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Supplementary material 2 from: Bruslund S, Leupen B, Shepherd CR, Nelson SS (2022) Online trade as a serious additional threat to the Critically Endangered silvery pigeon Columba argentina in Indonesia. Nature Conservation 46: 41-48. https://doi.org/10.3897/natureconservation.46.80064
Video 2
Correcting parentage relationships in the endangered California condor: Improving mean kinship estimates for conservation management
<p><span>Maintaining the existing biodiversity of endangered species is a goal of conservation management programs, and a major component of many collaborative efforts undertaken by zoos, field biologists, and conservation scientists. Over the past three decades, the San Diego Zoo has performed long-term genetic studies in support of the recovery program for the critically endangered California condor (<em>Gymnogyps californianus</em>). This work has included sex determination of hatchlings and parentage confirmation using microsatellite genotyping. This paper describes the genetic work associated with the California condor recovery program, which aims to provide a highly accurate pedigree for making informed captive pairing and release recommendations. Initial genotyping began after reintroduced California condors started reproducing, and the focus was on birds hatched from their wild-laid eggs. However, genetic analysis showed discrepancies relative to behavioral observations of wild birds, and led to the species-wide testing of all available samples. This genetic study has resolved instances of individual misidentifications and parental misassignments, verified the first cases of extra-pair paternity in this species, identified parentage where chicks were observed being raised by trios, and found two apparent de novo mutations in the captive condor population. Correcting the California condor pedigree according to genetic parental analysis has produced more accurate estimates of mean kinship values among living birds, ranking potential breeders according to their actual breeding value and helping managers to make informed decisions about captive pairing and release of condors in the wild.</span></p>
Data from: Temporal factors and distance to human settlement affect nest survival of the endangered Yellow-headed Parrot in Belize, Central America
<p>The endangered Yellow-headed Parrot (<em>Amazona oratrix</em>) has experienced a considerable reduction in abundance and distribution. Identifying natural and anthropogenic causes of nest failure is a critical step towards developing conservation actions that increase nest survival. In this study, we examined daily nest survival in relation to temporal, habitat and anthropogenic factors, as well as nest site properties. We monitored nests (<em>n </em>= 124) across six study sites in Belize during 2017 and 2018 and independently modeled the effects of predation, abandonment and poaching on daily nest survival rates. Overall, the estimated cumulative nest survival probability was 0.18 (95% CI = 0.12 – 0.25). Predation was the main cause of nest failure, followed by abandonment and poaching. Our results showed that nest predation and abandonment usually occurred early in the nesting cycle. Day within the nesting season negatively influenced daily survival for abandoned nests and had a quadratic effect on survival for poached nests.<strong> </strong>Poaching events occurred at a specific date range later in the season, with nests farther from the nearest human settlement having higher daily survival. Findings from this study highlight the additive mortality effect that nest poaching is having on Yellow-headed Parrot populations in Belize and show that managers can anticipate the timing and location of nests most vulnerable to poaching.<span> </span></p>
Supplementary material 3 from: Augsten M, Meyer PB, Freitas LB, Batista JAN, Stehmann JR (2022) Nicotiana gandarela (Solanaceae), a new species of 'tobacco' highly endangered from the Quadrilátero Ferrífero in Brazil. PhytoKeys 190: 113-129. https://doi.org/10.3897/phytokeys.190.76111
Figure S2
Supplementary material 2 from: Augsten M, Meyer PB, Freitas LB, Batista JAN, Stehmann JR (2022) Nicotiana gandarela (Solanaceae), a new species of 'tobacco' highly endangered from the Quadrilátero Ferrífero in Brazil. PhytoKeys 190: 113-129. https://doi.org/10.3897/phytokeys.190.76111
Figure S1
Figure 2 from: Augsten M, Meyer PB, Freitas LB, Batista JAN, Stehmann JR (2022) Nicotiana gandarela (Solanaceae), a new species of 'tobacco' highly endangered from the Quadrilátero Ferrífero in Brazil. PhytoKeys 190: 113-129. https://doi.org/10.3897/phytokeys.190.76111
Figure 2 Nicotiana gandarela Augsten & Stehmann A peculiar habitat of the species, the shaded sites in the base of the shaded ledge B seedlings growing in the site C habit highlighting the rosulate leaves and the scapose inflorescence D, E flowers in lateral and frontal view F 2-valvate capsule with many seeds. G seed with sinuous anticlinal walls (Scanning Electron Microscopy) D–G were obtained from plants of the type population (Augsten and Stehmann 1078, BHCB). Photos by JR Stehmann.
Supplementary material 1 from: Augsten M, Meyer PB, Freitas LB, Batista JAN, Stehmann JR (2022) Nicotiana gandarela (Solanaceae), a new species of 'tobacco' highly endangered from the Quadrilátero Ferrífero in Brazil. PhytoKeys 190: 113-129. https://doi.org/10.3897/phytokeys.190.76111
Table S1
Figure 3 from: Augsten M, Meyer PB, Freitas LB, Batista JAN, Stehmann JR (2022) Nicotiana gandarela (Solanaceae), a new species of 'tobacco' highly endangered from the Quadrilátero Ferrífero in Brazil. PhytoKeys 190: 113-129. https://doi.org/10.3897/phytokeys.190.76111
Figure 3 A main mountains of the Quadrilátero Ferrífero in Minas Gerais. Star indicates the Nicotiana gandarela Augsten & Stehmann occurrence site B Google Earth image showing the regional landscape associated with the N. gandarela site, the forest matrix impacted by a small village, and open mining. The red lines indicate mining concessions (Instituto Prístino: Atlas Digital Geoambiental [https://institutopristino.org.br/atlas/]).
Figure 1 from: Augsten M, Meyer PB, Freitas LB, Batista JAN, Stehmann JR (2022) Nicotiana gandarela (Solanaceae), a new species of 'tobacco' highly endangered from the Quadrilátero Ferrífero in Brazil. PhytoKeys 190: 113-129. https://doi.org/10.3897/phytokeys.190.76111
Figure 1 Bayesian 50% majority-rule consensus tree of 56 species of Nicotiana L. of the combined nuclear (ITS) and plastid (ndhF, trnLF, and trnSG) datasets. Numbers next to the nodes represent the posterior probabilities (PP) and bootstrap values. Section names (according to Knapp et al. 2004) are indicated on the right. Width of lines defined by PP values.
Transmissible cancer influences immune gene expression in an endangered marsupial, the Tasmanian devil (Sarcophilus harrisii)
<p>Understanding wildlife diseases' effects on populations requires insight into local environmental conditions, host defence mechanisms, host life-history trade-offs, pathogen population dynamics, and their interactions. The survival of Tasmanian devils (<em>Sarcophilus harrisii</em>) is challenged by a novel, fitness limiting pathogen, Tasmanian devil facial tumour disease (DFTD), a clonally transmissible, contagious cancer. In order to understand the devils' capacity to respond to DFTD, it is crucial to gain information on factors influencing the devils' immune system. By using RT-qPCR, we investigated how DFTD infection in association with intrinsic (sex and age) and environmental (season) factors influences the expression of 10 immune genes in Tasmanian devil blood. Our study showed that the expression of immune genes (both innate and adaptive) differed across seasons, a pattern that was altered when infected with DFTD. The expression of immunogbulins IgE and IgM:IgG showed downregulation in colder months in DFTD infected animals. We also observed strong positive association between the expression of an innate immune gene, CD16, and DFTD infection. Our results demonstrate that sampling across seasons, age groups and environmental conditions are beneficial when deciphering the complex eco-evolutionary interactions of not only conventional host-parasite systems, but also of host and diseases with high mortality rates, such as transmissible cancers.</p>
Data from: Up and down the blind alley: population divergence with scant gene flow in an endangered tropical lineage of Andean palms (Ceroxylon quindiuense clade: Ceroxyloideae)
[No abstract entered]
Data from: Causes and consequences of fine-scale population structure in a critically endangered freshwater seal
[No abstract entered]
Museomics contributes to the spatiotemporal assessment of genetic diversity and structure in wild and ex situ conservation organisms: a case study of three endangered coastal plants in Japan
<p><span>Understanding </span><span>the extent to which </span><span>genetic diversity of wild populations in ex</span> <span>situ</span><span> conservation can be retained is </span><span>crucial</span><span> for the management of </span><span>such</span><span> populations. Wild individuals collected in the target area in the past </span><span>and</span><span> present can be used to estimate the number of alleles lost over time in wild populations and</span><span> thereby</span><span> the number of alleles whose loss could be </span><span>prevented</span><span> by ex</span> <span>situ</span><span> conservation. </span><span>Here</span><span>, we assessed the genetic diversity of wild and ex</span> <span>situ</span><span> conservation populations of three endangered coastal herb species</span><span>,</span><span> <em>Cirsium maritimum</em> Makino (Asteraceae), <em>Linaria japonica</em> Miq. (Plantaginaceae</span><span>) and</span><span> <em>Suaeda glauca</em></span><span><em> </em>(Bunge) Bunge (Amaranthaceae), which are endangered </span><span>species on</span><span> Awaji Island, Hyogo Prefecture, Japan, via multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq). We </span><span>incorporated</span><span> the museomics approach, which </span><span>involves conducting</span><span> genetic analyses of museum specimens collected from the targeted wild populations in the past to estimate the temporal transition of genetic diversity in wild populations and the number of alleles maintai</span><span>ned in <em>ex situ</em></span><span> conservation. </span><span>Our </span><span>results </span><span>reveal</span><span> a declining trend in genetic diversity in the wild populations of all </span><span>investigated</span><span> species, although </span><span>this trend is </span><span>not significant. In all the species, </span><span>numerous</span><span> alleles were already lost in current wild populations, </span><span>whereas they</span><span> were </span><span>present</span><span> in the past wild and ex</span> <span>situ</span><span> conservation populations. Our study </span><span>indicates</span><span> that extinct alleles in current wild populations have been maintained in ex</span> <span>situ</span><span> conservation</span><span> by museomics approach. These </span><span>appro</span><span>aches </span><span>were effective in verifying</span><span> the genetic diversity retention effects of <em>ex</em></span><em> <span>situ</span></em><span> conservation populations.</span></p>
Data for: Quantifying patch-specific seed dispersal and local population dynamics to estimate population spread of an endangered plant species
<p>Dataset on seed dispersal and population spread for the paper</p> <p class="Default"><span><b>Quantifying patch-specific seed dispersal and local population dynamics to estimate population spread of an endangered plant species</b></span></p> <p>Jinlei Zhu<sup>1, 2,</sup> *, Karolína Hrušková<sup>1, 3</sup>, Hana Pánková<sup>1</sup>, Zuzana Münzbergová<sup>1, 3</sup></p> <p><sup>1</sup>Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic</p> <p class="Default"><span><sup>2</sup>Institute of Landscape and Plant Ecology, University of Hohenheim, Stuttgart, Germany</span></p> <p class="Default"><span><sup>3</sup>Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic</span></p> <p class="Default"><span>*Corresponding author: jinlei.zhu@uni-hohenheim.de</span></p> <p>Institute of Landscape and Plant Ecology</p> <p>University of Hohenheim</p> <p>Ottilie-Zeller-Weg 2, 70599 Stuttgart, Germany</p>
FIGURE 4 in Ternstroemia guerrerensis (Pentaphylacaceae), a new endangered cloud forest tree from Guerrero, Mexico
FIGURE 4. Distribution of T. guerrerensis in Guerrero, Mexico.
Supplementary material 1 from: Kneubühler J, Baggenstos M, Neubert E (2022) On the verge of extinction – revision of a highly endangered Swiss alpine snail with description of a new genus, Raeticella gen. nov. (Gastropoda, Eupulmonata, Hygromiidae). ZooKeys 1104: 69-91. https://doi.org/10.3897/zookeys.1104.82866
Calculated p-distances of the COI of the investigated specimens.
Supplementary material 2 from: Martínez-Domínguez L, Nicolalde-Morejón F, Vergara-Silva F, Stevenson DW (2022) Monograph of Ceratozamia (Zamiaceae, Cycadales): an endangered genus. PhytoKeys 208: 1-102. https://doi.org/10.3897/phytokeys.208.80382
Herbarium specimens for Ceratozamia sancheziae and C. zoquorum
Supplementary material 1 from: Martínez-Domínguez L, Nicolalde-Morejón F, Vergara-Silva F, Stevenson DW (2022) Monograph of Ceratozamia (Zamiaceae, Cycadales): an endangered genus. PhytoKeys 208: 1-102. https://doi.org/10.3897/phytokeys.208.80382
Glossary
FIGURE. A. Multi-partition plastome tree. B. 35S in Tulipa toktogulica (Liliaceae), a cryptic, endangered new species from the western Tien-Shan, Kyrgyzstan
FIGURE. A. Multi-partition plastome tree. B. 35S rDNA tree. New species shown in red on both trees.
Supplementary material 1 from: Saitoh K, Shindo K, Fujimoto Y, Takahashi K, Shimada T (2016) Mitochondrial genotyping of an endangered bitterling Acheilognathus typus (Cyprinidae). ZooKeys 623: 131-141. https://doi.org/10.3897/zookeys.623.8981
Table S1, Figure S1 : Explanation note: Table S1. Normalized haplotype composition of localities.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.