title: Phylogeography and support vector machine classification of colour variation in panther chameleons.
abstract: Lizards and snakes exhibit colour variation of adaptive value for thermoregulation, camouflage, predator avoidance, sexual selection and speciation. Furcifer pardalis, the panther chameleon, is one of the most spectacular reptilian endemic species in Madagascar, with pronounced sexual dimorphism and exceptionally large intraspecific variation in male coloration. We perform here an integrative analysis of molecular phylogeography and colour variation after collecting high-resolution colour photographs and blood samples from 324 F. pardalis individuals in locations spanning the whole species distribution. First, mitochondrial and nuclear DNA sequence analyses uncover strong genetic structure among geographically restricted haplogroups, revealing limited gene flow among populations. Bayesian coalescent modelling suggests that most of the mitochondrial haplogroups could be considered as separate species. Second, using a supervised multiclass support vector machine approach on five anatomical components, we identify patterns in 3D colour space that efficiently predict assignment of male individuals to mitochondrial haplogroups. We converted the results of this analysis into a simple visual classification key that can assist trade managers to avoid local population overharvesting.
authors.affiliation: Laboratory of Artificial and Natural Evolution (LANE), Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.|Swiss Institute of Bioinformatics, Geneva, Switzerland.
authors.forename: Djordje
authors.initials: D
authors.lastname: Grbic
authors.affiliation: Laboratory of Artificial and Natural Evolution (LANE), Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.
authors.forename: Suzanne V
authors.initials: SV
authors.lastname: Saenko
authors.affiliation: Département de Biologie Animale, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar.|Association Vahatra, Antananarivo, Madagascar.
authors.forename: Toky M
authors.initials: TM
authors.lastname: Randriamoria
authors.affiliation: Laboratory of Artificial and Natural Evolution (LANE), Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.
authors.forename: Adrien
authors.initials: A
authors.lastname: Debry
authors.affiliation: Département de Biologie Animale, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar.|Association Vahatra, Antananarivo, Madagascar.
authors.forename: Achille P
authors.initials: AP
authors.lastname: Raselimanana
authors.affiliation: Laboratory of Artificial and Natural Evolution (LANE), Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.|Swiss Institute of Bioinformatics, Geneva, Switzerland.
authors.forename: Michel C
authors.initials: MC
authors.lastname: Milinkovitch
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D002467:Cell Nucleus / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D005260:Female; D051456:Gene Flow; D005828:Genetics, Population; D008116:Lizards / Q000235:genetics*; D008270:Madagascar; D008297:Male; D008957:Models, Genetic; D008969:Molecular Sequence Data; D058974:Phylogeography; D010858:Pigmentation / Q000235:genetics*; D017422:Sequence Analysis, DNA; D060388:Support Vector Machine
chemical_list: D004272:DNA, Mitochondrial
keywords: Furcifer pardalis; colour patterns; panther chameleon; phylogeography; speciation; supervised learning; support vector machine classification