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Reconstructing Yeasts Phylogenies And Ancestors From Whole Genome Data, Bing Feng, Yu Lin, Lingxi Zhou, Yan Guo, Robert Friedman, Roufan Xia, Chao Liu, Jijun Tang
Reconstructing Yeasts Phylogenies And Ancestors From Whole Genome Data, Bing Feng, Yu Lin, Lingxi Zhou, Yan Guo, Robert Friedman, Roufan Xia, Chao Liu, Jijun Tang
Faculty Publications
Phylogenetic studies aim to discover evolutionary relationships and histories. These studies are based on similarities of morphological characters and molecular sequences. Currently, widely accepted phylogenetic approaches are based on multiple sequence alignments, which analyze shared gene datasets and concatenate/coalesce these results to a final phylogeny with maximum support. However, these approaches still have limitations, and often have conflicting results with each other. Reconstructing ancestral genomes helps us understand mechanisms and corresponding consequences of evolution. Most existing genome level phylogeny and ancestor reconstruction methods can only process simplified real genome datasets or simulated datasets with identical genome content, unique genome markers, …
Reconstructing Yeasts Phylogenies And Ancestors From Whole Genome Data, Bing Feng, Yu Ling, Lingxi Zhou, Roufan Xia, Fei Hu, Chao Liu
Reconstructing Yeasts Phylogenies And Ancestors From Whole Genome Data, Bing Feng, Yu Ling, Lingxi Zhou, Roufan Xia, Fei Hu, Chao Liu
Faculty Publications
Phylogenetic studies aim to discover evolutionary relationships and histories. These studies are based on similarities of morphological characters and molecular sequences. Currently, widely accepted phylogenetic approaches are based on multiple sequence alignments, which analyze shared gene datasets and concatenate/coalesce these results to a final phylogeny with maximum support. However, these approaches still have limitations, and often have conflicting results with each other. Reconstructing ancestral genomes helps us understand mechanisms and corresponding consequences of evolution. Most existing genome level phylogeny and ancestor reconstruction methods can only process simplified real genome datasets or simulated datasets with identical genome content, unique genome markers, …
The Statistical Need To Include Phylogeny In Trait-Based Analyses Of Community Composition, Daijiang Li, Anthony R. Ives
The Statistical Need To Include Phylogeny In Trait-Based Analyses Of Community Composition, Daijiang Li, Anthony R. Ives
Faculty Publications
© 2017 The Authors. Methods in Ecology and Evolution © 2017 British Ecological Society A growing number of studies incorporate functional trait information to analyse patterns and processes of community assembly. These studies of trait–environment relationships generally ignore phylogenetic relationships among species. When functional traits and the residual variation in species distributions among communities have phylogenetic signal, however, analyses ignoring phylogenetic relationships can decrease estimation accuracy and power, inflate type I error rates and lead to potentially false conclusions. Using simulations, we compared estimation accuracy, statistical power and type I error rates of linear mixed models (LMM) and phylogenetic linear …
Variation In Seed Size Is Structured By Dispersal Syndrome And Cone Morphology In Conifers And Other Nonflowering Seed Plants, Andrew B. Leslie, Jeremy M. Beaulieu, Sarah Mathews
Variation In Seed Size Is Structured By Dispersal Syndrome And Cone Morphology In Conifers And Other Nonflowering Seed Plants, Andrew B. Leslie, Jeremy M. Beaulieu, Sarah Mathews
Faculty Publications
© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust Seed size varies tremendously in plants and its evolution is influenced by multiple ecological and biological factors that are difficult to disentangle. In this study, we focus on understanding the role of seed dispersal by animals in the evolution of seed size in conifers, the most diverse extant nonflowering seed plant group. Relationships among seed size, dispersal syndrome, climate and cone morphology were analyzed across conifers using quantitative models of character evolution and phylogenetic regression techniques. Dispersal syndrome is a more consistent predictor of seed size within major extant …
Phylogenomics Using Formalin-Fixed And 100+ Year-Old Intractable Natural History Specimens, Sara Ruane, Christopher C. Austin
Phylogenomics Using Formalin-Fixed And 100+ Year-Old Intractable Natural History Specimens, Sara Ruane, Christopher C. Austin
Faculty Publications
© 2017 John Wiley & Sons Ltd Museum specimens provide a wealth of information to biologists, but obtaining genetic data from formalin-fixed and fluid-preserved specimens remains challenging. While DNA sequences have been recovered from such specimens, most approaches are time-consuming and produce low data quality and quantity. Here, we use a modified DNA extraction protocol combined with high-throughput sequencing to recover DNA from formalin-fixed and fluid-preserved snakes that were collected over a century ago and for which little or no modern genetic materials exist in public collections. We successfully extracted DNA and sequenced ultraconserved elements ((Formula presented.) = 2318 loci) …
Can Functional Traits Account For Phylogenetic Signal In Community Composition?, Daijiang Li, Anthony R. Ives, Donald M. Waller
Can Functional Traits Account For Phylogenetic Signal In Community Composition?, Daijiang Li, Anthony R. Ives, Donald M. Waller
Faculty Publications
© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust Phylogenetic and functional trait-based analyses inform our understanding of community composition, yet methods for quantifying the overlap in information derived from functional traits and phylogenies remain underdeveloped. Does adding traits to analyses of community composition reduce the phylogenetic signal in the residual variation? If not, then measured functional traits alone may be insufficient to explain community assembly. We propose a general statistical framework to quantify the proportion of phylogenetic pattern in community composition that remains after including measured functional traits. We then illustrate the framework with applications to two …