scholarly journals Whole-genomes from the extinct Xerces Blue butterfly reveal low diversity and long-term population decline

2021 ◽  
Author(s):  
Toni de-Dios ◽  
Claudia Fontsere ◽  
Pere Renom ◽  
Josefin Stiller ◽  
Laia Llovera ◽  
...  
Keyword(s):  
San Francisco ◽  
Demographic History ◽  
Population Decline ◽  
Distinct Species ◽  
Global Scale ◽  
Interglacial Period ◽  
Effective Population ◽  
White Spots ◽  
History Of ◽  
Historical Times

The Xerces Blue (Glaucopsyche xerces) is considered to be the first butterfly to become extinct at global scale in historical times. It was notable for its chalky lavender wings with conspicuous white spots on the ventral wings. The last individuals were collected in their restricted habitat, in the dunes near the Presidio military base in San Francisco, in 1941. To explore the demographic history of this iconic butterfly and to better understand why it went extinct, we sequenced at medium coverage the genomes of four 80 to 100-year-old Xerces Blue specimens and seven historic specimens of its closest relative, the Silvery Blue (G. lygdamus). We compared these to a novel annotated genome of the Green-Underside Blue (G. alexis). Phylogenetic relationships inferred from complete mitochondrial genomes indicate that Xerces Blue was a distinct species that diverged from the Silvery Blue lineage at least 850,000 years ago. Using nuclear genomes, we show that both species experienced population growth during the MIS 7 interglacial period, but the Xerces Blue decreased to a very low effective population size subsequently, a trend opposite to that observed in the Silvery Blue. Runs of homozygosity in the Xerces Blue were significantly greater than in the Silvery Blue, suggesting a higher incidence of inbreeding. In addition, the Xerces Blue carried a higher proportion of derived, putatively deleterious amino acid-changing alleles than the Silvery Blue. These results demonstrate that the Xerces Blue experienced more than 100 thousand years of population decline, prior to its human-induced final extinction.

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 Low Nucleotide Diversity in Chimpanzees and Bonobos

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1511-1518 ◽  
Author(s):  
Ning Yu ◽  
Michael I Jensen-Seaman ◽  
Leona Chemnick ◽  
Judith R Kidd ◽  
Amos S Deinard ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Nuclear Dna ◽  
Demographic History ◽  
Nuclear Genome ◽  
Limited Data ◽  
Effective Population ◽  
East Central ◽  
Dna Diversity ◽  
History Of ◽  
Mtdna Diversity

Abstract Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (π) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the π value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The π values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (Ne) in the human lineage after the human-chimpanzee divergence, because a reduction in Ne has a stronger effect on mtDNA diversity than on nuclear DNA diversity.

scholarly journals Comparing maternal genetic variation across two millennia reveals the demographic history of an ancient human population in southwest Turkey

2016 ◽  
Vol 3 (2) ◽  
pp. 150250 ◽  
Author(s):  
Claudio Ottoni ◽  
Rita Rasteiro ◽  
Rinse Willet ◽  
Johan Claeys ◽  
Peter Talloen ◽  
...  
Keyword(s):  
Demographic History ◽  
Population Decline ◽  
Fifth Century ◽  
Seventh Century ◽  
Human Occupation ◽  
Dna Variation ◽  
Genetic Discontinuity ◽  
History Of ◽  
The City ◽  
Modern Sample

More than two decades of archaeological research at the site of Sagalassos, in southwest Turkey, resulted in the study of the former urban settlement in all its features. Originally settled in late Classical/early Hellenistic times, possibly from the later fifth century BCE onwards, the city of Sagalassos and its surrounding territory saw empires come and go. The Plague of Justinian in the sixth century CE, which is considered to have caused the death of up to a third of the population in Anatolia, and an earthquake in the seventh century CE, which is attested to have devastated many monuments in the city, may have severely affected the contemporary Sagalassos community. Human occupation continued, however, and Byzantine Sagalassos was eventually abandoned around 1200 CE. In order to investigate whether these historical events resulted in demographic changes across time, we compared the mitochondrial DNA variation of two population samples from Sagalassos (Roman and Middle Byzantine) and a modern sample from the nearby town of Ağlasun. Our analyses revealed no genetic discontinuity across two millennia in the region and Bayesian coalescence-based simulations indicated that a major population decline in the area coincided with the final abandonment of Sagalassos, rather than with the Plague of Justinian or the mentioned earthquake.

scholarly journals The Genetic History of France

2019 ◽  
Author(s):  
Aude Saint Pierre ◽  
Joanna Giemza ◽  
Matilde Karakachoff ◽  
Isabel Alves ◽  
Philippe Amouyel ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Demographic History ◽  
Migration Routes ◽  
Effective Population ◽  
Genetic Studies ◽  
Independent Population ◽  
Genome Wide Data ◽  
Population Sizes ◽  
History Of ◽  
Exhaustive Study

ABSTRACTThe study of the genetic structure of different countries within Europe has provided significant insights into their demographic history and their actual stratification. Although France occupies a particular location at the end of the European peninsula and at the crossroads of migration routes, few population genetic studies have been conducted so far with genome-wide data. In this study, we analyzed SNP-chip genetic data from 2 184 individuals born in France who were enrolled in two independent population cohorts. Using FineStructure, six different genetic clusters of individuals were found that were very consistent between the two cohorts. These clusters match extremely well the geography and overlap with historical and linguistic divisions of France. By modeling the relationship between genetics and geography using EEMS software, we were able to detect gene flow barriers that are similar in the two cohorts and corresponds to major French rivers or mountains. Estimations of effective population sizes using IBDNe program also revealed very similar patterns in both cohorts with a rapid increase of effective population sizes over the last 150 generations similar to what was observed in other European countries. A marked bottleneck is also consistently seen in the two datasets starting in the fourteenth century when the Black Death raged in Europe. In conclusion, by performing the first exhaustive study of the genetic structure of France, we fill a gap in the genetic studies in Europe that would be useful to medical geneticists but also historians and archeologists.

scholarly journals Genomic evidence for the Old divergence of Southern European wolf populations

2020 ◽  
Vol 287 (1931) ◽  
pp. 20201206
Author(s):  
Pedro Silva ◽  
Marco Galaverni ◽  
Diego Ortega-Del Vecchyo ◽  
Zhenxin Fan ◽  
Romolo Caniglia ◽  
...  
Keyword(s):  
Canis Lupus ◽  
Common Ancestor ◽  
Demographic History ◽  
Population Decline ◽  
Divergence Times ◽  
Single Population ◽  
History Of ◽  
Fragmented Distribution ◽  
The Last Glacial Maximum ◽  
The Last Glacial

The grey wolf ( Canis lupus ) is one of the most widely distributed mammals in which a variety of distinct populations have been described. However, given their currently fragmented distribution and recent history of human-induced population decline, little is known about the events that led to their differentiation. Based on the analysis of whole canid genomes, we examined the divergence times between Southern European wolf populations and their ancient demographic history. We found that all present-day Eurasian wolves share a common ancestor ca 36 000 years ago, supporting the hypothesis that all extant wolves derive from a single population that subsequently expanded after the Last Glacial Maximum. We also estimated that the currently isolated European populations of the Iberian Peninsula, Italy and the Dinarics-Balkans diverged very closely in time, ca 10 500 years ago, and maintained negligible gene flow ever since. This indicates that the current genetic and morphological distinctiveness of Iberian and Italian wolves can be attributed to their isolation dating back to the end of the Pleistocene, predating the recent human-induced extinction of wolves in Central Europe by several millennia.

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 An insight into the evolutionary history of Indonesian cattle assessed by whole genome data analysis

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0241038
Author(s):  
Pita Sudrajad ◽  
Subiharta Subiharta ◽  
Yudi Adinata ◽  
Af’idatul Lathifah ◽  
Jun Heon Lee ◽  
...  
Keyword(s):  
Demographic History ◽  
Bos Indicus ◽  
Molecular Evidence ◽  
Effective Population ◽  
Genome Data ◽  
Bos Javanicus ◽  
History Of ◽  
Genome Data Analysis ◽  
Almost All ◽  
Insight Into

The domestication of Indonesian cattle was investigated through a study of their genetic diversity, up to the genome level. Little documentation exists regarding the history of domestication of Indonesian cattle and questions remain despite a growing body of molecular evidence. In this study, we genotyped seven Indonesian cattle breeds using an Illumina BovineSNP50 Bead Chip to provide insight into their domestication and demographic history in a worldwide population context. Our analyses indicated the presence of hybrid cattle, with Bos javanicus and Bos indicus ancestries being most prevalent, as well as purebred cattle. We revealed that all the breeds were interconnected through several migration events. However, their demographic status varied widely. Although almost all the Indonesian cattle had an effective population size higher than the minimum level required to ensure breed fitness, efforts are still needed to maintain their genetic variability and purity.

scholarly journals The Global History of Inequality

2019 ◽  
Vol 64 (2) ◽  
pp. 309-323
Author(s):  
Pim de Zwart
Keyword(s):  
Economic History ◽  
Demographic History ◽  
Economic Inequality ◽  
Global Scale ◽  
Governmental Organization ◽  
Occupy Movement ◽  
The Great Recession ◽  
The Us ◽  
The World ◽  
History Of

Inequality has increased in most Western countries since the early 1980s. In a recent report, the international non-governmental organization Oxfam noted that the twenty-six richest people in the world own as much wealth as the poorest fifty per cent of the world's population. Discontent with the growing disparities in wealth and income has soared in recent years, especially in the wake of the 2007/2008 financial crisis and the “Great Recession” that followed. The Occupy movement protested against the greed of the “one per cent”, referring to the highly skewed income distribution in the US. Former US president Barack Obama proclaimed the growth of within-country economic inequality as “the defining challenge of our time”. Yet, he enacted few policies that reduced inequality during his two terms in office; the Gini coefficient in the US actually increased slightly between 2007 and 2016. His successor, whose election has often been explained as a consequence of these high levels of inequality, has slashed taxes for the wealthy, probably causing further rises in inequality in the future. In this essay, I will review two recent economic history books that examine the historical roots of within-country inequality on a global scale: Branko Milanovic's Global Inequality (2016) and Walter Scheidel's The Great Leveler (2017). Formerly a lead economist at the World Bank, Milanovic is a well-known scholar working in the field of economic inequality, while Scheidel has a background as a specialist in the economic, social, and demographic history of antiquity.

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 Evidences of delayed size recovery in Araucaria angustifolia populations after post-glacial colonization of highlands in Southeastern Brazil

2008 ◽  
Vol 80 (3) ◽  
pp. 433-443 ◽  
Author(s):  
Valdir M. Stefenon ◽  
Hermann Behling ◽  
Oliver Gailing ◽  
Reiner Finkeldey
Keyword(s):  
Population Size ◽  
Demographic History ◽  
Southeastern Brazil ◽  
Effective Population ◽  
History Of ◽  
Natural Stands ◽  
Recovery Dynamics ◽  
The Relationship ◽  
Palynological Records ◽  
Small Effective Population Size

Up to date, little is known about the relationship between historical demography and the current genetic structure of A. Angus As a first effort towards overcoming this lack, microsatellite data scored in six populations and isozyme allele frequencies published for 11 natural stands of this species were analysed in order to assess molecular signatures of populations' demographic history. Signatures of genetic bottlenecks were captured in all analysed populations of southeastern Brazil. Among southern populations, signatures of small effective population size were observed in only three out of 13 populations. Southern populations likely experienced faster recovery of population size after migration onto highlands. Accordingly, current genetic diversity of the southern populations gives evidence of fast population size recovery. In general, demographic history of A. Angusmatches climatic dynamics of southern and southeastern Brazil during the Pleistocene and Holocene. Palynological records and reconstruction of the past climatic dynamics of southeastern and southern Brazil support the hypothesis of different population size recovery dynamics for populations from these regions.

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