•An efficient geometric method better calculates preferential concentration of particles.•A contractivity-preserving splitting method preserves the sum of the Lyapunov spectrum.•The centrifuge effect ...is also mimicked in the numerical solution.•Non-divergence-free interpolation can erroneously cluster particles.•Matrix-valued RBFs are equivalent to interpolation via regularized Stokeslets.
A geometric numerical method for simulating suspensions of spherical and non-spherical particles with Stokes drag is proposed. The method combines divergence-free matrix-valued radial basis function interpolation of the fluid velocity field with a splitting method integrator that preserves the sum of the Lyapunov spectrum while mimicking the centrifuge effect of the exact solution. We discuss how breaking the divergence-free condition in the interpolation step can erroneously affect how the volume of the particulate phase evolves under numerical methods. The methods are tested on suspensions of 104 particles evolving in a discrete cellular flow field. The results are that the proposed geometric methods generate more accurate and cost-effective particle distributions compared to conventional methods.
The Critically Endangered Cantor's giant softshell turtle Pelochelys cantorii is a freshwater turtle found in South and Southeast Asia. Its population is declining because of habitat destruction and ...alteration, and hunting for its meat. Data on the species’ ecology, behaviour, population size, distribution and threats are limited, and previous surveys undertaken in India have failed to detect individuals in the wild. This lack of data hinders strategic conservation planning. Ecologists and conservationists increasingly utilize local ecological knowledge to determine the status and gain insights into the ecology of threatened and rare species that are difficult to detect in field studies. To examine the historical and current occurrence of Cantor's giant softshell turtle, we conducted community interviews along the Chandragiri River in Kerala, India. With data from these interviews, we identified multiple sites where the species continues to occur. Older respondents and those that used the river for fishing and irrigation were more likely to report sightings of the species. Our findings also improved knowledge about the turtles’ seasonal and diel activity patterns. A network of key informants identified through the interviews provided information on turtle bycatch, sightings and nesting. This network is being utilized for the continued monitoring of the species and could help in devising evidence-based management strategies for softshell turtles in India. These methods can also be adopted more widely for other threatened species of freshwater turtles globally.
Human-driven extinction threatens entire lineages across the Tree of Life. Here we assess the conservation status of jawed vertebrate evolutionary history, using three policy-relevant approaches. ...First, we calculate an index of threat to overall evolutionary history, showing that we expect to lose 86-150 billion years (11-19%) of jawed vertebrate evolutionary history over the next 50-500 years. Second, we rank jawed vertebrate species by their EDGE scores to identify the highest priorities for species-focused conservation of evolutionary history, finding that chondrichthyans, ray-finned fish and testudines rank highest of all jawed vertebrates. Third, we assess the conservation status of jawed vertebrate families. We found that species within monotypic families are more likely to be threatened and more likely to be in decline than other species. We provide a baseline for the status of families at risk of extinction to catalyse conservation action. This work continues a trend of highlighting neglected groups-such as testudines, crocodylians, amphibians and chondrichthyans-as conservation priorities from a phylogenetic perspective.
Inaccurate taxonomic assessment of threatened populations can hinder conservation prioritization and management, with human‐mediated population movements obscuring biogeographic patterns and ...confounding reconstructions of evolutionary history. Giant salamanders were formerly distributed widely across China, and are interpreted as a single species, Andrias davidianus. Previous phylogenetic studies have identified distinct Chinese giant salamander lineages but were unable to associate these consistently with different landscapes, probably because population structure has been modified by human‐mediated translocations for recent commercial farming. We investigated the evolutionary history and relationships of allopatric Chinese giant salamander populations with Next‐Generation Sequencing methods, using historical museum specimens and late 20th‐century samples, and retrieved partial or near‐complete mitogenomes for 17 individuals. Samples from populations unlikely to have been affected by translocations form three clades from separate regions of China, spatially congruent with isolation by either major river drainages or mountain ranges. Pliocene–Pleistocene divergences for these clades are consistent with topographic modification of southern China associated with uplift of the Qinghai‐Tibet Plateau. General Mixed Yule Coalescent model analysis indicates that these clades represent separate species: Andrias davidianus (Blanchard, 1871) (northern Yangtze/Sichuan), Andrias sligoi (Boulenger, 1924) (Pearl/Nanling), and an undescribed species (Huangshan). Andrias sligoi is possibly the world's largest amphibian. Inclusion of additional reportedly wild samples from areas of known giant salamander exploitation and movement leads to increasing loss of biogeographic signal. Wild Chinese giant salamander populations are now critically depleted or extirpated, and conservation actions should be updated to recognize the existence of multiple species.
Giant salamanders were formerly distributed widely across China, and are interpreted as a single species, Andrias davidianus. We investigated the evolutionary history and relationships of allopatric Chinese giant salamander populations with Next‐Generation Sequencing methods, using historical museum specimens and late 20th century samples, and retrieved partial or near‐complete mitogenomes for 17 individuals. Samples cluster within three clades from separate regions of China, and represent three separate species, of which Andrias sligoi rather than Andrias davidianus is possibly the world's largest amphibian.
The fungal pathogen Batrachochytrium dendrobatidis (Bd) threatens amphibian biodiversity and ecosystem stability worldwide. Amphibian skin microbial community structure has been linked to the ...clinical outcome of Bd infections, yet its overall functional importance is poorly understood.
Microbiome taxonomic and functional profiles were assessed using high-throughput bacterial 16S rRNA and fungal ITS2 gene sequencing, bacterial shotgun metagenomics and skin mucosal metabolomics. We sampled 56 wild midwife toads (Alytes obstetricans) from montane populations exhibiting Bd epizootic or enzootic disease dynamics. In addition, to assess whether disease-specific microbiome profiles were linked to microbe-mediated protection or Bd-induced perturbation, we performed a laboratory Bd challenge experiment whereby 40 young adult A. obstetricans were exposed to Bd or a control sham infection. We measured temporal changes in the microbiome as well as functional profiles of Bd-exposed and control animals at peak infection.
Microbiome community structure and function differed in wild populations based on infection history and in experimental control versus Bd-exposed animals. Bd exposure in the laboratory resulted in dynamic changes in microbiome community structure and functional differences, with infection clearance in all but one infected animal. Sphingobacterium, Stenotrophomonas and an unclassified Commamonadaceae were associated with wild epizootic dynamics and also had reduced abundance in laboratory Bd-exposed animals that cleared infection, indicating a negative association with Bd resistance. This was further supported by microbe-metabolite integration which identified functionally relevant taxa driving disease outcome, of which Sphingobacterium and Bd were most influential in wild epizootic dynamics. The strong correlation between microbial taxonomic community composition and skin metabolome in the laboratory and field is inconsistent with microbial functional redundancy, indicating that differences in microbial taxonomy drive functional variation. Shotgun metagenomic analyses support these findings, with similar disease-associated patterns in beta diversity. Analysis of differentially abundant bacterial genes and pathways indicated that bacterial environmental sensing and Bd resource competition are likely to be important in driving infection outcomes.
Bd infection drives altered microbiome taxonomic and functional profiles across laboratory and field environments. Our application of multi-omics analyses in experimental and field settings robustly predicts Bd disease dynamics and identifies novel candidate biomarkers of infection. Video Abstract.
The interest in the welfare of zoo animals, from both the public and the scientific community, has long been biased towards mammals. However, growing evidence of the complex behavioural repertoires ...of less charismatic animals, such as reptiles, reveals the necessity to better comply with their welfare needs in captivity. Here, we present the effects of an enclosure change towards a more natural habitat in captive Galapagos tortoises (Chelonoidis spp.) held at ZSL London Zoo. Using behavioural observations, we found that the tortoises habituated to their new enclosure in six days. This represents the first quantification of habituation latency to a new enclosure in a reptile model to our knowledge—which is important information to adapt policies governing animal moves. The tortoises expressed time budgets more similar to those of wild individuals after their transition to the new enclosure. Interestingly, the hierarchy between the individuals was inverted and more stable after this change in environment. The tortoises interacted less often, which led to a decrease in the frequency of agonistic encounters. We also found that higher ambient sound volume was associated with increased likelihood of interactions turning into fights. Taken together, our results demonstrate the potential of appropriate enclosure design to improve reptile welfare.
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