A new balance index for phylogenetic trees

Mir, Arnau; Rosselló, Francesc; Rotger, Lucı ́a

doi:10.1016/j.mbs.2012.10.005

Cited by 64 publications

(122 citation statements)

References 33 publications

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“…Nucleotide substitution saturation was assessed using the Xia’s test 38 . The balance of the phylogenetic tree obtained under the best partitioning scheme was measured using the total cophenetic index 58 . PartitionFinder 59 was used to explore the partitioning schemes and evolutionary models for the standard DNA-based and the protein-based analyses.…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic evidence that both ancient vicariance and dispersal have contributed to the biogeographic patterns of anchialine cave shrimps

Jurado‐Rivera

Pons

Álvarez

et al. 2017

Sci Rep

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Cave shrimps from the genera Typhlatya, Stygiocaris and Typhlopatsa (Atyidae) are restricted to specialised coastal subterranean habitats or nearby freshwaters and have a highly disconnected distribution (Eastern Pacific, Caribbean, Atlantic, Mediterranean, Madagascar, Australia). The combination of a wide distribution and a limited dispersal potential suggests a large-scale process has generated this geographic pattern. Tectonic plates that fragment ancestral ranges (vicariance) has often been assumed to cause this process, with the biota as passive passengers on continental blocks. The ancestors of these cave shrimps are believed to have inhabited the ancient Tethys Sea, with three particular geological events hypothesised to have led to their isolation and divergence; (1) the opening of the Atlantic Ocean, (2) the breakup of Gondwana, and (3) the closure of the Tethys Seaway. We test the relative contribution of vicariance and dispersal in the evolutionary history of this group using mitochondrial genomes to reconstruct phylogenetic and biogeographic scenarios with fossil-based calibrations. Given that the Australia/Madagascar shrimp divergence postdates the Gondwanan breakup, our results suggest both vicariance (the Atlantic opening) and dispersal. The Tethys closure appears not to have been influential, however we hypothesise that changing marine currents had an important early influence on their biogeography.

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Section: Methodsmentioning

confidence: 99%

Phylogenetic evidence that both ancient vicariance and dispersal have contributed to the biogeographic patterns of anchialine cave shrimps

Jurado‐Rivera

Pons

Álvarez

et al. 2017

Sci Rep

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“…Balance has been one of the most studied tree shape metrics [12, 13], usually quantified by a balance index (examples in [14–17]), which depends only on tree topology. These indices have been used as tools to both test stochastic models of evolution and departures from them [18–24], and to assess the degree of imbalance of real phylogenies [9, 10, 19, 25–28].…”

Section: Introductionmentioning

confidence: 99%

The tree balance signature of mass extinction is erased by continued evolution in clades of constrained size with trait-dependent speciation

2017

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The kind and duration of phylogenetic topological “signatures” left in the wake of macroevolutionary events remain poorly understood. To this end, we examined a broad range of simulated phylogenies generated using trait-biased, heritable speciation probabilities and mass extinction that could be either random or selective on trait value, but also using background extinction and diversity-dependence to constrain clade sizes. In keeping with prior results, random mass extinction increased imbalance of clades that recovered to pre-extinction size, but was a relatively weak effect. Mass extinction that was selective on trait values tended to produce clades of similar or greater balance compared to random extinction or controls. Allowing evolution to continue past the point of clade-size recovery resulted in erosion and eventual erasure of this signal, with all treatments converging on similar values of imbalance, except for very intense extinction regimes targeted at taxa with high speciation rates. Return to a more balanced state with extended post-extinction evolution was also associated with loss of the previous phylogenetic root in most treatments. These results further demonstrate that while a mass extinction event can produce a recognizable phylogenetic signal, its effects become increasingly obscured the further an evolving clade gets from that event, with any sharp imbalance due to unrelated evolutionary factors.

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“…On the other hand, the topology of the least possible balanced binary reference taxonomy is a rooted caterpillar, as every internal node (and also the root) has one big descendant clade and one small (with only one node) descendant clade. Borrowing the notion of total cophenetic index for phylogenetic trees (Mir et al, 2013) to measure the balance of reference taxonomies, complete binary trees have indeed the minimum value while rooted caterpillars have the maximum value. Notice, however, that the total cophenetic index of the NCBI Taxonomy (Federhen, 2012(Federhen, , 2015 restricted to the standard taxonomic ranks (Kingdom, Phylum, Class, Order, Family, Genus, and Species) is 206,110,330,551, which represents only 0.00032060% of the interval between the minimum value (727,931) and the maximum value (64,288,827,123,576,010) for the number of taxa in the restricted NCBI Taxonomy.…”

Section: Taxonomic Annotation Using Imbalanced Reference Taxonomiesmentioning

confidence: 99%

Unbiased Taxonomic Annotation of Metagenomic Samples

Fosso¹,

Pesole²,

Rosselló³

et al. 2017

Bioinformatics Research and Applications

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The classification of reads from a metagenomic sample using a reference taxonomy is usually based on first mapping the reads to the reference sequences and then classifying each read at a node under the lowest common ancestor of the candidate sequences in the reference taxonomy with the least classification error. However, this taxonomic annotation can be biased by an imbalanced taxonomy and also by the presence of multiple nodes in the taxonomy with the least classification error for a given read. In this article, we show that the Rand index is a better indicator of classification error than the often used area under the receiver operating characteristic (ROC) curve and F-measure for both balanced and imbalanced reference taxonomies, and we also address the second source of bias by reducing the taxonomic annotation problem for a whole metagenomic sample to a set cover problem, for which a logarithmic approximation can be obtained in linear time and an exact solution can be obtained by integer linear programming. Experimental results with a proof-of-concept implementation of the set cover approach to taxonomic annotation in a next release of the TANGO software show that the set cover approach further reduces ambiguity in the taxonomic annotation obtained with TANGO without distorting the relative abundance profile of the metagenomic sample.

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A new balance index for phylogenetic trees

Cited by 64 publications

References 33 publications

Phylogenetic evidence that both ancient vicariance and dispersal have contributed to the biogeographic patterns of anchialine cave shrimps

Phylogenetic evidence that both ancient vicariance and dispersal have contributed to the biogeographic patterns of anchialine cave shrimps

The tree balance signature of mass extinction is erased by continued evolution in clades of constrained size with trait-dependent speciation

Unbiased Taxonomic Annotation of Metagenomic Samples

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