title: Estimation of effective population size in continuously distributed populations: there goes the neighborhood.
abstract: Use of genetic methods to estimate effective population size (Ne) is rapidly increasing, but all approaches make simplifying assumptions unlikely to be met in real populations. In particular, all assume a single, unstructured population, and none has been evaluated for use with continuously distributed species. We simulated continuous populations with local mating structure, as envisioned by Wright's concept of neighborhood size (NS), and evaluated performance of a single-sample estimator based on linkage disequilibrium (LD), which provides an estimate of the effective number of parents that produced the sample (Nb). Results illustrate the interacting effects of two phenomena, drift and mixture, that contribute to LD. Samples from areas equal to or smaller than a breeding window produced estimates close to the NS. As the sampling window increased in size to encompass multiple genetic neighborhoods, mixture LD from a two-locus Wahlund effect overwhelmed the reduction in drift LD from incorporating offspring from more parents. As a consequence, never approached the global Ne, even when the geographic scale of sampling was large. Results indicate that caution is needed in applying standard methods for estimating effective size to continuously distributed populations.
authors: Department of Plant Science and Landscape Architecture and Department of Entomology, University of Maryland, College Park, MD 20742, USA. mneel@umd.edu
authors: M C
authors: MC
authors: Neel
authors: K
authors: K
authors: McKelvey
authors: N
authors: N
authors: Ryman
authors: M W
authors: MW
authors: Lloyd
authors: R
authors: R
authors: Short Bull
authors: F W
authors: FW
authors: Allendorf
authors: M K
authors: MK
authors: Schwartz
authors: R S
authors: RS
authors: Waples
mesh_terms: D001947:Breeding; D005828:Genetics, Population; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D010375:Pedigree; D011156:Population Density
references: Genetics. 2011 Oct;189(2):633-44
references: 21840864
references: Mol Ecol Resour. 2008 Jan;8(1):103-6
references: 21585727
references: Genetics. 1997 Apr;145(4):1219-28
references: 9093870
references: J Fish Biol. 2009 Feb;74(2):403-17
references: 20735567
references: Heredity (Edinb). 1999 Aug;83 ( Pt 2):145-54
references: 10469202
references: Evolution. 1988 May;42(3):482-495
references: 28564013
references: Genetics. 1972 Apr;70(4):639-51
references: 5034774
references: J Fish Biol. 2009 Apr;74(5):1086-103
references: 20735621
references: Evol Appl. 2011 Jan;4(1):144-54
references: 25567959
references: Genetics. 2009 Aug;182(4):1233-49
references: 19528328
references: Evolution. 2004 Sep;58(9):1891-900
references: 15521449
references: Genetics. 1996 Sep;144(1):383-7
references: 8878701
references: Nat Rev Genet. 2009 Mar;10(3):195-205
references: 19204717
references: Genetics. 1943 Mar;28(2):114-38
references: 17247074
references: Mol Ecol Resour. 2008 Jul;8(4):753-6
references: 21585883
references: Evolution. 1995 Dec;49(6):1046-1054
references: 28568536
references: Genetics. 1931 Mar;16(2):97-159
references: 17246615
references: Mol Ecol. 2006 Oct;15(12):3601-15
references: 17032260
references: Philos Trans R Soc Lond B Biol Sci. 2005 Jul 29;360(1459):1395-409
references: 16048783
references: Theor Popul Biol. 1975 Oct;8(2):212-41
references: 1198353
references: Mol Ecol. 2012 Jun;21(12):2839-46
references: 22574758
references: Ecol Evol. 2012 Sep;2(9):2357-65
references: 23139893
references: Nat Genet. 2008 May;40(5):646-9
references: 18425127
references: Mol Ecol Resour. 2010 Jul;10(4):684-92
references: 21565073
references: Mol Ecol. 2003 Jul;12(7):1807-16
references: 12803633
references: Mol Ecol. 2005 Oct;14(11):3335-52
references: 16156807
references: Genetics. 2007 Jan;175(1):219-33
references: 17110487
references: Mol Ecol. 2002 Apr;11(4):699-709
references: 11972758
references: Mol Ecol Resour. 2008 Mar;8(2):299-301
references: 21585773
references: Genet Res (Camb). 2009 Dec;91(6):395-412
references: 20122296
references: Genetics. 2005 Jun;170(2):955-67
references: 15834143
references: Mol Ecol. 2008 Sep;17(17):3788-99
references: 18643879
references: Genetics. 2004 Feb;166(2):1081-92
references: 15020488
references: Genetics. 1973 Sep;75(1):213-9
references: 4762877
references: J Hered. 2008 Nov-Dec;99(6):694-5
references: 18703539
references: Mol Biol Evol. 2012 Mar;29(3):957-73
references: 22016575
references: Mol Ecol. 2009 May;18(10):2148-64
references: 19389175
references: Evolution. 2005 Aug;59(8):1633-8
references: 16329237
references: Genetics. 2004 Dec;168(4):2227-44
references: 15611188
references: Genetics. 1946 Jan;31:39-59
references: 21009706
references: Mol Ecol. 2009 Dec;18(23):4734-56
references: 19878454
references: Mol Ecol. 2010 Oct;19(19):4179-91
references: 20819159
references: Genetics. 1981 Jul;98(3):625-40
references: 17249104
references: Philos Trans R Soc Lond B Biol Sci. 1995 Jul 29;349(1327):49-59
references: 8748019
references: Evol Appl. 2010 May;3(3):244-62
references: 25567922
references: Proc Biol Sci. 2006 Jun 22;273(1593):1483-90
references: 16777742
references: Mol Ecol. 2007 Feb;16(4):737-51
references: 17284208
references: Mol Ecol Resour. 2011 Jan;11(1):5-18
references: 21429096