@article{fdi:010060838,
  title = {{N}on-invasive ancient {DNA} protocol for fluid-preserved specimens and phylogenetic systematics of the genus {O}restias ({T}eleostei : {C}yprinodontidae)},
  author = {{G}arrigos, {Y}. {E}. and {H}ugueny, {B}ernard and {K}oerner, {K}. and {I}banez, {C}. and {B}onillo, {C}. and {P}ruvost, {P}. and {C}ausse, {R}. and {C}ruaud, {C}. and {G}aubert, {P}hilippe},
  editor = {},
  language = {{ENG}},
  abstract = {{S}pecimens stored in museum collections represent a crucial source of morphological and genetic information, notably for taxonomically problematic groups and extinct taxa. {A}lthough fluid-preserved specimens of groups such as teleosts may constitute an almost infinite source of {DNA}, few ancient {DNA} protocols have been applied to such material. {I}n this study, we describe a non-invasive {G}uanidine-based ({G}u{SCN}) ancient {DNA} extraction protocol adapted to fluid-preserved specimens that we use to re-assess the systematics of the genus {O}restias ({C}yprinodontidae: {T}eleostei). {T}he latter regroups pupfishes endemic to the inter-{A}ndean basin that have been considered as a 'species flock', and for which the morphology-based taxonomic delimitations have been hotly debated. {W}e extracted {DNA} from the type specimens of {O}restias kept at the {M}useum {N}ational d'{H}istoire {N}aturelle of {P}aris, {F}rance, including the extinct species {O}. cuvieri. {W}e then built the first molecular (control region [{CR}] and rhodopsin [{RH}]) phylogeny including historical and recently collected representatives of all the {O}restias complexes as recognized by {P}arenti (1984a): agassizii, cuvieri, gilsoni and mulleri. {O}ur ancient {DNA} extraction protocol was validated after {PCR} amplification through an approach based on fragment-by-fragment chimera detection. {A}fter optimization, we were able to amplify < 200 bp fragments from both mitochondrial and nuclear {DNA} ({CR} and {RH}, respectively) from probably formalin-fixed type specimens bathed entirely in the extraction fluid. {M}ost of the individuals exhibited few modifications of their external structures after {G}u{SCN} bath. {O}ur approach combining type material and 'fresh' specimens allowed us to taxonomically delineate four clades recovered from the well-resolved {CR} tree into four redefined complexes: agassizii (sensu stricto, i.e. excluding luteus-like species), luteus, cuvieri and gilsoni. {T}he mulleri complex is polyphyletic. {O}ur phylogenetic analyses based on both mitochondrial and nuclear {DNA} revealed a main, deep dichotomy within the genus {O}restias, separating the agassizii complex from a clade grouped under shallow dichotomies as (luteus, (cuvieri, gilsoni)). {T}his 'deep and shallow' diversification pattern could fit within a scenario of ancient divergence between the agassizii complex and the rest of {O}restias, followed by a recent diversification or adaptive radiation within each complex during the {P}leistocene, in- and outside the {L}ake {T}iticaca. {W}e could not recover the reciprocal monophyly of any of the 15 species or morphotypes that were considered in our analyses, possibly due to incomplete lineage sorting and/or hybridization events. {A}s a consequence, our results starkly question the delineation of a series of diagnostic characters listed in the literature for {O}restias. {A}lthough not included in our phylogenetic analysis, the syntype of {O}. jussiei could not be assigned to the agassizii complex as newly defined. {T}he {CR} sequence of the extinct {O}. cuvieri was recovered within the cuvieri clade (same haplotype as one representative of {O}. pentlandii), so the mt{DNA} of the former species might still be represented in the wild.},
  keywords = {{A}ncient {DNA} ; ethanol-fixed specimen ; formalin-fixed specimen ; inter-{A}ndean basin ; museum collections ; phylogeny ; pupfishes ; species ; flock ; species complex ; {ANDES}},
  booktitle = {},
  journal = {{Z}ootaxa},
  volume = {3640},
  numero = {3},
  pages = {373--394},
  ISSN = {1175-5326},
  year = {2013},
  URL = {https://www.documentation.ird.fr/hor/fdi:010060838},
}