diff --git a/paper/paper.bib b/paper/paper.bib
index 9c400de508dbe0f916b8065b0a671a59caf7c012..b04600f98b9d3dada331bb72860b56b88b7fa2a3 100644
--- a/paper/paper.bib
+++ b/paper/paper.bib
@@ -1,17 +1,17 @@
@book{Cutter:2019,
Author = {{Cutter}, A.D.},
Publisher = {Oxford University Press},
- Title = {{A Primer of Molecular Population Genetics}},
+ Title = "{{A Primer of Molecular Population Genetics}}",
Year = 2019
}
@Article{Gautier:2017,
author = {{Gautier}, M., and {Klassmann}, A. and {Vitalis}, R.},
- title = {rehh2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure},
+ title = "{rehh2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure}",
journal = {Molecular Ecology Resources},
year = {2017},
volume = {17},
number = {1},
- pages = {78-90},
+ pages = {78-90}
}
@article{Jacobs:2016,
title="{Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps}",
@@ -32,6 +32,15 @@
year={2001},
doi={10.1038/ng1001-217}
}
+@article{Kelly:1997,
+ author = {{Kelly}, J.K.},
+ title = "{A test of neutrality based on interlocus associations}",
+ journal = {Genetics},
+ volume = {146},
+ number = {3},
+ pages = {1197-1206},
+ year = {1997}
+}
@article{Kim:2004,
title="{Linkage Disequilibrium as a Signature of Selective Sweeps}",
author={{Kim}, Y. and {Nielsen}, R.},
@@ -42,6 +51,16 @@
year={2004},
doi={10.1534/genetics.103.025387}
}
+@article{Liebert:2017,
+ author = {{Liebert}, A., and {Lopez}, S. and {Jones}, B.L. and {Montalva}, N. and {Gerbault}, P. and {Lau}, W. and {Thomas}, M.G. and {Bradman}, N. and {Maniatis}, N. and {Swallow}, D.M.},
+ title = "{World-wide distributions of lactase persistence alleles and the complex effects of recombination and selection}",
+ journal = {Human Genetics},
+ volume = {136},
+ number = {11-12},
+ pages = {1445-1453},
+ DOI = {10.1007/s00439-017-1847-y},
+ year = {2017}
+}
@article{Maynard:1974,
title="{The hitch-hiking effect of a favourable gene}",
author={{Maynard Smith}, J. and {Haigh}, J.},
@@ -49,20 +68,48 @@
volume={23},
number={1},
pages={23--35},
- year={1974},
+ year={1974}
+}
+@article{Nielsen:2005,
+ author = {{Nielsen}, R., and {Williamson}, S. and {Kim}, Y. and {Hubisz}, M.J. and {Clark}, A.G. and {Bustamante}, C.},
+ title = "{Genomic scans for selective sweeps using SNP data}",
+ journal = {Genome Research},
+ volume = {15},
+ number = {11},
+ pages = {1566-1575},
+ DOI = {10.1101/gr.4252305},
+ year = {2005}
}
@Article{Pfeifer:2014,
- title = {PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R},
+ title = "{PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R}",
journal = {Molecular Biology and Evolution},
year = {2014},
author = {{Pfeifer}, B., and {Wittelsbuerger}, U. and {Ramos-Onsins}, S.E. and {Lercher}, M.J.},
volume = {31},
pages = {1929-1936},
- doi = {10.1093/molbev/msu136},
+ doi = {10.1093/molbev/msu136}
+}
+@article {Rozas:2001,
+ author = {{Rozas}, J., and {Gullaud}, M. and {Blandin}, G. and {Aguad{\'e}}, M.},
+ title = "{DNA Variation at the rp49 Gene Region of Drosophila simulans: Evolutionary Inferences From an Unusual Haplotype Structure}",
+ volume = {158},
+ number = {3},
+ pages = {1147--1155},
+ year = {2001},
+ journal = {Genetics}
+}
+@article{Sabeti:2007,
+ author = {{Sabeti}, P.C., and {Varilly}, P. and {Fry}, B. and {Lohmueller}, J. and {Hostetter}, E. and {Cotsapas}, C. and {Xie}, X. and {Byrne}, E.H. and {McCarroll}, S.A. and {Gaudet}, R. and {Schaffner}, S.F. and {Lander}, Eric S.},
+ title = "{Genome-wide detection and characterization of positive selection in human populations}",
+ journal = {Nature},
+ volume = {449},
+ number = {7164},
+ pages = {913-918},
+ year = {2007}
}
@incollection{Vitti:2013,
author = {{Vitti}, J.J., and {Grossman}, S.R. and {Sabeti}, P.C.},
- title = {Detecting Natural Selection in Genomic Data},
+ title = "{Detecting Natural Selection in Genomic Data}",
booktitle = {Annual Review of Genetics},
publisher = {Annual Reviews},
year = 2013,
diff --git a/paper/paper.md b/paper/paper.md
index 54979d487b37807fbcdd22b6cc52d5b13fa1a5dd..cd4d99de37a21ceaba1ca32e6f13a21478b4ef1b 100644
--- a/paper/paper.md
+++ b/paper/paper.md
@@ -92,7 +92,7 @@ There are many statistics included in the package for adjusting for expected $r^
The output of the functions is in list format. The SNP positions and the values of the statistic(s) are stored in vectors of equal length in the list. Users can then identify outlying SNPs in their data that are candidate regions for selection.
-There are a few other R packages that can be used for selection scans, although none utilise the $Z_{\alpha}$ statistics described here. These include `PopGenome` [@Pfeifer:2014], which calcualtes Kelly's $Z_{nS}$ among other methods, and `rehh` [@Gautier:2017], which implements extended haplotype homozygosity (EHH) and related statistics.
+There are a few other R packages that can be used for single population selection scans, although none utilise the $Z_{\alpha}$ statistics described here. `PopGenome` has the advantage of being able to read in multiple standard genomic data formats and perform other analyses as well as selection scans [@Pfeifer:2014]. The scans it performs are the CL and CLR methods by @Nielsen:2005. It can also calculate Kelly’s $Z_{nS}$ [@Kelly:1997] and Rozas’ ZA/ZZ [@Rozas:2001] for LD, which are similar to the basic $Z_{\alpha}$ statistic; however, neither use an LD profile to correct for expected correlation. `rehh` is another package used for selection scans, and for single populations uses extended haplotype homozygosity (EHH) and related statistics [@Gautier:2017]. These are popular and easy to interpret methods; however, they are not as effective for soft sweeps [@Liebert:2017]. Variations in local recombination rate are accounted for by implementing the cross-population EHH (XP-EHH) [@Sabeti:2007], which requires another population to compare with [@Vitti:2013]. All these packages identify evidence of selective sweeps in different ways, and each have merits. It would be advisable to use a combination of approaches to achieve the most accurate and valid results.
# Conclusion
diff --git a/paper/paper.pdf b/paper/paper.pdf
index f99ae307e9eb67927bcee55ed1c4f0b8c54033e1..fc853bf401257c8d04e71225c6fa427d1d51cf5d 100644
Binary files a/paper/paper.pdf and b/paper/paper.pdf differ