Molecular Ecology Group

Department of Zoology

Professor William (Bill) Amos

Bill (right) & Joe Hoffman with a giant porcini mushroom

Email: w.amos@zoo.cam.ac.uk
Tel: +44 (0)1223 336616

Research Interests

I am interested in many aspects of evolutionary genetics. My early work focused on using techniques such as DNA fingerprinting to investigate breeding behaviour and population structure in marine mammals, particularly the long-finned pilot whale and the grey seal. Although this work continues, I have picked up and developed a number of other themes, illustrated by the publications below. These include: (a) research into how molecular markers, in particular microsatellites, evolve; (b) human population genetics; (c) the development of new statistical approaches to infer historical population structure; (d) a current vogue, trying to find out why it is so common to find a positive relationship between genetic heterozygosity and fitness; (e) a long-standing interest involves exploring an idea I had more than a decade ago that mutation rate is influenced by heterozygosity, with heterozygous sites being more mutable than equivalent homozygous sites – the evidence is accumulating! Along the way, I have often written my own bits of software to solve particular problems. These usually exist as Visual Basic Macros (see links below) for use in Microsoft Excel, and anyone is welcome to use them, with the standard proviso that I can accept no responsibility for problems arising from their use. I have done my best to eliminate bugs, but this does not mean that none exist! I very much welcome feedback on how the programs work and suggestions for improvements / changes.

Selected publications

What I feel are my most important publications to date:

  • Amos, W. 2011. Population-specific links between heterozygosity and the rate of human microsatellite evolution.   J. Mol. Evol. 72: 215-221
  • Amos, W., Flint, J. & Xu, X. 2008.  Heterozygosity increases microsatellite mutation rate, linking it to demographic history. BMC Genet. 9: 72
  • Amos, W.  2010.  Heterozygosity and mutation rate: evidence for an interaction and its implications. Bioessays 32: 82-90.

Marine Mammal Genetics

  • Amos, W., Barrett, J.A. & Dover, G.A. (1991) Breeding behaviour of pilot whales revealed by DNA fingerprinting. Heredity 67: 49-55
  • Amos, W., Schloetterer, C. & Tautz, D. (1993) Social structure of pilot whales revealed by analytical DNA typing. Science 260: 670-672
  • Amos, W., Twiss, S., Pomeroy, P. & Anderson, S.S. (1995) Mate fidelity in a polygynous mammal. Science268: 1897-1899
  • Valsecchi, E., Palsbøll, P., Hale, P., Glockner-Ferrari, D., Ferrari, M., Clapham, P., Larsen, F., Mattila, D., Sears, R., Sigurjonsson, J., Brown, M., Corkeron, P. & Amos, W. (1997). Microsatellite genetic distances between oceanic populations of the humpback whale (Megaptera novaeangliae). Mol. Biol. Evol.14:335-362
  • Amos, W. (1999) Cultural and genetic evolution in whales. Science 284: 2056-2057 technical comment (electronic appendix)
  • Worthington Wilmer, J, Allen, P.J., Pomeroy, P.P.,Twiss, S.D. & Amos, W. (1999). Where have all the fathers gone? An extensive microsatellite analysis of paternity in the grey seal (Halichoerus grypus). Mol. Ecol. 8: 1417-1430
  • Worthington Wilmer, J, Overall, A.J., Pomeroy, P.P.,Twiss, S.D. & Amos, W. (2000) Patterns of paternal relatedness in British grey seal colonies. Mol. Ecol. 9: 283-292
  • Fullard, K., Early, G., Heide-Jørgensen, M.P., Bloch, D., Rosing-Asvid, A. & Amos, W (2000) Population structure of long-finned pilot whales in the North Atlantic: a correlation with sea surface temperature? Mol. Ecol. 9: 949-958
  • Valsecchi, E., Hale, P., Corkeron, P. & Amos, W. (2002) Social structure in migrating humpback whales (Megaptera novaeangliae). Mol. Ecol. 11: 507-518
  • Gaggiotti, O.E., Jones, F., Amos, W., Harwood, J. & Nichols, R.A. (2002). Patterns of colonisation in a grey seal metapopulation. Nature 416: 424-427
  • Hoffman, J.I., Boyd, I.L., & Amos, W. (2003). Male reproductive strategy and the importance of maternal status in the Antarctic fur seal, Arctocephalus gazella. Evolution 57: 1917-1930
  • Hoffman, J.I., Mason, C., Amos, W., Loughlin, T.R. & Bickham, J.R. (2006). Deep genetic subdivision within a continuously distributed and highly vagile marine mammal, the Steller's sea lion (Eumetopias jubatus). Mol. Ecol. 15: 2821-2832
  • Hoffman, J.I., Boyd, I.L.B. & Amos, W. (2005). Does kin selection influence fostering behaviour in Antarctic fur seals (Arctocephalus gazella)? Proc. Roy. Soc. Lond. B. 272: 2017-2022
  • Hoffman, J.I., Trathan, P.N. & Amos, W. (2006). Genetic tagging reveals extreme site fidelity in territorial male Antarctic fur seals, Arctocephalus gazella Mol. Ecol. 15: 3841-3847
  • Hoffmann, J.I., Amos, W., Tratham, P.N., Forcada, J. (2007). Female fur seals show active choices for males who are heterozygous and unrelated. Nature 441: 912-914
  • Amos, W. 2007.  Mix and match – hybridisation reveals hidden complexity in seal breeding behaviour. Mol. Ecol. 16: 3066-306
  • Dasmahapatra, K.K., Hoffman, J.I. & Amos, W. 2009.  Pinniped phylogenetic relationships inferred using AFLP markers. Heredity 130: 168-177.

  • Hoffman, J.I., Dasmahapatra, K.K., Amos, W., Phillips, C.D., Gelatt, T.S. & Bickham, J.W.  2011.  Contrasting patterns of genetic diversity at three different genetic markers in a marine mammal metapopulation Mol. Ecol. (in press)

Microsatellite Evolution

  • Rubinsztein, D.C., Amos, W., Leggo, J., Goodburn, S., Jain, S., Ross, C.A., Li, S.H., Margolis, R.M. & Ferguson-Smith, M.A. (1995) Microsatellites are generally longer in humans compared to their homologues in non-human primates: evidence for directional evolution at microsatellite loci. Nature Genetics 10: 337-343
  • Amos, W., Rubinsztein, D.C. (1996). Microsatellites are subject to directional evolution. Nature Genetics 12: 13-14
  • Amos, W., Rubinsztein, D.C. (1996). Microsatellites show mutational bias and heterozygote instability. Nature Genet 13: 390-391
  • Cooper, G., Rubinsztein, D.C. & Amos, W. (1998) Ascertainment bias cannot entirely account for human microsatellites being longer than their chimpanzee homologues. Hum. Mol. Genet 7: 1425-1429
  • Amos, W. (1999). A comparative approach to the study of microsatellite evolution. In: Microsatellites: evolution and applications. Ed. Goldstein, D.B. & Schlötterer, C. Oxford University Press, Oxford
  • Cooper, G., Amos, W., Bellamy, R., Siddiqui, M.R., Frodsham, A., Hill, A.V.S. & Rubinsztein, D.C. 1999. An empirical exploration of the (dm)2 genetic distance for 213 human microsatellite markers. Am. J. Hum. Genet. 65: 1125-1133
  • Cooper, G., Burroughs, N.J., Rand, D.A., Rubinsztein, D.C. & Amos, W. (1999). Markov chain Monte Carlo analysis of human Y chromosome microsatellites provides evidence of biased mutation. Proc. Natl. Acad. Sci. USA 96: 11916-11921
  • Swinton, J. & Amos, W. (2002). Measurement of distributional asymmetry in allele frequency distributions of microsatellites. IMA J. Math. App. Med. Biol. 19: 257-273
  • Amos, W., Hutter, C.M., Schug, M.D., & Aquadro, C.F. (2003). Directional evolution of size coupled with ascertainment bias for variation in Drosophila microsatellites. Mol. Biol. Evol. 20: 660-662
  • Vowles, E.J. & Amos, W. (2004). Evidence for widespread convergent evolution around microsatellites. PloS Biol. 2(8): e199
  • Vowles, E.J. & Amos, W. (2006). Quantifying ascertainment bias and species-specific length differences in human and chimpanzee microsatellites using genome sequences. Mol. Biol. Evol. 23: 598-607
  • Kayser, M., Vowles, E.J., Kappei, D. & Amos, W. (2006). Microsatellite length differences between humans and chimpanzees at autosomal but not Y-chromosomal loci. Genetics 173: 2179-2186
  • Amos, W. & Clarke, A. 2008. Body temperature predicts maximum microsatellite length in mammals. Biol. Lett.4: 399-401
  • Amos, W., Flint, J. & Xu, X. 2008. Heterozygosity increases microsatellite mutation rate, linking it to demographic history. BMC Genet. 9: 72
  • Varela, M. & Amos, W. 2009. Evidence for non-independent evolution of adjacent microsatellites in the human genome. J. Mol. Biol.(in press)

  • Amos, W. 2010.  Even small SNP clusters are non-randomly distributed: is this evidence of mutational non-independence? Proc. R. Soc. B. 277: 1443-1449

  • Amos, W.  2010.  Mutation biases and mutation rate variation around very short human microsatellites revealed by human-chimpanzee-orangutan genomic sequence alignments.  J. Mol. Evol. 71: 192-201
  • Amos, W.  2011. Population-specific links between heterozygosity and the rate of human microsatellite evolution.   J. Mol. Evol. 72: 215-221

Human Population Genetics

  • Cooper, G., Amos, W., Hoffman, D. & Rubinsztein, D.C. (1996). Network analysis of human Y microsatellite haplotypes. Hum. Mol. Genet. 5: 1759-1766
  • Kirk, R., Furlong, R.A., Amos, W., Cooper, G., Rubinsztein, J.S., Walsh, C., Paykel, E.S.& Rubinsztein, D.C. (1999). Mitochondrial genetic analyses support selection against maternal lineages in bipolar affective disorder. Am. J. Hum. Genet. 65: 508-518
  • Bellamy, R., Beyers, N., McAdam, K. P. W. J., Ruwende, C., Gie, R., Samaai, P., Bester, D., Meyer, M., Corrah, T., Collin, M., Camidge1, D. R., Wilkinson, D., Hoal-van Helden, E., Whittle, H. C., Amos, W., van Helden, P. & Hill, A. V. S. (2000). Genetic susceptibility to tuberculosis in Africans: a genome-wide scan. Proc. Natl. Acad. Sci. USA 97: 8005-8009
  • Rosser, Z.H. (5 others), Amos, W. (56 others), (2000). Y-chromosomal diversity within Europe is clinal and influenced primarily by geography rather than language. Am. J. Hum. Genet. 67: 1526-1543
  • Amos, W. & Manica, A. (2006). Global genetic positioning: evidence for early human population centers in coastal habitats. Proc. Natl. Acad. Sci. USA 103: 820-824
  • Amos W., Jow H. & Burroughs N.J. (2006) 'Uncovering the male history of Britain' in, eds. Shuichi Matsumura, Peter Forster and Colin Renfrew "Simulations, Genetics and Human Prehistory – A Focus on Islands" McDonald Institute for Archaeology, Cambridge. (in press for 2006: to be published in the McDonald Institute Monograph Series)
  • Jow, H., Amos, W., Luo, H., Zhang, Y., Burroughs, N.J. (2006). A Markov chain Monte Carlo method for estimating population mixing using Y-chromosome markers: mixing of the Han people in China. Ann. Hum. Genet. 71: 407-420
  • Manica, A., Amos, W., Balloux, F., Hanihara, T. (2007). The effect of ancient population bottlenecks on human phenotypic variation. Nature 448: 346-348
  • Betti, L., Balloux, F., Amos, W., Hanihara, T. & Manica, A. 2009. Distance from Africa, not climate, explains within-population phenotypic diversity in humans. Proc. Roy. Soc. Lond. B. 276: 809-814
  • Amos, W. & Hoffman, J.I. 2010.  Evidence that two main bottleneck events shaped modern human genetic diversity. Proc. R. Soc. B. 277: 131-137
  • Amos, W.  & Bryant, C. 2011. Using human demographic history to infer natural selection reveals contrasting patterns on different families of immune genes. Proc. Roy. Soc. B. (in press)

Heterozygosity and Fitness

  • Amos, W., Worthington Wilmer, J &Kokko, H. (2001). Do female grey seals select genetically diverse mates? Anim. Behav. 62: 157-164
  • Krüger, O., Lindstrõm, J. & Amos, W. (2001). Maladaptive mate choice maintained by heterozygote advantage. Evolution 55: 1207-1214
  • Amos, W., Worthington Wilmer, J., Fullard, K., Burg, T.M., Croxall, J.P., Bloch, D. & Coulson, T. 2001. The influence of parental relatedness on reproductive success. Proc. Roy. Soc. Lond. B. 268: 2021-2027
  • Acevedo-Whitehouse, K., Gulland, F., Greig, D. & Amos, W. (2003). Inbreeding-dependent pathogen susceptibility in California sea lions. Nature 422: 35
  • Valsecchi, E., Amos, W., Raga, J.A., Podesta, M. & Sherwin, W. (2004). The effects of inbreeding on mortality during a morbillivirus outbreak in the Mediterranean striped dolphin (Stenella coeruleoalba). Animal Cons. 7: 139-146
  • Bean, K., Amos, W., Pomeroy, P.P., Twiss, S.D. Coulson T.N. & Boyd, I.L., (2004). Patterns of parental relatedness and pup survival in the grey seal (Halichoerus grypus). Mol. Ecol 13: 2365-2370
  • Hoffman, J.I., Boyd, I.L., & Amos, W. (2004). Exploring the relationship between parental relatedness and male reproductive success in the Antarctic fur seal Arctocephalus gazella. Evolution 58: 2087-2099
  • Seddon, N., Amos, W. & Tobias, J.A. (2004). Heterozygosity predicts territory size and song structure in a co-operatively breeding bird. Proc. Roy. Soc. Lond. B. 271: 1823-1829
  • Balloux, F., Amos, W. & Coulson, T.N. (2004). Does heterozygosity estimate inbreeding in real populations? Mol. Ecol. 13: 3021-3031
  • Acevedo-Whitehouse, K., Vicente, J., Höfle, U., Fernández-de-Mera, I.G., Amos, W. & Gortazar, C. (2005). Genetic resistance to infection and severity of bovine tuderculosis in wild boar. Mol. Ecol. 14: 3209-3217
  • Acevedo-Whitehouse, K., Spraker, T.R., Lyons, E., Melin, S.R., Gulland, F., DeLong, R.L. & Amos, W. (2006). Genetic heterozygosity, survival and pathogen resistance in California sea lion pups from San Miguel Island. Mol. Ecol. 15: 1973-1982
  • Hoffman, J.I., Forcada, J. & Amos, W. (2006). No relationship between microsatellite variation and neonatal fitness in Antarctic fur seals Arctocephalus gazella. Mol. Ecol. 15: 1996-2005
  • Ferreira, A.G.A. & Amos, W. (2006). Inbreeding depression and multiple regions showing heterozygote advantage in Drosophila melanogaster exposed to stress. Mol. Ecol. 15: 3885-3893
  • Boakes, E.H., Wang, J. Amos, W. 2007. An investigation of inbreeding depression and purging in captive pedigreed populations Heredity 98: 172-182.
  • Dasmahapatra, K.K., Lacy, R.C. & Amos, W. 2008. Estimating levels of inbreeding using AFLP markers. Heredity 100: 286-295
  • Rijks, J., Hoffman, J.I., Kuiken, T., Osterhaus, A.D.M.E. & Amos, W. 2008. Heterozygosity and lungworm burden in harbour seals (Phoca vitulina). Heredity100: 587-593
  • Lyons, E.J., Frodsham, A.J., Zhang, L., Hill, A.V.S. & Amos, W. 2009.  Consanguinity and susceptibility to infectious diseases in humans. Biol. Let. 5: 574-576

  • Amos, W. & Acevedo-Whitehouse, K. 2009.  A new test for genotype - fitness associations reveals a single microsatellite allele that strongly predicts the nature of tuberculosis infections in wild boar. Mol. Ecol. Res. 9: 1102-1111
  • Lyons, E.J., Amos, W., Berkley, J.A., Mwangi, I., Shafi, M., Williams, T.N., Newton, C.R., Peshu, N., Marsh, K., Scott, J.A.G. and Hill, A.V.S.  2009.  Homozygosity and Risk of Childhood Death due to Invasive Bacterial Disease BMC Medical Genet. 10: 55
  • Hoffman, J.I., Hanson, N., Forcada, J., Tratham, P.N. & Amos, W.  2010.  Getting long in the tooth: a strong positive correlation between canine size and heterozygosity in Antarctic fur seals Arctocephalus gazella J Hered. 101: 527-538
  • Hoffman, J.I., Forcada, J. & Amos, W.  2010.  Exploring the mechanisms underlying a heterozygosity-fitness correlation for canine size in the Antarctic fur seal Arctocephalus gazella.  J Hered. 101: 539-552
  • Cammen, K. Hoffman, J.I., Knapp, L.A., Harwood, J. & Amos, W.  2011.  Geographic variation of the major histocompatibility complex in Eastern Atlantic grey seals (Halichoerus grypus) Mol. Ecol. 20: 740-752

Miscellaneous

  • Amos, W. & Harwood, J. (1998). Factors affecting levels of genetic diversity in natural populations. Phil. Trans. Roy. Soc. B 353: 1-12
  • Valsecchi, E., Glockner-Ferrari, D., Ferrari, M. & Amos, W. (1998). Molecular analysis of the efficiency of sloughed skin sampling in whale population genetics.Mol. Ecol. 7: 1419-1422
  • McRae, S.B. & Amos, W. (1999). Can incest within cooperatively breeding groups be detected using DNA fingerprinting? Behav. Ecol. Sociobiol. 47: 104-107
  • Summers, K. & Amos, W. (1997). Behavioural, ecological and molecular genetic analyses of reproductive strategies in the Amazonian dart-poison from, Dentrobates ventrimaculatus. Behav. Ecol. 8: 260-267
  • Reed, J.Z., Tollit, D.J., Thompson, P.M. & Amos, W. (1997). Molecular scatology, the use of molecular genetic analysis to assign species, sex and individual identity to seal faeces. Mol. Ecol. 6: 225-234
  • Amos, W. & Balmford, A. 2001. When does conservation genetics matter? Heredity 87: 257-265
  • Johnson, P.C.D., Whitfield, J.A., Foster, W.A. & Amos, W. (2002). Clonal mixing in the soldier-producing aphid Pemphigus spyrothecae (Hemiptera: Aphididae). Mol. Ecol. 11: 1525-1531
  • Burg, T.M., Lomax, J., Almond, R., Brooke, M. deL. & Amos, W. (2003). Unravelling dispersal patterns in an expanding population of a highly mobile seabird, the northern fulmar. Proc. Roy. Soc. Lond. B. 270: 979-984
  • Gaggioitti, O.E., Brooks, S.P., Amos, W. & Harwood, J.H. (2003). Combining demongraphic, environmental and genetic data to test hypotheses about colonisation events in metapopulations. Mol. Ecol.13: 811-825
  • Madden, J., Lowe, T., Fuller, H., Coe, R., Dasmahapatra, K., Amos, W., & Dury, F. 2004. Neighbouring male spotted bowerbirds are not related, but do maraud each other. Anim. Behav. 68: 551-558
  • Braisher, T.L., Gemmell, N.J., Grenfell, B.T. & Amos, W. (2004). Host isolation and patterns of genetic variability in trichostrongylid nematode populations. Int. J. Parasitol. 34: 1197-1204
  • Hoffman, J.I. & Amos, W. (2005). Microsatellite genotyping errors: detection approaches, common sources and consequences for paternal exclusion. Mol. Ecol. 14: 599-612
  • Seddon, N., Amos, W., Adcock, G., Johnson, P., Kraaijeveld, K., Kraaijeveld-Smit, F., Lee, W., Senapathi, G.D., Tobias, J. & Mulder, R.A. (2005). Mating system, philopatry and patterns of kinship of kinship in the co-operatively breeding subdesert mesite Monias benschi. Mol. Ecol. 14: 3573-3583
  • Tan, S., Laughlin, S.B. & Amos, W. (2005). Captivity selects for smaller eyes. Curr. Biol. 15: R540-R542
  • Temple, H.J., Hoffman, J.I. & Amos, W. (2006). Dispersal, philopatry and inter-group relatedness: fine-scale genetic structure in the white-breasted thrasher Ramphocinclus brachyurus. Mol. Ecol. 15: 3449-3458
  • Amos, W., Hoffman, J.I., Frodsham, A., Zhang, L., Best, S. & Hill, A.V.S. (2006). Automated binning of microsatellite alleles: problems and solutions. Mol. Ecol. Notes 7: 10-14
  • Amos, W. (2006). The hidden value of missing data. Mol Biol. Evol. 23: 1995-1996
  • Amos, W. (2009). Sexual selection does not influence minisatellite mutation rate. BMC Evol. Biol. 9: 5
  • Temple, H.J., Hoffman, J.I. & Amos, W.  2009. Group structure, mating system and extra-group paternity in the co-operatively breeding whilte-breasted thrasher Rhamphocinclus brachyurus. Ibis151: 99-11
  • Parkes, K.A., Amos, W., Moore, N.W., Hoffman, J.I. & Moore, J. 2009. Population structure and speciation in the dragonfly Sympetrum striolatum/nigrescens: an analysis using AFLP markers. Eur. J. Entomol. 106: 179-184
  • Zieritz, A., Hoffman, J.I., Amos, W. & Aldridge, D.C. 2010. Phenotypic plasticity and genetic isolation-by-distance in the freshwater mussel Unio pictorum (Mollusca: Unionoida) Evol. Ecol. 24: 923-938
  • Munro, K., Hoffman, J.I., Amos, W. & Kilner, R.M.  2010.  Extreme promiscuity in the monomorphic, socially monogamous grey fantail Rhipidura albiscapa: female-choice or male bet-hedging? Ibis 152: 378-385
  • Brooke, M. de L., Welbergen, J.A., Mainwaring, M.M., van der Velde, M., Harts, A.M.F., Komdeur, J. & Amos, W.  2010.  Widespread autosome – sex chromosome fusions preserve genetic variability in an endangered larks J. Mol. Evol. 70: 242-246
  • Restif, O. & Amos, W.  2010.  The evolution of sex-specific immune defences. Proc. Roy. Soc. B. 277: 2247-2255

  • Nichols, H.J., Amos, W., Cant, M.A., Bell, M.B.V., Hodge, S.J.  2010. Top males gain high reproductive success by guarding more successful females in a cooperatively breeding mongoose Anim. Behav. 80: 649-657

  • Amos, W., Hoffman, J.I. & Discoll, E.E. 2010. Candidate genes versus genome-wide associations: which are better for detecting genetic susceptibility to infectious disease? Proc. Roy. Soc. B. (in press)
  • Skidmore, R., Leach, C., Hoffman, J.I., Amos, W. & Aldridge, D.C.  2010.  Conservation genetics of the endangered depressed river mussel, Pseudanodonta complanata, using Amplified Fragment Length Polymorphism (AFLP) markers.  Aquatic Cons. 20: 560-567
  • Discoll, E.E., Hoffman, J.I., Green, L.E., Medley, G.F. & Amos, W.  2011. Genetic factors that influence susceptibility to bovine tuberculosis in the British cattle herd identified by a candidate locus approach. PLoS ONE  (in press)

 

Computer Programs

1. FlexiBin This macro provides an aid to allele binning of microsatellite alleles, given a file of estimated fragment lengths such as is generated by an automated sequencer. For more information, see Amos, Hoffman et al. 2006. Mol. Ecol. Notes .

FlexiBinV2.xls
FlexiBin.doc

2. NewPatXL This macro conducts paternity and maternity analysis, allowing mismatches between parent and offspring and assessing significance using exhaustive randomisations. See Worthington Wilmer, J, Allen, P.J., Pomeroy, P.P.,Twiss, S.D. & Amos, W. 1999.

NewPatXL.xls
NewPatXL.doc

3. IRmacroN3
This macro calculates a number of different measures of heterozygosity for use in the analysis of heterozygosity-fitness calculations. These include IR, standardised heterozygosity and mean d-squared. It also estimates allele frequencies, null allele frequencies and checks for geneotyping errors due to miscalling of adjacent allele heterozygotes as homozygotes and vice versa. See Amos, W., Worthington Wilmer, J. et al 2001 (Proc. Roy. Soc. Lond. B)

IRmacroN4.xls
IRmacroN4.doc

4. DadShareV4 This macro estimates the level of shared paternity / maternity among groups of offspring where one or both parents are missing. It also determines the extent to which groups of offspring are compatible with a single parent / pair of parents.

DadShareV4.xls
DadShareV4.doc

5. GroupRelate This macro determines the extent to which individuals within a group are more related to each other than expected by chance, both overall and within and between the sexes. As elsewhere, significance is determined using extensive randomisations. For an example of use, see Valsecchi, E., Hale, P. Corkeron, P. & Amos, W. 2002. above.

GroupRelate.xls
GroupRelate.doc

6. FAFLP This program accepts AFLP data and estimates the inbreeding coefficient, F, for each individual, using an iterative process to circumvent the problem that estimates of band frequencies depend on the number of inbred individuals in the population. The citation for this program is: Dasmahapatra, K.K., Lacy, R.C. & Amos, W. 2008. Estimating levels of inbreeding using AFLP markers. Heredity 100: 286-295.

FAFLPcalc.xls
FAFLPcalc.doc

7. GEPHAST is an Excel macro that tests for single locus genotype-phenotype associations.  It represents an extension of the the general heterozygosity-fitness correlation test but operates on each locus separately.  The method is described in Amos, W. & Acevedo-Whitehouse, K. A. 2009 A new test for genotype - fitness associations reveals a single microsatellite allele that strongly predicts the nature of tuberculosis infections in wild boar. Mol. Ecol. Res. 9, 1102-1111.

GEPHAST.xls
GEPHAST.doc

 

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Computer Programs
Marine Mammal Genetics
Microsatellite Evolution
Human Population Genetics
Heterozygosity and Fitness
Miscellaneous publications

Microsatellite banding pattern