TreeBASE Search-Trees for study 2204

@ARTICLE{TreeBASE2Ref2141, author = {Brian D Farrell and Catherine R. Linnen}, title = {Comparison of methods for species-tree inference in the sawfly genus Neodiprion (Hymenoptera: Diprionidae)}, year = {2008}, keywords = {}, doi = {10.1080/10635150802580949}, url = {}, pmid = {}, journal = {Systematic Biology}, volume = {57}, number = {6}, pages = {876--890}, abstract = {Conifer-feeding sawflies in the genus Neodiprion provide an excellent opportunity to investigate the origin and maintenance of barriers to reproduction, but obtaining a phylogenetic estimate for comparative studies of Neodiprion speciation has proved difficult. Specifically, nonmonophyly within and discordance between individual gene trees, both of which are common in groups that diverged recently and/or rapidly, make it impossible to infer a species tree using methods that are designed to estimate gene trees. Therefore, in this study, we estimate relationships between members of the lecontei species group using four approaches that are intended to estimate species, not gene, trees: (1) minimize deep coalescences (MDC), (2) shallowest divergences (SD), (3) Bayesian estimation of species trees (BEST), and (4) a novel approach that combines concatenation with monophyly constraints (CMC). Multiple populations are sampled for most species and all four methods incorporate this intraspecific variation into estimates of interspecific relationships. We investigate the sensitivity of each method to taxonomic sampling, and, for the BEST method, we assess the impact of prior choice on species-tree inference. We also compare species-tree estimates to one another and to a morphologically-based hypothesis to identify clades that are supported by multiple analyses and lines of evidence. We find that both taxonomic sampling and method choice impact species-tree estimates and that, for these data, the BEST method is strongly influenced by ?? and branch-length priors. We also find that the CMC method is the least sensitive to taxonomic sampling. Finally, while interspecific genetic variation is low due to the recent divergence of the lecontei group, our results to date suggest that incomplete lineage sorting and interspecific gene flow are the main factors complicating species-tree inference in Neodiprion. Based on these analyses, we propose a phylogenetic hypothesis for the lecontei group. Finally, our results suggest that, even for very challenging groups like Neodiprion, an underlying species-tree signal can be extracted from multi-locus data so long as intraspecific variation is adequately sampled and methods that focus on the estimation of species trees are used.} }

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Trees for Study 2204

Citation title: "Comparison of methods for species-tree inference in the sawfly genus Neodiprion (Hymenoptera: Diprionidae)".

This study was previously identified under the legacy study ID S2212 (Status: Published).

Trees

ID	Tree Label	Tree Title	Tree Type	Tree Kind	Taxa
Tr3153	Fig. 2a	Neodiprion CMCmethod_LUdataset	Consensus	Species Tree	View Taxa
Tr3157	Fig. 2b	Neodiprion MDCmethod_LUdataset	Consensus	Species Tree	View Taxa
Tr3161	Fig. 2c	Neodiprion SDmethod_LUdataset	Single	Species Tree	View Taxa
Tr3166	Fig.3a	Neodiprion BESTmethod_ExemAdataset_exponentialprior	Consensus	Species Tree	View Taxa
Tr3167	Fig. 3b	Neodiprion BESTmethod_ExemBdataset_exponentialprior	Consensus	Species Tree	View Taxa
Tr3169	Fig. 3c	Neodiprion BESTmethod_MODdataset_exponentialprior	Consensus	Species Tree	View Taxa
Tr3172	Fig. 3d	Neodiprion BESTmethod_LUdataset_exponentialprior	Consensus	Species Tree	View Taxa
Tr3165	Fig. 3e	Neodiprion BESTmethod_ExemAdataset_coalescentprior	Consensus	Species Tree	View Taxa
Tr3168	Fig. 3f	Neodiprion BESTmethod_ExemBdataset_coalescentprior	Consensus	Species Tree	View Taxa
Tr3170	Fig. 3g	Neodiprion BESTmethod_MODdataset_coalescentprior	Consensus	Species Tree	View Taxa
Tr3171	Fig. 3h	Neodiprion BESTmethod_LUdataset_coalescentprior	Consensus	Species Tree	View Taxa
Tr3154	Fig. 5a supp.	Neodiprion CMCmethod_ExemAdataset	Consensus	Species Tree	View Taxa
Tr3155	Fig. 5b supp.	Neodiprion CMCmethod_ExemBdataset	Consensus	Species Tree	View Taxa
Tr3156	Fig. 5c supp.	Neodiprion CMCmethod_MODdataset	Consensus	Species Tree	View Taxa
Tr3158	Fig. 6a supp.	Neodiprion MDCmethod_ExemAdataset	Consensus	Species Tree	View Taxa
Tr3159	Fig. 6b supp.	Neodiprion MDCmethod_ExemBdataset	Consensus	Species Tree	View Taxa
Tr3160	Fig. 6c supp.	Neodiprion MDCmethod_MODdataset	Consensus	Species Tree	View Taxa
Tr3162	Fig. 7a supp.	Neodiprion SDmethod_ExemAdataset	Single	Species Tree	View Taxa
Tr3163	Fig. 7b supp.	Neodiprion SDmethod_ExemBdataset	Single	Species Tree	View Taxa
Tr3164	Fig. 7c supp.	Neodiprion SDmethod_MODdataset	Single	Species Tree	View Taxa