Landscape-level comparison of genetic diversity and differentiation in a small mammal inhabiting different fragmented landscapes of the Brazilian Atlantic Forest

Conservation Genetics

Volumn 14, Issue 2, 2013, Pages 355-367

  Balkenhol, Niko ^a,b   Pardini, Renata ^c   Cornelius, Cintia ^c,d   Fernandes, Fabiano ^a,c   Sommer, Simone ^a  

^a LEIBNIZ INSTITUTE FOR ZOO AND WILDLIFE RESEARCH   (Germany)

^b UNIVERSITY OF GÖTTINGEN   (Germany)

^c UNIVERSITY OF SÃO PAULO   (Brazil)

^d FEDERAL UNIVERSITY OF AMAZONAS   (Brazil)

Author keywords

Landscape connectivity; Landscape genetics; Marmosops incanus; Marsupial; Meta population; Model selection; Patch metrics

Indexed keywords

BIODIVERSITY; CONNECTIVITY; CONSERVATION GENETICS; ECOLOGICAL MODELING; GENE FLOW; GENETIC DIFFERENTIATION; GENETIC VARIATION; HABITAT FRAGMENTATION; HABITAT LOSS; LANDSCAPE ECOLOGY; MARSUPIAL; METAPOPULATION; PATCHINESS;

ATLANTIC FOREST; BRAZIL;

MAMMALIA; MARMOSOPS INCANUS; METATHERIA;

EID: 84875751269     PISSN: 15660621     EISSN: 15729737     Source Type: Journal    
DOI: 10.1007/s10592-013-0454-2     Document Type: Article

References (58)

1. Akaike H (1973) Information theory as an extension of the maximum likelihood principle. Second International symposium on Information Theory Akademiai Kiado, Budapest, pp 267-281.
2. Andrén H (1994) Effects of habitat fragmentation on birds and mammals in landscapes with different proportions of suitable habitat: a review. Oikos 71: 355-366.
3. Bailie J, Hilton-Taylor C, Stuart S (2004) IUCN Red List of threatened species. IUCN Publications Sercives Unit, Cambridge.
4. Burnham K, Anderson D (2002) Model selection and multimodel inference: a practical information-theoretic approach. Springer, New York.
5. Calabrese JM, Fagan WF (2004) A comparison-shopper's guide to connectivity metrics. Front Ecol Environ 2: 529-536.
6. Crawford NG (2010) SMOGD: software for the measurement of genetic diversity. Mol Ecol Resour 10: 556-557.
7. Cushman SA, Schwartz MK, Hayden J, McKelvey K (2006) Gene flow in complex landscapes: testing multiple hypotheses with causal modeling. Am Nat 168: 486-499.
8. Dias IMG, Amato G, Carvalho MRS, Cunha HM, Paglia AP, Desalle R, Fonseca CG (2008) Characterization of eight microsatellite loci in the woolly mouse opossum, Micoureus paraguayanus, isolated from Micoureus demerarae. Mol Ecol Resour 8: 345-347.
9. Dieringer D, Schlötterer C (2003) Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Mol Ecol Notes 3: 167-169.
10. Fahrig L (2002) Effect of habitat fragmentation on the extinction threshold: a synthesis. Ecol Appl 12: 346-353.
11. Fahrig L (2003) Effects of habitat fragmentation on biodiversity. Ann Rev Ecol Syst 34: 487-515.
12. Frankham R (2005) Genetics and extinction. Biol Conserv 126: 131-140.
13. Gerlach G, Jueterbock A, Kraemer P, Depperman J, Harmand P (2010) Calculations of population differentiation based on GST and D: forget GST but not all of statistics! Mol Ecol 19: 3845-3852.
14. Goslee SC, Urban DL (2007) The ecodist package for dissimilarity-based analysis of ecological data. J Stat Softw 22: 1-19.
15. Gotelli NJ, Colwell RK (2001) Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecol Lett 4: 379-391.
16. Gouin N, Westenberger SJ, Mahaney SM, Samollow PB (2005) Isolation and characterization of polymorphic microsatellite markers in the gray, short-tailed opossum (Monodelphis domestica). Mol Ecol Notes 5: 87-89.
17. Grivet D, Sork VL, Westfall RD, Davis FW (2008) Conserving the evolutionary potential of California valley oak (Quercus lobata Née): a multivariate genetic approach to conservation planning. Mol Ecol 17: 139-156.
18. Gustafson EJ, Parker GR (1994) Using an index of habitat patch proximity for landscape design. Landsc Urban Plan 29: 117-130.
19. Hanski I (1994) A practical model of metapopulation dynamics. J Anim Ecol 63: 151-162.
20. Hanski I (2011) Habitat loss, the dynamics of biodiversity, and a perspective on conservation. Ambio 40: 248-255.
21. Hedrick PW (2005) A standardized genetic differentiation measure. Evolution 59: 1633-1638.
22. Heller R, Siegesmund HR (2009) Relationship between three measures of genetic differentiation GST, DEST and G'ST: how wrong have we been? Mol Ecol 18: 2080-2083.
23. Hughes RA, Inouye BD, Johnson MTJ, Underwood N, Vellend M (2008) Ecological consequences of genetic diversity. Ecol Lett 11: 609-623.
24. Jenkins D, Carey M, Czerniewska J, Fletcher J, Hether T, Jones A, Knight S, Knox J et al (2010) A meta-analysis of isolation by distance: relic or reference standard for landscape genetics? Ecography 33: 315-320.
25. Jost L (2008) Gst and its relatives do not measure differentiation. Mol Ecol 17: 4015-4026.
26. Jousset A, Schmid B, Scheu S, Eisenhauer N (2011) Genotypic richness and dissimilarity opposingly affect ecosystem functioning. Ecol Lett 14: 537-545.
27. Kalinowski ST (2005) HP-RARE 1. 0: a computer program for performing rarefaction on measures of allelic richness. Mol Ecol Notes 5: 187-189.
28. Keyghobadi N (2007) The genetic implications of habitat fragmentation for animals. Can J Zool 85: 1049-1064.
29. Keyghobadi N, Roland J, Matter SF, Strobeck C (2005) Among- and within-patch components of genetic diversity respond at different rates to habitat fragmentation: an empirical demonstration. Proc R Soc B 272: 553-560.
30. Kindlmann P, Burel F (2008) Connectivity measures: a review. Land Ecol 23: 879-890.
31. Lange R, Durka W, Holzhauer SIJ, Wolters V, Dietköter T (2010) Differential threshold effects of habitat fragmentation on gene flow in two widespread species of bush crickets. Mol Ecol 19: 4936-4948.
32. Lavergne A, Douady C, Catzeflis FM (1999) Isolation and characterization of microsatellite loci in Didelphis marsupialis (Marsupialia: Didelphidae). Mol Ecol 8: 517-518.
33. Lindenmayer D, Hobbs R, Montague-Drake R, Alexandra J, Burgman M, Cale P, Calhoun A et al (2008) A checklist for ecological management of landscapes for conservation. Ecol Lett 11: 78-91.
34. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27: 209-220.
35. Meirmans PG, Hedrick PW (2011) Assessing population structure: FST and related measures. Mol Ecol Resour 11: 5-18.
36. Moilanen A, Hanski I (2001) On the use of connectivity measures in spatial ecology. Oikos 95: 235-260.
37. Moilanen A, Nieminen M (2002) Simple connectivity measures in spatial ecology. Ecology 84: 1131-1145.
38. Nei M (1978) Estimation of average heterozygosity and genetic distance from a number of individuals. Genetics 89: 538-590.
39. Noss RF (2006) Principles in conservation biology. Sinauer Associates, Inc, Sunderland.
40. Oosterhout CV, Hutchinson WF, Wills DPM, Shipley P (2004) Micro-Checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4: 535-538.
41. Pardini R, de Bueno AA, Gardner TA, Prado PI, Metzger JP (2010) Beyond the fragmentation threshold hypothesis: regime shifts in biodiversity across fragmented landscapes. PLoS ONE 5: e13666.
42. Püttker T, de Bueno AA, dos Santos de Barros C, Sommer S, Pardini R (2011) Immigration rates in fragmented landscapes-empirical evidence for the importance of habitat amount for species persistence. PLoS ONE 6: e27963.
43. R Development Core Team (2010) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna.
44. Radford JQ, Bennett AF, Cheers GJ (2005) Landscape-level thresholds of habitat cover for woodland-dependent birds. Biol Conserv 124: 317-337.
45. Raymond M, Rousset F (1995) GENEPOP (version 1. 2): population genetics software for exact tests and ecumenicism. J Hered 86: 248-249.
46. Robinson SJ, Samuel MD, Lopez DL, Shelton P (2012) The walk is never random: subtle landscape effects shape gene flow in a continuous white-tailed deer population in the Midwestern United States. Mol Ecol 21: 4190-4205.
47. Sommer S, Schmidt A, Fernandes F, Püttker T, Pardini R (2009) Development and characterization of microsatellite loci in the marsupial Marmosops incanus (Lund, 1840) of the Brazilian Atlantic rain forest using genome screening and restriction ligation. Added to Permanent Genetic Resources Database (1 May 2009-31 July 2009). Mol Ecol Resour 9: 1460-1466.
48. Swift TL, Hannon SJ (2010) Critical thresholds associated with habitat loss: a review of the concepts, evidence, and applications. Biol Rev 85: 35-53.
49. Taylor PD, Fahrig L, With KA (2006) Landscape connectivity: a return to the basics. In: Crooks KR, Sanayan M (eds) Connectivity conservation. Cambridge University Press, Cambridge, pp 29-43.
50. Templeton AR (2006) Population genetics and microevolutionary theory. Wiley, Hoboken.
51. Tischendorf L, Fahrig L (2000) How should we measure landscape connectivity? Land Ecol 15: 633-641.
52. Tischendorf L, Fahrig L (2001) On the use of connectivity measures in spatial ecology: a reply. Oikos 95: 152-155.
53. Varvio S, Chakraborty R, Nei M (1986) Genetic variation in subdivided populations and conservation genetics. Heredity 57: 189-198.
54. Wagenmakers EJ, Farrell S (2004) AIC model selection using Akaike weights. Psychon Bull Rev 11: 192-196.
55. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
56. With KA, King AW (1999a) Extinction thresholds for species in fractal landscapes. Conserv Biol 13: 314-326.
57. With KA, King AW (1999b) Dispersal success on fractal landscapes: a consequence of lacunarity thresholds. Land Ecol 14: 73-82.
58. Zuckerberg B, Porter WF (2010) Thresholds in the long-term responses of breeding birds to forest cover and fragmentation. Biol Conserv 143: 952-962.