TreeBASE Search-Matrices for study 13356

@ARTICLE{TreeBASE2Ref21325, author = {Ammon Corl and Hans Ellegren}, title = {Sampling strategies for species trees: The effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal}, year = {2013}, keywords = {*BEAST, effective population size, sex chromosomes, mtDNA, Z chromosome, Charadriiformes, shorebirds, phylogeny, gene tree, species tree}, doi = {}, url = {http://dx.doi.org/10.1016/j.ympev.2013.02.002}, pmid = {}, journal = {Molecular Phylogenetics and Evolution}, volume = {67}, number = {}, pages = {358--366}, abstract = {Systematists can now use multi-locus data to construct species trees that take into account the stochastic nature of gene tree divergence among populations. There is a need to evaluate the new methods for species tree reconstruction in order to determine what kinds of loci to use and the most effective sampling schemes in terms of numbers of genes and numbers of individuals per species. Here we study sampling strategies with an empirical data set for six shorebird species in which we sequenced 1 mitochondrial, 12 autosomal, and 12 Z-linked loci for >8 individuals/species. We found that sampling greater numbers of genes resulted in substantial improvements to the resolution of the species tree, but sampling greater numbers of individuals had minor effects. We found that Z-linked loci significantly outperformed autosomal loci at all levels of sampling, which likely resulted from the lower effective population size of the Z-linked loci. Therefore, sex-linked loci are likely to be a powerful tool for multi-locus phylogenetic studies. We found that adding a mitochondrial gene to a set of Z-linked or autosomal loci substantially improved the resolution of the tree. Overall, our results help evaluate how best to maximize phylogenetic resolution while minimizing the costs of sequencing and computation when performing species tree analyses.} }

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Matrices for Study 13356

Citation title: "Sampling strategies for species trees: The effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal".

Study name: "Sampling strategies for species trees: The effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal".

This study is part of submission 13356 (Status: Published).

Matrices

ID	Matrix Title	Description	Data type	NTAX	NCHAR	Taxa
M14301	Locus_29.41: Gene_PTPRD	Z-linked gene	Nucleic Acid	72	819	View Taxa
M14303	Locus_47.43: Gene_EF5	Z-linked gene	Nucleic Acid	72	480	View Taxa
M14304	Locus_50.99: Gene_UDP	Z-linked gene	Nucleic Acid	72	698	View Taxa
M14296	Locus_MB: Gene_MB	Autosomal gene	Nucleic Acid	72	637	View Taxa
M14302	Locus_31.46: Gene_FRAS1	Z-linked gene	Nucleic Acid	72	810	View Taxa
M14308	Locus_Aldob: Gene_Aldob	Z-linked gene	Nucleic Acid	72	588	View Taxa
M14293	Locus_6.1b: Gene_RasGEF1A	Autosomal gene	Nucleic Acid	72	722	View Taxa
M14306	Locus_73.07: Gene_ZNF608	Z-linked gene	Nucleic Acid	72	853	View Taxa
M14300	Locus_26.59: Gene_DOCK8	Z-linked gene	Nucleic Acid	72	686	View Taxa
M14297	Locus_TGFB2: Gene_TBFB2	Autosomal gene	Nucleic Acid	72	464	View Taxa
M14294	Locus_9.2: Gene_ATG4B_CHICK	Autosomal gene	Nucleic Acid	72	997	View Taxa
M14291	Locus_4.5b: Gene_NDST3	Autosomal gene	Nucleic Acid	72	958	View Taxa
M14286	Locus 1.1ny: Gene_Q5ZM32_CHICK	Autosomal gene	Nucleic Acid	72	451	View Taxa
M14295	Locus_IRF: Gene_IRF2	Autosomal gene	Nucleic Acid	72	623	View Taxa
M14305	Locus_69.74: Gene_DMXL1	Z-linked gene	Nucleic Acid	72	612	View Taxa
M14298	Locus_9.93: Gene_DNAJA5	Z-linked gene	Nucleic Acid	72	520	View Taxa
M14309	Locus_Musk: Gene_Musk	Z-linked gene	Nucleic Acid	72	605	View Taxa
M14287	Locus 2.3: Gene_MPP6	Autosomal gene	Nucleic Acid	72	640	View Taxa
M14289	Locus 3.3: Gene_Q6JLB2_CHICK	Autosomal gene	Nucleic Acid	72	509	View Taxa
M14310	Locus_COX1: Gene_COX1	mtDNA gene	Nucleic Acid	72	801	View Taxa
M14292	Locus_4.8c: Gene_CBPZ_CHICK	Autosomal gene	Nucleic Acid	72	930	View Taxa
M14288	Locus 2.7: Gene_RAB12	Autosomal gene	Nucleic Acid	72	626	View Taxa
M14307	Locus_7878620: Gene_PARP8	Z-linked gene	Nucleic Acid	72	1069	View Taxa
M14299	Locus_10.39: Gene_RANBP3L	Z-linked gene	Nucleic Acid	72	738	View Taxa
M14290	Locus 4.4: Gene_HMG-2	Autosomal gene	Nucleic Acid	72	790	View Taxa