Moose genomes reveal past glacial demography and the origin of modern lineages

Abstract Background Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America. Results We found that moose demographic history was greatly influenced by glacial cycles, with demographic responses to the Pleistocene/Holocene transition similar to other temperate ungulates. Our results further support that modern moose lineages trace their origin back to populations that inhabited distinct glacial refugia during the Last Glacial Maximum (LGM). Finally, we found that present day moose in Europe and North America show low to moderate inbreeding levels resulting from post-glacial bottlenecks and founder effects, but no evidence for recent inbreeding resulting from human-induced population declines. Conclusions Taken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies.

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Population structure and demographic history of the chukar partridge Alectoris chukar in China

Current Zoology ◽

10.1093/czoolo/59.4.458 ◽

2013 ◽

Vol 59 (4) ◽

pp. 458-474 ◽

Cited By ~ 2

Author(s):

Sen Song ◽

Shijie Bao ◽

Ying Wang ◽

Xinkang Bao ◽

Bei An ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

North America ◽

Demographic History ◽

Population Expansion ◽

Northwest China ◽

Population History ◽

Extant Species ◽

History Of ◽

Chukar Partridge

Abstract Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations’ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the chukar partridge Alec-toris chukar in north and northwest China. A 1,152 – 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of chukar experienced population expansion during 0.027 ? 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma).

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Large-scale geographic survey provides insights into the colonization history of a major aphid pest on its cultivated apple host in Europe, North America and North Africa

10.1101/2020.12.11.421644 ◽

2020 ◽

Author(s):

S.G. Olvera-Vazquez ◽

C. Remoue ◽

A. Venon ◽

A. Rousselet ◽

O. Grandcolas ◽

...

Keyword(s):

Gene Flow ◽

North America ◽

Genetic Differentiation ◽

North Africa ◽

Large Scale ◽

Demographic History ◽

High Genetic Diversity ◽

The North ◽

The Us ◽

History Of

With frequent host shifts involving the colonization of new hosts across large geographical ranges, crop pests are good models for examining the mechanisms of rapid colonization. The microbial partners of pest insects may be involved or affected by colonization, which has been little studied so far. We investigated the demographic history of the rosy apple aphid, Dysaphis plantaginea, a major pest of the cultivated apple (Malus domestica) in Europe, North Africa and North America, as well as the diversity of its endosymbiotic bacterial community. We genotyped a comprehensive sample of 714 colonies from Europe, Morocco and the US using mitochondrial (CytB and CO1), bacterial (16s rRNA and TrnpB), and 30 microsatellite markers. We detected five populations spread across the US, Morocco, Western and Eastern Europe, and Spain. Populations showed weak genetic differentiation and high genetic diversity, except the Moroccan and the North American that are likely the result of recent colonization events. Coalescent-based inferences releaved high levels of gene flow among populations during the colonization, but did not allow determining the sequence of colonization of Europe, America and Morroco by D. plantaginea, likely because of the weak genetic differentiation and the occurrence of gene flow among populations. Finally, we found that D. plantaginea rarely hosts any other endosymbiotic bacteria than its obligate nutritional symbiont Buchnera aphidicola. This suggests that secondary endosymbionts did not play any role in the rapid spread of the rosy apple aphid. These findings have fundamental importance for understanding pest colonization processes and implications for sustainable pest control programs.

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Declining Growth Rate of West Nile Virus in North America

Journal of Virology ◽

10.1128/jvi.02169-06 ◽

2006 ◽

Vol 81 (5) ◽

pp. 2531-2534 ◽

Cited By ~ 57

Author(s):

Katherine W. Snapinn ◽

Edward C. Holmes ◽

David S. Young ◽

Kristen A. Bernard ◽

Laura D. Kramer ◽

...

Keyword(s):

Growth Rate ◽

West Nile Virus ◽

North America ◽

Demographic History ◽

Data Sets ◽

Coding Region ◽

West Nile ◽

Region Data ◽

History Of ◽

The Mean

ABSTRACT To determine the demographic history of West Nile virus (WNV) in North America, we employed a coalescent method to envelope coding region data sets for the NY99 and WN02 genotypes. Although the observed genetic diversities in both genotypes were of approximately the same age, the mean rate of epidemiological growth of the WN02 population was approximately three times that of the NY99 population, a finding compatible with the recent dominance of the former genotype. However, there has also been a marked decrease in the recent growth rate of WN02, suggesting that WNV has reached its peak prevalence in North America.

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De novo chromosome level assembly of the mule deer (Odocoileus hemionus) genome

10.1101/2021.08.12.456132 ◽

2021 ◽

Author(s):

Sydney Lamb ◽

Adam M. Taylor ◽

Tabitha A. Hughes ◽

Brock R. McMillan ◽

Randy T. Larsen ◽

...

Keyword(s):

De Novo ◽

Demographic History ◽

Large Population ◽

Mule Deer ◽

Continuous Distribution ◽

Odocoileus Hemionus ◽

Chromosome Length ◽

Future Research ◽

A Genome ◽

Genomic Studies

The mule deer (Odocoileus hemionus) is an ungulate species that ranges from western Canada to central Mexico. Mule deer are an essential source of food for many predators, are relatively abundant, and commonly make broad migration movements. A clearer understanding of the mule deer genome can help facilitate knowledge of its population genetics, movements, and demographic history, aiding in conservation efforts. While mule deer are excellent candidates for population genomic studies because of their large population size, continuous distribution, and diversity of habitat, few genomic resources are currently available for this species. Here, we sequence and assemble the mule deer genome into a highly contiguous chromosome-length assembly for use in future research using long-read sequencing and Hi-C. We also provide a genome annotation and compare demographic histories of the mule deer and white-tail deer using PSMC. We expect this assembly to be a valuable resource in the continued study and conservation of mule deer.

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Demographic history and admixture dynamics in African Sahelian populations

Human Molecular Genetics ◽

10.1093/hmg/ddaa239 ◽

2020 ◽

Author(s):

Viktor Černý ◽

Cesar Fortes-Lima ◽

Petr Tříska

Keyword(s):

Demographic History ◽

Distribution Patterns ◽

Human Populations ◽

African Region ◽

Genetic Studies ◽

Genomic Studies ◽

History Of ◽

Sub Saharan ◽

High Degree ◽

The Impact

Abstract The Sahel/Savannah belt of Africa is a contact zone between two subsistence systems (nomadic pastoralism and sedentary farming) and of two groups of populations, namely Eurasians penetrating from northern Africa southwards and sub-Saharan Africans migrating northwards. Because pastoralism is characterised by a high degree of mobility, it leaves few significant archaeological traces. Demographic history seen through the lens of population genetic studies complements our historical and archaeological knowledge in this African region. In this review, we highlight recent advances in our understanding of demographic history in the Sahel/Savannah belt as revealed by genetic studies. We show the impact of food-producing subsistence strategies on population structure as well as the somewhat different migration patterns in the western and eastern part of the region. Genomic studies show that the gene pool of various groups of Sahelians consists in a complex mosaic of several ancestries. We also touch upon various signals of genetic adaptations such as lactase persistence, taste sensitivity, and malaria resistance, all of which have different distribution patterns among Sahelian populations. Overall, genetic studies contribute to gain a deeper understanding about the demographic and adaptive history of human populations in this specific African region and beyond.

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Diverse demographic histories in a guild of hymenopteran parasitoids

10.1101/2019.12.20.884403 ◽

2019 ◽

Author(s):

William Walton ◽

Graham N Stone ◽

Konrad Lohse

Keyword(s):

Population Size ◽

Sequence Data ◽

Demographic History ◽

Whole Genome Sequence ◽

Parasitoid Wasps ◽

Effective Population ◽

Glacial Cycles ◽

Genome Wide ◽

History Of ◽

Hymenopteran Parasitoids

AbstractSignatures of changes in population size have been detected in genome-wide variation in many species. However, the causes of such changes and the extent to which they are shared across co-distributed species remain poorly understood. During Pleistocene glacial maxima, many temperate European species were confined to southern refugia. While vicariance and range expansion processes associated with glacial cycles have been widely studied, little is known about the demographic history of refugial populations, and the extent and causes of demographic variation among codistributed species. We used whole genome sequence data to reconstruct and compare demographic histories during the Quaternary for Iberian refuge populations in a single ecological guild (seven species of chalcid parasitoid wasps associated with oak cynipid galls). We find support for large changes in effective population size (Ne) through the Pleistocene that coincide with major climate change events. However, there is little evidence that the timing, direction and magnitude of demographic change are shared across species, suggesting that demographic histories are largely idiosyncratic. Our results are compatible with the idea that specialist parasitoids attacking a narrow range of hosts experience greater fluctuations in Ne than generalists.

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Discovery of Drosophila melanogaster from Wild African Environments and Genomic Insights into Species History

10.1101/470765 ◽

2018 ◽

Cited By ~ 1

Author(s):

Quentin D. Sprengelmeyer ◽

Suzan Mansourian ◽

Jeremy D. Lange ◽

Daniel R. Matute ◽

Brandon S. Cooper ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Demographic History ◽

Historical Context ◽

Model Organism ◽

Widespread Species ◽

Wilderness Areas ◽

Genomic Studies ◽

History Of ◽

Sub Saharan ◽

Improved Model

A long-standing enigma concerns the geographic and ecological origins of the intensively studied vinegar fly, Drosophila melanogaster, a globally widespread species [1] which “has invariably appeared to be a strict human commensal” [2]. In spite of its sub-Saharan origins, this species has never been reported from undisturbed wilderness environments that might reflect its pre-commensal niche [3]. Here, we document the collection of 288 D. melanogaster individuals from African wilderness areas in Zambia, Zimbabwe, and Namibia. After sequencing the genomes of 17 flies collected from Kafue National Park, Zambia, we found reduced genetic diversity relative to town populations, elevated chromosomal inversion frequencies, and strong differences at specific genes including known insecticide targets. Combining these new genomes with prior data enabled us to gain novel insights into the history of this species’ geographic expansion. Our demographic estimates indicated that an expansion from southern Africa began approximately 10,000 years ago, with a Saharan crossing soon after, but expansion from the Middle East into Europe did not begin until roughly 1,400 years ago. This improved model of demographic history will provide a critical resource for future evolutionary and genomic studies of this key model organism. Our results add historical context to the species’ human association, and the opportunity to study wilderness populations opens the door for future studies on the biological basis of its adaptation to human environments.

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

10.1101/2021.11.18.468312 ◽

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.

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BIOGEOGRAPHY OF JACK PINE

Canadian Journal of Botany ◽

10.1139/b67-237 ◽

1967 ◽

Vol 45 (11) ◽

pp. 2201-2211 ◽

Cited By ~ 19

Author(s):

C. W. Yeatman

Keyword(s):

North America ◽

Pinus Banksiana ◽

Pinus Contorta ◽

Geographic Origin ◽

Glacial Refugia ◽

Jack Pine ◽

Hybrid Swarms ◽

Late Tertiary ◽

History Of ◽

Probable Origin

Interpretation of genetic variation associated with geographic origin must take into account the evolution and migratory history of the species being-studied. A literature survey was made to determine the probable origin of jack pine (pinus banksiana) and its migration from glacial refugia following the Wisconsin glacial maximum. Jack pine and contorta pine (Pinus contorta) became differentiated following cooling of the climate and crustal uplift in western North America in the late Tertiary. Modern hybrid swarms and introgression of jack pine and lodgepole pine (Pinus contorta var. lalifolia) east of the Rocky Mountains are of recent origin, dating from late post-glacial migration from the east and west respectively. Geological and paleobotanical evidence, particularly from fossil pollen depositions, indicate that jack pine survived glaciation in an extensive refugium centered on the Appalachian Highlands of eastern North America, and not in additional refugia south or west of the Great Lakes. This conclusion is consistent with the clinal pattern of geographic variation evident from genecological studies of the species.

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