scholarly journals Learning Genetic Population Structures Using Minimization of Stochastic Complexity

Entropy ◽  
2010 ◽  
Vol 12 (5) ◽  
pp. 1102-1124
Author(s):  
Jukka Corander ◽  
Mats Gyllenberg ◽  
Timo Koski
2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Guang Yao Fan ◽  
Yi Ye ◽  
Yi Ping Hou

Abstract Detecting population structure and estimating individual biogeographical ancestry are very important in population genetics studies, biomedical research and forensics. Single-nucleotide polymorphism (SNP) has long been considered to be a primary ancestry-informative marker (AIM), but it is constrained by complex and time-consuming genotyping protocols. Following up on our previous study, we propose that a multi-insertion-deletion polymorphism (Multi-InDel) with multiple haplotypes can be useful in ancestry inference and hierarchical genetic population structures. A validation study for the X chromosome Multi-InDel marker (X-Multi-InDel) as a novel AIM was conducted. Genetic polymorphisms and genetic distances among three Chinese populations and 14 worldwide populations obtained from the 1000 Genomes database were analyzed. A Bayesian clustering method (STRUCTURE) was used to discern the continental origins of Europe, East Asia, and Africa. A minimal panel of ten X-Multi-InDels was verified to be sufficient to distinguish human ancestries from three major continental regions with nearly the same efficiency of the earlier panel with 21 insertion-deletion AIMs. Along with the development of more X-Multi-InDels, an approach using this novel marker has the potential for broad applicability as a cost-effective tool toward more accurate determinations of individual biogeographical ancestry and population stratification.


Parasitology ◽  
1999 ◽  
Vol 119 (3) ◽  
pp. 295-302 ◽  
Author(s):  
C. M. DAVIES ◽  
J. P. WEBSTER ◽  
O. KRÜGER ◽  
A. MUNATSI ◽  
J. NDAMBA ◽  
...  

The genetic population structures of the freshwater snail Bulinus globosus and its trematode parasite Schistosoma haematobium from 8 river sites in the Zimbabwean highveld were compared using randomly amplified DNA(RAPD) markers. There was significant variability between snail populations collected at different sites, but schistosome populations only showed differentiation at a wider geographical scale (between 2 non-connected river systems). For snails, genetic distance was better correlated with proximity along rivers than absolute geographical separation. In contrast, schistosome genetic distance was better correlated with absolute geographical separation than proximity along rivers. These results are consistent with different dispersal mechanisms for snails and schistosomes and the implications for host–parasite coevolution are discussed.


2006 ◽  
Vol 151 (1) ◽  
pp. 31-39 ◽  
Author(s):  
Akira Iguchi ◽  
Shinpei Takai ◽  
Masahiro Ueno ◽  
Tsuneo Maeda ◽  
Takashi Minami ◽  
...  

2002 ◽  
Vol 80 (8) ◽  
pp. 875-884 ◽  
Author(s):  
Carolin Nuortila ◽  
Juha Tuomi ◽  
Kari Laine

Clonal propagation and limited dispersal of seeds lead to genetic population structures in which most potential mates are relatives. If the species suffers from inbreeding depression or is self-incompatible, the number of seeds matured per fruit may be limited by the lack of outcrossing by unrelated pollen. We tested for distance-related genetic structure by hand-pollinating plants at increasing distances and measuring fruit set (berries/pollinated flowers) and seed number per fruit in natural populations of bilberry (Vaccinium myrtillus L.) and lingonberry (Vaccinium vitis-idaea L.). Bagging of the flower buds without natural (pollination by insects) or hand-pollination yielded almost no fruit or seed, suggesting that the species are obligately insect pollinated. Self-pollination led to a significant reduction in seed number per fruit and increased seed abortion compared with cross-pollination. Moreover, seed number increased with increasing distance between the pollen donor and pollen recipient. Flight distances of bumblebees were estimated for bilberry by monitoring between-flower and, for lingonberry, between-inflorescence flight distances. About 90% of all flights were at distances of less than 1 m. At this distance, we observed less than the maximum seed number per fruit in hand-pollinations in both study species. Consequently, clonal growth is likely to be an important factor that constrains fruit and seed number in these species.Key words: bumblebee forage distance, clonal, hand-pollination, inter-parent distance, reproductive success, Vaccinium.


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