Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations

Corander, Jukka; Marttinen, Pekka; Sirén, Jukka; Tang, Jing

doi:10.1186/1471-2105-9-539

Cited by 783 publications

(646 citation statements)

References 36 publications

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“…Clustering analysis was run with Bayesian Analysis of Population Structure (BAPS) v6 (Corander, Marttinen, Siren, & Tang, 2008). The analysis used the linked loci option, the codon model of linkage, and variable K ( K ≤ 13; see Corander & Tang, 2007).…”

Section: Methodsmentioning

confidence: 99%

Phylogeographic mitogenomics of Atlantic codGadus morhua: Variation in and among trans‐Atlantic, trans‐Laurentian, Northern cod, and landlocked fjord populations

Lait

Marshall

Carr

2018

Ecology and Evolution

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The historical phylogeography, biogeography, and ecology of Atlantic cod (Gadus morhua) have been impacted by cyclic Pleistocene glaciations, where drops in sea temperatures led to sequestering of water in ice sheets, emergence of continental shelves, and changes to ocean currents. High‐resolution, whole‐genome mitogenomic phylogeography can help to elucidate this history. We identified eight major haplogroups among 153 fish from 14 populations by Bayesian, parsimony, and distance methods, including one that extends the species coalescent back to ca. 330 kya. Fish from the Barents and Baltic Seas tend to occur in basal haplogroups versus more recent distribution of fish in the Northwest Atlantic. There was significant differentiation in the majority of trans‐Atlantic comparisons (ΦST = .029–.180), but little or none in pairwise comparisons within the Northwest Atlantic of individual populations (ΦST = .000–.060) or defined management stocks (ΦST = .000–.023). Monte Carlo randomization tests of population phylogeography showed significantly nonrandom trans‐Atlantic phylogeography versus absence of such structure within various partitions of trans‐Laurentian, Northern cod (NAFO 2J3KL) and other management stocks, and Flemish Cap populations. A landlocked meromictic fjord on Baffin Island comprised multiple identical or near‐identical mitogenomes in two major polyphyletic clades, and was significantly differentiated from all other populations (ΦST = .153–.340). The phylogeography supports a hypothesis of an eastern origin of genetic diversity ca. 200–250 kya, rapid expansion of a western superhaplogroup comprising four haplogroups ca. 150 kya, and recent postglacial founder populations.

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Section: Methodsmentioning

confidence: 99%

Phylogeographic mitogenomics of Atlantic codGadus morhua: Variation in and among trans‐Atlantic, trans‐Laurentian, Northern cod, and landlocked fjord populations

Lait

Marshall

Carr

2018

Ecology and Evolution

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“…We also performed a Bayesian analysis of population structure using the software BAPS ver. 5 (Corander et al, 2008). We ran a population mixture analysis five times to check for convergence with the maximum number of genetically diverged groups K ¼ 32.…”

Section: Nuclear Its Data Analysismentioning

confidence: 99%

A large historical refugium explains spatial patterns of genetic diversity in a Neotropical savanna tree species

Souza

Collevatti

Lima‐Ribeiro

et al. 2016

Ann Bot

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Background and Aims The relative role of Pleistocene climate changes in driving the geographic distribution and genetic diversity of South American species is not well known, especially from open biomes such as the Cerrado, the most diverse tropical savanna, encompassing high levels of endemism. Here the effects of Quaternary climatic changes on demographic history, distribution dynamics and genetic diversity of Dimorphandra mollis, an endemic tree species widely distributed in the Cerrado, were investigated.Methods A total of 38 populations covering most of the distribution of D. mollis were analysed using internal transcribed spacer (ITS) sequences and nuclear microsatellite variation [simple sequence repeats (SSRs)]. The framework incorporated statistical phylogeography, coalescent analyses and ecological niche modelling (ENM).Key Results Different signatures of Quaternary climatic changes were found for ITS sequences and SSRs corresponding to different time slices. Coalescent analyses revealed large and constant effective population sizes, with high historical connectivity among the populations for ITS sequences and low effective population sizes and gene flow with recent population retraction for SSRs. ENMs indicated a slight geographical range retraction during the Last Glacial Maximum. A large historical refugium across central Brazil was predicted. Spatially explicit analyses showed a spatial cline pattern in genetic diversity related to the paleodistribution of D. mollis and to the centre of its historical refugium.Conclusions The complex genetic patterns found in D. mollis are the result of a slight geographical range retraction during the Last Glacial Maximum followed by population expansion to the east and south from a large refugium in the central part of the Cerrado. This historical refugium is coincident with an area predicted to be climatically stable under future climate scenarios. The identified refugium should be given high priority in conservation polices to safeguard the evolutionary potential of the species under predicted future climatic changes.

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“…We tested for the presence of cryptic microgeographic structure using the program BAPS version 5.3 (Corander et al, 2008), which identifies cryptic sub-structure by minimizing HWE and LD within each of k clusters. We used BAPS to estimate k within each CP using 15 runs wherein maximum k was constrained at the number of individuals genotyped.…”

Section: Cryptic Structurementioning

confidence: 99%

Heterozygote deficiencies in parasite populations: an evaluation of interrelated hypotheses in the raccoon tick, Ixodes texanus

2010

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Population genetics is increasingly being used to study the biology of parasites at the scales of both the host (infrapopulation, IP) and host population (component population, CP). In this study we tested three mechanistic hypotheses that could explain deviations from Hardy-Weinberg equilibrium (HWE) expectations due to heterozygote deficits (HDs) at the CP scale in raccoon ticks (Ixodes texanus; n ¼ 718) collected from raccoons (Procyon lotor; n ¼ 91) and genotyped at 11 microsatellite loci. These hypotheses were presence of technical issues (for example, null alleles), hierarchical structure (for example, host demography) and cryptic structure (for example, kin structure). Although statistical support for null alleles existed, their presence would also be expected to lead to an underestimation in levels of relatedness, and thus kin structure. However, we found the opposite pattern: significant HD at the IP scale being more likely in CPs with significant vs non-significant levels of kin structure. Our analyses revealed that pooling of kin groups could lead to highly variable levels of F IS among loci, a pattern usually suggestive of null alleles. We used Monte-Carlo (MC) simulations to show that the existence of subdivided breeding groups and high variance in individual reproductive success could adequately explain deviations from HWE in I. texanus. Thus, our results indicate that biological factors can lead to patterns that have usually been interpreted as technical issues (for example, null alleles), and that it is important to take such factors into consideration because loci deviating from HWE likely reflect the effects of real biological processes.

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Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations

Cited by 783 publications

References 36 publications

Phylogeographic mitogenomics of Atlantic codGadus morhua: Variation in and among trans‐Atlantic, trans‐Laurentian, Northern cod, and landlocked fjord populations

Phylogeographic mitogenomics of Atlantic codGadus morhua: Variation in and among trans‐Atlantic, trans‐Laurentian, Northern cod, and landlocked fjord populations

A large historical refugium explains spatial patterns of genetic diversity in a Neotropical savanna tree species

Heterozygote deficiencies in parasite populations: an evaluation of interrelated hypotheses in the raccoon tick, Ixodes texanus

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