Genetic variation over 10 000 years in Ctenomys: Comparative phylochronology provides a temporal perspective on rarity, environmental change and demography

Molecular Ecology

Volumn 20, Issue 22, 2011, Pages 4592-4605

  Chan, Yvonne L ^a   Hadly, Elizabeth A ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

Ancient DNA; Ctenomys haigi; Ctenomys sociabilis; Serial coalescent; Subterranean rodents; Temporal variation

Indexed keywords

ANIMAL; ARTICLE; BIOLOGICAL MODEL; COMPARATIVE STUDY; DNA SEQUENCE; ECOSYSTEM; ENVIRONMENT; FOSSIL; GENETIC VARIABILITY; GENETICS; HAPLOTYPE; PHYLOGENY; POPULATION GENETICS; RODENT;

ANIMALS; ECOSYSTEM; ENVIRONMENT; FOSSILS; GENETIC VARIATION; GENETICS, POPULATION; HAPLOTYPES; MODELS, GENETIC; PHYLOGENY; RODENTIA; SEQUENCE ANALYSIS, DNA;

EID: 80054119460     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2011.05295.x     Document Type: Article

References (77)

1. Anderson CNK, Ramakrishnan U, Chan YL, Hadly EA (2005) Serial SimCoal: a population genetic model for data from multiple populations and points in time. Bioinformatics, 21, 1733-1734.
2. Arnaud JF, Laval G (2004) Stability of genetic structure and effective population size inferred from temporal changes of microsatellite DNA polymorphisms in the land snail Helix aspersa (Gastropoda: Helicidae). Biological Journal of the Linnean Society, 82, 89-102.
3. Barnes I, Matheus P, Shapiro B, Jensen D, Cooper A (2002) Dynamics of pleistocene population extinctions in Beringian Brown Bears. Science, 295, 2267-2270.
4. Belle E, Ramakrishnan U, Mountain JL, Barbujani G (2006) Serial coalescent simulations suggest a weak genealogical relationship between Etruscans and modern Tuscans. Proceedings of the National Academy of Sciences, 103, 8012.
5. Bidau C, Lessa E, Ojeda R (2008a) Ctenomys haigi. In: IUCN 2011. IUCN Red List of Threatened Species. Version 2011.1. Available at: http://www.iucnredlist.org. Downloaded on 11 October 2011.
6. Bidau C, Lessa E, Ojeda R (2008b) Ctenomys sociabilis. In: IUCN 2011. IUCN Red List of Threatened Species. Version 2011.1. Available at: http://www.iucnredlist.org. Downloaded on 27 September 2011.
7. Brouat C, Chevallier H, Meusnier S, Noblecourt T, Rasplus J-Y (2004) Specialization and habitat: spatial and environmental effects on abundance and genetic diversity of forest generalist and specialist Carabus species. Molecular Ecology, 13, 1815-1826.
8. Campos PF, Willerslev E, Sher A et al. (2010) Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. Proceedings of the National Academy of Sciences, 107, 5675.
9. Castillo AH, Cortinas MN, Lessa EP (2005) Rapid diversification of South American tuco-tucos (Ctenomys; Rodentia, Ctenomyidae): contrasting mitochondrial and nuclea intron sequences. Journal of Mammalogy, 86, 170-179.
10. Chan YL, Lacey EA, Pearson OP, Hadly EA (2005) Ancient DNA reveals Holocene loss of genetic diversity in a South American rodent. Biology Letters, 1, 423-426.
11. Chan YL, Anderson CNK, Hadly EA (2006) Bayesian estimation of the timing and severity of a population bottleneck from ancient DNA. Public Library of Science Genetics, 2, e59.
12. Chesser RK, Baker RJ (1996) Effective sizes and dynamics of uniparentally and diparentally inherited genes. Genetics, 144, 1225-1235.
13. Clement M, Posada D, Crandall K (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657-1660.
14. Cooper A, Poinar HN (2000) Ancient DNA: do it right or not at all. Science, 289, 1139.
15. D’Elia G, Lessa EP, Cooke JA (1998) Geographic structure, gene flow, and maintenance of melanism in Ctenomys rionegrensis (Rodentia: Octodontida). Zeitschrift Fur Saugetierkunde, 63, 285-296.
16. Depaulis F, Orlando L, Hänni C (2009) Using classical population genetics tools with heterochroneous data: time matters! PLoS ONE, 4, e5541.
17. Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
18. Drummond AJ, Pybus OG, Rambaut A, Forsberg R, Rodrigo AG (2003) Measurably evolving populations. Trends in Ecology & Evolution, 18, 481-488.
19. Endler JA (1986) Natural Selection in the Wild. Princeton University Press, Princeton, New Jersey.
20. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47-50.
21. Faulkes CG, Abbott DH, O’Brien HP et al. (1997) Micro- and macrogeographical genetic structure of colonies of naked mole-rats Heterocephalus glaber. Molecular Ecology, 6, 615-628.
22. Frankham R, Ballou JD, Briscoe DA (2002) Introduction to Conservation Genetics. Cambridge University Press, Cambridge.
23. Gallardo MH, Köhler N, Araneda C (1995) Bottleneck effects in local populations of fossorial Ctenomys (Rodentia, Ctenomyidae) affected by vulcanism. Heredity, 74, 638-646.
24. Gilbert MTP, Drautz DI, Lesk AM et al. (2008) Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proceedings of the National Academy of Sciences, 105, 8327-8332.
25. Gimenez MD, Mirol PM, Bidau CJ, Searle JB (2002) Molecular analysis of populations of Ctenomys (Caviomorpha, Rodentia) with high karyotypic variability. Cytogenetic and Genome Research, 96, 130-136.
26. Hadly EA, Kohn MH, Leonard JA, Wayne RK (1998) A genetic record of population isolation in pocket gophers during Holocene climatic change. Proceedings of the National Academy of Sciences of the United States of America, 95, 6893-6896.
27. Hadly EA, Van Tuinen M, Chan Y, Heiman K (2003) Ancient DNA evidence of prolonged population persistence with negligible genetic diversity in an endemic tuco-tuco (Ctenomys sociabilis). Journal of Mammalogy, 84, 403-417.
28. Hadly EA, Ramakrishnan U, Chan YL et al. (2004) Genetic response to climatic change: insights from ancient DNA and phylochronology. Public Library of Science Biology, 2, 1600-1609.
29. Haldane JBSA (1930) Mathematical theory of natural and artificial selection. Proceedings of the Cambridge Philosophical Society, 26, 220-230.
30. Hardy C, Callou C, Vigne JD et al. (1995) Rabbit mitochondrial DNA diversity from prehistoric to modern times. Journal of Molecular Evolution, 40, 227-237.
31. Hasegawa M, Kishino K, Yano T (1985) Dating the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 22, 160-174.
32. Heusser CJ (1983) Palinologia de la secuencia sedimentaria de la Cueva Traful I (Provincia del Neuquen, Repulica Argentina). Praehistoria, 1, 206-210.
33. Ho SYW, Heupink TH, Rambaut A, Shapiro B (2007) Bayesian estimation of sequence damage in ancient DNA. Molecular Biology and Evolution, 24, 1416.
34. Hoelzer GA, Wallman J, Melnick DJ (1998) The effects of social structure, geographical structure, and population size on the evolution of mitochondrial DNA: II. Molecular clocks and the lineage sorting period. Journal of Molecular Evolution, 47, 21-31.
35. Hoffman EA, Schueler FW, Blouin MS (2004) Effective population sizes and temporal stability of genetic structure in Rana pipiens, the northern leopard frog. Evolution, 58, 2536-2545.
36. Hofreiter M, Jaenicke V, Serre D, von Haeseler A, Paabo S (2001) DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Research, 29, 4793-4799.
37. Hofreiter M, Serre D, Rohland N et al. (2004) Lack of phylogeography in European mammals before the last glaciation. Proceedings of the National Academy of Sciences of the United States of America, 101, 12963-12968.
38. Inchausti P, Halley J (2003) On the relation between temporal variability and persistence time in animal populations. Journal of Animal Ecology, 72, 899-908.
39. Kelley ST, Farrell BD, Mitton JB (2000) Effects of specialization on genetic differentiation in sister species of bark beetles. Heredity, 84, 218-227.
40. Kumar S, Tamura K, Nei M (2004) MEGA 3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics, 5, 150-163.
41. Lacey EA (2000) Spatial and social systems of subterranean rodents. In: Life Underground: The Biology of Subterranean Rodents (eds Lacey EA, Patton JL, Cameron GN), pp. 257-296. University of Chicago Press, Chicago, Illinois.
42. Lacey EA (2001) Microsatellite variation in solitary and social tuco-tucos: molecular properties and population dynamics. Heredity, 86, 628-637.
43. Lacey EA (2004) Sociality reduces individual direct fitness in a communally breeding rodent, the colonial tuco-tuco (Ctenomys sociabilis). Behavioural Ecology and Sociobiology, 56, 449-457.
44. Lacey EA, Wieczorek JR (2003) Ecology of sociality in rodents: a ctenomyid perspective. Journal of Mammalogy, 84, 1198-1211.
45. Lacey EA, Wieczorek JR (2004) Kinship in colonial tuco-tucos: evidence from group composition and population structure. Behavioural Ecology, 15, 988-996.
46. Lacey EA, Braude SH, Wieczorek JR (1997) Burrow sharing by colonial tuco-tucos (Ctenomys sociabilis). Journal of Mammalogy, 78, 556-562.
47. Lacey EA, Braude SH, Wieczorek JR (1998) Solitary burrow use by adult Patagonian tuco-tucos (Ctenomys haigi). Journal of Mammalogy, 79, 986-991.
48. Lande R (1988) Genetics and demography in biological conservation. Science, 241, 1455.
49. Leonard JA (2008) Ancient DNA applications for wildlife conservation. Molecular Ecology, 17, 4186-4196.
50. Lessios HA, Weinberg JR, Starczak VR (1994) Temporal variation in populations of the marine isopod Excirolana: how stable are gene frequencies and morphology? Evolution, 48, 549-563.
51. Markgraf V (1983) Late and postglacial vegetational and paleoclimatic changes in subantarctic, temperate, and arid environments in Argentina. Palynology, 7, 43-70.
52. McKinney ML (1997) How do rare species avoid extinction? A paleontological view. In: The Biology of Rarity (eds Kunin WE, Gaston KJ), pp. 110-129. Chapman & Hall, London.
53. Montero EAC, Silveira MJ (1983) Radiocarbon chronology of a tephra layer in Rio Traful Valley, Province of Neuquen, Argentina. Quaternary of South America and Antarctic Peninsula, 1, 135-150.
54. Montero EAC, Curzio DE, Silveira MJ (1983) La estratigrafia de la cueva Traful I (Provincia del Neuquen). Praehistoria, 1, 9-160.
55. Nielsen EE, Hansen MM, Loeschcke V (1999a) Analysis of DNA from old scale samples: technical aspects, applications and perspectives for conservation. Hereditas, 130, 265-276.
56. Nielsen EE, Hansen MM, Loeschcke V (1999b) Genetic variation in time and space: microsatellite analysis of extinct and extant populations of Atlantic salmon. Evolution, 53, 261-268.
57. O’Keefe K, Ramakrishnan U, van Tuinen M et al. (2009) Source-sink dynamics structure a common montane mammal. Molecular Ecology, 18, 4775-4789.
58. Pearson OP, Pearson AK (1981) La fauna mamiferos pequenos cerca de Cueva Traful, Argentina: pasado y presente. Praehistoria, 1, 211-224.
59. Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics, 14, 817-818.
60. Poulsen NA, Nielsen EE, Schierup MH, Loeschcke V, Grønkjaer P (2005) Long-term stability and effective population size in North Sea and Baltic Sea cod (Gadus morhua). Molecular Ecology, 15, 321-331.
61. Prost S, Anderson CNK (2011) TempNet: a method to display statistical parsimony networks for heterochronous DNA sequence data. Methods in Ecology and Evolution, DOI: 10.1111/j.2041-210X.2011.00129.x.
62. Prost S, Smirnov N, Fedorov VB et al. (2010) Influence of climate warming on arctic mammals? New insights from ancient DNA studies of the collared lemming Dicrostonyx torquatus PLoS ONE, 5, e10447.
63. Purvis A, Gittleman JL, Cowlishaw G, Mace GM (2000) Predicting extinction risk in declining species. Proceedings of the Royal Society B: Biological Sciences, 267, 1947-1952.
64. Rabinowitz D (1981) Seven forms of rarity. In: The Biological Aspects of Rare Plant Conservation (ed. Synge H), pp. 205-217. John Wiley & Sons, Chichester, UK.
65. Ramakrishnan U, Hadly EA (2009) Using phylochronology to reveal cryptic population histories: review and synthesis of 29 ancient DNA studies. Molecular Ecology, 18, 1310-1330.
66. Raymond M, Rousset F (1995) An exact test for population differentiation. Evolution, 49, 1280-1283.
67. Shapiro B, Drummond AJ, Rambaut A et al. (2004) Rise and fall of the Beringian steppe bison. Science, 306, 1561.
68. Sokal RR, Rohlf FJ (1995) Biometry, 3rd edn. W. H. Freeman and Company, New York, NY.
69. Steinberg EK, Patton JL (2000) Genetic structure and the geography of speciation in subterranean rodents: opportunities and constraints for evolutionary diversification. In: Life Underground: The Biology of Subterranean Rodents (eds Lacey EA, Patton JL, Cameron GN), pp. 301-331. University of Chicago Press, Chicago, IL.
70. Storz JF (1999) Genetic consequences of mammalian social structure. Journal of Mammalogy, 80, 553-569.
71. Stuiver M, Reimer PJ (1993) Extended 14C database and revised CALIB radiocarbon calibration program. Radiocarbon, 35, 215-230.
72. Tessier N, Bernatchez L (1999) Stability of population structure and genetic diversity across generations assessed by microsatellites among sympatrix populations of landlocked Atlantic salmon (Salmo salar L.). Molecular Ecology, 8, 169-179.
73. Thomas WK (1990) Spatial and temporal continuity of kangaroo rat populations shown by sequencing mitochondrial DNA from museum specimens. Journal of Molecular Evolution, 31, 101-112.
74. Valdiosera CE, García-Garitagoitia JL, Garcia N et al. (2008) Surprising migration and population size dynamics in ancient Iberian brown bears (Ursus arctos). Proceedings of the National Academy of Sciences, 105, 5123.
75. Villarosa G, Outes V, Hajduk A et al. (2006) Explosive volcanism during the Holocene in the Upper Limay River Basin: the effects of ashfalls on human societies, Northern Patagonia, Argentina. Quaternary International, 158, 44-57.
76. Whitlock MC (2005) Combining probability from independent tests: the weighted Z-method is superior to Fisher’s approach. Journal of Evolutionary Biology, 18, 1368-1373.
77. Woods CA, Kilpatrick CW (2005) Infraorder Hystricognathi. In: Mammal Species of the World, A Taxonomic and Geographic Reference (eds Wilson DE, Reeder DM), pp. 1538-1600. Johns Hopkids University Press, Baltimore, MD.