Estimating divergence times from DNA sequences

The patterns of genetic variation within and among individuals and populations can be used to make inferences about the evolutionary forces that generated those patterns. Numerous population genetic approaches have been developed in order to infer evolutionary history. Here, we present the “Two-Two (TT)” and the “Two-Two-outgroup (TTo)” methods; two closely related approaches for estimating divergence time based in coalescent theory. They rely on sequence data from two haploid genomes (or a single diploid individual) from each of two populations. Under a simple population-divergence model, we derive the probabilities of the possible sample configurations. These probabilities form a set of equations that can be solved to obtain estimates of the model parameters, including population split times, directly from the sequence data. This transparent and computationally efficient approach to infer population divergence time makes it possible to estimate time scaled in generations (assuming a mutation rate), and not as a compound parameter of genetic drift. Using simulations under a range of demographic scenarios, we show that the method is relatively robust to migration and that the TTo method can alleviate biases that can appear from drastic ancestral population size changes. We illustrate the utility of the approaches with some examples, including estimating split times for pairs of human populations as well as providing further evidence for the complex relationship among Neandertals and Denisovans and their ancestors.     

More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure

Here, we report the sequencing and analysis of eight complete mitochondrial genomes of chimpanzees (Pan troglodytes) from each of the three established subspecies (P. t. troglodytes, P. t. schweinfurthii and P. t. verus) and the proposed fourth subspecies (P. t. ellioti). Our population genetic analyses are consistent with neutral patterns of evolution that have been shaped by demography. The high levels of mtDNA diversity in western chimpanzees are unlike those seen at nuclear loci, which may reflect a demographic history of greater female to male effective population sizes possibly owing to the characteristics of the founding population. By using relaxed-clock methods, we have inferred a timetree of chimpanzee species and subspecies. The absolute divergence times vary based on the methods and calibration used, but relative divergence times show extensive uniformity. Overall, mtDNA produces consistently older times than those known from nuclear markers, a discrepancy that is reduced significantly by explicitly accounting for chimpanzee population structures in time estimation. Assuming the human–chimpanzee split to be between 7 and 5 Ma, chimpanzee time estimates are 2.1–1.5, 1.1–0.76 and 0.25–0.18 Ma for the chimpanzee/bonobo, western/(eastern + central) and eastern/central chimpanzee divergences, respectively.     

Phylogeny and divergence times of the Coluteoid clade with special reference to Colutea (Fabaceae) inferred from nrDNA ITS and two cpDNAs,matK and rpl32-trnL(UAG) sequences data

This study reconstructed the phylogeny of the Coluteoid clade using nrDNA ITS and plastid matK and rpl32-trnL_(UAG) sequences data. The analyses resolve a well-supported Coluteoid clade, as sister to Astragalus s.str. + Oxytropis, nested within the larger, strongly supported Astragalean clade. The Coluteoid clade is now composed of 12 genera including Podlechiella, Swainsona, Carmichaelia, Clianthus, Montigena, Phyllolobium, Lessertia, Sutherlandia, Sphaerophysa, Smirnowia, Eremosparton and Colutea. Within this clade, Podlechiella is the first diverging lineage followed by successive subclades of Carmichaelia + Clianthus + Swainsona, Phyllolobium, Lessertia + Sutherlandia, Sphaerophysa + Smirnowia + Eremosparton, and Colutea. We assigned the formal tribal name to this clade and redefined the tribe Coluteae. A diagnostic key to the genera of the tribe is presented. Astragalus cysticalyx and A. sinicus have no relationship with the Coluteoid clade, instead, they are nested in Astragalus s. str. Resolution within Colutea is rather low, but several smaller subclades with low to high supports are found in the genus. None of the large sections in Colutea are monophyletic. Divergence time estimates revealed that the Coluteoid clade originated in the Early Miocene (20.4 Mya). Most of its members were diverged during the Late Miocene to Pliocene. Colutea and Podlechiella form the youngest lineages where the diversification occurred in the Pliocene-Pleistocene.