Global assessment of effective population sizes: Consistent taxonomic differences in meeting the 50/500 rule.

Effective population size (Ne) is a particularly useful metric for conservation as it affects genetic drift, inbreeding and adaptive potential within populations. Current guidelines recommend a minimum Ne of 50 and 500 to avoid short-term inbreeding and to preserve long-term adaptive potential respectively. However, the extent to which wild populations reach these thresholds globally has not been investigated, nor has the relationship between Ne and human activities. Through a quantitative review, we generated a dataset with 4610 georeferenced Ne estimates from 3829 populations, extracted from 723 articles. These data show that certain taxonomic groups are less likely to meet 50/500 thresholds and are disproportionately impacted by human activities; plant, mammal and amphibian populations had a <54% probability of reaching N ̂ e = 50 and a <9% probability of reaching N ̂ e = 500. Populations listed as being of conservation concern according to the IUCN Red List had a smaller median N ̂ e than unlisted populations, and this was consistent across all taxonomic groups. N ̂ e was reduced in areas with a greater Global Human Footprint, especially for amphibians, birds and mammals, however relationships varied between taxa. We also highlight several considerations for future works, including the role that gene flow and subpopulation structure plays in the estimation of N ̂ e in wild populations, and the need for finer-scale taxonomic analyses. Our findings provide guidance for more specific thresholds based on Ne and help prioritise assessment of populations from taxa most at risk of failing to meet conservation thresholds.

Ongoing declines for the world's amphibians in the face of emerging threats.

Systematic assessments of species extinction risk at regular intervals are necessary for informing conservation action1,2. Ongoing developments in taxonomy, threatening processes and research further underscore the need for reassessment3,4. Here we report the findings of the second Global Amphibian Assessment, evaluating 8,011 species for the International Union for Conservation of Nature Red List of Threatened Species. We find that amphibians are the most threatened vertebrate class (40.7% of species are globally threatened). The updated Red List Index shows that the status of amphibians is deteriorating globally, particularly for salamanders and in the Neotropics. Disease and habitat loss drove 91% of status deteriorations between 1980 and 2004. Ongoing and projected climate change effects are now of increasing concern, driving 39% of status deteriorations since 2004, followed by habitat loss (37%). Although signs of species recoveries incentivize immediate conservation action, scaled-up investment is urgently needed to reverse the current trends.

Accuracy, limitations and cost efficiency of eDNA-based community survey in tropical frogs.

Rapid environmental change in highly biodiverse tropical regions demands efficient biomonitoring programmes. While existing metrics of species diversity and community composition rely on encounter-based survey data, eDNA recently emerged as alternative approach. Costs and ecological value of eDNA-based methods have rarely been evaluated in tropical regions, where high species richness is accompanied by high functional diversity (e.g., the use of different microhabitats by different species and life stages). We first tested whether estimation of tropical frogs' community structure derived from eDNA data is compatible with expert field assessments. Next, we evaluated whether eDNA is a financially viable solution for biodiversity monitoring in tropical regions. We applied eDNA metabarcoding to investigate frog species occurrence in five ponds in the Chiquitano dry forest region in Bolivia and compared our data with a simultaneous visual and audio encounter survey (VAES). We found that taxon lists and community structure generated with eDNA and VAES correspond closely, and most deviations are attributable to different species' life histories. Cost efficiency of eDNA surveys was mostly influenced by the richness of local fauna and the number of surveyed sites: VAES may be less costly in low-diversity regions, but eDNA quickly becomes more cost-efficient in high-diversity regions with many sites sampled. The results highlight that eDNA is suitable for large-scale biodiversity surveys in high-diversity areas if life history is considered, and certain precautions in sampling, genetic analyses and data interpretation are taken. We anticipate that spatially extensive, standardized eDNA biodiversity surveys will quickly emerge in the future.

Stem caecilian from the Triassic of Colorado sheds light on the origins of Lissamphibia.

The origin of the limbless caecilians remains a lasting question in vertebrate evolution. Molecular phylogenies and morphology support that caecilians are the sister taxon of batrachians (frogs and salamanders), from which they diverged no later than the early Permian. Although recent efforts have discovered new, early members of the batrachian lineage, the record of pre-Cretaceous caecilians is limited to a single species, Eocaecilia micropodia The position of Eocaecilia within tetrapod phylogeny is controversial, as it already acquired the specialized morphology that characterizes modern caecilians by the Jurassic. Here, we report on a small amphibian from the Upper Triassic of Colorado, United States, with a mélange of caecilian synapomorphies and general lissamphibian plesiomorphies. We evaluated its relationships by designing an inclusive phylogenetic analysis that broadly incorporates definitive members of the modern lissamphibian orders and a diversity of extinct temnospondyl amphibians, including stereospondyls. Our results place the taxon confidently within lissamphibians but demonstrate that the diversity of Permian and Triassic stereospondyls also falls within this group. This hypothesis of caecilian origins closes a substantial morphologic and temporal gap and explains the appeal of morphology-based polyphyly hypotheses for the origins of Lissamphibia while reconciling molecular support for the group's monophyly. Stem caecilian morphology reveals a previously unrecognized stepwise acquisition of typical caecilian cranial apomorphies during the Triassic. A major implication is that many Paleozoic total group lissamphibians (i.e., higher temnospondyls, including the stereospondyl subclade) fall within crown Lissamphibia, which must have originated before 315 million years ago.

In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River.

Analysis of environmental DNA (eDNA) enables the detection of species of interest from water and soil samples, typically using species-specific PCR. Here, we describe a method to characterize the biodiversity of a given environment by amplifying eDNA using primer pairs targeting a wide range of taxa and high-throughput sequencing for species identification. We tested this approach on 91 water samples of 40 mL collected along the Cuyahoga River (Ohio, USA). We amplified eDNA using 12 primer pairs targeting mammals, fish, amphibians, birds, bryophytes, arthropods, copepods, plants and several microorganism taxa and sequenced all PCR products simultaneously by high-throughput sequencing. Overall, we identified DNA sequences from 15 species of fish, 17 species of mammals, 8 species of birds, 15 species of arthropods, one turtle and one salamander. Interestingly, in addition to aquatic and semi-aquatic animals, we identified DNA from terrestrial species that live near the Cuyahoga River. We also identified DNA from one Asian carp species invasive to the Great Lakes but that had not been previously reported in the Cuyahoga River. Our study shows that analysis of eDNA extracted from small water samples using wide-range PCR amplification combined with high-throughput sequencing can provide a broad perspective on biological diversity.

Aquatic biodiversity assessment for the lazy.

The world is covered in DNA. In any ecosystem, extracellular DNA fragments can be found that once formed the genomes of a variety of micro- and macroorganisms. A few years ago, it was proposed to use this environmental DNA (eDNA) as a source of information on local vertebrate biodiversity (Ficetola et al. 2008; Taberlet et al. 2012). This idea offered an elegant solution to take up the gauntlet of rapidly increasing monitoring needs. Coupled with barcoding efforts, it promised to be cost-efficient in many respects, for example man-hours and taxonomic expertise. Ecologists and conservation biologists with an interest in aquatic ecosystems have enthusiastically adopted and pioneered this new method, producing dozens of eDNA studies. Most of these studies have, however, focused on a single or a few aquatic species. In this issue of Molecular Ecology, Valentini et al. (2016) move the field a step further by demonstrating that metabarcoding approaches - which simultaneously target large groups of organisms such as amphibians or fish - can match and sometimes even outperform other inventory methods.

Montane meadows in the Sierra Nevada: comparing terrestrial and aquatic assessment methods.

We surveyed montane meadows in the northern Sierra Nevada and southern Cascades for two field seasons to compare commonly used aquatic and terrestrial-based assessments of meadow condition. We surveyed (1) fish, (2) reptiles, (3) amphibians, (4) aquatic macroinvertebrates, (5) stream geomorphology, (6) physical habitat, and (7) terrestrial vegetation in 79 meadows between the elevations of 1,000 and 3,000 m. From the results of those surveys, we calculated five multi-metric indices based on methods commonly used by researchers and land management agencies. The five indices consisted of (1) fish only, (2) native fish and amphibians, (3) macroinvertebrates, (4) physical habitat, and (5) vegetation. We compared the results of the five indices and found that there were significant differences in the outcomes of the five indices. We found positive correlations between the vegetation index and the physical habitat index, the invertebrate index and the physical habitat index, and the two fish-based indices, but there were significant differences between indices in both range and means. We concluded that the five indices provided very different interpretations of the condition in a given meadow. While our assessment of meadow condition changed based on which index was used, each provided an assessment of different components important to the overall condition of a meadow system. Utilizing a multimetric approach that accounts for both terrestrial and aquatic habitats provides the best means to accurately assess meadow condition, particularly given the disproportionate importance of these systems in the Sierra Nevada landscape.

Inferring and testing hypotheses of cladistic character dependence by using character compatibility.

The notion that two characters evolve independently is of interest for two reasons. First, theories of biological integration often predict that change in one character requires complementary change in another. Second, character independence is a basic assumption of most phylogenetic inference methods, and dependent characters might confound attempts at phylogenetic inference. Previously proposed tests of correlated character evolution require a model phylogeny and therefore assume that nonphylogenetic correlation has a negligible effect on initial tree construction. This paper develops "tree-free" methods for testing the independence of cladistic characters. These methods can test the character independence model as a hypothesis before phylogeny reconstruction, or can be used simply to test for correlated evolution. We first develop an approach for visualizing suites of correlated characters by using character compatibility. Two characters are compatible if they can be used to construct a tree without homoplasy. The approach is based on the examination of mutual compatibilities between characters. The number of times two characters i and j share compatibility with a third character is calculated, and a pairwise shared compatibility matrix is constructed. From this matrix, an association matrix analogous to a dissimilarity matrix is derived. Eigenvector analyses of this association matrix reveal suites of characters with similar compatibility patterns. A priori character subsets can be tested for significant correlation on these axes. Monte Carlo tests are performed to determine the expected distribution of mutual compatibilities, given various criteria from the original data set. These simulated distributions are then used to test whether the observed amounts of nonphylogenetic correlation in character suites can be attributed to chance alone. We have applied these methods to published morphological data for caecilian amphibians. The analyses corroborate instances of dependent evolution hypothesized by previous workers and also identify novel partitions. Phylogenetic analysis is performed after reducing correlated suites to single characters. The resulting cladogram has greater topological resolution and implies appreciably less change among the remaining characters than does a tree derived from the raw data matrix.

Distribution of vasotocin- and mesotocin-like immunoreactivities in the brain of typhlonectes compressicauda (Amphibia, gymnophiona): further assessment of primitive and derived traits of amphibian neuropeptidergic systems.

To further assess primitive and derived conditions, we have studied the vasotocinergic (AVT) and mesotocinergic (MST) systems by immmunohistochemistry in the brain of Typhlonectes compressicauda. This species belongs to a separate order of amphibians which differs in several morphological and behavioral aspects from anurans and urodeles which have been studied previously. Nevertheless, the vasotocinergic and mesotocinergic systems of T. compressicauda are largely comparable to those of other amphibians. Apart from a well-developed hypothalamo-hypophyseal system, extrahypothalamic AVT-and MST-immunoreactive groups of cells and extensive networks of fibers were found. A major difference, however, is that neuropeptidergic cells in the caudal hypothalamus and the midbrain tegmentum of T. compressicauda contain MST, whereas those in corresponding locations contain AVT in anurans and urodeles. This suggests that certain neuropeptidergic cell groups in the gymnophionan brain have switched from AVT to MST gene expression, and, thereby, offers a new view on the functional significance of these neuropeptidergic systems.