scholarly journals Population Genomics and Structure of the Critically Endangered Mariana Crow (Corvus kubaryi)

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 187 ◽  
Author(s):  
Nandadevi Cortes-Rodriguez ◽  
Michael Campana ◽  
Lainie Berry ◽  
Sarah Faegre ◽  
Scott Derrickson ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Population Genomics ◽  
Population Decline ◽  
Management Strategies ◽  
Critically Endangered ◽  
Surprising Result ◽  
Single Nucleotide Variants ◽  
Genetic Structuring ◽  
Critically Endangered Species ◽  
A Genome

The Mariana Crow, or Åga (Corvus kubaryi), is a critically endangered species (IUCN -International Union for Conservation of Nature), endemic to the islands of Guam and Rota in the Mariana Archipelago. It is locally extinct on Guam, and numbers have declined dramatically on Rota to a historical low of less than 55 breeding pairs throughout the island in 2013. Because of its extirpation on Guam and population decline on Rota, it is of critical importance to assess the genetic variation among individuals to assist ongoing recovery efforts. We conducted a population genomics analysis comparing the Guam and Rota populations and studied the genetic structure of the Rota population. We used blood samples from five birds from Guam and 78 birds from Rota. We identified 145,552 candidate single nucleotide variants (SNVs) from a genome sequence of an individual from Rota and selected a subset of these to develop an oligonucleotide in-solution capture assay. The Guam and Rota populations were genetically differentiated from each other. Crow populations sampled broadly across their range on Rota showed significant genetic structuring – a surprising result given the small size of this island and the good flight capabilities of the species. Knowledge of its genetic structure will help improve management strategies to help with its recovery.

scholarly journals Conservation status and management insights from tracking a cryptic and Critically Endangered species of Orchidaceae

Oryx ◽  
2016 ◽  
Vol 51 (3) ◽  
pp. 441-450
Author(s):  
T. Kraaij ◽  
J. A. Baard ◽  
B. J. Crain
Keyword(s):  
Population Biology ◽  
Habitat Management ◽  
Conservation Status ◽  
Management Strategies ◽  
Growing Season ◽  
Iucn Red List ◽  
Critically Endangered ◽  
Physical Damage ◽  
Beneficial Effects ◽  
Critically Endangered Species

AbstractNinety-five percent of orchid species associated with fynbos shrublands of South Africa's Cape Floristic Kingdom have been assessed for the IUCN Red List, yet aspects of their demography and population biology remain poorly understood. We conducted a 6-year demographic study of the Critically Endangered Disa procera, a cryptic, terrestrial species from South Africa with a global population of c. 50 individuals known from a single location. We aimed to provide management recommendations that would facilitate its persistence. Our findings indicate that the population of D. procera is larger than previously thought, and the species occurs at two distinct locations. These orchids exhibit high interannual variation in population size and turnover of individuals, potentially indicative of a species with a short life span, and still meet the criteria for Critically Endangered status. The species benefits from disturbances, such as brush cutting along trails, or fire, which open up clearances in the vegetation. However, physical damage to plants during their aboveground growing season (September–January) is particularly detrimental and should be avoided in habitat management for the species. Fire had beneficial effects at the population and individual levels and is recommended at 10–25-year intervals, outside the orchid's growing season. The species exhibited comparatively high rates of fruit set (68%), suggesting that pollination limitation does not currently constrain its performance. Its patchy distribution may, however, indicate constraints on dispersal or recruitment. We recommend that management strategies should include continued protection and monitoring of both populations, studies on pollination, habitat requirements and mycorrhizal associates, and a prescribed disturbance regime.

scholarly journals The genome of the Balearic shearwater (Puffinus mauretanicus), a Critically Endangered seabird: a valuable resource for evolutionary and conservation genomics

2021 ◽  
Author(s):  
Cristian Cuevas Caballe ◽  
Joan Ferrer Obiol ◽  
Joel Vizueta ◽  
Meritxell Genovart ◽  
Jacob Gonzalez-Solis ◽  
...  
Keyword(s):  
Reference Genome ◽  
Conservation Status ◽  
Sharp Decrease ◽  
Night Vision ◽  
Critically Endangered ◽  
Conservation Genomics ◽  
Critically Endangered Species ◽  
A Genome ◽  
Long Read ◽  
Longline Fisheries

The Balearic shearwater (Puffinus mauretanicus) is the most threatened seabird in Europe. The fossil record suggests that human colonisation of the Balearic Islands resulted in a sharp decrease of the population size. Currently, populations continue to be decimated mainly due to predation by introduced mammals and bycatch in longline fisheries, and some studies predict their extinction by 2070. We present the first high-quality reference genome for the species which was obtained by a combination of short and long-read sequencing. Our hybrid assembly includes 4,169 scaffolds, with a scaffold N50 of 2.1 Mbp, a genome length of 1.2 Gbp, and BUSCO completeness of 96%, which is amongst the highest across sequenced avian species. This reference genome allowed us to study critical aspects relevant to the conservation status of the species, such as an evaluation of overall heterozygosity levels and the reconstruction of its historical demography. Our phylogenetic analysis using whole-genome information resolves current uncertainties in the order Procellariiformes systematics. Comparative genomics analyses uncover a set of candidate genes that may have played an important role into the adaptation to a pelagic lifestyle of Procellariiformes, including those for the enhancement of fishing capabilities, night vision and the development of natriuresis. This reference genome will be the keystone for future developments of genetic tools in conservation efforts for this Critically Endangered species.

scholarly journals Severe inbreeding and gene loss in the historical and extant population of the critically endangered Devils Hole pupfish

2021 ◽  
Author(s):  
David Tian ◽  
Bruce J. Turner ◽  
Christopher Herbert Martin
Keyword(s):  
Population Size ◽  
Stop Codon ◽  
Population Decline ◽  
Critically Endangered ◽  
Hypoxia Tolerance ◽  
Mitochondrial Activity ◽  
Low Oxygen ◽  
Genetic Rescue ◽  
A Genome ◽  
Devils Hole

Small populations with limited geographic distributions are predicted to be threatened by inbreeding and lack of genetic diversity, both of which may negatively impact fitness and exacerbate population decline. One of the most extreme natural examples is the Devils Hole pupfish (Cyprinodon diabolis), an iconic and critically endangered species with the smallest known habitat range of any vertebrate. This imperiled species has experienced severe declines in population size over the last thirty years and suffered major, repeated bottlenecks in 2007 and 2013, when the population sunk to 38 and 35 individuals, respectively. Here we sequenced contemporary and historical genomes of Devils Hole and neighboring Death Valley and Ash Meadows desert pupfishes to examine the genomic consequences of small population size. We found extreme inbreeding (FROH = 0.71 - 0.82) and increased genetic load in the Devils Hole pupfish. We also document unique fixed loss-of-function (LOF) alleles and deletions in genes associated with sperm motility, stress, and hypoxia within the extant Devils Hole pupfish population that likely reduce fitness. Comparisons between contemporary samples (2008 - 2012) and a genome sequenced from a 1980 formalin-fixed museum specimen suggest that inbreeding has increased 6% as the population has declined, but that many putatively deleterious variants have been segregating in the population since at least 1980. This includes a fixed early stop codon in cfap43 (n = 8/8 samples), which is associated with sperm flagellum defects and causes infertility in humans and mice. Out of ninety-four unique deletions, fifteen were detected within 2 kb of annotated genes. Five have roles in physiological responses to hypoxia and mitochondrial activity, such as redd1 (n = 7/7 samples), suggesting impaired hypoxia tolerance in this species despite the low oxygen concentrations of Devils Hole. We thus document one of the most extreme inbreeding events in a natural population and a set of candidate deleterious variants to inform management and potential genetic rescue in this conservation icon.

scholarly journals Genetic structure of Xiuning population of Isoetes sinensis， a critically endangered species in China

2004 ◽  
Vol 12 (6) ◽  
pp. 564-571
Author(s):  
Ye Qigang ◽  
CHEN Yuan-Yuan ◽  
Zuozhou Li ◽  
Hongwen Huang ◽  
Keyword(s):  
Genetic Structure ◽  
Endangered Species ◽  
Critically Endangered ◽  
Critically Endangered Species

Using hierarchies of cause to inform conservation of a naturally rare but critically endangered shrub Lasiopetalum pterocarpum (Malvaceae s.l.)

2009 ◽  
Vol 57 (5) ◽  
pp. 414 ◽  
Author(s):  
C. F. Wilkins ◽  
P. G. Ladd ◽  
B. J. Vincent ◽  
A. D. Crawford ◽  
L. W. Sage
Keyword(s):  
Life History ◽  
Seedling Recruitment ◽  
Management Strategies ◽  
Life History Strategy ◽  
Fruit Production ◽  
Critically Endangered ◽  
Active Management ◽  
Critically Endangered Species ◽  
Hand Pollination ◽  
In The Wild

Understanding the causes of rarity and ways of managing populations of rare species is essential for their successful conservation. The present study applies the conceptual model of a hierarchy of causes to Lasiopetalum pterocarpum E.M.Benn. & K.Shep. (a critically endangered species) to understand better its reproductive and ecological attributes, possible reasons for its rarity and to determine whether this model assists in developing management strategies. L. pterocarpum subpopulations from Serpentine National Park were censused to record abundance, plant health, phenology, flower and fruit production and the presence of any seed bank. These characteristics were matched to criteria in the hierarchies of cause model. There was no evidence of recent seedling recruitment at any subpopulation. Hand-pollination produced a flower-to-fruit conversion proportion similar to that found in the field and self- and cross-pollinations produced virtually the same fruit set. Seed store in soil from beneath the native subpopulations and at a translocation site showed seed was patchily distributed and infrequent. L. pterocarpum is an obligate seeder, killed by fire and dependent on disturbance to break seed dormancy. However, smoke has no effect on germination. Seed production does not constrain population growth, because seedling regeneration after fire in 1999 was prolific at sites where plants had been growing. In the hierarchies of cause framework, the main causes of rarity for this species are taxon ecology, life-history strategy and stochasticity. Thus, concentrating active management on factors related to life history such as mosaic patch burning, fencing after fire to exclude vertebrate grazers, weed control and establishment of translocated populations will aid the preservation of this species in the wild.

scholarly journals Low Diversity and Strong Genetic Structure Between Feeding and Nesting Areas in Brazil for the Critically Endangered Hawksbill Sea Turtle

2021 ◽  
Vol 9 ◽  
Author(s):  
Thyara Noely Simões ◽  
Ednilza Maranhão dos Santos ◽  
Alesandro Souza Santos ◽  
Fernanda Amato Gaiotto ◽  
Marco Antônio Costa ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Management Strategies ◽  
Species Conservation ◽  
Sea Turtle ◽  
Population Diversity ◽  
Critically Endangered ◽  
Marine Turtle ◽  
Northeastern Brazil ◽  
Loop Region ◽  
Low Diversity

Marine turtle nesting areas are characterized by receiving several females every year. The species Eretmochelys imbricata, known as hawksbill turtle is listed as Critically Endangered by the IUCN, and has been the target of studies on genetic structure and population diversity in nesting areas. Therefore, this study aimed to analyze the genetic diversity and haplotype composition of populations sampled in nesting areas from the coast of northeastern Brazil based on the mtDNA D-loop region. We used genetic information and compared it with data from feeding areas available in public databases. We recorded a total of six exclusive haplotypes in the nesting areas and 27 exclusive haplotypes for the feeding areas. The H_1 haplotype was shared in all nesting areas. The turtles of these regions had a low diversity and a genetic structure composed of five divergent groups separating the reproductive areas from the ones of feeding areas. Positive and significant geographical distance relationships were also recorded with FST values (r = 0.2302, p = 0.007). Our results revealed that hawksbill turtles from reproductive areas comprise a single population that needs management strategies to protect the threatened species, in addition to providing information that contributes to future actions for the species conservation.

scholarly journals Nimesulide Poisoning in White-Rumped Vulture Gyps Bengalensis in Gujarat, India

2021 ◽  
Author(s):  
Kanthan Nambirajan ◽  
Subramanian Muralidharan ◽  
Aditya Roy Ashimkumar ◽  
Shashikant Jadhav
Keyword(s):  
Indian Subcontinent ◽  
Population Decline ◽  
Critically Endangered ◽  
Gut Contents ◽  
High Concentration ◽  
Critically Endangered Species ◽  
Effective System ◽  
Wild Ass ◽  
The Government ◽  
Gyps Bengalensis

Abstract Catastrophic population decline of White-rumped Vulture due to use of a non-steroidal anti-inflammatory drug (NSAID), diclofenac throughout its distribution range is well documented. White-rumped Vulture was listed as Critically Endangered and only few thousands are remining. During 2019, there were two incidents of White-rumped Vulture death in Gujarat. In February 2019, two vultures were reported dead in Sanand, Gujarat and the death was suspected to be poisoning. Another two vultures were also reported to have died in Wild Ass Sanctuary, Dhrangadhra in October 2019. Tissues and gut contents of all four vultures were received for toxicological investigation and checked whether these vultures died due to NSAIDs. The tissues were analysed for thirteen NSAIDs. Of all the NSAIDs, nimesulide was detected in all the tissues analyzed in high concentration (17 - 1395 ng/g). Subsequently, these tissues were also screened for a set of mostly used toxic pesticides in India, and none of them was in toxic level. Visceral gout was also observed in all the four vultures during post-mortem. Elevated levels of nimesulide in tissues with clear symptoms of gout, indicated that the vultures died due to nimesulide poisoning. Although, other than diclofenac, many NSAIDs are toxic/suspected to be toxic to White-rumped Vultures, only nimesulide is reported with clear symptom of gout in wild dead White-rumped Vultures similar to diclofenac consistently in recent past. Considering the fact that nimesulide also acts similar to diclofenac leading to death in White-rumped Vulture, it seems that nimesulide is replacing diclofenac in case of White-rumped Vulture in Gujarat. Nimesulide is cause of concern in conservation of White-rumped Vultures. Hence, nimesulide should also be banned by the government for veterinary use in addition to diclofenac to conserve White-rumped Vulture in Indian subcontinent. Further, an effective system is recommended to be put in place to collect the tissues of dead Vultures for toxicological investigations, and eventual conservation of the critically endangered species.

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