A phylogenomic supermatrix of Galliformes (Landfowl) reveals biased branch lengths
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A phylogenomic supermatrix of Galliformes (Landfowl) reveals biased branch lengths. / Kimball, Rebecca T.; Hosner, Peter A.; Braun, Edward L.
In: Molecular Phylogenetics and Evolution, Vol. 158, 107091, 2021.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - A phylogenomic supermatrix of Galliformes (Landfowl) reveals biased branch lengths
AU - Kimball, Rebecca T.
AU - Hosner, Peter A.
AU - Braun, Edward L.
N1 - Funding Information: Funding was provided by the United States National Science Foundation (grants DEB-1118823 and DEB-1655683 to R.T.K. and E.L.B). P.A.H. has also received support from the Danish National Research Foundation (Center for Macroecology, Evolution, and Climate) and the Villum Foundation (Center for Global Mountain Biodiversity).
PY - 2021
Y1 - 2021
N2 - Building taxon-rich phylogenies is foundational for macroevolutionary studies. One approach to improve taxon sampling beyond individual studies is to build supermatricies of publicly available data, incorporating taxa sampled across different studies and utilizing different loci. Most existing supermatrix studies have focused on loci commonly sequenced with Sanger technology (“legacy” markers, such as mitochondrial data and small numbers of nuclear loci). However, incorporating phylogenomic studies into supermatrices allows problem nodes to be targeted and resolved with considerable amounts of data, while improving taxon sampling with legacy data. Here we estimate phylogeny from a galliform supermatrix which includes well-known model and agricultural species such as the chicken and turkey. We assembled a supermatrix comprising 4500 ultra-conserved elements (UCEs) collected as part of recent phylogenomic studies in this group and legacy mitochondrial and nuclear (intron and exon) sequences. Our resulting phylogeny included 88% of extant species and recovered well-accepted relationships with strong support. However, branch lengths, which are particularly important in down-stream macroevolutionary studies, appeared vastly skewed. Taxa represented only by rapidly evolving mitochondrial data had high proportions of missing data and exhibited long terminal branches. Conversely, taxa sampled for slowly evolving UCEs with low proportions of missing data exhibited substantially shorter terminal branches. We explored several branch length re-estimation methods with particular attention to terminal branches and conclude that re-estimation using well-sampled mitochondrial sequences may be a pragmatic approach to obtain trees suitable for macroevolutionary analysis.
AB - Building taxon-rich phylogenies is foundational for macroevolutionary studies. One approach to improve taxon sampling beyond individual studies is to build supermatricies of publicly available data, incorporating taxa sampled across different studies and utilizing different loci. Most existing supermatrix studies have focused on loci commonly sequenced with Sanger technology (“legacy” markers, such as mitochondrial data and small numbers of nuclear loci). However, incorporating phylogenomic studies into supermatrices allows problem nodes to be targeted and resolved with considerable amounts of data, while improving taxon sampling with legacy data. Here we estimate phylogeny from a galliform supermatrix which includes well-known model and agricultural species such as the chicken and turkey. We assembled a supermatrix comprising 4500 ultra-conserved elements (UCEs) collected as part of recent phylogenomic studies in this group and legacy mitochondrial and nuclear (intron and exon) sequences. Our resulting phylogeny included 88% of extant species and recovered well-accepted relationships with strong support. However, branch lengths, which are particularly important in down-stream macroevolutionary studies, appeared vastly skewed. Taxa represented only by rapidly evolving mitochondrial data had high proportions of missing data and exhibited long terminal branches. Conversely, taxa sampled for slowly evolving UCEs with low proportions of missing data exhibited substantially shorter terminal branches. We explored several branch length re-estimation methods with particular attention to terminal branches and conclude that re-estimation using well-sampled mitochondrial sequences may be a pragmatic approach to obtain trees suitable for macroevolutionary analysis.
U2 - 10.1016/j.ympev.2021.107091
DO - 10.1016/j.ympev.2021.107091
M3 - Journal article
C2 - 33545275
AN - SCOPUS:85101374494
VL - 158
JO - Molecular Phylogenetics and Evolution
JF - Molecular Phylogenetics and Evolution
SN - 1055-7903
M1 - 107091
ER -
ID: 272066698