Research and Publications
This page is out of date: please
see my google scholar page
and/or the Co-Lab publications page.
Note: try the on the arXiv links if the journal wants to charge you, or if you just like seeing the version I LaTeX'ed up myself.
- Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data,
CJ Battey,
Peter L Ralph,
and Andy Kern.
(on the bioRxiv)
- Spatial Population Genetics: It's About Time,
Gideon Bradburd,
and Peter L Ralph.
To appear, Annual Review of Ecology, Evolution, and Systematics, 2019.
(on the arXiv)
- An empirical approach to demographic inference with genomic data,
Peter L Ralph. Theoretical Population Biology, 2019.
(on the arXiv)
- Are populations like a circuit? Comparing isolation by resistance to a new coalescent-based method,
Erik Lundgren and Peter L Ralph.
Molecular Ecology Resources, 2019.
(on the bioRxiv)
- Limits to Genomic Divergence Under Sexually Antagonistic Selection,
Katja R Kasimatis, Peter L Ralph and
Patrick C Phillips.
Submitted, 2019.
(on the bioRxiv)
- Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes,
Benjamin C Haller,
Jared Galloway,
Jerome Kelleher,
Philipp W Messer, and Peter L Ralph.
Molecular Ecology Resources, November 2018.
(on the bioRXiv;
the simulation software SLiM;
and the python package pyslim)
- Efficient pedigree recording for fast population genetics simulation,
Jerome Kelleher,
Kevin Thornton,
Jaime Ashander, and
Peter Ralph.
PLoS Computational Biology, November 2018.
(on the bioRXiv;
the tools on github)
- The tempo of linked selection: emergence of a heterogeneous genomic landscape during a recent radiation of monkeyflowers,
Sean Stankowski, Madeline A Chase, Allison M Fuiten, Peter L Ralph, and Matthew A Streisfeld. To appear in PLoS Biology.
(on the bioRXiv)
- System drift and speciation,
Josh S Schiffman and Peter L Ralph. Submitted.
(on the bioRXiv)
- Demographic inference in a spatially-explicit ecological model from genomic data:
a proof of concept for the Mojave Desert Tortoise,
Jaime Ashander,
Peter Ralph,
Evan McCartney-Melstad,
H Bradley Shaffer.
Submitted.
(on the bioRXiv)
- Desert Tortoises in the Genomic Age: Population Genetics and the Landscape,
H Bradley Shaffer.
Evan McCartney-Melstad,
Peter L Ralph,
Gideon Bradburd,
Erik Lundgren,
Jannet Vu,
Bridgette Hagerty,
Fran Sandmeier,
Chava Weitzman,
and C. Richard Tracy.
Report for the CDFW.
(on the bioRxiv)
- Inferring Continuous and Discrete Population Genetic Structure Across Space,
Gideon Bradburd,
Graham Coop, and Peter Ralph, Genetics, September 2018.
(on the bioRXiv; conStruct on github)
- Local PCA shows how the effect of population structure differs along the genome, Han Li and Peter Ralph.
Genetics, January 2019.
(on the bioRXiv; and on github, including the R package)
- Predicting Responses to Contemporary Environmental Change Using Evolutionary Response Architectures, Rachael A. Bay, Noah Rose, Rowan Barrett, Louis Bernatchez, Cameron K. Ghalambor, Jesse R. Lasky, Rachel B. Brem, Stephen R. Palumbi, and Peter Ralph, American Naturalist, March 2017.
- Beyond clines: lineages and haplotype blocks in hybrid zones, Alisa Sedghifar, Yaniv Brandvain, and Peter Ralph, Molecular Ecology, May 2016.
(on the bioRXiv; on github)
- Adaptation in isolated populations: when does it happen and when can we tell?, Jessica Crisci, Matt Dean, and Peter Ralph, Molecular Ecology, June 2016.
(on the bioRXiv; scripts on datadryad)
- A Spatial Framework for Understanding Population Structure and Admixture., Gideon Bradburd, Peter L. Ralph, and Graham Coop, PLoS Geneticson the bioRXiv; SpaceMix on github; reviewed at the Molecular Ecologist)
- The Spatial Mixing of Genomes in Secondary Contact Zones, Alisa Sedghifar, Yaniv Brandvain, Peter Ralph, and Graham Coop, Genetics, September 2015.
(on the bioRXiv)
- The role of standing variation in geographic convergent adaptation, Peter Ralph and Graham Coop, American Naturalist, October 2015.
(on the bioRXiv, and on github)
- Convergent evolution during local adaptation to patchy landscapes, Peter Ralph and Graham Coop, PLoS Genetics, November 2015.
(on the bioRXiv, and on github)
- Independent molecular basis of convergent highland adaptation in maize, Shohei Takuno, Peter Ralph, Kelly Swarts, Rob J Elshire, Jeffrey C Glaubitz, Edward S. Buckler, Matthew B Hufford, and Jeff Ross-Ibarra, Genetics, June 2015.
(on the bioRXiv, and on github)
- Sexual selection targets cetacean pelvic bones, James P. Dines, Erik Otárola-Castillo, Peter Ralph, Jesse Alas, Timothy Daley, Andrew D. Smith, and Matthew D. Dean, Evolution, October 2014.
(pdf, and code on github)
- Conflation of short identity-by-descent segments bias their inferred length distribution, Charleston W.K. Chiang, Peter Ralph, and John Novembre,
G3: Genes, Genomes, Genetics, May 2016.
(on the arXiv)
- Disentangling the effects of geographic and ecological isolation on genetic differentiation, Gideon Bradburd, Peter Ralph and Graham Coop, Evolution, July 2013.
(Gideon's talk on this reviewed at nothing in biology makes sense)
(on the arXiv; the R package, BEDASSLE)
- The geography of recent genetic ancestry across Europe, Peter Ralph andGraham Coop, PLoS Biology 11(5) 2013: e1001555. (experimental html version; individual full size supplemental figures: S3, S4, S5, and S8 (225 pages)) (our summary plus discussion at haldane's sieve; also discussed at the Loom, nature news, dienekes, gene expression, and eurogenes) (on the arXiv)
- Patterns of Neutral Diversity Under General Models of Selective Sweeps, Graham Coop and Peter Ralph, Genetics, June 2012. Code available on gcbias.org. (on the arXiv)
- Is your phylogeny informative? Measuring the power of comparative methods, with Carl Boettiger, Peter Ralph and Graham Coop, Evolution, January 2012. Code available on github. (on the arXiv)
- Stochastic population growth in spatially heterogeneous environments, Steve Evans, Peter Ralph, Sebastian J. Schreiber and Arnab Sen, Journal of Mathematical Biology, January 2012. (on the arXiv)
- Transcriptional regulation: Effects of promoter proximal pausing on speed, synchrony and reliability, Alistair Boettiger, Peter Ralph and Steve Evans. PLoS Computational Biology, May 2011. (on the arXiv)
- Parallel adaptation: One or many waves of advance of an advantageous allele?, Peter Ralph and Graham Coop. Genetics Vol. 186, pp. 647-668, October 2010. (on the arXiv) and (reviewed by Daniel Wilson, John Hawks, Luke Jostins, and various at Faculty of 1000)
- Dynamics of the time to the most recent common ancestor in a large branching population, Steve Evans and Peter Ralph. Annals of Applied Probability vol. 20, no. 1, 1-25. (pdf) (on the arXiv)
- Seed dispersal kernel estimation without fecundities, Peter Ralph, a brief commentary in Molecular Ecology, April 2008. (also note Juan Jose Robledo-Arnuncio's reply, which makes some good points)
- Brownian motion on time scales, basic hypergeometric functions, and some continued fractions of Ramanujan Shankar Bhamidi, Steve Evans, Ron Peled, and Peter Ralph; published in: Deborah Nolan and Terry Speed, eds., Probability and Statistics: Essays in Honor of David A. Freedman, IMS Collections 2008, Vol. 2, 42-75. (on the arXiv) Also see this page for some pictures, the paper, and the slides from a presentation.
- A Lesser Frigatebird (Fregata ariel) in California: a first for the state and a fourth for North America, Brian J. Sullivan, Marshall J. Iliff, Peter Ralph, C.J. Ralph, and Steven J. Kelling, in North American Birds, 61 (4) 2008. (pdf)
- Growth and Activity Patterns in a Backyard Population of the Banana Slug, Ariolimax columbianus, Anita K. Pearson, Peter Ralph and Oliver P. Pearson, in The Veliger 48 (3), 2006. (pdf)
Also, my thesis (May 2009), broken up (conveniently?) into four chapters, which are self-contained, except for the references, which are all in the bibliography (sorry).
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