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opencc-zeroMay 2022View details →

Comparing genome-based estimates of relatedness for use in pedigree-based conservation management

Researchers have long debated which estimator of relatedness best captures the degree of relationship between two individuals. In the genomics era, this debate continues, with relatedness estimates being sensitive to the methods used to generate markers, marker quality, and levels of diversity in sampled individuals. Here, we compare six commonly used genome-based relatedness estimators (kinship genetic distance (KGD), Wang Maximum Likelihood (TrioML), Queller and Goodnight (Rxy), Kinship INference for Genome-wide association studies (KING-robust), and Pairwise Relatedness (RAB), allele-sharing co-ancestry (AS)) across five species bred in captivity–including three birds and two mammals–with varying degrees of reliable pedigree data, using reduced-representation and whole genome resequencing data. Genome-based relatedness estimates varied widely across estimators, sequencing methods, and species, yet the most consistent results for known first order relationships were found using Rxy, RAB, and AS. However, AS was found to be less consistently correlated with known pedigree relatedness than either Rxy or RAB. Our combined results indicate there is not a single genome-based estimator that is ideal across different species and data types. To determine the most appropriate genome-based relatedness estimator for each new dataset, we recommend assessing the relative: (1) correlation of candidate estimators with known relationships in the pedigree and (2) precision of candidate estimators with known first-order relationships. These recommendations are broadly applicable to conservation breeding programs, particularly where genome-based estimates of relatedness can complement and complete poorly pedigreed populations. Given a growing interest in the application of wild pedigrees, our results are also applicable to in-situ wildlife management.

opencc-zeroMay 2022View details →

Sequence conservation and structural features that are common within TRP channels

TRP proteins are a large family of cation-selective channels, surpassed in variety only by voltage-gated potassium channels. Detailed molecular mechanisms governing how membrane voltage, ligand binding, or temperature can induce conformational changes promoting the open state in TRP channels are still a matter of debate. Aiming to unveil distinctive structural features common to the transmembrane domains within the TRP family, we performed phylogenetic reconstruction, sequence statistics, and structural analysis over a large set of TRP channel genes. Here we report an exceptionally conserved set of residues. This fingerprint is composed of twelve residues localized at equivalent three-dimensional positions in TRP channels from the different subtypes. Moreover, these amino acids are arranged in three groups, connected by a set of aromatics located at the core of the transmembrane structure. We hypothesize that differences in the connectivity between these different groups of residues harbors the apparent differences in coupling strategies used by TRP subgroups.

Random forest modelling of multi-scale, multi-species habitat associations within KAZA transfrontier conservation area using spoor data

As landscape-scale conservation models grow in prominence, assessments of how wildlife utilise multiple-use landscapes are required to inform effective conservation and management planning. Such efforts should strive to incorporate multi-species perspectives to maximise value for conservation, and should account for scale to accurately capture species-environment relationships. We show that the random forest machine learning algorithm can be used to model large-scale sign-based data in a multi-scale framework. We used this method to investigate scale-dependent habitat associations for 16 mammal species of high conservation importance across the southern Kavango Zambezi (KAZA) Transfrontier Conservation Area in Botswana and Zimbabwe. Our findings revealed substantial variation in the factors shaping habitat use across species, and illustrate that different species often have divergent responses to the same environmental and anthropogenic factors, and differ in the scales at which they respond to them. For all variables across all species, scale optimisation most often selected our largest scale. Precipitation, soil nutrients, and vegetation appeared to be the most important factors determining mammal distributions, likely through their associations with food resources for herbivores and, in turn, prey availability for carnivores. Anthropogenic pressures also had an important influence on habitat use, with many species selecting against areas with high cattle density. The variety of relationships with human density indicated that species vary in their tolerance of humans. We found a consistent positive relationship with areas under high protection, and negative relationship with unprotected and less-strictly protected areas. Policy implications: This study highlights the importance of adopting a multi-scale, multi-species approach for critical decision-making processes that depend on understanding wildlife distributions and habitat associations, such as protected area, corridor, and buffer zone prioritisation. We use our findings to identify changing rainfall patterns and increasing livestock numbers as two emerging trends that may impact wildlife distributions, both within sub-Saharan Africa and on a global scale.

Augmentation and conservation biological control of Tetranychus urticae on hops in Ohio

The twospotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae), is a key pest on hops grown in the Midwestern USA, where hop production is a new industry, and little research has been done on the management of T. urticae. In 2016 and 2017, we conducted an experiment to determine the efficacy of augmentative biological control of T. urticae populations on the cultivar 'Cascade' at four hop yards. In both years, treatments compared Neoseiulus fallacis Garman (Acari: Phytoseiidae), released at a high rate and a low rate, and an untreated control, with eight replicates in 2016 and 17 replicates in 2017. Additional treatments in 2016 evaluated Galendromus occidentalis Nesbitt (Acari: Phytoseiidae) released at a high and a low rate. The target low rate in both years was one predator per ten T. urticae. The target high rate was one predator per five T. urticae in 2016, and one predator per two T. urticae in 2017. When weekly monitoring showed that the population reached an action threshold of one T. urticae per ten leaves, predatory mites were released. If the T. urticae population continued to increase, a second release was made. By the time of harvest, the cumulative number of mite-days for T. urticae did not differ significantly among treatments in either year. Hop yields showed a significant treatment effect in 2016, with higher yield where the high rate of G. occidentalis was released than in other treatments, but yields did not show any significant treatment effect in 2017. In 2017, we also conducted an exclusion experiment at four hop yards in Ohio, to determine the services provided by predators already present in hop yards, as well as the ability of the combination of predatory mites, N. fallacis and Neoseiulus californicus McGregor (Acari: Phytoseiidae), to suppress T. urticae by augmentative releases at three different predator to prey ratios: zero to ten, one to ten, and two to ten. Samples were paired; one leaf was covered with a fine mesh bag and one leaf was left uncovered, in each of 50 replicates. After two weeks, the average number of T. urticae motiles on the open leaves that received zero phytoseiids was significantly less than the starting number of ten, suggesting that ambient predation is capable of suppressing T. urticae populations. The average number of T. urticae motiles on the enclosed leaves that received two phytoseiids was also significantly less than the starting number of ten, while the average number of T. urticae motiles on the enclosed leaf that received one phytoseiid was not, showing that a ratio of one phytoseiid to five T. urticae is effective at reducing T. urticae populations. Our experiments showed that when T. urticae is found at low to moderate densities, naturally occurring predators are able to suppress their populations in Ohio hop yards. Augmentation using phytoseiid mites did not have a consistent beneficial effect on yields. Given that naturally occurring predators are important in the suppression of T. urticae populations, future studies thus might concentrate on conservation biological control.

Data accessibility for conservation implications of genetic structure in the narrowest endemic quillwort from the Eastern Amazon

The quillwort Isoetes cangae is a critically endangered species occurring in a single lake in Serra dos Carajás, Eastern Amazon. Low genetic diversity and small effective population sizes (Ne) is expected for narrow endemic species (NES). Here, we evaluated genetic diversity, population structure, and Ne of I. cangae to provide information for conservation programs. Conservation biology studies centered in a single‐species show some limitations but they are still useful considering the limited time and resources available for the protection of species at risk of extinction. Our analyses were based on 55 individuals collected from the Amendoim lake and 35,638 neutral SNPs. Our results indicated a single panmictic population, moderate levels of genetic diversity, and effective population size (Ne) in the order of thousands, contrasting the expected for NES. Negative FIS values were also found, suggesting that I. cangae is not under risk of inbreeding depression. Our findings imply that I. cangae contains enough genetic diversity to ensure evolutionary potential, all individuals should be treated as one demographic unit.

Genomic analyses show extremely perilous conservation status of African and Asiatic cheetahs (Acinonyx jubatus)

We live in a world characterised by biodiversity loss and global environmental change. The extinction of large carnivores can have ramifying effects on ecosystems like an uncontrolled increase in wild herbivores, which in turn can have knock-on impacts on vegetation regeneration and communities. Cheetahs (Acinonyx jubatus) serve important ecosystem functions as apex predators; yet, they are quickly heading towards an uncertain future. Threatened by habitat loss, human-wildlife conflict, and illegal trafficking, there are only approximately 7,100 individuals remaining in nature. We present the most comprehensive genome-wide analysis of cheetah phylogeography and conservation genomics to date, assembling samples from nearly the entire current and past species' range. We show that their phylogeography is more complex than previously thought, and that East African cheetahs (A. j. raineyi) are genetically distinct from Southern African individuals (A. j. jubatus), warranting their recognition as a distinct subspecies. We found strong genetic differentiation between all classically recognised subspecies, thus refuting earlier findings that cheetahs show only little differentiation. The strongest differentiation was observed between the Asiatic and all the African subspecies. We detected high inbreeding in the Critically Endangered Iranian (A. j. venaticus) and North-western (A. j. hecki) subspecies, and show that overall cheetahs, along with snow leopards, have the lowest genome-wide heterozygosity of all the big cats. This further emphasizes the cheetah's perilous conservation status. Our results provide novel and important information on cheetah phylogeography that can support evidence-based conservation policy decisions to help protect this species. This is especially relevant in light of ongoing and proposed translocations across subspecies boundaries, and the increasing threats of illegal trafficking.

opencc-by-4.0Jun 2022View details →

Data from: Using functional traits to identify conservation priorities for the world's crocodylians

Over half of all crocodylians are threatened with extinction, with many species considered to be functionally extinct throughout their historical ranges. How such losses impact crocodylian functional diversity (FD) and its conservation is poorly understood, but can be investigated using measurable traits. Where such information is unavailable, phylogenetic diversity (PD) has been proposed as an effective strategy to capture FD, but this assumption is not well tested. We constructed a global trait database for 28 extant crocodylians [uploaded here], and quantified their functional diversity, distinctiveness and groupings. Functionally distinctive crocodylians include the most and least evolutionarily distinct species, likely because unusual trait values and combinations can be produced by both evolutionary isolation and evolutionarily recent adaptive radiation. We identified four functional groups of crocodylians, within which species have similar ecological roles.  Highly distinctive species, such as the gharial, fit less well into functional groups. We combined functional distinctiveness and threat ranking scores to prioritise species for conservation. The metric is termed EcoDGE (Ecologically Distinct and Globally Endangered), and we tested how well it operates to preserve crocodylian FD amongst extant Crocodylia. Under current extinction scenarios, 32-38% of crocodylian FD might be lost within 100 years. Losses increase to 48% if all threatened species go extinct, with Asia identified as a hotspot of threatened FD in crocodylians. Highly-threatened distinctive species lead this extinction scenario, exacerbated by clusters of species sharing traits linked to high extinction risk. These traits include habitat specialism and lower reproductive investment; in contrast, species that tolerate climate extremes are more resilient. Prioritising at-risk species based on functional distinctiveness and threat status appears to be an effective way to conserve present-day crocodylian diversity. Conservation prioritisation based on the EcoDGE metric performed well to minimize projected losses in FD. Among extant crocodylians, FD losses are projected when high diversity overlaps with high extrinsic threats. We then examined the utility of PD-based measures as surrogates for FD conservation, to better understand the advantages and drawbacks of such substitutions. A PD-based measure such as the EDGE metric, provided an effective tool to capture functional diversity in our tests.

Landscape conservation as a strategy for recovering biodiversity: lessons from a long-term program of pasture restoration in the southern Atlantic Forest

Although ecological restoration has entered the global agenda to reverse different anthropogenic disturbances, we still know little about how this solution interacts with other conservation strategies, to avoid the progressive loss of species and ecosystem services. Here we evaluate one of the pioneering restoration programs in the southern Brazilian Atlantic Forest, where the combination of conservation and restoration efforts have been carried out for 20 years. Specifically, we tested how landscape characteristics, restoration strategies and environmental characteristics affect the results of the restoration of pastures. We established 65 circular plots (total 4.0 ha) along restoration areas (3-10 years) and sampled trees and shrubs composing the canopy (DBH > 5cm) and understory (DBH< 5cm, height > 1.3m). We analyzed the landscape metrics (proportion of old-growth forests in 200 m, 500m and 1000m buffers around each plot; and area and distance of the nearest-neighboring old-growth forests). We explored the multiple effects of landscape, restoration strategy (reforestation, natural regeneration) and environmental variables (soil, pasture grass types) on the species composition and multiple diversity metrics of restoration areas. The species composition was very similar among restoration ages and restoration strategies. We found positive and strong effects of old-growth forest (200 m buffer) proportion on the species richness and Shannon diversity (canopy and understory), aboveground biomass (canopy) and functional diversity (understory) of restoration areas. The restoration strategies affected forest structure, and, in general, the reforestation strategy increased aboveground biomass, Shannon, functional and phylogenetic diversities (in canopy), and percentage of endemic species and biomass (understory), when compared to natural regeneration. The 20 year-experience in the southern Atlantic Forest showed that programs focused on landscape conservation associated with a mixture of restoration strategies (i.e. natural regeneration in larger areas and active restoration in more disturbed sites) , can be an efficient strategy to ensure biodiversity and ecosystem services in tropical landscapes. Synthesis and applications: To manage degraded tropical lands and achieve global targets for biodiversity and ecosystem services, it is necessary to first ensure the conservation of natural remnants and then use multiple restoration strategies in less resilient areas.

Assessing the conservation priority of freshwater lake sites based on taxonomic, functional and environmental uniqueness

Aim: We propose a novel approach that considers taxonomic uniqueness, functional uniqueness and environmental uniqueness, and show how it can be used in guiding conservation planning. We illustrate the approach using data for lake biota and environment. Location: Lake Puruvesi, Finland. Methods: We sampled macrophytes and macroinvertebrates from the same 18 littoral sites. By adapting the original 'ecological uniqueness' approach, we used distance‒based methods to calculate measures of taxonomic (LCBD‒t), functional (LCBD‒f) and environmental (LCEH) uniqueness for each site. We also considered the numbers and locations of the sites needed to protect up to 70% of total variation in taxonomic, functional or environmental features in the studied part of the lake. Results: Relationships between taxonomic (LCBD‒t), functional (LCBD‒f) and environmental (LCEH) uniqueness were generally weak, and only the relationship between macrophyte LCBD‒t and LCBD‒f was statistically significant. Overall, however, if the whole biotic dataset was considered, macroinvertebrate LCBD‒f values showed a consistent positive relationship with macrophyte LCBD‒f. Depending on the measure of site uniqueness, between one third to one half of the sites could help protect up to 70% of the ecological uniqueness of the studied part of Lake Puruvesi. Main conclusions: Although the dataset examined originated from a large lake system, the approach we proposed here can be applied in different ecosystems and at various spatial scales. An important consideration is that a set of sites has been sampled using the same methods, resulting in species and environmental matrices that can be analysed using the methodological approach proposed here. This framework can be easily applied to grid‒based data, sets of islands, or sets of forest fragments. We suggest that the approach based on taxonomic, functional and environmental uniqueness will be a useful tool in guiding nature conservation and ecosystem management, especially if associated with meta‒system ideas or network thinking.

To a charismatic rescue: Designing a blueprint to steer fishing cat conservation for safeguarding Indian wetlands

Wetland conservation in the Indo-tropics can benefit from the protection of the charismatic Fishing Cat. India, supporting ∼ 40% of its known range, is a stronghold for the species. Here, using multiple information sources we outline a framework to safeguard fishing cats in India. Specifically, we a) estimated district-level Conservation priority scores (using presence records, and habitat suitability and habitat connectivity) to identify ecologically important habitats, b) estimated state-level Conservation likelihood scores assessing the success potential of any conservation intervention, c) collated district-level Conservation initiative information identifying ongoing efforts for species and/or habitat conservation. We consecutively assessed the spatial congruence between (a), (b) and (c) to delineate species' conservation areas and corresponding action goals (blueprint). Using information on habitat suitability, we also delineated survey landscapes. Although Fishing Cat records were found in 12 Indian states, only a small proportion of the state area was identified harbouring optimal habitat for the species. Three broad habitat clusters - Terai arc, Eastern coast, and Brahmaputra floodplains - were identified, with overall high habitat connectivity. Most districts ranking high in Conservation priority scored low in Conservation likelihood. Districts with Fishing Cat presence (n = 60) were delineated into four tiers of action landscapes and the majority of districts classified as survey landscapes (n = 156) were found in the Terai arc. We use our results to recommend and discuss conservation actions for districts identified in our blueprint. Flagship species conservation approach has substantial potential to enrich wetland conservation, for which our blueprint can act as a baseline.

The GENOMES UNCOUPLED1 protein has an ancient, highly conserved role but not in retrograde signalling

The pentatricopeptide repeat protein GENOMES UNCOUPLED1 (GUN1) is required for chloroplast-to-nucleus signalling in response to plastid stress during chloroplast development in Arabidopsis thaliana but its exact molecular function remains unknown. Current data on GUN1 function is limited to Arabidopsis, so we set out to investigate the origin and evolution of the land plant GUN1 proteins. We retrieved GUN1 sequences from 76 phylogenetically diverse land plants and developed a GUN1 sequence profile using hmmbuild (<a href="http://hmmer.org/">http://hmmer.org</a>). We then used this profile to systematically analyse the presence/absence of GUN1 sequences in transcriptomes from land plants and streptophyte algae. This dataset includes the GUN1 profile we developed, the code we used to analyse the results of screening over 500,000 PPR protein sequences with the profile, and an alignment of the 893 GUN1 sequences that we obtained. We used this data to show that GUN1 is an ancient protein that is highly conserved across land plants but missing from the Rafflesiaceae that lack chloroplast genomes. Our findings suggest that GUN1 is an ancient protein that evolved within the streptophyte algal ancestors of land plants before the first plants colonised land more than 470 million years ago. This dataset also includes transcript count data from an RNA-seq experiment looking at gene expression in liverwort Marchantia polymorpha wild type and Mpgun1 mutant spore samples grown in the presence or absence of spectinomycin. We used this data to show that GUN1 does not act significantly in chloroplast retrograde signalling in the liverwort M. polymorpha. Its primary role is likely to be in chloroplast gene expression and its role in chloroplast retrograde signalling probably evolved more recently.

opencc-by-4.0Dec 2021View details →

Comparing conservation and animal welfare professionals' perspectives on domestic cat management (data and scripts)

This repository contains the final datasets and R scripts to run the analyses and create the plots in the main text of this publication.

opencc-zeroJul 2022View details →

Data from: Conservation and convergence of genetic architecture in the adaptive radiation of anolis lizards

The G matrix, which quantifies the genetic architecture of traits, is often viewed as an evolutionary constraint. However, G can evolve in response to selection and may also be viewed as a product of adaptive evolution. Convergent evolution of G in similar environments would suggest that G evolves adaptively, but it is difficult to disentangle such effects from phylogeny. Here, we use the adaptive radiation of Anolis lizards to ask whether convergence of G accompanies the repeated evolution of habitat specialists, or ecomorphs, across the Greater Antilles. We measured G in seven species representing three ecomorphs (trunk-crown, trunk-ground, and grass-bush). We found that the overall structure of G does not converge. Instead, the structure of G is well conserved and displays a phylogenetic signal consistent with Brownian motion. However, several elements of G showed signatures of convergence, indicating that some aspects of genetic architecture have been shaped by selection. Most notably, genetic correlations between limb traits and body traits were weaker in long-legged trunk-ground species, suggesting effects of recurrent selection on limb length. Our results demonstrate that common selection pressures may have subtle but consistent effects on the evolution of G, even as its overall structure remains conserved.

opencc-by-4.0Jul 2022View details →

EXAMPLE: Lattice-based equation of state tables with three conserved charges (BSQ)

These table is intended to provide an example format of the equation of state expected for the CCAKE hydrodynamic code which propagates conserved charge densities for baryon number \(B\), net strangeness \(S\), and electric charge \(Q\).  They are included primarily for demonstration purposes and no claim is made as to the accuracy of their contents.

opencc-zeroAug 2022View details →

Species as conservation umbrellas: a case study with lesser prairie-chicken (Tympanuchus pallidicinctus) in the southern Great Plains of North America

Qualitative index of conservation benefit conferred by management for the lesser prairie chicken on non-target at-risk wildlife species.

opencc-by-4.0Sep 2022View details →

Data associated with manuscript titled "Landscape predictors of Human-Leopard conflicts in and around Annapurna Conservation Area."

The data set belongs to the research conducted in Annapurna Conservation Area regarding Human Leopard Conflict (HLC).

opencc-zeroSep 2022View details →

Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana Parry) with implications for rare species conservation

Understanding the contribution of neutral and adaptive evolutionary processes to population differences is often necessary for better-informed management and conservation of rare species. In this study, we focused on Pinus torreyana Parry (Torrey pine), one of the world's rarest pines, endemic to one island and one mainland population in California. Small population size, low genetic diversity, and susceptibility to abiotic and biotic stresses suggest Torrey pine may benefit from inter-population genetic rescue to preserve the species' evolutionary potential. We leveraged reduced representation sequencing to tease apart the respective contributions of stochastic and deterministic evolutionary processes to population differentiation. We applied these data to model spatial and temporal demographic changes in effective population sizes and genetic connectivity, to assess loci possibly under selection, and to evaluate genetic rescue as a potential conservation strategy. Overall, we observed exceedingly low standing variation reflecting consistently low effective population sizes across time and limited genetic differentiation suggesting maintenance of gene flow following divergence. However, genome scans identified more than 2000 candidate SNPs for divergent selection. Combined with previous observations indicating population phenotypic differentiation, this indicates natural selection has likely contributed to the evolution of population genetic differences. Thus, while reduced genetic diversity, small effective population size, and genetic connectivity between populations suggest genetic rescue could mitigate the adverse effects of rarity, divergent selection suggests genetic mixing could disrupt adaptation. Further work evaluating the fitness consequences of inter-population admixture is necessary to empirically evaluate the trade-offs associated with genetic rescue in Torrey pine.

opencc-by-4.0Jun 2023View details →

Conservation networks do not match ecological requirements of amphibians

Supplementary files of the paper Matutini et al. 2023 (https://doi.org/10.1101/2022.07.18.500425) Dataset sample and R script

opencc-zeroSep 2022View details →

Monarch butterfly roost site variables and habitat conservation

The criteria that Monarchs use to select specific roost sites, and the landscape context where those sites are found, have received little study. We developed ecological niche models for the Atlantic Flyway roost sites using modeling algorithms, citizen scientist observations, and environmental variables that are known to affect Monarchs in the adult stage prior to migration. These models can be used to help prioritize survey and conservation efforts for Monarchs in areas most suitable for their roosting. We conducted a vulnerability assessment of predicted suitable roost habitat, assessed the connectivity of the habitat with Morphological Spatial Pattern Analysis, used Zonation software to create a relative value ranking of the Atlantic flyway region for Monarch roost site conservation, and mapped areas of high conservation value in the flyway in regards to their current predicted vulnerability.