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Hybridization inference using PhyloNetA data set of 4,000 random (every fourth) GFs, that are putatively in linkage equilibrium, was created to calculate rooted ML trees with RAxML as described earlier. The trees were pruned to contain one individual of each ursine species plus the ABC- brown bear to reduce computational complexity of the ML analyses. Maximum likelihood networks in a coalescent framework, thus incorporating ILS and gene flow, were inferred using PhyloNet32,64 allowing 0, 1 and 2 reticulations in 50 runs and returning the five best networks.Estimation of heterozygosity, past effective population size and divergence timesIn order to calculate the amount of heterozygous sites as well as their distribution in all the bear genomes, their genomes were fragmented into 10 Mb regions using custom Perl scripts. The number of heterozygous sites was counted using a custom Perl script and plotted as distributions using R. The pairwise sequentially Markovian coalescent (PSMC)34 analysis assessed past changes in effective population size over time. We used default parameters and 100 bootstrap replicates assuming a generation time for brown and polar bears of ten years, and six years for the other bear species for the PSMC analysis. We selected a mutation rate of 1 × 10−8 changes/site/generation for all species. These parameters were used in previous brown and polar bear analyses10 and enable comparability between the studies. A generation time of six years has been shown for the American black bear65 and was deemed realistic for the other relatively small-bodied bears. The mutation rate is close to a pedigree-based mutation rate of 1.1 × 10−8 changes/site/generation in humans66 that is considered to be typical for mammals. We also estimated the divergence time for all the bear species (Supplementary methods).
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Felis (all other ‘small’ catsHowever, the classification of the Felidae family is difficult, in part because of the difficulty in distinguishing species by their phenotype and morphology – they all look remarkably similar and, for example, it is extremely difficult for even trained experts to differentiate the skull of a lion from that of a tiger. More recent genetic investigations have suggested eight distinct clusterings or lineages within the Felidae family which could therefore form the basis of their reclassification in the future.Common featuresAll cats have evolved as predatory hunting mammals with particularly keen senses of hearing, sight and smell. Anatomical characteristics such as the rounded head and skeletal structure suggest that all the 37 recognised species within the Felidae family evolved from a common ancestor, probably living in Asia around 10-12 million years ago. There has been a rapid expansion and diversity of the Felidae family during the past 10 to 11 million years and by 3 million years ago there was a wide variety of cats populating all regions of the earth except the Arctic, Antarctic and Australia. The rise and fall of sea levels over many millennia helped both to create conditions where Felidae species could migrate and occupy other geographical locations (when sea levels were low) and isolate the development of species (when sea levels were high). The widespread migration of ancestral cats was probably made easier by their natural behaviour to disperse and seek their own territory, and also the need to follow the prey species they hunted on.
