I have a long-standing interest in the use of genetic markers to elucidate population structure and breeding behaviour, originally in marine mammals, coupled with studies on how these markers evolve. Since the 1990's I have developed the idea that heterozygous sites attract additional mutations at and around them, creating a link between evolutionary rate and population size. It was testing this hypothesis that led me to the prediction that mutation rate in humans would have dropped as a result of the large loss of variability that occurred during the out of Africa event, and thence to an alternative model to inter-breeding that could explain why non-Africans are closer to Neanderthals than Africans. Work in this area has pre-occupied me for more than a decade but challenging the idea that many humans carry Neanderthal legacies has proved near-impossible! Below is a document summarising many of my ideas, analyses and reasons why these legacies appear to be near-zero. To make this as self-contained and easy to share as possible, I start with a very brief bio.
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A while back I was invited to present my work on Neanderthal introgression (or lack thereof) via Zoom at UCL. Below is a link to a recording of this seminar where I outline some of the strongest results and why I came into this area of research in the first place.
In addition to the work on the question of Neanderthal introgression, I have two large studies of natural populations. The first is the genetic analysis of mink culled in major project that aims to eradicate this invasive pest from East Anglia and, eventually, from the UK. Mink predation is the major reason behind catastrophic declines in water vole numbers but they also eat kingfishers and pretty much any other species they dispersal patterns and identify kin clusters to inform can catch along the banks of rivers where they live. My work aims to inform trapping strategies. I am also interested in fungi and particularly porcini, Boletus edulis. I have assembled a database of over 4,000 samples, often sampled from under the same trees over periods of up to 15 years. My aim is to understand how this species evolves, including adaptation to its various host trees, dispersal and competition between genets.
Biography
I joined the Department of Zoology in 1996 from the Department of Genetics, Cambridge, where I had been joint head of the Molecular Ecology Research Group with Josephine Pemberton.
Research
Data
Detecting climate-linked selection
Below is the accessory data file for the following paper where we explore a new method for estimating selection in the human genome:
- Raj, S.M., Pagani, L., Gallego Romero, I., Kivisild, T. & Amos, W. 2013. A general linear model-based approach for inferring selection to climate. BMC Genetics
This file contains a list of human genes along with their locations and the strength of evidence we found for links to various climate variables.
Boxer Dog Genetics
Publications
The following are the four publications that I feel are my most important ones to date. All relate to my hypothesis that mutation rates are influenced by heterozygosity. The 2013 paper in particular presents evidence that human mutation rate was reduced as heterozygosity was lost when we moved out of Africa. I hope you find it convincing but if you are not convinced I’d love to hear why not!
Amos W. 2013. Variation in heterozygosity predicts variation in human substitution rates between populations, individuals and genomic regions. PLoS ONE 8(4), e63048.
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.
These are arranged according to the broad areas in which I work.
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. Science 268: 1897-1899.
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
Hoffman, J.I., Amos, W., Tratham, P.N., Forcada, J. 2007. Female fur seals show active choice 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: 3066-3068
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)
de Assunção-Franco, M., Hoffman, J.I., Harwood, J. & Amos, W. 2012. MHC genotype and near-deterministic mortality in grey seals. Sci. Rep. 2: 659
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
Microsatellite Evolution and Heterozygote Instability
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. J. Mol. Biol. 68: 160-170
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.
Varela, M.A. & Amos, W. 2010. Heterogeneous distribution of SNPs in the human genome: microsatellites as predictors of nucleotide diversity and divergence. Genomics 95: 151-159
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
Amos, W. 2013. Variation in heterozygosity predicts variation in human substitution rates between populations, individuals and genomic regions. PLoS ONE 8(4): e63048. doi:10.1371/journal.pone.0063048
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
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. 14:355-362
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. 278: 1587-1594
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., Lindström, 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). Heredity 100: 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
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
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
Bovine tuberculosis
Amos, W., Hoffman, J.I. & Discoll, E.E. 2011. Candidate genes versus genome-wide associations: which are better for detecting genetic susceptibility to infectious disease? Proc. Roy. Soc. B. 278: 1183-1188
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 6: e18806
Amos, W., Brooks-Pollock, E., Blackwell, R., Driscoll, E., Nelson-Flower, M. & Conlan, A.J.K. 2013. Genetic predisposition to pass the standard SICCT test for bovine tuberculosis in British cattle. PLoS ONE 8(3): e58245. doi:10.1371/journal.pone.0058245
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: 99-112
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
Restif, O. & Amos, W. 2010. The evolution of sex-specific immune defences. Proc. Roy. Soc. B. 277: 2247-2255
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)
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
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
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 .
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.
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)
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.
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.
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.
