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371 results for “Ecology and Evolution”
Genomics of extreme ecological specialists: multiple convergent evolution but no genetic divergence between ecotypes of Maculinea alcon butterflies
<p>Biotic interactions are often acknowledged as catalysers of genetic divergence and eventual explanation of processes driving species richness. We address the question, whether extreme ecological specialization is always associated with lineage sorting, by analysing polymorphisms in morphologically similar ecotypes of the myrmecophilous butterfly <em>Maculinea alcon</em>. The ecotypes occur in either hygric or xeric habitats, use different larval host plants and ant species, but no significant distinctive molecular traits have been revealed so far. We apply genome-wide RAD-sequencing to specimens originating from both habitats across Europe in order to get a view of the potential evolutionary processes at work. Our results confirm that genetic variation is mainly structured geographically but not ecologically — specimens from close localities are more related to each other than populations of each ecotype from distant localities. However, we found two loci for which the association with xeric versus hygric habitats is supported by segregating alleles, suggesting convergent evolution of habitat preference. Thus, ecological divergence between the forms probably does not represent an early stage of speciation, but may result from independent recurring adaptations involving few genes. We discuss the implications of these results for conservation and suggest preserving biotic interactions and main genetic clusters.</p>
Data from: Padfield et al. (2016) Rapid evolution of metabolic traits explains thermal adaptation in phytoplankton. Ecology letters.
<p>This repository provides the data from the TPC and logistic growth curves from the paper:</p> <p>Padfield, D., Yvon‐Durocher, G., Buckling, A., Jennings, S., & Yvon‐Durocher, G. (2016). Rapid evolution of metabolic traits explains thermal adaptation in phytoplankton. Ecology letters, 19(2), 133-142.</p> <p>metadata.pdf gives a more detailed explanation of the data.</p>
Data and code from "Black-throated blue warblers (Setophaga caerulescens) exhibit diet flexibility and track seasonal changes in insect availability" Kaiser et al. 2024 Ecology and Evolution
Changes in leaf phenology from warming spring and autumn temperatures have lengthened the temperate zone growing ‘green’ season and breeding window for migratory birds in North America. However, the fitness benefits of an extended breeding season will depend, in part, on whether species have sufficient dietary flexibility to accommodate seasonal changes in prey availability. We used fecal DNA metabarcoding to test the hypothesis that seasonal changes in the diets of the insectivorous, migratory black-throated blue warbler (Setophaga caerulescens) track changes in the availability of arthropod prey at the Hubbard Brook Experimental Forest, New Hampshire, USA. We examined changes across the breeding season and along an elevation gradient encompassing a two-week difference in green season length. From 98 fecal samples, we identified 395 taxa from 17 arthropod orders; 242 were identified to species, with Cecrita guttivitta (saddled prominent moth), Theridion frondeum (eastern long-legged cobweaver), and Philodromus rufus (white-striped running crab spider) occurring at the highest frequency. We found significant differences in diet composition between survey periods and weak differences among elevation zones. Variance in diet composition was highest late in the season, and diet richness and diversity were highest early in the season. Diet composition was associated with changes in prey availability surveyed over the green season. However, several taxa occurred in diets more or less than expected relative to their frequency of occurrence from survey data, suggesting that prey selection or avoidance sometimes accompanies opportunistic foraging. This study demonstrates that black-throated blue warblers exhibit diet flexibility and track seasonal changes in prey availability, which has implications for migratory bird responses to climate-induced changes in insect communities with longer green seasons. These data were gathered as part of the Hubbard Brook Ecosystem Study (HB
Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation
<p>Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all ~6000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our 'backbone-and-patch' approach to tree-building applies a newly assembled 31-gene supermatrix to two levels of Bayesian inference: (i) backbone relationships and ages among major lineages, using fossil node- or tip-dating; and (ii) species-level 'patch' phylogenies with non-overlapping in-groups that each correspond to one representative lineage in the backbone. Species unsampled for DNA are either excluded ('DNA-only' trees) or imputed within taxonomic constraints using branch lengths drawn from local birth-death models ('completed' trees). Joining time-scaled patches to backbones results in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. We compare our phylogenetic trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (i) node ages are broadly concordant among studies, and (ii) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous 'supertree' approaches where unresolved nodes led to branch length artifacts. Credible sets of mammalian phylogenetic history are now available for download at <a href="http://vertlife.org/phylosubsets">http://vertlife.org/phylosubsets</a>, enabling investigations of long-standing questions in comparative biology.</p>
Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation
Open the record for dataset details and reuse information.
Data from: Breaking Barriers? Ethnicity and socioeconomic background impact on early career progression in the fields of ecology and evolution
<p>The academic disciplines of Science, Technology, Engineering and Mathematics (STEM) have long suffered from a lack of diversity. While in recent years there has been some progress in addressing the underrepresentation of women in STEM subjects, other characteristics that have the potential to impact on equality of opportunity have received less attention. In this study, we surveyed 188 early career scientists (ECRs), defined as within ten years of completing their PhD, in the fields of ecology, evolutionary biology, behaviour, and related disciplines. We examined associations between ethnicity, age, sexual orientation, sex, socioeconomic background, and disability, with measures of career progression, namely publication record, number of applications made before obtaining a postdoc, type of contract, and number of grant applications made. We also queried respondents on perceived barriers to progression, and potential ways of overcoming them. Our key finding was that socioeconomic background and ethnicity were associated with measures of career progression. While there was no difference in the number of reported first-authored papers on PhD completion, ethnic minority respondents reported fewer other-authored papers. In addition, ECRs from a lower socioeconomic background were more likely to report being in teaching and research positions, rather than research only positions, the latter being perceived as more prestigious by some institutions. We discuss our findings in the context of possible inequality of opportunity. We hope that this study will stimulate wider discussion, and help to inform strategies to address the underrepresentation of minority groups in the fields of ecology and evolution, and STEM subjects more widely.</p>
Supporting Data from Ecological Opportunities and Constraints in the Evolution of Diatoms
<p>2016-02-01<br /> Teofil Nakov</p> <p>Data and code for Nakov, Ruck, Alverson: Ecological opportunities and constraints in the evolution of diatom</p> <p>This packet contains the following files:</p> <p>1. Sequence alignment for 540 diatoms and 2 Bolidomonas: Nakov-etal-542-taxon-alignment-clean.fasta<br /> 2. The constraint topology used in tree searches: Nakov-etal-constraint-small-clades.phylip<br /> 3. Alignment partition file: Nakov-etal-tiger-partitions-rax<br /> 4. Character data for 540 diatoms and 2 Bolidomonas: Nakov-etal-542-taxon-discrete-characters.csv<br /> 5. The best tree from 420 RAxML optimizations: Nakov-etal-RAxML_bestTree.opt_89<br /> 6. 99 additional trees used in the analyses: Nakov-etal-99-randomly-sampled-unique-trees.newick<br /> 7. All 100 trees converted into chronograms: Nakov-etal-100-chronograms-smooth-1000.newick<br /> 8. Script with random seeds for RAxML optimizations: Nakov-etal-RAxML-calls-for-420-optimizations<br /> 9. R scripts with random seeds: Nakov-etal-R-scripts.zip (three scripts: equal-rates, independent, and coordinated + paint regimes models)<br /> 10. TreePL control file: Nakov-etal-TreePL-control-file.txt</p>
Supporting voucher images for Phylogeny, ecology, morphological evolution, and reclassification of the diatom orders Surirellales and Rhopalodiales
<p>A compressed directory of images of voucher specimens used for sequencing and phylogenetic analysis.</p>
Data from: Mating environments mediate the evolution of behavioral isolation during ecological speciation
<p>The evolution of behavioral isolation is often the first step towards speciation. While past studies show that behavioral isolation will sometimes evolve as a by-product of divergent ecological selection, we lack a more nuanced understanding of factors that may promote or hamper its evolution. The environment in which mating occurs may be important in mediating whether behavioral isolation evolves for two reasons. Ecological speciation could occur as a direct outcome of different sexual interactions being favored in different mating environments. Alternatively, mating environments may vary in the constraint they impose on traits underlying mating interactions, such that populations evolving in a 'constraining' mating environment would be less likely to evolve behavioral isolation than populations evolving in a less constraining mating environment. In the latter, mating environment is not the direct cause of behavioral isolation but rather permits its evolution only if other drivers are present. We test these ideas with a set of 28 experimental fly populations, each of which evolved under one of two mating environments and one of two larval environments. Counter to the prediction of ecological speciation by mating environment, behavioral isolation was not maximal between populations evolved in different mating environments. Nonetheless, mating environment was an important factor as behavioral isolation evolved among populations from one mating environment but not among populations from the other. Though one mating environment was conducive to the evolution of behavioral isolation, it was not sufficient: assortative mating only evolved between populations adapting to different larval environments within that mating environment, indicating a role for ecological speciation. Intriguingly, the mating environment that promoted behavioral isolation is characterized by less sexual conflict compared to the other mating environment. Our results suggest that mating environments plays a key role in mediating ecological speciation via other axes of divergent selection.</p>
Data from: Interactions between sexual signaling, thermoregulation and body size drive ecology and evolution of wing colors in Odonata
<p>This dataset consists of images of the fore and hind wings (and associated metadata) of 4091 individual odonate specimens, and thus over 8000 wings, imaged on a commercially-available Epson desktop flatbed scanner and color-calibrated using a color-checker, comprising the Targeted Odonata Wing Digitization dataset (TOWD; <a href="https://digitizingdragonflies.org/">https://digitizingdragonflies.org/</a>) The odonates imaged are all from the Nearctic, and represent 343 species. </p> <p>In this dataset, 47% of images come from the Alabama Museum of Natural History (ALMNH), 19% from the PhD thesis collection of William Kuhn (now housed at the American Museum of Natural History, AMNH), 19% from the collection of the late Michael L. May, and 13% from Jessica Ware’s Rutgers-University Newark collection (now housed at the AMNH). </p> <p>Files are individual PNGs where transparency is the background. </p> <p>Metadata includes species, sex, and county. </p>
Ecology and evolution of chlamydial symbionts of arthropods
<p><strong>The phylum Chlamydiae consists of obligate intracellular bacteria including major human pathogens and diverse environmental representatives. Here we investigated the Rhabdochlamydiaceae which is predicted to be the largest and most diverse chlamydial family, with the few known members infecting arthropod hosts. Using published 16S rRNA gene sequence data we identified at least 388 genus-level lineages containing about 14 051 putative species within this family. We show that rhabdochlamydiae are mainly found in freshwater and soil environments, suggesting the existence of diverse, yet unknown hosts. Next, we created a comprehensive genome dataset including metagenome assembled genomes classified as members of the family Rhabdochlamydiaceae, and we determined the genome sequences of two Rhabdochlamydia species, R. porcellionis infecting the woodlouse Porcellio scaber, and R. oedothoracis associated with the dwarf spider Oedothorax gibbosus. Comparative analysis of basic genome features and gene content with reference genomes of well-studied chlamydial families with known host ranges, namely Parachlamydiaceae (protist hosts) and Chlamydiaceae (human and other vertebrate hosts) suggested a distinct niche for members of the Rhabdochlamydiaceae. We propose that members of the family represent intermediate stages of adaptation of chlamydiae from protists to vertebrate hosts. Within the genus Rhabdochlamydia pronounced genome size reduction could be observed (1.49-1.93 Mb). The abundance and genomic distribution of transposases suggests transposable element expansion and subsequent gene inactivation as a mechanism of genome streamlining during adaptation to new hosts. Together, this study provides first insights into the molecular ecology, genomic diversity and evolution of representatives of one of the most successful chlamydial families.</strong></p>
Data and JAGS-code for "Michel et al 2022 Ecology and Evolution - Reduced habitat quality increases intrinsic but not ecological costs of reproduction"
<p><strong>Abstract</strong></p> <p>Although the costs of reproduction are predicted to vary with the quality of the breeding habitat thereby affecting population dynamics and life-history trade-offs, empirical evidence for this pattern remains sparse and equivocal. Costs of reproduction can operate through immediate ecological mechanisms or through delayed intrinsic mechanisms. Ignoring these separate pathways might hinder the identification of costs and the understanding of their consequences. We experimentally investigated the survival costs of reproduction for adult little owls (<em>Athene noctua</em>) within a gradient of habitat quality. We supplemented food to nestlings, thereby relieving the parents’ effort for brood provisioning. We used radio-tracking and Bayesian multi-state modelling based on marked recapture and dead recovery to estimate survival rates of adult little owls across the year as a function of food supplementation and habitat characteristics. Food supplementation to nestlings during the breeding season increased parental survival not only during the breeding season but also during the rest of the year. Thus, the low survival of parents of unfed broods likely represents both, strong ecological and strong intrinsic costs of reproduction. However, while immediate ecological costs occurred also in high quality habitats, intrinsic costs carrying over to the post-breeding period occurred only in low quality habitats. Our results suggest that immediate costs resulting from ecological mechanisms such as predation, are high also in territories of high habitat quality. Long-term costs resulting from intrinsic trade-offs, however, are only paid in low quality habitats. Consequently, differential effects of habitat quality on immediate ecological and delayed intrinsic mechanisms can mask the increase of costs of reproduction in low quality breeding habitats. Intrinsic costs may represent an underrated mechanism of habitat quality affecting adult survival rate thereby considerably accelerating population decline in degrading habitats. This study therefore highlights the need for a long-term perspective to fully assess the costs of reproduction and the role of habitat quality in modifying these costs.</p>
Data from: Ecology and evolution of blood oxygen-carrying capacity in birds
Blood oxygen-carrying capacity is one of important determinants of oxygen amounts supplied to the tissues per unit time and plays a key role in oxidative metabolism. In wild vertebrates, blood oxygen-carrying capacity is most commonly measured with the total blood haemoglobin concentration (Hb) and haematocrit (Hct), which is the volume percentage of red blood cells in blood. Here, I used published estimates of avian Hb and Hct (nearly one thousand estimates from 300 species) to examine macroevolutionary patterns in blood oxygen-carrying capacity of blood in birds. Phylogenetically-informed comparative analysis indicated that blood oxygen-carrying capacity was primarily determined by species distribution (latitude and elevation) and morphological constraints (body mass). I found little support for the effect of life history components on blood oxygen-carrying capacity, except for a positive association of Hct with clutch size. Hb was also positively associated with diving behaviour, but I found no effect of migratoriness on either Hb or Hct. Fluctuating selection was identified as the major force shaping the evolution of blood oxygen-carrying capacity. The results offer novel insights into the evolution of Hb and Hct in birds, as well as they provide a general, phylogenetically-robust support for some long-standing hypotheses in avian ecophysiology.
Frontiers in Ecology and Evolution 01 frontiersin.org Why grazing and soil matter for dry grassland diversity: New insights from multigroup structural equation modeling of micro-patterns
<p>Grazing is recognized as a major process driving the composition of plant<br> communities in grasslands, mostly due to the heterogeneous removal of<br> plant species and soil compaction that results in a mosaic of small patches<br> called micro-patterns. To date, no study has investigated the differences in<br> composition and functioning among these micro-patterns in grasslands in<br> relation to grazing and soil environmental variables at the micro-local scale.<br> In this study, we ask (1) To what extent are micro-patterns different from each<br> other in terms of species composition, species richness, vegetation volume,<br> evenness, and functioning? and (2) based on multigroup structural equation<br> modeling, are those differences directly or indirectly driven by grazing and soil<br> characteristics? We focused on three micro-patterns of the Mediterranean dry<br> grassland of the Crau area, a protected area traditionally grazed in the South-<br> East of France. From 70 plant community relevés carried out in three micro-<br> patterns located in four sites with different soil and grazing characteristics,<br> we performed univariate, multivariate analyses and applied structural equation<br> modeling for the first time to this type of data. Our results show evidence<br> of clear differences among micro-pattern patches in terms of species<br> composition, vegetation volume, species richness, evenness, and functioning<br> at the micro-local scale. These differences are maintained not only by direct<br> and indirect effects of grazing but also by several soil variables such as fine<br> granulometry. Biological crusts appeared mostly driven by these soil variables,<br> whereas reference and edge communities are mostly the result of different<br> levels of grazing pressure revealing three distinct functioning specific to each<br> micro-pattern, all of them coexisting at the micro-local scale in the studied<br> Mediterranean dry grassland. This first overview of the multiple effects of<br> grazing and soil characteristics on communities in micro-patterns is discussed<br> within the scope of the conservation of dry grasslands plant diversity.</p>
Eye morphology contributes to the ecology and evolution of the avian tree of life
<p>The avian eye is the single most important external anatomical trait for interpreting light environments by birds and varies widely in size and shape across the avian tree of life. The attached dataset provides measurements on eye size taken from preserved museum specimens for roughly one third of the avian tree of life (N = 3,475 species). The original dataset was collected by Stanley Ritland and Alice Hutchinson and archived as appendices in Stanley Ritland's Dissertation from the University of Chicago (1982): "The Allometry of the Vertebrate Eye".</p>
FIGURE 18 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 18. Ancestral state reconstruction of prey capture strategies and prey type preference in stem and crown Mysticeti. Topology follows Gatesy et al. (2013) and Fordyce and Marx (2018). Details on the tree can be found in Appendix 1. All data matrices and complete trees with branch lengths can be found in the Supplementary Information (https://doi.org/10.6086/d14671).
FIGURE 3 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 3. Anatomical features associated with suction feeding in walrus (Odobenus rosmarus skull, from Jefferson et al., 2015) and North Sea beaked whale (Mesoplodon bidens skull, authors' work).
FIGURE 11 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 11. Sirenia stem and familial level diversity through time. "Protosirenidae / Prorastomidae" includes all taxa that are not included in the two extant groups. Dashed vertical lines: black, epoch boundaries; gray, age boundaries.
FIGURE 7 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 7. Pinnipedimorpha stem taxa and familial level diversity through time. "Stem-Pinnipedimorpha" includes all stem taxa that are not included in Desmatophocidae and the three extant groups. Dashed vertical lines: black, epoch boundaries; gray, age boundaries.
FIGURE 5 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 5. Anatomical features associated with grazing in African manatee (Trichechus senegalensis skull, from Werth, 2000), Desmostylia (Paleoparadoxia skull, public domain), and aquatic sloth (Thalassocnus sp. skull, modified from de Muizon et al., 2004).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.