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The implications of lineage-specific rates for divergence time estimation
<p>Rate variation adds considerable complexity to divergence time estimation in molecular phylogenies. Here, we evaluate the impact of lineage-specific rates—which we define as among-branch-rate-variation that acts consistently across the entire genome. We compare its impact to residual rates—defined as among-branch-rate-variation that shows a different pattern of rate variation at each sampled locus, and gene-specific rates—defined as variation in the average rate across all branches at each sampled locus. We show that lineage-specific rates lead to erroneous divergence time estimates, regardless of how many loci are sampled. Further, we show that stronger lineage-specific rates lead to increasing error. This contrasts to residual rates and gene-specific rates, where sampling more loci significantly reduces error. If divergence times are inferred in a Bayesian framework, we highlight that error caused by lineage-specific rates significantly reduces the probability that the 95% highest posterior density includes the correct value, and leads to sensitivity to the prior. Use of a more complex rate prior—which has recently been proposed to model rate variation more accurately—does not affect these conclusions. Finally, we show that the scale of lineage-specific rates used in our simulation experiments is comparable to that of an empirical data set for the angiosperm genus Ipomoea. Taken together, our findings demonstrate that lineage-specific rates cause error in divergence time estimates, and that this error is not overcome by analyzing genomic scale multilocus data sets.</p>
Data from: Laboratory rearing of Anopheles arabiensis: impact on genetic variability and implications for Sterile Insect Technique (SIT) based mosquito control in northern Sudan
Background: Mosquito colony populations often show significant changes in their population genetic make-up compared to the field populations that were used as founding source. Most of the changes that have been reported are indicators of depletion in the overall genetic diversity of the colony populations. The Sterile Insect Techniques programme of mosquito control that is underway in Northern Sudan uses sterilized males produced from a laboratory-maintained colony population. The genetic diversity of an advanced generation of this colony population was quantitatively assessed and compared to the field population from which the colony was derived. Methods: Anopheles arabiensis mosquito samples from the 13th generation of the colony, and from the locality that was the source of the first generation of the colony, were genotyped at 11 microsatellite loci distributed throughout the species' genome. Standard population genetic analyses were carried out to quantify and compare their population genetic make-up and diversities. Results: The colony samples showed significant reduction in the total number of alleles, the numbers of rare and private alleles, and the fractions of heterozygote individuals at all the loci. The pattern of change is consistent with the expected effect of the use of a small number of mosquitoes when the colony was established. Departure from Hardy–Weinberg equilibrium in the direction of homozygote excess was observed at some loci and attributed to the presence of null-alleles. Conclusions: This study highlights the need for broad sampling when initiating colony populations and for ongoing assessment of the population genetic make-up of colony populations. Previous assessments of survivorship, dispersive behaviour and swarm formation indicate that the inbreeding and reduced genetic variability reported in this study may not have had direct fitness consequences yet. However, noting the lessons learned in other SIT programmes about the impact of colonization on male sexual behaviour and longevity, as well as other inbreeding related adverse effects, a systematic investigation of these potential effects is recommended because they have direct impact on the ultimate success of the programme.
Data from: Local and landscape-scale heterogeneity shape spotted wing drosophila (Drosophila suzukii) activity and natural enemy abundance: implications for trophic interactions
Like natural enemies, invasive polyphagous pests may respond positively to local and landscape-scale diversity, making them more serious challenges to sustainable management than specialists. Yet the current view of landscape effects on pests rarely considers perennial systems or polyphagous pests. We investigated Drosophila suzukii (SWD) and natural enemy distributions and trophic interactions in blueberry systems of the southeast US in relation to local management and landscape structure. Fields were nested in 1-km landscapes along gradients of crop and forest heterogeneity (landscape compositional diversity) and field border and crop border lengths (landscape configurational diversity). Yeast-sugar bait traps were used to collect SWD and canopy suction sampling for natural enemies. Management practices at the local scale did not influence SWD abundance, but natural enemy abundance was higher in organic systems and fields with vegetation present between rows. Landscape configurational diversity and greater proportion of non-cropping habitat promoted higher SWD populations. Natural enemy communities were composed of highly generalized species, and contrary to our predictions, we observed lower abundances in landscapes with higher proportion of non-cropping area. Few predators were detected to have fed on SWD, and communities were dominated by predators with low specialization on prey in blueberry. Our results indicate that local and landscape features in blueberry landscapes have differential effects on a polyphagous pest and generalist natural enemies. Our initial analysis of predator diets, using a metabarcoding approach, suggests spatial structure in specialization on prey with high diversity of prey in predators collected in forested margins.
Data from: Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation
Background: The greater bamboo lemur (Prolemur simus) is a member of the Family Lemuridae that is unique in their dependency on bamboo as a primary food source. This Critically Endangered species lives in small forest patches in eastern Madagascar, occupying a fraction of its historical range. Here we sequence the genome of the greater bamboo lemur for the first time, and provide genome resources for future studies of this species that can be applied across its distribution. Results: Following whole genome sequencing of five individuals we identified over 152,000 polymorphic single nucleotide variants (SNVs), and evaluated geographic structuring across nearly 19k SNVs. We characterized a stronger signal associated with a north-south divide than across elevations for our limited samples. We also evaluated the demographic history of this species, and infer a dramatic population crash. This species had the largest effective population size (estimated between ~900,000 to one million individuals) between approximately 60,000-90,000 years before present (ybp), during a time in which global climate change affected terrestrial mammals worldwide. We also note the single sample from the northern portion of the extant range had the largest effective population size around 35,000 ybp. Conclusions: From our whole genome sequencing we recovered an average genomic heterozygosity of 0.0037%, comparable to other lemurs. Our demographic history reconstructions recovered a probable climate-related decline (60-90,000 ybp), followed by a second population decrease following human colonization, which has reduced the species to a census size of approximately 1,000 individuals. The historical distribution was likely a vast portion of Madagascar, minimally estimated at 44,259 km2, while the contemporary distribution is only ~1,700 km2. The decline in effective population size of 89-99.9% corresponded to a vast range retraction. Conservation management of this species is crucial to retain genetic diversity across the remaining isolated populations.
Data from: Ecological disturbance influences adaptive divergence despite high gene flow in golden perch (Macquaria ambigua): implications for management and resilience to climate change
Populations that are adaptively divergent but maintain high gene flow may have greater resilience to environmental change as gene flow allows the spread of alleles that have already been tested elsewhere. In addition, populations naturally subjected to ecological disturbance may already hold resilience to future environmental change. Confirming this necessitates ecological genomic studies of high dispersal, generalist species. Here we perform one such study on golden perch (Macquaria ambigua) in the Murray-Darling Basin (MDB), Australia using a genome-wide SNP dataset. The MDB spans across arid to wet and temperate to sub-tropical environments, with low to high ecological disturbance in the form of low to high hydrological variability. We found high gene flow across the basin and three populations with low neutral differentiation. Genotype-environment association analyses detected adaptive divergence predominantly linked to an arid region with highly variable riverine flow, and candidate loci included functions related to fat storage, stress and molecular or tissue repair. The high connectivity of golden perch in the MDB will likely allow locally adaptive traits in its most arid and hydrologically variable environment to spread and be selected in localities that are predicted to become arid and hydrologically variable in future climates. High connectivity in golden perch is likely due to their generalist life history and efforts of fisheries management. Our study adds to growing evidence of adaptation in the face of gene flow, and highlights the importance of considering ecological disturbance and adaptive divergence in biodiversity management.
Data from: Adaptive landscape and functional diversity of Neotropical cichlids: implications for the ecology and evolution of Cichlinae (Cichlidae; Cichliformes)
Morphological, lineage and ecological diversity can vary substantially even among closely related lineages. Factors that influence morphological diversification, especially in functionally relevant traits, can help to explain the modern distribution of disparity across phylogenies and communities. Multivariate axes of feeding functional morphology from 75 species of Neotropical cichlid and a stepwise-AIC algorithm were used to estimate the adaptive landscape of functional morphospace in Cichlinae. Adaptive landscape complexity and convergence, as well as the functional diversity of Cichlinae, were compared with expectations under null evolutionary models. Neotropical cichlid feeding function varied primarily between traits associated with ram feeding vs. suction feeding/biting and secondarily with oral jaw muscle size and pharyngeal crushing capacity. The number of changes in selective regimes and the amount of convergence between lineages was higher than expected under a null model of evolution, but convergence was not higher than expected under a similarly complex adaptive landscape. Functional disparity was compatible with an adaptive landscape model, whereas the distribution of evolutionary change through morphospace corresponded with a process of evolution towards a single adaptive peak. The continentally distributed Neotropical cichlids have evolved relatively rapidly towards a number of adaptive peaks in functional trait space. Selection in Cichlinae functional morphospace is more complex than expected under null evolutionary models. The complexity of selective constraints in feeding morphology has likely been a significant contributor to the diversity of feeding ecology in this clade.
Data from: Root elemental composition in Chinese forests: implications for biogeochemical niche differentiation
1. Trait-based community analysis provides a new approach to integrate functional ecology with community ecology. However, our understanding of the linkages between root chemical traits and community chemical diversity and assembly is still in its infancy. 2. Environmental filtering and niche differentiation are two opposite driving forces of community assembly based on deterministic niche processes. We hypothesize that environmental filtering is a strong driver of root chemical assembly at a large spatial scale, whereas biogeochemical niche differentiation drives root chemical traits divergence among co-occurring species at site scale. 3. We analyzed the concentrations of 15 elements in the fine roots of 281 species across five forest types of China. Discriminant analysis was used to measure the degree of similarity of root chemical traits at the community level and biogeochemical niche differentiation at the species level. 4. Root chemical traits at the community level showed a systematic shift along environmental gradients. The growth rate-related dimension represented by root P and Ca was the most important niche dimension associated with community root chemical assembly, driven by large-scale environmental filters, particularly soils and climate. Biogeochemical niche differentiation of co-occurring species could be a consequence of reducing nutrient competition, especially the competition for nitrogen. 5. Root chemical traits provide a new dimension for assessing the functional niche and may help improve our understanding of the underlying mechanisms of root chemical assembly from the local to the biome scale.
Data from: Ecological and evolutionary implications of allometric growth in stomach size of brachyuran crabs
Individual characteristics often scale allometrically with organismal body size and the form of this scaling can be influenced by ecological and evolutionary factors. Examining the specific form of this scaling can therefore yield important insights into organismal ecology and evolution and the ability of organisms to respond to future environmental changes. We examine the allometric scaling of stomach volume with body mass for 17 species of brachyuran crabs. We also examine how this scaling is influenced by dietary strategy, maximum body size, and activity level, all while controlling for phylogenetic relationships between the species. We show that the slope and intercept of the allometric scaling relationships vary across species and are influenced by all three ecological factors examined here, as well as by evolutionary relationships. These results highlight potential divergent strategies in stomach growth taken by different groups of crabs and highlight potential limitations that may be imposed on the ability of this group of organisms to respond to warming trends expected with climate change.
Data from: Postglacial range expansion shaped the spatial genetic structure in a marine habitat-forming species: implications for conservation plans in the Eastern Adriatic Sea
Aim: Understanding how historical and contemporary processes shaped and maintain spatial patterns of genetic diversity is a major goal for conservation biologists. Here, we characterized the pattern of neutral genetic diversity and we inferred underlying processes in the habitat-forming octocoral Paramuricea clavata in the Adriatic Sea, a peculiar phylogeographic region of the Mediterranean Sea. Location: Eastern coast of the Adriatic Sea. Methods: We genotyped seven microsatellites in 454 individuals of P. clavata from 13 populations recolonized after the last glacial maximum (LGM). We estimated the levels of contemporary connectivity and genetic drift and we reconstructed the demographic history of these populations. Results: The pattern of spatial genetic structure resulted from the combination of hierarchical genetic clusters and isolation by distance (IBD). A significant decrease in genetic diversity and an increase of the frequencies of individual alleles likely due to allele surfing from the south to the north of the area were observed as expected after a postglacial sequential recolonization. Based on maximum likelihood analyses, the foundation of these populations was not linked to dramatic change in population size. Main conclusion: Oceanographic barriers to gene flow combined to the restricted dispersal of P. clavata likely maintain the hierarchical structure and the IBD pattern. We suggest that the latitudinal genetic gradient results from a northward 'serial founder events' recolonization. By integrating patterns and processes, we bridge the gap between the evolutionary and the conservation biology of P. clavata, providing management guidelines, which will benefit the associated coralligenous biodiversity.
Data from: Black abalone (Haliotis cracherodii) population structure shifts through deep time: Management implications for southern California's northern Channel Islands
For over 10,000 years, black abalone (Haliotis cracherodii) were an important resource in southern California, first for coastal Native Americans, then beginning in the nineteenth century, as one of the state's first commercial shellfisheries. By 1993, after years of heavy fishing, rising sea surface temperatures (SST), and the spread of withering syndrome (WS), black abalone populations declined dramatically, resulting in the closure of the Alta California fishery. After nearly 25 years of management and recovery efforts, black abalone are showing signs of ecological rebound along some Channel Island shorelines. These include the presence of juvenile abalone and increasing densities, largely from data collected by Channel Islands National Park (CINP) monitoring efforts that began in 1985. In an effort to apply deeper historical perspectives to modern fisheries management and restoration, we analyzed black abalone size data from San Miguel Island at prehistoric and historical archeological sites spanning the last 10,000 years and compared these populations to those described by CINP biologists between 1985 and 2013. We found a statistically significant relationship between SST and black abalone size distributions during the ancient record, along with dramatic shifts in population size structure toward larger individuals between the nineteenth century and modern periods. A pattern of larger mean black abalone sizes was identified during warm SSTs, when compared against intervals of cooler SSTs. Synthesis and applications. Our study provides a deep historical perspective of abalone population size distributions, patterns within these distributions through time, and parallels to modern abalone populations. Our results may help managers determine whether the current (and future) size and age structure of intertidal black abalone populations around the northern Channel Islands are "natural" and healthy, measured against the 10,000 year history of black abalone fishing in southern California.
Data from: A new species of burnetiid (Therapsida, Burnetiamorpha) from the early Wuchiapingian of South Africa and implications for the evolutionary ecology of the family Burnetiidae.
Burnetiidae is a family of basal therapsids that is known from late Permian-aged (Lopingian) sequences from southern and eastern Africa and European Russia. Recent discoveries of related genera within the broader clade Burnetiamorpha have added to our understanding of morphological variation in the group but have eroded the list of characters defining the family Burnetiidae. We describe a new burnetiid taxon, Leucocephalus wewersi gen. et sp. nov., and argue that Burnetiidae can be defined by, among other characters, the presence of two bosses on the ventrolateral surface of suborbital bar and zygomatic arch, high skull angulation between the orbits, and a median frontal crest that becomes wider and lower posteriorly. The new specimen was found in the early Wuchiapingian Tropidostoma Assemblage Zone of the Main Karoo Basin and, along with previous discoveries, indicates that the family reached its greatest diversity and abundance in the early Wuchiapingian. Diversity declined into the later Wuchiapingian and Changhsingian. Although the clade Burnetiamorpha, including the family Burnetiidae, contains at least 11 genera, each of these is exceptionally rare, with most represented by only one specimen. This could be attributed to a genuine ecological characteristic or may be the result of biogeographic factors, particularly if the Main Karoo Basin was on the periphery of their range.
Data from: Resurrecting an extinct salmon evolutionarily significant unit: archived scales, historical DNA, and implications for restoration
Archival scales from 603 sockeye salmon (Oncorhynchus nerka), sampled from May to July 1924 in the lower Columbia River, were analyzed for genetic variability at 12 microsatellite loci, and compared to 17 present-day O. nerka populations—exhibiting either anadromous (sockeye salmon) or non-anadromous (kokanee) life histories—from throughout the Columbia River Basin, including areas upstream of impassable dams built subsequent to 1924. Statistical analyses identified four major genetic assemblages of sockeye salmon in the 1924 samples. Two of these putative historical groupings were found to be genetically similar to extant evolutionarily significant units (ESUs) in the Okanogan and Wenatchee rivers (pairwise FST = 0.004 and 0.002, respectively) and assignment tests were able to allocate 77% of the fish in these two historical groupings to the contemporary Okanogan River and Lake Wenatchee ESUs. A third historical genetic grouping was most closely aligned with contemporary sockeye salmon in Redfish Lake, Idaho, although the association was less robust (pairwise FST = 0.060). However, a fourth genetic grouping did not appear to be related to any contemporary sockeye salmon or kokanee population, assigned poorly to the O. nerka baseline, and had distinctive early return migration-timing suggesting that this group represented a putative historical ESU originating in headwater lakes in British Columbia that was likely extirpated sometime after 1924. The lack of a contemporary O. nerka population possessing the genetic legacy of this extinct ESU indicates that efforts to reestablish early-migrating sockeye salmon to the headwater lakes region of the Columbia River will be difficult.
Data from: Population genetic structure and its implications for adaptive variation in memory and the hippocampus on a continental scale in food-caching black-capped chickadees
Food-caching birds rely on stored food to survive the winter and spatial memory has been shown to be critical in successful cache recovery. Both spatial memory and the hippocampus, an area of the brain involved in spatial memory, exhibit significant geographic variation linked to climate-based environmental harshness and the potential reliance on food caches for survival. Such geographic variation has been suggested to have a heritable basis associated with differential selection. Here, we ask whether population genetic differentiation and potential isolation among multiple populations of food-caching black-capped chickadees is associated with differences in memory and hippocampal morphology by exploring population genetic structure within and among groups of populations that are divergent to different degrees in hippocampal morphology. Using mitochondrial DNA and 583 AFLP loci, we found that population divergence in hippocampal morphology is not significantly associated with neutral genetic divergence or geographic distance, but instead is significantly associated with differences in winter climate. These results are consistent with variation in a history of natural selection on memory and hippocampal morphology that creates and maintains differences in these traits regardless of population genetic structure and likely associated gene flow.
Data from: Use it or lose it: reproductive implications of ecological specialization in a haematophagous ectoparasite
Using experimentally induced disruptive selection, we tested two hypotheses regarding the evolution of specialization in parasites. The 'trade-off' hypothesis suggests that adaptation to a specific host may come at the expense of a reduced performance when exploiting another host. The alternative 'relaxed selection' hypothesis suggests that the ability to exploit a given host would deteriorate when becoming obsolete. Three replicate populations of a flea Xenopsylla ramesis were maintained on each of two rodent hosts, Meriones crassus and Dipodillus dasyurus, for nine generations. Fleas maintained on a specific host species for a few generations substantially decreased their reproductive performance when transferred to an alternative host species, whereas they generally did not increase their performance on their maintenance host. The results support the 'relaxed selection' hypothesis of the evolution of ecological specialization in haematophagous ectoparasites, while suggesting that trade-offs are unlikely drivers of specialization. Further work is needed to study the extent by which the observed specializations are based on epigenetic or genetic modifications.
Data from: Bias associated with the detectability of the coral-eating pest crown-of-thorns seastar and implications for reef management
Outbreaks of the predator crown-of-thorns seastar (COTS) Acanthaster planci cause widespread coral mortality across the Indo-Pacific. Like many marine invertebrates, COTS is a nocturnal species whose cryptic behaviour during the day can affect its detectability, particularly in structurally complex reef habitats that provide many refuges for benthic creatures. We performed extensive day and night surveys of COTS populations in coral reef habitats showing differing levels of structural complexity and COTS abundance. We tested whether estimations of COTS density varied between day and night observations, and if the differences were related to changes in COTS abundance, reef structural complexity, and the spatial scale of observation. Estimations of COTS density were on average 27% higher at night than during the day. Differences in COTS detection varied with changing seastar abundance but not reef structural complexity or scale of observation. Underestimation of COTS abundance in daytime was significant for a broad seastar density range, thus potentially affecting most outbreak events. Our study suggests that portions of COTS populations can be undetected during conventional surveys and control campaigns, which are exclusively conducted by day, and significantly affect the trajectory of coral reefs. Accounting for bias in COTS detection can strengthen coral reef management broadly.
Data from: A basal lithostrotian titanosaur (Dinosauria: Sauropoda) with a complete skull: implications for the evolution and paleobiology of Titanosauria
We describe Sarmientosaurus musacchioi gen. et sp. nov., a titanosaurian sauropod dinosaur from the Upper Cretaceous (Cenomanian–Turonian) Lower Member of the Bajo Barreal Formation of southern Chubut Province in central Patagonia, Argentina. The holotypic and only known specimen consists of an articulated, virtually complete skull and part of the cranial and middle cervical series. Sarmientosaurus exhibits the following distinctive features that we interpret as autapomorphies: (1) maximum diameter of orbit nearly 40% rostrocaudal length of cranium; (2) complex maxilla–lacrimal articulation, in which the lacrimal clasps the ascending ramus of the maxilla; (3) medial edge of caudal sector of maxillary ascending ramus bordering bony nasal aperture with low but distinct ridge; (4) 'tongue-like' ventral process of quadratojugal that overlaps quadrate caudally; (5) separate foramina for all three branches of the trigeminal nerve; (6) absence of median venous canal connecting infundibular region to ventral part of brainstem; (7) subvertical premaxillary, procumbent maxillary, and recumbent dentary teeth; (8) cervical vertebrae with 'strut-like' centroprezygapophyseal laminae; (9) extremely elongate and slender ossified tendon positioned ventrolateral to cervical vertebrae and ribs. The cranial endocast of Sarmientosaurus preserves some of the most complete information obtained to date regarding the brain and sensory systems of sauropods. Phylogenetic analysis recovers the new taxon as a basal member of Lithostrotia, as the most plesiomorphic titanosaurian to be preserved with a complete skull. Sarmientosaurus provides a wealth of new cranial evidence that reaffirms the close relationship of titanosaurs to Brachiosauridae. Moreover, the presence of the relatively derived lithostrotian Tapuiasaurus in Aptian deposits indicates that the new Patagonian genus represents a 'ghost lineage' with a comparatively plesiomorphic craniodental form, the evolutionary history of which is missing for at least 13 million years of the Cretaceous. The skull anatomy of Sarmientosaurus suggests that multiple titanosaurian species with dissimilar cranial structures coexisted in the early Late Cretaceous of southern South America. Furthermore, the new taxon possesses a number of distinctive morphologies—such as the ossified cervical tendon, extremely pneumatized cervical vertebrae, and a habitually downward-facing snout—that have rarely, if ever, been documented in other titanosaurs, thus broadening our understanding of the anatomical diversity of this remarkable sauropod clade. The latter two features were convergently acquired by at least one penecontemporaneous diplodocoid, and may represent mutual specializations for consuming low-growing vegetation.
Data from: Temperature drives abundance fluctuations, but spatial dynamics is constrained by landscape configuration: implications for climate-driven range shift in a butterfly
1. Prediction of species distributions in an altered climate requires knowledge on how global- and local-scale factors interact to limit their current distributions. Such knowledge can be gained through studies of spatial population dynamics at climatic range margins. 2. Here, using a butterfly (Pyrgus armoricanus) as model species, we first predicted based on species distribution modelling that its climatically suitable habitats currently extend north of its realized range. Projecting the model into scenarios of future climate, we showed that the distribution of climatically suitable habitats may shift northward by an additional 400 km in the future. 3. Second, we used a 13-year monitoring data set including the majority of all habitat patches at the species' northern range margin to assess the synergetic impact of temperature fluctuations and spatial distribution of habitat, microclimatic conditions and habitat quality, on abundance and colonisation-extinction dynamics. 4. The fluctuation in abundance between years was almost entirely determined by the variation in temperature during the species' larval development. In contrast, colonisation and extinction dynamics were better explained by patch area, between-patch connectivity, and host plant density. This suggests that the response of the species to future climate change may be limited by future land-use and how its host plants respond to climate change. It is thus probable that dispersal limitation will prevent P. armoricanus from reaching its potential future distribution. 5. We argue that models of range dynamics should consider the factors influencing metapopulation dynamics, especially at the range edges, and not only broad-scale climate. It includes factors acting at the scale of habitat patches such as habitat quality and microclimate, and landscape-scale factors such as the spatial configuration of potentially suitable patches. Knowledge of population dynamics under various environmental conditions, and the incorporation of realistic scenarios of future land-use, appear thus essential to provide predictions useful for actions mitigating the negative effects of climate change.
Data from: Visual effects in great bowerbird sexual displays and their implications for signal design
It is often assumed that the primary purpose of a male's sexual display is to provide information about quality, or to strongly stimulate prospective mates, but other functions of courtship displays have been relatively neglected. Male great bowerbirds (Ptilonorhynchus nuchalis) construct bowers that exploit the female's predictable field of view (FOV) during courtship displays by creating forced perspective illusions, and the quality of illusion is a good predictor of mating success. Here, we present and discuss two additional components of male courtship displays that use the female's predetermined viewpoint: (i) the rapid and diverse flashing of coloured objects within her FOV and (ii) chromatic adaptation of the female's eyes that alters her perception of the colour of the displayed objects. Neither is directly related to mating success, but both are likely to increase signal efficacy, and may also be associated with attracting and holding the female's attention. Signal efficacy is constrained by trade-offs between the signal components; there are both positive and negative interactions within multicomponent signals. Important signal components may have a threshold effect on fitness rather than the often assumed linear relationship.
Data from: Mechanisms and implications of a type IV functional response for short-term intake rate of dry matter in large mammalian herbivores
1. The functional response (i.e. the relationship between consumers' intake rate and resource density) is central in plant-herbivore interactions. Its shape and the biological processes leading to it have significant implications for both foraging theory and ecology of grazing systems. 2. A type IV functional response (i.e. dome-shaped relationship) of short-term intake rate of dry matter (intake while grazing) has rarely been reported for large herbivores and the conditions that can lead to it are poorly understood. 3. We report a type IV functional response observed in heifers grazing monocultures of Cynodon sp. and Avena strigosa. The mechanisms and consequences of this type of functional response for grazed system dynamics are discussed. 4. Intake rate was higher at intermediate than at short or tall sward heights in both grass species. The type IV functional response resulted from changes in bite mass instead of a longer time needed to encounter and process bites. Thus, the decrease of intake rate of dry matter in tall swards is not explained by a shift from process 3 (potential bites are concentrated and apparent) to process 2 (potential bites are apparent but dispersed, Spalinger & Hobbs 1992). Bite mass was smaller in tall than in intermediate swards due to a reduction of bite volume possibly caused by the greater proportion of stem and sheath acting as a physical barrier to bite formation. 5. It is generally accepted that potential bites are abundant and apparent in most grassland and meadow systems, as they were in the present experiments. Therefore, a type IV response of intake rate not directly related to digestive constraints may determine the dynamics of intake and defoliation under a much larger set of conditions than previously thought. These results have implications for foraging theory and stability of grazing systems. For example, if animals prefer patches of intermediate stature that yield the highest intake rate, grazing should lead to the widely observed bimodal distribution of plant mass per unit area, even when tall patches are not of significantly lower digestive quality than the pasture average.
Data from: Genetic specificity of a plant-insect food web: implications for linking genetic variation to network complexity
Theory predicts that intraspecific genetic variation can increase the complexity of an ecological network. To date, however, we are lacking empirical knowledge of the extent to which genetic variation determines the assembly of ecological networks, as well as how the gain or loss of genetic variation will affect network structure. To address this knowledge gap, we used a common garden experiment to quantify the extent to which heritable trait variation in a host plant determines the assembly of its associated insect food web (network of trophic interactions). We then used a resampling procedure to simulate the additive effects of genetic variation on overall food-web complexity. We found that trait variation among host-plant genotypes was associated with resistance to insect herbivores, which indirectly affected interactions between herbivores and their insect parasitoids. Direct and indirect genetic effects resulted in distinct compositions of trophic interactions associated with each host-plant genotype. Moreover, our simulations suggest that food-web complexity would increase by 20% over the range of genetic variation in the experimental population of host plants. Taken together, our results indicate that intraspecific genetic variation can play a key role in structuring ecological networks, which may in turn affect network persistence.
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.