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opennotspecifiedSep 2014View details →

FIG. 5 in Current status of the Crocodile Lizard Shinisaurus crocodilurus Ahl, 1930 in Vietnam with implications for conservation measures

FIG. 5 Slash and burn practices in Tay Yen Tu NR, Vietnam. (A) example of forest fire; (B) burned area cleared for agricultural purposes or exploration by the paper industry. Photos: M. Bernardes & M. van Schingen.

opennotspecifiedSep 2014View details →

FIG. 1 in Current status of the Crocodile Lizard Shinisaurus crocodilurus Ahl, 1930 in Vietnam with implications for conservation measures

FIG. 1 Shinisaurus crocodilurus in its natural habitat in Tay Yen Tu NR, Vietnam. Photo: M. van Schingen.

opennotspecifiedSep 2014View details →

FIG. 4 in Current status of the Crocodile Lizard Shinisaurus crocodilurus Ahl, 1930 in Vietnam with implications for conservation measures

FIG. 4 Distribution of different age classes of S. crocodilurus in Vietnam. (A) Frequency of observed juveniles, subadults and adults from three nature reserves, p <0.001; (B) Frequency shift (of juveniles, subadults and adults) in Tay Yen Tu NR between 2010 and 2013, p <0.05.

opencc-zeroJan 2022View details →

Conspecific attraction for conservation and management of terrestrial breeding birds: current knowledge and future research directions

Conspecific presence can indicate the location or quality of resources, and animals settling near conspecifics often gain fitness benefits. This can result in adaptive conspecific attraction during breeding habitat selection as demonstrated in numerous terrestrial, territorial birds. There is growing interest in using simulated conspecific social cues (e.g., decoys, broadcasted vocalizations) to manage bird distributions, yet it remains unclear when this approach is likely to succeed. We reviewed published studies to evaluate whether the strength of conspecific attraction in terrestrial birds is mediated by characteristics of species (life history traits), simulated cues (e.g., timing and duration), sites (e.g., quality), and how conspecific attraction was measured. We identified 31 experiments that simulated social cues and compared conspecific settlement between treatment and control sites. We then used phylogenetically controlled meta-regression to assess impacts of 19 moderators on settlement. Nearly all species included in these experiments were migratory passerines, and social cues generally had a strong, positive influence on their settlement decisions, as the odds of site occupancy were 3.12× (95% CI = 0.81, 11.69) greater in treatment sites relative to control sites. Within this group, conspecific attraction was evolutionarily conserved with ≥ 25.5% (CI = 5.1%, 65.4%) of the variance in treatment effects explained by phylogenetic relatedness. However, we found no evidence that any covariates influenced the response to social cues, and we posit this stems from limited research specifically designed to identify the mechanisms mediating conspecific attraction. We therefore developed a research agenda that provides a framework for testing mechanistic hypotheses regarding how cue characteristics, species traits, and spatial contexts may mediate attraction to conspecifics. Evaluating these hypotheses will greatly advance the field by helping managers understand when, where, and why simulating social cues can be used to enhance populations of species that are of conservation concern.

opencc-zeroDec 2021View details →

Collaboration for conservation: assessing country-wide carnivore occupancy dynamics from sparse data

Aim: Assessing the distribution and persistence of species across their range is a crucial component of wildlife conservation. It demands data at adequate spatial scales and over extended periods of time, which may only be obtained through collaborative efforts, and the development of methods that integrate heterogeneous datasets. We aimed to combine existing data on large carnivores to evaluate population dynamics and improve knowledge on their distribution nationwide. Location: Botswana Methods: Between 2010 – 2016, we collated data on African wild dog, cheetah, leopard, brown and spotted hyaena, and lion gathered with different survey methods by independent researchers across Botswana. We used a multi-species, multi-method dynamic occupancy model to analyse factors influencing occupancy, persistence, and colonisation, while accounting for imperfect detection. Lastly, we used the gained knowledge to predict the probability of occurrence of each species countrywide. Results: Wildlife areas and communal rangelands had similar occupancy probabilities for most species. Large carnivore occupancy was low in commercial farming areas and where livestock density was high, except for brown hyaena. Lion occupancy was negatively associated with human density; lion and spotted hyena occupancy was high where rainfall was high, while the opposite applied to brown hyaena. Lion and leopard occupancy remained constant countrywide over the study period. African wild dog and cheetah occupancy declined over time in the south and north, respectively, whereas both hyaena species expanded their ranges. Countrywide predictions identified the highest occupancy for leopards and lowest for the two hyaena species. Main Conclusions: We highlight the necessity of data sharing and propose a generalisable analytical method that addresses the challenges of heterogeneous data common in ecology. Our approach, which enables a comprehensive multi-species assessment at large spatial and temporal scales, supports the development of data-driven conservation guidelines and the implementation of evidence-based management strategies nationally and internationally.

opencc-zeroFeb 2022View details →

Taxonomy based on limited genomic markers may underestimates species diversity of rockhopper penguins and threaten their conservation

Delimiting recently diverged species is challenging. During speciation, genetic differentiation may be distributed unevenly across the genome, as different genomic regions can be subject to different selective pressures and evolutionary histories. Reliance on limited numbers of genetic markers that may be underpowered can make species delimitation even more challenging, potentially resulting in taxonomic inconsistencies. Rockhopper penguins of the genus Eudyptes comprise three broadly recognized taxa: northern (E. moseleyi), southern (E. chrysocome), and eastern rockhopper (E. filholi). Their taxonomic status has been controversial for decades, with researchers disagreeing about whether E. chrysocome and E. filholiare distinct species or conspecific. Our goal is to evaluate genome-wide patterns of divergence to evaluate genetic differentiation and species delimitation in rockhopper penguins, and to assess which mechanisms may underlie previous discordance among nuclear versus mitochondrial analyses. We generated reduced-representation genomic libraries using Double Digest Restriction-site Associated DNA (ddRAD) sequencing to evaluate genetic differentiation, contemporary migration rates and admixture among colonies of rockhopper penguins. The extent of genetic differentiation among the three taxa was consistently higher than population-level genetic differentiation found within these and other penguin species. There was no evidence of admixture among the three taxa, suggesting the absence of ongoing gene flow among them. Species delimitation analyses based on molecular data, along with other lines of evidence, provide strong support for the taxonomic distinction of three species of rockhopper penguins. Our results provide strong support for the existence of three distinct species of rockhopper penguins. The recognition of this taxonomic diversity is crucial for the management and conservation of this widely distributed species group. This study illustrates that widespread dispersive seabird lineages lacking obvious morphological differences may nevertheless have complex evolutionary histories and comprise cryptic species diversity.

FIGURE 1 in Description of three new Boulenophrys species from eastern Guangdong, China, emphasizing the urgency of ecological conservation in this region (Anura, Megophryidae)

FIGURE 1. Map showing the known distribution sites of Boulenophrys species in eastern Guangdong, China.

FIGURE 4 in Description of three new Boulenophrys species from eastern Guangdong, China, emphasizing the urgency of ecological conservation in this region (Anura, Megophryidae)

FIGURE 4. The paratypes of Boulenophrys puningensis sp. nov. in life. A–B: male paratype, SYS a007649; C–D: female paratype, SYS a007647; E–F: female paratype, SYS a007648.

FIGURE 2 in Description of three new Boulenophrys species from eastern Guangdong, China, emphasizing the urgency of ecological conservation in this region (Anura, Megophryidae)

FIGURE 2. ML tree based on the partial DNA sequences of the mitochondrial 16S rRNA and COI genes, with Bootstrap Support (BS) / Posterior Probabilities (PP) at nodes. '-' means BS <70 or PP <90.

opencc-by-4.0Jan 2022View details →

The benefits of coastal adaptation through conservation of foreshore vegetation Supplementary data

This data consists of the first global scale assessment of the benefits of conserving foreshore vegetation as a means of adaptation to future projections of change in coastal flood risk. In doing so, we extend the current knowledge on the economic feasibility of implementing global scale Nature-based Solutions. We show that globally foreshore vegetation can contribute to a large decrease in both absolute and relative flood risk (13% of present-day, and 8.5% of future conditions in 2080 of global flood risk). Although the analysis of the results give a first proxy of the flood risk reduction benefits of conserving foreshore vegetation at the global scale, it shows promising results for including nature-based and hybrid adaptation measures in coastal adaptation schemes.

opencc-zeroFeb 2022View details →

Conserving on the edge: genetic variation and structure in northern populations of the endangered plant Dracocephalum ruyschiana L. (Lamiaceae)

Loss of biodiversity is accelerating, including the loss of genetic diversity. Conservation of small, isolated populations may be important, as they can provide valuable contributions to overall genetic variation and long-term viability of species. Furthermore, such populations may play an essential role in adaptation to new environments following changes in e.g. land-use and climate. Dracocephalum ruyschiana is a threatened plant species throughout its European distribution, but 25% of the European populations are situated within Norway. Therefore, the species has its own action plan in Norway, which includes demographic monitoring. However, this monitoring does not cover genetic variation nor is the selection of monitored populations based on genetic differentiation, therefore this fundamental level of biodiversity is overlooked. We analyzed 43 sites using 96 SNPs developed for D. ruyschiana, to investigate whether the monitored populations cover the genetic variation and differentiation found within the Norwegian distribution. The results show structuring and differentiation between populations and indicate that there are at least four distinct genetic groups, of which only two are covered extensively by current demographic monitoring. We suggest that two sites representing the two other genetic groups should be included in the national monitoring program to better conserve the genetic variation found in the Norwegian population of D. ruyschiana. Overall, our results highlight the importance of an integrated, interdisciplinary framework to better monitor and conserve biodiversity at several levels.

opencc-by-4.0Feb 2022View details →

Assessing taxonomic, functional, and phylogenetic diversity of giant clams across the Indo-Pacific for conservation prioritisation

Datasets and R scripts

opencc-by-4.0Mar 2022View details →

Biogenesis, conservation and function of miRNA in liverworts

Recent findings on liverwort micro RNA repertoire, Marchantia miRNA gene organization, biogenesis, functions, and microprocessor, auxiliary, and regulatory proteins involved in miRNA biogenesis

FIGURE 5 in Astragalus nigriceps (Fabaceae, Papilionoideae): an emended description with new data on distribution and conservation status

FIGURE 5. Distribution maps of Astragalus nigriceps. A) Geographical position of the study area in Central Kopet Dagh Mountains; B) Distribution map of the collected specimens around Iran-Turkmenistan borders; C) GeoCAT distribution map of the species, and estimation of Extent of Occurrence (EOO) and Area of Occupancy (AOO), with maximum distance of 70 km between pairs of points, based on IUCN Red List Criteria.

FIGURE 4 in Astragalus nigriceps (Fabaceae, Papilionoideae): an emended description with new data on distribution and conservation status

FIGURE 4. Some details of morphological characters in Astragalus nigriceps. A) Racemes, covered by black and white hairs; B) Petals (standard, keel, and wings); C) Stipule, covered by black hairs; D) Various hairs on calyx tube and teeth; E) Fruiting stage with legumes. Scale bars: A–B, and E=10 mm; C–D=1 mm. Herbarium specimens: A–D: Joharchi & Memariani 46837-FUMH; E: Joharchi & Ghahremaninejad 34738-b-FUMH.

FIGURE 3 in Astragalus nigriceps (Fabaceae, Papilionoideae): an emended description with new data on distribution and conservation status

FIGURE 3. Astragalus nigriceps in its natural habitat. A) Aselmeh Mountains in NE Iran, where newly discovered populations of A. nigriceps are found on mountain slopes with open Juniperus polycarpos var. turcomanica woodlands; B) Habit; C) Inflorescence; D) Close-up view of the flowers.

opennotspecifiedJan 2022View details →

Figure 1 in Filling Linnean shortfalls increases endemicity patterns: conservation and biogeographical implications for the extreme case of Liolaemus (Liolaemidae, Squamata) species

Figure 1. Distribution of L. dorbignyi in 2000 (left) and the current (2020) distribution of L. dorbignyi, L. huayra, L. inti, L. scrocchii and L. vulcanus, species that were all considered populations of L. dorbignyi in 2000 (right).

opennotspecifiedJan 2022View details →

Figure 3 in Filling Linnean shortfalls increases endemicity patterns: conservation and biogeographical implications for the extreme case of Liolaemus (Liolaemidae, Squamata) species

Figure 3. Species composition and extent of occurrence within the 11 well-studied species clades of Liolaemus, across the three studied periods (1980, 2000 and 2020). Coloured circles indicate the extent of occurrence of each species based on the thresholds of B1criteria of IUCN (green <20 000 km2 = LC/NT; yellow <5000 km2 = VU; orange <500 km2 = EN; red> 500 km2 = CR). Pie charts show the proportion of the studied species for each period corresponding to each conservation status based on the B1 criteria of IUCN.

opencc-by-4.0Mar 2022View details →

Taxonomic revision of Chinemys pani (Testudines: Geoemydidae) from the Pleistocene of Taiwan and its implications of conservation paleobiology

Proper taxonomic identification is critical to our understanding of biodiversity and the underlying evolutionary history. Here we re-examine the cast of the holotype of Chinemys pani, a geoemydid turtle from the Pleistocene of Taiwan; the actual specimen was not curated appropriately after the original publication and was most likely lost. Our results provide substantial evidence to show that Chinemys panishould be identified as Mauremys reevesii. The replica, though not ideal, preserves various morphological features that allow reliable taxonomic identification to Mauremys reevesii, including the presence of three longitudinal keels on the carapace, the second to sixth neural bones anteriorly short-sided, the lack of movable plastral hinge. In addition, we also confirm that the original diagnostic features that established the new taxon: Chinemys pani– are polymorphic characters of Mauremys reevesii. Our taxonomic revision of a Pleistocene geoemydid turtle from Taiwan resolves the debate on whether Mauremys reevesiishould be a native turtle in Taiwan instead of an introduced invasive species. More importantly, this study offers new insights into the origin of modern biodiversity in Taiwan and gives a straightforward example of how fossils can be applied to conservation policies.Proper taxonomic identification is critical to our understanding of biodiversity and the underlying evolutionary history. Here we re-examine the cast of the holotype of Chinemys pani, a geoemydid turtle from the Pleistocene of Taiwan; the actual specimen was not curated appropriately after the original publication and was most likely lost. Our results provide substantial evidence to show that Chinemys panishould be identified as Mauremys reevesii. The replica, though not ideal, preserves various morphological features that allow reliable taxonomic identification to Mauremys reevesii, including the presence of three longitudinal keels on the carapace, the second to sixth neural bones anteriorly short-sided, the lack of movable plastral hinge. In addition, we also confirm that the original diagnostic features that established the new taxon: Chinemys pani– are polymorphic characters of Mauremys reevesii. Our taxonomic revision of a Pleistocene geoemydid turtle from Taiwan resolves the debate on whether Mauremys reevesiishould be a native turtle in Taiwan instead of an introduced invasive species. More importantly, this study offers new insights into the origin of modern biodiversity in Taiwan and gives a straightforward example of how fossils can be applied to conservation policies.