Ancestral admixture is the main determinant of global biodiversity in fission yeast

Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodiversity within all globally known strains of Schizosaccharomyces pombe arose through admixture between two divergent ancestral lineages. Initial hybridization occurred ~20 sexual outcrossing generations ago consistent with recent, human-induced migration at the onset of intensified transcontinental trade. Species-wide heritable phenotypic variation was explained near-exclusively by strain-specific arrangements of alternating ancestry components with evidence for transgressive segregation. Reproductive compatibility between strains was likewise predicted by the degree of shared ancestry. To assess the genetic determinants of ancestry block distribution across the genome, we characterized the type, frequency and position of structural genomic variation (SV) using nanopore and single-molecule real time sequencing, discovering over 800 SVs. Despite being associated with double-strand break initiation points, SV exerted overall little influence on the introgression landscape or on reproductive compatibility that exist between strains. In contrast, we find strongly increased statistical linkage between ancestral populations that is consistent with negative epistatic selection shaping genomic ancestry combinations during the course of hybridization. This study provides a detailed, experimentally tractable example that genomes of natural populations are mosaics reflecting different evolutionary histories. Exploiting genome-wide heterogeneity in the history of ancestral recombination and lineage-specific mutations sheds new light on the population history of S. pombe and highlights the importance of hybridization as a creative force in generating biodiversity.

Download Full-text

Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast

Molecular Biology and Evolution ◽

10.1093/molbev/msz126 ◽

2019 ◽

Vol 36 (9) ◽

pp. 1975-1989 ◽

Cited By ~ 14

Author(s):

Sergio Tusso ◽

Bart P S Nieuwenhuis ◽

Fritz J Sedlazeck ◽

John W Davey ◽

Daniel C Jeffares ◽

...

Keyword(s):

Single Molecule ◽

Phenotypic Variation ◽

Natural Populations ◽

Strand Break ◽

Transgressive Segregation ◽

Genomic Variation ◽

Population History ◽

Structural Genomic ◽

History Of ◽

Reproductive Compatibility

Abstract Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodiversity within all globally known strains of Schizosaccharomyces pombe arose through admixture between two divergent ancestral lineages. Initial hybridization was inferred to have occurred ∼20–60 sexual outcrossing generations ago consistent with recent, human-induced migration at the onset of intensified transcontinental trade. Species-wide heritable phenotypic variation was explained near-exclusively by strain-specific arrangements of alternating ancestry components with evidence for transgressive segregation. Reproductive compatibility between strains was likewise predicted by the degree of shared ancestry. To assess the genetic determinants of ancestry block distribution across the genome, we characterized the type, frequency, and position of structural genomic variation using nanopore and single-molecule real-time sequencing. Despite being associated with double-strand break initiation points, over 800 segregating structural variants exerted overall little influence on the introgression landscape or on reproductive compatibility between strains. In contrast, we found strong ancestry disequilibrium consistent with negative epistatic selection shaping genomic ancestry combinations during the course of hybridization. This study provides a detailed, experimentally tractable example that genomes of natural populations are mosaics reflecting different evolutionary histories. Exploiting genome-wide heterogeneity in the history of ancestral recombination and lineage-specific mutations sheds new light on the population history of S. pombe and highlights the importance of hybridization as a creative force in generating biodiversity.

Download Full-text

Whales and Men: genetic inferences uncover a detailed history of hunting in bowhead whale

10.1101/2020.04.09.033191 ◽

2020 ◽

Cited By ~ 1

Author(s):

TB Hoareau

Keyword(s):

Population Change ◽

Natural Populations ◽

Late Glacial ◽

Population History ◽

Bowhead Whale ◽

The Arctic ◽

Arctic Seas ◽

The North ◽

Time Calibration ◽

History Of

AbstractAfter millennia of hunting and a population collapse, it is still challenging to understand the genetic consequences of whaling on the circumarctic bowhead whale. Here I use published modern mtDNA sequences from the Bering-Chukchi-Beaufort population and a new time calibration to show that late–glacial climate changes and whaling have been the major drivers of population change. Cultures that hunted in the Arctic Seas from as early as 5000 years ago appear to be responsible for successive declines of the population growth, bringing the effective size down to 38% of its pristine population size. The Thules and the Basques (year 1000–1730) who only hunted in the North Atlantic had a major impact on this North Pacific population, indicating that bowhead whale stocks respond to harvesting as a single population unit. Recent positive growth is inferred only after the end of commercial whaling in 1915, and for levels of harvesting that are close to the current annual quota of 67 whales. By unfolding the population history of the bowhead whale, I provide compelling evidence that mtDNA yields critical yet undervalued information for management and conservation of natural populations.

Download Full-text

Recombination Disequilibrium in Ideal and Natural Populations

10.1101/035121 ◽

2015 ◽

Author(s):

Yuan-De Tan

Keyword(s):

Random Mating ◽

Natural Populations ◽

Population History ◽

Human Populations ◽

Linkage Maps ◽

Multiple Loci ◽

Breeding Populations ◽

Mating Population ◽

History Of ◽

Population Recombination

Following Hardy-Weinberg disequilibrium (HWD) occurring at a single locus and linkage disequilibrium (LD) between two loci in generations, we here proposed the third genetic disequilibrium in population: recombination disequilibrium (RD). RD is a measurement of crossover interference among multiple loci in a random mating population. In natural populations besides recombination interference, RD may also be due to selection, mutation, gene conversion, drift and/or migration. Therefore, similarly to LD, RD will also reflect the history of natural selection and mutation. In breeding populations, RD purely results from recombination interference and hence can be used to build or evaluate and correct a linkage map. Several practical examples from F2, testcross and human populations indeed demonstrate that RD is useful for measuring recombination interference between two short intervals and evaluating linkage maps. As with LD, RD will be important for studying genetic mapping, association of haplotypes with disease, plant breading and population history.

Download Full-text

The Population History of Britain and Ireland 1500-1750

Population Studies ◽

10.1080/0032472031000149416 ◽

1996 ◽

Vol 50 (2) ◽

pp. 284-285

Author(s):

Eilidh Garrett

Keyword(s):

Population History ◽

History Of

Download Full-text

Phenotypic variation and covariation among natural populations ofArabidopsis thalianain North Xinjiang

Biodiversity Science ◽

10.3724/sp.j.1003.2010.497 ◽

2010 ◽

Vol 18 (5) ◽

pp. 497

Author(s):

Li Lei ◽

Liu Tong ◽

Liu Bin ◽

Liu Zhongquan ◽

Si Langming ◽

...

Keyword(s):

Phenotypic Variation ◽

Natural Populations ◽

North Xinjiang

Download Full-text

Update on the Boundaries of the Curly Birch Range

Lesnoy Zhurnal (Forestry Journal) ◽

10.37482/0536-1036-2020-6-9-21 ◽

2020 ◽

pp. 9-21

Author(s):

L.V. Vetchinnikova ◽

◽

A.F. Titov ◽

◽

Keyword(s):

Population Size ◽

Natural Populations ◽

Forest Tree ◽

Published Data ◽

Population Approach ◽

Key Factors ◽

History Of ◽

Individual Trees ◽

Karelian Birch

The article reports on the application of the best known principles for mapping natural populations of curly (Karelian) birch Betula pendula Roth var. carelica (Mercklin) Hämet-Ahti – one of the most appealing representatives of the forest tree flora. Relying on the synthesis and analysis of the published data amassed over nearly 100 years and the data from own full-scale studies done in the past few decades almost throughout the area where curly birch has grown naturally, it is concluded that its range outlined in the middle of the 20th century and since then hardly revised is outdated. The key factors and reasons necessitating its revision are specified. Herewith it is suggested that the range is delineated using the population approach, and the key element will be the critical population size below which the population is no longer viable in the long term. This approach implies that the boundaries of the taxon range depend on the boundaries of local populations (rather than the locations of individual trees or small clumps of trees), the size of which should not be lower than the critical value, which is supposed to be around 100–500 trees for curly birch. A schematic map of the curly birch range delineated using this approach is provided. We specially address the problem of determining the minimum population size to secure genetic diversity maintenance. The advantages of the population approach to delineating the distribution range of curly birch with regard to its biological features are highlighted. The authors argue that it enables a more accurate delineation of the range; shows the natural evolutionary history of the taxon (although it is not yet officially recognized as a species) and its range; can be relatively easily updated (e.g. depending on the scope of reintroduction); should be taken into account when working on the strategy of conservation and other actions designed to maintain and regenerate this unique representative of the forest tree flora.

Download Full-text

Mitochondrial phylogeography and population history of finless porpoises in Sino-Japanese waters

Biological Journal of the Linnean Society ◽

10.1111/j.1095-8312.2008.0932.x ◽

2008 ◽

Vol 95 (1) ◽

pp. 193-204 ◽

Cited By ~ 21

Author(s):

GUANG YANG ◽

LI GUO ◽

MICHAEL W. BRUFORD ◽

FUWEN WEI ◽

KAIYA ZHOU

Keyword(s):

Population History ◽

History Of ◽

Japanese Waters

Download Full-text

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

Animal Biology ◽

10.1163/157075610x523314 ◽

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.

Download Full-text