Genetic monitoring informs conservation status and trend of Arctic grayling at the southern edge of their distribution

2020 ◽  
Vol 77 (12) ◽  
pp. 1934-1942
Author(s):  
Ryan P. Kovach ◽  
Andrew R. Whiteley ◽  
Matthew E. Jaeger ◽  
Sally Painter ◽  
Angela Lodmell ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Conservation Status ◽  
Temporal Trends ◽  
Genetic Data ◽  
Genetic Monitoring ◽  
Evolutionary Status ◽  
Effective Population ◽  
Conservation Action ◽  
Arctic Grayling ◽  
Conservation Concern

The number of effective breeders (Nb) has been touted as a means to monitor freshwater fishes, but the realized application of Nb has been limited. Using genetic monitoring data for two Arctic grayling (Thymallus arcticus) populations of conservation concern, we describe temporal trends in genetic variation and Nb, determine how sampling and variance in reproductive success influence estimates of Nb, and quantify the relationship among Nb, effective population size (Ne), and adult abundance (Nc). Temporal trends in allelic richness (AR) and Nb tracked known or suspected population trajectories. Nb increased in one population where there has been extensive conservation action, and both Nb and AR tracked a decline in the other population where harsh winter conditions have resulted in overwinter mortality events. After accounting for population demography, Ne estimates for each population were 190.7 and 308.8. Overall, this study demonstrates that temporal genetic data effectively resolve demographic and evolutionary status and trend in Arctic grayling, provides insight into the demographic factors that influence genetic variation, and emphasizes the value of temporal genetic data for conservation and management.

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.

Archival DNA reveals cryptic biodiversity within the Spotted Shag (Phalacrocorax punctatus) from New Zealand

The Condor ◽  
2019 ◽  
Vol 121 (3) ◽  
Author(s):  
Nicolas J Rawlence ◽  
Matt J Rayner ◽  
Tim G Lovegrove ◽  
Debbie Stoddart ◽  
Melanie Vermeulen ◽  
...  
Keyword(s):  
New Zealand ◽  
Conservation Management ◽  
Species Conservation ◽  
Genetic Data ◽  
Mitochondrial Control Region ◽  
Phylogenetic Structure ◽  
Management Guidelines ◽  
Conservation Concern ◽  
Cryptic Biodiversity ◽  
Archival Dna

Abstract Genetic data are increasingly being used to prioritize species conservation in a fiscally constrained age of seemingly boundless conservation crises. Such data can also reveal previously cryptic biodiversity requiring further revision of conservation management guidelines. Using a combination of mitochondrial (control region) and nuclear (beta fibrinogen intron 7) DNA, and morphology, we reveal that the endemic New Zealand Spotted Shag (Phalacrocorax punctatus) complex exhibits phylogenetic structure that is decoupled from previously recorded qualitative morphological variation. Crucially, the most genetically distinct populations within P. punctatus are from northern New Zealand; recent surveys show that these populations, which house important genetic diversity within Spotted Shags, are in danger of being extirpated. In contrast, we find the previously phenotypically differentiated nominate (P. punctatus punctatus) and Blue (P. punctatus oliveri) Shag subspecies show no genetic and morphological separation, and are of least conservation concern.

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.

Quantifying genetic variation at the molecular level

2019 ◽  
pp. 34-66
Author(s):  
Asher D. Cutter
Keyword(s):  
Genetic Variation ◽  
Dna Sequences ◽  
Migration Rate ◽  
Population Genetic ◽  
Quantitative Methods ◽  
Molecular Level ◽  
Effective Population ◽  
Fundamental Properties ◽  
Site Frequency Spectrum ◽  
Population Genetic Variation

Chapter 3, “Quantifying genetic variation at the molecular level,” introduces quantitative methods for measuring variation directly in DNA sequences to help decipher fundamental properties of populations and what they can tell us about evolution. It provides an overview of the evolutionary factors that contribute to genetic variation, like mutational input, effective population size, genetic drift, migration rate, and models of migration. This chapter surveys the principal ways to measure and summarize polymorphisms within a single population and across multiple populations of a species, including heterozygosity, nucleotide polymorphism estimators of θ‎, the site frequency spectrum, and F ST, and by providing illustrative natural examples. Populations are where evolution starts, after mutations arise as the spark of population genetic variation, and Chapter 3 describes how to quantify the variation to connect observations to predictions about how much polymorphism there ought to be under different circumstances.

scholarly journals Genetic data improve the assessment of the conservation status based only on herbarium records of a Neotropical tree

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
André Carneiro Muniz ◽  
José Pires Lemos-Filho ◽  
Renata Santiago de Oliveira Buzatti ◽  
Priciane Cristina Correa Ribeiro ◽  
Fernando Moreira Fernandes ◽  
...  
Keyword(s):  
Conservation Status ◽  
Genetic Data ◽  
Neotropical Tree

scholarly journals Genetic Diversity of Indigenous Pigs from South China Area Revealed by SNP Array

Animals ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 361 ◽  
Author(s):  
Shuqi Diao ◽  
Shuwen Huang ◽  
Zhiting Xu ◽  
Shaopan Ye ◽  
Xiaolong Yuan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Conservation Status ◽  
Snp Array ◽  
Size Analysis ◽  
Selection Signatures ◽  
Effective Population ◽  
Low Genetic Diversity ◽  
Indigenous Pigs

To investigate the genetic diversity, population structure, extent of linkage disequilibrium (LD), effective population size (Ne), and selection signatures in indigenous pigs from Guangdong and Guangxi in China, 226 pigs belonging to ten diverse populations were genotyped using single nucleotide polymorphism (SNP) chips. The genetic divergence between Chinese and Western pigs was determined based on the SNP chip data. Low genetic diversity of Dahuabai (DHB), Luchuan (LC), Lantang (LT), and Meihua (MH) pigs, and introgression of Western pigs into Longlin (LL), MH, and Yuedonghei (YDH) pigs were detected. Analysis of the extent of LD showed that indigenous pigs had low LD when pairwise SNP distance was short and high LD when pairwise SNP distance was long. Effective population size analysis showed a rapid decrease for Chinese indigenous pigs, and some pig populations had a relatively small Ne. This result indicated the loss of genetic diversity in indigenous pigs, and introgression from Western commercial pigs. Selection signatures detected in this study overlapped with meat quality traits, such as drip loss, intramuscular fat content, meat color b*, and average backfat thickness. Our study deepened understanding of the conservation status and domestication of Chinese indigenous pigs.

scholarly journals A globally threatened shark, Carcharias taurus, shows no population decline in South Africa

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Juliana D. Klein ◽  
Aletta E. Bester-van der Merwe ◽  
Matthew L. Dicken ◽  
Arsalan Emami-Khoyi ◽  
Kolobe L. Mmonwa ◽  
...  
Keyword(s):  
South Africa ◽  
Census Data ◽  
Demographic History ◽  
Conservation Status ◽  
Population Decline ◽  
Multilocus Genotype ◽  
Population Declines ◽  
Effective Population ◽  
Anthropogenic Pressures ◽  
Carcharias Taurus

Abstract Knowledge about the demographic histories of natural populations helps to evaluate their conservation status, and potential impacts of natural and anthropogenic pressures. In particular, estimates of effective population size obtained through molecular data can provide useful information to guide management decisions for vulnerable populations. The spotted ragged-tooth shark, Carcharias taurus (also known as the sandtiger or grey nurse shark), is widely distributed in warm-temperate and subtropical waters, but has suffered severe population declines across much of its range as a result of overexploitation. Here, we used multilocus genotype data to investigate the demographic history of the South African C. taurus population. Using approximate Bayesian computation and likelihood-based importance sampling, we found that the population underwent a historical range expansion that may have been linked to climatic changes during the late Pleistocene. There was no evidence for a recent anthropogenic decline. Together with census data suggesting a stable population, these results support the idea that fishing pressure and other threats have so far not been detrimental to the local C. taurus population. The results reported here indicate that South Africa could possibly harbour the last remaining, relatively pristine population of this widespread but vulnerable top predator.

scholarly journals Morphometric Variation as an Indicator of Genetic Interactions Between Black-Capped and Carolina Chickadees at a Contact Zone in the Appalachian Mountains

The Auk ◽  
2000 ◽  
Vol 117 (2) ◽  
pp. 427-444 ◽  
Author(s):  
Gene D. Sattler ◽  
Michael J. Braun
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Markers ◽  
Hybrid Zone ◽  
Morphological Variation ◽  
Genetic Data ◽  
Mixed Ancestry ◽  
Morphometric Variation ◽  
Average Gene ◽  
Hybridization And Introgression

AbstractWe studied hybridization and introgression between Black-capped (Poecile atricapillus) and Carolina (P. carolinensis) chickadees along two transects in the Appalachians using four genetic markers and multivariate analysis of morphology. Genetic data revealed that at least 58% of the birds in the center of each transect were of mixed ancestry and that recombinant genotypes predominated among hybrids, demonstrating that hybridization is frequent and that many hybrids are fertile. Genetic clines generally were steep and coincident in position, but introgression was evident well beyond the range interface. Introgression was higher at the one autosomal locus surveyed than in mitochondrial DNA or in two sex-linked markers, suggesting that the hybrid zone is a conduit for gene flow between the two forms at some loci. On a broad scale, morphometric variation was concordant with genetic variation. Clines in morphological variation based on principal components (PC) scores were steep and coincident with genetic clines. Also, a strong correlation within a population between PC scores and an individual's genetic makeup suggested that a large amount of morphological variation was genetically determined. However, morphological analysis indicated that hybrids were uncommon on one transect, whereas genetic data clearly showed that they were common on both. In addition, patterns of morphological variation were equivocal regarding introgression across the hybrid zone. Thus, genetic data provided a complementary and more detailed assessment of hybridization, largely due to the discrete nature of genetic variation. Genetic markers are useful in understanding hybridization and introgression, but diagnostic markers may underestimate average gene flow if selection against hybrids maintains steep clines at diagnostic loci. To gain a clearer picture of the genome-wide effects of hybridization, a much larger number of loci must be assayed, including non-diagnostic ones.

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