scholarly journals Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō

2021 ◽  
Author(s):  
Yasmin Foster ◽  
Ludovic Dutoit ◽  
Stefanie Grosser ◽  
Nicolas Dussex ◽  
Brodie J Foster ◽  
...  
Keyword(s):  
Endangered Species ◽  
Genotyping By Sequencing ◽  
Small Population ◽  
Critically Endangered ◽  
Island Population ◽  
Nucleotide Polymorphisms ◽  
Critically Endangered Species ◽  
Increased Risk ◽  
Population Sizes ◽  
Extant Population

Abstract Events of inbreeding are inevitable in critically endangered species. Reduced population sizes and unique life-history traits can increase the severity of inbreeding, leading to declines in fitness and increased risk of extinction. Here, we investigate levels of inbreeding in a critically endangered flightless parrot, the kākāpō (Strigops habroptilus), wherein a highly inbred island population and one individual from the mainland of New Zealand founded the entire extant population. Genotyping-by-sequencing (GBS), and a genotype calling approach using a chromosome-level genome assembly, identified a filtered set of 12,241 single-nucleotide polymorphisms (SNPs) among 161 kākāpō, which together encompass the total genetic potential of the extant population. Multiple molecular-based estimates of inbreeding were compared, including genome-wide estimates of heterozygosity (FH), the diagonal elements of a genomic-relatedness matrix (FGRM), and runs of homozygosity (RoH, FRoH). In addition, we compared levels of inbreeding in chicks from a recent breeding season to examine if inbreeding is associated with offspring survival. The density of SNPs generated with GBS was sufficient to identify chromosomes that were largely homozygous with RoH distributed in similar patterns to other inbred species. Measures of inbreeding were largely correlated and differed significantly between descendants of the two founding populations. However, neither inbreeding nor ancestry was found to be associated with reduced survivorship in chicks, owing to unexpected mortality in chicks exhibiting low levels of inbreeding. Our study highlights important considerations for estimating inbreeding in critically endangered species, such as the impacts of small population sizes and admixture between diverse lineages.

Whole-chloroplast analysis as an approach for fine-tuning the preservation of a highly charismatic but critically endangered species, Wollemia nobilis (Araucariaceae)

2016 ◽  
Vol 64 (8) ◽  
pp. 654 ◽  
Author(s):  
Abigail Greenfield ◽  
Hannah McPherson ◽  
Tony Auld ◽  
Sven Delaney ◽  
Catherine A. Offord ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Endangered Species ◽  
Fine Tuning ◽  
Critically Endangered ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Critically Endangered Species ◽  
Single Difference ◽  
Variant Detection ◽  
Nuclear Loci

The critically endangered Wollemia nobilis W.G. Jones, K.D. Hill & J.M. Allen is endemic to Wollemi National Park north of Sydney (Australia). All known wild individuals are restricted to four sites in a single canyon system. W. nobilis can reproduce sexually but at all sites individual clumps can be multi-stemmed from a common base. In the first genetic study of this species, no genetic variation was found across multiple genetic marker types representing hundreds of nuclear loci, indicating this species is characterised by very low genetic variation. In this study we searched for variation across the chloroplast using shotgun sequencing, bioinformatic extraction of chloroplast DNA and variant detection. Six chloroplast single nucleotide polymorphisms were detected, producing three chlorotypes. Chlorotype 1 is found in every individual surveyed at Sites 1 and 3, and in individuals from Sites 2 and 4. Chlorotype 2 – the most distinct chlorotype – was found in two individuals from Site 4. Chlorotype 3 consists of a single difference from Chlorotype 1 and may represent a somaclonal mutant. These findings will guide management and translocation of this critically endangered species. This study provides a practical template that is highly informative and easily applicable to other taxa in similar circumstances.

Eugenia alletiana (Myrtaceae), a new critically endangered species endemic to the island of Mauritius

Phytotaxa ◽  
2013 ◽  
Vol 94 (1) ◽  
pp. 1 ◽  
Author(s):  
CLÁUDIA BAIDER ◽  
F. B. VINCENT FLORENS
Keyword(s):  
Endangered Species ◽  
Small Population ◽  
Red List ◽  
Alien Plants ◽  
Critically Endangered ◽  
Invasive Alien Plants ◽  
International Union ◽  
Diagnostic Features ◽  
Critically Endangered Species ◽  
Apical Pore

Eugenia alletiana, a new endemic species from Mauritius, is described and its ecology and conservation is discussed. The morphological diagnostic features for Eugenia alletiana are chartaceous, discoloured leaves, very thin terminal branchlets, flowers solitary or in fascicles of 2–3 flowers, totally fused hypanthium without apical pore or calyptra, that encloses the numerous stamens (> 500) and petals before anthesis; seed enclosed in a woody endocarp with a lamellated outer surface. The species should be considered as Critically Endangered (CR) according to the Red List Criteria of the International Union for the Conservation of Nature. This assessment is based on the plant’s restricted distribution, very small population size, a habitat sustaining degradation by invasive alien plants and animals and predation of immature fruits and seeds by invasive alien monkeys and rats respectively leading to a weak regeneration.

Where have all the sawfishes gone? Perspectives on declines of these Critically Endangered species in Sri Lanka

2021 ◽  
Author(s):  
Akshay Tanna ◽  
Daniel Fernando ◽  
Ramajeyam Gobiraj ◽  
Buddhi M. Pathirana ◽  
Sahan Thilakaratna ◽  
...  
Keyword(s):  
Sri Lanka ◽  
Endangered Species ◽  
Critically Endangered ◽  
Critically Endangered Species

scholarly journals The Oral Bacterial Community in Melanophryniscus admirabilis (Admirable Red-Belly Toads): Implications for Conservation

2021 ◽  
Vol 9 (2) ◽  
pp. 220
Author(s):  
Michele Bertoni Mann ◽  
Janira Prichula ◽  
Ícaro Maia Santos de Castro ◽  
Juliana Mello Severo ◽  
Michelle Abadie ◽  
...  
Keyword(s):  
Endangered Species ◽  
Bacterial Community ◽  
High Throughput Sequencing ◽  
Dietary Diversity ◽  
Natural Habitat ◽  
Critically Endangered ◽  
Personal Genome ◽  
Oral Microbiota ◽  
Critically Endangered Species ◽  
Anthropogenic Environment

Melanophryniscus admirabilis (admirable red-belly toad) is a microendemic and critically endangered species found exclusively along 700 m of the Forqueta River, in a fragment of the Atlantic Forest of southern Brazil. One of the greatest concerns regarding the conservation of this species is the extensive use of pesticides in areas surrounding their natural habitat. In recent years, the adaptation and persistence of animal species in human-impacted environments have been associated with microbiota. Therefore, the present study aimed to characterize the oral bacterial community of wild M. admirabilis and to address the question of how this community might contribute to this toad’s adaptation in the anthropogenic environment as well as its general metabolic capabilities. A total of 11 oral samples collected from wild M. admirabilis were characterized and analyzed via high-throughput sequencing. Fragments of the 16S rRNA variable region 4 (V4) were amplified, and sequencing was conducted using an Ion Personal Genome Machine (PGM) System with 316 chips. A total of 181,350 sequences were obtained, resulting in 16 phyla, 34 classes, 39 orders, and 77 families. Proteobacteria dominated (53%) the oral microbiota of toads, followed by Firmicutes (18%), Bacteroidetes (17%), and Actinobacteria (5%). No significant differences in microbial community profile from among the samples were reported, which suggests that the low dietary diversity observed in this population may directly influence the bacterial composition. Inferences of microbiome function were performed using PICRUSt2 software. Important pathways (e.g., xenobiotic degradation pathways for pesticides and aromatic phenolic compounds) were detected, which suggests that the bacterial communities may serve important roles in M. admirabilis health and survival in the anthropogenic environment. Overall, our results have important implications for the conservation and management of this microendemic and critically endangered species.

scholarly journals High survival rate of a critically endangered species, the Azores Bullfinch Pyrrhula murina, as a contribution to population recovery

2010 ◽  
Vol 151 (3) ◽  
pp. 627-636 ◽  
Author(s):  
David Monticelli ◽  
Ricardo Ceia ◽  
Ruben Heleno ◽  
Hugo Laborda ◽  
Sergio Timóteo ◽  
...  
Keyword(s):  
Survival Rate ◽  
Endangered Species ◽  
Critically Endangered ◽  
High Survival ◽  
Population Recovery ◽  
High Survival Rate ◽  
Critically Endangered Species

scholarly journals Effects of Lead on Ultrastructure of Isoetes sinensis Palmer (Isoetaceae), a Critically Endangered Species in China

PLoS ONE ◽  
2015 ◽  
Vol 10 (9) ◽  
pp. e0139231 ◽  
Author(s):  
Guohua Ding ◽  
Chunye Li ◽  
Xu Han ◽  
Chunyu Chi ◽  
Dawei Zhang ◽  
...  
Keyword(s):  
Endangered Species ◽  
Critically Endangered ◽  
Critically Endangered Species

Genomic characteristics of critically endangered Chimonobambusa hirtinoda C.S. Chao & K.M. Lan

2021 ◽  
Vol 50 (1) ◽  
pp. 69-77
Author(s):  
Tengfei Shen ◽  
Youmiao Zheng ◽  
Zimou Sun ◽  
Meng Xu
Keyword(s):  
Endangered Species ◽  
Frequency Analysis ◽  
Natural Habitat ◽  
Gc Content ◽  
Critically Endangered ◽  
Critically Endangered Species ◽  
Phylogenetic Studies ◽  
Ssr Loci ◽  
Ecological Conservation ◽  
Repeat Rate

With its unique square-shaped culm, Chimonobambusa hirtinoda C.S. Chao & K.M. Lan is a critically endangered species, and its natural habitat is solely restricted to Doupeng Mountain in Guizhou, China. Two small-insert libraries from C. hirtinoda were constructed and sequenced. Approximately 127.83 Gb of highquality reads were generated and assembled into 9,320,997 contigs with a N50 length of 213bp, thereby producing 8,867,344 scaffolds with total length of 2.01 Gb. An estimated genome size of C. hirtinode was 2.86 Gb on the basis of k-mer frequency analysis, with the GC content of 45.40%. The repeat rate and heterozygous ratio were 74.11 and 1.48% in C. hirtinoda genome, respectively. Finally, 65,398 SSR loci were identified in the assembled contigs, including 58.66% tri-nucleotide, 27.42% di-nucleotide, 7.94% tetranucleotide, 3.67% penta-nucleotide, and 2.31% hexa-nucleotide. Results of this study are useful not only for ecological conservation of C. hirtinoda, but also for phylogenetic studies.

Novelties in Begonia (Begoniaceae) from the campos rupestres of Serra do Padre Ângelo, Minas Gerais, Brazil: a new species and a new record

Phytotaxa ◽  
2021 ◽  
Vol 510 (1) ◽  
Author(s):  
LUDOVIC JEAN CHARLES KOLLMANN ◽  
PAULO MINATEL GONELLA
Keyword(s):  
New Species ◽  
High Elevation ◽  
Iucn Red List ◽  
Minas Gerais ◽  
Small Population ◽  
Critically Endangered ◽  
Campos Rupestres ◽  
Rock Outcrops ◽  
Critically Endangered Species ◽  
Minas Gerais State

Begonia piranga (Begoniaceae) is a new narrowly endemic species from the campos rupestres of Serra do Padre Ângelo, a quartzitic massif in Conselheiro Pena, eastern Minas Gerais state, Brazil. Description, diagnosis, taxonomic comments, detailed illustrations, field photographs, and a provisional IUCN Red List Assessment are provided. The new species is considered Critically Endangered due to its restricted occurrence in high elevation rock outcrops, small population size, and decline in the quality of the habitat. Begonia vasconcelosiana, another Critically Endangered species, is also newly reported here for Serra do Padre Ângelo. These discoveries add to the increasing list of novelties from Serra do Padre Ângelo, reinforcing the urge for conservation actions to protect the endemic flora of this Serra and other areas of campos rupestres in eastern Minas Gerais state.

Lymania involucrata (Bromeliaceae: Bromelioideae), a new ornamental species from Bahia, Brazil

Phytotaxa ◽  
2021 ◽  
Vol 489 (2) ◽  
pp. 209-215
Author(s):  
EVERTON HILO DE SOUZA ◽  
LIDYANNE Y. S. AONA ◽  
FERNANDA V. D. SOUZA ◽  
ELTON M. C. LEME
Keyword(s):  
New Species ◽  
Endangered Species ◽  
Atlantic Forest ◽  
Critically Endangered ◽  
Critically Endangered Species ◽  
Ornamental Species ◽  
Shape And Size

The authors describe, discuss, and illustrate Lymania involucrata, a new ornamental species from the Atlantic Forest in the municipality of Igrapiúna, Bahia, Brazil, here considered a critically endangered species. The new species is morphologically related to L. brachycaulis but clearly diffe According to Sousa rs from it by the well-developed, involucral primary bracts and the distinct shape and size of inflorescence, primary branches, and flowers. A map of the distribution of the species and taxonomic comments are presented.

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