Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus.

@article{Kates2018AllelePH,
  title={Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus.},
  author={H. Kates and Matthew G. Johnson and E. Gardner and N. Zerega and N. Wickett},
  journal={American journal of botany},
  year={2018},
  volume={105 3},
  pages={
          404-416
        }
}
PREMISE OF THE STUDY Untapped information about allele diversity within populations and individuals (i.e., heterozygosity) could improve phylogenetic resolution and accuracy. Many phylogenetic reconstructions ignore heterozygosity because it is difficult to assemble allele sequences and combine allele data across unlinked loci, and it is unclear how reconstruction methods accommodate variable sequences. We review the common methods of including heterozygosity in phylogenetic studies and present… Expand
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References

SHOWING 1-10 OF 50 REFERENCES
PoMo: An Allele Frequency-Based Approach for Species Tree Estimation
TLDR
This work uses a POlymorphisms-aware phylogenetic MOdel that has been shown to efficiently estimate mutation rates and fixation biases from within and between-species variation data and extends this model to perform efficient estimation of species trees. Expand
Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics.
TLDR
This study attempts to resolve cheirogaleid phylogeny, focusing especially on the mouse lemurs, by employing a large multilocus data set and shows that phylogenetic results are substantially influenced by the selection of alleles in the concatenation process. Expand
Phylogeny of Conradina and Related Southeastern Scrub Mints (Lamiaceae) Based on GapC Gene Sequences
TLDR
This work isolated three members of the nuclear GapC gene family and used two approaches to concatenate the two heterozygous GapC loci with ITS and plastid data sets from a previous study and carried out combined analyses, which did not resolve species relationships. Expand
Low-coverage, whole-genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery1
TLDR
This study substantially increases the genomic resources available for Artocarpus and Moraceae and demonstrates the value of low-coverage de novo assemblies for nonmodel organisms with moderately large genomes. Expand
Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants
TLDR
This study demonstrates that phylogenetic signal is highly variable in phylogenomic data sampled across related species and poses challenges when conducting species tree analyses on large genomic and transcriptomic datasets. Expand
Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing.
TLDR
A high-throughput protocol and an associated bioinformatics pipeline that is able to generate nuclear data quickly and conveniently that makes it easy and economical to study the phylogenetics of polyploids, and facilitates investigation of broad patterns ofpolyploid evolution. Expand
HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment1
TLDR
HybPiper is developed as a user-friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies in Artocarpus. Expand
Constructing phylogenies in the presence of intra-individual site polymorphisms (2ISPs) with a focus on the nuclear ribosomal cistron.
TLDR
It is envisage that this 2ISP-informative approach will greatly aid phylogenetic inference using any nuclear DNA regions that contain polymorphisms within individuals (including consensus sequences generated from NGS), especially at the intrageneric or intraspecific level. Expand
Inferring phylogeny despite incomplete lineage sorting.
TLDR
Improved methods to reconstruct phylogeny near the species level will require a shift to a compound model that considers not only nucleotide or character state substitutions, but also the population genetics processes of lineage sorting. Expand
L. A. S. JOHNSON REVIEW No. 2 Use of nuclear genes for phylogeny reconstruction in plants
TLDR
Advantages of low-copy nuclear sequences include a higher rate of evolution than for organellar sequences, the potential to accumulate datasets from multiple unlinked loci, and bi-parental inheritance. Expand
...
1
2
3
4
5
...