Computational problems in molecular systematics

DeSalle, Rob; Wray, Charles G.; Absher, Robin

doi:10.1007/978-3-0348-7527-1_21

Cited by 13 publications

(5 citation statements)

References 49 publications

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“…Both have been the source of debate recently (Hickson et al, 2000;Lutzoni et al, 2000;and citations therein). Sequence alignment typically is accomplished by one of several computer programs, yet different optimal alignments may be favored by different programs and by different parameter values (Fitch and Smith, 1983;Lake, 1991;Mindell, 1991;Wheeler and Gladstein, 1991;Gatesy et al, 1993;DeSalle et al, 1994;Wheeler, 1995;Morrison and Ellis, 1997;Hickson et al, 2000;Lutzoni et al, 2000). The key parameter that can be modified for all programs is the cost ratio for opening and extending a gap.…”

Section: Summary and Perspectivesmentioning

confidence: 99%

Molecular Phylogenetics of the Chiropteran Family Vespertilionidae

Hoofer

Bussche

2003

Acta Chiropterologica

189

168

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Section: Summary and Perspectivesmentioning

confidence: 99%

Molecular Phylogenetics of the Chiropteran Family Vespertilionidae

Hoofer

Bussche

2003

Acta Chiropterologica

189

168

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“…When the amount of gaps is large due to excessive amounts of indels, MJ can create complicated cyclic structures that are almost impossible to interpret. Consequently, it has been recommended to minimize gap sites prior to analysis (Bandelt et al, 1999), but this can be a very subjective process (DeSalle et al, 1994). Moreover, gaps can be phylogenetically informative, improve branch support, and even change a topology (Simmons and Norton, 2014, Nagy et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

Topological incongruence between Median-Joining Networks and Bayesian inference phylogenies

Kong

Sánchez-Pacheco

Murphy

2022

Preprint

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Inferring phylogenies among intraspecific individuals often yields unresolved relationships (i.e., polytomies). Consequently, methods that compute distance-based abstract networks, like Median-Joining Networks (MJNs), are thought to be more appropriate tools for reconstructing such relationships than traditional trees. MJNs visualize all routes of relationships in the form of cycles, if needed, when traditional approaches cannot resolve them. However, the MJN method is a distance-based phenetic approach that does not involve character transformations and makes no reference to ancestor—descendant relationships. Although philosophical and theoretical arguments challenging the implication that MJNs reflect phylogenetic signal in the traditional sense have been presented elsewhere, an empirical comparison with a character-based approach is needed given the increasing popularity of MJN analysis in evolutionary biology. Here, we use the conservative Approximately Unbiased (AU) test to compare 85 cases of branching patterns of cycle-free MJNs and Bayesian Inference (BI) phylogenies using datasets from 55 empirical studies. By rooting the MJN analyses to provide directionality, analyses find substantial disagreement between computed MJNs and posterior distributions on BI phylogenies. The branching patterns in MJNs and BI phylogenies show significantly different relationships in 37.6% of cases. Among the relationships that were not significantly different, 96.2% show different sets of relationships. Our results indicate that the two methods provide different measures of relatedness in a phylogenetic sense. Finally, our analyses also support previous observations of the statistical hypothesis testing by reconfirming the over-conservativeness of the Shimodaira–Hasegawa test versus the AU test.

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“…334 VAN DEN BUSSCHE, HOOFER, AND HANSEN Because many parameters can affect the alignment of multiple sequences, thereby affecting the resulting phylogenetic tree (DeSalle et al, 1994;Wheeler, 1995), we performed four alignments with CLUSTAL X ( Thompson et al, 1997), each differing in cost ratios for opening gap and extending gap (5:4, 10:4, 20:8, and 30:5). All alignments were refined by considering deduced amino acid sequences and exon boundaries established in previous studies and allowing only triplet gaps within coding regions.…”

Section: Methodsmentioning

confidence: 99%