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Figure 4 from: França RC, Morais M, França FGR, Rödder D, Solé M (2020) Snakes of the Pernambuco Endemism Center, Brazil: diversity, natural history and conservation. ZooKeys 1002: 115-158. https://doi.org/10.3897/zookeys.1002.50997

Figure 4 Snake species from the Pernambuco Endemism Center. ATantilla melanocephalaBApostolepis cearensisCApostolepis longicaudataDAtractus maculatusEAtractus potschiFBoiruna sertanejaGCaaeteboia sp. HDipsas mikaniiIDipsas neuwiediJDipsas sazimaiKDipsas variegataLErythrolamprus aesculapiiMErythrolamprus almadensisNErythrolamprus poecilogyrusOErythrolamprus reginae. Photograph credits: Frederico França (A, B, G, H, I), Anderson A. Santos (C, N), Rafaela França (D, E, J, K, L, M, O), Paulo R. S. Freitas (F).

Figure 3 from: França RC, Morais M, França FGR, Rödder D, Solé M (2020) Snakes of the Pernambuco Endemism Center, Brazil: diversity, natural history and conservation. ZooKeys 1002: 115-158. https://doi.org/10.3897/zookeys.1002.50997

Figure 3 Snake species from the Pernambuco Endemism Center. ABoa constrictorBCorallus hortulanusCEpicrates assisiDEpicrates cenchriaEChironius carinatusFChironius exoletusGChironius flavolineatus, HDendrophidion atlanticaIDrymarchon coraisJDrymoluber dichrousKLeptophis ahaetullaLPalusophis bifossatusMOxybelis aeneusNSpilotes pullatusOSpilotes sulphureus. Photograph credits: Frederico França (A, B, E, F, G, J, L, M, N, O), Vanessa Nascimento (D), Davi Pantoja (C, H, I), Rafaela França (K).

Figure 11 from: França RC, Morais M, França FGR, Rödder D, Solé M (2020) Snakes of the Pernambuco Endemism Center, Brazil: diversity, natural history and conservation. ZooKeys 1002: 115-158. https://doi.org/10.3897/zookeys.1002.50997

Figure 11 Geographic distribution records for snakes of the Pernambuco Endemism Center (PEC). AXenodon merremii and X. rabdocephalusBXenopholis scalaris and X. undulatusCMicrurus corallinus, M. ibiboboca and M. potyguaraDEpictia borapeliotesEAmerotyphlops amoipira and A. arenensisFA. brongersmianus and A. paucisquamusGBothrops bilineatus and B. erythromelasHB. leucurus and B. muriciensisICrotalus durissus and Lachesis muta.

Figure 2 from: França RC, Morais M, França FGR, Rödder D, Solé M (2020) Snakes of the Pernambuco Endemism Center, Brazil: diversity, natural history and conservation. ZooKeys 1002: 115-158. https://doi.org/10.3897/zookeys.1002.50997

Figure 2 Vegetation physiognomies found in the Pernambuco Endemism Center. A forest B forest interior C Coastal Restingas D mangroves, E tabuleiros F Brejos Nordestinos. Photograph credits: Ivan L. Sampaio, in the Barra de Gramame (A), Frederico França, in the APA da Barra do Rio Mamanguape (B, C), Marcelo Melo, in the APA da Barra do Rio Mamanguape (D), Frederico França, in the Reserva Biológica Guaribas (E) and Adonias Teixeira, in the Parque Estadual Mata do Pau-Ferro (F).

Figure 10 from: França RC, Morais M, França FGR, Rödder D, Solé M (2020) Snakes of the Pernambuco Endemism Center, Brazil: diversity, natural history and conservation. ZooKeys 1002: 115-158. https://doi.org/10.3897/zookeys.1002.50997

Figure 10 Geographic distribution records for snakes of the Pernambuco Endemism Center (PEC). AHydrodynastes gigas and Lygophis dilepisBImantodes cenchoa and Leptodeira annulataCOxyrhopus guibei and O. petolariusDO. trigeminusEPhilodryas nattereri, P. olfersii and P. patagoniensisFPhimophis guerini and Pseudoboa nigraGPsomophis joberti, Sibon nebulatus and Siphlophis compressusHTaeniophallus affinis and T. occipitalisIThamnodynastes almae, T. hypoconia, T. pallidus and T. phoenix.

Figure 1 from: França RC, Morais M, França FGR, Rödder D, Solé M (2020) Snakes of the Pernambuco Endemism Center, Brazil: diversity, natural history and conservation. ZooKeys 1002: 115-158. https://doi.org/10.3897/zookeys.1002.50997

Figure 1 Map of the location of the Pernambuco Endemism Center, with the original coverage of Atlantic Forest (gray), and the actual remnants (green).

Figure 6 from: França RC, Morais M, França FGR, Rödder D, Solé M (2020) Snakes of the Pernambuco Endemism Center, Brazil: diversity, natural history and conservation. ZooKeys 1002: 115-158. https://doi.org/10.3897/zookeys.1002.50997

Figure 6 Snake species from the Pernambuco Endemism Center. APseudoboa nigraBPsomophis joberti, CSibon nebulatusDSiphlophis compressusETaeniophallus affinisFTaeniophallus occipitalisGThamnodynastes almaeHThamnodynastes hypoconiaIThamnodynastes pallidusJThamnodynastes phoenixKXenodon merremiiLXenodon rabdocephalusMXenopholis scalarisNXenopholis undulatusOMicrurus corallinus. Photograph credits: Frederico França (A, B, C, D, F, H, K, N), Vanessa Nascimento (L), Samuel Cardoso (G), Davi Pantoja (M), Rafaela França (I), Anderson A. Santos (E), Paulo R. S. Freitas (J), Adrian Garda (O).

Figure 8 from: França RC, Morais M, França FGR, Rödder D, Solé M (2020) Snakes of the Pernambuco Endemism Center, Brazil: diversity, natural history and conservation. ZooKeys 1002: 115-158. https://doi.org/10.3897/zookeys.1002.50997

Figure 8 Geographic distribution records for snakes of the Pernambuco Endemism Center (PEC). ALiotyphlops trefautiBBoa constrictor and Corallus hortulanusCEpicrates cenchria and E. assisiDChironius carinatus and C. exoletusEChironius flavolineatus and Dendrophidion atlanticaFDrymarchon corais and Drymoluber dichrousGLeptophis ahaetulla and Palusophis bifossatusHOxybelis aeneus and Tantilla melanocephalaISpilotes sulphureus and S. pullatus.

Figure 7 from: França RC, Morais M, França FGR, Rödder D, Solé M (2020) Snakes of the Pernambuco Endemism Center, Brazil: diversity, natural history and conservation. ZooKeys 1002: 115-158. https://doi.org/10.3897/zookeys.1002.50997

Figure 7 Snake species from the Pernambuco Endemism Center. AMicrurus ibibobocaBMicrurus potyguaraCEpictia borapeliotesDAmerotyphlops arenensisEAmerotyphlops brongersmianusFAmerotyphlops paucisquamusGBothrops bilineatusHBothrops erythromelasIBothrops leucurusJBothrops muriciensisKCrotalus durissusLLachesis muta. Photograph credits: Frederico França (A, B, E, F, H, I, K, L), Ivan L. Sampaio (C), Gentil A. Pereira Filho (D), Willianilson Pessoa (J), Rafaela França (G).

Identifying conservation priorities in a defaunated tropical biodiversity hotspot

Aim: Unsustainable hunting is leading to widespread defaunation across the tropics. To mitigate against this threat with limited conservation resources, stakeholders must make decisions on where to focus anti-poaching activities. Identifying priority areas in a robust way allows decision-makers to target areas of conservation importance, therefore maximizing the impact of conservation interventions. Location: Annamite mountains, Vietnam and Laos. Methods: We conducted systematic landscape-scale surveys across five study sites (four protected areas, one unprotected area) using camera-trapping and leech-derived environmental DNA. We analyzed detections within a Bayesian multi-species occupancy framework to evaluate species responses to environmental and anthropogenic influences. Species responses were then used to predict occurrence to unsampled regions. We used predicted species richness maps and occurrence of endemic species to identify areas of conservation importance for targeted conservation interventions. Results: Analyses showed that habitat-based covariates were uninformative. Our final model therefore incorporated three anthropogenic covariates as well as elevation, which reflects both ecological and anthropogenic factors. Conservation-priority species tended to found in areas that are more remote now or have been less accessible in the past, and at higher elevations. Predicted species richness was low and broadly similar across the sites, but slightly higher in the more remote site. Occupancy of the three endemic species showed a similar trend. Main conclusion: Identifying spatial patterns of biodiversity in heavily-defaunated landscapes may require novel methodological and analytical approaches. Our results indicate to build robust prediction maps it is beneficial to sample over large spatial scales, use multiple detection methods to increase detections for rare species, include anthropogenic covariates that capture different aspects of hunting pressure, and analyze data within a Bayesian multi-species framework. Our models further suggest that more remote areas should be prioritized for anti-poaching efforts to prevent the loss of rare and endemic species.

Supplementary material 3 from: Demant L, Bergmeier E, Walentowski H, Meyer P (2020) Suitability of contract-based nature conservation in privately-owned forests in Germany. Nature Conservation 42: 89-112. https://doi.org/10.3897/natureconservation.42.58173

Table S3

Supplementary material 1 from: Demant L, Bergmeier E, Walentowski H, Meyer P (2020) Suitability of contract-based nature conservation in privately-owned forests in Germany. Nature Conservation 42: 89-112. https://doi.org/10.3897/natureconservation.42.58173

Table S1

Supplementary material 2 from: Demant L, Bergmeier E, Walentowski H, Meyer P (2020) Suitability of contract-based nature conservation in privately-owned forests in Germany. Nature Conservation 42: 89-112. https://doi.org/10.3897/natureconservation.42.58173

Table S2

Data from: Loss of sweet taste despite the conservation of sweet receptor genes in insectivorous bats

The evolution of taste perception is usually associated with the ecology and dietary changes of organisms. However, mismatches between feeding ecology and taste receptor evolution have been identified in some vertebrate animals. One example is the sweet taste receptor gene Tas1r2. Previous analysis of partial sequences has revealed that Tas1r2 has undergone equally strong purifying selection between insectivorous and frugivorous bats. To test whether the sweet taste function is also important in bats with contrasting diets, we examined the complete coding sequences of both sweet taste receptor genes (Tas1r2 and Tas1r3) in 34 representative bat species. Although these two genes are highly conserved between frugivorous and insectivorous bats at the sequence level, our behavioral experiments revealed that an insectivorous bat (Myotis ricketti) showed no preference for natural sugars, whereas the frugivorous species (Rousettus leschenaultii) showed strong preferences for sucrose and fructose. Furthermore, while both sweet taste receptor genes are expressed in the taste tissue of insectivorous and frugivorous bats, our cell-based assays revealed striking functional divergence: the sweet taste receptors of frugivorous bats are able to respond to natural sugars whereas those of insectivorous bats are not, which is consistent with the behavioral preference tests, suggesting that functional evolution of sweet taste receptors is closely related to diet. This comprehensive study suggests that using sequence conservation alone could be misleading in inferring protein and physiological function, and highlights the power of combining behavioral experiments, expression analysis, and functional assays in molecular evolutionary studies.

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FIGURE 1 in Nomenclatural changes and two new species in the leafhopper genus Usanus DeLong (Hemiptera: Cicadellidae) with notes on conservation status

FIGURE 1. Distribution of the endemic Athysanini leafhopper genus Usanus DeLong in Mexico.

Field evidence reveals conservative water use of poplars under high aerosol conditions in Beijing

<ol> <li>Anthropogenic aerosols could alter multiple meteorological processes such as radiation regime and air temperature, thereby modifying plant transpiration. However, the lack of field observations at the leaf- and plant-level hinders our ability to understand how aerosols could affect plant water use. </li> <li>Aerosol concentrations in northern China fluctuates periodically over a wide range<a name="_Hlk47963537">.</a> Taking advantage of this unique natural experiment opportunity, we conducted a full series of supporting physiological and environmental measurements to explore aerosols' effect on leaf transpiration and sap flow in the field using poplar trees (Populus × canadensis Moench).</li> <li>We found that high aerosol concentrations suppressed sun-leaf transpiration by reducing leaf-to-air vapor pressure deficit (VPDleaf) while not affecting shade-leaf transpiration, mainly because the negative effect of reduced VPDleaf on transpiration offset the positive effects of the increased stomatal conductance (gs). As aerosol concentration increases, the gs of both sun and shade leaves decreased more rapidly with an increase in VPDleaf, which caused their transpiration rates to become less sensitive to VPDleaf. Similarly, aerosols reduced sap flow density and its sensitivity to VPD. </li> <li>Synthesis. Our study provided observational evidence on aerosols' effects on plant transpiration at the leaf and canopy scales. The reduced transpiration and stronger stomatal control indicated that plant water use becomes more conservative under elevated aerosol concentrations.</li> </ol>

Data from: Conserving the genetic diversity of condemned populations: optimizing collections and translocation

We generated SNP genotype data from two endangered plant species, Pimelea spicata and Eucalyptus sp. Cattai. For each, we genotyped plants from a population that was 'condemned,' or that would soon be destoyed. We used the genotype data to design ex situ germplasm collections that preserved the diversity in the condemned populations, in ways that were optimized. Here, we provide an archive of these SNP genotype data, and the code that was used to analyse these data, including the optimizations.

Evolution of conserved noncoding sequences in Arabidopsis thaliana

Recent pangenome studies have revealed that a large fraction (>20%) of the gene content within a species exhibits presence-absence variation (PAV). However, coding regions alone provide an incomplete assessment of functional genomic sequence variation at the species level. Little to no attention has been paid to noncoding regulatory regions in pangenome studies, though these sequences directly modulate gene expression and phenotype. To uncover regulatory genetic variation, we generated chromosome-scale genome assemblies for thirty Arabidopsis thaliana accessions from multiple distinct habitats and characterized species level variation in Conserved Noncoding Sequences (CNS). Our analyses uncovered not only evidence for PAV and Positional Variation (PosV) but that diversity in CNS is non-random, with variants shared across different accessions. Using evolutionary analyses and chromatin accessibility data, we provide further evidence supporting conserved and variable CNS roles in gene regulation. Characterizing species-level diversity in all functional genomic sequences may later uncover previously unknown mechanistic links between genotype and phenotype.

Supplementary material 3 from: Manjarrés-Hernández A, Guisande C, García-Roselló E, Heine J, Pelayo-Villamil P, Pérez-Costas E, González-Vilas L, González-Dacosta J, R. Duque S, Granado-Lorencio C, Lobo JM (2021) Predicting the effects of climate change on future freshwater fish diversity at global scale. Nature Conservation 43: 1-24. https://doi.org/10.3897/natureconservation.43.58997

Appendix 2

Supplementary material 4 from: Manjarrés-Hernández A, Guisande C, García-Roselló E, Heine J, Pelayo-Villamil P, Pérez-Costas E, González-Vilas L, González-Dacosta J, R. Duque S, Granado-Lorencio C, Lobo JM (2021) Predicting the effects of climate change on future freshwater fish diversity at global scale. Nature Conservation 43: 1-24. https://doi.org/10.3897/natureconservation.43.58997

Appendix 3