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Data from: Increasing the fish diversity of the Triassic faunas of Gondwana: a new redfieldiiform (Actinopterygii) from the Middle Triassic of Argentina and its palaeobiogeographical implications
A new actinopterygian, Calaichthys tehul gen. et sp. nov. is described on the basis of a few, well-preserved specimens from the Anisian Cerro de Las Cabras Formation, Cuyo Basin in Mendoza Province. The new genus shows a combination of primitive characters (e.g. deep posterior region of the maxilla contacting the preopercle, a suspensorium backwardly oriented) and more advanced characters (e.g. distally segmented fin rays, hemiheterocercal caudal fin) and is thus considered to be a 'subholostean' fish. The new taxon is assigned to Redfieldiiformes on the basis of its single branchiostegal plate-like ray, a median gular plate, pectoral fins with stout, stiff, mainly non-segmented and distally branched fin rays, long and robust fringing fulcra in all fins, basal fulcra bordering both lobes of the caudal fin, and opposite dorsal and anal fins. Calaichthys is characterized by a combination of characters some of which are unique among redfieldiiforms (i.e. strongly ornamented but thin scales with a serrated posterior margin, smooth skull roof bones, extrascapulars with a bifid posterior margin, three suborbital bones, a hatchet-shaped preopercle, rectangular and slender opercle, deep mouth gape, entopterygoid and ectopterygoid with small pointed teeth disposed in several series, unornamented rostral bone, massive pectoral fins and delicate dorsal, pelvic and anal fins). Calaichthys provides novel information about the anatomy of redfieldiiforms, in particular in relation with the fins and associated scaly elements, as well as the scale morphology and their disposition over the body. Our work confirms for the first time that redfieldiiforms occur in South America. Redfieldiiforms seem to have originated in Gondwana and shown two diversity peaks: in the Anisian and the Carnian. Calaichthys is coeval with those redfieldiiforms of the Middle Triassic (Anisian) of Africa and Australia dwelling in ephemeral lakes.
Data from: Revision of the New World species of the millipede-parasitic genus Myriophora Brown (Diptera: Phoridae)
The New World species of the millipede-parasitic genus Myriophora Brown are revised. Sixty-five species based on the female sex are treated, mostly from the Neotropical Region. Of these, fifty-seven are new to science: Myriophora alexandrae sp. nov., Myriophora alienipennis sp. nov., Myriophora angustifascia sp. nov., Myriophora annetteae sp. nov., Myriophora annulata sp. nov., Myriophora bicuspidis sp. nov., Myriophora bilsae sp. nov., Myriophora bimaculata sp. nov., Myriophora borealis sp. nov., Myriophora brevitarsus sp. nov., Myriophora browni sp. nov. Hash, Myriophora brunneipleuron sp. nov., Myriophora communis sp. nov., Myriophora curvata sp. nov., Myriophora curvicacumen sp. nov., Myriophora dennisoni sp. nov., Myriophora discalis sp. nov., Myriophora diversa sp. nov., Myriophora dividida sp. nov., Myriophora dolionatis sp. nov., Myriophora flavicosta sp. nov., Myriophora fuscidorsum sp. nov., Myriophora gigantea sp. nov., Myriophora gobaleti sp. nov., Myriophora harwoodi sp. nov., Myriophora hebes sp. nov., Myriophora heratyi sp. nov., Myriophora inaequalisetarum sp. nov., Myriophora infirmata sp. nov., Myriophora jeffersoni sp. nov., Myriophora kerri sp. nov., Myriophora kungae sp. nov., Myriophora longisetarum sp. nov., Myriophora luteitergum sp. nov., Myriophora magnilabellum sp. nov., Myriophora misionesensis sp. nov., Myriophora nigra sp. nov., Myriophora nigralinea sp. nov., Myriophora obscuritergum sp. nov., Myriophora pallida sp. nov., Myriophora parva sp. nov., Myriophora pectinata sp. nov., Myriophora perpendicularis sp. nov., Myriophora plana sp. nov., Myriophora porrasae sp. nov., Myriophora porrecta sp. nov., Myriophora reminatis sp. nov., Myriophora scopulata sp. nov., Myriophora simplex sp. nov., Myriophora sinesplendida sp. nov., Myriophora smithi sp. nov., Myriophora spicaphora sp. nov., Myriophora spicaticonus sp. nov., Myriophora tenuis sp. nov., Myriophora uruguaiensis sp. nov., Myriophora vancouverensis sp. nov., Myriophora wellsorum sp. nov. The first key to the species of Myriophora is provided.
Data from: New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems
Metabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized for taxonomic resolution, minimal bias in amplification of the target organism group and short sequence length. Using bioinformatic tools, we developed metabarcodes for several groups of organisms: fungi, bryophytes, enchytraeids, beetles and birds. The ability of these metabarcodes to amplify the target groups was systematically evaluated by (1) in silico PCRs using all standard sequences in the EMBL public database as templates, (2) in vitro PCRs of DNA extracts from surface soil samples from a site in Varanger, northern Norway, and (3) in vitro PCRs of DNA extracts from permanently frozen sediment samples of late-Pleistocene age (~ 16 000–50 000 yr BP) from two Siberian sites, Duvanny Yar and Main River. Comparison of the results from the in silico PCR with those obtained in vitro showed that the in silico approach offered a reliable estimate of the suitability of a marker. All target groups were detected in the environmental DNA, but we found large variation in the level of detection among the groups and between modern and ancient samples. Success rates for the Pleistocene samples were highest for fungal DNA, whereas bryophyte, beetle and bird sequences could also be retrieved, but to a much lesser degree. The metabarcoding approach has considerable potential for biodiversity screening of modern samples and also as a paleoecological tool.
Data from: A new taxon of cistecephalid dicynodont from the upper Permian Kundaram Formation of India
A new cistecephalid dicynodont, Sauroscaptor tharavati gen. et sp. nov., is described from the upper Permian Kundaram Formation of India. This taxon is represented by specimens formerly referred to the African dicynodont genera Cistecephalus and Emydops. Sauroscaptor can be distinguished from other cistecephalids by the extremely posterior position of the pineal foramen (overhanging the edge of the occiput), bipartite nuchal crest, and relatively narrow skull roof. The recognition of Sauroscaptor as a distinct cistecephalid taxon adds to the increasing evidence for high levels of basinal endemism in this family. However, dicynodont biogeographical patterns are complex, and there is no simple relationship between inferred dispersal ability based on body size and levels of endemicity within clades.
Data from: A new theory of plant-microbe nutrient competition resolves inconsistencies between observations and model predictions
Terrestrial plants assimilate anthropogenic CO2 through photosynthesis and synthesizing new tissues. However, sustaining these processes requires plants to compete with microbes for soil nutrients, which therefore calls for an appropriate understanding and modeling of nutrient competition mechanisms in Earth System Models (ESMs). Here, we survey existing plant-microbe competition theories and their implementations in Earth System Models (ESMs). We found no consensus regarding the representation of nutrient competition and that observational and theoretical support for current implementations are weak. To reconcile this situation, we applied the Equilibrium Chemistry Approximation (ECA) theory to plant-microbe nitrogen competition in a detailed grassland 15N tracer study and found that competition theories in current ESMs fail to capture observed patterns and the ECA prediction simplifies the complex nature of nutrient competition and quantitatively matches the 15N observations. Since plant carbon dynamics are strongly modulated by soil nutrient acquisition, we conclude that (1) predicted nutrient limitation effects on terrestrial carbon accumulation by existing ESMs may be biased and (2) our ECA-based approach may improve predictions by mechanistically representing plant-microbe nutrient competition.
Data from: The influence of selection on MHC DQA and DQB haplotypes in the endemic New Zealand Hector's and Māui dolphins
Strong balancing selection on the Major Histocompatibility Complex (MHC) can lead to different patterns in gene frequencies and neutral genomic variation within species. We investigated diversity and geographic structure of MHC genes DQA and DQB, as well as their inferred functional haplotypes, from two regional populations (East and West Coast) of the endangered Hector's dolphin (Cephalorhynchus hectori hectori) and the critically endangered Māui dolphin (Cephalorhynchus hectori maui) (West Coast, North Island), and contrasted these results with patterns from neutral microsatellites. The Māui had the lowest number of alleles for DQA (2) and DQB (3), consistent with strong genetic drift acting on this remnant population. However, the two retained DQA alleles are amongst the most divergent combinations of all four alleles found across the Hector's metapopulation, potentially reflecting the retention of divergent alleles due to balancing selection. The high frequency of the divergent DQB04 allele also gave this population the highest nucleotide diversity for DQB. Strong differentiation was evident for DQA, DQB, and DQA-DQB haplotypes between the regional populations of Hector's dolphins (FST>0.213) and both subspecies (FST>0.311). Differentiation was generally greater than observed at neutral microsatellite loci, suggesting the influence of selection between geographically proximate East and West Coast populations. This might be the result of spatial differences in directional selection on those opposite coastlines. Additionally, measures of the ratio of non-synonymous to synonymous substitutions (dN/dS) were consistent with balancing selection over evolutionary time. Together, these results suggest a complex interplay of balancing selection, directional selection, local fidelity, and genetic drift.
Data from: A new species of Chiasmocleis (Microhylidae, Gastrophryninae) from the Atlantic Forest of Espírito Santo State, Brazil
Among Neotropical microhylids, the genus Chiasmocleis is exceptionally diverse. Most species of Chiasmocleis were described in recent years based on external morphology, but recent studies using molecular data did not support the monophyly of the species groups clustered based on feet webbing. Furthermore, a phylogeographic study of C. lacrimae estimated high genetic divergence and low gene flow among populations across small geographic ranges. Increasing the molecular and geographic sampling, and incorporating morphological data, we identified new cryptic species. Herein, we used novel genetic and morphological data to describe a new species of Chiasmocleis.
Data from: Multiple stressors and the potential for synergistic loss of New England salt marshes
Climate change and other anthropogenic stressors are converging on coastal ecosystems worldwide. Understanding how these stressors interact to affect ecosystem structure and function has immediate implications for coastal planning, however few studies quantify stressor interactions. We examined past and potential future interactions between two leading stressors on New England salt marshes: sea-level rise and marsh crab (Sesarma reticulatum) grazing driven low marsh die-off. Geospatial analyses reveal that crab-driven die-off has led to an order of magnitude more marsh loss than sea-level rise between 2005 and 2013. However, field transplant experimental results suggest that sea-level rise will facilitate crab expansion into higher elevation marsh platforms by inundating and gradually softening now-tough high marsh peat, exposing large areas to crab-driven die-off. Taking interactive effects of marsh softening and concomitant overgrazing into account, we estimate that even modest levels of sea-level rise will lead to levels of salt marsh habitat loss that are 3x greater than the additive effects of sea-level rise and crab-driven die-off would predict. These findings highlight the importance of multiple stressor studies in enhancing mechanistic understanding of ecosystem vulnerabilities to future stress scenarios and encourage managers to focus on ameliorating local stressors to break detrimental synergisms, reduce future ecosystem loss, and enhance ecosystem resilience to global change.
Data from: Population genetic analyses using 10 new polymorphic microsatellite loci confirms genetic subdivision within the olm, Proteus anguinus
We provide a comparative population genetic study of the elusive amphibian, Proteus anguinus, by comparing the genetic diversity and divergence among four cave populations (96 individuals) sampled in the Dinaric Karst of Croatia. We developed 10 variable microsatellite markers using pyrosequencing and applied them to the four selected populations belonging to four different cave systems. The results showed strong genetic differentiation between the four caves corroborating with previous findings suggesting that Proteus might comprises several unrecognized taxa. Our results confirmed that gene flow should be high within the caves, whereas it is low between hydrographic systems since geological periods. Finally, we conclude that the high genetic subdivision suggests the necessity of treating the four studied Proteus populations as evolutionary significant units.
Data from: A new oviraptorid (Dinosauria: Theropoda) from the Upper Cretaceous of southern China
This paper describes a new oviraptorid dinosaur taxon, Ganzhousaurus nankangensis gen. et sp. nov., based on a specimen collected from the Upper Cretaceous Nanxiong Formation of Nankang County, Ganzhou City, Jiangxi Province, southern China. This new taxon is distinguishable from other oviraptorids based on the following unique combination of primitive and derived features: relatively shallow dentary; absence of fossa or pneumatopore on lateral surface of dentary; weakly downturned anterior mandibular end; shallow depression immediately surrounding anterior margin of external mandibular fenestra; external mandibular fenestra subdivided by anterior process of surangular; dentary posteroventral process slight-ly twisted and positioned on mandibular ventrolateral surface; shallow longitudinal groove along medial surface of den-tary posteroventral process; angular anterior process wider transversely than deep dorsoventrally; sharp groove along ventrolateral surface of angular anterior process; ventral border of external mandibular fenestra formed mainly by angular; ventral flange along distal half of metatarsal II; and arctometatarsal condition absent. Phylogenetic analysis places Ganzhousaurus nankangensis gen. et sp. nov. in the clade Oviraptoridae, together with Oviraptor, Citipati, Rinchenia and the unnamed Zamyn Khondt oviraptorid.
Data from: New insights into New World biogeography: an integrated view from the phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies
Understanding the biogeographic origins and temporal sequencing of groups within a region or of lineages within an ecosystem can yield important insights into evolutionary dynamics and ecological processes. Fifty years ago, Ernst Mayr generated comprehensive—if limited—inferences about the origins of the New World avifaunas, including the importance of pre-Isthmian dispersal between North and South America. Since then, methodological advances have improved our ability to address many of the same questions, but the phylogenies upon which such analyses should be based have been incompletely sampled or fragmentary. Here, we report a near-species-level phylogeny of the diverse (~832 species) New World clade Emberizoidea—the group that includes the familiar sparrows, cardinals, blackbirds, wood-warblers, tanagers, and their close relatives—to our knowledge the largest essentially complete (≥95%) phylogenetic hypothesis for any group of organisms. Biogeographic analyses based on this tree suggest initial dispersal into the New World via Beringia, with rapid subsequent diversification, including early dispersal of 1 lineage (the tanagers, Thraupidae) into South America. We found substantial dispersal between North and South America prior to closure of the Isthmus of Panama, but with a notable increase afterward, with a directional bias from north to south. With much greater detail and historical rigor, these analyses largely confirm Mayr's speculations based on taxonomy, resolving outstanding ambiguity regarding the continental origins of some groups such as the Emberizidae and Icteridae. The phylogeny reported here will be a resource of broad utility for addressing additional evolutionary and ecological questions with this diverse group.
Data from: New SNPs for population genetic analysis reveal possible cryptic speciation of eastern Australian sea mullet (Mugil cephalus)
Sustainable management of sea mullet (Mugil cephalus) fisheries needs to account for recent observations of regional-scale differentiation. Population genetic analysis is sought to assess the situation of this ecologically and economically important fish species in eastern Australian waters. Here, we report (i) new population genetic markers [single nucleotide polymorphisms (SNPs) and potential microsatellites], (ii) first estimates of spatial genetic differentiation and (iii) prospective power tests for designing more comprehensive studies. Six DNA samples from three sampling regions (North Queensland, South Queensland and central New South Wales) on the eastern coast of Australia were used to prepare restriction site associated DNA (RAD) tag libraries from genomic DNA digested with EcoRI and MseI. A pooled sample of regional RAD tag libraries was sequenced using the Roche GS-FLX Titanium platform. A total of 172 837 raw reads (17.4 Mbp) were retrieved, 95 500 of which were used to discover 1267 SNPs and 1417 microsatellites. A subset of 161 SNPs was validated based on 63 additional DNA samples genotyped using the Sequenom MassArray (iPLEX Gold chemistry). Altogether 92 SNPs (57%) were confirmed, with 40% of these marking fixed variants between northern and southern sampling regions. Our preliminary findings indicate a multispecies fishery stock of M. cephalus in eastern Australian waters, but suggest that strong genetic differentiation occurs north of major fishing grounds. Low potential differentiation within major fishing grounds (e.g. FST = 0.0025) can be resolved with a likely power ≥67% by using standard sample sizes of 50 and validated subsets of available markers.
Data from: Description of a new species of Petrolisthes in the Indo-West Pacific with a redefinition of P. hastatus Stimpson, 1858 and resurrection of P. inermis (Heller, 1862) (Crustacea, Anomura, Porcellanidae)
The porcellanid crab Petrolisthes hastatus Stimpson, 1858, has been traditionally viewed as a highly variable species with a wide distribution in the West Pacific. For more than a century there has been taxonomic confusion of this species with morphologically similar taxa, some of which were synonymized with Stimpson's taxon. We redefine P. hastatus, resurrect P. inermis as a valid species, discuss the status of P. tenkatei De Man, 1893, and describe a new species as P. elegantissimus from Indonesia.
Data from: De novo transcriptome analysis of the common New Zealand stick insect Clitarchus hookeri (Phasmatodea) reveals genes involved in olfaction, digestion and sexual reproduction
Phasmatodea, more commonly known as stick insects, have been poorly studied at the molecular level for several key traits, such as components of the sensory system and regulators of reproduction and development, impeding a deeper understanding of their functional biology. Here, we employ de novo transcriptome analysis to identify genes with primary functions related to female odour reception, digestion, and male sexual traits in the New Zealand common stick insect Clitarchus hookeri (White). The female olfactory gene repertoire revealed ten odorant binding proteins with three recently duplicated, 12 chemosensory proteins, 16 odorant receptors, and 17 ionotropic receptors. The majority of these olfactory genes were over-expressed in female antennae and have the inferred function of odorant reception. Others that were predominantly expressed in male terminalia (n = 3) and female midgut (n = 1) suggest they have a role in sexual reproduction and digestion, respectively. Over-represented transcripts in the midgut were enriched with digestive enzyme gene families. Clitarchus hookeri is likely to harbour nine members of an endogenous cellulase family (glycoside hydrolase family 9), two of which appear to be specific to the C. hookeri lineage. All of these cellulase sequences fall into four main phasmid clades and show gene duplication events occurred early in the diversification of Phasmatodea. In addition, C. hookeri genome is likely to express γ-proteobacteria pectinase transcripts that have recently been shown to be the result of horizontal transfer. We also predicted 711 male terminalia-enriched transcripts that are candidate accessory gland proteins, 28 of which were annotated to have molecular functions of peptidase activity and peptidase inhibitor activity, two groups being widely reported to regulate female reproduction through proteolytic cascades. Our study has yielded new insights into the genetic basis of odour detection, nutrient digestion, and male sexual traits in stick insects. The C. hookeri reference transcriptome, together with identified gene families, provides a comprehensive resource for studying the evolution of sensory perception, digestive systems, and reproductive success in phasmids.
Data from: MonotomidGen – A matrix-based interactive key to the New World genera of Monotomidae (Coleoptera, Cucujoidea)
A matrix-based Lucid key is presented for the twelve genera of Monotomidae (Coleoptera: Cucujoidea) represented in the New World. A general overview is given for the features and technical specifications of an original interactive key for the identification of these genera. The list of terminal taxa included with the key provides a current summary of monotomid generic diversity for the Nearctic and Neotropical regions.
Data from: A new species of logperch endemic to Tennessee (Percidae: Etheostomatinae: Percina)
Percina apina, the Tennessee Logperch, is described as a new species endemic to Tennessee and distributed in the Duck River system and Whiteoak Creek. The earliest collection records for Percina apina date to 1971 and the species was identified as Percina burtoni, the Blotchside Logperch. A phylogenetic analysis of mitochondrial DNA (mtDNA) published in 2006 showed that populations identified as Percina burtoni in the Duck River system and Whiteoak Creek were a new and undescribed species. In this study, we test the hypothesis that Percina burtoni is composed of multiple species through analyses of mtDNA, nuclear genetic variation, and traditional meristic trait morphology. Our analyses of morphological divergence, nuclear genotypes, mtDNA gene trees, and comparisons with other sister species pairs of logperches confirm the distinctiveness of Percina apina. Morphologically, Percina apina is distinguished from Percina burtoni through higher average numbers of lateral line scales (93.1 versus 89.9); pored lateral line scales (91.6 versus 88.8); rows of transverse scales (38.1 versus 33.6); and scales around the caudal peduncle (36.2 versus 33.5). The two species also differ in patterns of pigmentation; the lateral blotches in Percina apina are typically wider than high, whereas the blotches tend to be higher than wide in Percina burtoni. We recommend that future species descriptions of North American freshwater fishes leverage available genetic resources and include molecular phylogenetic assessments in analyses of taxon distinctiveness. In addition, we advocate the deposition of morphological data used in species descriptions to online data repositories to ensure that other researchers are able to evaluate and modify hypotheses of species delimitations.
Data from: Peperomia (Piperaceae) from Trindade Island: a new species based on morphological and molecular data
Peperomia is one of the largest genera of basal angiosperms, with about 1,600 species, distributed pantropically. The Brazilian oceanic island of Trindade is located about 1,200km off the Brazilian coast; its maximum altitude is 620ma.s.l. and its area is 9.28km2. Among the 113 species of vascular plants reported for Trindade Island there are two species of Peperomia: Peperomia beckeri, an endemic species known only from the type specimen; and Peperomia glabella.We re-evaluated specimens attributed to P. glabella from Trindade Island and compared them to specimens from the continent. The comparison included morphological analyses of the vegetative and reproductive organs, and a molecular phylogenetic study using the molecular markers trnK/matK and ITS. The trnK/matK marker showed significant differences between Peperomia from the mainland and Trindade. Together, these studies showed that the Peperomia occurring on Trindade is a species that differs both from those previously recorded on Trindade Island and from those on the continent, leading us to describe a new species. Peperomia segregata is endemic to Trindade, and would likely be considered critically endangered according to the IUCN criteria.
Data from: New bothremydid turtle (Testudines, Pleurodira) from the Paleocene of north-eastern Colombia
A new turtle, Puentemys mushaisaensis, from the middle to late Paleocene Cerrejón Formation of Colombia, is described on the basis of a partial skull and many partial to nearly complete carapaces and plastrons representing multiple ontogenetic stages. Whereas P. mushaisaensis is unique in aspects of its shell morphology, it shares many diagnostic characteristics of bothremydid pleurodirans, including a long exoccipital-quadrate contact, a very low and rounded almost circular carapace, and a thinner internal bone cortex than that of the external cortex in both the carapace and plastron. With a maximum carapacial length of 151 cm, P. mushaisaensis is the largest known bothremydid turtle and represents the first occurrence of bothremydids in the Paleogene of South American tropics. Results from a cladistic analysis of bothremydids indicate that P. mushaisaensis shares a close relationship with Foxemys mechinorum from the Late Cretaceous of Europe, indicating a wide-spread geographical distribution for bothremydines during the Late Cretaceous–Paleocene.
Data from: A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents
Introduction: The PCR-based analysis of homologous genes has become one of the most powerful approaches for species detection and identification, particularly with the recent availability of Next Generation Sequencing platforms (NGS) making it possible to identify species composition from a broad range of environmental samples. Identifying species from these samples relies on the ability to match sequences with reference barcodes for taxonomic identification. Unfortunately, most studies of environmental samples have targeted ribosomal markers, despite the fact that the mitochondrial Cytochrome c Oxidase subunit I gene (COI) is by far the most widely available sequence region in public reference libraries. This is largely because the available versatile ("universal") COI primers target the 658 barcoding region, whose size is considered too large for many NGS applications. Moreover, traditional barcoding primers are known to be poorly conserved across some taxonomic groups. Results: We first design a new PCR primer within the highly variable mitochondrial COI region, the "mlCOIintF" primer. We then show that this newly designed forward primer combined with the "jgHCO2198" reverse primer to target a 313 bp fragment performs well across metazoan diversity, with higher success rates than versatile primer sets traditionally used for DNA barcoding (i.e. LCO1490/HCO2198). Finally, we demonstrate how the shorter COI fragment coupled with an efficient bioinformatics pipeline can be used to characterize species diversity from environmental samples by pyrosequencing. We examine the gut contents of three species of planktivorous and benthivorous coral reef fish (family: Apogonidae and Holocentridae). After the removal of dubious COI sequences, we obtained a total of 334 prey Operational Taxonomic Units (OTUs) belonging to 14 phyla from 16 fish guts. Of these, 52.5% matched a reference barcode (>98% sequence similarity) and an additional 32% could be assigned to a higher taxonomic level using Bayesian assignment. Conclusions: The molecular analysis of gut contents targeting the 313 COI fragment using the newly designed mlCOIintF primer in combination with the jgHCO2198 primer offers enormous promise for metazoan metabarcoding studies. We believe that this primer set will be a valuable asset for a range of applications from large-scale biodiversity assessments to food web studies.
Data from: A worldwide perspective on the population structure and genetic diversity of bottlenose dolphins (Tursiops truncatus) in New Zealand
Bottlenose dolphins (Tursiops truncatus) occupy a wide range of coastal and pelagic habitats throughout tropical and temperate waters worldwide. In some regions, "inshore" and "offshore" forms or ecotypes differ genetically and morphologically, despite no obvious boundaries to interchange. Around New Zealand, bottlenose dolphins inhabit 3 coastal regions: Northland, Marlborough Sounds, and Fiordland. Previous demographic studies showed no interchange of individuals among these populations. Here, we describe the genetic structure and diversity of these populations using skin samples collected with a remote biopsy dart. Analysis of the molecular variance from mitochondrial DNA (mtDNA) control region sequences (n = 193) showed considerable differentiation among populations (Fst = 0.17, Φst = 0.21, P < 0.001) suggesting little or no female gene flow or interchange. All 3 populations showed higher mtDNA diversity than expected given their small population sizes and isolation. To explain the source of this variation, 22 control region haplotypes from New Zealand were compared with 108 haplotypes worldwide representing 586 individuals from 19 populations and including both inshore and offshore ecotypes as described in the Western North Atlantic. All haplotypes found in the Pacific, regardless of population habitat use (i.e., coastal or pelagic), are more divergent from populations described as inshore ecotype in the Western North Atlantic than from populations described as offshore ecotype. Analysis of gene flow indicated long-distance dispersal among coastal and pelagic populations worldwide (except for those haplotypes described as inshore ecotype in the Western North Atlantic), suggesting that these populations are interconnected on an evolutionary timescale. This finding suggests that habitat specialization has occurred independently in different ocean basins, perhaps with Tursiops aduncus filling the ecological niche of the inshore ecotype in some coastal regions of the Indian and Western Pacific Oceans.
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.