scholarly journals Diversity and Paleodemography of the Addax (Addax nasomaculatus), a Saharan Antelope on the Verge of Extinction

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1236
Author(s):  
Elisabeth Hempel ◽  
Michael V. Westbury ◽  
José H. Grau ◽  
Alexandra Trinks ◽  
Johanna L. A. Paijmans ◽  
...  
Keyword(s):  
Population Size ◽  
Population History ◽  
Phylogeographic Structure ◽  
Recent Common Ancestor ◽  
Mitochondrial Genomes ◽  
Effective Population ◽  
Mammal Species ◽  
Human Disturbances ◽  
Most Recent Common Ancestor ◽  
History Of

Since the 19th century, the addax (Addax nasomaculatus) has lost approximately 99% of its former range. Along with its close relatives, the blue antelope (Hippotragus leucophaeus) and the scimitar-horned oryx (Oryx dammah), the addax may be the third large African mammal species to go extinct in the wild in recent times. Despite this, the evolutionary history of this critically endangered species remains virtually unknown. To gain insight into the population history of the addax, we used hybridization capture to generate ten complete mitochondrial genomes from historical samples and assembled a nuclear genome. We found that both mitochondrial and nuclear diversity are low compared to other African bovids. Analysis of mitochondrial genomes revealed a most recent common ancestor ~32 kya (95% CI 11–58 kya) and weak phylogeographic structure, indicating that the addax likely existed as a highly mobile, panmictic population across its Sahelo–Saharan range in the past. PSMC analysis revealed a continuous decline in effective population size since ~2 Ma, with short intermediate increases at ~500 and ~44 kya. Our results suggest that the addax went through a major bottleneck in the Late Pleistocene, remaining at low population size prior to the human disturbances of the last few centuries.

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.

scholarly journals Introgression makes waves in inferred histories of effective population size

2017 ◽  
Author(s):  
John Hawks
Keyword(s):  
Gene Flow ◽  
Population Size ◽  
Effective Population Size ◽  
Population History ◽  
Human Populations ◽  
Effective Population ◽  
History Of ◽  
Or Gene ◽  
Time Of Origin ◽  
Past Population

AbstractHuman populations have a complex history of introgression and of changing population size. Human genetic variation has been affected by both these processes, so that inference of past population size depends upon the pattern of gene flow and introgression among past populations. One remarkable aspect of human population history as inferred from genetics is a consistent “wave” of larger effective population size, prior to the bottlenecks and expansions of the last 100,000 years. Here I carry out a series of simulations to investigate how introgression and gene flow from genetically divergent ancestral populations affect the inference of ancestral effective population size. Both introgression and gene flow from an extinct, genetically divergent population consistently produce a wave in the history of inferred effective population size. The time and amplitude of the wave reflect the time of origin of the genetically divergent ancestral populations and the strength of introgression or gene flow. These results demonstrate that even small fractions of introgression or gene flow from ancient populations may have large effects on the inference of effective population size.

scholarly journals Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe

2019 ◽  
Vol 5 (6) ◽  
pp. eaaw5873 ◽  
Author(s):  
Stéphane Peyrégne ◽  
Viviane Slon ◽  
Fabrizio Mafessoni ◽  
Cesare de Filippo ◽  
Mateja Hajdinjak ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Nuclear Dna ◽  
Population History ◽  
The Other ◽  
Genomic Sequences ◽  
Recent Common Ancestor ◽  
Mitochondrial Lineage ◽  
Most Recent Common Ancestor ◽  
History Of ◽  
Genetic Continuity

Little is known about the population history of Neandertals over the hundreds of thousands of years of their existence. We retrieved nuclear genomic sequences from two Neandertals, one from Hohlenstein-Stadel Cave in Germany and the other from Scladina Cave in Belgium, who lived around 120,000 years ago. Despite the deeply divergent mitochondrial lineage present in the former individual, both Neandertals are genetically closer to later Neandertals from Europe than to a roughly contemporaneous individual from Siberia. That the Hohlenstein-Stadel and Scladina individuals lived around the time of their most recent common ancestor with later Neandertals suggests that all later Neandertals trace at least part of their ancestry back to these early European Neandertals.

scholarly journals Inference of Historical Population-Size Changes with Allele-Frequency Data

2019 ◽  
Vol 10 (1) ◽  
pp. 211-223 ◽  
Author(s):  
Michael Lynch ◽  
Bernhard Haubold ◽  
Peter Pfaffelhuber ◽  
Takahiro Maruki
Keyword(s):  
Population Size ◽  
Probability Distributions ◽  
Daphnia Pulex ◽  
Population History ◽  
Effective Population ◽  
Size Change ◽  
Conceptual Approach ◽  
Population Genomic ◽  
Population Sizes ◽  
History Of

With up to millions of nearly neutral polymorphisms now being routinely sampled in population-genomic surveys, it is possible to estimate the site-frequency spectrum of such sites with high precision. Each frequency class reflects a mixture of potentially unique demographic histories, which can be revealed using theory for the probability distributions of the starting and ending points of branch segments over all possible coalescence trees. Such distributions are completely independent of past population history, which only influences the segment lengths, providing the basis for estimating average population sizes separating tree-wide coalescence events. The history of population-size change experienced by a sample of polymorphisms can then be dissected in a model-flexible fashion, and extension of this theory allows estimation of the mean and full distribution of long-term effective population sizes and ages of alleles of specific frequencies. Here, we outline the basic theory underlying the conceptual approach, develop and test an efficient statistical procedure for parameter estimation, and apply this to multiple population-genomic datasets for the microcrustacean Daphnia pulex.

scholarly journals Population Divergence Times and Historical Demography in red Knots and Dunlins

The Condor ◽  
2005 ◽  
Vol 107 (3) ◽  
pp. 497-513 ◽  
Author(s):  
Deborah M. Buehler ◽  
Allan J. Baker
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Recent Common Ancestor ◽  
Divergence Times ◽  
Population Divergence ◽  
Restricted Gene Flow ◽  
Genetic Evolution ◽  
Effective Population ◽  
Calidris Canutus ◽  
Most Recent Common Ancestor

Abstract We employed Bayesian coalescent modeling of samples of mitochondrial control region sequences in two species of shorebird, Red Knots (Calidris canutus) and Dunlins (Calidris alpina) to estimate evolutionary effective population size, population divergence times, and time to most recent common ancestor of genes in the samples. The gene trees for the two species contrast sharply: knot haplotypes were connected in a shallow, star phylogeny whereas Dunlin haplotypes were related in a deeper bifurcating genealogy. Divergence times of populations representing all six subspecies of knots are estimated to have occurred within the last 20 000 (95% CI: 5600–58 000) years, and evolutionary effective population sizes of females are small (Nef = 2000–14 000). We hypothesized that breeding knots were restricted to unglaciated regions of Eurasia during the last glacial maximum, and gradually expanded eastwards into Alaska, the high Canadian Arctic and Greenland as the ice melted. Population divergence times in Dunlins are much older (58 000–194 000 ybp) and effective population size has historically been higher in major lineages (Nef = 12 000–44 000). We conclude that Dunlin populations were not severely reduced in size in the last 200 000 years, and major lineages have differentiated under restricted gene flow for a much longer time than knots. Knots present a snapshot of genetic evolution in the last 20 000 years, whereas Dunlins display patterns of genetic evolution over an order of magnitude longer time frame. Tiempos de Divergencia Poblacional e Historia Demográfica en Calidris canutus y C. alpina Resumen. Aplicamos modelos Bayesianos de coalescencia en una muestra de secuencias de la región de control mitocondrial de dos especies de playeros, Calidris canutus y C. alpina, para estimar el tamaño efectivo de la población, los tiempos de divergencia entre poblaciones y la distancia cronológica al antepasado común más reciente de los genes muestreados. Los árboles genealógicos de las dos especies contrastan fuertemente: los haplotipos de C. canutus están conectados superficialmente siguiendo un patrón filogenético en forma de estrella, mientras que los haplotipos de C. alpina se relacionan de manera más profunda, mostrando patrones de genealogía bifurcados. Se estima que la divergencia poblacional de las seis subespecies de C. canutus tuvo lugar durante los últimos 20 000 años aproximadamente, y los tamaños efectivos de la población de hembras son pequeños (Nef = 2000–14 000). Presumimos que la reproducción de C. canutus estuvo restringida sólo a regiones de Eurasia que estuvieron libres de hielo durante el último máximo glacial y se expandieron gradualmente hacia el este de Alaska, el Ártico canadiense y Groenlandia cuando el hielo se derritió. Los tiempos de divergencia poblacional en C. alpina son más antiguos (58 000–194 000), y el tamaño efectivo de la población ha sido históricamente más alto en los linajes principales (Nef = 12 000–44 000). Concluimos que las poblaciones de C. alpina no mostraron reducciones serias en los últimos 200 000 años, y que sus linajes se han diferenciado por un período de tiempo mucho más prolongado que los de C. canutus. Los patrones encontrados para C. canutus representan una imagen de evolución genética ocurrida durante los últimos 20 000 años, mientras que los patrones de C. alpina indican la ocurrencia de evolución genética durante un período de tiempo diez veces más largo.

scholarly journals Recent effective population size in Eastern European plain Russians correlates with the key historical events

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ural Yunusbaev ◽  
Arslan Ionusbaev ◽  
Giyoun Han ◽  
Hyung Wook Kwon
Keyword(s):  
Population Size ◽  
Ethnic Group ◽  
Effective Population Size ◽  
Ural Region ◽  
Population History ◽  
Eastern European ◽  
Effective Population ◽  
History Of ◽  
Key Events ◽  
Volga Ural Region

Abstract Effective population size reflects the history of population growth, contraction, and structuring. When the effect of structuring is negligible, the inferred trajectory of the effective population size can be informative about the key events in the history of a population. We used the IBDNe and DoRIS approaches, which exploit the data on IBD sharing between genomes, to reconstruct the recent effective population size in two population datasets of Russians from Eastern European plain: (1) ethnic Russians sampled from the westernmost part of Russia; (2) ethnic Russians, Bashkirs, and Tatars sampled from the Volga-Ural region. In this way, we examined changes in effective population size among ethnic Russians that reside in their historical area at the West of the plain, and that expanded eastward to come into contact with the indigenous peoples at the East of the plain. We compared the inferred demographic trajectories of each ethnic group to written historical data related to demographic events such as migration, war, colonization, famine, establishment, and collapse of empires. According to IBDNe estimations, 200 generations (~6000 years) ago, the effective size of the ancestral populations of Russians, Bashkirs, and Tatars hovered around 3,000, 30,000, and 8,000 respectively. Then, the ethnic Russians exponentially grew with increasing rates for the last 115 generations and become the largest ethnic group of the plain. Russians do not show any drop in effective population size after the key historical conflicts, including the Mongol invasion. The only exception is a moderate drop in the 17th century, which is well known in Russian history as The Smuta. Our analyses suggest a more eventful recent population history for the two small ethnic groups that came into contact with ethnic Russians in the Volga-Ural region. We found that the effective population size of Bashkirs and Tatars started to decrease during the time of the Mongol invasion. Interestingly, there is an even stronger drop in the effective population size that coincides with the expansion of Russians to the East. Thus, 15–20 generations ago, i.e. in the 16–18th centuries in the trajectories of Bashkirs and Tatars, we observe the bottlenecks of four and twenty thousand, respectively. Our results on the recent effective population size correlate with the key events in the history of populations of the Eastern European plain and have importance for designing biomedical studies in the region.

scholarly journals Harmful mutation load in the mitochondrial genomes of cattle breeds

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Population Size ◽  
Artificial Selection ◽  
Deleterious Mutation ◽  
Genetic Diseases ◽  
Mitochondrial Genomes ◽  
Deleterious Mutations ◽  
Founder Population ◽  
Mutation Load ◽  
Effective Population ◽  
Cattle Breeds

Abstract Objective Domestication of wild animals results in a reduction in the effective population size, and this could affect the deleterious mutation load of domesticated breeds. Furthermore, artificial selection will also contribute to the accumulation of deleterious mutations due to the increased rate of inbreeding among these animals. The process of domestication, founder population size, and artificial selection differ between cattle breeds, which could lead to a variation in their deleterious mutation loads. We investigated this using mitochondrial genome data from 364 animals belonging to 18 cattle breeds of the world. Results Our analysis revealed more than a fivefold difference in the deleterious mutation load among cattle breeds. We also observed a negative correlation between the breed age and the proportion of deleterious amino acid-changing polymorphisms. This suggests a proportionally higher deleterious SNPs in young breeds compared to older breeds. Our results highlight the magnitude of difference in the deleterious mutations present in the mitochondrial genomes of various breeds. The results of this study could be useful in predicting the rate of incidence of genetic diseases in different breeds.

scholarly journals The Ancestry of a Sample of Sequences Subject to Recombination

Genetics ◽  
1999 ◽  
Vol 151 (3) ◽  
pp. 1217-1228 ◽  
Author(s):  
Carsten Wiuf ◽  
Jotun Hein
Keyword(s):  
Genetic Distance ◽  
Population Size ◽  
Upper Bound ◽  
Recombination Rate ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Sequence Length ◽  
Most Recent Common Ancestor ◽  
The Mean ◽  
Mean Time

Abstract In this article we discuss the ancestry of sequences sampled from the coalescent with recombination with constant population size 2N. We have studied a number of variables based on simulations of sample histories, and some analytical results are derived. Consider the leftmost nucleotide in the sequences. We show that the number of nucleotides sharing a most recent common ancestor (MRCA) with the leftmost nucleotide is ≈log(1 + 4N Lr)/4Nr when two sequences are compared, where L denotes sequence length in nucleotides, and r the recombination rate between any two neighboring nucleotides per generation. For larger samples, the number of nucleotides sharing MRCA with the leftmost nucleotide decreases and becomes almost independent of 4N Lr. Further, we show that a segment of the sequences sharing a MRCA consists in mean of 3/8Nr nucleotides, when two sequences are compared, and that this decreases toward 1/4Nr nucleotides when the whole population is sampled. A measure of the correlation between the genealogies of two nucleotides on two sequences is introduced. We show analytically that even when the nucleotides are separated by a large genetic distance, but share MRCA, the genealogies will show only little correlation. This is surprising, because the time until the two nucleotides shared MRCA is reciprocal to the genetic distance. Using simulations, the mean time until all positions in the sample have found a MRCA increases logarithmically with increasing sequence length and is considerably lower than a theoretically predicted upper bound. On the basis of simulations, it turns out that important properties of the coalescent with recombinations of the whole population are reflected in the properties of a sample of low size.

Phylogeographic structure and gene flow of Himalayan snowcock (Tetraogallus himalayensis)

2010 ◽  
Vol 60 (4) ◽  
pp. 449-465
Author(s):  
Wen Longying ◽  
Zhang Lixun ◽  
An Bei ◽  
Luo Huaxing ◽  
Liu Naifa ◽  
...  
Keyword(s):  
Demographic History ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Population Expansion ◽  
Population History ◽  
Tibet Plateau ◽  
Phylogeographic Structure ◽  
Mitochondrial Cytochrome B ◽  
History Of ◽  
Qinghai Tibet Plateau

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.

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