si+ plants. Aphid abundance was twice as high on Si+ plants compared to Si- plants and was positively correlated with silicon-stimulated plant growth. Si+ plants accumulated more than twice as much silicon as Si- plants, but did not have higher silicon concentrations because of dilution effects linked to the rapid growth of Si+ plants. Si+ plants showed a 65% increase in synthesis of essential foliar amino acids, probably due to increased levels of root nodulation. These results suggest that increased silicon supply makes M. sativa more susceptible to A. pisum, mainly because of increased plant growth and resource availability (i.e. essential amino acids). While silicon augmentation of the Poaceae frequently improves herbivore defence, the current study illustrates that this cannot be assumed for other plant families where the beneficial effects of silicon on plant growth and nutrition may promote herbivore performance in some instances.

Data from: Random sequences are an abundant source of bioactive RNAs or peptides

It is generally assumed that new genes arise through duplication and/or recombination of existing genes. The probability that a new functional gene could arise out of random non-coding DNA is so far considered to be negligible, as it seems unlikely that such an RNA or protein sequence could have an initial function that influences the fitness of an organism. Here, we have tested this question systematically, by expressing clones with random sequences in Escherichia coli and subjecting them to competitive growth. Contrary to expectations, we find that random sequences with bioactivity are not rare. In our experiments we find that up to 25% of the evaluated clones enhance the growth rate of their cells and up to 52% inhibit growth. Testing of individual clones in competition assays confirms their activity and provides an indication that their activity could be exerted by either the transcribed RNA or the translated peptide. This suggests that transcribed and translated random parts of the genome could indeed have a high potential to become functional. The results also suggest that random sequences may become an effective new source of molecules for studying cellular functions, as well as for pharmacological activity screening.

opencc-zeroDec 2013View details →

Data from: Microsatellite abundance across the Anthozoa and Hydrozoa in the phylum Cnidaria

Background: Microsatellite loci have high mutation rates and thus are indicative of mutational processes within the genome. By concentrating on the symbiotic and aposymbiotic cnidarians, we investigated if microsatellite abundances follow a phylogenetic or ecological pattern. Individuals from eight species were shotgun sequenced using 454 GS-FLX Titanium technology. Sequences from the three available cnidarian genomes (Nematostella vectensis, Hydra magnipapillata and Acropora digitifera) were added to the analysis for a total of eleven species representing two classes, three subclasses and eight orders within the phylum Cnidaria. Results: Trinucleotide and tetranucleotide repeats were the most abundant motifs, followed by hexa- and dinucleotides. Pentanucleotides were the least abundant motif in the data set. Hierarchical clustering and log likelihood ratio tests revealed a weak relationship between phylogeny and microsatellite content. Further, comparisons between cnidaria harboring intracellular dinoflagellates and those that do not, show microsatellite coverage is higher in the latter group. Conclusions: Our results support previous studies that found tri- and tetranucleotides to be the most abundant motifs in invertebrates. Differences in microsatellite coverage and composition between symbiotic and non-symbiotic cnidaria suggest the presence/absence of dinoflagellates might place restrictions on the host genome.

opencc-zeroDec 2017View details →

Data from: Nest survival in year-round breeding tropical Red-capped Larks (Calandrella cinerea) increases with higher nest abundance but decreases with higher invertebrate availability and rainfall

Nest survival is critical to breeding in birds and plays an important role in life-history evolution and population dynamics. Studies evaluating the proximate factors involved in explaining nest survival and the resulting temporal patterns are biased in favor of temperate regions. Yet, such studies are especially pertinent to the tropics, where nest predation rates are typically high and environmental conditions often allow for year-round breeding. To tease apart the effects of calendar month and year, population-level breeding activity and environmental conditions, we studied nest survival over a 64-month period in equatorial, year-round breeding red-capped larks Calandrella cinerea in Kenya. We show that daily nest survival rates varied with time, but not in a predictable seasonal fashion among months or consistently among years. We found negative influences of flying invertebrate biomass and rain on nest survival and higher survival of nests when nests were more abundant, which suggests that nest predation resulted from incidental predation. Although an increase in nest predation is often attributed to an increase in nest predators, we suggest that in our study, it may be caused by altered predator activity resulting from increased activity of the primary prey, invertebrates, rather than activity of the red-capped larks. Our results emphasize the need to conduct more studies in Afro-tropical regions because proximate mechanisms explaining nest predation can be different in the unpredictable and highly variable environments of the tropics compared with the relatively predictable seasonal changes found in temperate regions. Such studies will aid in better understanding of the environmental influences on life-history variation and population dynamics in birds.

opencc-zeroSep 2019View details →

Data from: Bird species diversity in Altai riparian landscapes: wood cover plays a key role for avian abundance

Aims: We aim to understand bird richness and variation in species composition (beta diversity) along a 630 km riparian landscape in the Altai Mountains of China, and to test whether vegetation cover is the main explanation of species diversity. Methods: We selected nine regions along a gradient of natural vegetation change. Bird surveys and environmental measurements were conducted at 10 points in each of the nine regions. We collected environmental land cover variables such as wood cover (area proportion of trees and shrubs with saplings in habitats; here trees are woody plant with a single trunk and higher than 3m, shrubs and saplings are distinguished from trees by their multiple trunks and shorter height) and tree cover, and two climate factors which were Annual Mean Temperature (AMT) and Annual Precipitation (AP). We used Liner Regression Models to explore the correlation between bird species richness and environmental variables. We used Sørensen's dissimilarity index to measure birds' beta diversity, and quantified the contribution of environmental variables to this pattern using a Canonical Correspondence Analysis (CCA). Results: Wood cover was the strongest predictor of overall, insectivore and omnivore bird richness. Regions with wood cover contained more bird species. Beta diversity was overall high in the studied regions, and turnover components occupied a major part of beta diversity. Wood cover and AP were significant predictors of bird species composition explaining 33.24% of bird beta diversity together. Conclusions: Wood vegetation including trees, shrubs and saplings, rather than only trees, contains high bird richness. High beta diversity suggests that expansion of the existing nature reserves is needed in the riparian landscapes to capture the variation in bird species composition. Thus all wood cover in the overall riparian landscapes of Altai Mountains should be protected from farming and grazing to improve bird conservation outcomes.

opencc-zeroDec 2013View details →

Data from: Genomic repeat abundances contain phylogenetic signal

A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilising comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution.

Data from: Linking intra-specific trait variation to community abundance dynamics improves ecological predictability by revealing a growth-defence trade-off

1.Intraspecific trait change, including altered behaviour or morphology, can drive temporal variation in inter-specific interactions and population dynamics. In turn, variation in species' interactions and densities can alter the strength and direction of trait change. The resulting feedback between species′ traits and abundance permits a wide range of community dynamics that would not be expected from ecological theories purely based on species abundances. Despite the theoretical importance of these interrelated processes, unambiguous experimental evidence of how intraspecific trait variation modifies species interactions and population dynamics and how this feeds back to influence trait variation is currently required. 2.We investigate the role of trait-mediated demography in determining community dynamics and examine how ecological interactions influence trait change. We concurrently monitored the dynamics of community abundances and individual traits in an experimental microbial predator-prey-resource system. Using this data, we parameterized a trait dependent community model to identify key ecologically relevant traits and to link trait dynamics with those of species abundances. 3.Our results provide clear evidence of a feedback between trait change, demographic rates and species dynamics. The inclusion of trait-abundance feedbacks into our population model improved the predictability of ecological dynamics from r-squared of 34% to 57% and confirmed theoretical expectations of density dependent population growth and species interactions in the system. 4.Additionally, our model revealed that the feedbacks were underpinned by a trade-off between population growth and anti-predatory defence. High predator abundance was linked to a reduction in prey body size. This prey size decrease was associated with a reduction in its rate of consumption by predators and a decrease in its resource consumption. 5.Modelling trait-abundance feedbacks allowed us to pinpoint the underlying life history trade-off which links trait and abundance dynamics. These results show that accounting for trait-abundance feedbacks has the potential to improve understanding and predictability of ecological dynamics.

opencc-by-4.0Feb 2024View details →

zenodo28/100

Abundant genetic variation is retained in many laboratory schistosome populations - Code and data

Code and data used for the generation of figures in manuscript.