Comparative landscape genetics of two river frog species occurring at different elevations on Mount Kilimanjaro

Molecular Ecology

Volumn 23, Issue 20, 2014, Pages 4989-5002

  Zancolli, Giulia ^a,b   Rödel, Mark Oliver ^c,d   Steffan Dewenter, Ingolf ^a   Storfer, Andrew ^b,e  

^a UNIVERSITY OF WÜRZBURG   (Germany)

^b WASHINGTON STATE UNIVERSITY   (United States)

^c LEIBNIZ INSTITUTE FOR EVOLUTION AND BIODIVERSITY SCIENCE   (Germany)

^d BERLIN BRANDENBURG INSTITUTE OF ADVANCED BIODIVERSITY RESEARCH BBIB   (Germany)

^e BANGOR UNIVERSITY   (United Kingdom)

Author keywords

amphibians; amplified fragment length polymorphism; anthropogenic disturbance; climate change; gene flow; tropical mountains

Indexed keywords

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ANIMAL; BIOLOGICAL MODEL; CLASSIFICATION; DNA BARCODING; ECOSYSTEM; GENE FLOW; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; POPULATION DYNAMICS; POPULATION GENETICS; RANIDAE; RIVER; TANZANIA;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; ANIMALS; DNA BARCODING, TAXONOMIC; ECOSYSTEM; GENE FLOW; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; MODELS, GENETIC; POPULATION DYNAMICS; RANIDAE; RIVERS; TANZANIA;

EID: 84907893122     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12921     Document Type: Article

References (87)

1. Allendorf FW, Luikart GH, Aitken SN, (2013) Conservation and the Genetics of Populations, 2nd edn. Wiley-Blackwell, West Sussex.
2. Anderson EC, Thompson EA, (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics, 160, 1217-1229.
3. Barej MF, Rödel MO, Loader SP, et al,. (2014) Light shines through the spindrift-Phylogeny of African torrent frogs (Amphibia, Anura, Petropedetidae). Molecular Phylogenetics and Evolution, 71, 261-273.
4. Berthier K, Galan M, Foltête JC, Charbonnel N, Cosson JF, (2005) Genetic structure of the cyclic fossorial water vole (Arvicola terrestris): landscape and demographic influences. Molecular Ecology, 14, 2861-2871.
5. Bonin A, Ehrich D, Manel S, (2007) Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionists. Molecular Ecology, 16, 3737-3758.
6. Castillo JA, Epps CW, Davis AR, Cushman SA, (2014) Landscape effects on gene flow for a climate-sensitive montane species, the American pika. Molecular Ecology, 23, 843-856.
7. Channing A, (2004) Afrana angolensis (Bocage, 1866). In: Atlas and Red Data Book of the Frogs of South Africa, Lesotho and Swaziland (eds, Minter LR, Burger M, Harrison JA, Braack HH, Bishop PJ, Kloepfer D,), pp. 270-271. Smithsonian Institution, Washington, District of Columbia.
8. Channing A, Howell KM, (2006) Amphibians of East Africa. Cornell University Press, New York City, New York.
9. Clarke KR, Ainsworth M, (1993) A method of linking multivariate community structure to environmental variables. Marine Ecology Progress Series, 92, 205-219.
10. Clarke RT, Rothery P, Raybould AF, (2002) Confidence limits for regression relationships between distance matrices: estimating gene flow with distance. Journal of Agricultural Biological and Environmental Statistics, 7, 361-372.
11. Coulon A, Guillot G, Cosson JF, (2006) Genetic structure is influenced by landscape features: empirical evidence from a roe deer population. Molecular Ecology, 15, 1669-1679.
12. Dobzhansky TG, (1937) Genetics and the Origin of Species. Columbia University Press, New York City, New York.
13. Dubey S, Shine R, (2010) Restricted dispersal and genetic diversity in populations of an endangered montane lizard (Eulamprus leuraensis, Scincidae). Molecular Ecology, 19, 886-897.
14. Eterovick PC, Yazbeck GM, Dergam JA, Kalapothakis E, (2009) Small scale population structure in the treefrog Bokermannohyla saxicola (Bokermann, 1964) (Anura, Hylidae). South American Journal of Herpetology, 4, 235-244.
15. Evanno G, Regnaut S, Goudet J, (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14, 2611-2620.
16. Excoffier L, Smouse PE, Quattro JM, (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes-application to human mitochondrial-DNA restriction data. Genetics, 131, 479-491.
17. Falush D, Stephens M, Pritchard JK, (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes, 7, 574-578.
18. Forero-Medina G, Terborgh J, Socolar SJ, Pimm SL, (2011) Elevational ranges of birds on a tropical montane gradient lag behind warming temperatures. PLoS ONE, 6, e28535.
19. Funk WC, Blouin MS, Corn PS, et al,. (2005) Population structure of Columbia spotted frogs (Rana luteiventris) is strongly affected by the landscape. Molecular Ecology, 14, 483-496.
20. Gessler PE, Moore ID, McKenzie NJ, Ryan PJ, (1995) Soil-landscape modelling and spatial prediction of soil attributes. International Journal of Geographical Information Systems, 9, 421-432.
21. Giordano AR, Ridenhour BJ, Storfer A, (2007) The influence of altitude and topography on genetic structure in the long-toed salamander (Ambystoma macrodactylum). Molecular Ecology, 16, 1625-1637.
22. Gosner KL, (1960) A simplified table for staging anuran embryos and larvae with notes on identification. Herpetologica, 16, 183-190.
23. Guarnizo CE, Cannatella DC, (2013) Genetic divergence within frog species is greater in topographically more complex regions. Journal of Zoological Systematics and Evolutionary Research, 51, 333-340.
24. Guarnizo CE, Cannatella DC, (2014) Geographic determinants of gene flow in two sister species of tropical andean frogs. Journal of Heredity, 105, 216-225.
25. Gurka MJ, (2006) Selecting the best linear mixed model under REML. The American Statistician, 60, 19-26.
26. Hemp A, (2006) Continuum or zonation? Altitudinal gradients in the forest vegetation of Mt. Kilimanjaro. Plant Ecology, 184, 27-42.
27. Hirao AS, Kudo G, (2004) Landscape genetics of alpine snowbed-plants: comparisons along geographic and snowmelt gradients. Heredity, 93, 290-298.
28. Holderegger R, Wagner HH, (2008) Landscape genetics. BioScience, 58, 199-207.
29. Hubisz M, Falush D, Stephens M, Pritchard JK, (2009) Inferring weak population structure with the assistance of sample group information. Molecular Ecology Resources, 9, 1322-1332.
30. Huff DR, Peakall R, Smouse PE, (1993) RAPD variation within and among natural populations of outcrossing buffalograss Buchloe dactyloides (Nutt) Engelm. Theoretical and Applied Genetics, 86, 927-934.
31. Kershenbaum A, Blank L, Sinai I, Merilä J, Blaustein L, Templeton AR, (2014) Landscape influences on dispersal behaviour: a theoretical model and empirical test using the fire salamander, Salamandra infraimmaculata. Oecologia, 175, 509-520.
32. Kimble SJA, Rhodes OE Jr, Williams RN, (2014) Unexpectedly low rangewide population structure of the imperiled eastern box turtle Terrapene c. Carolina. PLoS ONE, 9, e92274.
33. Konvicka M, Maradova M, Benes J, Fric Z, Kepka P, (2003) Uphill shifts in distribution of butterflies in the Czech Republic: effects of changing climate detected on a regional scale. Global Ecology and Biogeography, 12, 403-410.
34. La Sorte FA, Jetz W, (2010) Projected range contractions of montane biodiversity under global warming. Proceedings of the Royal Society London Series B: Biological Sciences, 277, 3401-3410.
35. Lambrechts C, Woodley B, Hemp A, Hemp C, Nnyiti P, (2002) Aerial Survey of the Threats to Mt. Kilimanjaro Forests. UNDP, Dar es Salaam, Tanzania.
36. Larkin MA, Blackshields G, Brown NP, et al,. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
37. Lötters S, Drewes R, Pickersgill M, (2004) Amietia wittei. 2013 IUCN Red List of Threatened Species. Version 2013.2. Available at: www.iucnredlist.org.
38. Lynch M, Milligan BG, (1994) Analysis of population genetic structure with RAPD markers. Molecular Ecology, 3, 91-99.
39. Lynn SG, Lindle C, (2002) The effect of anthropogenic habitat modification on habitat use by Afrana angolensis along the Dodwe River, Tanzania. African Journal of Herpetology, 51, 69-73.
40. Manel S, Holderegger R, (2013) Ten years of landscape genetics. Trends in Ecology and Evolution, 28, 614-621.
41. Manel S, Schwartz MK, Luikart G, Taberlet P, (2003) Landscape genetics: combining landscape ecology and population genetics. Trends in Ecology and Evolution, 18, 189-197.
42. Measey GJ, Galbusera P, Breyne P, Matthysen E, (2007) Gene flow in a direct-developing, leaf litter frog between isolated mountains in the Taita Hills, Kenya. Conservation Genetics, 8, 1177-1188.
43. Monsen KJ, Blouin MS, (2004) Extreme isolation by distance in a montane frog Rana cascadae. Conservation Genetics, 5, 827-835.
44. Murphy MA, Dezzani R, Pilliod DS, Storfer A, (2010) Landscape genetics of high mountain frog metapopulations. Molecular Ecology, 19, 3634-3649.
45. Nosil P, Vines TH, Funk DJ, (2005) Perspective: reproductive isolation caused by natural selection against immigrants from divergent habitats. Evolution, 59, 705-719.
46. Oksanen J, Blanchet FG, Kindt R, et al,. (2010) vegan: community ecology package version 2.0. Available at: http://cran.r-project.org
47. Orelien JG, Edwards LJ, (2008) Fixed-effect variable selection in linear mixed models using statistics. Computational Statistics & Data Analysis, 52, 1896-1907.
48. Parmesan C, (1996) Climate and species' range. Nature, 382, 765-766.
49. Parmesan C, (2006) Ecological and evolutionary responses to recent climate change. Annual Review of Ecology, Evolution, and Systematics, 37, 637-669.
50. Pauli H, Gottfried M, Grabherr G, (1996) Effects of climate change on mountain ecosystems-upward shifting of alpine plants. World Resource Review, 8, 382-390.
51. Peakall R, Smouse PE, (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics, 28, 2537-2539.
52. Peaty D, (2012) Kilimanjaro tourism and what it means for local porters and for the local environment. Journal of Ritsumeikan Social Sciences and Humanities, 4, 1-11.
53. Pérez-Espona S, Pérez-Barberia FJ, McLeod JE, Jiggins CD, Gordon IJ, Pemberton JM, (2008) Landscape features affect gene flow of Scottish Highland red deer (Cervus elaphus). Molecular Ecology, 17, 981-996.
54. Poynton J, Channing A, Howell K, Largen M, Drewes R, Lötters S, (2004) Amietia angolensis. 2013 IUCN Red List of Threatened Species. Version 2013.2. Available at: www.iucnredlist.org.
55. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
56. Pritchard JK, Wen X, Falush D, (2010) Documentation for structure software: Version 2.3.
57. R Development Core Team (2012) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. Available at: http://www.R-project.org/.
58. Radespiel U, Rakotondravony R, Chikhi L, (2008) Natural and anthropogenic determinants of genetic structure in the largest remaining population of the endangered golden-brown mouse lemur, Microcebus ravelobensis. American Journal of Primatology, 70, 860-870.
59. Raxworthy CJ, Pearson RG, Rabibisoa N, et al,. (2008) Extinction vulnerability of tropical montane endemism from warming and upslope displacement: a preliminary appraisal for the highest massif in Madagascar. Global Change Biology, 14, 1703-1720.
60. Richardson JL, (2012) Divergent landscape effects on population connectivity in two co-occurring amphibian species. Molecular Ecology, 21, 4437-4451.
61. Ricketts TH, Dinerstein E, Boucher T, et al,. (2005) Pinpointing and preventing imminent extinctions. Proceedings of the National Academy of Sciences USA, 102, 18497-18501.
62. Riley SJ, DeGloria SD, Elliot R, (1999) A terrain ruggedness index that quantifies topographic heterogeneity. Intermountain Journal of Sciences, 5, 23-27.
63. Savage WK, Fremier AK, Shaffer HB, (2010) Landscape genetics of alpine Sierra Nevada salamanders reveal extreme population subdivision in space and time. Molecular Ecology, 19, 3301-3314.
64. Slatkin M, (2005) Seeing ghosts: the effect of unsampled populations on migration rates estimated for sampled populations. Molecular Ecology, 14, 67-73.
65. Smouse PE, Long JC, Sokal RR, (1986) Multiple-regression and correlation extensions of the Mantel test of matrix correspondence. Systematic Zoology, 35, 627-632.
66. Spear SF, Storfer A, (2008) Landscape genetic structure of coastal tailed frogs (Ascaphus truei) in protected vs. managed forests. Molecular Ecology, 17, 4642-4656.
67. Spear SF, Storfer A, (2010) Anthropogenic and natural disturbance lead to differing patterns of gene flow in the Rocky Mountain tailed frog, Ascaphus montanus. Biological Conservation, 143, 778-786.
68. Spear SF, Peterson CR, Matocq MD, Storfer A, (2005) Landscape genetics of the blotched tiger salamander (Ambystoma tigrinum melanostictum). Molecular Ecology, 14, 2553-2564.
69. Stevens VM, Verkenne C, Vandewoestijne S, Wesselingh RA, Baguette M, (2006) Gene flow and functional connectivity in the natterjack toad. Molecular Ecology, 15, 2333-2344.
70. Storfer A, Murphy MA, Evans JS, et al,. (2007) Putting the 'landscape' in landscape genetics. Heredity, 98, 128-142.
71. Storfer A, Murphy MA, Spear SF, Holderegger R, Waits LP, (2010) Landscape genetics: where are we now? Molecular Ecology, 19, 3496-3514.
72. Tallmon DA, Funk WC, Dunlap WW, Allendorf FW, (2000) Genetic differentiation among long-toed salamander (Ambystoma macrodactylum) populations. Copeia, 2000, 27-35.
73. Tamura K, Peterson D, Peterson N, et al,. (2011) Mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731-2739.
74. Trumbo DR, Spear SF, Baumsteiger J, Storfer A, (2013) Rangewide landscape genetics of an endemic Pacific northwestern salamander. Molecular Ecology, 22, 1250-1266.
75. Urban MC, Tewksbury JJ, Sheldon KS, (2012) On a collision course: competition and dispersal differences create no-analogue communities and cause extinctions during climate change. Proceedings of the Royal Society London Series B: Biological Sciences, 279, 2072-2080.
76. Van Strien MJ, Keller D, Holderegger R, (2012) A new analytical approach to landscape genetic modelling: least-cost transect analysis and linear mixed models. Molecular Ecology, 21, 4010-4023.
77. Vekemans X, Beauwens T, Lemaire M, Roldán-Ruiz I, (2002) Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Molecular Ecology, 11, 139-151.
78. Velo-Antõn G, Parra JL, Parra-Olea G, Zamudio KR, (2013) Tracking climate change in a dispersal-limited species: reduced spatial and genetic connectivity in a montane salamander. Molecular Ecology, 22, 3261-3278.
79. Verbeke G, Molenberghs G, (2000) Linear Mixed Models for Longitudinal Data. Springer, New York City, New York.
80. Vos P, Hogers R, Bleeker M, et al,. (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research, 23, 4407-4414.
81. Whitlock R, Hipperson H, Mannarelli M, Butlin RK, Burke T, (2008) An objective, rapid and reproducible method for scoring AFLP peak-height data that minimizes genotyping error. Molecular Ecology Resources, 8, 725-735.
82. Wright S, (1942) Isolation by distance. Genetics, 28, 114-138.
83. Yang RC, (2004) A likelihood-based approach to estimating and testing for isolation by distance. Evolution, 58, 1839-1845.
84. Zancolli G, Steffan-Dewenter I, Rödel MO, (2014a) Amphibian diversity on the roof of Africa: unveiling the effects of habitat degradation, altitude and biogeography. Diversity and Distributions, 20, 297-308.
85. Zancolli G, Rödel M, Steffan-Dewenter I, Storfer A, (2014b) Data from: comparative landscape genetics of two river frog species occurring at different elevations on Mount Kilimanjaro. Dryad Digital Repository. doi: 10.51061/dryad.9pb01.
86. Zhao S, Dai Q, Fu J, (2009) Do rivers function as genetic barriers for the plateau wood frog at high elevations? Journal of Zoology, 279, 270-276.
87. Zhivotovsky LA, (1999) Estimating population structure in diploids with multilocus dominant DNA markers. Molecular Ecology, 8, 907-913.