Ten slotte hebben we een puma 36 reeks analyses uitgevoerd om de demografische geschiedenis van poema's te onderzoeken.We hebben neutraliteitstests uitgevoerd (Tajima's D, Fu & Li 'D * en F *, Fu's F's) met DnaSP, evenals een analyse van de verkeerde combinatie (Rogers en Harpending, 1992; Schneider and Excoffier, 1999) met Arlequin.
Daarnaast gebruikten we het programma Beast 1.6.1 (Drummond en Rambaut, 2007) om schattingen van coalescentie-tijden en demografie uit het verleden uit te voeren. We definieerden het beste model puma cali sneakers van nucleotidesubstitutie voor onze dataset, namelijk HKY (Hasegawa et al. , 1985) G-model, gebruikmakend van het Akaike Information Criterion (AIC, Akaike, 1974) geïmplementeerd in jModelTest puma witte sneaker 0.1 (Posada, 2008). Onze eerste set Beast-runs was gericht op het schatten van de moleculaire kloksnelheid voor ons segment in poema-afstammingslijnen.
De BSP-analyses werden alleen uitgevoerd voor sets (i) en (ii), omdat hun grotere steekproefomvang robuustere demografische gevolgtrekkingen mogelijk maakte De MCMC-parameters waren hetzelfde als in de eerste set Beast-analyses.
Geografische verdeling van de puma vikky stacked hier geanalyseerde Puma-concolormonsters Blauwe lijnen geven drie grote rivieren aan De verschillende kleuren geven de zeven groepen aan die met de AMOVA zijn geïdentificeerd (zie tekst en tabel 3 voor details): Noord-Centraal-Amerika Noord-Amerika (NCA NA, in lichtroze ), Zuid-Centraal-Amerika (SCA, in donkerroze), Noord-Zuid-Amerika (NSA, in donkergroen), Centraal-Noordoost-Zuid-Amerika (CNESA, in mediumgroen), Oost-Zuid-Amerika (ESA, in lichtgroen), puma 44 Centraal-Zuid-Zuid-Amerika (CSSA, in lichtblauw) en Zuidwest-Zuid-Amerika (SWSA, in paars).
Toen de P. yagouaroundi-sequenties werden gebruikt als outgroups in het netwerk (Figuur 2A), werden ze door 85 mutatiestappen verbonden met puma haplotype H01, wat deze positie voor de puma-mtDNA-wortel ondersteunde.
Haplotype H01 wordt gevonden in centraal Zuid-Amerika (Paraguay, evenals de Braziliaanse staten MS, SP en MG), en verschilt met minstens zes mutatiestappen van de belangrijkste haplotypes in Noord- en Midden-Amerika. Toen de M. trumani-sequentie in de netwerk (Figuur 2B), werd de lengte van de sequentie-uitlijning teruggebracht tot 286 bp om overeen te komen met het segment dat beschikbaar is voor deze outgroup.
ÿþThe puma is an iconic new balance 992 predator that ranges throughout the Americas, occupying diverse habitats. Previous phylogeographic analyses have revealed that it exhibits moderate levels of genetic structure across its range, with few of the classically recognized subspecies being supported as distinct demographic units. Moreover, most of the species' molecular diversity was found to be in South America.
Within the mtDNA, the NADH dehydrogenase subunit 5 ( ND5 ) new balance 990 grey gene has been successfully used in phylogenetic and phylogeographic studies of felids and other carnivores ( e.g. Culver et al. , 2000 ; new balance 624 Trinca et al. , 2012 ).
In a previous study focusing on pumas ( Culver et al. , 2000 ), three mtDNA segments were employed ( ND5 , 16S and ATP8 ). Of these, ND5 showed the highest polymorphic content in this species, based on new balance 410 a segment spanning 318 bp. A new primer set for this gene was designed specifically for carnivores ( Trigo et al. , 2008 ), amplifying a longer fragment ( ca. 750 bp) and exhibiting successful amplification new balance 247 mens across several families ( e.g. Felidae, Mustelidae, Mephitidae, Procyonidae [unpublished data]).
Given that the geographic sampling of South American pumas was limited in that first study, we aimed here to expand the representation of the various regions of this sub-continent, so as to allow refined inferences of population structure, maternal gene flow and demographic history.
In addition to expanding the geographic coverage of South American regions to refine inferences on patterns of matrilineal subdivision, we have performed novel analyses on puma demographic history, which revealed consistent evidence of a recent population expansion in South America, prior to re-colonization of North America.
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