Dit werd uitgevoerd met het programma Alleles in Space puma fenty creeper (AIS) (Miller, 2005), waarbij het aandeel van verschillen (dwz een p-afstandsequivalent) werd gebruikt om de genetische afstandsmatrix en 10.000 permutaties te genereren om de statistische significantie te beoordelen. We gebruikten ook AIS om voer een ruimtelijke autocorrelatieanalyse uit van de dataset, met behulp van 11 afstandsklassen, gelijkgemaakte steekproefgroottes over klassen en 10.000 permutaties om de significantie te beoordelen.
Daarnaast gebruikten we het programma Beast 1.6.1 (Drummond en Rambaut, 2007) om schattingen van coalescentie-tijden en demografie puma badslippers uit het verleden uit te voeren. We definieerden het beste model van nucleotidesubstitutie voor onze dataset, namelijk HKY (Hasegawa et al. , 1985) G-model, gebruikmakend van het Akaike Information puma for baby Criterion (AIC, Akaike, 1974) geïmplementeerd in jModelTest 0.1 (Posada, 2008). Onze eerste set Beast-runs was gericht op het schatten van de moleculaire kloksnelheid voor ons segment in poema-afstammingslijnen.
We gingen uit van een Bayesiaanse skyline en een strikte moleculaire klok, waarvan de evolutionaire snelheid was gebaseerd op de schatting die was afgeleid van de eerste analyseronde. We puma babys beoordeelden de t MRCA voor vier verschillende monstersets: (i) volledige steekproef; (ii) Zuid Alleen Amerika; (iii) Noord- en Midden-Amerika (NA NCA); en (iv) een subset van 24 NA NCA-monsters die een regionaal endemische subclade vormden in het haplotype-netwerk, wat wijst op autochtone diversificatie (zie Resultaten).
Na verwijdering van opgenomen primersequenties en fragmentranden van lage kwaliteit werden dubbelstrengs sequenties voor een segment van 669 bp van het mtDNA ND5-gen verkregen voor 156 puma california sneakers poema-individuen bemonsterd in Zuid-Amerika, 17 uit Midden-Amerika en 13 uit Noord-Amerika ( Tabel S1, figuur 1).
Er werden matige tot hoge niveaus van haplotype-diversiteit waargenomen, terwijl de nucleotide-diversiteit vrij laag was (tabel 2).
A) Analyse van de volledige dataset (669 bp) De pijl geeft het punt aan waar de outgroep P. yagouaroundi is verbonden B) Analyse van een subset van de nucleotideplaatsen die overlappen met de Miracinonyx trumani-sequentie (286 bp). geef de punten aan waar de outgroup-taxa zich bij het netwerk aansluiten: P. yagouaroundi (in grijs; 32 mutatiestappen vanaf het verbindingspunt) en M. trumani (in zwart; 19 stappen vanaf het verbindingspunt).
The puma ( Puma concolor Linnaeus, 1771) new balance 501 womens is a large felid that ranges throughout the Americas, exhibiting the broadest latitudinal distribution of any terrestrial mammal ( Nowak, 1999 ). Pumas have remarkable dispersal capabilities ( Maehr et al. , 2002 ; Beier et al. , 2003 ) and successfully occupy a diverse array of habitats, illustrating their potential to adapt to the breadth of environmental conditions occurring across the continent, from tropical forests and marshes to dry scrubland and cold Andean or Patagonian biomes ( Redford and Eisenberg, 1992 ; new balance 574 red Nowak, 1999 ). Pumas are solitary and territorial, with large home ranges. Females tend to occupy smaller areas and disperse shorter distances, thus being more philopatric than males ( Logan new balance 993 mens and Sweanor, 2001 ; Maehr et al. , 2002 ).
Overall, the species' ecological flexibility and dispersal capabilities have the potential to induce broad genetic connectivity across large geographic areas, unless historical barriers have limited gene flow among populations.
Four of these subspecies were distributed in South America, indicating that most of the species' historical subdivision occurred in that subcontinent. new balance 1080 mens In addition, the genetic diversity within South America was found to be larger than in Central and North America, suggesting that pumas from the latter subcontinent actually derive from a recent re-colonization event, following extinction in North America in the Late Pleistocene (ca. 10,000 12,000 years ago).
Within the mtDNA, the NADH dehydrogenase subunit 5 ( ND5 ) gene has been successfully used in phylogenetic and phylogeographic studies of felids and other carnivores ( e.g. Culver et al. , 2000 new balance cruz v2 ; Trinca et al. , 2012 ).
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.
To select a marker that would provide suitable information levels, we initially examined the mtDNA fragments used in previous studies, especially those involving Neotropical felids ( e.g. Eizirik et al. , 1998 , 2001 ; Johnson et al. , 1998 , 1999 ; Culver et al. , 2000 ).
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