17 Works

Data from: A generalized K statistic for estimating phylogenetic signal from shape and other high-dimensional multivariate data

Dean C. Adams
Phylogenetic signal is the tendency for closely related species to display similar trait values due to their common ancestry. Several methods have been developed for quantifying phylogenetic signal in univariate traits and for sets of traits treated simultaneously, and the statistical properties of these approaches have been extensively studied. However, methods for assessing phylogenetic signal in high-dimensional multivariate traits like shape are less well developed, and their statistical performance is not well characterized. In this...

Data from: A method for analysis of phenotypic change for phenotypes described by high-dimensional data

Michael L. Collyer, David J. Sekora & Dean C. Adams
The analysis of phenotypic change is important for several evolutionary biology disciplines, including phenotypic plasticity, evolutionary developmental biology, morphological evolution, physiological evolution, evolutionary ecology and behavioral evolution. It is common for researchers in these disciplines to work with multivariate phenotypic data. When phenotypic variables exceed the number of research subjects—data called ‘high-dimensional data’—researchers are confronted with analytical challenges. Parametric tests that require high observation to variable ratios present a paradox for researchers, as eliminating variables...

Data from: Maternal effects influence phenotypes and survival during early life stages in an aquatic turtle

Timothy S. Mitchell, Jessica A. Maciel & Fredric J. Janzen
Offspring phenotypic variation can be substantially influenced by non-genetic factors such as maternal effects, which ultimately can influence organismal fitness. For oviparous organisms that lack parental care, oviposition-site choice and egg size are maternal effects that can greatly affect offspring traits. Yet, few studies examine the consequences of these traits in the wild. We manipulated the contents of natural painted turtle nests such that offspring spent two life stages (incubation and hibernation) in either maternally-selected...

Data from: Maintenance of genetic diversity in an introduced island population of Guanacos after seven decades and two severe demographic bottlenecks: implications for camelid conservation

Benito A. González, Pablo Orozco-TerWengel, Rainer Von Borries, Warren E. Johnson, William L. Franklin & Juan C. Marín
Fifteen Guanacos were introduced to Staats Island in Falklands/Malvinas archipelago from Patagonia in the 1930s. After introduction, the Guanaco population increased to almost 400 animals that retained a footprint of the founding effect and bottleneck reflected in the genetic status of this isolated population. The goals of this study were to (i) make a genetic assessment of this island population through comparisons with mainland populations and simulation, and (ii) assess the likely source population of...

Data from: Pleiotropy can be effectively estimated without counting phenotypes through the rank of genotype-phenotype map

Xun Gu
Though pleiotropy, the capability of a gene affecting multiple phenotypes, has been well-known as one of common gene properties, a quantitative estimation remains a great challenge, simply because of the phenotype complexity. Not surprisingly, it is hard for general readers to understand how, without counting phenotypes, gene pleiotropy can be effectively estimated from the genetics data. In this article we extensively discussed the Gu-2007-method (Genetics 175: 1813-1822) that estimated pleiotropy from the protein sequence analysis....

Data from: Hallauer's Tusón: a decade of selection for tropical- to-temperate phenological adaptation in maize

Juliana E. C. Teixeira, Teclemariam Weldekidan, Natalia De Leon, Sherry Flint-Garcia, James B. Holland, Nick Lauter, Seth C. Murray, Wenwei Xu, David A. Hessel, Adrienne E. Kleintop, James A. Hawk, Arnel R. Hallauer & Randall J. Wisser
Crop species exhibit an astounding capacity for environmental adaptation, but genetic bottlenecks resulting from intense selection for adaptation and productivity can lead to a genetically vulnerable crop. Improving the genetic resiliency of temperate maize depends upon the use of tropical germplasm, which harbors a rich source of natural allelic diversity. Here, the adaptation process was studied in a tropical maize population subjected to 10 recurrent generations of directional selection for early flowering in a single...

Data from: Assessing approaches for inferring species trees from multi-copy genes

Ruchi Chaudhary, Bastien Boussau, J. Gordon Burleigh & David Fernández-Baca
With the availability of genomic sequence data, there is increasing interest in using genes with a possible history of duplication and loss for species tree inference. Here we assess the performance of both non-probabilistic and probabilistic species tree inference approaches using gene duplication and loss and coalescence simulations. We evaluated the performance of gene tree parsimony (GTP) based on duplication (Only-dup), duplication and loss (Dup-loss), and deep coalescence (Deep-c) costs, the NJst distance method, the...

Data from: Swimming against the tide: resilience of a riverine turtle to recurrent extreme environmental events

Abigail M. Jergenson, David A. W. Miller, Lorin A. Neuman-Lee, Daniel A. Warner & Fredric J. Janzen
Extreme environmental events (EEE) are likely to exert deleterious effects on populations. From 1996-2012 we studied the nesting dynamics of a riverine population of painted turtles (Chrysemys picta) that experienced seven years with significantly definable spring floods. We used capture-mark-recapture methods to estimate the relationships between >5-m and >6-m flood events and population parameters. Contrary to expectations, flooding was not associated with annual differences in survival, recruitment, or annual population growth rates of the adult...

Data from: A method for assessing phylogenetic least squares models for shape and other high-dimensional multivariate data

Dean C. Adams
Studies of evolutionary correlations commonly utilize phylogenetic regression (i.e., independent contrasts and phylogenetic generalized least squares) to assess trait covariation in a phylogenetic context. However, while this approach is appropriate for evaluating trends in one or a few traits, it is incapable of assessing patterns in highly-multivariate data, as the large number of variables relative to sample size prohibits parametric test statistics from being computed. This poses serious limitations for comparative biologists, who must either...

Data from: Range-wide analysis of genetic structure in a widespread, highly mobile species (Odocoileus hemionus) reveals the importance of historical biogeography

Emily K. Latch, Dawn M. Reding, James R. Heffelfinger, Olin E. Rhodes & Carlos H. Alcalá-Galván
Highly mobile species that thrive in a wide range of habitats are expected to show little genetic differentiation across their range. A limited but growing number of studies have revealed that patterns of broad-scale genetic differentiation can and do emerge in vagile, continuously distributed species. However, these patterns are complex and often shaped by both historical and ecological factors. Comprehensive surveys of genetic variation at a broad scale and at high resolution are useful for...

Data from: Functionally reciprocal mutations of the prolactin signalling pathway define hairy and slick cattle

Matthew D. Littlejohn, Kristen M. Henty, Tiplady Kathryn, Thomas Johnson, Chad Harland, Thomas Lopdell, Richard G. Sherlock, Wanbo Li, Steven D. Lukefahr, Bruce C. Shanks, Dorian J. Garrick, Russel G. Snell, Richard J. Spelman & Stephen R. Davis
WGS Variants from 556 NZ Dairy Animals Chr23:30627379-40627379rtg_3.3.1_556_animal_Chr23:30627379-40627379_for_dryad.vcf.gzExome Variants in Multiple Breeds Chr20:34783594-42331973GATK-10MB-Window-Exomes.vcf.gzHairy syndrome genotypes and phenotypesGenotypes and phenotype used for genome-wide analysis of the hairy syndrome, Plink binary format (.bim .bed .fam)gen_phen_data_for_paper.zipHairy bull progeny TaqMan resultsHairy_bull_progeny_TaqMan_results.txtphysiological phenotypesphysiological_phenos.zipDFAM association results for 628,279 SNPDFAM_assoc_results.zipPhased genotypes and phenotypes for 82 Senepol crossbreedsphased_gen_phen_data_slick.zip

Data from: Re-evaluating neonatal-age models for ungulates: does model choice affect survival estimates?

Troy W. Grovenburg, Kevin L. Monteith, Christopher N. Jacques, Robert W. Klaver, Christopher S. DePerno, Todd J. Brinkman, Kyle B. Monteith, Sophie L. Gilbert, Joshua B. Smith, Vernon C. Bleich, Christopher C. Swanson & Jonathan A. Jenks
New-hoof growth is regarded as the most reliable metric for predicting age of newborn ungulates, but variation in estimated age among hoof-growth equations that have been developed may affect estimates of survival in staggered-entry models. We used known-age newborns to evaluate variation in age estimates among existing hoof-growth equations and to determine the consequences of that variation on survival estimates. During 2001–2009, we captured and radiocollared 174 newborn (≤24-hrs old) ungulates: 76 white-tailed deer (Odocoileus...

Data from: Hydric conditions during incubation influence phenotypes of neonatal reptiles in the field

Brooke L. Bodensteiner, Timothy S. Mitchell, Jeramie T. Strickland & Fredric J. Janzen
Phenotypic variation is strongly impacted by environmental conditions experienced during development. Substantial laboratory research has shown that reptiles with flexible-shelled eggs are particularly sensitive to hydric conditions, yet research on nests in the wild is sparse. In this two-year field experiment, we explore the influence of hydric conditions during incubation on phenotypic traits of hatchling painted turtles (Chrysemys picta). Using a split-clutch design, we created two artificial nests adjacent to each maternally-selected nest site. Half...

Data from: Ecomorphological variation in male and female wall lizards and the macroecolution of sexual dimorphism in relation to habitat use

Antigoni Kaliontzopoulou, Miguel A. Carretero & Dean C. Adams
Understanding how phenotypic diversity evolves is a major interest of evolutionary biology. Habitat use is an important factor in the evolution of phenotypic diversity of many animal species. Interestingly, male and female phenotypes have been frequently shown to respond differently to environmental variation. At the macroevolutionary level, this difference between the sexes is frequently analyzed by using phylogenetic comparative tools to assess variation in sexual dimorphism (SD) across taxa in relation to habitat. A shortcoming...

Data from: Sexual selection targets cetacean pelvic bones

James P. Dines, Erik Otárola-Castillo, Peter Ralph, Jesse Alas, Timothy Daley, Andrew D. Smith & Matthew D. Dean
Male genitalia evolve rapidly, probably as a result of sexual selection. Whether this pattern extends to the internal infrastructure that influences genital movements remains unknown. Cetaceans (whales and dolphins) offer a unique opportunity to test this hypothesis: since evolving from land-dwelling ancestors, they lost external hind limbs and evolved a highly reduced pelvis which seems to serve no other function except to anchor muscles that maneuver the penis. Here we create a novel morphometric pipeline...

Data from: Permutation tests for phylogenetic comparative analyses of high-dimensional shape data: what you shuffle matters

Dean C. Adams & Michael L. Collyer
Evaluating statistical trends in high-dimensional phenotypes poses challenges for comparative biologists, because the high-dimensionality of the trait data relative to the number of species can prohibit parametric tests from being computed. Recently, two comparative methods were proposed to circumvent this difficulty. One obtains phylogenetic independent contrasts for all variables, and statistically evaluates the linear model by permuting the PICs of the response data. The other uses a distance-based approach to obtain coefficients for generalized least...

Data from: Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle

Jared Egan Decker, Stephanie D. McKay, Megan M. Rolf, JaeWoo Kim, Antonio Molina Alcalá, Tad S. Sonstegard, Olivier Hanotte, Anders Götherström, Christopher M. Seabury, Lisa Praharani, Masroor Ellahi Babar, Luciana Correia De Almieda Regitano, Mehmet Ali Yildiz, Michael P. Heaton, Wan-Sheng Liu, Chu-Zhao Lei, James M. Reecy, Muhammad Saif-Ur-Rehman, Robert D. Schnabel & Jeremy F. Taylor
The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns...

Registration Year

  • 2014

Resource Types

  • Dataset


  • Iowa State University
  • Texas A&M University
  • United States Department of Agriculture
  • Western Kentucky University
  • United States Fish and Wildlife Service
  • Pennsylvania State University
  • North West Agriculture and Forestry University
  • University of Alabama at Birmingham
  • University of Liège
  • Universidad de Sonora