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opencc-zeroMay 2020View details →

Data from: Pollen limitation in the endangered Chinese endemic species Sinocalycanthus chinensis

Pollen limitation negatively impacts endangered and endemic plants with small fragmented populations, such as Sinocalycanthus chinensis, an endangered plant endemic to China. In this study, we analyzed the pollen limitation of the S. chinensis Damingshan (DMS) population in 2006, 2009, and 2010, and crossed plants with mates separated by different distances, both within and between populations. The DMS population exhibited strong pollen limitation in fruit set, seed set, and seeds per fruit in 2006, 2009, and 2010. The average accumulated pollen limitation (for fruit set times seeds per fruit) was 0.510 ± 0.180. Progeny crossed with pollen from intermediate neighboring plants within the same population (separated by 30 – 50 m from pollen recipients) had the lowest fitness. No optimal outcrossing distance was found within the DMS population. Progeny from crosses with the SXW and DLS populations performed relatively better, while those from crosses with QLF and LXS populations performed worse. Compared with average reproductive success, outbreeding depression was found in progeny from crosses with the LXS and QLF populations. Reproductive success from pure self-pollination indicated S. chinensis is self-compatible. Geitonogamous selfing increased reproductive success. Based on geitonogamous selfing, the proportion of selfed offspring was relatively high. These results provide basic references for the conservation of this species.

opencc-zeroDec 2018View details →

Data from: Soil microbiomes underlie population persistence of an endangered plant species

Microbiomes can dramatically alter individual plant performance, yet how these effects influence higher order processes is not well resolved. In particular, little is known about how microbiome effects on individual plants alter plant population dynamics, a question critical to imperiled species conservation. Here, we integrate bioassays, multidecadal demographic data, and integral projection modeling to determine how the presence of the natural soil microbiome underlies plant population dynamics. Simulations indicated that the presence of soil microbiomes boosted population growth rates (λ) of the endangered Hypericum cumulicola by 13% on average, the difference between population growth versus decline in 76% of patches. The greatest benefit (47% increase in λ) occurred in low nutrient, high elevation habitats, suggesting that the soil microbiome may help expand H. cumulicola's distribution to include these stressful habitats. Our results demonstrate that soil microbiomes can significantly affect plant population growth and persistence, and support the incorporation of soil microbiomes into conservation planning. plant population growth and persistence, and support the incorporation of soil microbiomes into conservation planning.

opencc-zeroDec 2023View details →

High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species

With populations of threatened and endangered species declining worldwide, efforts are being made to generate high-quality genomic records of these species before they are lost forever. Here, we demonstrate that data from single Oxford Nanopore Technologies (ONT) MinION flow cells can, even in the absence of highly accurate short DNA-read polishing, produce high-quality de novo plant genome assemblies adequate for downstream analyses, such as synteny and ploidy evaluations, paleodemographic analyses, and phylogenomics. This study focuses on three North American ash tree species in the genus Fraxinus (Oleaceae) that were recently added to the International Union for Conservation of Nature (IUCN) Red List as critically endangered. Our results support a whole genome triplication at the base of the Oleaceae as well as a subsequent whole genome duplication shared by Syringa, Osmanthus, Olea, and Fraxinus. Finally, we demonstrate the use of ONT long-read sequencing data to reveal patterns in demographic history.

opencc-zeroOct 2021View details →

Do nest boxes breed the target species or its competitors? A case study of a critically endangered bird

Nest boxes are widely used for habitat restoration. Unfortunately, competitors of the target species may exploit nest boxes, creating perverse outcomes. Avoiding habitats preferred by nontarget species, while favoring those of the target species, requires an adaptive management approach if limited information about species preferences is available when deploying boxes. Using nest boxes intended for Swift Parrots Lathamus discolor, we identify factors associated with nontarget species occupancy (Common Starling Sturnus vulgaris and Tree Martin Petrochelidon nigricans) in newly deployed boxes in 2016, and then again after 3 years had elapsed in 2019. Box occupancy by different species depended on the interaction between distance of individual boxes to the forest edge and year. Although the target species exploited similar numbers of nest boxes in both years, competitors were the main beneficiaries of established boxes. A subordinate native nest competitor increased box occupancy likelihood at greater distances from forest edges in both years, but the relationship was stronger in 2019. Introduced Common Starlings S. vulgaris were most likely to occupy boxes close to forest edges, but the magnitude of this relationship was much greater for established than newly deployed boxes. We suggest that permanent box deployments for Swift Parrots may produce perverse outcomes by increasing nesting habitat for Common Starlings. We suggest that for species that only use cavities for part of their life cycle, managers should limit access to boxes outside of critical times to reduce the likelihood that pest populations can exploit restoration efforts and create new problems.

opencc-by-4.0Dec 2021View details →

Map 1 in Clusia falcata (Clusiaceae), an endangered species with exceptionally narrow leaves endemic to Chiapas, Mexico

Map 1. Distribution map of Clusia falcata in Chiapas, Mexico.

opencc-zeroDec 2016View details →

Data from: Genetic diversity and divergence in the fountain darter (Etheostoma fonticola): implications for conservation of an endangered species

The endangered fountain darter Etheostoma fonticola is found only in the Comal and San Marcos rivers in the Guadalupe River basin in central Texas, USA. Comal River fountain darters were believed to be extir- pated following a severe drought in the 1950s and were reintroduced in the early 1970s using 457 darters from the San Marcos River. In this study we used 23 microsatellite loci to describe and evaluate the genetic diversity, population structure and effective population size (Ne) of fountain darters. We also evaluated the genetic effect of the Comal River reintroduction and the influence of low-head dams (dams) on dispersal in both rivers. Bayesian analysis of individual genotypes and Analysis of Molecular Variation supported two distinct populations concordant with the two rivers. Estimates of Ne were much smaller (<10 %) than census size (Nc) in both rivers but did not indicate the populations are at risk of an immediate and rapid loss of genetic diversity. Coalescent-based estimates of the genetically effective number of founders (Nf) for the Comal River averaged about 49 darters and, together with the indices of genetic diversity and the bottleneck test (heterozygosity excess) results, were consistent with a founder event following the reintroduction in the Comal River. Finally, our results regarding the influence of dams on fountain darter dispersal were equivocal and did not support a conclusion. We recommend this issue be examined further as part of the fountain darter recovery program.

opencc-by-4.0Feb 2022View details →

Fig. 6 in Two new remarkable and endangered catfish species of the genus Cambeva (Siluriformes, Trichomycteridae) from southern Brazil

Fig. 6. Type locality of Cambeva betabelardense sp. nov.

opencc-by-4.0Feb 2022View details →

Fig. 4 in Two new remarkable and endangered catfish species of the genus Cambeva (Siluriformes, Trichomycteridae) from southern Brazil

Fig. 4. Type locality of Cambeva alphabelardense sp. nov.

opencc-zeroAug 2022View details →

Strong isolation by distance among local populations of an endangered butterfly species (Euphydryas aurinia)

The marsh fritillary (Euphydryas aurinia) is a critically endangered butterfly species in Denmark known to be particularly vulnerable to habitat fragmentation due to its poor dispersal capacity. We identified and genotyped 318 novel SNP loci across 273 individuals obtained from 10 small and fragmented populations in Denmark using a genotyping-by-sequencing (GBS) approach to investigate its population genetic structure. Our results showed clear genetic substructuring and highly significant population differentiation based on genetic divergence (FST) among the 10 populations. The populations clustered in three overall clusters and due to further substructuring among these, it was possible to clearly distinguish six clusters in total. We found highly significant deviations from Hardy-Weinberg equilibrium due to heterozygote deficiency within every population investigated which indicates substructuring and/or inbreeding (due to mating among closely related individuals). The stringent filtering procedure that we have applied to our genotype quality could have overestimated the heterozygote deficiency and the degree of substructuring of our clusters but is allowing relative comparisons of the genetic parameters among clusters. Genetic divergence increased significantly with geographic distance, suggesting limited gene flow at spatial scales comparable to the dispersal distance of individual butterflies and strong isolation by distance. Altogether, our results clearly indicate that the marsh fritillary populations are genetically isolated. Further, our results highlight that the relevant spatial scale for conservation of rare, low mobile species may be smaller than previously anticipated.

opencc-zeroAug 2022View details →

Data: Detecting preservation and reintroduction sites for endangered plant species using a two-step modelling and field approach

To withstand the surge of species loss worldwide, (re)introduction of endangered plant species has become an increasingly common technique in conservation biology. Successful (re)introduction plans, however, require identifying sites that provide the optimal ecological conditions for the target species to thrive. In this study, we propose a two-step approach to identify appropriate (re)introduction sites. The first step involves modelling the niche and distribution of the species with bioclimatic and topographical predictors, both at continental and at national scales. The second step consists of refining these bioclimatic predictions by analysing stationary ecological parameters, such as soil conditions, and relating them to population-level fitness values. We demonstrate this methodology using Swiss populations of the lady's slipper orchid (Cypripedium calceolus L., Orchidaceae), for which conservation plans have existed for years but have generally been unfruitful. Our workflow identified sites for future (re)introductions based on the species requirements for mid-to-sunny light conditions and specific soil physico-chemical properties, such as basic to neutral pH and low soil organic matter content. Our findings show that by combining wide-scale bioclimatic modelling with fine scale field measurements it is possible to carefully identify the ecological requirements of a target species for successful (re)introductions.

Fig. 8 in Captive individuals of endangered Philippine raptors maintain native feather mites (Acariformes: Pterolichoidea) species

Fig. 8. Pseudogabucinia nisaeti sp. n. female. A – dorsal view, B – ventral view.

Fig. 5 in Captive individuals of endangered Philippine raptors maintain native feather mites (Acariformes: Pterolichoidea) species

Fig. 5. Pseudalloptinus pithecophagae sp. n. female. A – dorsal view, B – ventral view.

Fig. 2 in Captive individuals of endangered Philippine raptors maintain native feather mites (Acariformes: Pterolichoidea) species

Fig. 2. Hieracolichus philippinensis sp. n. female. A – dorsal view, B – ventral view.

Fig. 1 in Captive individuals of endangered Philippine raptors maintain native feather mites (Acariformes: Pterolichoidea) species

Fig. 1. Hieracolichus philippinensis sp. n. male. A – dorsal view, B – ventral view.

Fig. 4 in Captive individuals of endangered Philippine raptors maintain native feather mites (Acariformes: Pterolichoidea) species

Fig. 4. Pseudalloptinus pithecophagae sp. n. male. A – dorsal view, B – ventral view.

Fig. 7 in Captive individuals of endangered Philippine raptors maintain native feather mites (Acariformes: Pterolichoidea) species

Fig. 7. Pseudogabucinia nisaeti sp. n. male. A – dorsal view, B – ventral view.

opencc-by-4.0Dec 2010View details →

Fig.1 in Preliminary Studies On The Genetic Diversity Of An Endemic And Endangered Species Saussurea Esthonica Baer Ex Rupr. In Latvia

Fig.1 Genetic diversity measures between populations based on retrotransposon markers