A Characterization of the Set of Species Trees that Produce Anomalous Ranked Gene Trees

Degnan, J.H.; Rosenberg, Noah A.; Stadler, Tanja

doi:10.1109/tcbb.2012.110

Cited by 16 publications

(36 citation statements)

References 20 publications

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“…The ranked gene tree in Figure 1(A) matches the ranked species tree, while the ranked gene tree in Figure 1(B) does not. In spite of the results of this paper, caterpillar gene trees can be ARGTs (Degnan et al, 2012a), i.e., a caterpillar gene tree can be more probable than a matching ranked gene tree, even though it must be less probable than the matching unranked gene tree.…”

Section: Anomalous Ranked and Unrooted Gene Treesmentioning

confidence: 60%

“…Recently, the concept of anomalous gene trees has also been extended to ranked gene trees (Degnan et al, 2012a;Disanto and Rosenberg, 2014) and unrooted gene trees (Degnan, 2013).…”

Section: Anomalous Ranked and Unrooted Gene Treesmentioning

confidence: 99%

“…A ranked gene tree topology encodes the relative timing of the branches, so that, as an example, the ranked gene tree topologies in Figure 1(A) and (B) are distinct because the ordering of the (a, b) and (c, d) coalescences are reversed, even though the unranked gene tree topologies are the same. An anomalous ranked gene tree (ARGT) is a ranked gene tree that is more probable than the ranked gene tree that matches the ranked species tree (Degnan et al, 2012a). The ranked gene tree in Figure 1(A) matches the ranked species tree, while the ranked gene tree in Figure 1(B) does not.…”

Section: Anomalous Ranked and Unrooted Gene Treesmentioning

confidence: 99%

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There are no caterpillars in a wicked forest

Degnan

Rhodes

2015

Theoretical Population Biology

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Species trees represent the historical divergences of populations or species, while gene trees trace the ancestry of individual gene copies sampled within those populations. In cases involving rapid speciation, gene trees with topologies that differ from that of the species tree can be most probable under the standard multispecies coalescent model, making species tree inference more difficult. Such anomalous gene trees are not well understood except for some small cases. In this work, we establish one constraint that applies to trees of any size: gene trees with "caterpillar" topologies cannot be anomalous. The proof of this involves a new combinatorial object, called a population history, which keeps track of the number of coalescent events in each ancestral population.

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Section: Anomalous Ranked and Unrooted Gene Treesmentioning

confidence: 60%

“…Recently, the concept of anomalous gene trees has also been extended to ranked gene trees (Degnan et al, 2012a;Disanto and Rosenberg, 2014) and unrooted gene trees (Degnan, 2013).…”

Section: Anomalous Ranked and Unrooted Gene Treesmentioning

confidence: 99%

Section: Anomalous Ranked and Unrooted Gene Treesmentioning

confidence: 99%

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There are no caterpillars in a wicked forest

Degnan

Rhodes

2015

Theoretical Population Biology

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“…While a robust phylogeny is needed to study diversification and adaptation in such groups, phylogenetic analysis of close relatives can be problematic. Discordance between gene trees and species trees is more likely when speciation is recent and the effective population size of the ancestral population is large relative to the age of the species (Kubatko and Degnan 2007; Degnan et al, 2012). This discordance can arise through hybridization, gene duplication and loss, and incomplete lineage sorting (Maddison 1997; Degnan and Rosenberg 2009; Knowles and Kubatko 2010; Nakhleh 2013).…”

Section: Introductionmentioning

confidence: 99%

Colonization and diversification of aquatic insects on three Macaronesian archipelagos using 59 nuclear loci derived from a draft genome

Rutschmann

Detering

Simon

et al. 2016

Preprint

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29The study of processes driving diversification requires a fully sampled and well resolved 30 phylogeny. Multilocus approaches to the study of recent diversification provide a powerful 31 means to study the evolutionary process, but their application remains restricted because 32 multiple unlinked loci with suitable variation for phylogenetic or coalescent analysis are not 33 available for most non-model taxa. Here we identify novel, putative single-copy nuclear DNA 34 (nDNA) phylogenetic markers to study the colonization and diversification of an aquatic 35 insect species complex, Cloeon dipterum L. 1761 (Ephemeroptera: Baetidae), in Macaronesia. 36 Whole-genome sequencing data from one member of the species complex were used to 37 identify 59 nDNA loci (32,213 base pairs), followed by Sanger sequencing of 29 individuals 38 sampled from 13 islands of three Macaronesian archipelagos. Multispecies coalescent 39 analyses established six putative species. Three island species formed a monophyletic clade, 40 with one species occurring on the Azores, Europe and North America. Ancestral state 41 reconstruction indicated at least two colonization events from the mainland (Canaries, 42Azores) and one within the archipelago (between Madeira and the Canaries). Random subsets 43 of the 59 loci showed a positive linear relationship between number of loci and node support. 44In contrast, node support in the multispecies coalescent tree was negatively correlated with 45 mean number of phylogenetically informative sites per locus, suggesting a complex 46 relationship between tree resolution and marker variability. Our approach highlights the value 47 of combining coalescent-based phylogeography, species delimitation, and phylogenetic 48 reconstruction to resolve recent diversification events in an archipelago species complex. 49

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“…This is in spite of the fact that simple formulas exist for relating the number of duplication-loss events and the number of deep coalescence events (Zhang 2011), which, at first glance, might suggest that parsimony methods would always infer one event over the other (for further discussion, see Supplemental Material S5). Furthermore, while we have demonstrated that DLCpar performs well under a variety of species tree parameters, more study is needed in the ''anomaly zone'' of species histories in which anomalous gene trees (AGTs) exist, that is, where the gene tree most likely to evolve under a coalescent model differs from the species tree topology (Degnan and Rosenberg 2006;Degnan et al 2012;Degnan 2013). Within an anomaly zone, it has been shown that species trees reconstructed using democratic vote (Degnan and Rosenberg 2006), greedy consensus ), maximum likelihood from concatenated sequences (Kubatko and Degnan 2007), and minimizing-deepcoalescence (Than and Rosenberg 2011) methods are inconsistent, meaning that the estimated species tree topology is incorrect in the limit as the number of sampled gene trees goes to infinity.…”

Section: Discussionmentioning

confidence: 99%

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees

et al. 2013

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Accurate gene tree-species tree reconciliation is fundamental to inferring the evolutionary history of a gene family. However, although it has long been appreciated that population-related effects such as incomplete lineage sorting (ILS) can dramatically affect the gene tree, many of the most popular reconciliation methods consider discordance only due to gene duplication and loss (and sometimes horizontal gene transfer). Methods that do model ILS are either highly parameterized or consider a restricted set of histories, thus limiting their applicability and accuracy. To address these challenges, we present a novel algorithm DLCpar for inferring a most parsimonious (MP) history of a gene family in the presence of duplications, losses, and ILS. Our algorithm relies on a new reconciliation structure, the labeled coalescent tree (LCT), that simultaneously describes coalescent and duplication-loss history. We show that the LCT representation enables an exhaustive and efficient search over the space of reconciliations, and, for most gene families, the least common ancestor (LCA) mapping is an optimal solution for the species mapping between the gene tree and species tree in an MP LCT. Applying our algorithm to a variety of clades, including flies, fungi, and primates, as well as to simulated phylogenies, we achieve high accuracy, comparable to sophisticated probabilistic reconciliation methods, at reduced run time and with far fewer parameters. These properties enable inferences of the complex evolution of gene families across a broad range of species and large data sets.

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A Characterization of the Set of Species Trees that Produce Anomalous Ranked Gene Trees

Cited by 16 publications

References 20 publications

There are no caterpillars in a wicked forest

There are no caterpillars in a wicked forest

Colonization and diversification of aquatic insects on three Macaronesian archipelagos using 59 nuclear loci derived from a draft genome

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees

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