The phylogeny of the subgroups within the melanogaster species group: Likelihood tests on COI and COII sequences and a Bayesian estimate of phylogeny

Lewis, Robyn; Beckenbach, Andrew T.; Mooers, Arne Ø.

doi:10.1016/j.ympev.2005.02.018

Cited by 37 publications

(36 citation statements)

References 41 publications

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“…Phylogenetic relationships within the melanogaster species group and subgroup have proven difficult to resolve (Ko et al, 2003;Kopp, 2006;Kopp and True, 2002b;Lewis et al, 2005). In this study, we find strong support for Topology II within the melanogaster subgroup, i.…”

Section: Discussion Phylogenetic Relationships Within the Melanogastesupporting

confidence: 52%

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Phylogenetic incongruence in the Drosophila melanogaster species group

Wong

Jensen

Pool

et al. 2007

Molecular Phylogenetics and Evolution

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Drosophila melanogaster and its close relatives are used extensively in comparative biology. Despite the importance of phylogenetic information for such studies, relationships between some melanogaster species group members are unclear due to conflicting phylogenetic signals at different loci. In this study, we use twelve nuclear loci (eleven coding and one non-coding) to assess the degree of phylogenetic incongruence in this model system. We focus on two nodes: (1) The node joining the D. erecta-D. orena, D. melanogaster-D. simulans, and D. yakuba-D. teissieri lineages, and (2) The node joining the lineages leading to the melanogaster, takahashii, and eugracilis subgroups. We find limited evidence for incongruence at the first node; our data, as well as those of several previous studies, strongly support monophyly of a clade consisting of D. erecta-D. orena and D. yakuba-D. teissieri. By contrast, using likelihood based tests of congruence, we find robust evidence for topological incongruence at the second node. Different loci support different relationships among the melanogaster, takahashii and eugracilis subgroups, and the observed incongruence is not easily attributable to homoplasy, non-equilibrium base composition, or positive selection on a subset of loci. We argue that lineage sorting in the common ancestor of these three subgroups is the most plausible explanation for our observations. Such lineage sorting may lead to biased estimation of tree topology and evolutionary rates, and may confound inferences of positive selection.Drosophila melanogaster and its relatives have been used extensively in studies of genetic and morphological variation within and between species. For example, inferences concerning the relative roles of drift, purifying selection, and positive selection in shaping patterns of genetic variation in D. melanogaster often benefit from comparisons to the closely related species D. simulans and D. yakuba (e.g., McDonald and Kreitman, 1991). Similarly, comparative morphologists have used D. melanogaster and its relatives to study the evolution of a number of traits, e.g., genital morphology (Kopp and True, 2002a) and pigmentation (Wittkopp et al., 2002;Prud'homme et al., 2006).Opportunities for, and interest in, using the genus Drosophila in comparative biology is likely to grow in the near future. The availability of complete genome sequences for twelve members of the genus Drosophila (http://species.flybase.net), as well as for several other dipterans, promises to facilitate genome scale studies of molecular evolution. These comparative data will allow for the detection of functionally important genomic regions, as indicated by high levels of conservation or by the signature of positive, diversifying selection. Moreover, the application of genetic and transgenic techniques developed in D. melanogaster to other species will facilitate studies of evolution and development. *Corresponding author: Address: Department of Molecular Biology and Genetics, Biotechnology Building, Co...

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Section: Discussion Phylogenetic Relationships Within the Melanogastesupporting

confidence: 52%

“…Phylogenetic relationships within the melanogaster species group and subgroup have proven difficult to resolve (Ko et al, 2003;Kopp, 2006;Kopp and True, 2002b;Lewis et al, 2005 (Fig. 5).…”

Section: Phylogenetic Relationships Within the Melanogaster Subgroupmentioning

confidence: 99%

Phylogenetic incongruence in the Drosophila melanogaster species group

Wong

Jensen

Pool

et al. 2007

Molecular Phylogenetics and Evolution

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“…Differences in the number of taxa and the number of genes can have an effect on phylogenetic accuracy [19]. In many previous phylogenetic treatments of this species complex, representatives of only 4 species or less were included [4] [7] [13] [14] [15] [16] [17] [20]. Incomplete or insufficient taxon sampling has led to major inconsistencies in phylogenetic reconstructions [20] [21] [22] [23] [24].…”

Section: Introductionmentioning

confidence: 99%

“…On the other hand, differing sets of genetic markers were selected in previous studies, the most previous investigations were based on no more than two genetic markers [9] [11] [12] [15] [16] [17], phylogenetic hypotheses deduced from small amounts of sequence data would be incongruent or pool support [25]. Moreover, highly conserved genetic markers were involved in some analyses [3] [7] [13] [14] but some authors suggested that fast-evolving DNA regions were prior to analysis the molecular phylogenies of closely related species [26]. Although the phylogenetic relationships of these five members were deduced from 17 loci [18], the hypothesis that "increasing sampling outside the group may decrease accuracy" [27] may have applied; therefore, Yang (2012) did not resolve this complex problem.…”

Section: Introductionmentioning

confidence: 99%

Increase Data Characters to Construct the Molecular Phylogeny of the <i>Drosophila auraria</i> Species Complex

Li¹,

Li²,

Zeng³

et al. 2017

OJGen

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Previous phylogenetic analyses of the auraria species complex have led to conflicting hypotheses concerning their relationship; therefore the addition of new sequence data is necessary to discover the phylogeny of this species complex. Here we present new data derived from 22 genes to reconstruct the phylogeny of the auraria species complex. A variety of statistical tests, as well as maximum likelihood mapping analysis, were performed to estimate data quality, suggesting that all genes had a high degree of contribution to resolve the phylogeny. Individual locus was analyzed using maximum likelihood (ML), and the concatenated dataset (21,882 bp) were analyzed using partitioned maximum likelihood (ML) and Bayesian analyses. Separated analysis produced various phylogenetic relationships. Phylogenetic topologies from ML and Bayesian analysis based on concatenated dataset show that D. subauraria was well supported as the first species by separated analysis, concatenated dataset analysis, and some previous analysis, then followed by D. auraria and D. biauraria, D. quadraria and D. triauraria. The close relationships of D. quadraria and D. triauraria were consistent with most previous studies. The phylogenetic position of the D. auraria and D. biauraria will be resolved by more data sets.

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“…The species history of the genus Drosophila has been the subject of numerous studies, and the consensus from the literature suggests that the relationship of the 12 sequenced species is well resolved, with the exception of the species within the Dmel species subgroup and perhaps the placement of the Hawaiian species, D. grimshawi, and the virilis-repleta species, D. virilis and D. mojavenis [1][2][3][4][5]. Within the Dmel species group, the placement of D. erecta (Dere) and D. yakuba (Dyak) relative to the Dmel lineage has been the subject of numerous conflicting studies [1][2][3][6][7][8][9][10][11][12][13][14][15].…”

Section: Introductionmentioning

confidence: 99%

Whole Genome Phylogeny of the Drosophila melanogaster Species Subgroup: Widespread Discordance with Species Tree & Evidence for Incomplete Lineage Sorting

Pollard¹,

Iyer²,

Moses³

2005

PLoS Genet

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The phylogenetic relationship of the now fully sequenced species Drosophila erecta and D. yakuba with respect to the D. melanogaster species complex has been a subject of controversy. All three possible groupings of the species have been reported in the past, though recent multi-gene studies suggest that D. erecta and D. yakuba are sister species. Using the whole genomes of each of these species as well as the four other fully sequenced species in the subgenus Sophophora, we set out to investigate the placement of D. erecta and D. yakuba in the D. melanogaster species group and to understand the cause of the past incongruence. Though we find that the phylogeny grouping D. erecta and D. yakuba together is the best supported, we also find widespread incongruence in nucleotide and amino acid substitutions, insertions and deletions, and gene trees. The time inferred to span the two key speciation events is short enough that under the coalescent model, the incongruence could be the result of incomplete lineage sorting. Consistent with the lineage-sorting hypothesis, substitutions supporting the same tree were spatially clustered. Support for the different trees was found to be linked to recombination such that adjacent genes support the same tree most often in regions of low recombination and substitutions supporting the same tree are most enriched roughly on the same scale as linkage disequilibrium, also consistent with lineage sorting. The incongruence was found to be statistically significant and robust to model and species choice. No systematic biases were found. We conclude that phylogenetic incongruence in the D. melanogaster species complex is the result, at least in part, of incomplete lineage sorting. Incomplete lineage sorting will likely cause phylogenetic incongruence in many comparative genomics datasets. Methods to infer the correct species tree, the history of every base in the genome, and comparative methods that control for and/or utilize this information will be valuable advancements for the field of comparative genomics.

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The phylogeny of the subgroups within the melanogaster species group: Likelihood tests on COI and COII sequences and a Bayesian estimate of phylogeny

Cited by 37 publications

References 41 publications

Phylogenetic incongruence in the Drosophila melanogaster species group

Phylogenetic incongruence in the Drosophila melanogaster species group

Increase Data Characters to Construct the Molecular Phylogeny of the <i>Drosophila auraria</i> Species Complex

Whole Genome Phylogeny of the Drosophila melanogaster Species Subgroup: Widespread Discordance with Species Tree & Evidence for Incomplete Lineage Sorting

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The phylogeny of the subgroups within the melanogaster species group: Likelihood tests on COI and COII sequences and a Bayesian estimate of phylogeny

Cited by 37 publications

References 41 publications

Phylogenetic incongruence in the Drosophila melanogaster species group

Phylogenetic incongruence in the Drosophila melanogaster species group

Increase Data Characters to Construct the Molecular Phylogeny of the &lt;i&gt;Drosophila auraria&lt;/i&gt; Species Complex

Whole Genome Phylogeny of the Drosophila melanogaster Species Subgroup: Widespread Discordance with Species Tree & Evidence for Incomplete Lineage Sorting

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Increase Data Characters to Construct the Molecular Phylogeny of the <i>Drosophila auraria</i> Species Complex