scholarly journals Genotyping-in-Thousands by sequencing of archival fish scales reveals maintenance of genetic variation following a severe demographic contraction in kokanee salmon

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Christopher Setzke ◽  
Carmen Wong ◽  
Michael A. Russello
Keyword(s):  
Wildlife Conservation ◽  
Dna Analysis ◽  
Population Decline ◽  
Allelic Diversity ◽  
Biodiversity Loss ◽  
Poor Quality ◽  
Population History ◽  
Effective Population ◽  
High Coverage ◽  
Kokanee Salmon

AbstractHistorical DNA analysis of archival samples has added new dimensions to population genetic studies, enabling spatiotemporal approaches for reconstructing population history and informing conservation management. Here we tested the efficacy of Genotyping-in-Thousands by sequencing (GT-seq) for collecting targeted single nucleotide polymorphism genotypic data from archival scale samples, and applied this approach to a study of kokanee salmon (Oncorhynchus nerka) in Kluane National Park and Reserve (KNPR; Yukon, Canada) that underwent a severe 12-year population decline followed by a rapid rebound. We genotyped archival scales sampled pre-crash and contemporary fin clips collected post-crash, revealing high coverage (> 90% average genotyping across all individuals) and low genotyping error (< 0.01% within-libraries, 0.60% among-libraries) despite the relatively poor quality of recovered DNA. We observed slight decreases in expected heterozygosity, allelic diversity, and effective population size post-crash, but none were significant, suggesting genetic diversity was retained despite the severe demographic contraction. Genotypic data also revealed the genetic distinctiveness of a now extirpated population just outside of KNPR, revealing biodiversity loss at the northern edge of the species distribution. More broadly, we demonstrated GT-seq as a valuable tool for collecting genome-wide data from archival samples to address basic questions in ecology and evolution, and inform applied research in wildlife conservation and fisheries management.

Large effective population size and temporal genetic stability in Atlantic cod (Gadus morhua) in the southern Gulf of St. Lawrence

2010 ◽  
Vol 67 (10) ◽  
pp. 1585-1595 ◽  
Author(s):  
Nina Overgaard Therkildsen ◽  
Einar Eg Nielsen ◽  
Douglas P. Swain ◽  
Jes Søe Pedersen
Keyword(s):  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Population Decline ◽  
Allelic Diversity ◽  
Estimation Methods ◽  
Effective Population ◽  
Commercial Fish

Worldwide, many commercial fish stocks have experienced dramatic declines due to overfishing. Such fisheries-induced population reductions could potentially erode the genetic diversity of marine fish populations. Based on analyses of DNA extracted from archived and contemporary samples, this paper compares the genetic variability at nine microsatellite loci in a Canadian population of Atlantic cod ( Gadus morhua ) over 80 years, spanning from before the fishery intensified to now when the population is at historically low abundance. Extensively validated genetic data from the temporally spaced samples were used to estimate the effective population size. Over the period, we observed no loss of either heterozygosity or allelic diversity. Several of the estimation methods applied could not distinguish the effective population size from infinity, and the lower 95% confidence limit on estimates was generally >500, suggesting that the effective population size is probably considerably larger than this. Hence, it appears that the southern Gulf of St. Lawrence cod stock has maintained genetic variability to sustain future evolution despite a dramatic population decline.

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 Population Genomics of American Mink Using Whole Genome Sequencing Data

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 258
Author(s):  
Karim Karimi ◽  
Duy Ngoc Do ◽  
Mehdi Sargolzaei ◽  
Younes Miar
Keyword(s):  
Population Genomics ◽  
Association Studies ◽  
American Mink ◽  
Population History ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Effective Population ◽  
Cross Validation Error

Characterizing the genetic structure and population history can facilitate the development of genomic breeding strategies for the American mink. In this study, we used the whole genome sequences of 100 mink from the Canadian Centre for Fur Animal Research (CCFAR) at the Dalhousie Faculty of Agriculture (Truro, NS, Canada) and Millbank Fur Farm (Rockwood, ON, Canada) to investigate their population structure, genetic diversity and linkage disequilibrium (LD) patterns. Analysis of molecular variance (AMOVA) indicated that the variation among color-types was significant (p < 0.001) and accounted for 18% of the total variation. The admixture analysis revealed that assuming three ancestral populations (K = 3) provided the lowest cross-validation error (0.49). The effective population size (Ne) at five generations ago was estimated to be 99 and 50 for CCFAR and Millbank Fur Farm, respectively. The LD patterns revealed that the average r2 reduced to <0.2 at genomic distances of >20 kb and >100 kb in CCFAR and Millbank Fur Farm suggesting that the density of 120,000 and 24,000 single nucleotide polymorphisms (SNP) would provide the adequate accuracy of genomic evaluation in these populations, respectively. These results indicated that accounting for admixture is critical for designing the SNP panels for genotype-phenotype association studies of American mink.

Ancient DNA Analysis of the Thulamela Remains: Deciphering the Migratory Patterns of a Southern African Population

2019 ◽  
Vol 17 (2) ◽  
pp. 161-172
Author(s):  
Molebogeng Bodiba ◽  
Maryna Steyn ◽  
Paulette Bloomer ◽  
Morongwa N. Mosothwane ◽  
Frank Rühli ◽  
...  
Keyword(s):  
Iron Age ◽  
Dna Analysis ◽  
Poor Quality ◽  
Archaeological Sites ◽  
Genetic Groups ◽  
African Populations ◽  
Ancient Dna Analysis ◽  
Migratory Patterns ◽  
African Iron Age ◽  
Adna Analysis

Abstract Ancient DNA (aDNA) analysis was employed to obtain information on the population relationships of the two Thulamela individuals (AD 1400-1700) and six other skeletons from various archaeological sites of the southern African Iron Age – Tuli (Botswana), Nwanetsi, Makgope, Happy Rest and Stayt. Although sequences were short, it seems that the Thulamela female aligns somewhat more with eastern populations as opposed to the male who aligns more with western groups. This result is not surprising given that the two individuals were buried at the same site but their burials were hundreds of years apart. It was also possible to identify genetic links between the Iron Age individuals and modern southern African populations (e.g. some of the skeletons assessed showed maternal genetic similarities to present-day Sotho/Tswana groups) and to separate the samples into at least two genetic groups. Poor quality and quantity of DNA meant that only haplogroups, not subhaplogroups, of the individuals could be traced.

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.

Spatial and temporal genetic diversity of the Texas kangaroo rat, Dipodomys elator (Rodentia: Heteromyidae)

2019 ◽  
Vol 100 (4) ◽  
pp. 1169-1181 ◽  
Author(s):  
Russell S Pfau ◽  
Jim R Goetze ◽  
Robert E Martin ◽  
Kenneth G Matocha ◽  
Allan D Nelson
Keyword(s):  
Genetic Diversity ◽  
Genetic Drift ◽  
Isolation By Distance ◽  
Extinction Risk ◽  
Allelic Diversity ◽  
Effective Population ◽  
Kangaroo Rat ◽  
Time Periods ◽  
Mtdna Diversity ◽  
Using Data

Abstract The Texas kangaroo rat (Dipodomys elator) is listed as a threatened species in Texas because of its scarcity and small geographic range. We assessed patterns of genetic diversity in D. elator that could affect extinction risk or influence management decisions. Specific objectives included: 1) document levels of genetic diversity, 2) document the degree and patterns of genetic divergence among localities, and 3) compare levels of genetic diversity between different time periods at the same locality. Portions of the mitochondrial genome (mtDNA; control region, cytochrome c oxidase subunit I, and cytochrome b) were sequenced and nuclear microsatellites were examined. Low mtDNA diversity was observed, which could be explained by an historical, species-wide genetic bottleneck. In contrast, microsatellites exhibited ample variation, and analyses were conducted using data from 11 loci and four populations (designated Quanah, Iowa Park, Vernon, and Harrold). Allelic diversity and heterozygosity were similar between populations and temporal samples. Estimates of effective population size (Ne) ranged from 5 to 856, depending on method and population, with Iowa Park showing consistently lower values than Quanah. All methods addressing population structure indicated that the Iowa Park population was divergent from the others, with Vernon and Harrold showing a somewhat intermediate relationship but with a closer affiliation with Quanah than Iowa Park, despite their closer proximity to Iowa Park. This pattern did not conform to isolation by distance, thus genetic drift appears to have played a greater role than gene flow in establishing genetic structure. There was much less difference between temporal samples compared to geographic samples, indicating that genetic drift has had only minimal impacts in shifting allelic frequencies over the time periods examined (17–36 years).

scholarly journals Fragmented Integration: The Nova Scotia Steel and Coal Company and the Anatomy of an Urban-Industrial Landscape, c. 1912

2013 ◽  
Vol 22 (2) ◽  
pp. 139-158
Author(s):  
L. D. McCann
Keyword(s):  
Nova Scotia ◽  
Population Decline ◽  
Urban System ◽  
Poor Quality ◽  
Iron And Steel ◽  
Spatial Strategies ◽  
Industrial Landscape ◽  
Long Run ◽  
Regional Markets ◽  
And Control

This paper examines how forces of fragmentation within the Maritimes contribute a partial but important explanation of the urban-industrial collapse that marked the region in the early 20th century. Specifically, weaknesses that affected the spatial strategies of the vertically-integrated industrial giant, the Nova Scotia Steel and Coal Company, provide evidence of limited interaction within the Maritime urban system. Profits from exporting staples, pig iron, and steel products to foreign and national markets, although initially aided by tidewater location and control over all phases of production, were not sufficient to overcome, in the long-run, such forces of fragmentation as dispersed and limited regional markets, increased costs of producing poor quality resources, or the minimal presence of external economies. With "Scotia's" eventual demise, towns like Sydney Mines, Trenton, and New Glasgow suffered economic and population decline.

scholarly journals Information on population trends and biological constraints from bat counts in roost cavities: a 22-year case study of a pipistrelle bats (Pipistrellus pipistrellus Schreber) hibernaculum

2015 ◽  
Vol 42 (1) ◽  
pp. 35 ◽  
Author(s):  
Christian Kerbiriou ◽  
Jean François Julien ◽  
Sophie Monsarrat ◽  
Philippe Lustrat ◽  
Alexandre Haquart ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Population Size ◽  
Spatial Scales ◽  
Population Decline ◽  
Current Trend ◽  
Biodiversity Loss ◽  
Population Trends ◽  
Railway Tunnel ◽  
Biodiversity Indicators ◽  
Pipistrellus Pipistrellus

Context According to the current trend of biodiversity loss, information on population trends at large temporal and spatial scales is necessary. However, well documented animal population dynamics are generally based on intensive protocols requiring animal manipulation, which can be impossible to conduct in species for which conservation is a concern. Aims For many bat species, an alternative approach entails performing an appropriate analysis of counts in roost cavities. Because of managers’ perception of chaotic variations through time, relatively few count monitoring surveys are regularly analysed. Here, we present the analysis of a twenty-two-year survey of a large hibernaculum of pipistrelle bats (Pipistrellus pipistrellus) located in a railway tunnel in Paris, France. Methods We propose that using combinations of population-dynamics modelling using demographic parameters from the literature and statistical analyses helps with identifying the biological and methodological effects underlying the dynamics observed in census analyses. Key results We determined that some of the observed year-to-year variations of population size cannot be explained only by the intrinsic dynamics of the population. In particular, in 1993–94, the population size increased by >40%, which should have implied a massive immigration. This change coincided with the end of the operation of the railway line. After consideration of a drastic trend of population decline (7% year–1), we were able to detect this event and several environmental effects. Specifically, the winter conditions and the temperature in July affected the colony size, presumably because of aggregative behaviour and reproduction success, respectively. Conclusions Emigration–immigration processes might have preponderant effects on population dynamics. In addition, our analysis demonstrated that (1) the study population suffered a large decline, (2) a combination of human disturbance and meteorological variation explains these dynamics and (3) emigration–immigration processes have preponderant effects on the population dynamics. Implications To conduct a meaningful analysis of non-standard time series and provide a source of data for implementing biodiversity indicators, it is necessary to include (1) the local knowledge of the people involved in the field surveys in these analyses (the existence of disturbances and site protections) and (2) meteorological information for the appropriate seasons of the year.

scholarly journals Mobile elements reveal small population size in the ancient ancestors of Homo sapiens

2010 ◽  
Vol 107 (5) ◽  
pp. 2147-2152 ◽  
Author(s):  
Chad D. Huff ◽  
Jinchuan Xing ◽  
Alan R. Rogers ◽  
David Witherspoon ◽  
Lynn B. Jorde
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Dna Sequences ◽  
Mobile Element ◽  
Small Population ◽  
Mobile Elements ◽  
Population History ◽  
Recent Common Ancestor ◽  
Demographic Model ◽  
Effective Population

The genealogies of different genetic loci vary in depth. The deeper the genealogy, the greater the chance that it will include a rare event, such as the insertion of a mobile element. Therefore, the genealogy of a region that contains a mobile element is on average older than that of the rest of the genome. In a simple demographic model, the expected time to most recent common ancestor (TMRCA) is doubled if a rare insertion is present. We test this expectation by examining single nucleotide polymorphisms around polymorphic Alu insertions from two completely sequenced human genomes. The estimated TMRCA for regions containing a polymorphic insertion is two times larger than the genomic average (P < <10−30), as predicted. Because genealogies that contain polymorphic mobile elements are old, they are shaped largely by the forces of ancient population history and are insensitive to recent demographic events, such as bottlenecks and expansions. Remarkably, the information in just two human DNA sequences provides substantial information about ancient human population size. By comparing the likelihood of various demographic models, we estimate that the effective population size of human ancestors living before 1.2 million years ago was 18,500, and we can reject all models where the ancient effective population size was larger than 26,000. This result implies an unusually small population for a species spread across the entire Old World, particularly in light of the effective population sizes of chimpanzees (21,000) and gorillas (25,000), which each inhabit only one part of a single continent.

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