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

2020 ◽  
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

AbstractKnowledge 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, it was 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 Inferring the Demographic History of Japanese Eel (Anguilla japonica) from Genomic Data: Insights for Conservation and Fisheries Management

2021 ◽  
Author(s):  
Leanne Faulks ◽  
Prashant Kaushik ◽  
Shoji Taniguchi ◽  
Masashi Sekino ◽  
Reiichiro Nakamichi ◽  
...  
Keyword(s):  
Population Size ◽  
Environmental Conditions ◽  
Wildlife Conservation ◽  
Demographic History ◽  
Population Decline ◽  
Anguilla Japonica ◽  
Japanese Eel ◽  
Population Declines ◽  
Effective Population ◽  
History Of

Assessing the status or population size of species is a key task for wildlife conservation and the sustainable management of harvested species. In particular, assessing historical changes in population size provides an evolutionary perspective on current population dynamics and can help distinguish between anthropogenic and natural causes for population decline. Japanese eel (Anguilla japonica) is an endangered yet commercially important catadromous fish species. Here we assess the demographic history of Japanese eel using the pairwise and multiple sequentially Markovian coalescent methods. The analyses indicate a reduction in effective population size (Ne) from 38 000 to 10 000 individuals between 4 and 1 Ma, followed by an increase to 80 000 individuals, between 1 Ma and 22-30 kya. Approximately 22-30 kya there is evidence for a reduction in Ne to approximately 60 000 individuals. These events are likely due to changes in environmental conditions, such as sea level and oceanic currents, especially around the last glacial maximum (19-33 kya). The results of this study suggest that Japanese eel has experienced at least two population bottlenecks, interspersed by a period of population growth. This pattern of demographic history may make Japanese eel sensitive to current and future population declines. Conservation management of Japanese eel should focus on practical ways to prevent further population decline and the loss of genetic diversity that is essential for the species to adapt to changing environmental conditions such as climate change.

scholarly journals Coalescent models at small effective population sizes and population declines are positively misleading

2019 ◽  
Author(s):  
M. Elise Lauterbur
Keyword(s):  
Genetic Diversity ◽  
Sample Size ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Relationships ◽  
Population Decline ◽  
Population Declines ◽  
Effective Population ◽  
Analytical Approximations ◽  
Population Sizes

AbstractPopulation genetics employs two major models for conceptualizing genetic relationships among individuals – outcome-driven (coalescent) and process-driven (forward). These models are complementary, but the basic Kingman coalescent and its extensions make fundamental assumptions to allow analytical approximations: a constant effective population size much larger than the sample size. These make the probability of multiple coalescent events per generation negligible. Although these assumptions are often violated in species of conservation concern, conservation genetics often uses coalescent models of effective population sizes and trajectories in endangered species. Despite this, the effect of very small effective population sizes, and their interaction with bottlenecks and sample sizes, on such analyses of genetic diversity remains unexplored. Here, I use simulations to analyze the influence of small effective population size, population decline, and their relationship with sample size, on coalescent-based estimates of genetic diversity. Compared to forward process-based estimates, coalescent models significantly overestimate genetic diversity in oversampled populations with very small effective sizes. When sampled soon after a decline, coalescent models overestimate genetic diversity in small populations regardless of sample size. Such overestimates artificially inflate estimates of both bottleneck and population split times. For conservation applications with small effective population sizes, forward simulations that do not make population size assumptions are computationally tractable and should be considered instead of coalescent-based models. These findings underscore the importance of the theoretical basis of analytical techniques as applied to conservation questions.

scholarly journals A case study on trade in threatened Tiger Geckos (Goniurosaurus) in Vietnam including updated information on the abundance of the Endangered G. catbaensis

2019 ◽  
Vol 33 ◽  
pp. 1-19 ◽  
Author(s):  
Hai Ngoc Ngo ◽  
Truong Quang Nguyen ◽  
Tien Quang Phan ◽  
Mona van Schingen ◽  
Thomas Ziegler
Keyword(s):  
International Trade ◽  
Conservation Status ◽  
Iucn Red List ◽  
Red List ◽  
Effective Population ◽  
Anthropogenic Pressures ◽  
Wild Fauna ◽  
Distribution Ranges ◽  
Long Bay ◽  
The U.S

Tiger geckos of the genusGoniurosaurusare considered as a susceptible reptile group, due to their restricted distribution ranges, specialisation to specific microhabitats and generally low population densities. While still new species have been discovered recently,Goniurosaurusspecies are threatened by extinction through habitat loss and collection for the pet trade. Of the 19 described species, for only eight species, the conservation status has been assessed within the IUCN Red List between 2016 and 2018 and all have been classified in the threat categories VU (Vulnerable), EN (Endangered) and CR (Critically Endangered).Goniurosaurusspp. are popular in the international pet market at least since the 1990s and several species experienced local extirpations as a consequence of massive over-collection in the past. However, tiger geckos have not been paid much attention for conservation, amongst others, due to the lack of comprehensive knowledge on their conservation status and biology. This study provides an overview of international trade inGoniurosaurusbased on available data from 1999 to 2018 in the U.S. as well as data from online surveys and interviews in Europe and Vietnam, with the main focus on species native to Vietnam. All five tiger gecko species known from Vietnam were found in the local trade as wild captures for the national and international market and / or in the U.S. and Europe for relatively higher prices. We found that entire trade chains are very long (including several transfers and dealers involved) and that keeping and transport happen under poor conditions. We herein provide updated information on the abundance of the Endangered Cat Ba Tiger Gecko, which was recently shown to not only occur at its type locality, Cat Ba Island, Hai Phong City, North Vietnam, but also to inhabit small offshore islands in the Ha Long Bay, Quang Ninh Province. While the wild effective population was found to be relatively stable on four islands in Ha Long Bay, consisting of about 124 and 129 individuals in July 2017 and April 2018, respectively, the abundance of other sub-populations, impacted by anthropogenic pressures were found to be very low (2–10 individuals). Based on our findings, we propose stringent conservation measures to more efficiently protect wild tiger gecko populations, such as the inclusion in the Governmental Decree in Vietnam, the assessment of remaining species in the IUCN Red List of Threatened Species and the inclusion in the Appendices of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES).

scholarly journals Holocene Population Decline and Conservation Implication for the Western Hercules Beetle, Dynastes grantii (Coleoptera, Scarabaeidae)

2019 ◽  
Vol 110 (5) ◽  
pp. 629-637 ◽  
Author(s):  
Jen-Pan Huang
Keyword(s):  
United States ◽  
Genetic Structure ◽  
Population Size ◽  
Demographic History ◽  
Population Decline ◽  
Southwestern United States ◽  
Effective Population ◽  
Mogollon Rim ◽  
Major Factors ◽  
Forest Habitats

Abstract The Western Hercules beetle (Dynastes grantii) is endemic to the highland forest habitats of southwestern United States and northern Mexico. The habitats harbor many endemic species, but are being threatened by rapid climate change and urban development. In this study, the genetic structure of D. grantii populations from southwestern United States was investigated. Specifically, genomic data from double-digest restriction-site-associated DNA sequencing libraries were utilized to test whether geographically distant populations from the Mogollon Rim (Arizona [N = 12 individuals] and New Mexico [N = 10 individuals]) are genetically structured. The study also estimated the effective population size of the Mogollon Rim populations based on genetic diversity. The results indicated that the 2 geographic populations from the Mogollon Rim were not genetically structured. A population size reduction was detected since the end of the last glacial period, which coincided with a reduction of forest habitat in the study area. The results implied that the connectivity and the size of highland forest habitats in the Mogollon Rim could have been the major factors shaping the population genetic structure and demographic history of D. grantii. The Western Hercules beetle could be a useful flagship species for local natural history education and to promote the conservation of highland forest habitats.

scholarly journals The conservation status and population decline of the African penguin deconstructed in space and time

2020 ◽  
Author(s):  
Richard B. Sherley ◽  
Robert J. M. Crawford ◽  
Andrew D. de Blocq ◽  
Bruce M. Dyer ◽  
Deon Geldenhuys ◽  
...  
Keyword(s):  
South African ◽  
Conservation Status ◽  
Population Decline ◽  
Iucn Red List ◽  
Population Declines ◽  
Posterior Density ◽  
Conservation Action ◽  
Space And Time ◽  
African Penguin ◽  
Highest Posterior Density

AbstractUnderstanding changes in abundance is crucial for conservation, but population growth rates often vary over space and time. We use 40 years of count data (1979–2019) and Bayesian state-space models to assess the African penguin Spheniscus demersus population under IUCN Red List Criterion A. We deconstruct the overall decline in time and space to identify where urgent conservation action is needed. The global African penguin population met the threshold for Endangered with a high probability (97%), having declined by almost 65% since 1989. An historical low of ~17,900 pairs bred in 2019. Annual declines were faster in the South African population (−4.2%, highest posterior density interval, HPDI: −7.8 to −0.6%) than the Namibian one (−0.3%, HPDI: −3.3 to +2.6%), and since 1999 were almost 10% at South African colonies north of Cape Town. Over the 40-year period, the Eastern Cape colonies went from holding ~25% of the total penguin population to ~40% as numbers decreased more rapidly elsewhere. These changes coincided with an altered abundance and availability of the main prey of African penguins. Our results underline the dynamic nature of population declines in space as well as time and highlight which penguin colonies require urgent conservation attention.

scholarly journals Demographic history of the fragmented yellowthroated bulbul (Pycnonotus xantholaemus) population in the Deccan Peninsula, India

2020 ◽  
Vol 43 ◽  
pp. 199-207
Author(s):  
A Jha ◽  
K Vasudevan
Keyword(s):  
Demographic History ◽  
Population Decline ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Mitochondrial Control Region ◽  
Haplotype Network ◽  
Genetic Connectivity ◽  
Founder Population ◽  
Effective Population ◽  
Genetic Structuring

The yellow-throated bulbul (YTB) is an endemic passerine restricted to scrub forests along hill slopes with exposed rocky outcrops in the Deccan Peninsula, India. It is found in small, discontinuous populations and is vulnerable to extinction due to ongoing habitat loss and subsequent population decline. To assess the genetic connectivity and past demography, we sequenced 1050 nucleotide base pairs of the mitochondrial control region of 60 individuals that represent distinct populations in the geographic range of the species. We recovered 39 haplotypes defined by 81 variable sites. Haplotype diversity was high with low nucleotide diversity, suggesting rapid population growth from a founder population with a small effective population size. The negative values of Tajima’s D and Fu’s Fs and small positive value of Ramos-Onsins and Rozas’ R2 suggest deviation from neutrality and population expansion. The haplotype network and demographic expansion parameters further suggest historical population expansion. Mismatch analysis statistics and Bayesian skyline plots estimate population expansion during the late Pleistocene. Although the species presently occurs in small, disconnected we found no structuring of the population. Dispersal events are the most likely explanation for the absence of genetic structuring in the YTB population. These results represent important data for the design of a conservation plan for this endemic and globally threatened species.

scholarly journals Conservation Status and Historical Relatedness of South African Communal Indigenous Goat Populations Using Genome-Wide Snp Marker

2020 ◽  
Author(s):  
Tlou Caswell Chokoe ◽  
Khanyi Hadebe ◽  
Farai Muchadeyi ◽  
Khathutshelo Nephawe ◽  
Edgar Dzomba ◽  
...  
Keyword(s):  
Negative Impact ◽  
Demographic History ◽  
Conservation Status ◽  
Snp Marker ◽  
Conservation Strategies ◽  
Effective Population ◽  
North West ◽  
Genome Wide ◽  
A Genome ◽  
Indigenous Goat

Abstract Background: Indigenous goats forms the majority of populations in smallholder; low input, low output production systems and are considered an important genetic resource due to their adaptability to different production environments and support communal farming. Effective population size (Ne), inbreeding levels, and the runs of homozygosity (ROHs) are effective tools for exploring the genetic diversity and understanding the demographic history in efforts to support breeding strategies to use and conserve genetic resources. Results: Across populations, the current Ne of Gauteng was the lowest at 371 animals, while the historical Ne across populations suggests that the ancestor Ne has decreased by 53.86%, 44.58%, 42.16% and 41.16% in Free State (FS), North West (NW), Limpopo (LP) and Gauteng (GP), respectively, over the last 971 generations. Genomic inbreeding levels related to ancient kinship (FROH >5Mb) was highest in FS (0.08±0.09) and lowest for Eastern Cape (EC) (0.02±0.02). A total of 871 ROH island regions which include important environmental adaptation and hermo-tolerance genes such as IL10RB, IL23A, FGF9, IGF1, EGR1, MTOR and MAPK3 were identified (occurring in over 20% of the samples) in FS (n = 37), GP (n = 42), NW (n = 2) populations only. The mean length of ROH across populations was 7.76Mb and ranged from 1.61Mb KwaZulu-Natal (KZN) to 98.05Mb (GP and NW). Distribution of ROH according to their size showed that the majority (n = 1949) of the detected ROH were >5Mb in length than the other categories. Assuming two hypothetical ancestral populations, the population from KZN and LP are revealed, supporting PC 1. The genomes of KZN and LP shared an origin but have substantial admixture from the EC and NW populations.Conclusions: These findings indicated a greater negative impact of inbreeding in recent times which is important for planning conservation strategies. It was revealed that the occurrence of high Ne and autozygosity varied largely across breeds in communal indigenous goat populations at different recent and ancient events when a genome-wide SNP marker was used.

scholarly journals Rapid population declines of Himalayan Griffon Gyps himalayensis in Upper Mustang, Nepal

2009 ◽  
Vol 19 (1) ◽  
pp. 99-107 ◽  
Author(s):  
RAJU ACHARYA ◽  
RICHARD CUTHBERT ◽  
HEM SAGAR BARAL ◽  
KARAN BAHADUR SHAH
Keyword(s):  
South Asia ◽  
Conservation Status ◽  
Population Decline ◽  
Population Trends ◽  
Himalayan Region ◽  
Veterinary Drug ◽  
Mountainous Region ◽  
Population Declines ◽  
Breeding Area ◽  
Population Collapse

SummaryThe population collapse of resident Gyps vulture species in South Asia, caused by the use of a veterinary drug diclofenac, has highlighted an urgent need to monitor numbers of other vulture species in the region. This study assessed population trends of Himalayan Griffon Gyps himalayensis in the mountainous region of Upper Mustang, Nepal, which is an important breeding area for the species. Vultures were surveyed in 2002, 2004 and 2005 by recording the number of birds sighted along 188 km of transects, and observing numbers of birds at breeding colonies. The number of birds recorded per day and per kilometre of transect declined by 67% and 70% respectively over the period of study. The number of active nests declined by 84% from 2002 to 2005. The veterinary drug diclofenac was available in pharmacies in the Mustang region. Young Himalayan Griffons, which migrate to the lowland areas of Nepal and, in increasing numbers to India, are highly likely to be subject to diclofenac poisoning. If this rate of population decline occurs throughout the Himalayan region, the conservation status of the species will need to be urgently reassessed.

scholarly journals Conservation priorities in an endangered estuarine seahorse are informed by demographic history

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Thomas Kalama Mkare ◽  
Bettine Jansen van Vuuren ◽  
Peter R. Teske
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Demographic History ◽  
Conservation Status ◽  
Limited Range ◽  
The Other ◽  
Conservation Priorities ◽  
Population Declines ◽  
Term Survival

AbstractHistorical demographic events shape genetic diversity that remains evident in the genomes of contemporary populations. In the case of species that are of conservation concern, this information helps to unravel evolutionary histories that can be critical in guiding conservation efforts. The Knysna seahorse, Hippocampus capensis, is the world’s most endangered seahorse species, and it presently survives in only three estuaries on the South African south coast. Factors that contributed to the species becoming endangered are unclear; additionally, the lack of information on whether the three populations should be managed separately because of potential long-term isolation hampers effective management efforts. In the present study, we reconstructed the seahorses’ demographic history using a suite of microsatellite loci. We found that the largest population (Knysna Estuary) has colonised the other estuaries relatively recently (< 450 years ago), and that its population size is comparatively large and stable. Neither of the other two populations shows signs of long-term reductions in population size. The high conservation status of the species is thus a result of its limited range rather than historical population declines. Our findings indicate that the long-term survival of H. capensis depends primarily on the successful management of the Knysna population, although the other estuaries may serve as reservoirs of genetic diversity.

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