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Chen ZZ, Harada Y, Nakamura Y, Wang L. Faster Exact Computation of rSPR Distance via Better Approximation. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 17:916-929. [PMID: 30387740 DOI: 10.1109/tcbb.2018.2878731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Due to hybridization events in evolution, studying two different genes of a set of species may yield two related but different phylogenetic trees for the set of species. In this case, we want to measure the dissimilarity of the two trees. The rooted subtree prune and regraft (rSPR) distance of the two trees has been used for this purpose. The problem of computing the rSPR distance of two given trees has many applications but is NP-hard. Accordingly, a number of programs have been developed for solving the problem either exactly or approximately. In this paper, we develop two new programs one of which solves the problem exactly and outperforms the previous best (namely, Whidden et al.'s rSPR-v1.3.0) significantly, while the other solves the problem approximately and outputs significantly better lower and upper bounds on the rSPR distance of the two given trees than the previous best due to Schalekamp et al. Our programs can be downloaded at http://rnc.r.dendai.ac.jp/rspr.html.
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Huson DH, Linz S. Autumn Algorithm-Computation of Hybridization Networks for Realistic Phylogenetic Trees. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:398-410. [PMID: 26955052 DOI: 10.1109/tcbb.2016.2537326] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A minimum hybridization network is a rooted phylogenetic network that displays two given rooted phylogenetic trees using a minimum number of reticulations. Previous mathematical work on their calculation has usually assumed the input trees to be bifurcating, correctly rooted, or that they both contain the same taxa. These assumptions do not hold in biological studies and "realistic" trees have multifurcations, are difficult to root, and rarely contain the same taxa. We present a new algorithm for computing minimum hybridization networks for a given pair of "realistic" rooted phylogenetic trees. We also describe how the algorithm might be used to improve the rooting of the input trees. We introduce the concept of "autumn trees", a nice framework for the formulation of algorithms based on the mathematics of "maximum acyclic agreement forests". While the main computational problem is hard, the run-time depends mainly on how different the given input trees are. In biological studies, where the trees are reasonably similar, our parallel implementation performs well in practice. The algorithm is available in our open source program Dendroscope 3, providing a platform for biologists to explore rooted phylogenetic networks. We demonstrate the utility of the algorithm using several previously studied data sets.
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Ottenburghs J, Megens HJ, Kraus RHS, van Hooft P, van Wieren SE, Crooijmans RPMA, Ydenberg RC, Groenen MAM, Prins HHT. A history of hybrids? Genomic patterns of introgression in the True Geese. BMC Evol Biol 2017; 17:201. [PMID: 28830337 PMCID: PMC5568201 DOI: 10.1186/s12862-017-1048-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/11/2017] [Indexed: 12/19/2022] Open
Abstract
Background The impacts of hybridization on the process of speciation are manifold, leading to distinct patterns across the genome. Genetic differentiation accumulates in certain genomic regions, while divergence is hampered in other regions by homogenizing gene flow, resulting in a heterogeneous genomic landscape. A consequence of this heterogeneity is that genomes are mosaics of different gene histories that can be compared to unravel complex speciation and hybridization events. However, incomplete lineage sorting (often the outcome of rapid speciation) can result in similar patterns. New statistical techniques, such as the D-statistic and hybridization networks, can be applied to disentangle the contributions of hybridization and incomplete lineage sorting. We unravel patterns of hybridization and incomplete lineage sorting during and after the diversification of the True Geese (family Anatidae, tribe Anserini, genera Anser and Branta) using an exon-based hybridization network approach and taking advantage of discordant gene tree histories by re-sequencing all taxa of this clade. In addition, we determine the timing of introgression and reconstruct historical effective population sizes for all goose species to infer which demographic or biogeographic factors might explain the observed patterns of introgression. Results We find indications for ancient interspecific gene flow during the diversification of the True Geese and were able to pinpoint several putative hybridization events. Specifically, in the genus Branta, both the ancestor of the White-cheeked Geese (Hawaiian Goose, Canada Goose, Cackling Goose and Barnacle Goose) and the ancestor of the Brent Goose hybridized with Red-breasted Goose. One hybridization network suggests a hybrid origin for the Red-breasted Goose, but this scenario seems unlikely and it not supported by the D-statistic analysis. The complex, highly reticulated evolutionary history of the genus Anser hampered the estimation of ancient hybridization events by means of hybridization networks. The reconstruction of historical effective population sizes shows that most species showed a steady increase during the Pliocene and Pleistocene. These large effective population sizes might have facilitated contact between diverging goose species, resulting in the establishment of hybrid zones and consequent gene flow. Conclusions Our analyses suggest that the evolutionary history of the True Geese is influenced by introgressive hybridization. The approach that we have used, based on genome-wide phylogenetic incongruence and network analyses, will be a useful procedure to reconstruct the complex evolutionary histories of many naturally hybridizing species groups. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1048-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jente Ottenburghs
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands.
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Robert H S Kraus
- Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Am Obstberg, 1D-78315, Radolfzell, Germany.,Department of Biology, University of Konstanz, D-78457, Constance, Germany
| | - Pim van Hooft
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands
| | - Sipke E van Wieren
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands
| | - Richard P M A Crooijmans
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Ronald C Ydenberg
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands.,Centre for Wildlife Ecology, Simon Fraser University, V5A 1S6, Burnaby, BC, Canada
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Herbert H T Prins
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands
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Willems M, Tahiri N, Makarenkov V. A new efficient algorithm for inferring explicit hybridization networks following the Neighbor-Joining principle. J Bioinform Comput Biol 2014; 12:1450024. [PMID: 25219384 DOI: 10.1142/s0219720014500243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Several algorithms and software have been developed for inferring phylogenetic trees. However, there exist some biological phenomena such as hybridization, recombination, or horizontal gene transfer which cannot be represented by a tree topology. We need to use phylogenetic networks to adequately represent these important evolutionary mechanisms. In this article, we present a new efficient heuristic algorithm for inferring hybridization networks from evolutionary distance matrices between species. The famous Neighbor-Joining concept and the least-squares criterion are used for building networks. At each step of the algorithm, before joining two given nodes, we check if a hybridization event could be related to one of them or to both of them. The proposed algorithm finds the exact tree solution when the considered distance matrix is a tree metric (i.e. it is representable by a unique phylogenetic tree). It also provides very good hybrids recovery rates for large trees (with 32 and 64 leaves in our simulations) for both distance and sequence types of data. The results yielded by the new algorithm for real and simulated datasets are illustrated and discussed in detail.
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Affiliation(s)
- Matthieu Willems
- Département d'informatique, Université du Québec à Montréal, Case postale 8888, Succursale Centre-ville, Montréal (Québec) H3C 3P8, Canada
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Affiliation(s)
- Zhi-Zhong Chen
- Division of Information System Design, Tokyo Denki University, Ishizaka, Hatoyama, Hiki, Saitama, Japan
| | - Lusheng Wang
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR, People's Republic of China
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