Current Research Projects
Conservation Genetics
Evolutionary Genetics of Vector and Parasite Populations
Invasion Biology
Development of Molecular Markers for Novel Organisms
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Before 2001
After 2001
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Dr. Adalgisa Caccone
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YIBS-Molecular Systemtics Conservation Genetics Laboratory
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DNA Analysis Facility on Science Hill
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Yale Department of EEB

Galapagos Tortoises Papers (1999-2008):

Reviews/book chapters:
Powell, JR. and A. Caccone 2006. A quick guide to Galapagos tortoises. Current Biology, 16: R144-145.

Powell, JR. and A. Caccone. 2008. CSI tortoise: unraveling the mystery of mysteries. Galapagos News. 26:8-9.

Parent, C, E. A. CACCONE and K. Petren. 2008. Colonization and diversification of Galápagos terrestrial fauna: a phylogenetic and biogeographical synthesis.

Transactions of the Royal Society of London, series B,  Evolution on Pacific islands: Darwin's Legacy” S. Trewick and R. Cowie (eds.).

Ciofi, C., A. CACCONE, LB. Beheregaray, MC. Milinkovitch, M. Russello and JR. Powell. “Genetics and conservation on islands: the Galápagos giant tortoise as a case study” in “Population Genetics for Animal Conservation” (Bertorelle, Bruford, Chemini, Hauffe, and Vernesi, eds). Cambridge University Press (In press).


Caccone A, JP. Gibbs, V. Ketmaier, El. Suatoni, JR. Powell. 1999. Origin and evolutionary relationships of giant Gálapagos tortoises. Proceedings National Academy of Sciences  (PNAS) USA, 96: 13223-13228.

Caccone, A., G. Gentile, JP. Gibbs, TH. Fritts, HL. Snell, and JR. Powell. 2002. Phylogeography and history of Giant Galapagos Tortoises. Evolution 56, 2052-2066.

Ciofi, C., M. Milinkovitch, JP. Gibbs, A. Caccone, JR. Powell. 2002. Nuclear DNA microsatellite analysis of genetic divergence among and within island populations of giant Galápagos tortoises. Molecular Ecology 11:2265-2283.

Beherengary, LB, C. Ciofi, A. Caccone, J. P. Gibbs, and J. R. Powell. 2003. Genetic divergence, phylogeography and conservation units of Giant tortoises from Santa Cruz and Pinzon, Galápagos islands. Conservation Genetics, 4:31-46

Beheregaray, LB, C. Ciofi, Geist, D., Gibbs, J, Powell, J.R, and A. Caccone. 2003. Genes record a prehistorical volcano eruption in the Galápagos. Science, 302: 75.

Burns, CT, C. Ciofi, LB. Beheregaray, TH. Fritts, JP. Gibbs., C. Marquez, MC. Milinkovitch, JR. Powell and A. Caccone. 2003. The origin of captive Galápagos tortoises based on DNA analysis: Implications for the management of natural populations. Animal Conservation, 6(4): 329-37.

Beheregaray, LB, JP. Gibbs, N. Havill, TH. Fritts, JR. Powell, and A. Caccone. 2004. Giant tortoises are not so slow: Rapid diversification by recent volcanism in Galápagos. PNAS 101: 6514-6519.

Milinkovitch, M., D. Monteyne, JP. Gibbs, TH. Fritts, W. Tapia, HL. Snell, R. Tiedemann, A. Caccone and J.R. Powell. 2003. Genetic analysis of a successful repatriation program: Giant Galápagos tortoises. Proc. Royal. Soc. London B, 271:341-345).

Caccone, A, G. Gentile, C. Burns, E. Sezzi, W. Bergman, and JR. Powell. 2004. Extreme difference in rate of mitochondrial and nuclear DNA evolution in a large ectotherm, Galápagos tortoises. Molecular Phylogenetics and Evolution 31: 794-798.

Russello, M, S. Glaberman, C. Marquez, JR. Powell, and A. Caccone. 2005. A novel taxon of Giant tortoises in conservation peril. Biology Letters 1(3):287-290.

Ciofi, C., KA. Wilson, LB. Beheregeray, C. Marquez, JP. Gibbs, W. Tapia, HL. Snell, A. Caccone and JR. Powell Phylogeographic history and gene flow among giant Galápagos tortoises on southern Isabela island. Genetics 172: 1727-1744.

Milinkovitch, MC., D. Monteyne, M. Russello, JP. Gibbs, HL. Snell, W. Tapia, C. Marquez, A. Caccone and J. R. Powelll. 2007. Giant Galápagos Tortoises: Molecular Genetic Analysis Reveals Contamination in a Repatriation Program of an Endangered Taxon” BMC Ecology 2007, 7:2 (15 February 2007) .

Russello, M, LB. Beheregaray, JP. Gibbs, T. Fritts, N. Havill, JR. Powell, and A. Caccone. 2007.  Lonesome George is not alone among Galápagos Tortoises. Current Biology 17: 317-318.

Russello,M.A., C. Hyseni, J. P. Gibbs, S. Cruz, C. Marquez, W. Tapia, P. Velensky, J. R. Powell and A. 2007. Caccone. Lineage identification of Galápagos tortoises in captivity worldwide. Animal Conservation (Published article online: 30-May-2007).

Chiari, Y., B. Wang, H. Rushmeier, A. Caccone. Reconstruction of the 3D carapace shape for morphometric analyses of turtles. Biological Journal of the Linnean Society (in press).

Poulakakis, N., S.Glaberman, M.Russello*, L. B. Beheregaray, C. Ciofi, J. R. Powell, and A. CACCONE. Rediscovery of an extinct species of giant Galápagos tortoise. PNAS (in press).

Marine Iguana Papers

Hanley, T., and A. CACCONE. 2005. Development of primers for the characterization of the mitochondrial control region of Galápagos land and marine iguanas (Conolophus and Amblyrhynchus). Molecular Ecology Notes 5:599-601.

Steinfartz, S., S. Glaberman, D. Lanterbecq, C. Marquez, K. Rassmann, and A. CACCONE. 2007.  Genetic impact of a severe El Niño event on Galápagos marine iguanas. PloS ONE 2: e1285.

Glaberman, S. and A. CACCONE. 2008. Species-specific evolution of class I MHC genes of iguans (Order: Squamata;Subfamily: Iguaninae) Immunogenetics 60.

Glaberman, S., S. Steinfartz, D. Lanterbecq, T. C. Hanley, C. Marquez, H. L. Snell, K. Dion, H. M. Snell, and A. CACCONE. 2008. Mitochondrial control region sequences reveal complex phylogeographic patterns and excessive homoplasy in Galápagos marine iguanas (Amblyrhynchus cristatus). Mol. Ecol. (Submitted)

Glaberman, S., M. A. Moreno, and A. CACCONE. 2008. Patterns of squamate MHC evolution based on class II genes from Galápagos marine iguanas (Amblyrhynchus cristatus). Mol. Biol. And Evol. (submitted).

Aldabra Tortoises papers:

CACCONE, A., G. Amato, O. C. Gratry, J. Behler, J.R. Powell.  1999. A molecular phylogeny of four endangered Madagascar tortoises based on mtDNA sequences.Molecular Phylogenetics and Evolution, 12: 1-9.

Palkovacs, E. , J. Gerlach, and A. CACCONE. 2002. The evolutionary origin of Indian Ocean tortoises (Dypsochelys). Molecular Phylogenetics and Evolution, 24: 216-227.

Palkovacs, E.P., M. Mendez, C. Ciofi, J. Gerlach, and A. CACCONE. Are the native Giant tortoises from the Seychelles really extinct? A genetic perspective based on mtDNA and microsatellite data. Molecular Ecology 12: 1403-1413.

Karanth, P.K., S. Glaberman, E. Palkovacs, A. CACCONE, and A. Yoder. 2005. Seychelles tortoises are they a distinct species? DNA from sub-fossil material sheds lights on this issue. Amphibia and Reptilia, 26: 116-121.

Balmer, O., C. Ciofi, D. A. Galbraith, I. R. Swingland, G. R. Zug  and A. CACCONE. Population genetic structure in Aldabra giant tortoises. Mol. Ecol. (submitted).

Amur Tigers

Russello, MA, E. Gladyshev, D. Miquelle, and A. CACCONE. 2004. Potential genetic consequences of a recent bottleneck in the Amur tiger of the Russian Far East. Conservation Genetics 5:707-713.
Henry, P., D. Miquelle, T. Sugimoto, A. CACCONE, M.A. Russello. Conservation genetics of Amur Tigers(Panthera tigris altaica): population structure in the Russian Far East and representation in captivity. In prep.

Conservation Genetics papers:

Russello M.A., P. Brazaitis, J. Gratten, G.J. Watkins-Colwell, and A. CACCONE. 2006. Molecular assessment of the genetic integrity, distinctiveness and phylogeographic context of the saltwater crocodile (Crocodylus porosus) on Palau. Conservation Genetics, 8: 777-787.

Palkovacs, EP, AJ. Oppenheimer, E. Gladyshev, JE Toepfer, G. Amato, T. Chase, and A. CACCONE 2004. Phylogeography of the Greater Prairie Chicken (Tympanuchus cupido) Including the Extinct Heath Hen: Potential Implications for Conservation and Management. Molecular Ecology 13: 1759-1769.

Anopheles gambiae

Powell, J. R., A. CACCONE, V. Petrarca, A. della Torre, and M. Coluzzi.  1999. Population structure, speciation, and introgression in the Anopheles gambiae complex.  Parassitologia 41:101-113.

Gentile G., M. Slotman, V. Ketmaier, J.R. Powell, and A. CACCONE. 2001. Attempts to molecularly distinguish cryptic taxa in Anopheles gambiae s.s.Insect Molecular Biology 10 (1): 25-32

Gentile, G., A. Della Torre, B. Maegga, J.R. Powell, and A. CACCONE. 2002. Genetic differentiation in the African malaria vector, Anopheles gambiae s.s., and the problem of taxonomic status. Genetics, 161:1561-1578

della Torre, A., C. Costantini, N.J. Besansky, A. CACCONE, V. Petrarca, J.R. Powell, and M. Coluzzi.2002. Speciation Within Anopheles gambiae: The Glass is Half Full. Science 248: 115-117.

Santolamazza F A. della Torre and A. CACCONE. 2004. A new PCR-RFLP method to identify An. arabiensis from An. gambiae and its two molecular forms from DNA templates of poor quality. Am. J. of Trop. Med. and Hyg., 70: 604-606.

Gentile G, Santolamazza F, Fanello C, Petrarca V, CACCONE A, Della Torre A .2004. variation in an intron sequence of the voltage gated sodium channel gene correlates with genetic differentiation between Anopheles gambiae s.s. molecular forms. Insect Mol Biol: 13: 371-377.

Marshall, J. C,, J.R. Powell, and A. CACCONE. 2005. Phylogenetic relationships of five   major malaria (Plasmodium falciparum) vectors within the mosquito subgenus Cellia. Am. J. of Trop. Med and Hyg., 73: 749-752.

Pinto, J.,  A. Lynd, N. Elissa, M.J. Donnelly, C. Costa, G. Gentile, A. CACCONE, and V.E. do Rosário. 2006. Co-occurrence of East and West African kdr mutations suggests high levels of resistance to pyrethroid insecticides in Anopheles gambiae from Libreville, Gabon. Med. and Vet. Entomol, 20:27-32.

Slotman, M. A., M. Mendez, A. dellaTorre, Y. Toure’, G. Dolo, and A. CACCONE. 2006. AFLP analysis indicates genetic differentiation between the Bamako and Savanna chromosomal forms of Anopheles gambiae. Am. J. of Trop. Med and Hyg., 74:641-648.

Schielke, E., C. Costantini, G. Carchini, N'falé Sagnon, J.R.Powell, and A. CACCONE. 2007. Development of a molecular assay to detect predation on Anopheles gambiae complex larval stages. Am J. of Trop. Med and Hyg Sep 2007; 77: 464 - 466.

Slotman, M. A. Parmakelis, J. Marshall, P. Awono-Ambene, C. Antonio-Nkondjio, F. Simard, A. CACCONE, and J.R. Powell. 2007. Adaptive Evolution in the Anti-Malarial Immune Gene LRIM1 in Anopheles arabiensis. PloS One Genetics (August 2007, issue 8, e793).

Moreno M,  P. Salgueiro, J.L. Vicente, J. Cano, P.J. Berzosa, A. De Lucio A, F. Simard, CACCONE A, V.E. Do Rosario, J. Pinto J  and A. Benito. 2007. Genetic population structure of Anopheles gambiae in Equatorial Guinea. Malaria Journal 2007, 6:137 (15 October 2007).

Pinto, J., A. Lynd, J.L. Vicente, F. Santolamazza, N.P. Randle, G. Gentile, M. Moreno, F. Simard, J.D. Charlwood, A. CACCONE, A. della Torre and M. J. Donnelly. 2007. Multiple origin of knockdown resistence in the Afrotropical mosquito vector Anopheles gambiae. Plos ONE 11:e1243.

Parmakelis, A., M. A. Russello, A. CACCONE, C. Brisola Marcondes, J. Costa, O. P. Forattini, M. Sallum, R. C. Wilkerson, and J. R. Powell. 2008.  Historical analysis of a near disaster: anopheles gambiae in Brazil. Am J. of Trop. Med and Hyg., 78 (1): 176-178.

Santolamazza, F., , M. Calzetta, J. Etang2, E. Barrese1, I. Dia, A. CACCONE, M.J. Donnelly, V. Petrarca, F. Simard, J. Pinto, A. della Torre. 2008. Distribution of knock-down resistance mutations in Anopheles gambiae (Diptera: Culicidae) molecular forms in west and central-west Africa. Malaria Journal 2008, 7:74.

Parmakelis, A.,, M.A. Slotman, J.C. Marshall, P.H. Awono-Ambene, C. Antonio-Nkondjio, F. Simard, A. CACCONE, and J.R. Powell . 2008. The molecular evolution of four anti-malarial immune genes in the Anopheles gambiae species complex. BMC Evolutionary Biology 2008, 8:79 (06 Mar 2008).

Oliveira, E., Salgueiro P., Pålsson K., Vicente J.L., Arez A.P., Jaenson T., do Rosário V., CACCONE A., Pinto J. 2008. High Levels of hybridisation between molecular forms of Anopheles gambiae from Guinea Bissau. Submitted. J.of Med. Entomol.(In press).

Marshall, J.C.,, J. Pinto, J. D. Charlwood, G. Gentile, F. Santolamazza, F. Simard, A. della Torre, M. J. Donnelly, and A. CACCONE. 2008. Exploring the origin and degree of genetic isolation of An. gambiae from the islands of São Tomé and Príncipe: implications for testing transgenic-based vector control. Evolutionary Applications (in press).

Aedes aegypti

Slotman, M.A., N. B. Kelly, L. C. Harrington, S. Kitthawee, J. W. Jones, T. W. Scott, A. Caccone, and J.R. Powell. 2006. Polymorphic microsatellites markers for studies of Aedes aegypti (Diptera Culicidae), the vector of dengue and yellow fever. Molecular Ecology Notes, 7: 168-171.



Balmer, O., C. Palma, A. MacLeod, A. CACCONE. 2008. Characterization of di-, tri-, and tetranucleotide microsatellite markers with perfect repeats for Trypanosoma brucei and related species.Molecular Ecology Notes 6:508-510.

Abila, P.A., M. A. Slotman, A. Parmakelis, K. B. Dion, A. S. Robinson, V. B. Muwanika, J. CK Enyaru, L.M. Okedi, S. Aksoy and A. CACCONE. 2008.  High levels of genetic differentiation between Ugandan Glossina fuscipes fuscipes populations separated by Lake Kyoga. Plos Emerging Tropical Diseases . PLoS Neglected Tropical Diseases 2(5): e242 doi:10.1371/journal.pntd.0000242121

Brown, J.E. .K.J. Komatsu1, P.P. Abila, A.S. Robinson, L.M. Okedi, Naomi Dyer, M.J. Donnelly, M.A. Slotman and A. CACCONE. 2008. Polymorphic microsatellite markers for the tsetse fly Glossina fuscipes fuscipes (Diptera: glossinidae), a vector of human African trypanosomiasis. Molecular Ecology Resources (in press).

Invasion Biology

Havill, N.P.,M. E. Montgomery, G.Yu,  S. Shiyake, A. CACCONE. 2006.  Mitochondrial DNA from hemlock woolly adelgids, Adelges tsugae (Hemiptera, Adelgidae), suggests cryptic speciation and pinpoints the source  of introduction to eastern North America. Ann. of the Entomol. Soc. of America, 99(2): 195-203.

Evolutionary and behavioural ecology

Halverson, M.A, D. K. Skelly, and A. CACCONE. 2006. Kin Distribution among wood frog (Rana sylvatica) larvae in the wild. Molecular Ecology 15: 1139-1146.
Jounhyoung Lee, Jonathan Marshall, Oswald J. Schmitz, and A. CACCONE.2006.  Genetic divergence of Connecticut Melanoplus femurrubrum populations. J. of Heredity 97:290-293
Halverson, M.A, D. K. Skelly, and A. CACCONE. 2006.  Inbreeding linked to amphibian survival the wild but not in the laboratory. J. of Heredity 97: 499-507.
Garren, M., S. M.Walsh, A. CACCONE, and N. Knowlton. 2006. Patterns of association between Symbiodinium and members of the Montastraea annularis species complex on spatial scales ranging from within colonies to between geographic regions. Coral Reefs, 25: 503-512
Palkovacs,E.P., K. B. Dion, D. M. Post, and A. CACCONE. 2008. Independent evolution of landlocked alewife populations and rapid, parallel evolution of phenotypic traits. Molecular Ecology, Volume 17: 582-597.

Phylogeography and Phylogenetics

Reviews/Book Chapters

Beheregaray,L. and A. CACCONE. 2007. Cryptic Biodiversity in a Changing World. Invited minireview. J. of Biology, 6:9 (doi:10.I 186/jbiol60). 21 December 2007. Highly Assessed label of BioMed central.

Allegrucci G., A. CACCONE, V. Sbordoni. Cytochrome b sequence divergence in the European Sea Bass (Dicentrarchus labrax) and phylogenetic relationships among some Perciformes species.
              J. of Zool. Syst. and Evol. Res. , 37:149-156.
CACCONE A  and V. Sbordoni.  2001. Molecular biogeography, evolutionary rates, and morphological adaptation to cave life: a case study using Bathysciine beetles and sequence data from the mitochondrial COI gene.Evolution   55(10: 122-130.).
Ketmaier, V., R. Argano, and A. CACCONE. 2003. Phylogeography and molecular rates of subterranean aquatic Stenasellid Isopods with a peri-Tyrrhenian distribution. Molecular Ecology 12: 547-555.
Vicario, S., A. CACCONE, and J. Gauthier. 2003. Xantusiid "Night" lizards: a puzzling phylogenetic problem revisited using likelihood-based Bayesian methods on mtDNA sequences. Molecular Phylogenetics and Evolution, 26: 243-261.
Roth R., C. Dick, M. R. Lemes, C. Navarro, A. CACCONE, and E. Bermingham. 2003. Genetic structure of Mesoamerican populations of Big-leaf mahogany (Swietenia macrophylla) inferred from microsatellite analysis.
            Molecular Ecology, 12: 2885-2894.
Pinou,, D., S. Vicario, M. Mendez, and A. CACCONE. 2004. Relict Snakes of North America and their relationship to the Caenophidia using Likelihood-Based Bayesian Methods on Mitochondrial Sequences. Mol. Phylog. and Evol., 32:563-574.
LeonardJ.A., N. Rohland, S.Glaberman , R. C. Fleischer, S. Pääbo, A. CACCONE and M. Hofreiter.  2005. How a Zebra Lost its Stripes: 20 Years of Ancient DNA and the Origin of the Quagga. Biology Letters 1(3): 291-295.
Ketmaier, V., F. Giusti, A. CACCONE. 2006. Molecular phylogeny and historical biogeography of the land snail genus Solatopupa (Pulmonata) in the peri-Tyrrhenian area.Mol. Phylog. And Evol.,39:439-451.
Poulakakis, N., A. Parmakelis, P. Lymberakis, M. Mylonas, E. Zouros, D. S. Reese, S. Glaberman, A. CACCONE. 2006. Ancient DNA forces reconsideration of evolutionary history of Mediterranean pygmy elephantids. Biology Letters, 2 451-454.
Suatoni, E. S. Vicario, S. Rice, T. Snell, and A. CACCONE. 2006. An analysis of species boundary and biogeographic patterns in the salt water rotifer, Brachionus plicatilis. Mol. Phylogen. and Evol. 41: 86-98.
Steinfartz, S, S. Vicario, J. W. Arntzen and A. CACCONE.2006. A Bayesian approach on molecules, morphology and behavior: reconsidering evolutionary patterns in Triturus newts (Amphibia: Salamandridae)”. J. of Exp. Zoology (Mol.Dev.Evol), 306B: 1-24.
Poulakakis, N., A. Parmakelis, P. Lymberakis, M. Mylonas, E. Zouros, D. S. Reese, S. Glaberman, A. CACCONE. 2006. Reply. It remains a mammoth DNA fragment.         Biology Letters. 3, 60-63.
Gentile, G., C. Vernesi, S. Vicario, E. Pecchioli, G. Bertorelle, A. CACCONE, and V. Sbordoni. 2008. MtDNA variation in roe deer from Italy (Capreolus capreolus): evidence of admixture in one of the last C.c.italicus populations from central-southern Italy. J. of Italian Zoology (in press).