scholarly journals Low worldwide genetic diversity in the basking shark ( Cetorhinus maximus )

2006 ◽  
Vol 2 (4) ◽  
pp. 639-642 ◽  
Author(s):  
A Rus Hoelzel ◽  
Mahmood S Shivji ◽  
Jennifer Magnussen ◽  
Malcolm P Francis
Keyword(s):  
Genetic Diversity ◽  
North Atlantic ◽  
Effective Population ◽  
Mitochondrial Dna Control Region ◽  
Significant Differentiation ◽  
Low Genetic Diversity ◽  
Eastern North Atlantic ◽  
Globally Distributed ◽  
Basking Shark ◽  
Cetorhinus Maximus

The basking shark ( Cetorhinus maximus ) is found in temperate waters throughout the world's oceans, and has been subjected to extensive exploitation in some regions. However, little is known about its current abundance and genetic status. Here, we investigate the diversity of the mitochondrial DNA control region among samples from the western North Atlantic, eastern North Atlantic, Mediterranean Sea, Indian Ocean and western Pacific. We find just six haplotypes defined by five variable sites, a comparatively low genetic diversity of π =0.0013 and no significant differentiation between ocean basins. We provide evidence for a bottleneck event within the Holocene, estimate an effective population size ( N e ) that is low for a globally distributed species, and discuss the implications.

scholarly journals Population structure and genetic diversity of non-native aoudad populations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sunčica Stipoljev ◽  
Toni Safner ◽  
Pavao Gančević ◽  
Ana Galov ◽  
Tina Stuhne ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Control Region ◽  
Effective Population ◽  
The Czech Republic ◽  
Mitochondrial Dna Control Region ◽  
Mountain Ranges ◽  
Spanish Populations ◽  
Microsatellite Alleles ◽  
Shared Alleles ◽  
Number Of Individuals

AbstractThe aoudad (Ammotragus lervia Pallas 1777) is an ungulate species, native to the mountain ranges of North Africa. In the second half of the twentieth century, it was successfully introduced in some European countries, mainly for hunting purposes, i.e. in Croatia, the Czech Republic, Italy, and Spain. We used neutral genetic markers, the mitochondrial DNA control region sequence and microsatellite loci, to characterize and compare genetic diversity and spatial pattern of genetic structure on different timeframes among all European aoudad populations. Four distinct control region haplotypes found in European aoudad populations indicate that the aoudad has been introduced in Europe from multiple genetic sources, with the population in the Sierra Espuña as the only population in which more than one haplotype was detected. The number of detected microsatellite alleles within all populations (< 3.61) and mean proportion of shared alleles within all analysed populations (< 0.55) indicates relatively low genetic variability, as expected for new populations funded by a small number of individuals. In STRUCTURE results with K = 2–4, Croatian and Czech populations cluster in the same genetic cluster, indicating joined origin. Among three populations from Spain, Almeria population shows as genetically distinct from others in results, while other Spanish populations diverge at K = 4. Maintenance of genetic diversity should be included in the management of populations to sustain their viability, specially for small Czech population with high proportion of shared alleles (0.85) and Croatian population that had the smallest estimated effective population size (Ne = 5.4).

scholarly journals Low genetic diversity in the endangered Taxus yunnanensis following a population bottleneck, a low effective population size and increased inbreeding

2016 ◽  
Vol 65 (1) ◽  
pp. 59-66 ◽  
Author(s):  
Y. C. Miao ◽  
Z. J. Zhang ◽  
J. R. Su
Keyword(s):  
Genetic Diversity ◽  
Habitat Fragmentation ◽  
Population Size ◽  
Effective Population Size ◽  
Spatial Genetic Structure ◽  
Population Bottleneck ◽  
Effective Population ◽  
Taxus Yunnanensis ◽  
Low Genetic Diversity ◽  
Two Populations

Abstract Taxus yunnanensis, which is an endangered tree that is considered valuable because it contains the effective natural anticancer metabolite taxol and heteropolysaccharides, has long suffered from severe habitat fragmentation. In this study, the levels of genetic diversity in two populations of 136 individuals were analyzed based on eleven polymorphic microsatellite loci. Our results suggested that these two populations were characterized by low genetic diversity (NE = 2.303/2.557; HO = 0.168/0.142; HE = 0.453/0.517), a population bottleneck, a low effective population size (Ne = 7/9), a high level of inbreeding (FIS = 0.596/0.702), and a weak, but significant spatial genetic structure (Sp = 0.001, b = −0.001*). Habitat fragmentation, seed shadow overlap and limited seed and pollen dispersal and potential selfing may have contributed to the observed gene tic structure. The results of the present study will enable development of practical conservation measures to effectively conserve the valuable genetic resources of this endangered plant.

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.

Nuclear and cytoplasmic genetic diversity reveals long-term population decline in Abies semenovii, an endemic fir of central Asia

2012 ◽  
Vol 42 (12) ◽  
pp. 2142-2152 ◽  
Author(s):  
Svetlana A. Semerikova ◽  
Martin Lascoux ◽  
Vladimir L. Semerikov
Keyword(s):  
Genetic Diversity ◽  
Central Asia ◽  
Population Decline ◽  
Population Expansion ◽  
Nuclear Marker ◽  
Effective Population ◽  
Species Status ◽  
Siberian Fir ◽  
Low Genetic Diversity

The genus Abies is one of the largest conifer genera and many of the marginal species remain poorly characterized. Abies semenovii B. Fedtsch. is a rare mountain fir species from central Asia, and its species status is still disputed. We used both nuclear (allozymes and AFLP) and chloroplastic (cpSSR) markers to show that A. semenovii deserves to be considered as a species and that its low genetic diversity justifies more a proactive conservation policy. First, A. semenovii was significantly differentiated from the Siberian fir Abies sibirica Ledeb. and we did not detect gene flow between the two species. Second, A. semenovii has a very low nuclear genetic diversity, suggesting a prolonged restricted effective population size. Abies semenovii had low cpSSR diversity too but the identification of seven closely related haplotypes suggests that these mutations accumulated recently during a phase of population expansion. This agrees well with the palynological record and is in contrast with the situation observed in another rare Eurasian fir endemic to Kamchatka, Abies gracilis Kom., which was devoid of variation in cpSSRs but that also had a more substantial nuclear marker diversity than A. semenovii, thereby suggesting a more recent but less severe population bottleneck.

scholarly journals The pattern of neutral molecular variation under the background selection model.

Genetics ◽  
1995 ◽  
Vol 141 (4) ◽  
pp. 1619-1632 ◽  
Author(s):  
D Charlesworth ◽  
B Charlesworth ◽  
M T Morgan
Keyword(s):  
Genetic Diversity ◽  
Genomic Region ◽  
Stochastic Simulations ◽  
Background Selection ◽  
Effective Population ◽  
Frequency Spectra ◽  
Low Genetic Diversity ◽  
Neutral Locus ◽  
Large Populations ◽  
Site Diversity

Abstract Stochastic simulations of the infinite sites model were used to study the behavior of genetic diversity at a neutral locus in a genomic region without recombination, but subject to selection against deleterious alleles maintained by recurrent mutation (background selection). In large populations, the effect of background selection on the number of segregating sites approaches the effect on nucleotide site diversity, i.e., the reduction in genetic variability caused by background selection resembles that caused by a simple reduction in effective population size. We examined, by coalescence-based methods, the power of several tests for the departure from neutral expectation of the frequency spectra of alleles in samples from randomly mating populations (Tajima's, Fu and Li's, and Watterson's tests). All of the tests have low power unless the selection against mutant alleles is extremely weak. In Drosophila, significant Tajima's tests are usually not obtained with empirical data sets from loci in genomic regions with restricted recombination frequencies and that exhibit low genetic diversity. This is consistent with the operation of background selection as opposed to selective sweeps. It remains to be decided whether background selection is sufficient to explain the observed extent of reduction in diversity in regions of restricted recombination.

scholarly journals Low genetic variation is associated with low mutation rate in the giant duckweed

2018 ◽  
Author(s):  
Shuqing Xu ◽  
Jessica Stapley ◽  
Saskia Gablenz ◽  
Justin Boyer ◽  
Klaus J. Appenroth ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Mutation Rate ◽  
Spontaneous Mutation ◽  
Effective Population ◽  
Spontaneous Mutation Rate ◽  
Low Genetic Diversity ◽  
Genome Wide ◽  
Census Population Size

AbstractMutation rate and effective population size (Ne) jointly determine intraspecific genetic diversity, but the role of mutation rate is often ignored. We investigate genetic diversity, spontaneous mutation rate andNein the giant duckweed (Spirodela polyrhiza). Despite its large census population size, whole-genome sequencing of 68 globally sampled individuals revealed extremely low within-species genetic diversity. Assessed under natural conditions, the genome-wide spontaneous mutation rate is at least seven times lower than estimates made for other multicellular eukaryotes, whereasNeis large. These results demonstrate that low genetic diversity can be associated with large-Nespecies, where selection can reduce mutation rates to very low levels, and accurate estimates of mutation rate can help to explain seemingly counterintuitive patterns of genome-wide variation.One Sentence SummaryThe low-down on a tiny plant: extremely low genetic diversity in an aquatic plant is associated with its exceptionally low mutation rate.

Genetic Diversity and Place in the General Phylogeographic Structure of Capercaillie, Tetrao Urogallus (Galliformes, Phasianidae), from Belarus

2019 ◽  
Vol 53 (5) ◽  
pp. 385-398
Author(s):  
K. V. Homel ◽  
T. E. Pavlushchick ◽  
M. E. Nikiforov ◽  
E. E. Kheidorova ◽  
M. G. Dmitrenok ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Molecular Marker ◽  
Human Activities ◽  
Phylogeographic Structure ◽  
Tetrao Urogallus ◽  
Biological Resource ◽  
Effective Population ◽  
Mitochondrial Dna Control Region ◽  
Intraspecific Structure

Abstract We report on the assessment of the level of genetic diversity of the capercaillie in Belarus. This species of birds is a valuable biological resource, and also acts as a natural indicator for the state of large forests and the degree of their disturbance by human activities. Two subspecies of the capercaillie —Tetrao urogallus major (C. L. Brehm, 1831) and Tetrao urogallus pleskei (Stegmann, 1926) have been described for Belarus. The first domain of the mitochondrial DNA control region was used as the molecular marker for the study. An additional assessment of the level of genetic diversity of the capercaillie was carried out by calculating the effective size of its population (Ne) in Belarus. We found that the absence of subspecific structure is characteristic for all samples of the capercaillie from Belarus. The data on the intraspecific structure and genetic diversity of the capercaillie from Belarus allows us to considerits population in the central and eastern parts of the country as stable and sustainable. This can be explained by its inclusion in the general phylogeographic structure of birds of the boreal lineage. The low values of the effective population size for the partially isolated capercaillie population from the western part of the country indicate the need for increased attention and further monitoring of that population.

Archival tagging of a basking shark, Cetorhinus maximus, in the western North Atlantic

2004 ◽  
Vol 84 (4) ◽  
pp. 795-799 ◽  
Author(s):  
Gregory B. Skomal ◽  
Grayson Wood ◽  
Nick Caloyianis
Keyword(s):  
United States ◽  
North Carolina ◽  
North Atlantic ◽  
Shelf Edge ◽  
Eastern United States ◽  
Temperature Preference ◽  
South West ◽  
Basking Shark ◽  
Cetorhinus Maximus ◽  
Tracking Period

A 6·1-m long female basking shark (Cetorhinus maximus) was tagged 73 km east of Nantucket Island, Massachusetts on 27 September 2001 with a pop-up archival transmitting tag. The tag detached prematurely on 6 December 2001 in an area approximately 800 km south-west of the tag site off the coast of North Carolina. The basking shark was vertically active for the 71-d tracking period, moving through depths and temperatures ranging from the surface to 320 m and 5·8 to 21·0°C, respectively. The shark displayed temporal variation in its residence depth and exhibited a marked temperature preference, with 72% of the temperature observations between 15·0 and 17·5°C. This track provides evidence that the basking shark associates with the continental shelf and shelf edge off the south-eastern United States during autumn. Moreover, it corroborates previous studies indicating that the basking shark remains active and does not hibernate during autumn.

scholarly journals Conservation concerns associated with low genetic diversity for K’gari–Fraser Island dingoes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
G. C. Conroy ◽  
R. W. Lamont ◽  
L. Bridges ◽  
D. Stephens ◽  
A. Wardell-Johnson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Factors ◽  
Conservation Management ◽  
Future Research ◽  
Effective Population ◽  
Tissue Samples ◽  
Island Populations ◽  
Low Genetic Diversity ◽  
Sample Set

AbstractThe dingo population on world heritage-listed K’gari-Fraser Island (K’gari) is amongst the most well-known in Australia. However, an absence of population genetic data limits capacity for informed conservation management. We used 9 microsatellite loci to compare the levels of genetic diversity and genetic structure of 175 K’gari dingo tissue samples with 264 samples from adjacent mainland regions. Our results demonstrated that the K'gari population has significantly lower genetic diversity than mainland dingoes (AR, HE, PAR; p < 0.05) with a fourfold reduction in effective population size (Ne = 25.7 vs 103.8). There is also strong evidence of genetic differentiation between the island and mainland populations. These results are in accordance with genetic theory for small, isolated, island populations, and most likely the result of low initial diversity and founder effects such as bottlenecks leading to decreased diversity and drift. As the first study to incorporate a large sample set of K’gari dingoes, this provides invaluable baseline data for future research, which should incorporate genetic and demographic monitoring to ensure long-term persistence. Given that human-associated activities will continue to result in dingo mortality, it is critical that genetic factors are considered in conservation management decisions to avoid deleterious consequences for this iconic dingo population.

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