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Data from: Living on the edge: exploring the role of coastal refugia in the Alexander Archipelago of Alaska
Although islands are of long-standing interest to biologists, only a handful of studies have investigated the role of climatic history in shaping evolutionary diversification in high latitude archipelagos. In this study of the Alexander Archipelago (AA) of Southeast Alaska, we address the impact of glacial cycles on geographic genetic structure for three mammals co-distributed along the North Pacific Coast. We examined variation in mitochondrial and nuclear loci for long-tailed voles (Microtus longicaudus), northwestern deermice (Peromyscus keeni), and dusky shrews (Sorex monticola), and then tested hypotheses derived from Species Distribution Models, reconstructions of paleo-shorelines, and island area and isolation. In all three species, we identified paleoendemic clades that likely originated in coastal refugia, a finding consistent with other paleoendemic lineages identified in the region such as ermine. Although there is spatial concordance at the regional level for endemism, finer scale spatial and temporal patterns are less clearly defined. Demographic expansion across the region for these distinctive clades is also evident and highlights the dynamic history of Late Quaternary contraction and expansion that characterizes high latitude species.
Data from: Contrasting habitat and landscape effects on the fitness of a long-lived grassland plant under forest encroachment: do they provide evidence for extinction debt?
1. Habitat loss, fragmentation and transformation threaten the persistence of many species worldwide. Population and individual fitness are often compromised in small, degraded and isolated habitats, but extinction can be a slow process and extinction debts are common. 2. Long-lived species are prone to persist as remnant populations in low quality habitats for a long time, but the population and individual-level mechanisms of extinction debt remain poorly explored so far. 3. We here investigate the mechanisms involved in the long-term persistence of the common grassland specialist, long-lived, clonal plant Aphyllanthes monspeliensis L. (Asparagaceae). after forest encroachment into semi-natural Mediterranean calcareous grasslands in Catalonia (NE Iberian Peninsula). For this purpose we assess vegetative (aboveground and belowground) and reproductive plant performance indicators and their habitat and landscape (current and historical) drivers. 4. We confirm the existence of an extinction debt for this species, since current plant frequency is related to historical but not current connectivity, and we also find a positive effect of historical connectivity on seed set. In addition, current tree cover negatively affects individual size and aboveground/belowground biomass ratio, and biotic soil acidification leads to a reduction in the flowering probability of individuals and stems. 5. However, we also find that current connectivity negatively affects flowering and that tree cover enhances seed set. The forestation process, thus, also exerts a positive effect on some fitness traits, probably by providing a moister environment. 6. Synthesis. Habitat loss and deterioration result in a decreased vegetative performance of Aphyllanthes monspeliensis, a grassland specialist, but show contrasting effects on its reproductive performance. However, further forest encroachment would increase light competition and soil acidification, threatening its persistence and promoting the payment of the extinction debt if no conservation measures are taken.
Data from: Explaining high-diversity death assemblages: undersampling of the living community, out-of-habitat transport, time-averaging of rare taxa, and local extinction
Molluscan benthic assemblages provide unique opportunities for understanding both spatial and temporal patterns of biodiversity. Species richness in the shell remains found at a site (i.e. the death assemblage) is typically several times higher than in the counterpart living assemblage, reflecting a complex history of settlement, dissemination and decomposition post-mortem. We used high-density temporal and spatial sampling (>37'000 individuals representing 196 taxa) of a shallow (5-8 m) nearshore sandy habitat off the coast of south-east Sardinia (Italy, Mediterranean Sea) to study the factors responsible for differences in the relative diversity of living and death assemblages. We found that death assemblages at all sites were considerably more diverse than living communities (1.5-3.5x more dead than living taxa after sample-size standardization), with 78% of all taxa solely recovered as empty shells, resulting in low live-dead agreement. By carefully filtering the raw data and combining them with habitat information extracted from the literature, we disentangled the major causes of this discordance and quantified their individual effects. Increased dead diversities could not be attributed to undersampling of the living community, but instead resulted from three phenomena of decreasing importance: the post-mortem, out-of-habitat transport of non-indigenous taxa (57% of dead-only taxa were allochthonous), the time-averaged presence of rare indigenous taxa (40% of dead-only taxa), and the likely local extirpation of a small number of species (3% of dead-only taxa). Our approach demonstrates how ecological inferences based on death assemblages can be improved by restricting analyses to demonstrably indigenous taxa, and highlights how mollusc shell remains can be used to provide information over both ecological and evolutionary timescales.
Data from: Color vision varies more among populations than among species of live-bearing fish from South America
Background: Sensory Bias models for the evolution of mate preference place a great emphasis on the role of sensory system variation in mate preferences. However, the extent to which sensory systems vary across- versus within-species remains largely unknown. Here we assessed whether color vision varies in natural locations where guppies (Poecilia reticulata) and their two closest relatives, Poecilia parae and Poecilia picta, occur in extreme sympatry and school together. All three species base mate preferences on male coloration but differ in the colors preferred. Results: Measuring opsin gene expression, we found that within sympatric locations these species have similar color vision and that color vision differed more across populations of conspecifics. In addition, all three species differ across populations in the frequency of the same opsin coding polymorphism that influences visual tuning. Conclusions: Together, this shows sensory systems vary considerably across populations and supports the possibility that sensory system variation is involved in population divergence of mate preference.
Data from: Dominance, gender, and season influence food patch use in a group-living, solitary foraging canid
In patchy environments, foragers adopt different strategies to acquire resources depending on their internal state and external physical and social environment: this has important fitness consequences. Linking individual variation in patch use to tangible characteristics is key to understand many higher-level ecological processes. We studied patch use by red foxes (Vulpes vulpes) in the city of Bristol, UK. We placed camera traps in gardens where householders provisioned foxes (patches) to investigate whether 1) foxes discriminated between patches based on food availability, quantified as provisioning frequency (predictability) and the energy value of provisioned food; and 2) individual patch use varied with dominance, gender, and season. Increased frequency of provisioning encouraged more foxes to visit and to stay longer in patches. All foxes visited the most predictable patches first each day, but females were more selective and generally more efficient foragers than males. Females increased foraging effort during cub rearing, whereas males reduced patch use in the dispersal and mating season. Dominants and subordinates shared patches spatiotemporally, possibly facilitated by relatedness and familiarity between group members. However, dominants visited more food patches on their territory, spent more time in predictable patches and fed earlier than subordinates. Subordinates may compensate for competition by visiting patches of lower quality or outside their territory, which is inefficient and risky. Our results demonstrate gender differences in behavioral motivation, show how subordinates forego foraging efficiency to mitigate intra-group competition and reveal how human provisioning influences fox space use in urban areas.
Data from: Living on a volcano's edge: genetic isolation of an extremophile terrestrial metazoan
Communities of organisms inhabiting extreme terrestrial environments provide a unique opportunity to study evolutionary forces that drive population structure and genetic diversity under the combined challenges posed by multiple geogenic stressors. High abundance of an invasive pantropical earthworm (and the absence of indigenous lumbricid species) in the Furnas geothermal field (Sao Miguel Island, Azores) indicates its remarkable tolerance to high soil temperature, exceptionally high carbon dioxide and low oxygen levels, and elevated metal bioavailability, conditions which are lethal for the majority of terrestrial metazoans. Mitochondrial and nuclear markers were used to analyze the relationship between populations living inside and outside the geothermal field. Results showed that Pontoscolex corethrurus (Annelida, Oligochaeta, Glossoscolecidae) to be a genetically heterogeneous complex within the Sao Miguel landscape and is probably differentiated into cryptic species. The population exposed to the hostile soil conditions within the volcanic caldera possesses the lowest within-population mitochondrial diversity but an unexpectedly high degree of nuclear variability with several loci evidencing positive selection, parameters indicative of a genetically unique population only distantly related to conspecifics living outside the caldera. In conclusion, P. corethrurus inhabiting active volcanic soil is a discrete extremophile population that has evolved by tolerating a mixture of non-anthropogenic chemical and physical stressors.
Data from: Exploring an alternative explanation for the second phase of viral decay: infection of short-lived cells in a drug-limited compartment during HAART
Most HIV-infected patients who initiate combination antiretroviral therapy experience a viral load decline in several phases. These phases are characterized by different rates of viral load decay that decrease when transitioning from one phase to the next. There is no consensus as to the origin of these phases. One hypothesis put forward is that short- and long-lived infected cells are responsible for the first and second phases of decay, respectively. However, significant differences in drug concentrations are observed in monocytes from various tissues, suggesting the first two phases of decay in viral loads could instead be attributed to short-lived cells being differently exposed to drugs. Compared to a well-exposed compartment, new cell infection can be expected in a compartment with limited drug exposure, thus leading to a slower viral load decay with potential virologic failure and drug resistance. In the current study, the latter hypothesis was investigated using a model of viral kinetics. Empirical datasets were involved in model elaboration and parameter estimation. In particular, susceptibility assay data was used for an in vitro to in vivo extrapolation based on the expected drug concentrations inside physiological compartments. Results from numerical experiments of the short-term evolution of viral loads can reproduce the first two phases of viral decay when allowing new short-lived cell infections in an unidentified drug-limited compartment. Model long-term predictions are however less consistent with clinical observations. For the hypothesis to hold, efavirenz, tenofovir and emtricitabine drug exposure in the drug-limited compartment would have to be very low compared to exposure in peripheral blood. This would lead to significant long-term viral growth and the frequent development of resistant strains, a prediction not supported by clinical observations. This suggests that the existence of a drug-limited anatomical compartment is unlikely, by itself, to explain the second phase of viral load decay.
Data from: Telomere length is repeatable, shortens with age and reproductive success, and predicts remaining lifespan in a long-lived seabird
<p>Telomeres are protective caps at the end of chromosomes, and their length is positively correlated with individual health and lifespan across taxa. Longitudinal studies have provided mixed results regarding the within-individual repeatability of telomere length. While some studies suggest telomere length to be highly dynamic and sensitive to resource-demanding or stressful conditions, others suggest that between-individual differences are mostly present from birth and relatively little affected by the later environment. This dichotomy could arise from differences between species, but also from methodological issues. In our study, we used the highly reliable Terminal Restriction Fragment analysis method to measure telomeres over a 10-year period in adults of a long-lived seabird, the common tern (<i>Sterna hirundo</i>). Telomeres shortened with age within individuals. The individual repeatability of age-dependent telomere length was high (> 0.53), and independent of the measurement interval (i.e. 1 <i>vs.</i> 6 years). A small (R<sup>2</sup> = 0.01), but significant part of the between-individual variation in telomere length was, however, explained by the number of fledglings produced in the previous year, while reproduction in years prior to the previous year had no effect. We confirmed that age-dependent telomere length predicted an individual's remaining lifespan. Overall, our study suggests that the majority of between-individual variation in adult telomere length is consistent across adult life, and that a smaller part of the variation can be explained by dynamic factors, such as reproduction.</p>
Data from: Are 2D space-use analyses adapted to animals living in 3D environments? A case study on a fish shoal
Methodologies enabling the monitoring of animal movement and behavior in 3-dimensions (3D; x, y, z, the latter accounting for the vertical dimension) are becoming increasingly accessible and can be deployed on entire groups of animals inhabiting 3D habitats. When 2-dimensional (2D; x, y) space-use analyses are used on such groups, their spatial organization is represented as a planar projection of individuals' space-use. Movement on the vertical dimension is ignored and could biased ecological inference made from the spatial structure of the group. We used a digital imaging technique to track movements and feeding behavior of individual animals within a free-range aggregation of juvenile drift-feeding fish (Galaxias anomalus) in 3D and at fine spatiotemporal scales. We estimated spatiotemporal overlap of space-use and feeding territories between group-members using 2D (x, y) and 3D spatial analysis to: (1) describe the spatial structure of the group, (2) identify patterns of resource partitioning, and (3) investigate the relationship between space-use overlap and feeding behavior. We found that overlapping ratios of space-use and feeding territories were over-estimated in 2D, while 3D analysis of space-use provided evidence of spatial partitioning between group-members. We also found that, regardless of the computation used, the overlapping ratios of space-use were positively correlated with overlapping ratios of feeding territories while no effect was found on feeding activity. In conclusion, whilst 3D analysis provided valuable information on the spatial structure of a group, inferences on the ecological function of space-use can also be obtained from 2D analysis.
Data from: Daily foraging patterns in free-living birds: exploring the predation-starvation trade-off
Daily patterns in the foraging behaviour of birds are assumed to balance the counteracting risks of predation and starvation. Predation risks are a function of the influence of weight on flight performance and foraging behaviours that may expose individuals to predators. Although recent research sheds light on daily patterns in weight gain, little data exist on daily foraging routines in free-living birds. In order to test the predictions of various hypotheses about daily patterns of foraging, we quantified the activity of four species of passerines in winter using radio frequency identification receivers built into supplemental feeding stations. From records of 472,368 feeder visits by tagged birds, we found that birds generally started to feed before sunrise and continued to forage at a steady to increasing rate throughout the day. Foraging in most species terminated well before sunset, suggesting their desired level of energy reserves was being reached before the end of the day. These results support the risk-spreading theorem over a long-standing hypothesis predicting bimodality in foraging behaviour purportedly driven by a tradeoff between the risks of starvation and predation. Given the increased energetic demands experienced by birds during colder weather, our results suggest that birds' perceptions of risk are biased towards starvation avoidance in winter.
Data from: Artificial light at night does not affect telomere shortening in a developing free-living songbird: a field experiment
Artificial light at night (ALAN) is an increasingly pervasive anthropogenic disturbance factor. ALAN can seriously disrupt physiological systems that follow circadian rhythms, and may be particularly influential early in life, when developmental trajectories are sensitive to stressful conditions. Using great tits (Parus major) as a model species, we experimentally examined how ALAN affects physiological stress in developing nestlings. We used a repeated-measure design to assess effects of ALAN on telomere shortening, body mass, tarsus length and body condition. Telomeres are repetitive nucleotide sequences that protect chromosomes from damage and malfunction. Early life telomere shortening can be accelerated by environmental stressors, and has been linked to later-life declines in survival and reproduction. We also assayed nitric oxide, as an additional metric of physiological stress, and determined fledging success. Change in body condition between day 8 and 15 differed according to treatment. Nestlings exposed to ALAN displayed a trend towards a decline in condition, whereas control nestlings displayed a trend towards increased condition. This pattern was driven by a greater increase in tarsus length relative to mass in nestlings exposed to ALAN. Nestlings in poorer condition and nestlings that were smaller than their nest mates had shorter telomeres. However, exposure to ALAN was unrelated to telomere shortening, and also had no effect on nitric oxide concentrations or fledging success. Thus, exposure to ALAN may not have led to sufficient stress to induce telomere shortening. Indeed, plasticity in other physiological systems could allow nestlings to maintain telomere length despite moderate stress. Alternatively, the cascade of physiological and behavioral responses associated with light exposure may have no net effect on telomere dynamics.
Data from: Ecomorphological determinations in the absence of living analogs: the predatory behavior of the marsupial lion (Thylacoleo carnifex) as revealed by elbow-joint morphology
Thylacoleo carnifex, or the "pouched lion" (Mammalia: Marsupialia: Diprotodontia: Thylacoleonidae) was a carnivorous marsupial that inhabited Australia during the Pleistocene. Although today all authors agree that Thylacoleo had a hypercarnivorous diet, the way in which it killed its prey remains uncertain. Here we use geometric morphometrics to capture the shape of the elbow joint (i.e., the posterior articular surface of the distal humerus) in a wide sample of extant mammals of known behavior to determine how elbow anatomy reflects forearm use. We then employ this information to investigate the predatory behavior of Thylacoleo. A Principal Components Analysis indicates that Thylacoleo is the only carnivorous mammal to cluster with extant taxa that have an extreme degree of forearm maneuverability, such as primates and arboreal xenarthrans (pilosans). A Canonical Variates Analysis confirms that Thylacoleo had forearm maneuverability intermediate between wombats (terrestrial) and arboreal mammals, and a much greater degree of maneuverability than any living carnivoran placental. A Linear Discriminant Analysis computed to separate the elbow morphology of arboreal mammals from terrestrial ones shows that Thylacoleo was primarily terrestrial but with some climbing abilities. We infer from our results that Thylacoleo used its forelimbs for grasping or manipulating prey to much higher degree than its supposed extant placental counterpart, the African lion (Panthera leo). The use of the large and retractable claw on the semi-opposable thumb of Thylacoleo for potentially slashing and disemboweling prey is discussed in the light of this new evidence.
Data from: Sex-specific pathways of parental age effects on offspring lifetime reproductive success in a long-lived seabird
The conditions under which individuals are reared vary and sensitivity of offspring to such variation is often sex-dependent. Parental age is one important natal condition with consequences for aspects of offspring fitness, but reports are mostly limited to short-term fitness consequences and do not take into account offspring sex. Here we used individual-based data from a large colony of a long-lived seabird, the common tern Sterna hirundo, to investigate longitudinal long-term fitness consequences of parental age in relation to both offspring and parental sex. We found that recruited daughters from older mothers suffered from reduced annual reproductive success. Recruited sons from older fathers were found to suffer from reduced lifespan. Both effects translated to reductions in offspring lifetime reproductive success. Besides revealing novel sex-specific pathways of trans-generational parental age effects on offspring fitness, which inspire studies of potential underlying mechanisms, our analyses show that reproductive senescence is only observed in the common tern when including trans-generational age effects. In general, our study shows that estimates of selective pressures underlying the evolution of senescence, as well as processes such as age-dependent mate choice and sex allocation, will depend on whether causal trans-generational effects exist and are taken into account.
Data from: Living near the edge: being close to mature forest increases the rate of succession in beetle communities
In increasingly fragmented landscapes, it is important to understand how mature forest affects adjacent secondary forest (forest influence). Forest influence on ecological succession of beetle communities is largely unknown. We investigated succession and forest influence using 235 m long transects across boundaries between mature and secondary forest at 15 sites, sampling a chronosequence of three forest age classes (5-10, 23-29 and 42-46 years since clearcutting) in tall eucalypt forest in Tasmania. Our results showed that ground-dwelling beetle communities showed strong successional changes, and in the oldest secondary forests, species considered indicators of mature forest had re-colonised to abundance levels similar to those observed within adjacent mature forest stands. However, species composition also showed forest influence gradients in all age classes. Forest influence was estimated to extend 13 m and 20 m in the youngest and intermediate aged secondary forests, respectively. However, the estimated effect extended to at least 176 m in the oldest secondary forest. Our environmental modelling suggests that leaf litter, microclimate and soil variables were all important in explaining the spatial variation in beetle assemblages, and the relative importance of factors varied between secondary forest age classes. Mature forest beetle communities can recolonise successfully from the edge and our results provide a basis for land managers to build mature habitat connectivity into forest mosaics typical of production forests. Our results also indicate the importance of forest influence in determining potential conservation value of older secondary forest for beetles.
Data from: Genetic divergence and signatures of natural selection in marginal populations of a keystone, long-lived conifer, eastern white pine (Pinus strobus) from northern Ontario
Marginal populations are expected to provide the frontiers for adaptation, evolution and range shifts of plant species under the anticipated climate change conditions. Marginal populations are predicted to show genetic divergence from central populations due to their isolation, and divergent natural selection and genetic drift operating therein. Marginal populations are also expected to have lower genetic diversity and effective population size (Ne) and higher genetic differentiation than central populations. We tested these hypotheses using eastern white pine (Pinus strobus) as a model for keystone, long-lived widely-distributed plants. All 614 eastern white pine trees, in a complete census of two populations each of marginal old-growth, central old-growth, and central second-growth, were genotyped at 11 microsatellite loci. The central populations had significantly higher allelic and genotypic diversity, latent genetic potential (LGP) and Ne than the marginal populations. However, heterozygosity and fixation index were similar between them. The marginal populations were genetically diverged from the central populations. Model testing suggested predominant north to south gene flow in the study area with curtailed gene flow to northern marginal populations. Signatures of natural selection were detected at three loci in the marginal populations; two showing divergent selection with directional change in allele frequencies, and one balancing selection. Contrary to the general belief, no significant differences were observed in genetic diversity, differentiation, LGP, and Ne between old-growth and second-growth populations. Our study provides information on the dynamics of migration, genetic drift and selection in central versus marginal populations of a keystone long-lived plant species and has broad evolutionary, conservation and adaptation significance.
Data from: Within-individual plasticity explains age-related decrease in stress response in a short-lived bird
A crucial problem for every organism is how to allocate energy between competing life-history components. The optimal allocation decision is often state-dependent and mediated by hormones. Here, we investigated how age, a major state variable affects individuals' hormonal response to a standardized stressor: a trait that may reflect allocation between self-maintenance and reproduction. We caught free-living house sparrows and measured their hormonal (corticosterone) response to capture stress in consecutive years. Using a long-term ringing dataset, we determined the age of the birds, and we partitioned the variation into within- and among-individual age components to investigate the effects of plasticity versus selection or gene flow, respectively, on the stress response. We found large among-individual variation in the birds' hormone profiles, but overall, birds responded less strongly to capture stress as they grew older. These results suggest that stress responsiveness is a plastic trait that may vary within individuals in an adaptive manner, and natural selection may act on the reaction norms producing optimal phenotypic response in the actual environment and life-history stage.
Data from: Warming impacts on early life stages increase the vulnerability and delay the population recovery of a long-lived habitat-forming macroalga
1. Understanding the combined effects of global and local stressors is crucial for conservation and management, yet challenging due to the different scales at which these stressors operate. Here we examine the effects of one of the most pervasive threats to marine biodiversity, ocean warming, on the early life stages of the habitat-forming macroalga Cystoseira zosteroides, its long-term consequences for population resilience and its combined effect with physical stressors. 2. First, we performed a controlled laboratory experiment exploring the impacts of warming on early life stages. Settlement and survival of germlings were measured at 16ºC (control), 20ºC and 24ºC and both processes were affected by increased temperatures. Then, we integrated this information into stochastic, density-dependent integral projection models (IPM). 3. Recovery time after a minor disturbance significantly increased in warmer scenarios. The stochastic population growth rate (λs) was not strongly affected by warming alone, as high adult survival compensated for thermal-induced recruitment failure. Nevertheless, warming coupled with recurrent physical disturbances had a strong impact on λs and population viability. 4. Synthesis: The impact of warming effects on early stages may significantly decrease the natural ability of habitat-forming algae to rebound after major disturbances. These findings highlight that, in a global warming context, populations of deep-water macroalgae will become more vulnerable to further disturbances, and stress the need to incorporate abiotic interactions into demographic models.
Data from: A new approach to study local adaptation in long-lived organisms: virtual transplant experiments
1. Despite the importance of local adaptation and the extended literature that has addressed it, there are few methods available to explore local adaptation across large temporal scales. However, long-term patterns are likely to be essential to understanding adaptation in long-lived species, such as trees. 2. Here, we propose a methodology named 'virtual transplant experiment' (VTE), which uses long-term climatic variability to explore local adaptation to climate in natural tree populations. VTEs evaluate the historical response of populations to their local climate and to climates representative of conditions in other populations. We tested our methodology using simulated data and applied it in two case studies on: (i) Pinus nigra populations at the edge of the species distribution, where previous research has suggested strong climate adaptation, and (ii) Fagus sylvatica mesic populations, where parallel experiments showed no adaptation to macroclimate. 3. VTE results from simulated and real-world data matched our expectations, suggesting that the method accurately identified the patterns of local adaptation to climate in tree populations. VTEs consistently discriminated locally adapted populations in synthetic data with a known degree of local adaptation. As expected, P. nigra populations showed adaptation to local climate in the VTE, while F. sylvatica populations showed no overall local advantage. 4. Our method provides a new way to test for local adaptation over time scales encompassing the complete lifespan of trees. VTEs can complement current methods to study local adaptation by adding the ability to explore the long-term response to local climate in natural populations. The advantages and limitations of the different approaches to studying local adaptation stress the importance of combining multiple approaches to test for local adaptation in long-lived organisms.
Data from: Speciation slowing down in widespread and long-living tree taxa: insights from the tropical timber tree genus Milicia (Moraceae)
The long generation time and large effective size of widespread forest tree species can result in slow evolutionary rate and incomplete lineage sorting, complicating species delimitation. We addressed this issue with the African timber tree genus Milicia that comprises two morphologically similar and often confounded species: M. excelsa, widespread from West to East Africa, and M. regia, endemic to West Africa. We combined information from nuclear microsatellites (nSSRs), nuclear and plastid DNA sequences, and morphological systematics to identify significant evolutionary units and infer their evolutionary and biogeographical history. We detected five geographically coherent genetic clusters using nSSRs and three levels of genetic differentiation. First, one West African cluster matched perfectly with the morphospecies M. regia, which formed a monophyletic clade at both DNA sequences. Second, a West African M. excelsa cluster formed a monophyletic group at plastid DNA and was more related to M. regia than to Central African M. excelsa, but shared many haplotypes with the latter at nuclear DNA. Third, three Central African clusters appeared little differentiated and shared most of their haplotypes. Although gene tree paraphyly could suggest a single species in Milicia following the Phylogenetic Species Concept, the existence of mutual haplotypic exclusivity and non-admixed genetic clusters in the contact area of the two taxa indicate strong reproductive isolation, and thus, two species following the Biological Species Concept. Molecular dating of the first divergence events showed that speciation in Milicia is ancient (Tertiary), indicating that long-living tree taxa exhibiting genetic speciation may remain similar morphologically.
Data from: Cryptic lineages in the Wolf Cardinalfish living in sympatry on remote coral atolls
Coral reef health and biodiversity is under threat worldwide due to rapid climate change. However, much of the inter- and intra-specific diversity of coral reefs are undescribed even in well studied taxa such as fish. Delimiting previously unrecognised diversity is important for understanding the processes that generate and sustain biodiversity in coral reef ecosystems and informing strategies for their conservation and management. Many taxa that inhabit geographically isolated coral reefs rely on self-recruitment for population persistence, providing the opportunity for the evolution of unique genetic lineages through divergent selection and reproductive isolation. Many such lineages in corals and fish are morphologically similar or indistinguishable. Here, we report the discovery and characterisation of cryptic lineages of the Wolf Cardinalfish, Cheilodipterus artus, from the coral atolls of northwest Australia using multiple molecular markers from mitochondrial (CO1 and D-loop) and nuclear (microsatellites) DNA. Concordant results from all markers identified two highly divergent lineages that are morphologically cryptic and reproductively isolated. These lineages co-occurred at daytime resting sites, but the relative abundance of each lineage was strongly correlated with wave exposure. It appears, therefore, that fish from each lineage are better adapted to different microhabitats. Such cryptic and ecologically based diversity appears to be common in these atolls and may well aid resilience of these systems. Our results also highlight that underwater surveys based on visual identification clearly underestimate biodiversity, and that a taxonomic revision of the Cheilodipterus genus is necessary.
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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.