A well-tested set of primers to amplify regions spread across the avian genome

Kimball, Rebecca T.; Braun, Edward L.; Barker, F. Keith; Bowie, Rauri C. K.; Braun, Michael J.; Chojnowski, Jena L.; Hackett, Shannon J.; Han, Kin Lan; Harshman, John; Heimer-Torres, Victoria; Holznagel, Wallace E.; Huddleston, Christopher J.; Marks, Ben D.; Miglia, Kathleen J.; Moore, William S.; Reddy, Srinivas K.; Sheldon, Frederick H.; Smith, Jordan V.; Witt, Christopher C.; Yuri, Tamaki

doi:10.1016/j.ympev.2008.11.018

Cited by 165 publications

(104 citation statements)

References 34 publications

Supporting

Mentioning

103

Contrasting

Order By: Relevance

“…We simulated 1000 base pair (bp) sequences (a typical length for many markers; [45][46][47] using each gene tree in SeqGen [48], assuming the HKY model of evolution with a range of parameters that are typical of vertebrate introns. We established ranges of parameter values from empirical studies (Supplementary Material) and then chose values for our simulated regions randomly from these distributions.…”

Section: Simulationsmentioning

confidence: 99%

Error in Phylogenetic Estimation for Bushes in the Tree of Life

Patel

Kimball²,

Braun³

2013

Phylogenetics Evolutionary

104

View full text Add to dashboard Cite

Many rapid radiations, or bushes, throughout the Tree of Life remain unresolved. Here, we investigated how the shape of a bush interacts with two key processes -coalescence and mutation -that can lead to errors in phylogenetic inference under specific conditions. For this study, we focused on the tradeoff between sampling more individuals per species and sampling more loci as well as the utility of a species tree method based upon gene tree reconciliation and the concatenation of multiple loci for resolving bushes. We examined different bush shapes, varying both the speciation rate during the radiation and the depth of the radiation, to encompass a broad range of situations. Using simulations based upon parameters derived from empirical studies, we investigated the performance of phylogenetic analyses under different conditions to identify approaches with the greatest potential to resolve difficult phylogenies. Sampling a single individual for more loci outperformed sampling multiple individuals for one locus in all cases except the most recent radiations. We found that error due to homoplastic mutations increased with depth, while error due to the coalescent process remained unchanged. These simulations also revealed that, for certain ancient bushes, analyses of concatenated data matrices surprisingly resulted in more accurate phylogenies than gene tree reconciliation. The poor performance of gene tree reconciliation in this study appeared to reflect the poor estimation of gene trees, not the superiority of concatenation per se. Our results suggest concatenation remains a useful approximate method for species tree estimation, even for rapid evolutionary radiations. However, improved estimation of gene trees combined with use of gene tree reconciliation has the greatest potential for resolving the remaining bushes of the Tree of Life.

show abstract

Section: Simulationsmentioning

confidence: 99%

Error in Phylogenetic Estimation for Bushes in the Tree of Life

Patel

Kimball²,

Braun³

2013

Phylogenetics Evolutionary

104

View full text Add to dashboard Cite

show abstract

“…We sequenced 15 autosomal and two Z-linked introns (Friesen et al, 1999;Shapiro and Dumbacher, 2001;Primmer et al, 2002;Backström et al, 2006Backström et al, , 2008Kimball et al, 2009) (Table 1). We collected 13-24 allele copies in the 17 introns for each species (mean ¼ 18.5 for F. parva and 22.2 for F. albicilla; Table 1).…”

Section: Sequence Data Collection and Analysesmentioning

confidence: 99%

Distinguishing the effects of selection from demographic history in the genetic variation of two sister passerines based on mitochondrial–nuclear comparison

Hung

Zink

2014

Heredity

View full text Add to dashboard Cite

Determining the mechanisms responsible for the distribution of genetic diversity in natural populations has occupied a central role in molecular evolution. Our study was motivated by the unprecedented observation that a widespread Eurasian flycatcher, Ficedula albicilla, exhibited no variation at the mitochondrial DNA (mtDNA) ND2 gene in 75 individuals sampled over a 5000-km distance. In contrast, its sister species, F. parva, had low but considerably higher levels of mtDNA variation. We assessed whether natural selection or demographic factors could explain the absence of mtDNA variation in F. albicilla. Eighteen nuclear genes were sequenced to estimate the two species' phylogeographic histories, and for comparison to the mtDNA data. Multilocus coalescence analyses suggested that F. albicilla experienced a population expansion perhaps following a population bottleneck. Simulations based on this demographic history, however, did not replicate the extremely low level of mtDNA variation. Historical range changes based on ecological niche models also failed to explain the observed mtDNA patterns. Neutrality tests (DHEW and ML-HKA) suggested a non-neutral pattern in the mtDNA of F. albicilla. We found a transmembrane-skewed distribution of nonsynonymous substitutions between the two species, three of which caused functional change; the results implied that positive selection could have targeted mtDNA. Several lines of evidence support selection rather than demographic history as the main force influencing the patterns of mtDNA variation. Despite the influence of natural selection, many of the phylogeographic inferences derived from mtDNA were robust, including species limits and a high level of gene flow among populations within species.

show abstract

“…Microsatellite development can now be achieved rapidly for very little work and $US1000-2000 using next-generation sequencing, and costs will continue to fall (Abdelkrim et al 2009). It is also tractable to apply the same or equivalent markers among species and obtain quantitatively comparable estimates of population demography, for example using resources based on comparing the Chicken genome with genomes of other birds including the Zebra Finch (Hillier et al 2004;Backström et al 2008;Karaiskou et al 2008;Kimball et al 2009). These have made available many hundreds of coding exons, non-coding introns and untranslated regions, for application to any bird.…”

Section: The Genomics Revolution and Associated Technical Advancementioning

confidence: 99%

Towards modelling persistence of woodland birds: the role of genetics

Sunnucks

2011

Emu - Austral Ornithology

View full text Add to dashboard Cite

Abstract. Assessing how environmental change affects the probability of persistence of organisms requires an understanding of dispersal through, and occupation of, landscapes, and the associated demographic outcomes. Projections of differences in persistence probability can then be made under different scenarios of land-use and global environmental change. Rates and distances of dispersal, and demographic change and trajectories, are difficult to measure accurately, but genetic approaches can make major contributions. For two decades the field of molecular ecology has been providing useful life-history information relevant to population management, including key ecological attributes such as disease-resistance and thermal biology, mobility, dispersal and gene flow, habitat connectivity, the spatial and temporal scales of population processes, and demography. Genetic estimators of these factors could be employed to a much greater extent than they are currently. To facilitate this increased use, genetic estimates of functional connectivity (mobility and gene flow of organisms) and demography need to be integrated directly into decision-making processes. Population genetics is well suited to Bayesian approaches, with associated benefits including the ability to consider many factors, and estimation of error and parameter sensitivities. Genetic estimators based on the mobility and reproductive success of individual organisms and their key ecological traits can make unique contributions alongside other types of data into agent-based, spatially explicit modelling approaches of real landscape scenarios at the range of scales needed by managers. Virtually all the tools to do this exist. It is imperative that genetic samples be collected for contemporary and future analyses.

show abstract

A well-tested set of primers to amplify regions spread across the avian genome

Cited by 165 publications

References 34 publications

Error in Phylogenetic Estimation for Bushes in the Tree of Life

Error in Phylogenetic Estimation for Bushes in the Tree of Life

Distinguishing the effects of selection from demographic history in the genetic variation of two sister passerines based on mitochondrial–nuclear comparison

Towards modelling persistence of woodland birds: the role of genetics

Contact Info

Product

Resources

About