Find research datasets worth reusing

Data from: The challenge of accurately documenting bee species richness in agroecosystems: bee diversity in eastern apple orchards

Bees are important pollinators of agricultural crops, and bee diversity has been shown to be closely associated with pollination, a valuable ecosystem service. Higher functional diversity and species richness of bees have been shown to lead to higher crop yield. Bees simultaneously represent a mega-diverse taxon that is extremely challenging to sample thoroughly and an important group to understand because of pollination services. We sampled bees visiting apple blossoms in 28 orchards over 6 years. We used species rarefaction analyses to test for the completeness of sampling and the relationship between species richness and sampling effort, orchard size, and percent agriculture in the surrounding landscape. We performed more than 190 h of sampling, collecting 11,219 specimens representing 104 species. Despite the sampling intensity, we captured <75% of expected species richness at more than half of the sites. For most of these, the variation in bee community composition between years was greater than among sites. Species richness was influenced by percent agriculture, orchard size, and sampling effort, but we found no factors explaining the difference between observed and expected species richness. Competition between honeybees and wild bees did not appear to be a factor, as we found no correlation between honeybee and wild bee abundance. Our study shows that the pollinator fauna of agroecosystems can be diverse and challenging to thoroughly sample. We demonstrate that there is high temporal variation in community composition and that sites vary widely in the sampling effort required to fully describe their diversity. In order to maximize pollination services provided by wild bee species, we must first accurately estimate species richness. For researchers interested in providing this estimate, we recommend multiyear studies and rarefaction analyses to quantify the gap between observed and expected species richness.

Data from: Taxonomic challenges in freshwater fishes: a mismatch between morphology and DNA barcoding in fish of the north-eastern part of the Congo basin

This study evaluates the utility of DNA barcoding to traditional morphology-based species identifications for the fish fauna of the north-eastern Congo basin. We compared DNA sequences (COI) of 821 samples from 206 morphologically identified species. Best match, best close match and all species barcoding analyses resulted in a rather low identification success of 87.5%, 84.5% and 64.1%, respectively. The ratio 'nearest-neighbour distance/maximum intraspecific divergence' was lower than 1 for 26.1% of the samples, indicating possible taxonomic problems. In ten genera, belonging to six families, the number of species inferred from mtDNA data exceeded the number of species identified using morphological features; and in four cases indications of possible synonymy were detected. Finally, the DNA barcodes confirmed previously known identification problems within certain genera of the Clariidae, Cyprinidae and Mormyridae. Our results underscore the large number of taxonomic problems lingering in the taxonomy of the fish fauna of the Congo basin and illustrate why DNA barcodes will contribute to future efforts to compile a reliable taxonomic inventory of the Congo basin fish fauna. Therefore, the obtained barcodes were deposited in the reference barcode library of the Barcode of Life Initiative.

Data from: Transgenerational plasticity following a dual pathogen and stress challenge in fruit flies

Background: Phenotypic plasticity operates across generations, when the parental environment affects phenotypic expression in the offspring. Recent studies in invertebrates have reported transgenerational plasticity in phenotypic responses of offspring when the mothers had been previously exposed to either live or heat-killed pathogens. Understanding whether this plasticity is adaptive requires a factorial design in which both mothers and their offspring are subjected to either the pathogen challenge or a control, in experimentally matched and mismatched combinations. Most prior studies exploring the capacity for pathogen-mediated transgenerational plasticity have, however, failed to adopt such a design. Furthermore, it is currently poorly understood whether the magnitude or direction of pathogen-mediated transgenerational responses will be sensitive to environmental heterogeneity. Here, we explored the transgenerational consequences of a dual pathogen and stress challenge administered in the maternal generation in the fruit fly, Drosophila melanogaster. Prospective mothers were assigned to a non-infectious pathogen treatment consisting of an injection with heat-killed bacteria or a procedural control, and a stress treatment consisting of sleep deprivation or control. Their daughters and sons were similarly assigned to the same pathogen treatment, prior to measurement of their reproductive success. Results: We observed transgenerational interactions involving pathogen treatments of mothers and their offspring, on the reproductive success of daughters but not sons. These interactions were unaffected by sleep deprivation. Conclusions: The direction of the transgenerational effects was not consistent with that predicted under a scenario of adaptive transgenerational plasticity. Instead, they were indicative of expectations based on terminal investment.

opencc-zeroDec 2016View details →

Data from: Do cryptic species matter in macroecology? Sequencing European groundwater crustaceans yields smaller ranges but does not challenge biodiversity determinants

Ecologists increasingly rely on molecular delimitation methods (MMs) to identify species boundaries, thereby potentially increasing the number of putative species because of the presence of morphologically cryptic species. It has been argued that cryptic species could challenge our understanding of what determine large-scale biodiversity patterns which have traditionally been documented from morphology alone. Here, we used morphology and three MMs to derive four different sets of putative species among the European groundwater crustaceans. Then, we used regression models to compare the relative importance of spatial heterogeneity, productivity and historical climates, in shaping species richness and range size patterns across sets of putative species. We tested three predictions. First, MMs would yield many more putative species than morphology because groundwater is a constraining environment allowing little morphological changes. Second, for species richness, MMs would increase the importance of spatial heterogeneity because cryptic species are more likely along physical barriers separating ecologically similar regions than along resource gradients promoting ecologically-based divergent selection. Third, for range size, MMs would increase the importance of historical climates because of reduced and asymmetrical fragmentation of large morphological species ranges at northern latitudes. MMs yielded twice more putative species than morphology and decreased by 10-fold the average species range size. Yet, MMs strengthened the mid-latitude ridge of high species richness and the Rapoport effect of increasing range size at higher latitudes. Species richness predictors did not vary between morphology and MMs but the latter increased the proportion of variance in range size explained by historical climates. These findings demonstrate that our knowledge of groundwater biodiversity determinants is robust to overlooked cryptic species because the latter are homogeneously distributed along environmental gradients. Yet, our findings call for incorporating multiple species delimitation methods into the analysis of large-scale biodiversity patterns across a range of taxa and ecosystems.

Data from: Benefits and challenges of scaling up expansion of marine protected area networks in the Verde Island Passage, Central Philippines

Locally-established marine protected areas (MPAs) have been proven to achieve local-scale fisheries and conservation objectives. However, since many of these MPAs were not designed to form ecologically-connected networks, their contributions to broader-scale goals such as complementarity and connectivity can be limited. In contrast, integrated networks of MPAs designed with systematic conservation planning are assumed to be more effective—ecologically, socially, and economically—than collections of locally-established MPAs. There is, however, little empirical evidence that clearly demonstrates the supposed advantages of systematic MPA networks. A key reason is the poor record of implementation of systematic plans attributable to lack of local buy-in. An intermediate scenario for the expansion of MPAs is scaling up of local decisions, whereby locally-driven MPA initiatives are coordinated through collaborative partnerships among local governments and their communities. Coordination has the potential to extend the benefits of individual MPAs and perhaps to approach the potential benefits offered by systematic MPA networks. We evaluated the benefits of scaling up local MPAs to form networks by simulating seven expansion scenarios for MPAs in the Verde Island Passage, central Philippines. The scenarios were: uncoordinated community-based establishment of MPAs; two scenarios reflecting different levels of coordinated MPA expansion through collaborative partnerships; and four scenarios guided by systematic conservation planning with different contexts for governance. For each scenario, we measured benefits through time in terms of achievement of objectives for representation of marine habitats. We found that: in any governance context, systematic networks were more efficient than non-systematic ones; systematic networks were more efficient in broader governance contexts; and, contrary to expectations but with caveats, the uncoordinated scenario was slightly more efficient than the coordinated scenarios. Overall, however, coordinated MPA networks have the potential to be more efficient than the uncoordinated ones, especially when coordinated planning uses systematic methods.

opencc-zeroDec 2017View details →

Data from: Challenges of NGS in conservation management: insights from long-term monitoring of corridor effects on the genetic diversity of mouse lemurs in a fragmented landscape

Long-term genetic monitoring of populations is essential for efforts aimed at preserving genetic diversity of endangered species. Here, we employ a framework of long-term genetic monitoring to evaluate the effects of fragmentation and the effectiveness of the establishment of corridors in restoring population connectivity and genetic diversity of mouse lemurs Micocebus ganzhorni. To this end, we supplement estimates of neutral genetic diversity with the assessment of adaptive genetic variability of the MHC. In addition, we address the challenges of long-term genetic monitoring of functional diversity by comparing the genotyping performance and estimates of MHC variability generated by SSCP/Sanger-sequencing with those obtained by high throughput sequencing (NGS, Illumina), an issue that is particularly relevant when previous work serves as a baseline for planning management strategies that aim to ensure the viability of a population. We report that SSCP greatly underestimates individual diversity and that discrepancies in estimates of MHC diversity attributable to the comparisons of traditional and NGS genotyping techniques can influence the conclusions drawn from conservation management scenarios. Evidence of migration among fragments in Mandena suggests that mouse lemurs are robust to the process of fragmentation and that the effect of corridors is masked by ongoing gene flow. Nonetheless, results based on a larger number of shared private alleles at neutral loci between fragment pairs found after the establishment of corridors in Mandena suggest that gene flow is augmented as a result of enhanced connectivity. Our data points out that despite low effective population size, M. ganzhorni maintains high individual heterozygosity at neutral loci and at MHC II DRB gene and that selection plays a predominant role in maintaining MHC diversity. These findings highlight the importance of long-term genetic monitoring in order to disentangle between the processes of drift and selection maintaining adaptive genetic diversity in small populations.

Data from: Repetitive flanking sequences challenge SSR marker development: a case study in the lepidopteran Melanargia galathea

Microsatellite DNA families (MDF) are stretches of DNA that share similar or identical sequences beside nuclear simple-sequence repeat (nSSR) motifs, potentially causing problems during nSSR marker development. Primers positioned within MDFs can bind several times within the genome and might result in multiple banding patterns. It is therefore common practice to exclude MDF loci in the course of marker development. Here, we propose an approach to deal with multiple primer binding sites by purposefully positioning primers within the detected repetitive element. We developed a new protocol to determine the family type and the primer position in relation to MDFs using the software packages RepARK and RepeatMasker together with an in-house R script. We re-evaluated newly developed nSSR markers for the lepidopteran Marbled White (Melanargia galathea) and explored the implications of our results with regard to published data sets of the butterfly Ephydryas aurinia, the grasshopper Stethophyma grossum, the conifer Pinus cembra, and the crucifer Arabis alpina. For M. galathea, we show that it is not only possible to develop reliable nSSR markers for MDF loci, but even to benefit from their presence in some cases: We used one unlabeled primer, successfully binding within an MDF, for two different loci in a multiplex PCR, combining this family primer with uniquely binding and fluorescently labeled primers outside of MDFs, respectively. As MDFs are abundant in many taxa, we propose to consider these during nSSR marker development in taxa concerned. Our new approach might help in reducing the number of tested primers during nSSR marker development.

opencc-zeroDec 2012View details →

Data from: The challenge of species delimitation at the extremes: diversification without morphological change in Philippine sun skinks

Species represent one of the fundamental units of the evolutionary process, and an accurate understanding of species diversity is essential to studies across a wide range of biological subdisciplines. However, delimiting species remains challenging in evolutionary radiations where morphological diversification is rapid and accompanied by little genetic differentiation or when genetic lineage divergence is not accompanied by morphological change. We investigate the utility of a variety of recently developed approaches to examine genetic and morphological diversity, and delimit species in a morphologically conserved group of Southeast Asian lizards. We find that species diversity is vastly underestimated in this unique evolutionary radiation, and find an extreme case where extensive genetic divergence among lineages has been accompanied by little to no differentiation in external morphology. Although we note that different conclusions can be drawn when species are delimited using molecular phylogenetics, coalescent-based methods, or morphological data, it is clear that the use of a pluralistic approach leads to a more comprehensive appraisal of biodiversity, and greater appreciation for processes of diversification in this biologically important geographic region. Similarly, our approach demonstrates how recently developed methodologies can be utilized to obtain robust estimates of species limits in "non-adaptive" or "cryptic" evolutionary radiations.

opencc-zeroJul 2019View details →

Data from: Differential gene expression analysis of symbiotic and aposymbiotic Exaiptasia anemones under immune challenge with Vibrio coralliilyticus

Anthozoans are a class of Cnidarians that includes scleractinian corals, anemones and their relatives. Despite a global rise in disease epizootics impacting scleractinian corals, little is known about the immune response of this key group of invertebrates. To better characterize the anthozoan immune response, we used the model anemone Exaiptasia pallida to explore the genetic links between the anthozoan-algal symbioses and immunity in a two-factor RNA-Seq experiment using both symbiotic and aposymbiotic(menthol-bleached) Exaiptasia pallida exposed to the bacterial pathogen Vibrio coralliilyticus. Multivariate and univariate analyses of Exaiptasia gene expression demonstrated that exposure to live Vibrio coralliilyticus had strong and significant impacts on transcriptome-wide gene expression for both symbiotic and aposymbiotic anemones, but we did not observe strong interactions between symbiotic state and Vibrio exposure. There were 4,164 significantly differentially expressed (DE) genes for Vibrio exposure, 1,114 DE genes for aposymbiosis, and 472 DE genes for the additive combinations of Vibrio and aposymbiosis. KEGG enrichment analyses identified 11 pathways - involved in immunity (5), transport and catabolism (4) and cell growth and death (2) - that were enriched due to both Vibrio and/or aposymbiosis. Immune pathways showing strongest differential expression included complement, coagulation, nucleotide-binding and oligomerization domain (NOD), and Toll for Vibrio exposure and coagulation and apoptosis for aposymbiosis.

opencc-zeroDec 2012View details →

Data from: Differential gene expression in Acromyrmex leaf-cutting ants after challenges with two fungal pathogens

Social insects in general and leaf-cutting ants in particular have increased selection pressures on their innate immune system due to their social lifestyle and monoclonality of the symbiotic fungal cultivar. As this symbiosis is obligate for both parties, prophylactic behavioural defences against infections are expected to increase either ant survival or fungus-garden survival, but also to possibly trade off when specific infections differ in potential danger. We examined the effectiveness of prophylactic behaviours and modulations of innate immune defences by a combination of inoculation bioassays and genome-wide transcriptomic studies (RNA-Seq), using an ant pathogen (Metarhizium brunneum) and a fungus-garden pathogen (Escovopsis weberi) and administering inoculations both directly and indirectly (via the symbiotic partner). Upon detection of pathogen conidia, ant workers responded by increasing both general activity and the frequency of specific defence behaviours (self-grooming, allo-grooming, garden-grooming) independent of the pathogen encountered. This trend was also evident in the patterns of gene expression change. Both direct and indirect (via fungus garden) inoculations with Metarhizium induced a general up-regulation of gene expression, including a number of well-known immune-related genes. In contrast, direct inoculation of the fungus garden by Escovopsis induced an overall down-regulation of ant gene expression, whereas indirect inoculation (via the ants) did not, suggesting that increased activity of ants to remove this fungus-garden pathogen is costly and involves trade-offs with the activation of other physiological pathways.

opencc-zeroDec 2013View details →

Data from: Critically endangered island endemic or peripheral population of a widespread species? Conservation genetics of Kikuchi's gecko and the global challenge of protecting peripheral oceanic island endemic vertebrates

Aim: To highlight the significant conservation challenge of evaluating peripheral endemic vertebrates in island archipelago systems and to assess empirically the complexities of approaches to conservation genetic studies across political and biogeographic boundaries. To demonstrate the poignant need for international collaboration and coordination when species delimitation problems with high conservation concern involve island endemics with biogeographically peripheral ranges. Location: Southeast Asia, Lanyu Island, Taiwan, and the Philippines. Methods: Genetic samples were collected and sequenced for one mitochondrial gene and five nuclear loci for species of the Gekko mindorensis-G. kikuchii species complex in Southeast Asia. We used maximum likelihood and Bayesian phylogenetic methods and coalescent-based species delimitation analyses to estimate phylogeographic relationships, construct multilocus haplotype networks and test putative species boundaries. Results: Phylogenetic and population genetic analyses suggest that Kikuchi's Gecko may represent a peripheral population of a widespread species distributed from the northern Philippines to Taiwan. However, we identify a discrepancy between inferences of species boundaries resulting from methods based on allele frequencies versus coalescent-based methods that incorporate evolutionary history. Coalescent-based analyses suggest that G. kikuchii may be a distinct evolutionary lineage. Our study underscores the need for coalescent-based methods in conjunction with population genetic approaches for conservation genetic assessments of widespread species. Main conclusions: This study joins a few recent works suggesting that Philippine-derived anomalies in the fauna of Lanyu (and possibly greater Taiwan) are worthy of careful reconsideration. Determining whether each is the result of recent human-mediated introduction or (possibly more ancient) natural dispersal should be the goal of future studies on this seldom-conceived biogeographic relationship. Isolated species endemic to islands on the outer periphery of biogeographic and political regions represent particular conservation challenges. This is especially true if a species occurs on an isolated island that is allied biogeographically with one nation, but politically administered by another.

Data from: Accounting for uncertainty in gene tree estimation: summary-coalescent species tree inference in a challenging radiation of Australian lizards

Accurate gene tree inference is an important aspect of species tree estimation in a summary-coalescent framework. Yet, in empirical studies, inferred gene trees differ in accuracy due to stochastic variation in phylogenetic signal between targeted loci. Empiricists should, therefore, examine the consistency of species tree inference, while accounting for the observed heterogeneity in gene tree resolution of phylogenomic data sets. Here, we assess the impact of gene tree estimation error on summary-coalescent species tree inference by screening ${\sim}2000$ exonic loci based on gene tree resolution prior to phylogenetic inference. We focus on a phylogenetically challenging radiation of Australian lizards (genus Cryptoblepharus, Scincidae) and explore effects on topology and support. We identify a well-supported topology based on all loci and find that a relatively small number of high-resolution gene trees can be sufficient to converge on the same topology. Adding gene trees with decreasing resolution produced a generally consistent topology, and increased confidence for specific bipartitions that were poorly supported when using a small number of informative loci. This corroborates coalescent-based simulation studies that have highlighted the need for a large number of loci to confidently resolve challenging relationships and refutes the notion that low-resolution gene trees introduce phylogenetic noise. Further, our study also highlights the value of quantifying changes in nodal support across locus subsets of increasing size (but decreasing gene tree resolution). Such detailed analyses can reveal anomalous fluctuations in support at some nodes, suggesting the possibility of model violation. By characterizing the heterogeneity in phylogenetic signal among loci, we can account for uncertainty in gene tree estimation and assess its effect on the consistency of the species tree estimate. We suggest that the evaluation of gene tree resolution should be incorporated in the analysis of empirical phylogenomic data sets. This will ultimately increase our confidence in species tree estimation using summary-coalescent methods and enable us to exploit genomic data for phylogenetic inference.

opencc-zeroDec 2011View details →

Data from: Discrimination of hybrid classes using cross-species amplification of microsatellite loci: methodological challenges and solutions in Daphnia

Microsatellite markers are important tools in population, conservation and forensic studies and are frequently used for species delineation, the detection of hybridization and introgression. Therefore, marker sets that amplify variable DNA regions in two species are required; however, cross-species amplification is often difficult, as genotyping errors such as null alleles may occur. In order to estimate the level of potential misidentifications based on genotyping errors, we compared the occurrence of parental alleles in laboratory and natural Daphnia hybrids (Daphnia longispina group). We tested a set of twelve microsatellite loci with regard to their suitability for unambiguous species and hybrid class identification using F1 hybrids bred in the laboratory. Further, a large set of 44 natural populations of D. cucullata, D. galeata and D. longispina (1715 individuals) as well as their interspecific hybrids were genotyped to validate the discriminatory power of different marker combinations. Species delineation using microsatellite multi-locus genotypes produced reliable results for all three studied species using assignment tests. D. galeata x cucullata hybrid detection was limited due to three loci exhibiting D. cucullata specific null alleles which most likely are caused by differences in primer binding sites of parental species. Overall discriminatory power in hybrid detection was improved when a subset of markers was identified that amplifies equally well in both species.

Data from: Migrating songbirds on stopover prepare for, and recover from, oxidative challenges posed by long-distance flight

Managing oxidative stress is an important physiological function for all aerobic organisms, particularly during periods of prolonged high metabolic activity, such as long-distance migration across ecological barriers. However, no previous study has investigated the oxidative status of birds at different stages of migration and whether that oxidative status depends on the condition of the birds. In this study, we compared (1) energy stores and circulating oxidative status measures in (a) two species of Neotropical migrants with differing migration strategies that were sampled at an autumn stopover site before an ecological barrier; and (b) a species of trans-Saharan migrant sampled at a spring stopover site after crossing an ecological barrier; and (2) circulating oxidative measures and indicators of fat metabolism in a trans-Saharan migrant after stopovers of varying duration (0–8 nights), based on recapture records. We found fat stores to be positively correlated with circulating antioxidant capacity in Blackpoll Warblers and Red-eyed Vireos preparing for fall migration on Block Island, USA, but uncorrelated in Garden Warblers on the island of Ponza, Italy, after a spring crossing of the Sahara Desert and Mediterranean Sea. In all circumstances, fat stores were positively correlated with circulating lipid oxidation levels. Among Garden Warblers on the island of Ponza, fat anabolism increased with stopover duration while oxidative damage levels decreased. Our study provides evidence that birds build antioxidant capacity as they build fat stores at stopover sites before long flights, but does not support the idea that antioxidant stores remain elevated in birds with high fuel levels after an ecological barrier. Our results further suggest that lipid oxidation may be an inescapable hazard of using fats as the primary fuel for flight. Yet, we also show that birds on stopover are capable of recovering from the oxidative damage they have accrued during migration, as lipid oxidation levels decrease with time on stopover. Thus, the physiological strategy of migrating songbirds may be to build prophylactic antioxidant capacity in concert with fuel stores at stopover sites before a long-distance flight, and then repair oxidative damage while refueling at stopover sites after long-distance flight.

opencc-by-4.0Jun 2021View details →

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Taxonomic profiles of the CAMI 2 Challenge datasets: marine, plant-associated, strain madness

Taxonomic profiles including participant submissions for the CAMI 2 Challenge datasets: marine, plant-associated, strain madness. See <a href="https://www.microbiome-cosi.org/cami">https://www.microbiome-cosi.org/cami</a> and <a href="https://data.cami-challenge.org/participate">https://data.cami-challenge.org/participate</a>.

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Taxonomic binnings of the CAMI 2 Challenge datasets: marine, plant-associated, strain madness

Taxonomic binnings including participant submissions for the CAMI 2 Challenge datasets: marine, plant-associated, strain madness. See <a href="https://www.microbiome-cosi.org/cami">https://www.microbiome-cosi.org/cami</a> and <a href="https://data.cami-challenge.org/participate">https://data.cami-challenge.org/participate</a>.

opencc-by-4.0Jun 2021View details →

opencc-zeroDec 2013View details →

Data from: Enhanced male coloration after immune challenge increases reproductive potential

In many animal species, females select a mate on the basis of the expression of secondary sexual traits. A prevalent theory suggests that male ornaments are reliable indicators of immunocompetence, because the cost of immune function prevents cheating. However, sexual signalling is a component of males' reproductive effort, and an immune challenge may also alter the organism's perceived future prospects and hence their signalling effort. In this study, to investigate the consequences of mounting an immune response on signalling effort, blue-footed booby males (Sula nebouxii) during courtship were inoculated with diphtheria–tetanus vaccine. We found that, after this immune challenge, on average males increased their signalling effort but lost more body mass compared to control males. Importantly, vaccination affected the partner's reproductive decisions: compared to control females, females paired with vaccinated males laid eggs earlier, and increased clutch volume in early pairs. Overall, our results suggest that blue-footed booby males invest more in sexual signals when future breeding opportunities are at risk, eliciting a greater reproductive investment by their partners. Increased signaling effort by infected individuals may contrast the idea of sexual ornaments as signals of infection status.

opencc-zeroDec 2016View details →

Data from: Joint histology in Alligator mississippiensis challenges the identification of synovial joints in fossil archosaurs and inferences of cranial kinesis

Archosaurs, like all vertebrates, have different types of joints that allow or restrict cranial kinesis, such as synovial joints and fibrous joints. In general, synovial joints are more kinetic than fibrous joints, because the former possess a fluid-filled cavity and articular cartilage that facilitate movement. Even though there is a considerable lack of data on the microstructure and the structure–function relationships in the joints of extant archosaurs, many functional inferences of cranial kinesis in fossil archosaurs have hinged on the assumption that elongated condylar joints are (i) synovial and/or (ii) kinetic. Cranial joint microstructure was investigated in an ontogenetic series of American alligators, Alligator mississippiensis. All the presumably synovial, condylar joints found within the head of the American alligator (the jaw joint, otic joint and laterosphenoid–postorbital (LS–PO) joint) were studied by means of paraffin histology and undecalcified histology paired with micro-computed tomography data to better visualize three-dimensional morphology. Results show that among the three condylar joints of A. mississippiensis, the jaw joint was synovial as expected, but the otherwise immobile otic and LS–PO joints lacked a synovial cavity. Therefore, condylar morphology does not always imply the presence of a synovial articulation nor mobility. These findings reveal an undocumented diversity in the joint structure of alligators and show that crocodylians and birds build novel, kinetic cranial joints differently. This complicates accurate identification of synovial joints and functional inferences of cranial kinesis in fossil archosaurs and tetrapods in general.

Data from: Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: a case-study in Carex sect. Racemosae

PREMISE OF THE STUDY: Relationships among closely related and recently diverged taxa can be especially difficult to resolve. Here we use both Sanger sequencing and next-generation RADseq data sets to estimate phylogenetic relationships among species of Carex section Racemosae (Cyperaceae), a clade largely restricted to high latitudes and elevations. Interest in relationships among these taxa derives from questions about the species' biogeographic histories and possible links between diversification and Pleistocene glaciations. METHODS: A combination of approaches and molecular markers were used to estimate relationships among Carex species within sect. Racemosae and taxa from closely related sections. Nuclear and chloroplast loci generated by Sanger sequencing were analyzed with *BEAST, and SNP data from RADseq loci were analyzed as a concatenated data set using maximum likelihood and as independent loci using SVDquartets. KEY RESULTS: Sanger sequencing data sets resolved relationships among taxa at intermediate phylogenetic depths (albeit with low levels of support). Only the RADseq data resolved relationships with strong support at all phylogenetic depths. Moreover, different methods and data partitions of the RADseq data resulted in nearly identical topologies. Carex sect. Racemosae is a strongly supported clade, although a handful of species were found to group with closely related sections. Herbarium specimens up to 35 yr old successfully produced informative RADseq data. CONCLUSIONS: Despite the short read lengths of RADseq data, they nevertheless resolved relationships that Sanger sequencing data did not. Resolution of the phylogenetic relationships among recently and rapidly diversifying taxa within sect. Racemosae clades suggest a role for the Pleistocene glaciations in clade diversification.