Inferring rooted species trees from unrooted gene trees using approximate Bayesian computation

Alanzi, Ayed R. A.; Degnan, J.H.

doi:10.1016/j.ympev.2017.07.017

Cited by 12 publications

(29 citation statements)

References 67 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Interestingly, for distinguishing the two species trees, the frequency of the matching unrooted gene tree ((a, b) , c, (d, e)) is not helpful. Instead, it is frequencies of nonmatching unrooted gene trees that are useful for inferring the rooted species tree [26]. This paper examines features of the distribution of unrooted topological gene trees that occur under the multispecies coalescent model on a species tree, for deriving asymptotic (i.e., large numbers of loci) UMDC behavior from unrooted gene trees for four taxa and five taxa.…”

Section: Introductionmentioning

confidence: 99%

Statistical inconsistency of the unrooted minimize deep coalescence criterion

Alanzi

Degnan

2021

PLoS ONE

Self Cite

View full text Add to dashboard Cite

Species trees, which describe the evolutionary relationships between species, are often inferred from gene trees, which describe the ancestral relationships between sequences sampled at different loci from the species of interest. A common approach to inferring species trees from gene trees is motivated by supposing that gene tree variation is due to incomplete lineage sorting, also known as deep coalescence. One of the earliest methods motivated by deep coalescence is to find the species tree that minimizes the number of deep coalescent events needed to explain discrepancies between the species tree and input gene trees. This minimize deep coalescence (MDC) criterion can be applied in both rooted and unrooted settings. where either rooted or unrooted gene trees can be used to infer a rooted species tree. Previous work has shown that MDC is statistically inconsistent in the rooted setting, meaning that under a probabilistic model for deep coalescence, the multispecies coalescent, for some species trees, increasing the number of input gene trees does not make the method more likely to return a correct species tree. Here, we obtain analogous results in the unrooted setting, showing conditions leading to inconsistency of the MDC criterion using the multispecies coalescent model with unrooted gene trees for four taxa and five taxa.

show abstract

Section: Introductionmentioning

confidence: 99%

Statistical inconsistency of the unrooted minimize deep coalescence criterion

Alanzi

Degnan

2021

PLoS ONE

Self Cite

View full text Add to dashboard Cite

show abstract

“…Genetic distances (D A ) and fixation index (Fst) values in Mongolian and other populations were calculated with DISPAN (15) and Genepop software v. 4.0 (16), respectively. Heat maps were drawn by R software v. 3.4.3 (17) based on the D A and Fst values, and phylogeny trees were drawn by MEGA software v. 6.0 (18) and Phylip software v. 3.69 (19-21). Principal components analysis (PCA) was performed by using and MVSP software v. 3.1 (22).…”

Section: Methodsmentioning

confidence: 99%

Multiple genetic analyses to investigate the polymorphisms of Chinese Mongolian population with an efficient short tandem repeat panel

et al. 2019

View full text Add to dashboard Cite

Aim To determine allele frequencies and forensic statistics of 22 autosomal short tandem repeat loci in Chinese Mongolian population. Methods Blood specimens were collected from 134 unrelated healthy Mongolian individuals, and 22 short tandem repeat loci were co-amplified and genotyped. Allele frequencies and forensic parameters were calculated, and population genetic differences were analyzed among Mongolian population and other eight Chinese populations: Northern Han, Guangdong Han, Chengdu Han, Xinjiang Hui, Xinjiang Uygur, Hainan Li, Qinghai Tibetan, and Hainan Han. Results All the loci were in the Hardy-Weinberg equilibrium, and after Bonferroni correction there was no linkage disequilibrium between them. The allele frequencies of these 22 loci were between 0.0037 and 0.3657. This panel had high discriminating power and genetic polymorphism in the Mongolian population, with combined power of discrimination of 0.999999999999999999999999998399 and combined probability of exclusion of 0.9999999999566925. Structure analysis showed no evidence that these nine Chinese populations had different component distribution. However, genetic distance analysis showed significant differences among them ( P < 0.05). Conclusion The combined application of these 22 loci could be useful for forensic purposes in the Mongolian population. Mongolian population had smaller genetic distances from the populations in northern China (Northern Han, Xinjiang Uygur, and Xinjiang Hui) than from the populations in Hainan province (Hainan Han and Hainan Li populations).

show abstract

“…67 without using an outgroup. Although this method has been tested using approximate Bayesian computation (Alanzi and Degnan 2017), it is expected that using an outgroup (if available) to ultimately root the tree (or network) will typically be easier than inferring the root directly from the unrooted trees. SNaQ (Solís-Lemus and Ané 2016) is able to infer some rooted information (direction of some hybridization edges) in networks from unrooted trees.…”

Section: Rooted Versus Unrooted Networkmentioning

confidence: 99%

Modeling Hybridization Under the Network Multispecies Coalescent

Degnan

2018

Systematic Biology

100

View full text Add to dashboard Cite

Simultaneously modeling hybridization and the multispecies coalescent is becoming increasingly common, and inference of species networks in this context is now implemented in several software packages. This article addresses some of the conceptual issues and decisions to be made in this modeling, including whether or not to use branch lengths and issues with model identifiability. This article is based on a talk given at a Spotlight Session at Evolution 2017 meeting in Portland, Oregon. This session included several talks about modeling hybridization and gene flow in the presence of incomplete lineage sorting. Other talks given at this meeting are also included in this special issue of Systematic Biology.

show abstract

Inferring rooted species trees from unrooted gene trees using approximate Bayesian computation

Cited by 12 publications

References 67 publications

Statistical inconsistency of the unrooted minimize deep coalescence criterion

Statistical inconsistency of the unrooted minimize deep coalescence criterion

Multiple genetic analyses to investigate the polymorphisms of Chinese Mongolian population with an efficient short tandem repeat panel

Modeling Hybridization Under the Network Multispecies Coalescent

Contact Info

Product

Resources

About