scholarly journals State of Shark and Ray Genomics in an Era of Extinction

2021 ◽  
Vol 8 ◽  
Author(s):  
Jessica Pearce ◽  
Matthew W. Fraser ◽  
Ana M. M. Sequeira ◽  
Parwinder Kaur
Keyword(s):  
Conservation Status ◽  
Marine Species ◽  
Chromosome Length ◽  
Cultural Significance ◽  
Conservation Genomics ◽  
Genomic Resources ◽  
A Genome ◽  
Sampling Protocols ◽  
Threatened Taxa ◽  
Data Deficient

Chondrichthyan species (sharks, rays, skates, and chimeras) are a class of high ecological, economic, and cultural significance, and yet they are the most threatened taxa in the marine environment. The creation of reference chromosome-length genome assemblies allows for conservation genomics methods, such as population and ecological genomics, to be utilized. Despite being greatly threatened and of great importance in maintaining ecosystem function, chondrichthyan species have been repeatedly absent from conservation-based genome sequencing projects. Less than 1% of these species have a genome sequence, despite their almost 50% either threatened or Data Deficient conservation status. Most notably, there are seven orders within this class without any genome representation. In this review, we identify gaps in chondrichthyan genomic resources and demonstrate how the lack of genomic resources for this major taxonomic class is limiting the conservation of these already difficult to conserve species. We highlight other applications for chondrichthyans genomics, such as evolutionary and developmental biology. Likely, the mismatching sampling protocols and limited computational skills and communication between fields have been preventing the integration of marine and molecular sciences. Here, we propose that this field is in dire need to move forward quickly to increase protection for marine species and ecosystems through improved collaboration between marine, molecular, and computer sciences.

scholarly journals Bivalves (Mollusca: Bivalvia) in Malaysian Borneo: status and threats

2021 ◽  
Vol 13 (11) ◽  
pp. 19553-19565
Author(s):  
Abdulla-Al-Asif ◽  
Hadi Hamli ◽  
Abu Hena Mustafa Kamal ◽  
Mohd Hanafi Idris ◽  
Geoffery James Gerusu ◽  
...  
Keyword(s):  
Conservation Status ◽  
Species Conservation ◽  
Marine Species ◽  
Iucn Red List ◽  
Conservation Strategies ◽  
Future Research ◽  
Bivalve Species ◽  
Bivalve Molluscs ◽  
Data Deficient ◽  
Malaysian Borneo

Species checklists enlist the species existing within a distinct geographical biome and assist as an indispensable input for evolving conservation and administration strategies. The arenas of conservation ecology and biology face the challenge of exaggerated biodiversity, accredited to the non-recognition of taxonomic inconsistencies. The study’s goals are to organize all scattered taxonomic information regarding bivalve molluscs from Malaysian Borneo, i.e. Sarawak and Sabah, under one umbrella. Available literature regarding Malaysian Borneo was reviewed. The published taxonomic data on bivalve species, conservation status, inconsistencies, habitats (marine, fresh, and brackish), research aspects, threats, and conservation strategies are presented. A critical review of the checklists and distributional records of the class Bivalvia from Malaysian Borneo and subsequent validation of species names with the World Register of Marine Species (WoRMS) database revealed that currently 76 bivalve species from 12 orders and other entities, 18 superfamilies, and 27 families have been recorded from the area. Twenty-six inconsistencies with WoRMS were found, and the corrected names are presented. The study indicates most of the enlisted bivalve species have not been evaluated by the IUCN Red List authority and have ‘Least Concern’ or ‘Data Deficient’ status for Malaysian Borneo. To date, published documents on conservation decision strategies and guidelines for future research are not good enough. Nevertheless, potential threats and their remedies for bivalves in the enriched Malaysian Borneo ecosystems are discussed herein. 

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 Global extinction risk for seahorses, pipefishes and their near relatives (Syngnathiformes)

Oryx ◽  
2021 ◽  
pp. 1-10
Author(s):  
Riley A. Pollom ◽  
Gina M. Ralph ◽  
Caroline M. Pollock ◽  
Amanda C.J. Vincent
Keyword(s):  
Threatened Species ◽  
Habitat Degradation ◽  
Extinction Risk ◽  
Conservation Status ◽  
Field Research ◽  
Selective Extraction ◽  
Iucn Red List ◽  
Point Estimate ◽  
Conservation Action ◽  
Data Deficient

Abstract Few marine taxa have been comprehensively assessed for their conservation status, despite heavy pressures from fishing, habitat degradation and climate change. Here we report on the first global assessment of extinction risk for 300 species of syngnathiform fishes known as of 2017, using the IUCN Red List criteria. This order of bony teleosts is dominated by seahorses, pipefishes and seadragons (family Syngnathidae). It also includes trumpetfishes (Aulostomidae), shrimpfishes (Centriscidae), cornetfishes (Fistulariidae) and ghost pipefishes (Solenostomidae). At least 6% are threatened, but data suggest a mid-point estimate of 7.9% and an upper bound of 38%. Most of the threatened species are seahorses (Hippocampus spp.: 14/42 species, with an additional 17 that are Data Deficient) or freshwater pipefishes of the genus Microphis (2/18 species, with seven additional that are Data Deficient). Two species are Near Threatened. Nearly one-third of syngnathiformes (97 species) are Data Deficient and could potentially be threatened, requiring further field research and evaluation. Most species (61%) were, however, evaluated as Least Concern. Primary threats to syngnathids are (1) overexploitation, primarily by non-selective fisheries, for which most assessments were determined by criterion A (Hippocampus) and/or (2) habitat loss and degradation, for which assessments were determined by criterion B (Microphis and some Hippocampus). Threatened species occurred in most regions but more are found in East and South-east Asia and in South African estuaries. Vital conservation action for syngnathids, including constraining fisheries, particularly non-selective extraction, and habitat protection and rehabilitation, will benefit many other aquatic species.

scholarly journals Conservation Status of Marine Biodiversity in Oceania: An Analysis of Marine Species on the IUCN Red List of Threatened Species

2011 ◽  
Vol 2011 ◽  
pp. 1-14 ◽  
Author(s):  
Beth A. Polidoro ◽  
Cristiane T. Elfes ◽  
Jonnell C. Sanciangco ◽  
Helen Pippard ◽  
Kent E. Carpenter
Keyword(s):  
Threatened Species ◽  
Environmental Changes ◽  
Extinction Risk ◽  
Conservation Status ◽  
Marine Species ◽  
Iucn Red List ◽  
Red List ◽  
Marine Biodiversity ◽  
Conservation Priorities ◽  
Conservation Action

Given the economic and cultural dependence on the marine environment in Oceania and a rapidly expanding human population, many marine species populations are in decline and may be vulnerable to extinction from a number of local and regional threats. IUCN Red List assessments, a widely used system for quantifying threats to species and assessing species extinction risk, have been completed for 1190 marine species in Oceania to date, including all known species of corals, mangroves, seagrasses, sea snakes, marine mammals, sea birds, sea turtles, sharks, and rays present in Oceania, plus all species in five important perciform fish groups. Many of the species in these groups are threatened by the modification or destruction of coastal habitats, overfishing from direct or indirect exploitation, pollution, and other ecological or environmental changes associated with climate change. Spatial analyses of threatened species highlight priority areas for both site- and species-specific conservation action. Although increased knowledge and use of newly available IUCN Red List assessments for marine species can greatly improve conservation priorities for marine species in Oceania, many important fish groups are still in urgent need of assessment.

scholarly journals Co-occurring cryptic species pose challenges for conservation: a case study of the African dwarf crocodile (Osteolaemusspp.) in Cameroon

Oryx ◽  
2014 ◽  
Vol 49 (4) ◽  
pp. 584-590 ◽  
Author(s):  
Nicole L. Smolensky
Keyword(s):  
Cryptic Species ◽  
Conservation Status ◽  
Taxonomic Revision ◽  
Single Species ◽  
Conservation Strategies ◽  
Encounter Rates ◽  
Distribution Maps ◽  
Species Complexes ◽  
Threatened Taxa ◽  
Population Structures

AbstractThe conservation status of threatened taxa may be obfuscated by the detection of cryptic species complexes, in both vertebrate and invertebrate species. African dwarf crocodiles (Osteolaemusspp.) are hunted throughout their range but their conservation status is unknown. Few population assessments have been carried out and there has been a taxonomic revision of the number of species in the genus. The similar morphologies ofOsteolaemus tetraspisandOsteolaemus osbornipose a challenge for conservation in Cameroon, where they are still managed as a single species. Nocturnal spotlight surveys were conducted in three regions during August–November 2010 and December 2011–February 2012 to provide population assessments ofO. tetraspisandO. osborniand raise awareness of the two species in Cameroon. The mean encounter rates ofO. tetraspisandO. osborniwere 1.02 ± SD 1.34 (65 individuals in 39 surveys) and 0.61 ± SD 0.38 (three in four surveys) crocodiles per km, respectively. TheO. tetraspispopulation comprised juveniles predominantly and had a male-biased sex ratio. The fewO. osbornidetected comprised both adults and juveniles. Both species are threatened in Cameroon, based on low encounter rates, young population structures and the threats of habitat loss and hunting pressure. This study provides distribution maps and serves as a baseline to quantify population trends and inform conservation strategies.

scholarly journals Functional genetic diversity in an exploited marine species and its relevance to fisheries management

2021 ◽  
Vol 288 (1945) ◽  
pp. 20202398
Author(s):  
Eleni L. Petrou ◽  
Angela P. Fuentes-Pardo ◽  
Luke A. Rogers ◽  
Melissa Orobko ◽  
Carolyn Tarpey ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Isolation By Distance ◽  
Chromosomal Rearrangements ◽  
High Mobility ◽  
Marine Species ◽  
Clupea Harengus ◽  
Pacific Herring ◽  
Reproductive Timing ◽  
Cultural Significance ◽  
Ecological Processes

The timing of reproduction influences key evolutionary and ecological processes in wild populations. Variation in reproductive timing may be an especially important evolutionary driver in the marine environment, where the high mobility of many species and few physical barriers to migration provide limited opportunities for spatial divergence to arise. Using genomic data collected from spawning aggregations of Pacific herring ( Clupea pallasii ) across 1600 km of coastline, we show that reproductive timing drives population structure in these pelagic fish. Within a specific spawning season, we observed isolation by distance, indicating that gene flow is also geographically limited over our study area. These results emphasize the importance of considering both seasonal and spatial variation in spawning when delineating management units for herring. On several chromosomes, we detected linkage disequilibrium extending over multiple Mb, suggesting the presence of chromosomal rearrangements. Spawning phenology was highly correlated with polymorphisms in several genes, in particular SYNE2 , which influences the development of retinal photoreceptors in vertebrates. SYNE2 is probably within a chromosomal rearrangement in Pacific herring and is also associated with spawn timing in Atlantic herring ( Clupea harengus ). The observed genetic diversity probably underlies resource waves provided by spawning herring. Given the ecological, economic and cultural significance of herring, our results support that conserving intraspecific genetic diversity is important for maintaining current and future ecosystem processes.

scholarly journals Distribution update, conservation status and color in life of the rare Amazonian snake, Eutrachelophis papilio Zaher and Prudente 2019 (Serpentes: Xenodontini)

2020 ◽  
Vol 50 (3) ◽  
pp. 252-255
Author(s):  
Nathalie CITELI ◽  
Mariana DE-CARVALHO ◽  
Reuber BRANDÃO
Keyword(s):  
Convex Polygon ◽  
Conservation Status ◽  
Biological Data ◽  
Distribution Area ◽  
Minimum Convex Polygon ◽  
Human Footprint ◽  
Data Deficient ◽  
First Time ◽  
Polygon Method ◽  
Anthropic Pressure

ABSTRACT The rare Amazonian snake Eutrachelophis papilio is known from only five individuals, from four localities, belonging to its type-series, the more recent collected over 10 years ago. Here, we expand its distribution and describe its color in life for the first time. We also provide an estimate of its distribution area using the minimum convex polygon method and identify the values of anthropic pressure within its known distribution range with the Human Footprint Index. The new occurrence is located 291 km from the nearest known locality and its distribution is associated with pristine forests. Considering its rarity, and the absence of demographic and biological data, we suggest that the species should be classified as Data Deficient by IUCN criteria.

scholarly journals First records of bats (Mammalia: Chiroptera) from Son La city, Northwestern Vietnam, with remarks on their conservation status

2019 ◽  
Vol 41 (3) ◽  
Author(s):  
Dao Nhan Loi
Keyword(s):  
Threatened Species ◽  
Conservation Status ◽  
Natural Habitats ◽  
Farming Area ◽  
Northwestern Region ◽  
Data Deficient ◽  
The City

Son La is a well-known city in the Northwestern region of Vietnam for its outstanding landscapes. It contains a variety of ecosystems ranging from farming area, valleys, forests on hills and karst with cave systems. Natural habitats of the city would be suitable for many bat species. However, bats of the city were not included in any literature. Between March 2014 and June 2018, we conducted a series of bat surveys in this city using mist nets and harp traps. Results from our study indicated that Son La city is a home to at least 21 bat species belonging to 9 genera, 6 families. Of which, Rhinolophus thomasi was listed as “VU” (Vulnerable) in the 2007 Red Book of Vietnam and Myotis annamiticus was listed in the IUCN Redlist of the Threatened Species as “DD” (Data Deficient). This paper provides the first data on bats of Son La city with morphological measurements and conservation status of each recorded species.

scholarly journals Sumberdaya Kuda Laut (Hippocampus spp.) di Perairan Pulau Bintan, Teluk Lampung dan Pulau Tanakeke

2019 ◽  
Vol 4 (1) ◽  
pp. 27
Author(s):  
Masayu Rahmia Anwar Putri ◽  
Astri Suryandari ◽  
Joni Haryadi
Keyword(s):  
Marine Species ◽  
Literature Study ◽  
South Sulawesi ◽  
Lack Of Information ◽  
Management Measures ◽  
Data Deficient ◽  
Study Sites ◽  
Habitat Damage ◽  
Over Exploitation ◽  
Sexually Mature

<strong>Seahorse Resources (Hippocampus spp.) in the Waters of Bintan Island, Lampung Bay and Tanakeke Island</strong>.Information on seahorse resources is very limited, from 35 species of marine species listed on the IUCN redlist, 20 species are listed as "data deficient" which illustrates the lack of information related to sea horses, even for highly exploited species. This research was conducted to inventory sea horse resources (<em>Hippocampus</em> spp.), covering spesies information, size, sex ratio and density of seahorses from three potential locations, they are Bintan Island, Lampung and Tanakeke Island Waters. Field observation for seahorse resources was conducted at Bintan Island (Riau Islands Province) in March 2016, Lampung Bay (Lampung Province) in May 2016 and Tanakeke Islands (Takalar Regency, South Sulawesi) in June 2016 by purposive sampling method, interview with fisherman and collector and also literature study. A total of 5 seahorse species were found in three research locations, 4 species found in Bintan waters <em>(H. comes</em>, <em>H. spinossisimus</em>, <em>H. hystrix</em> and <em>H. kuda</em>), 2 species found in Lampung Bay (<em>H. comes</em> and <em>H. kuda</em>) and only 1 species found in Tanakeke (<em>H.barbouri</em>). Most of seahorse found during the study were categorized as sexually mature, dominated with seahorse 11-12 cm in size. The different types and densities of seahorses in the three study sites are supported by differences in habitat where seahorses are occupied. The density of seahorses tended to be low due to over-exploitation, environmental change and habitat damage. Management measures based on biological aspects and ecological conditions of each region need to be carried out for sustainable seahorse fisheries.

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