Population structure and colonization history of the olive fly, Bactrocera oleae (Diptera, Tephritidae)

Species from the steppe region of Eastern Europe likely colonized northwestern Europe in connection with agriculture after 6500 BP. The striped field mouse ( Apodemus agrarius Pallas, 1783), is a steppe-derived species often found in human crops. It is common on the southern Danish islands of Lolland and Falster, which have been isolated from mainland Europe since approximately 10 300–8000 BP. Thus, this species could have been brought in with humans in connection with agriculture, or it could be an earlier natural invader. We sequenced 86 full mitochondrial genomes from the northwestern range of the striped field mouse, analysed phylogenetic relationships and estimated divergence time. The results supported human-induced colonization of Denmark in the Subatlantic or Subboreal period. A newly discovered population from Central Jutland in Denmark diverged from Falster approximately 100–670 years ago, again favouring human introduction. One individual from Sweden turned out to be a recent introduction from Central Jutland.

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The origin and colonization history of the barley scald pathogen Rhynchosporium secalis

Journal of Evolutionary Biology ◽

10.1111/j.1420-9101.2007.01347.x ◽

2007 ◽

Vol 20 (4) ◽

pp. 1311-1321 ◽

Cited By ~ 35

Author(s):

P. C. BRUNNER ◽

S. SCHÜRCH ◽

B. A. MCDONALD

Keyword(s):

Rhynchosporium Secalis ◽

Colonization History ◽

History Of

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A novel coalescent method insensitive to population structure

10.1101/2020.11.30.405431 ◽

2020 ◽

Author(s):

Zeqi Yao ◽

Kehui Liu ◽

Shanjun Deng ◽

Xionglei He

Keyword(s):

Population Structure ◽

Phylogenetic Tree ◽

Simulated Data ◽

Structured Populations ◽

Population History ◽

Cell Populations ◽

Developmental History ◽

Coalescent Analysis ◽

History Of ◽

Larger Sample

AbstractConventional coalescent inferences of population history make the critical assumption that the population under examination is panmictic. However, most populations are structured. This complicates the prevailing coalescent analyses and sometimes leads to inaccurate estimates. To develop a coalescent method unhampered by population structure, we perform two analyses. First, we demonstrate that the coalescent probability of two randomly sampled alleles from the immediate preceding generation (one generation back) is independent of population structure. Second, motivated by this finding, we propose a new coalescent method: i-coalescent analysis. i-coalescent analysis computes the instantaneous coalescent rate (iCR) by using a phylogenetic tree of sampled alleles. Using simulated data, we broadly demonstrate the capability of i-coalescent analysis to accurately reconstruct population size dynamics of highly structured populations, although we find this method often requires larger sample sizes for structured populations than for panmictic populations. Overall, our results indicate i-coalescent analysis to be a useful tool, especially for the inference of population histories with intractable structure such as the developmental history of cell populations in the organs of complex organisms.

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Effect of population structure and migration when investigating genetic continuity using ancient DNA

10.1101/052548 ◽

2016 ◽

Author(s):

NM Silva ◽

S Kreutzer ◽

C Papageorgopoulou ◽

M Currat

Keyword(s):

Population Structure ◽

Ancient Dna ◽

Isolated Populations ◽

Hunter Gatherers ◽

History Of ◽

Genetic Continuity ◽

Population Continuity ◽

Local Hunter ◽

And Migration ◽

Genetic Pool

AbstractRecent advances in sequencing techniques provide means to access direct genetic snapshots from the past with ancient DNA data (aDNA) from diverse periods of human prehistory. Comparing samples taken in the same region but at different time periods may indicate if there is continuity in the peopling history of that area or if a large genetic input, such as an immigration wave, has occurred. Here we propose a new modeling approach for investigating population continuity using aDNA, including two fundamental elements in human evolution that were absent from previous methods: population structure and migration. The method also considers the extensive temporal and geographic heterogeneity commonly found in aDNA datasets. We compare our spatially-explicit approach to the previous non-spatial method and show that it is more conservative and thus suitable for testing population continuity, especially when small, isolated populations, such as prehistoric ones, are considered. Moreover, our approach also allows investigating partial population continuity and we apply it to a real dataset of ancient mitochondrial DNA. We estimate that 91% of the current genetic pool in central Europe entered the area with immigrant Neolithic farmers, but a genetic contribution of local hunter-gatherers as large as 83% cannot be entirely ruled out.

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