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Data from: Assessing thermal adaptation using family-based association and FST-outlier tests in a threatened trout
Discovering genetic markers associated with phenotypic or ecological characteristics can improve our understanding of adaptation and guide conservation of key evolutionary traits. The Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) of the northern Great Basin Desert, USA, demonstrated exceptional tolerance to high temperatures in the desert lakes where it resided historically. This trait is central to a conservation hatchery effort to protect the genetic legacy of the nearly extinct lake ecotype. We genotyped full‐sibling families from this conservation broodstock and samples from the only two remaining, thermally distinct, native lake populations at 4,644 new single nucleotide polymorphisms (SNPs). Family‐based genome‐wide association testing of the broodstock identified nine and 26 SNPs associated with thermal tolerance (p < 0.05 and p < 0.1), measured in a previous thermal challenge experiment. Genes near the associated SNPs had complex functions related to immunity, growth, metabolism and ion homeostasis. Principal component analysis using the thermotolerance‐related SNPs showed unexpected divergence between the conservation broodstock and the native lake populations at these loci. FST outlier tests on the native lake populations identified 18 loci shared between two or more of the tests, with two SNPs identified by all three tests (p < 0.01); none overlapped with loci identified by association testing in the broodstock. A recent history of isolation and the complex genetic and demographic backgrounds of Lahontan cutthroat trout probably limited our ability to find shared thermal tolerance loci. Our study extends the still relatively rare application of genomic tools testing for markers associated with important phenotypic or environmental characteristics in species of conservation concern.
Data from: Testing the species–genetic diversity correlation in the Aegean archipelago: towards a haplotype-based macroecology?
A positive correlation between species and genetic diversity (SGDC) has been proposed, consistent with neutral predictions in macroecology. We assessed the SGDC in tenebrionid beetle communities of the Aegean archipelago on fifteen islands of different sizes, distances to mainland, and ages of isolation. Alpha- and beta-diversity of species and haplotypes were assessed using sequences of >1000 individuals (mitochondrial Cytochrome Oxidase I and nuclear Muscular Protein 20) to test the SGDC. We show that: (i) there is a strong species-area and haplotype-area relationship; (ii) species richness in island communities is correlated with intraspecific genetic diversity in the constituent species except when island size or distance to mainland are factored out in partial correlations; (iii) community similarity declines exponentially at an increasing rate when calculated based on species, nuclear and mtDNA haplotypes; and (iv) distance decay of community similarity is slower in dispersive sand-dwelling lineages compared to less dispersive lineages that are not sand-obligate. Taken together, these correlated patterns at the species and haplotype level are consistent with individual-based stochastic dispersal proposed by neutral theories of biodiversity. The results also demonstrate the utility of haplotype data for exploring macroecological patterns in poorly known biota and predicting large-scale biodiversity patterns based on genetic inventories of local samples.
Data from: Testing a post-copulatory pre-zygotic reproductive barrier in a passerine species pair
Sexual selection may drive speciation, but most research focuses on pre-copulatory sexual selection, overlooking post-copulatory processes. Post-copulatory sexual selection in allopatric populations could drive divergence in post-copulatory pre-zygotic (PCPZ) phenotypes, limiting gene flow upon secondary contact. Here, we performed in vitro experiments examining one potential PCPZ barrier between two closely related passerine species, house sparrows (Passer domesticus) and Spanish sparrows (Passer hispaniolensis). In birds, crossing in the vagina may be particularly challenging for sperm, so we tested the effect of female reproductive tract fluids on sperm swimming speed and motility. If a PCPZ barrier exists at this stage of the fertilization process, heterospecific female fluids are predicted to reduce sperm swimming speed or motility relative to conspecific female fluid. We found that house sparrow female fluids affected the two species' sperm asymmetrically, depending on the control sperm velocity and male species. Overall, however, sperm performed equally in conspecific and heterospecific female fluids, and the species had similar sperm morphology and sperm swimming performance. Low divergence in PCPZ phenotypes between species, perhaps because post-copulatory sexual selection is stabilizing or only moderately strong in these taxa, may be insufficient to cause an overall PCPZ barrier. Reinforcement may be unlikely to drive PCPZ barriers for this species pair, because relatively effective pre-copulatory barriers exist between the species, and because hybrids can be quite successful. Testing the role of PCPZ barriers in birds with more divergent PCPZ phenotypes will improve our understanding of speciation in passerines.
Data from: How do patients and health workers interact around malaria rapid diagnostic testing, and how are the tests experienced by patients in practice? A qualitative study in western Uganda
Background: Successful scale-up in the use of malaria rapid diagnostic tests (RDTs) requires that patients accept testing and treatment based on RDT results and that healthcare providers treat according to test results. Patient-provider communication is a key component of quality care, and leads to improved patient satisfaction, higher adherence to treatment and better health outcomes. Voiced or perceived patient expectations are also known to influence treatment decision-making among healthcare providers. While there has been a growth in literature on provider practices around rapid testing for malaria, there has been little analysis of inter-personal communication around the testing process. We investigated how healthcare providers and patients interact and engage throughout the diagnostic and treatment process, and how the testing service is experienced by patients in practice. Methods: This research was conducted alongside a larger study which explored determinants of provider treatment decision-making following negative RDT results in a rural district (Kibaale) in mid-western Uganda, ten months after RDT introduction. Fifty-five patients presenting with fever were observed during routine outpatient visits at 12 low-level public health facilities. Observation captured communication practices relating to test purpose, results, diagnosis and treatment. All observed patients or caregivers were immediately followed up with in-depth interview. Analysis followed the 'framework' approach. A summative approach was also used to analyse observation data. Results: Providers failed to consistently communicate the reasons for carrying out the test, and particularly to RDT-negative patients, a diagnostic outcome or the meaning of test results, also leading to confusion over what the test can detect. Patients appeared to value testing, but were frustrated by the lack of communication on outcomes. RDT-negative patients were dissatisfied by the absence of information on an alternative diagnosis and expressed uncertainty around adequacy of proposed treatment. Conclusions: Poor provider communication practices around the testing process, as well as limited inter-personal exchange between providers and patients, impacted on patients' perceptions of their proposed treatment. Patients have a right to health information and may be more likely to accept and adhere to treatment when they understand their diagnosis and treatment rationale in relation to their perceived health needs and visit expectations.
Data from: Higher rates of pre‐breeding condition gain positively impacts clutch size: a mechanistic test of the condition‐dependent individual optimization model
1. A combination of timing of and body condition (i.e., mass) at arrival on the breeding grounds interact to influence the optimal combination of the timing of reproduction and clutch size in migratory species. This relationship has been formalized by Rowe et al. in a condition-dependent individual optimization model (American Naturalist, 1994, 143, 689-722), which has been empirically tested and validated in avian species with a capital-based breeding strategy. 2. This model makes a key, but currently untested prediction; that variation in the rate of body condition gain will shift the optimal combination of laying date and clutch size. This prediction is essential because it implies that individuals can compensate for the challenges associated with late timing of arrival or poor body condition at arrival on the breeding grounds through adjustment of their life history investment decisions, in an attempt to maximize fitness. 3. Using an 11-year data set in arctic-nesting common eiders (Somateria mollissima), quantification of fattening rates using plasma triglycerides (an energetic metabolite), and a path analysis approach, we test this prediction of this optimization model; controlling for arrival date and body condition, females that fatten more quickly will adjust the optimal combination of lay date and clutch size, in favour of a larger clutch size. 4. As predicted, females fattening at higher rates initiated clutches earlier and produced larger clutch sizes, indicating that fattening rate is an important factor in addition to arrival date and body condition in predicting individual variation in reproductive investment. However, there was no direct effect of fattening rate on clutch size (i.e., birds laying on the same date had similar clutch sizes, independent of their fattening rate). Instead, fattening rate indirectly affected clutch size via earlier lay dates, thus not supporting the original predictions of the optimization model. 5. Our results demonstrate that variation in the rate of condition gain allows individuals to shift flexibly along the seasonal decline in clutch size to presumably optimize the combination of laying date and clutch size.
Data from: An updated global dataset for diet preferences in terrestrial mammals: testing the validity of extrapolation
1. Diet is a key trait of an organism's life history that influences a broad spectrum of ecological and evolutionary processes. Kissling et al. (2014) compiled a species-specific dataset of diet preferences of mammals for 38% of a total of 5364 terrestrial mammalian species assessed for the International Union for Conservation of Nature's Red List, to facilitate future studies. The authors imputed dietary data for the remaining 62% by using extrapolation from phylogenetic relatives. 2. We collected dietary information for 1261 mammalian species for which data were extrapolated by Kissling et al. (2014), in order to evaluate the success with which such extrapolation can predict true diets. 3. The extrapolation method devised by Kissling et al. (2014) performed well for broad dietary categories (consumers of plants and animals). However, the method performed inconsistently, and sometimes poorly, for finer dietary categories, varying in accuracy in both dietary categories and mammalian orders. 4. The results of the extrapolation performance serve as a cautionary tale. Given the large variation in extrapolation performance, we recommend a more conservative approach for inferring mammalian diets, whereby dietary extrapolation is implemented only when there is a high degree of phylogenetic conservatism for dietary traits. Phylogenetic comparative methods can be used to detect and measure phylogenetic signal in diet. If data for species are needed, then only the broadest feeding categories should be used. This would ensure a greater level of accuracy and provide a more robust dataset for further ecological and evolutionary analysis.
Data from: Experimental manipulation reveals a trade-off between weapons and testes
Theory predicts a trade-off between sexually-selected weapons used to secure mates and post-copulatory traits used to maximize fertilization success. However, individuals that have a greater capacity to acquire resources from the environment may invest more in both pre- and post-copulatory traits, and trade-offs may not be readily apparent. Here, we manipulate the phenotype of developing individuals to examine allocation trade-offs between weapons and testes in Mictis profana (Hemiptera: Coreidae), a species where the hind legs are sexually selected weapons used in contests over access to females. We experimentally prevented males from developing weapons by inducing them to autotomize their hind legs before the final molt to adulthood. We compared trait expression in this group to males where autotomy was induced in the mid legs, which are presumably not under sexual selection to the same extent. We found males without weapons invested proportionally more in testes mass than those with their mid legs removed. Males that developed to adulthood without weapons did not differ from the mid leg removal group in other traits potentially under pre-copulatory sexual selection, other post-copulatory traits, or naturally selected traits. In addition, a sample of adult males from the same population in the wild revealed a positive correlation between investment in testes and weapons. Our study presents a critical contribution to a growing body of literature suggesting the allocation of resources to pre- and post-copulatory sexual traits is influenced by a resource allocation trade-off and that this trade-off may only be revealed with experimental manipulation.
Data from: No place like home? A test of the natal habitat-biased dispersal hypothesis in Scandinavian wolves
Natal dispersal is an important mechanism for the viability of populations. The influence of local conditions or experience gained in the natal habitat could improve fitness if dispersing individuals settle in an area with similar habitat characteristics. This process, defined as "natal habitat-biased dispersal" (NHBD), has been used to explain distribution patterns in large carnivores, but actual studies evaluating it are rare. We tested whether gray wolf Canis lupus territory establishment was influenced by the habitat characteristics of the natal territory using the long-term monitoring of the Scandinavian wolf population. We paired the locations of natal and established territories, accounted for available habitats along the dispersing route, and compared their habitat characteristics for 271 wolves during 1998-2012. Wolves with the shortest dispersal distances established in natal-like habitat types more than expected by chance, whereas wolves that dispersed longer distances did not show NHBD. The pattern was consistent for male and female wolves, with females showing more NHBD than males. Chances to detect NHBD increased with the size of habitat defined as available. This highlights the importance of considering the biological characteristics of the studied species when defining habitat availability. Our methodological approach can prove useful to inform conservation and management to identify habitats to be selected by reintroduced or naturally expanding populations.
Data from: Testing the efficiency of nested barriers to dispersal in the Mediterranean high mountain plant Edraianthus graminifolius (Campanulaceae)
Due to strong spatial heterogeneity and limited Pleistocene glaciation, the Balkan Peninsula is a major European biodiversity hotspot. Surprisingly little, however, is known about patterns and processes of intraspecific diversification of its biota in general and of high altitude species in particular. A well-suited system to test hypotheses with respect to various isolating factors acting at different geographic scales and to explore full-range phylogeographic patterns on the Balkan Peninsula is Edraianthus graminifolius (Campanulaceae), distributed in the western Balkan mountain systems, the southwestern Carpathians and the Apennine Peninsula. To this end, we used a dense population sampling and employed Amplified Fragment Length Polymorphism (AFLP) markers and plastid DNA sequences supplemented by ecological niche modelling. The strongest splits were inferred to separate southern and northern Balkan populations from the central ones, from where range extension occurred to the Carpathians and, in more recent times, once or twice to the Apennine Peninsula. The three genetic groups in the western Balkan Peninsula were remarkably congruent among molecular markers suggesting that the barriers to gene flow acted over long time periods facilitating allopatric differentiation. Each main group of Balkan populations contained genetically and geographically distinct subgroups, which likely are the result of local refugia during warmer periods. Evidently, the topographically highly complex and during the last glacial maximum only locally glaciated Balkan Peninsula is a hotspot of species richness and endemism as well as a sanctuary of intraspecific genetic diversity, even if the underlying causes remain insufficiently understood.
Data from: Breeding synchrony and predator specialization: a test of the predator swamping hypothesis in seabirds
Reproductive synchrony is a widespread phenomenon that is predicted to be adaptive for prey with specialist predators but not for those with generalist ones. I tested this prediction in three polar seabird species characterized by different levels of predator specialization. In the Antarctic petrel, for which the only predator was highly specialized, hatching dates were highly synchronous and chicks that hatched close to the mean hatching date had a higher survival. In black-legged kittiwakes and Brünnich's guillemots, whose predators were generalists, breeding was less synchronous and there was no fitness advantage in hatching close to the mean. This study emphasizes the potential importance of the relative timing of reproduction for individual fitness and supports the hypothesis that the adaptive value of breeding synchrony depends on the predator functional response.
Data from: Testing the link between perceived and actual risk of predation: mosquito oviposition site selection and egg predation by native and introduced fish
1. According to the threat-sensitivity hypothesis, prey avoidance behaviour should reflect the magnitude of predation risk. Since predation can strongly affect reproduction success, ovipositing females are expected to adaptively adjust their predator-avoidance response, or local breeding patch selectivity, in accordance with the perceived level of threat posed for their progeny by specific predators. However, association between avoidance and predation can be disrupted when the prey and the predator lack spatio-temporal opportunities to co-evolve, such as in cases of non-native predator introductions. 2. We examined the interactions between mosquitoes (from the genus Culex) and three species of sympatric predaceous freshwater fish, a native cyprinid (Barbus paludinosus), a cichlid (Pseudocrenilabrus philander), and an introduced poeciliid, the Western mosquitofish (Gambusia affinis). 3. In an outdoor mesocosm experiment we quantified patterns of Culex oviposition site selection across fish species using free-roaming, caged, and fish-free treatments. In a complementary laboratory experiment we tested the effectiveness of each fish species as predators of mosquito eggs and larvae. 4. Synthesis and applications. We found evidence for: (i) mosquito egg raft predation by free- roaming fish; (ii) fish-specific avoidance by ovipositing Culex and (iii) a positive association between fish-specific oviposition avoidance and fish-specific efficiency as an egg predator. These results contribute towards a better understanding of predator-prey coevolution, predator-borne cue recognition, and suggest local native fish, the Southern mouthbrooder (Pseudocrenilabrus philander), as an alternative to Gambusia for the biocontrol of Culex mosquitoes.
Data from: The effects of temporal resolution on species turnover and on testing metacommunity models
Patterns of low temporal turnover in species composition found within long paleoecological time series contrast with the high turnover predicted by dispersal-limited neutral metacommunity models and thus have been used to support non-neutral models. However, predictions assume temporal resolution on the scale of a season or year whereas individual fossil assemblages are typically time-averaged to decadal or centennial time scales. Here, we simulate the effects of time averaging by building time-averaged assemblages from local dispersal-limited non-averaged (living) assemblages and compare the predicted species turnover with observed patterns in mollusk and ostracod fossil records. Time averaging substantially reduces temporal turnover such that neutral predictions converge with those of trade-off and density-dependent models, and tends to decrease species dominance and increase the proportion of rare species. Observed turnover rates are comparable to an appropriately scaled neutral model: patterns of high community stability can be produced or reinforced by time averaging alone. The community attributes of local time-averaged assemblages approach those of the metacommunity. Time-averaged assemblages are thus unlikely to capture attributes arising from processes operating at small spatial scales, but should do well at capturing the turnover and diversity parameters of metacommunities, and thus will be a valuable basis for analyzing the large-scale processes that determine metacommunity evolution.
Data from: Sticky genomes: using NGS evidence to test hybrid speciation hypotheses
Hypotheses of hybrid origin are common. Here we use next generation sequencing to test a hybrid hypothesis for a non-model insect with a large genome. We compared a putative hybrid triploid stick insect species (Acanthoxyla geisovii) with its putative paternal diploid taxon (Clitarchus hookeri), a relationship that provides clear predictions for the relative genetic diversity within each genome. The parental taxon is expected to have comparatively low allelic diversity that is nested within the diversity of the hybrid daughter genome. The scale of genome sequencing required was conveniently achieved by extracting mRNA and sequencing cDNA to examine expressed allelic diversity. This allowed us to test hybrid-progenitor relationships among non-model organisms with large genomes and different ploidy levels. Examination of thousands of independent loci avoids potential problems produced by the silencing of parts of one or other of the parental genomes, a phenomenon sometimes associated with the process of stabilisation of a hybrid genome. Transcript assembles were assessed for evidence of paralogs and/or alternative splice variants before proceeding. Comparison of transcript assemblies was not an appropriate measure of genetic variability, but by mapping reads back to clusters derived from each species we determined levels of allelic diversity. We found greater cDNA sequence diversity among alleles in the putative hybrid species (Acanthoxyla geisovii) than the non-hybrid. The allelic diversity within the putative paternal species (Clitachus hookeri) nested within the hybrid-daughter genome, supports the current view of a hybrid-progenitor relationship for these stick insect species. Next generation sequencing technology provides opportunities for testing evolutionary hypotheses with non-model organisms, including, as here, genomes that are large due to polyploidy
Data from: Testing the role of mating preference in a case of incomplete ecological speciation with gene flow
Mating preference can evolve as a side effect of ecological adaptation and simultaneously contribute to speciation in certain scenarios. However, theoretical predictions have been difficult to test experimentally because there has not been any simple way to relate empirical and theoretical parameters. Recently, it has been shown that the r coefficient and other statistics can be used to estimate mating preference in wild-captured mating pairs. In the present work we use these estimators to test whether mating preference has significantly increased in a context favorable for ecological divergence. We perform the study using two groups of samples from populations of the marine gastropod Littorina saxatilis: 1) a group of bimodal populations affected by ecological divergence, and 2) a group of unimodal populations. The results show that mating preference (unlike the trait affected by the preference) does not increase when two ecotypes meet and mate in sympatry, which suggests that mating preference must be controlled by strong stabilizing natural selection, and/or limited by mating cost. This would suggest that mating preference would rarely contribute to speciation under the face of gene flow in these ecotypes.
Data from: Testing hypotheses of mitochondrial gene-tree paraphyly: unraveling mitochondrial capture of the Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) by the Taiwan Scimitar Babbler (P. musicus)
Species-level paraphyly inferred from mitochondrial gene trees is a prevalent phenomenon in taxonomy and systematics, but there are several potential causes that are not easily explained by currently used methods. The present study aims to test the underlying causes behind the observed paraphyly of Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) via statistical analyses of four mitochondrial (mtDNA) and nine nuclear (nuDNA) genes. Mitochondrial gene trees show paraphyly of P. ruficollis with respect to the Taiwan Scimitar Babbler (P. musicus), but nuclear genealogies support a sister-group relationship. Predictive coalescent simulations imply several hypothetical explanations, the most likely being mitochondrial capture of P. ruficollis by P. musicus for the observed cyto-nuclear incongruence. Further Approximate Bayesian Computation suggests a unidirectional introgression model with substantial level of gene flow from P. ruficollis to P. musicus during their initial divergence during the Late Pleistocene. This specific observation frames several potential causes for incongruent outcomes of mitochondrial and nuclear introgression in general, and on the whole, our results underscore the strength of multiple independent loci for species delimitation and importance of testing hypotheses that explain disparate causes of mitochondrial gene-tree paraphyly.
Data from: Oxidation of linoleic and palmitic acid in pre-hibernating and hibernating common noctule bats revealed by 13C breath testing
Mammals fuel hibernation by oxidizing saturated and unsaturated fatty acids from triacylglycerols in adipocytes, yet the relative importance of these two categories as an oxidative fuel may change during hibernation. We studied the selective use of fatty acids as an oxidative fuel in noctule bats (<i>Nyctalus noctula</i>). Pre-hibernating noctule bats that were fed 13C-enriched linoleic acid (LA) showed 12 times higher tracer oxidation rates compared to conspecifics fed 13C-enriched palmitic acid (PA). After this experiment, we supplemented the diet of bats with the same fatty acids on 5 subsequent days to enrich their fat depots with the respective tracer. We then compared the excess 13C enrichment (APE) in breath of bats for torpor and arousal events during early and late hibernation. We observed higher APE values in breath of bats fed 13C-enriched LA than in bats fed 13C-enriched PA for both states, torpor and arousal, and also for both periods. Thus, hibernating bats oxidized selectively endogenous LA instead of PA, most likely because of faster transportation rates of PUFA compared with SFA. We did not observe changes in APE values in the breath of torpid animals between early and late hibernation. Skin temperature of torpid animals increased by 0.7oC between early and late hibernation in bats fed PA, whereas it decreased by -0.8oC in bats fed LA, highlighting that endogenous LA may fulfil two functions when available in excess: serving as an oxidative fuel and supporting cell membrane functionality.
Data from: A test of the "flexible stem" model of evolution: ancestral plasticity, genetic accommodation, and morphological divergence in the threespine stickleback radiation
If an ancestral stem group repeatedly colonizes similar environments, developmental plasticity specific to that group should consistently give rise to similar phenotypes. Parallel selection on those similar phenotypes could lead to the repeated evolution of characteristic ecotypes, a property common to many adaptive radiations. A key prediction of this "flexible stem" model of adaptive radiation is that patterns of phenotypic divergence in derived groups should mirror patterns of developmental plasticity in their common ancestor. The threespine stickleback radiation provides an excellent opportunity to test this prediction because the marine form is representative of the ancestral stem group, which has repeatedly given rise to several characteristic ecotypes. We examined plasticity of several aspects of shape and trophic morphology in response to diets characteristic of either the derived benthic or limnetic ecotypes. When marine fish were reared on alternative diets, plasticity of head and mouth shape paralleled phenotypic divergence between the derived ecotypes, supporting the flexible stem model. Benthic and limnetic fish exhibited patterns of plasticity similar to the marine population; however, some differences in population means were present, as well as subtle differences in shape plasticity in the benthic population, indicating a role for genetic accommodation in this system.
Data from: Evidence for contemporary and historical gene flow between guppy populations in different watersheds, with a test for associations with adaptive traits
In dendritic river systems, gene flow is expected to occur primarily within watersheds. Yet, rare cross‐watershed transfers can also occur, whether mediated by (often historical) geological events or (often contemporary) human activities. We explored these events and their potential evolutionary consequences by analyzing patterns of neutral genetic variation (microsatellites) and adaptive phenotypic variation (male color) in wild guppies (Poecilia reticulata) distributed across two watersheds in northern Trinidad. We found the expected signatures of within‐watershed gene flow; yet we also inferred at least two instances of cross‐watershed gene flow—one in the upstream reaches and one further downstream. The upstream cross‐watershed event appears to be very recent (41 ± 13 years), suggesting dispersal via recent flooding or undocumented human‐mediated transport. The downstream cross‐watershed event appears to be considerably older (577 ± 265 years), suggesting a role for rare geological or climatological events. Alongside these strong signatures of both contemporary and historical gene flow, we found little evidence of impacts on presumably adaptive phenotypic differentiation, except perhaps in the one instance of very recent cross‐watershed gene flow. Selection in this system seems to overpower gene flow—at least on the spatiotemporal scales investigated here.
Data from: Testing the CREA 'rule' in Galliformes
Recent comparative studies have indicated the existence of a common cranial evolutionary allometric (CREA) pattern in mammals and birds, in which smaller species have relatively smaller faces and bigger braincases than larger species. In these studies, cranial allometry was tested using a multivariate regression between shape (described using landmarks coordinates) and size (i.e. centroid size), after accounting for phylogenetic relatedness. Alternatively, cranial allometry can be determined by comparing the sizes of two anatomical parts using a bivariate regression analysis. In this analysis, a slope higher or lower than 1 indicates the existence of positive or negative allometry, respectively. Thus, in those species that support the CREA 'rule', positive allometry is expected for the association between face size and braincase size, which would indicate that larger species have disproportionally larger faces. In the present study, I applied these two approaches to explore cranial allometry in 83 Galliformes (Aves, Galloanserae), ranging in body weight from 30 g to 2.5 kg. The multivariate regression between shape and centroid size revealed the existence of a significant allometric pattern resembling CREA, whereas the second analysis revealed a negative allometry for beak size and braincase size (i.e. contrary to the CREA 'rule', larger galliform species have disproportionally shorter beaks than smaller galliform species). This study suggests that the presence of CREA may be overestimated when using cranium size as the standard measurement.
Data from: How do foragers decide when to leave a patch? A test of alternative models under natural and experimental conditions
1. A forager's optimal patch-departure time can be predicted by the prescient marginal value theorem (pMVT), which assumes they have perfect knowledge of the environment, or by approaches such as Bayesian-updating and learning rules, which avoid this assumption by allowing foragers to use recent experiences to inform their decisions. 2. In understanding and predicting broader scale ecological patterns, individual-level mechanisms, such as patch-departure decisions, need to be fully elucidated. Unfortunately, there are few empirical studies that compare the performance of patch-departure models that assume perfect knowledge with those that do not, resulting in a limited understanding of how foragers decide when to leave a patch. 3. We tested the patch-departure rules predicted by fixed-rule, pMVT, Bayesian-updating and learning models against one another, using patch residency times recorded from 54 chacma baboons (Papio ursinus) across two groups in natural (n = 6,594 patch visits) and field-experimental (n = 8,569) conditions. 4. We found greater support in the experiment for the model based on Bayesian-updating rules, but greater support for the model based on the pMVT in natural foraging conditions. This suggests that foragers may place more importance on recent experiences in predictable environments, like our experiment, where these experiences provide more reliable information about future opportunities.5. Furthermore, the effect of a single recent foraging experience on patch residency times was uniformly weak across both conditions. This suggests that foragers' perception of their environment may incorporate many previous experiences, thus approximating the perfect knowledge assumed by the pMVT. Foragers may, therefore, optimise their patch-departure decisions in line with the pMVT through the adoption of rules similar to those predicted by Bayesian-updating.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.