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Data from: Antagonistic relationships between intron content and codon usage bias of genes in three mosquito species: functional and evolutionary implications
Genome biology of mosquitoes holds potential in developing knowledge-based control strategies against vector-borne diseases such as malaria, dengue, West Nile Virus and others. Although the genomes of three major vector mosquitoes have been sequenced, attempts to elucidate the relationship between intron and codon usage bias across species in phylogenetic contexts are limited. In this study, we investigated the relationship between intron content and codon bias of orthologous genes among three vector mosquito species. We found an antagonistic relationship between codon usage bias and the intron number of genes in each mosquito species. The pattern is further evident among the intronless and the intron-containing orthologous genes associated with either low or high codon bias among the three species. Furthermore, the co-variance between codon bias and intron number has a directional component associated with the species phylogeny when compared with other non-mosquito insects. By applying a maximum likelihood based continuous regression method, we show that codon bias and intron content of genes vary among the insects in a phylogeny dependent manner but with no evidence of adaptive radiation or species-specific adaptation. We discuss the functional and evolutionary significance of antagonistic relationships between intron content and codon bias.
Data from: A chloroplast tree for Viburnum (Adoxaceae) and its implications for phylogenetic classification and character evolution
Premise of the study: Despite recent progress, significant uncertainties remain concerning relationships among early-branching lineages within Viburnum (Adoxaceae). This has prohibited a new classification, and has hindered studies of character evolution and the increasing use of Viburnum in addressing a wide range of ecological and evolutionary questions. We hoped to resolve these issues by sequencing whole plastid genomes for representative species and combining these with molecular data previously obtained from an expanded taxon sample. Methods: We performed paired-end Illumina sequencing of plastid genomes of 22 Viburnum species, and combined these data with a 10-gene dataset to infer phylogenetic relationships for 113 species. We used the results to devise a comprehensive phylogenetic classification and to analyze the evolution of eight morphological characters that vary among early-branching lineages. Key results: With greatly increased levels of confidence in most of the early branches, we propose a phylogenetic classification of Viburnum, providing formal phylogenetic definitions for 30 clades, including 13 with ICN names, eight with previously proposed informal names, and nine newly proposed names for major branches. Our parsimony reconstructions of bud structure, leaf margins, inflorescence form, ruminate endosperm, extrafloral nectaries, glandular trichomes, palisade anatomy, and pollen exine showed varying levels of homoplasy, but collectively provided morphological support for some, though not all, of the major clades. Conclusions: Our study demonstrates the value of next generation plastid sequencing, the ease of creating a formal phylogenetic classification, and the utility of such a system in describing patterns of character evolution.
Data from: Adaptive genetic potential and plasticity of trait variation in the foundation prairie grass Andropogon gerardii across the US Great Plains' climate gradient: Implications for climate change and restoration
<p>Plant response to climate depends on a species' adaptive potential. To address this, we used reciprocal gardens to detect genetic and environmental plasticity effects on phenotypic variation and combined with genetic analyses. Four reciprocal garden sites were planted with three regional ecotypes of <i>Andropogon gerardii</i>, a dominant Great Plains prairie grass, using dry, mesic, wet ecotypes originating from western KS to Illinois that span 500 to 1,200 mm rainfall year<sup>-1</sup>. We aimed to answer: (1) What is the relative role of genetic constraints and phenotypic plasticity in controlling phenotypes? 2) When planted in the home site, is there a trait syndrome for each ecotype? 3) How are genotypes and phenotypes structured by climate? (4) What are implications of these results for response to climate change and use of ecotypes for restoration? Surprisingly, we did not detect consistent local adaptation. Rather, we detected co-gradient variation primarily for most vegetative responses. All ecotypes were stunted in western KS. Eastward, the wet ecotype was increasingly robust relative to other ecotypes. In contrast, fitness showed evidence for local adaptation in wet and dry ecotypes with wet and mesic ecotypes producing little seed in western KS. Earlier flowering time in the dry ecotype suggests adaptation to end of season drought. Considering ecotype traits in home site, the dry ecotype was characterized by reduced canopy area and diameter, short plants, and low vegetative biomass and putatively adapted to water limitation. The wet ecotype was robust, tall with high biomass and wide leaves putatively adapted for the highly competitive, light-limited Eastern Great Plains. Ecotype differentiation was supported by random forest classification and PCA. We detected genetic differentiation and outlier genes associated primarily with precipitation. We identified candidate gene GA1 for which allele frequency associated with plant height. Sourcing of climate adapted ecotypes should be considered for restoration.</p>
Data from: Hemocyanin gene family evolution in spiders (Araneae), with implications for phylogenetic relationships and divergence times in the infraorder Mygalomorphae
Hemocyanins are multimeric copper-containing hemolymph proteins involved in oxygen binding and transport in all major arthropod lineages. Most arachnids have seven primary subunits (encoded by paralogous genes a–g), which combine to form a 24-mer (4 × 6) quaternary structure. Within some spider lineages, however, hemocyanin evolution has been a dynamic process with extensive paralog duplication and loss. We have obtained hemocyanin gene sequences from numerous representatives of the spider infraorders Mygalomorphae and Araneomorphae in order to infer the evolution of the hemocyanin gene family and estimate spider relationships using these conserved loci. Our hemocyanin gene tree is largely consistent with the previous hypotheses of paralog relationships based on immunological studies, but reveals some discrepancies in which paralog types have been lost or duplicated in specific spider lineages. Analyses of concatenated hemocyanin sequences resolved deep nodes in the spider phylogeny and recovered a number of clades that are supported by other molecular studies, particularly for mygalomorph taxa. The concatenated data set is also used to estimate dates of higher-level spider divergences and suggests that the diversification of extant mygalomorphs preceded that of extant araneomorphs. Spiders are diverse in behavior and respiratory morphology, and our results are beneficial for the comparative analyses of spider respiration. Lastly, the conserved hemocyanin sequences allow for the inference of spider relationships and ancient divergence dates.
Data from: Microform-scale variations in peatland permeability and their ecohydrological implications
1. The acrotelm-catotelm model of peatland hydrological and biogeochemical processes posits that the permeability of raised bogs is largely homogenous laterally but varies strongly with depth through the soil profile; uppermost peat layers are highly permeable while deeper layers are, effectively, impermeable. 2. We measured down-core changes in peat permeability, plant macrofossil assemblages, dry bulk density and degree of humification beneath two types of characteristic peatland microform – ridges and hollows – at a raised bog in Wales. Six 14C dates were also collected for one hollow and an adjacent ridge. 3. Contrary to the acrotelm-catotelm model, we found that deeper peat can be as highly permeable as near-surface peat and that its permeability can vary by more than an order of magnitude between microforms over horizontal distances of 1-5 metres. 4. Our palaeo-ecological data paint a complicated picture of microform persistence. Some microforms can remain in the same position on a bog for millennia, growing vertically upwards as the bog grows. However, adjacent areas on the bog (< 10 m distant) show switches between microform type over time, indicating a lack of persistence. 5. Synthesis. We suggest that the acrotelm-catotelm model should be used cautiously; spatial variations in peatland permeability do not fit the simple patterns suggested by the model. To understand how peatlands as a whole function both hydrologically and ecologically it is necessary to understand how patterns of peat physical properties and peatland vegetation develop and persist.
Data from: Internal cranial anatomy of Early Triassic species of †Saurichthys (Actinopterygii: †Saurichthyiformes): implications for the phylogenetic placement of †saurichthyiforms
Background: †Saurichthyiformes was a successful group of latest Permian-Middle Jurassic predatory actinopterygian fishes and constituted important and widely-distributed components of Triassic marine and freshwater faunas. Their systematic affinities have long been debated, with †saurichthyiforms often being aligned with chondrosteans, a group today comprising sturgeons and paddlefishes. However, their character-rich endocranial anatomy has not been investigated in detail since the first half of the 20th century. Since that time, major advances have occurred in terms of our understanding of early actinopterygian anatomy, as well as techniques for extracting morphological data from fossils. Results: We used µCT to study the internal cranial anatomy of two of the stratigraphically oldest representatives of †Saurichthys, from the Early Triassic of East Greenland and Nepal. Our work revealed numerous previously unknown characters (e.g., cryptic oticooccipital fissure; intramural diverticula of braincase; nasobasal canals; lateral cranial canal; fused dermohyal), and permitted the reevalution of features relating to the structure of cranial fossae, basicranial circulation and opercular anatomy of the genus. Critically, we reinterpret the former †saurichthyiform opercle as an expanded subopercle. For comparison, we also produced the first digital models of a braincase and endocast of a sturgeon (A. brevirostrum). New information from these taxa was included in a broad phylogenetic analysis of Actinopterygii. †Saurichthyiforms are resolved as close relatives of †Birgeria, forming a clade that constitutes the immediate sister group of crown actinopterygians. However, these and other divergences near the actinopterygian crown node are weakly supported. Conclusions: Our phylogeny disagrees with the historically prevalent hypothesis favoring the chondrostean affinities of †saurichthyiforms. Previously-proposed synapomorphies uniting the two clades, such as the closure of the oticooccipital fissure, the posterior extension of the parasphenoid, and the absence of an opercular process are widespread amongst actinopterygians. Others, like those relating to basicranial circulation, are found to be based on erroneous interpretations. Our work renders the †saurichthyiform character complex adequately understood, and permits detailed comparisons with other early crown actinopterygians. Our phylogenetic scheme highlights outstanding questions concerning the affinity of many crown actinopterygians, such as the Paleozoic-early Mesozoic deep-bodied forms, which are largely caused by lack of endoskeletal data.
Data from: Molecular phylogenetics of Braconidae (Hymenoptera: Ichneumonoidea) based on multiple nuclear genes and implications for classification
This study examined subfamilial relationships within Braconidae, using 4kb of sequence data for 139 taxa. Genetic sampling included previously used markers for phylogenetic studies of Braconidae (28S and 18S rDNA) as well as new nuclear protein-coding genes (CAD and ACC). Maximum likelihood and Bayesian inference of the concatenated dataset recovered a robust phylogeny, particularly for early divergences within the family. This study focused primarily on non-cyclostome subfamilies, but the monophyly of the cyclostome complex was strongly supported. There was evidence supporting an independent clade, termed the aphidioid complex as sister to the cyclostome complex of subfamilies. Maxfischeria was removed from Helconinae and placed within its own subfamily within the aphidioid complex. Most relationships within the cyclostome complex were poorly supported, likely due to lower taxonomic sampling within this group. Similar to other studies, there was strong support for the alysioid subcomplex containing Gnamptodontinae, Alysiinae, Opiinae, and Exothecinae. Cenocoeliinae was recovered as sister to all other subfamilies within the euphoroid complex. Planitorus and Mannokeraia, previously placed in Betylobraconinae and Masoninae, respectively, were moved to the Euphorinae and may share a close affiliation with Neoneurinae. Neoneurinae and Ecnomiinae were placed as tribes within Euphorinae. A sister relationship between the microgastroid and sigalphoid complexes was also recovered. Within the helconoid complex was a well-supported lineage parasitic on lepidopteran larvae (macrocentroid subcomplex). Helconini was raised to subfamily status and was recovered as sister to the macrocentroid subcomplex. Blacinae was demoted to tribal status and placed within the newly circumscribed subfamily Brachistinae, which also contains the tribes Diospilini, Brulleiini, and Brachistini, all formerly in Helconinae.
Data from: Conserved but flexible modularity in the zebrafish skull: implications for craniofacial evolvability
Morphological variation is the outward manifestation of development and provides fodder for adaptive evolution. Because of this contingency, evolution is often thought to be biased by developmental processes and functional interactions among structures, which are statistically detectable through forms of covariance among traits. This can take the form of substructures of integrated traits, termed modules, which together comprise patterns of variational modularity. While modularity is essential to an understanding of evolutionary potential, biologists currently have little understanding of its genetic basis, nor its temporal dynamics over generations. To address these open questions we compared patterns of craniofacial modularity among laboratory strains, defined mutant lines and a wild population of zebrafish (Danio rerio). Our findings suggest that relatively simple genetic changes can have profound effects on covariance, without greatly affecting craniofacial shape. Moreover, we show that instead of completely deconstructing the covariance structure among sets of traits, mutations cause shifts among seemingly latent patterns of modularity suggesting that the skull may be predisposed toward a limited number of phenotypes. This new insight may serve to greatly increase the evolvability of a population by providing a range of 'preset' patterns of modularity that can appear readily and allow for rapid evolution.
Data from: Ontogenetic trajectories of septal spacing in Early Jurassic belemnites from Germany and France, and their palaeobiological implications
Based on well-preserved belemnites, the ontogenetic trajectories of septal spacing between succeeding chambers were analysed. In the examined species (Passaloteuthis laevigata, Parapassaloteuthis zieteni and Pseudohasitites longiformis) that come from Buttenheim, Germany, and Lixhausen, France, the ontogenetic trajectories of septal spacing follow exponentially increasing trends with no decreasing phase of septal crowding during the earliest ontogenetic stage. The absence of a decreasing trend at the earliest ontogenetic stage is a unique character in contrast with those in modern cuttlefish and ancient and modern nautiloids, in which the decreasing trends are related to hatching events. These ontogenetic septal spacing trends suggest that the belemnite hatchlings had only a protoconch with no chamber. These belemnite hatchlings with no chamber and therefore small embryonic shell diameter are similar to those of ammonoids. Significant difference in a statistical test that compared the protoconch size between the two localities, might suggest that there was limited transportation at the embryonic stage, although it could also just indicate differences in regional environmental conditions, age and/or degree of time averaging which might differ between the examined taxa.
Data from: Atypical panmixia in a European dolphin species (Delphinus delphis); implications for the evolution of diversity across oceanic boundaries.
Despite the scarcity of geographical barriers in the ocean environment, delphinid cetaceans often exhibit marked patterns of population structure on a regional scale. The European coastline is a prime example, with species exhibiting population structure across well defined environmental boundaries. Here we undertake a comprehensive population genetic study on the European common dolphin (Delphinus delphis, based on 492 samples and 15 loci) and establish that this species shows exceptional panmixia across most of the study range. We found differentiation only between the eastern and western Mediterranean, consistent with earlier studies, and here use Approximate Bayesian Computations to explore different scenarios to explain the observed pattern. Our results suggest that a recent population bottleneck likely contributed significantly to the differentiation of the Eastern Mediterranean population (in Greek waters). This interpretation is consistent with independent census data which suggests a sharp population decline in the recent past. The implication is that an unperturbed population may currently show panmixia across the full study range. This exception to the more typical pattern of population structure seen for other regional dolphin species (and for common dolphin populations elsewhere in the world) suggests particular ecological or life history traits distinct to this species in European waters.
Data from: Fine-scale appendage structure of the Cambrian trilobitomorph Naraoia spinosa and its ontogenetic and ecological implications
<p>Trilobitomorphs are a species-rich Palaeozoic arthropod assemblage that unites trilobites with several other lineages that share similar appendage structure. Post-embryonic development of the exoskeleton is well documented for some trilobitomorphs, especially trilobites, but little is known of the ontogeny of their soft parts, limiting understanding of their autecology. Here we document appendage structure of the Cambrian naraoiid trilobitomorph Naraoia spinosa by computed microtomography, resulting in three-dimensional reconstructions of appendages at both juvenile and adult stages. The adult has dense, strong spines on the protopods of post-antennal appendages, implying a predatory/scavenging behavior. Absence of such gnathobasic structures but instead tiny protopodal bristles and a number of endopodal setae suggests a detritus-feeding strategy for the juvenile. Our data add strong morphological evidence for ecological-niche shifting by Cambrian arthropods during their life cycles. A conserved number of appendages across the sampled developmental stages demonstrates that Naraoia ceased budding off new appendages by the mid-juvenile stage.</p> <p> </p> <p> </p>
Data from: A novel, bounding gait in swimming turtles: implications for aquatic locomotor diversity
Turtles are an iconic lineage in studies of animal locomotion, typifying the use of slow, alternating footfalls during walking. Alternating movements of contralateral limbs are also typical during swimming gaits for most freshwater turtles. Here, we report a novel gait in turtles, in which the pleurodire Emydura subglobosa swims using a bounding gait that coordinates bilateral protraction of both forelimbs with bilateral retraction of both hindlimbs. Use of this bounding gait is correlated with increased limb excursion and decreased stride frequency, but not increased velocity when compared to standard swimming strokes. Bounding by E. subglobosa provides a second example of a non-mammalian lineage that can use bounding gaits, and may give insight into the evolution of aquatic flapping. Parallels in limb muscle fascicle properties between bounding turtles and crocodylids suggest a possible musculoskeletal mechanism underlying the use of bounding gaits in particular lineages.
Data from: Allometric convergence in savanna trees and implications for plant scaling models in variable ecosystems
Theoretical models of allometric scaling provide frameworks for understanding and predicting how and why the morphology and function of organisms vary with scale. It remains unclear, however, if the predictions of 'universal' scaling models for vascular plants hold across diverse species in variable environments. Phenomena such as competition and disturbance may drive allometric scaling relationships away from theoretical predictions based on an optimized tree. Here, we use a hierarchical Bayesian approach to calculate tree-specific, species-specific, and 'global' (i.e. interspecific) scaling exponents for several allometric relationships using tree- and branch-level data harvested from three savanna sites across a rainfall gradient in Mali, West Africa. We use these exponents to provide a rigorous test of three plant scaling models (Metabolic Scaling Theory (MST), Geometric Similarity, and Stress Similarity) in savanna systems. For the allometric relationships we evaluated (diameter vs. length, aboveground mass, stem mass, and leaf mass) the empirically calculated exponents broadly overlapped among species from diverse environments, except for the scaling exponents for length, which increased with tree cover and density. When we compare empirical scaling exponents to the theoretical predictions from the three models we find MST predictions are most consistent with our observed allometries. In those situations where observations are inconsistent with MST we find that departure from theory corresponds with expected tradeoffs related to disturbance and competitive interactions. We hypothesize savanna trees have greater length-scaling exponents than predicted by MST due to an evolutionary tradeoff between fire escape and optimization of mechanical stability and internal resource transport. Future research on the drivers of systematic allometric variation could reconcile the differences between observed scaling relationships in variable ecosystems and those predicted by ideal models such as MST.
Data from: A nation-wide survey of neonicotinoid insecticides in agricultural land with implications for agri-environment schemes
1. Neonicotinoids are the most widely used class of insecticides globally. However, the link between farming practices and the extent of contamination of soils and crops by neonicotinoid insecticides, as well as and the extent of such contamination in organic fields and ecological focus areas (EFAs) are currently unclear. 2. We measured the concentrations of five neonicotinoid insecticides (imidacloprid, clothianidin, thiamethoxam, thiacloprid, acetamiprid) in 702 soil and plant samples in 169 cultivated fields and EFAs from 62 conventional, integrated production and organic farms distributed over the entire lowland of Switzerland. 3. We detected neonicotinoids in 93% of organic soils and crops, and more than 80% of EFA soils and plants – two types of arable land supposedly free of insecticides. We also tested 16 samples of organic seeds, of which 14 were positive for neonicotinoids. 4. Finally, we calculated hazard quotients (HQs) and potentially affected fractions for 72 beneficial and 12 pest species. Under a field-realistic scenario, we found that between 5.3 and 8.6% of above-ground invertebrate species may be exposed to lethal concentrations of clothianidin, and 31.6 to 41.2% to sublethal concentrations, in "integrated production" and conventional fields. We also found that 1.3 to 6.8% (up to 12.5% based on HQs) of the beneficial invertebrate species may be exposed to sublethal concentrations of neonicotinoids in EFAs and organic fields. In contrast, no pest species would be exposed to lethal concentrations, even under a worst-case scenario. 5. Synthesis and applications. Our study suggests that diffuse contamination by neonicotinoids may harm a significant fraction of non-target beneficial species. The use of neonicotinoids on crops may threaten biodiversity in refuge areas, while also potentially jeopardizing the practice of organic farming by impeding the biological control of pests. Based on our results, we call for a reduction in the dispersion and overuse of neonicotinoid insecticides in order to prevent any detrimental effects on biodiversity and ecosystem services associated with agroecosystems.
Data from: Variation in species light acquisition traits under fluctuating light regimes: implications for non‐equilibrium coexistence
Resource distribution heterogeneity offers niche opportunities for species with different functional traits to develop and potentially coexist. Available light (photosynthetically active radiation or PAR) for suspended algae (phytoplankton) may fluctuate greatly over time and space. Species-specific light acquisition traits capture important aspects of the ecophysiology of phytoplankton and characterize species growth at either limiting or saturating daily PAR supply. Efforts have been made to explain phytoplankton coexistence using species-specific light acquisition traits under constant light conditions, but not under fluctuating light regimes that should facilitate non-equilibrium coexistence. In the well-mixed, hypertrophic Lake TaiHu (China), we incubated the phytoplankton community in bottles placed either at fixed depths or moved vertically through the water column to mimic vertical mixing. Incubations at constant depths received only the diurnal changes in light, while the moving bottles received rapidly fluctuating light. Species-specific light acquisition traits of dominant cyanobacteria (Anabaena flos-aquae, Microcystis spp.) and diatom (Aulacoseira granulata, Cyclotella pseudostelligera) species were characterized from their growth-light relationships that could explain relative biomasses along the daily PAR gradient under both constant and fluctuating light. Our study demonstrates the importance of interspecific differences in affinities to limiting and saturating light for the coexistence of phytoplankton species in spatially heterogeneous light conditions. Furthermore, we observed strong intraspecific differences in light acquisition traits between incubation under constant and fluctuating light – leading to the reversal of light utilization strategies of species. This increased the niche space for acclimated species, precluding competitive exclusion. These observations could enhance our understanding of the mechanisms behind the Paradox of the Plankton.
Data from: Pedigree analysis reveals a generational decline in reproductive success of captive Tasmanian devil (Sarcophilus harrisii): implications for captive management of threatened species
Captive breeding programs are an increasingly popular tool to augment the conservation of threatened wild populations. Many programs keep detailed pedigrees, which are used to prescribe breeding targets to meet demographic and genetic goals. Annual breeding targets are based on previous productivity, but do not account for changes in reproductive success that may occur over generations in captivity and which may impair the ability of a program to meet its goals. We utilise a large studbook from the Tasmanian devil (Sarcophilus harrisii) captive breeding program to investigate biological, genetic and environmental factors that affect variation in reproductive success among individuals and over generations of captive breeding. Reproductive success declined with increasing generations in captivity: wild-born females had a 56.5% chance of producing a litter compared to a 2.8% chance for generation 5 captive-born females (N = 182) and when they did, wild-born females produced more offspring (3.1 joeys, 95% CI: 2.76 - 3.38, compared to 2.7 joeys, 95% CI: 2.55 - 2.90, in captive-born females [N = 105]). Reproductive success also declined as dam age at first breeding increased. Our results reveal a conflict with the widely-cited conservation strategy to limit opportunity for selection by extending generation length through delaying reproduction, as captive breeding programs that delay female breeding with this goal in mind risk reduced productivity. Our data demonstrate the benefit of pedigree analysis to identify biological processes that reveal crucial trade-offs with conservation best-practice.
Testing size-frequency distributions as a method of ontogenetic aging: a life history assessment of hadrosaurid dinosaurs from the Dinosaur Park Formation of Alberta, Canada, with implications for hadrosaurid paleoecology
<p class="MsoNoSpacing">Hadrosaurid dinosaurs, the dominant large-bodied terrestrial herbivores in most Laurasian Late Cretaceous ecosystems, have an exceptional fossil record consisting of many species known from partial ontogenetic series making them an ideal clade with which to conduct life history studies. Previous research considered the Dinosaur Park Formation (DPF) of Alberta as an attritional, or time-averaged, sample and interpreted size-frequency distribution of long bones collected from the DPF with three size classes to suggest that hadrosaurids from the DPF attained near-asymptotic body size in under three years. This conflicted with previously published osteohistological estimates of 6+ years for penecontemporaneous hadrosaurids from the Two Medicine Formation (TMF) of Montana suggesting either extreme variation in hadrosaurid growth rates or that size-frequency distributions and/or osteohistology and growth modeling inaccurately estimate ontogenetic age.</p> <p>We tested the validity of the previously proposed size-age relationship of hadrosaurids from the DPF by significantly increasing sample size and combining data from size-frequency distributions and osteohistology across multiple long bones elements. The newly constructed size-frequency distributions typically reveal four relatively distinct size-frequency peaks that, when integrated with the osteohistological data, aligned with growth marks. The yearling size class was heavily underrepresented in the size-frequency distribution. If not due to preservation, this suggests that either juvenile (< 2 years of age) hadrosaurids from the DPF had increased survivorship following an initially high nestling mortality rate, or that yearlings were segregated from adults. A growth curve analysis revealed asymptotic body size was attained in approximately 7 years, which is consistent with hadrosaurids from the TMF. The data suggest size-frequency distributions of attritional samples underestimate age and overestimate growth rates, but when paired with osteohistology can provide unique life history insights.</p>
Data from: Preservation-induced morphological change in salamanders and failed DNA extraction from a decades-old museum specimen: implications for Plethodon ainsworthi
<p>Natural history collections are important data repositories, but different chemical treatments of specimens can influence morphological measurements and DNA extraction, complicating taxonomic and conservation decisions dependent upon these data. One such example is the Bay Springs Salamander (<i>Plethodon ainsworthi</i>), the only United States amphibian categorized as Extinct by the IUCN.<i> </i>Recent research has proposed that <i>P. ainsworthi </i>is an invalid taxon, arguing that the 55-year-old type specimens' morphological distinctiveness from syntopic <i>P. mississippi</i> is a preservation artifact. To address this controversy, we tested for morphological changes across five experimental treatments in proxy <i>P. shermani</i> specimens, and we re-examined the datasets used to support the invalidity of <i>P. ainsworthi</i>. We also tested recently developed DNA extraction techniques on the putatively formalin-fixed <i>P. ainsworthi</i> holotype. We used Bayesian models to demonstrate that preservation method can differentially bias morphological measurements, with most methods causing lower estimates of mass and modestly higher estimates of snout-vent-length:head width ratio. These results are broadly consistent with previous studies of other vertebrates, but inconsistent with the hypothesis that <i>P. ainsworthi </i>type specimens are actually poorly preserved <i>P. mississippi</i>. Attempts to extract DNA from the <i>P. ainsworthi</i> holotype unfortunately proved unsuccessful, preventing conclusive resolution of its status and emphasizing the limitations of promising new methods. Nonetheless, we tentatively recommend continued recognition of <i>P. ainsworthi</i> as a valid but possibly extinct taxon. More generally, we invite all authors who study preserved specimens to recognize and report how certain chemical treatments might impact their results.</p>
Data from: Integrative taxonomy improves understanding of native beneficial fauna: revision of the Nearctic Peristenus pallipes complex (Hymenoptera: Braconidae) and implications for release of exotic biocontrol agents
The Nearctic Peristenus pallipes complex (Hymenoptera: Braconidae) consists of two species groups that are further divided into nine species, separated largely using ecological rather than morphological differences. The species are re-examined with an integrative approach using morphometric multivariate ratios, molecular (COI and CytB), and ecological data to test the validity of the nine species. The data support only three valid species [P. dayi Goulet, P. mellipes (Cresson) and P. howardi Shaw] rather than nine. New synonymies include: P. braunae Goulet under P. dayi Goulet 2006 syn.n.; P. carcamoi Goulet, P. otaniae Goulet and P. pseudopallipes (Loan) under P. mellipes (Cresson) syn.n., and finally P. broadbenti Goulet 2006 and P. gillespiei Goulet 2006 under P. howardi Shaw 1999 syn.n. In light of these taxonomic revisions, the biology and distributions of the Nearctic P. pallipes complex are updated, resulting in three morphologically variable, widespread, multivoltine species rather than nine largely univoltine species with patchy distributions. The integrative taxonomic approach used here allowed for a more accurate delineation of native fauna and their potential to be competitively displaced by foreign biocontrol agents.
Data from: Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition
We explore the tree of mammalian mtDNA sequences, using particularly the LogDet transform on amino acid sequences, the distance Hadamard transform, and the Closest Tree selection criterion. The amino acid composition of different species show significant differences, even within mammals. After compensating for these differences, nearest-neighbor bootstrap results suggest that the tree is locally stable, though a few groups show slightly greater rearrangements when a large proportion of the constant sites are removed. Many parts of the trees we obtain agree with those on published protein ML trees. Interesting results include a preference for rodent monophyly. The detection of a few alternative signals to those on the optimal tree were obtained using the distance Hadamard transform (with results expressed as a Lento plot). One rearrangement suggested was the interchange of the position of primates and rodents on the optimal tree. The basic stability of the tree, combined with two calibration points (whale/cow and horse/rhinoceros), together with a distant secondary calibration from the mammal/bird divergence, allows inferences of the times of divergence of putative clades. Allowing for sampling variances due to finite sequence length, most major divergences amongst lineages leading to modern orders, appear to occur well before the Cretaceous/Tertiary (K/T) boundary. Implications arising from these early divergences are discussed, particularly the possibility of competition between the small dinosaurs and the new mammal clades.
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.