Using supernetworks to distinguish hybridization from lineage-sorting

Holland, Barbara R.; Benthin, Steffi; Lockhart, Peter J.; Moulton, Vincent; Huber, Katharina T.

doi:10.1186/1471-2148-8-202

Cited by 108 publications

(88 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This problem has attracted much interest (Sang and Zhong, 2000;Buckley et al, 2006;Holland et al, 2008), and yet few effective approaches exist for distinguishing these processes. Fortunately the range-wide sampling with mtDNA and microsatellite markers facilitates some level of resolution.…”

Section: Hybridization or Incomplete Lineage Sorting?mentioning

confidence: 99%

Surgeons and suture zones: Hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes

DiBattista

Whitney

Craig

et al. 2016

Molecular Phylogenetics and Evolution

View full text Add to dashboard Cite

Surgeons and suture zones: Hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes, Molecular Phylogenetics and Evolution (2016), doi: http:// dx.doi.org/10. 1016/j.ympev.2016.04.036 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. . japonicus and A. nigricans) are distinguishable only at a population or subspecies level (Φ ST = 0.6533, P < 0.001). Little population structure was observed within species, with evidence of recent population expansion across all four geographic ranges. We detected sharing of mtDNA haplotypes between species and extensive hybridization based on microsatellites, consistent with later generation hybrids but also the effects of allele homoplasy. Despite extensive introgression, 98% of specimens had 3 concordance between mtDNA lineage and species identification based on external morphology, indicating that species integrity may not be eroding. The A. nigricans complex demonstrates a range of outcomes from incomplete speciation to secondary contact to decreasing hybridization with increasing evolutionary depth.

show abstract

Section: Hybridization or Incomplete Lineage Sorting?mentioning

confidence: 99%

Surgeons and suture zones: Hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes

DiBattista

Whitney

Craig

et al. 2016

Molecular Phylogenetics and Evolution

View full text Add to dashboard Cite

show abstract

“…However, Holder et al showed later that this statistic fails to reliably distinguish between the two processes [42]. More recently, Holland et al proposed to use supernetworks for this task [43].…”

Section: To Network or Not To Network That Is The Questionmentioning

confidence: 99%

Evolutionary Phylogenetic Networks: Models and Issues

Nakhleh

2010

Problem Solving Handbook in Computational Biology and Bioinformatics

View full text Add to dashboard Cite

Phylogenetic networks are special graphs that generalize phylogenetic trees to allow for modeling of non-treelike evolutionary histories. The ability to sequence multiple genetic markers from a set of organisms and the conflicting evolutionary signals that these markers provide in many cases, have propelled research and interest in phylogenetic networks to the forefront in computational phylogenetics. Nonetheless, the term 'phylogenetic network' has been generically used to refer to a class of models whose core shared property is tree generalization. Several excellent surveys of the different flavors of phylogenetic networks and methods for their reconstruction have been written recently. However, unlike these surveys, this chapter focuses specifically on one type of phylogenetic networks, namely evolutionary phylogenetic networks, which explicitly model reticulate evolutionary events. Further, this chapter focuses less on surveying existing tools, and addresses in more detail issues that are central to the accurate reconstruction of phylogenetic networks.

show abstract

“…Despite advances in both fields (e.g. Balvočiūtė et al 2014;Salichos et al 2014;Yang et al 2013), the interface between trees and networks has rarely been bridged (Holland & Moulton 2003;Holland et al 2008;Huber et al 2016). The decision to use trees or networks is usually not dependent on any arguments over the superiority of one approach over the other (but see Morrison 2014), but rather the evolutionary complexity of the group under investigation and the resulting dataset.…”

Section: Textmentioning

confidence: 99%

Intertwining phylogenetic trees and networks

Schliep

Potts

Morrison

et al. 2016

Preprint

View full text Add to dashboard Cite

The fields of phylogenetic tree and network inference have dramatically advanced in the last decade, but independently with few attempts to bridge them. Here we provide a framework, implemented in the PHANGORN library in R, to transfer information between trees and networks.This includes: 1) identifying and labelling equivalent tree branches and network edges, 2) transferring branch support to network edges, and 3) mapping bipartition support from a sample of trees (e.g. from bootstrapping or Bayesian inference) onto network edges. The ability to readily combine tree and network information should lead to more comprehensive evolutionary comparisons and conclusions.

show abstract

Using supernetworks to distinguish hybridization from lineage-sorting

Cited by 108 publications

References 39 publications

Surgeons and suture zones: Hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes

Surgeons and suture zones: Hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes

Evolutionary Phylogenetic Networks: Models and Issues

Intertwining phylogenetic trees and networks

Contact Info

Product

Resources

About