PSA: Software for parental structure analysis of seed or seedling patches

Molecular Ecology Resources

Volumn 12, Issue 6, 2012, Pages 1180-1189

  Robledo Arnuncio, J J ^a   Grivet, D ^a   Smouse, P E ^b   Sork, V L ^c  

^a Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria   (Spain)

^b RUTGERS UNIVERSITY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Gene flow; Genetic structure; Kinship; Parentage; Pericarp; Seed and pollen dispersal

Indexed keywords

ARTICLE; BIOLOGY; COMPUTER PROGRAM; GENETICS; GENOTYPE; INHERITANCE; METHODOLOGY; MOLECULAR BIOLOGY; PLANT; PLANT SEED; SEEDLING;

COMPUTATIONAL BIOLOGY; GENOTYPE; INHERITANCE PATTERNS; MOLECULAR BIOLOGY; PLANTS; SEEDLING; SEEDS; SOFTWARE;

ANIMALIA;

EID: 84867564327     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12005     Document Type: Article

References (37)

1. Baskin CC, Baskin JM (2000) Seeds: Ecology, Biogeography and Evolution of Dormancy and Germination. Academic Press Inc., San Diego.
2. Blouin MS (2003) DNA-based methods for pedigree reconstruction and kinship analysis in natural populations. Trends in Ecology and Evolution, 18, 503-511.
3. Burczyk J, Adams WT, Birkes DS, Chybicki IJ (2006) Using genetic markers to directly estimate gene flow and reproductive success parameters in plants on the basis of naturally regenerated seedlings. Genetics, 173, 363-372.
4. Chybicki I, Burczyk J (2010) NM+: software implementing parentage-based models for estimating gene dispersal and mating patterns in plants. Molecular Ecology Resources, 10, 1071-1075.
5. Ellstrand NC, Elam DR (1993) Population genetics of small population size: implications for plant conservation. Annual Review of Ecology and Systematics, 23, 217-242.
6. Fenner M (1992) Seeds: The Ecology of Regeneration in Plant Communities. CAB International, Wallingford.
7. Gerber S, Chabrier P, Kremer A (2003) FaMoz: a software for parentage analysis using dominant, codominant and uniparentally inherited markers. Molecular Ecology Notes, 3, 479-481.
8. Godoy JA, Jordano P (2001) Seed dispersal by animals: exact identification of source trees with endocarp DNA microsatellites. Molecular Ecology, 10, 2275-2283.
9. Goto S, Shimatani K, Yoshimaru H, Takahashi Y (2006) Fat-tailed gene flow in the dioecious canopy tree species Fraxinus mandshurica var. japonica revealed by microsatellites. Molecular Ecology, 15, 2985-2996.
10. Grivet D, Smouse PE, Sork VL (2005) A novel approach to an old problem: tracking dispersed seeds. Molecular Ecology, 14, 3585-3595.
11. Grivet D, Robledo-Arnuncio JJ, Smouse PE, Sork VL (2009) Relative contribution of contemporary pollen and seed dispersal to the effective parental size of seedling populations of Californian valley oak (Quercus lobata, Née). Molecular Ecology, 18, 3967-3979.
12. Hardy OJ, Vekemans X (2002) spagedi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular Ecology Notes, 2, 618-620.
13. Howe GT, Miriti MN (2004) When seed dispersal matters. BioScience, 54, 651-660.
14. Ibarra-Manríquez G, Martínez Ramos M, Oyama K (2001) Seedling functional types in a lowland rain forest in Mexico. American Journal of Botany, 88, 1801-1812.
15. Irwin AJ, Hamrick JL, Godt MJW, Smouse PE (2003) A multiyear estimate of the effective pollen donor pool for Albizia julibrissin. Heredity, 90, 187-194.
16. Iwaizumi MG, Watanabe A, Ubukata M (2007) Use of different seed tissues for separate biparentage identification of dispersed seeds in conifers: confirmations and practices for gene flow in Pinus densiflora. Canadian Journal of Forest Research, 37, 2022-2030.
17. Jones OR, Wang J (2010) colony: aprogram for parentage and sibship inference from multilocus genotype data. Molecular Ecology Resources, 10, 551-555.
18. Kalinowski ST, Wagner AP, Taper ML (2006) ml-relate: a computer program for maximum likelihood estimation of relatedness and relationship. Molecular Ecology Resources, 6, 575-579.
19. Karubian J, Sork VL, Roorda T, Duraes R, Smith TB (2010) Destination-based seed dispersal homogenizes genetic structure of a tropical palm. Molecular Ecology, 19, 1745-1753.
20. Ledig FT (1992) Human impacts on genetic diversity in forest ecosystems. Oikos, 63, 87-108.
21. Loiselle BA, Sork VL, Nason J, Graham C (1995) Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). American Journal of Botany, 82, 1420-1425.
22. Lowe AJ, Boshier D, Ward M, Bacles CFE, Navarro C (2005) Genetic resource impacts of habitat loss and degradation; reconciling empirical evidence and predicted theory for neotropical trees. Heredity, 95, 255-273.
23. Marshall TC, Slate J, Kruuk LEB, Pemberton JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology, 7, 639-655.
24. Nielsen R, Tarpy DR, Reeve K (2003) Estimating effective paternity number in social insects and the effective number of alleles in a population. Molecular Ecology, 12, 3157-3164.
25. Queller DC, Goodnight KF (1989) Estimating relatedness using genetic markers. Evolution, 43, 258-275.
26. Robledo-Arnuncio JJ, Austerlitz F, Smouse PE (2006) A new method of estimating the pollen dispersal curve independently of effective density. Genetics, 173, 1033-1045.
27. Rousset F (2008) genepop'007: a complete re-implementation of the genepop software for Windows and Linux. Molecular Ecology Resources, 8, 103-106.
28. Rousset F, Leblois R (2012) Likelihood-based inferences under isolation by distance: two-dimensional habitats and confidence intervals. Molecular Biology and Evolution, 29, 957-973.
29. Smouse PE, Robledo-Arnuncio JJ (2005) Measuring the genetic structure of the pollen pool as the probability of paternal identity. Heredity, 94, 640-649.
30. Smouse PE, Sork VL, Scofield DG, Grivet D (2012) Using seedling and pericarp tissues to determine maternal parentage of dispersed Valley oak recruits. Journal of Heredity, 103, 250-259.
31. Sork VL, Nason J, Campbell DR, Fernandez JF (1999) Landscape approaches to historical and contemporary gene flow in plants. Trends in Ecology & Evolution, 14, 219-224.
32. Thomas PA (2000) Trees: Their Natural History. Cambridge University Press, Cambridge.
33. Vander Wall SB (2001) The evolutionary ecology of nut dispersal. The Botanical Review, 67, 74-117.
34. Wang J (2011) coancestry: a program for simulating, estimating and analysing relatedness and inbreeding coefficients. Molecular Ecology Resources, 11, 141-145.
35. Wang BC, Sork VL, Leong MT, Smith TB (2007) Hunting of mammals reduces seed removal and dispersal of the afrotropical tree Antrocaryon klaineanum (Anacardiaceae). Biotropica, 39, 340-347.
36. Wilcock C, Neiland R (2002) Pollination failure in plants: why it happens and when it matters. Trends in Plant Science, 7, 270-277.
37. Ziegenhagen B, Liepelt S, Kuhlenkamp V, Fladung M (2003) Molecular identification of individual oak and fir trees from maternal tissues of their fruits or seeds. Trees Structure and Function, 17, 345-350.