Modelos de distribución de especies y estado de conservación de murciélagos amenazados en la región tumbesina de Ecuador y Perú / Species distribution models and conservation status of threatened bats in the Tumbesian region of Ecuador and Perú

Resumen Introducción: La biodiversidad se está perdiendo a un ritmo acelerado como resultado del cambio global. Herramientas como los modelos de distribución de especies (MDEs) han sido ampliamente usados para mejorar el conocimiento sobre el estado de conservación de las especies y ayudar a desarrollar estrategias de gestión para mitigar la pérdida de biodiversidad. Objetivo: Determinar cómo la distribución potencial predicha por los MDEs para ocho especies de murciélagos amenazados difiere de los mapas de distribución reportados por la UICN. También, inferir el área de distribución y estado de endemismo de cada especie, y evaluar la importancia de la región tumbesina para su conservación. Métodos: Basados en registros de presencia del rango global de las especies, usamos MDEs para evaluar el estado de conservación de estas ocho especies en la región tumbesina de Ecuador y Perú. Resultados: Las áreas estimadas por los MDEs eran 35-78 % más pequeñas para cuatro especies (Eptesicus innoxius, Lophostoma occidentale, Platalina genovensium y Lonchophylla hesperia) y 26-1 600 % más grandes para tres especies (Amorphochilus schnablii, Promops davisoni y Rhogeessa velilla) que aquellas reportadas por la UICN. Para Tomopeas ravus, el área estimada por el MDE y la UICN fue similar, pero difirió en la distribución espacial. Los MDEs coincidieron con áreas de endemismo informadas por autores previos para E. innoxius, R. velilla y T. ravus, pero fueron diferentes para A. schnablii, P. genovensium, P. davisoni y L. hesperia, debido en parte a las distribuciones proyectadas para estas últimas especies en valles secos interandinos según los MDEs. Conclusiones: La región tumbesina representa una porción significativa (40-96 %) de la distribución predicha de siete de las ocho especies estudiadas, subrayando la importancia de esta región para la conservación de murciélagos. Nuestros resultados muestran las probables distribuciones para estas especies y proporcionan una base importante para identificar vacíos de investigación y desarrollar medidas de conservación para murciélagos amenazados en el punto caliente de biodiversidad de Tumbes.

Abstract Introduction: Biodiversity is being lost at an accelerating rate because of global change. Tools such as species distribution models (SDMs) have been widely used to improve knowledge about species' conservation status and help develop management strategies to mitigate biodiversity loss. SDMs are especially important for species with restricted distributions, such as endemic species. Objective: To determine how potential distribution predicted by SDMs for eight threatened bat species differed from the distribution maps reported by the IUCN. Also, to infer the area of distribution and state of endemism of each specie, and to evaluate the importance of the Tumbesian region for their conservation. Methods: Based on presence records across the species' entire ranges, we used SDMs to assess the conservation status of these eight species in the Tumbesian region of Ecuador and Peru. Results: The areas estimated by SDMs were 35-78 % smaller for four species (Eptesicus innoxius, Lophostoma occidentale, Platalina genovensium and Lonchophylla hesperia) and 26-1 600 % larger for three species (Amorphochilus schnablii, Promops davisoni and Rhogeessa velilla) than those reported by the IUCN. For Tomopeas ravus, the area estimated by the SDM and IUCN was similar but differed in spatial distribution. SDMs coincided with areas of endemism reported by previous authors for E. innoxius, R. velilla, and T. ravus, but were different for A. schnablii, P. genovensium, P. davisoni, and L. hesperia, due in part to projected distributions for these latter species in dry inter-Andean valleys according to the SDMs. Conclusions: The Tumbesian region represents a significant portion (40-96 %) of the predicted distribution of seven of the eight species studied, underscoring the importance of this region for bat conservation. Our results show likely distributions for these species and provide an important basis for identifying research gaps and developing conservation measures for threatened bats in the Tumbes biodiversity hotspot.

Investigating the reproductive strategies of Deuterocohnia meziana (Bromeliaceae), an endangered and restricted species from South American rocky outcrops.

Studies of reproductive biology and resources availability to floral visitors by plant species are important to understand the plant-pollinator interactions that drive species adaptation. We aim to understand the relationship between reproduction mechanisms of Deuterocohnia meziana (Bromeliaceae) and pollinators. The species occurs in Bolivia and Paraguay, and it is the only species of the genus found in Brazil, where it is restricted to ironstone outcrops. These areas are currently threatened by the iron mining industry. Additionally, they face risks from fire occurrence and grazing by cattle. We analyzed the floral biology, reproductive system, phenology, and pollination ecology of a natural population of Deuterocohnia meziana, from ironstone outcrops in Brazil. The species exhibits diurnal anthesis, with stigma receptive throughout anthesis, and 77% of pollen viability. Deuterocohnia meziana produces relatively large amounts of nectar, especially early in the morning (32.8 ± 9.4 µl), with a mean sugar concentration of 23.5 (± 3.2) ºBrix. It is self-incompatible with a peak flowering occurring in August (dry season), although flowers are observed continuously throughout the year. The species exhibits two types of inflorescences, young and mature, among which an average of 13.1 and 3.6 flowers open per day, respectively. Hummingbirds and bees are the effective pollinators, although butterflies and ants also visit D. meziana flowers. The species is reliant on exogenous pollen and pollinators for fruit set. The continuous conservation of D. meziana populations and their communities is essential for preserving plant-pollinator mutualism and the floral community adapted to ironstone outcrops.

Rangewide occupancy of a flagship species, the Coastal California Gnatcatcher (Polioptila californica californica) in southern California: Habitat associations and recovery from wildfire.

The Coastal California Gnatcatcher (Polioptila californica californica), a federally threatened species, is a flagship species for regional conservation planning in southern California (USA). An inhabitant of coastal sage scrub vegetation, the gnatcatcher has declined in response to habitat loss and fragmentation, exacerbated by catastrophic wildfires. We documented the status of gnatcatchers throughout their California range and examined post-fire recovery of gnatcatchers and their habitat. We used GIS to develop a habitat suitability model for Coastal California Gnatcatchers using climate and topography covariates and selected over 700 sampling points in a spatially balanced manner. Bird and vegetation data were collected at each point between March and May in 2015 and 2016. Presence/absence of gnatcatchers was determined during three visits to points, using area searches within 150 x 150 m plots. We used an occupancy framework to generate Percent Area Occupied (PAO) by gnatcatchers, and analyzed PAO as a function of time since fire. At the regional scale in 2016, 23% of the points surveyed were occupied by gnatcatchers, reflecting the effect of massive wildfires in the last 15 years. Similarly, PAO in the post-fire subset of points was 24%, with the highest occupancy in unburned (last fire <2002) habitat. Positive predictors of occupancy included percent cover of California sagebrush (Artemisia californica), California buckwheat (Eriogonom fasciculatum), and sunflowers (Encelia spp., Bahiopsis laciniata), while negative predictors included laurel sumac (Malosma laurina) and total herbaceous cover; in particular, non-native grasses. Our findings indicate that recovery from wildfire may take decades, and provide information to speed up recovery through habitat restoration.

In Vitro Propagation of Threatened Agave Species Using a Two-Stage System.

Agaves are plants with multiple possibilities of use and are naturally tolerant to low water availability conditions and high temperatures. This makes them species of great interest in the context of the necessary substitution of crops due to climate change. Unfortunately, the overexploitation of wild specimens has endangered many species of the genus that have not been domesticated or cultivated intensively. In vitro mass culture and propagation techniques have emerged as a very efficient option to produce agave plants that can be used without damage to the natural populations. A protocol is presented here for the in vitro micropropagation of agaves in a two-stage process. In the first step, clusters of slightly differentiated shoots are generated from stem segments cultivated on a semisolid medium added with cytokinin. In a second step, these shoot clusters are cultured in temporary immersion bioreactors where they grow and complete their differentiation, and then the shoots are rooted and transferred to soil. This protocol has been successfully applied to several threatened species of the Agave genus.

A high-quality chromosome-level genome assembly of the endangered tree Kmeria septentrionalis.

Kmeria septentrionalis is a critically endangered tree endemic to Guangxi, China, and is listed on the International Union for Conservation of Nature's Red List. The lack of genetic information and high-quality genome data has hindered conservation efforts and studies on this species. In this study, we present a chromosome-level genome assembly of K. septentrionalis. The genome was initially assembled to be 2.57 Gb, with a contig N50 of 11.93 Mb. Hi-C guided genome assembly allowed us to anchor 98.83% of the total length of the initial contigs onto 19 pseudochromosomes, resulting in a scaffold N50 of 135.08 Mb. The final chromosome-level genome, spaning 2.54 Gb, achieved a BUSCO completeness of 98.9% and contained 1.67 Gb repetitive elements and 35,927 coding genes. This high-quality genome assembly provides a valuable resource for understanding the genetic basis of conservation-related traits and biological properties of this endangered tree species. Furthermore, it lays a critical foundation for evolutionary studies within the Magnoliaceae family.

Southern marsh deer (Blastocerus dichotomus) populations assessed using Amplicon Sequencing on fecal samples.

Populations in isolated and small fragments lose genetic variability very fast and are usually of conservation concern because they are at greater risk of local extinction. The largest native deer in South America, Blastocerus dichotomus (Illiger, 1815), is a Vulnerable species according to the IUCN categorization, which inhabits tropical and subtropical swampy areas. In Argentina, its presence has been restricted to four isolated fragments. Here we examine the genetic diversity and differentiation among three of them, including the three different patches that form the southernmost population, using 18 microsatellite markers genotyped by Amplicon Sequencing of DNA extracted from fecal samples. Genetic diversity was low (HE < 0.45) in all three populations studied. We found three genetic clusters compatible with the geographic location of the samples. We also found a metapopulation dynamics that involves the patches that make up the southernmost population, with evidence of a barrier to gene flow between two of them. Our results point to the creation of a corridor as a necessary and urgent management action. This is the first study, at the population level, employing microsatellite genotyping by Amplicon Sequencing with non-invasive samples in an endangered species.

Habitat occupancy of the threatened Diademed Plover (Phegornis mitchellii) is not affected by llama grazing or peatland size, but declines with peatland humidity.

Many habitat-specialist organisms occur in distinct, patchy habitat, yet do not occupy all patches, and an important question is why apparently suitable habitat remains unoccupied. We examined factors influencing patch occupancy in near-threatened, little-known Diademed Plovers (Phegornis mitchellii), arguably the bird most specialized to life in High Andean peatlands. Andean peatlands are well-suited to occupancy modelling because they are discrete patches of humid habitat within a matrix of high-altitude steppe. We hypothesized that Diademed Plovers occupy preferably larger and more humid peatlands, and avoid peatlands used for grazing by llamas and vicuñas, which may trample vegetation and nests. From December 2021 to February 2022 (breeding season), we conducted plover occupancy surveys (2-4) on 40 peatlands at Lagunas de Vilama, a landscape of arid steppe and wetlands above 4,500 m in NW Argentina. We measured peatland size, grazing pressure, topographic and remotely-sensed variables that correlate with humidity, and incorporated these as covariates in occupancy models. Occupancy models showed that more than 50% of the studied peatlands were used by Diademed Plovers and most showed signs of reproduction, highlighting the importance of the Vilama Wetlands for Diademed Plover conservation. Within peatlands, Diademed Plovers were most often associated with headwaters. The top ranked occupancy model included constant detection, random spatial effects, and a single occupancy covariate: mean NDWI (Normalized Difference Water Index, an index correlated with water content and humidity) over the previous three years. Contrary to our prediction, Diademed Plovers preferred less water-saturated peatlands (lower NDWI), possibly to avoid nest flooding. This may be especially important in wet years, like the year when we conducted our surveys. Neither peatland size nor grazing by llamas and vicuñas affected peatland use by Diademed Plovers, suggesting that llama grazing at current levels may be compatible with plover conservation. For organisms that specialize on humid habitats, such as peatlands, factors affecting occupancy may vary temporally with variation in climate, and we recommend follow-up surveys across multi-year timescales to untangle the impact of climate on animals' use of humid habitats.

Climate change can disproportionately reduce habitats of stream fishes with restricted ranges in southern South America.

Freshwater fishes are among the most threatened taxa worldwide owing to changes in land use, species introductions, and climate change. Although more than half of the freshwater fishes in the Chilean Mediterranean ecoregion are considered vulnerable or endangered, still little is known about their biogeography. Fishes of the family Perciliidae are endemic of this region and ideal cases to study potential implications of global warming given their endangered conservation status, small size, restricted range, and limited dispersal capacity in fragmented habitats. Here, we model the spatial distribution of habitats for Percilia irwini and P. gillissi under current (1970-2000) and future (2050-2080) climatic scenarios (SSP245, SSP585). We implement maximum entropy (MaxEnt) models adapted for stream networks using high-resolution datasets of selected geophysical and climatic variables. At present, both species inhabit relatively low-quality habitats. In the future (SSP585), suitable habitats for P. irwini are predicted to be reduced drastically (99%) with potential local extirpations in its northern range. Similarly, up to 62% of suitable habitats for P. gillissi would also be reduced in the future. Our study provides insights about assessing future threats and vulnerability of endemic, endangered, range-restricted, and small-bodied freshwater species in this region and elsewhere.

Endangered bird species of one of the last remnants of lowland Atlantic Forest in Rio de Janeiro state, Brazil: pressures and preservation measures.

The lowland Atlantic Forest, at altitudes of below 500 m, is highly fragmented, and is home to many threatened species of birds. The Brazilian state of Rio de Janeiro has a high concentration of threatened birds in the Americas and is an important residual of the dense ombrophilous formations of the Atlantic Forest, which includes the Reserva Biológica União, a high priority area for conservation of Atlantic Forest birds. This study compiled empirical and secondary records of threatened birds in this reserve and discusses potential factors determining their local occurrence. Since 2008, regular observations, including transect surveys and mist-netting, in addiction to secondary data, have provided records of 306 bird species, of which 49 appear on red lists at some level (state, national or global), including 34 listed as endangered, of which 13 are listed globally, eight of them dependent on well-conserved lowland rainforest. Future studies should include new areas of the reserve, with the aim of confirming the presence of additional threatened species. The long-term conservation of this fauna will depend not only on the adequate management of the reserve, but also the reestablishment of its connectivity with adjacent forest fragments and upland areas in the state.

Chromosome-Level Assembly and Annotation of the Genome of the Endangered Giant Patagonian Bumble Bee Bombus dahlbomii.

This article describes a genome assembly and annotation for Bombus dahlbomii, the giant Patagonian bumble bee. DNA from a single, haploid male collected in Argentina was used for PacBio (HiFi) sequencing, and Hi-C technology was then used to map chromatin contacts. Using Juicer and manual curation, the genome was scaffolded into 18 main pseudomolecules, representing a high-quality, near chromosome-level assembly. The sequenced genome size is estimated at 265 Mb. The genome was annotated based on RNA sequencing data of another male from Argentina, and BRAKER3 produced 15,767 annotated genes. The genome and annotation show high completeness, with >95% BUSCO scores for both the genome and annotated genes (based on conserved genes from Hymenoptera). This genome provides a valuable resource for studying the biology of this iconic and endangered species, as well as for understanding the impacts of its decline and designing strategies for its preservation.

Labor of a free-living buffy-tufted marmoset (Callithrix aurita) at a Wildlife Rehabilitation Center in southeastern Brazil.

Callithrix aurita is an endangered small primate endemic to the Atlantic Forest. The present work reports the labor of a free-living C. aurita, through observation of its length and offspring viability. A conservative treatment was used to maintain fetal viability, in view of the species conservation importance.

Climate change introduces threatened killer whale populations and conservation challenges to the Arctic.

The Arctic is the fastest-warming region on the planet, and the lengthening ice-free season is opening Arctic waters to sub-Arctic species such as the killer whale (Orcinus orca). As apex predators, killer whales can cause significant ecosystem-scale changes. Setting conservation priorities for killer whales and their Arctic prey species requires knowledge of their evolutionary history and demographic trajectory. Using whole-genome resequencing of 24 killer whales sampled in the northwest Atlantic, we first explored the population structure and demographic history of Arctic killer whales. To better understand the broader geographic relationship of these Arctic killer whales to other populations, we compared them to a globally sampled dataset. Finally, we assessed threats to Arctic killer whales due to anthropogenic harvest by reviewing the peer-reviewed and gray literature. We found that there are two highly genetically distinct, non-interbreeding populations of killer whales using the eastern Canadian Arctic. These populations appear to be as genetically different from each other as are ecotypes described elsewhere in the killer whale range; however, our data cannot speak to ecological differences between these populations. One population is newly identified as globally genetically distinct, and the second is genetically similar to individuals sampled from Greenland. The effective sizes of both populations recently declined, and both appear vulnerable to inbreeding and reduced adaptive potential. Our survey of human-caused mortalities suggests that harvest poses an ongoing threat to both populations. The dynamic Arctic environment complicates conservation and management efforts, with killer whales adding top-down pressure on Arctic food webs crucial to northern communities' social and economic well-being. While killer whales represent a conservation priority, they also complicate decisions surrounding wildlife conservation and resource management in the Arctic amid the effects of climate change.

Predictive modelling reveals Australian continental risk hotspots for marine debris interactions with key threatened species.

Anthropogenic debris is a global threat that impacts threatened species through various lethal and sub-lethal consequences, as well as overall ecosystem health. This study used a database of over 24,000 beach surveys of marine debris collated by the Australian Marine Debris Initiative from 2012 to 2021, with two key objectives: (1) identify variables that most influence the occurrence of debris hotspots on a continental scale and (2) use these findings to identify likely hotspots of interaction between threatened species and marine debris. The number of particles found in each beach survey was modelled alongside fifteen biological, social, and physical spatial variables including land use, physical oceanography, population, rainfall, distance to waste facilities, ports, and mangroves to identify the significant drivers of debris deposition. The model of best fit for predicting debris particle abundance was calculated using a generalized additive model. Overall, debris was more abundant at sites near catchments with high annual rainfall (mm), intensive land use (km2), and that were nearer to ports (km) and mangroves (km). These results support previous studies which state that mangroves are a significant sink for marine debris, and that large ports and urbanized catchments are significant sources for marine debris. We illustrate the applicability of these models by quantifying significant overlap between debris hotspots and the distributions for four internationally listed threatened species that exhibit debris interactions; green turtle (26,868 km2), dugong (16,164 km2), Australian sea lion (2903 km2) and Flesh-footed Shearwater (2413 km2). This equates to less than 1% (Flesh-footed Shearwater, Australian sea lion), over 2% (green sea turtle) and over 5% (dugong) of their habitat being identified as areas of high risk for marine debris interactions. The results of this study hold practical value, informing decision-making processes, managing debris pollution at continental scales, as well as identifying gaps in species monitoring.

Sediment source and dose influence the larval performance of the threatened coral Orbicella faveolata.

The effects of turbidity and sedimentation stress on early life stages of corals are poorly understood, particularly in Atlantic species. Dredging operations, beach nourishment, and other coastal construction activities can increase sedimentation and turbidity in nearby coral reef habitats and have the potential to negatively affect coral larval development and metamorphosis, reducing sexual reproduction success. In this study, we investigated the performance of larvae of the threatened Caribbean coral species Orbicella faveolata exposed to suspended sediments collected from a reef site in southeast Florida recently impacted by dredging (Port of Miami), and compared it to the performance of larvae exposed to sediments collected from the offshore, natal reef of the parent colonies. In a laboratory experiment, we tested whether low and high doses of each of these sediment types affected the survival, settlement, and respiration of coral larvae compared to a no-sediment control treatment. In addition, we analyzed the sediments used in the experiments with 16S rRNA gene amplicon sequencing to assess differences in the microbial communities present in the Port versus Reef sediments, and their potential impact on coral performance. Overall, only O. faveolata larvae exposed to the high-dose Port sediment treatment had significantly lower survival rates compared to the control treatment, suggesting an initial tolerance to elevated suspended sediments. However, significantly lower settlement rates were observed in both Port treatments (low- and high-dose) compared to the control treatment one week after exposure, suggesting strong latent effects. Sediments collected near the Port also contained different microbial communities than Reef sediments, and higher relative abundances of the bacteria Desulfobacterales, which has been associated with coral disease. We hypothesize that differences in microbial communities between the two sediments may be a contributing factor in explaining the observed differences in larval performance. Together, these results suggest that the settlement success and survival of O. faveolata larvae are more readily compromised by encountering port inlet sediments compared to reef sediments, with potentially important consequences for the recruitment success of this species in affected areas.

Unlocking the Genetic Identity of Endangered Paphiopedilum Orchids: A DNA Barcoding Approach.

Orchids of the genus Paphiopedilum, also called slippers, are among the most valued representatives of the Orchidaceae family due to their aesthetic qualities. Due to overexploitation, deforestation, and illegal trade in these plants, especially in the vegetative phase, Paphiopedilum requires special protection. This genus is listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora. Their precise identification is of great importance for the preservation of genetic resources and biodiversity of the orchid family (Orchidaceae). Therefore, the main objective of the study was to investigate the usefulness of the DNA barcoding technique for the identification of endangered orchids of the genus Paphiopedilum and to determine the effectiveness of five loci: matK, rbcL, ITS2, atpF-atpH and trnH-psbA as potential molecular markers for species of this genus. Among single locus barcodes, matK was the most effective at identifying species (64%). Furthermore, matK, ITS2, matK + rbcL, and matK + trnH-psbA barcodes can be successfully used as a complementary tool to identify Paphiopedilum orchids while supporting morphological data provided by taxonomists.

Transcriptomic Analysis Reveals Adaptive Evolution and Conservation Implications for the Endangered Magnolia lotungensis.

Magnolia lotungensis is an extremely endangered endemic tree in China. To elucidate the genetic basis of M. lotungensis, we performed a comprehensive transcriptome analysis using a sample integrating the plant's bark, leaves, and flowers. De novo transcriptome assembly yielded 177,046 transcripts and 42,518 coding sequences. Notably, we identified 796 species-specific genes enriched in organelle gene regulation and defense responses. A codon usage bias analysis revealed that mutation bias appears to be the primary driver of selection in shaping the species' genetic architecture. An evolutionary analysis based on dN/dS values of paralogous and orthologous gene pairs indicated a predominance of purifying selection, suggesting strong evolutionary constraints on most genes. A comparative transcriptomic analysis with Magnolia sinica identified approximately 1000 ultra-conserved genes, enriched in essential cellular processes such as transcriptional regulation, protein synthesis, and genome stability. Interestingly, only a limited number of 511 rapidly evolving genes under positive selection were detected compared to M. sinica and Magnolia kuangsiensis. These genes were enriched in metabolic processes associated with adaptation to specific environments, potentially limiting the species' ability to expand its range. Our findings contribute to understanding the genetic architecture of M. lotungensis and suggest that an insufficient number of adaptive genes contribute to its endangered status.

A multi-tissue de novo transcriptome assembly and relative gene expression of the vulnerable freshwater salmonid Thymallus ligericus.

Freshwater ecosystems are among the most endangered ecosystems worldwide. While numerous taxa are on the verge of extinction as a result of global changes and direct or indirect anthropogenic activity, genomic and transcriptomic resources represent a key tool for comprehending species' adaptability and serve as the foundation for conservation initiatives. The Loire grayling, Thymallus ligericus, is a freshwater European salmonid endemic to the upper Loire River basin. The species is comprised of fragmented populations that are dispersed over a small area and it has been identified as a vulnerable species. Here, we provide a multi-tissue de novo transcriptome assembly of T. ligericus. The completeness and integrity of the transcriptome were assessed before and after redundancy removal with lineage-specific libraries from Eukaryota, Metazoa, Vertebrata, and Actinopterygii. Relative gene expression was assessed for each of the analyzed tissues, using the de novo assembled transcriptome and a genome-based analysis using the available T. thymallus genome as a reference. The final assembly, with a contig N50 of 1221 and Benchmarking Universal Single-Copy Orthologs (BUSCO) scores above 94%, is made accessible along with structural and functional annotations and relative gene expression of the five tissues (NCBI SRA and FigShare databases). This is the first transcriptomic resource for this species, which provides a foundation for future research on this and other salmonid species that are increasingly exposed to environmental stressors.

The first complete mitochondrial genome of the critically endangered Malaysian giant turtle, Orlitia borneensis (Testudines: Geoemydidae).

We present here the complete mitochondrial sequence of the critically endangered Malaysian giant turtle, Orlitia borneensis. The assembled mitochondrial genome includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes (rRNAs), and one control region. This mitochondrial genome has been archived in the NCBI GenBank with accession number OQ808845. The Batagur control region is relatively smaller than O. borneensis and closer to Aldabrachelys gigantea, which suggests potentially that O. borneensis has undergone an expansion in the control region.