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Data from: Direct detection of male quality can facilitate the evolution of female choosiness and indicators of good genes: evolution across a continuum of indicator mechanisms
The evolution of mating displays as indicators of male quality has been the subject of extensive theoretical and empirical research for over four decades. Research has also addressed the evolution of female mate choice favoring such indicators. Yet, much debate still exists about whether displays can evolve through the indirect benefits of female mate choice. Here, we use a population genetic model to investigate how the extent to which females can directly detect male quality influences the evolution of female choosiness and male displays. We use a continuum framework that incorporates indicator mechanisms that are traditionally modelled separately. Counter to intuition, we find that intermediate levels of direct detection of male quality can facilitate, rather than impede, the evolution of female choosiness and male displays in broad regions of this continuum. We examine how this evolution is driven by selective forces on genetic quality and on the display, and find that direct detection of male quality results in stronger indirect selection favoring female choosiness. Our results imply that displays maybe more likely to evolve when female choosiness has already evolved to discriminate perceptible forms of male quality. They also highlight the importance of considering general female choosiness, as well as preference, in studies of "good genes".
Data from: Mitochondrial haplotypes indicate parapatric-like phylogeographic structure in blue-spotted maskray (Neotrygon kuhlii) from the Coral Triangle region
Phylogeographic structure was investigated in the blue-spotted maskray, Neotrygon kuhlii, focusing on the Coral Triangle region. We used as genetic marker a 519-bp fragment of the cytochrome c-oxidase subunit I (COI) gene, sequenced in a total of 147 individuals from 26 sampling locations. The parsimony network of COI haplotypes was split into seven distinct clades within the Coral Triangle region. Different clades had exclusive but contiguous geographic distributions, indicating parapatric-like phylogeographic structure. Strong genetic differences were also inferred between local populations within a clade, where reciprocal monophyly between geographically adjacent samples was observed on several instances. Nearly 25% of the total molecular variance could be ascribed to differences between geographic samples within a clade, whereas interclade variation accounted for >65% of the total variance. The strong phylogeographic structure observed within a clade can be explained by either sedentarity or female philopatry. We interpret the parapatric distribution of clades as the joint result of 1) expansion from refuge populations at times of low sea level, and 2) possible enhanced competition between individuals from different clades, or assortative mating, or hybrid zones, along lines of secondary contact. The parapatric-like structure uncovered in the present study parallels regional differences at nuclear marker loci, thus pointing to incipient speciation within Coral Triangle N. kuhlii.
Data from: Proxies in practice: calibration and validation of multiple indices of animal abundance
The abundance of individuals in a population is a fundamental metric in basic and applied ecology, but sampling protocols yielding precise and unbiased estimates of abundance are often cost prohibitive. Proxies of abundance are therefore common, but require calibration and validation. There are many ways to calibrate a proxy, and it is not obvious which will perform best. We use data from eight populations of Chinook salmon (Oncorhynchus tshawytscha) on the Oregon coast where multiple proxies of abundance were obtained contemporaneously with independent mark-recapture estimates. We combined multiple proxy values associated with a single level of abundance into a univariate index and then calibrated that index to mark-recapture estimates using several different techniques. We tested our calibration methods using leave-one-out cross validation and simulation. Our cross-validation analysis did not definitively identify a single best calibration technique for all populations, but we could identify consistently inferior approaches. The simulations suggested that incorporating the known mark-recapture uncertainty into the calibration technique added bias and imprecision. Cross validation techniques should be used to test multiple methods of calibrating multiple proxies to an estimate of abundance. Critical uncertainties with the application of calibrated proxies still exist, and cost-benefit analysis should be performed to help identify optimal monitoring designs.
Data from: Survival of the fattest? Indices of body condition do not predict viability in the brown anole (Anolis sagrei)
1. Measures of body mass and length are commonly used to derive indices of condition, which are often assumed to reflect the energetic state of an animal and, by extension, to predict its fitness. However, the relationship between condition and fitness is rarely quantified, and the appropriate method(s) for deriving indices of condition are frequently debated. 2. Data from a decade of mark-recapture studies involving over 4,600 individual lizards (Anolis sagrei) and 41 replicates of selection across seven populations were used to test the common assumption that condition, as estimated from body mass and length, is a strong predictor of adult survival, an important component of fitness. Inferences about natural selection were compared between two alternative indices of condition: the popular residual index (Ri), and the scaled mass index (Mi), which was recently proposed as a more appropriate method. 3. Linear, quadratic, and correlational selection gradients obtained using Ri and Mi were highly correlated with one another. Relative to variance in selection among replicates and to error associated with the estimation of selection gradients, variance due to the use of alternative condition indices was minor and effectively negligible. 4. Contrary to the intuitive prediction that individuals in better condition should exhibit higher survival, there was no evidence for strong or consistent linear (directional) selection for higher condition indices in either males or females. Significant quadratic (stabilizing or disruptive) selection on condition was similarly rare in both sexes. Correlational selection favored combinations of large size and high condition in males, but not females. 5. Collectively, these results indicate that inferences about natural selection may be robust to the choice between indices of condition, but that indices of condition can be unreliable as proxies for fitness, particularly when relationships between fitness components and condition are contingent upon interactions with other traits.
Data from: Genetic diversity and structure of Lolium perenne ssp. multiflorum in California vineyards and orchards indicates potential for spread of herbicide resistance via gene flow
Management of agroecosystems with herbicides imposes strong selection pressures on weedy plants leading to the evolution of resistance against those herbicides. Resistance to glyphosate in populations of Lolium perenne L. ssp. multiflorum is increasingly common in California, USA, causing economic losses and the loss of effective management tools. To gain insights into the recent evolution of glyphosate resistance in L. perenne in perennial cropping systems of northwest California and to inform management, we investigated the frequency of glyphosate resistance and the genetic diversity and structure of 14 populations. The sampled populations contained frequencies of resistant plants ranging from 10% to 89%. Analyses of neutral genetic variation using microsatellite markers indicated very high genetic diversity within all populations regardless of resistance frequency. Genetic variation was distributed predominantly among individuals within populations rather than among populations or sampled counties, as would be expected for a wide-ranging outcrossing weed species. Bayesian clustering analysis provided evidence of population structuring with extensive admixture between two genetic clusters or gene pools. High genetic diversity and admixture, and low differentiation between populations, strongly suggests the potential for spread of resistance through gene flow and the need for management that limits seed and pollen dispersal in L. perenne.
Data from: More taxonomists describing significantly fewer species per unit effort may indicate that most species have been discovered
Recent studies show that there are more taxonomists describing species in recent decades than before. However, whether the rate of increase in number of taxonomists is greater than the rate of new species description has been questioned. We found a statistically significant decline in the proportion of species being described per number of taxonomists (i.e. authors of recent species descriptions) during the past century for (a) families of insects that had been stated not to show this trend, and (b) a sample of over 0.5 million marine, terrestrial and freshwater species. We suggest that this decreased 'catch' of species per taxonomic effort, despite scientists' greater ability to explore and sample habitats, means it is getting harder to discover new species, and supports recent studies suggesting that two-thirds of all species have been named.
Data from: A multilevel society of herring-eating killer whales indicates adaptation to prey characteristics
Non-social factors can influence animal social structure. In killer whales (Orcinus orca), fish- versus mammal-eating ecological differences are regarded as key ecological drivers of their multilevel society, including group size, but the potential importance of specific target prey remains unclear. Here, we investigate the social structure of herring-eating killer whales in Iceland and compare it to the described social structures of primarily salmon- and seal-eating populations in the Northeast Pacific, which form stable coherent basic units nested within a hierarchical multilevel society. Using 29023 photographs collected over 6 years, we examined the association patterns of 198 individuals combining clustering, social network structure, and temporal patterns of association analysis. The Icelandic population had largely weak but non-random associations, which were not completely assorted by known ranging patterns. A fission–fusion dynamic of constant and temporary associations was observed but this was not due to permanent units joining. The population-level society was significantly structured but not in a clear hierarchical tier system. Social clusters were highly diverse in complexity and there were indications of subsclusters. There was no indication of dispersal nor strong sex differences in associations. These results indicate that the Icelandic herring-eating killer whale population has a multilevel social structure without clear hierarchical tiers or nested coherent social units, different from other populations of killer whales. We suggest that local ecological context, such as the characteristics of the specific target prey (e.g., predictability, biomass, and density) and subsequent foraging strategies may strongly influence killer whale social association patterns.
Data from: Approximate Bayesian computation analysis of EST-associated microsatellites indicates that the broadleaved evergreen tree Castanopsis sieboldii survived the Last Glacial Maximum in multiple refugia in Japan
Climatic changes have played major roles in plants' evolutionary history. Glacial oscillations have been particularly important, but some of their effects on plants' populations are poorly understood, including the numbers and locations of refugia in Asian warm temperate zones. In the present study, we investigated the demographic history of the broadleaved evergreen tree species Castanopsis sieboldii (Fagaceae) during the last glacial period in Japan. We used approximate Bayesian computation (ABC) for model comparison and parameter estimation for the demographic modelling using 27 EST associated microsatellites. We also performed the species distribution modelling (SDM). The results strongly support a demographic scenario that the Ryukyu Islands and the western parts in the main islands (Kyushu and western Shikoku) were derived from separate refugia and the eastern parts in the main islands and the Japan Sea groups were diverged from the western parts prior to the coldest stage of the Last Glacial Maximum (LGM). Our data indicate that multiple refugia survived at least one in the Ryukyu Islands, and the other three regions of the western and eastern parts and around the Japan Sea of the main islands of Japan during the LGM. The SDM analysis also suggests the potential habitats under LGM climate conditions were mainly located along the Pacific Ocean side of coastal region. Our ABC-based study helps efforts resolve the demographic history of a dominant species in warm temperate broadleaved forests during and after the last glacial period, which provides a basic model for future phylogeographical studies using this approach.
Data from: Projected population proximity indices (30km) for 2005, 2030 & 2050
This data package includes nine population proximity index layers for 2005, 2030 and 2050, for rural, urban and total populations. The layers are distributed as 1km GeoTIFFs and GeoJPGss at 1km. The aim of these layers is to describe the population which may be likely to visit a specific locality where access is determined by Euclidean distance. By using the layers alongside other geographic datasets relating to disease risk it may help identify where people may come into contact with a disease. Human population layers are often used in models to identify risk areas where humans and viruses interact, however most pathogens are not restricted to areas of human habitation: many are found in lesser populated areas such as forests. This dataset will help identify less populated areas that may well still receive high visitor numbers. The layers have been projected to 2030 and 2050 to enable projections of human/disease interfaces in the medium-term which are required to inform policy makers at country and continental level. Urban and rural populations have been separated into individual layers as in some cases it is useful to distinguish between the behaviour and associated risks attributed to the different population segments. There may be a different risk of contacting diseases in rural habitats for rural workers than for than urban visitors.
Data from: Phylogenetic and population genetic analyses of Phaeosphaeria nodorum and its close relatives indicate cryptic species and an origin in the Fertile Crescent
The origin of the fungal wheat pathogen Phaeosphaeria nodorum remains unclear despite earlier intensive global population genetic and phylogeographical studies. We sequenced 1,683 bp distributed across three loci in 355 globally distributed Phaeosphaeria isolates, including 74 collected in Iran near the center of origin of wheat. We identified nine phylogenetically distinct clades, including two previously unknown species tentatively named P1 and P2 collected in Iran. Coalescent analysis indicates that P1 and P2 are sister species of P. nodorum and the other Phaeosphaeria species identified in our analysis. Two species, P. nodorum and P. avenaria f. sp. tritici 1 (Pat1), comprised ∼85% of the sampled isolates, making them the dominant wheat-infecting pathogens within the species complex. We designed a PCR-RFLP assay to distinguish P. nodorum from Pat1. Approximately 4% of P. nodorum and Pat1 isolates showed evidence of hybridization. Measures of private allelic richness at SSR and sequence loci suggest that the center of origin of P. nodorum coincides with its host in the Fertile Crescent. We hypothesize that the origin of this species complex is also in the Fertile Crescent, with four species out of nine found exclusively in the Iranian collections.
Data from: Endothermic mosasaurs? Possible thermoregulation of Late Cretaceous mosasaurs (Reptilia, Squamata) indicated by stable oxygen isotopes in fossil bioapatite in comparison with coeval marine fish and pelagic seabirds
The thermoregulatory style of Late Cretaceous mosasaurs has become a highly controversial subject in vertebrate palaeontology. These extinct marine reptiles have previously been described as poikilothermic, endothermic or gigantothermic. Here we analyse three genera of mosasaurs from the Mooreville Chalk in Alabama (USA) of differing body mass, and compare their δ18OPO4 derived body temperatures (Tb) with those of coeval poikilothermic fish (Enchodus) and endothermic pelagic seabirds (Ichthyornis). Results show that all mosasaurs, Clidastes (Tb = 33.1°C), Platecarpus (Tb = 36.3°C), and Tylosaurus (Tb = 34.3°C), had elevated average body temperatures in relation to those of the fish (Tb = 28.3°C) and were closer to those of Ichthyornis (Tb = 38.6°C). The temperatures calculated for Enchodus compare well with previously reported temperature estimates for the Mooreville Chalk and the Tb of Ichthyornis compares well with temperatures that have been reported for modern seabirds, suggesting that this method provides accurate results. Finally, although there are small differences of body temperature among mosasaur genera, these are independent of size, and thus inferred body mass, suggesting that mosasaurs were not gigantotherms, but rather endotherms.
Data from: At least some meiofaunal species are not everywhere. Indication of geographic, ecological and geological barriers affecting the dispersion of species of Ototyphlonemertes (Nemertea, Hoplonemertea)
Most meiofaunal species are known to have a broad distribution with no apparent barriers to their dispersion. However, different morphological and/or molecular methods supported patterns of diversity and distribution that may be different among taxa while also conflicting within the same group. We accurately assessed the patterns of geographic distribution in actual genetic species of a marine meiofaunal animal model: Ototyphlonemertes. Specimens were collected from several sites around Europe, Northern and Central America, Southern America, Pacific Islands and Asia. We sequenced regions of two mitochondrial and two nuclear genes. Using single-gene, a concatenated data set, multilocus approaches and different DNA taxonomy methods, we disentangled the actual diversity and the spatial structures of haplotypes and tested the possible correlation between genetic diversity and geographic distance. The results show (i) the importance of using several genes to uncover both diversity and highlight phylogeographic relationships among species and that (ii) independent genetic evolutionary entities have a narrower distribution than morphological species. Moreover, (iii) a Mantel test supported a positive correlation between genetic and geographical distance. By sampling from the two sides of Isthmus of Panama, we were additionally able to identify lineage divergence times that are concordant with vicariance mechanisms caused by the geological closure of the seaway across the Isthmus. We therefore propose that in addition to distance, other geological and ecological conditions are also barriers to the dispersion of and gene flow in marine meiofaunal organisms.
Data from: Life-history strategies indicate live-bearing in Nothosaurus (Sauropterygia)
In Sauropterygia, a diverse group of Mesozoic marine reptiles, fossil evidence of viviparity (live‐bearing) only exists for Pachypleurosauria and Plesiosauria, and was assumed to also be the case for nothosaurs. Previous studies have successfully applied an extant squamate model to sauropterygian life‐history traits. In extant squamates, oviparity and viviparity are associated with differences in life‐history trait combinations. We establish growth curves for Nothosaurus specimens based on their humeral histology. We then analyse life‐history traits derived from these curves and compare inferred traits to those of modern squamates and pachypleurosaurs to assess their reproduction mode. We show that birth to adult size ratios (i.e. birth size divided by the mother's size) provide good estimates of clutch sizes in extant squamates and in viviparous extinct marine reptiles, but these ratios cannot discriminate viviparous and oviparous squamates. Thus, large ratios do not indicate viviparity in fossil taxa to which the extant squamate model is applicable. Applying differences in birth size, age at maturation, and maximum longevity that are observed between extant viviparous and oviparous squamates to our Nothosaurus sample, we identified 7 out of 24 specimens as being potentially viviparous. Conversely, they suggested oviparity for many nothosaurs but also for many pachypleurosaur samples. Under the assumption that the entire clade Pachypleurosauria was viviparous, the majority of nothosaurs would also have been viviparous as they comprised trait combinations similar to those seen in pachypleurosaurs. Overall, this suggests that within nothosaurs and pachypleurosaurs both reproduction modes existed in different taxa.
Data from: Quantifying the climatic niche of symbiont partners in a lichen symbiosis indicates mutualist-mediated niche expansions
The large distributional areas and ecological niches of many lichenized fungi may in part be due to the plasticity in interactions between the fungus (mycobiont) and its algal or cyanobacterial partners (photobionts). On the one hand, broad-scale phylogenetic analyses show that partner compatibility in lichens is rather constrained and shaped by reciprocal selection pressures and codiversification independent of ecological drivers. On the other hand, sub-species-level associations among lichen symbionts appear to be environmentally structured rather than phylogenetically constrained. In particular, switching between photobiont ecotypes with distinct environmental preferences has been hypothesized as an adaptive strategy for lichen-forming fungi to broaden their ecological niche. The extent and direction of photobiont-mediated range expansions in lichens, however, have not been examined comprehensively at a broad geographic scale. Here we investigate the population genetic structure of Lasallia pustulata symbionts at sub-species-level resolution across the mycobiont's Europe-wide range, using fungal MCM7 and algal ITS rDNA sequence markers. We show that variance in occurrence probabilities in the geographic distribution of genetic diversity in mycobiont-photobiont interactions is closely related to changes in climatic niches. Quantification of niche extent and overlap based on species distribution modeling and construction of Hutchinsonian climatic hypervolumes revealed that combinations of fungal-algal interactions change at the sub-species level along latitudinal temperature gradients and in Mediterranean climate zones. Our study provides evidence for symbiont-mediated niche expansion in lichens. We discuss our results in the light of symbiont polymorphism and partner switching as potential mechanisms of environmental adaptation and niche evolution in mutualisms.
Data from: Ants as ecological indicators of rainforest restoration: community convergence and the development of an Ant Forest Indicator Index in the Australian wet tropics
Ecosystem restoration can help reverse biodiversity loss, but whether faunal communities of forests undergoing restoration converge with those of primary forest over time remains contentious. There is a need to develop faunal indicators of restoration success that more comprehensively reflect changes in biodiversity and ecosystem function. Ants are an ecologically dominant faunal group and are widely advocated as ecological indicators. We examine ant species and functional group responses on a chronosequence of rainforest restoration in northern Australia, and develop a novel method for selecting and using indicator species. Four sampling techniques were used to survey ants at 48 sites, from grassland, through various ages (1–24 years) of restoration plantings, to mature forest. From principal components analysis of seven vegetation metrics, we derived a Forest Development Index (FDI) of vegetation change along the chronosequence. A novel Ant Forest Indicator Index (AFII), based on the occurrences of ten key indicator species associated with either grassland or mature forest, was used to assess ant community change with forest restoration. Grasslands and mature forests supported compositionally distinct ant communities at both species and functional levels. The AFII was strongly correlated with forest development (FDI). At forest restoration sites older than 5–10 years that had a relatively closed canopy, ant communities converged on those of mature rainforest, indicating a promising restoration trajectory for fauna as well as plants. Our findings reinforce the utility of ants as ecological indicators and emphasize the importance of restoration methods that achieve rapid closed-canopy conditions. The novel AFII assessed restoration status from diverse and patchily distributed species, closely tracking ant community succession using comprehensive species-level data. It has wide applicability for assessing forest restoration in a way that is relatively independent of sampling methodology and intensity, and without a need for new comparative data from reference sites.
Data from: Genotyping of Coxiella burnetii from domestic ruminants and human in Hungary: indication of various genotypes
Background: Information about the genotypic characteristic of Coxiella burnetii from Hungary is lacking. The aim of this study is to describe the genetic diversity of C. burnetii in Hungary and compare genotypes with those found elsewhere. A total of 12 samples: (cattle, n = 6, sheep, n = 5 and human, n = 1) collected from across Hungary were studied by a 10-loci multispacer sequence typing (MST) and 6-loci multiple-locus variable-number of tandem repeat analysis (MLVA). Phylogenetic relationships among MST genotypes show how these Hungarian samples are related to others collected around the world. Results: Three MST genotypes were identified: sequence type (ST) 20 has also been identified in ruminants from other European countries and the USA, ST28 was previously identified in Kazakhstan, and the proposed ST37 is novel. All MST genotypes yielded different MLVA genotypes and three different MLVA genotypes were identified within ST20 samples alone. Two novel MLVA types 0-9-5-5-6-2 (AG) and 0-8-4-5-6-2 (AF) (Ms23-Ms24-Ms27-Ms28-Ms33-Ms34) were defined in the ovine materials correlated with ST28 and ST37. Samples from different parts of the phylogenetic tree were associated with different hosts, suggesting host-specific adaptations. Conclusions: Even with the limited number of samples analysed, this study revealed high genetic diversity among C. burnetii in Hungary. Understanding the background genetic diversity will be essential in identifying and controlling outbreaks.
M Dwarf Flare Continuum Variations on One-Second Timescales: Calibrating and Modeling of ULTRACAM Flare Color Indices
<p>These files contain the ULTRACAM light curves, the ULTRACAM flare color indices, the APO/DIS spectral data, and the NMSU 1-m U-band photometry from "M Dwarf Flare Continuum Variations on One-Second Timescales: Calibrating and Modeling of ULTRACAM Flare Color Indices", Kowalski, A. F., Mathioudakis, M., Hawley, S. L., Wisniewski, J. P., Dhillon, V. S., Marsh, T. R., Hilton, E. J., & Brown, B. P., 2016, Astrophysical Journal in press. See the included ReadMe file for detailed information on the files.</p>
FIGURE 7. Phylogenetic tree from Bayesian analysis. Thick branches indicate posterior probabilities over 80 in Revision of the Ranitomeya fantastica species complex with description of two new species from Central Peru (Anura: Dendrobatidae)
FIGURE 7. Phylogenetic tree from Bayesian analysis. Thick branches indicate posterior probabilities over 80.
FIGURE 8. Study area. The thick line indicates the border between administration regions. 1 in Two new species of Parameletus Bengtsson, 1908 (Ephemeroptera: Siphlonuridae), and notes on other species from the Far East of Russia
FIGURE 8. Study area. The thick line indicates the border between administration regions. 1 – Primorskiy Kray, 2 – Khabarovskiy Kray, 3 – Sakhalinskaya Oblast', 4 – Magadanskaya Oblast', 5 – Kamchatskaya Oblast', 6 – Chukotka, 7 – Evreiskaya Autonomous Oblast', 8 – Amurskaya Oblast', 9 – Chitinskaya Oblast', 10 – Republic Sakha Yakutia.
FIGURE 5 in Electric organ discharges of South African Marcusenius species (Teleostei: Mormyridae) and their effectiveness as indicators of local species diversity
FIGURE 5. Male. Discriminant analysis (DA) of characters of the electric organ discharge (EOD) waveform of five male samples of South African Marcusenius species, compared to M. devosi specimens from Kenya (D symbols). B, S and P symbols, M. pongolensis specimens from different South African locations; K symbols, M. krameri. EOD waveform characters that were included in DA as given in Table 2, but Ndur excluded because of irrelevance in the male sample.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.