Martyna Molak

ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis

SUMMARY Relaxed molecular clocks allow the phylogenetic estimation of evolutionary timescales even when substitution rates vary among branches. In analyses of large multigene datasets, it is often appropriate to use multiple relaxed-clock models to accommodate differing patterns of rate variation among genes. We present ClockstaR, a method for selecting the number of relaxed clocks for multigene datasets. AVAILABILITY ClockstaR is freely available for download at http://sydney.edu.au/science/biology/meep/software/.

Phylogenetic Estimation of Timescales Using Ancient DNA: The Effects of Temporal Sampling Scheme and Uncertainty in Sample Ages

In recent years, ancient DNA has increasingly been used for estimating molecular timescales, particularly in studies of substitution rates and demographic histories. Molecular clocks can be calibrated using temporal information from ancient DNA sequences. This information comes from the ages of the ancient samples, which can be estimated by radiocarbon dating the source material or by dating the layers in which the material was deposited. Both methods involve sources of uncertainty. The performance of bayesian phylogenetic inference depends on the information content of the data set, which includes variation in the DNA sequences and the structure of the sample ages. Various sources of estimation error can reduce our ability to estimate rates and timescales accurately and precisely. We investigated the impact of sample-dating uncertainties on the estimation of evolutionary timescale parameters using the software BEAST. Our analyses involved 11 published data sets and focused on estimates of substitution rate and root age. We show that, provided that samples have been accurately dated and have a broad temporal span, it might be unnecessary to account for sample-dating uncertainty in Bayesian phylogenetic analyses of ancient DNA. We also investigated the sample size and temporal span of the ancient DNA sequences needed to estimate phylogenetic timescales reliably. Our results show that the range of sample ages plays a crucial role in determining the quality of the results but that accurate and precise phylogenetic estimates of timescales can be made even with only a few ancient sequences. These findings have important practical consequences for studies of molecular rates, timescales, and population dynamics.

Time‐dependent estimates of molecular evolutionary rates: evidence and causes

We are writing in response to a recent critique by Emerson & Hickerson ( ), who challenge the evidence of a time‐dependent bias in molecular rate estimates. This bias takes the form of a negative relationship between inferred evolutionary rates and the ages of the calibrations on which these estimates are based. Here, we present a summary of the evidence obtained from a broad range of taxa that supports a time‐dependent bias in rate estimates, with a consideration of the potential causes of these observed trends. We also describe recent progress in improving the reliability of evolutionary rate estimation and respond to the concerns raised by Emerson & Hickerson ( ) about the validity of rates estimated from time‐structured sequence data. In doing so, we hope to dispel some misconceptions and to highlight several research directions that will improve our understanding of time‐dependent biases in rate estimates.

Evaluating the Impact of Post-Mortem Damage in Ancient DNA: A Theoretical Approach

The growth of ancient DNA research has offered exceptional opportunities and raised great expectations, but has also presented some considerable challenges. One of the ongoing issues is the impact of post-mortem damage in DNA molecules. Nucleotide alterations and DNA strand breakages lead to a significant decrease in the quantity of DNA molecules of useful length in a sample and to errors in the final DNA sequences obtained. We present a model of age-dependent DNA damage and quantify the influence of that damage on subsequent steps in the sequencing process, including the polymerase chain reaction and cloning. Calculations using our model show that deposition conditions, rather than the age of a sample, have the greatest influence on the level of DNA damage. In turn, this affects the probability of interpreting an erroneous (possessing damage-derived mutations) sequence as being authentic. We also evaluated the effect of post-mortem damage on real data sets using a Bayesian phylogenetic approach. According to our study, damage-derived sequence alterations appear to have little impact on the final DNA sequences. This indicates the effectiveness of current methods for sequence authentication and validation.

Prolonged decay of molecular rate estimates for metazoan mitochondrial DNA

Evolutionary timescales can be estimated from genetic data using the molecular clock, often calibrated by fossil or geological evidence. However, estimates of molecular rates in mitochondrial DNA appear to scale negatively with the age of the clock calibration. Although such a pattern has been observed in a limited range of data sets, it has not been studied on a large scale in metazoans. In addition, there is uncertainty over the temporal extent of the time-dependent pattern in rate estimates. Here we present a meta-analysis of 239 rate estimates from metazoans, representing a range of timescales and taxonomic groups. We found evidence of time-dependent rates in both coding and non-coding mitochondrial markers, in every group of animals that we studied. The negative relationship between the estimated rate and time persisted across a much wider range of calibration times than previously suggested. This indicates that, over long time frames, purifying selection gives way to mutational saturation as the main driver of time-dependent biases in rate estimates. The results of our study stress the importance of accounting for time-dependent biases in estimating mitochondrial rates regardless of the timescale over which they are inferred.

Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon‐date and calibration error into Bayesian phylogenetic analyses of ancient DNA

Studies of DNA from ancient samples provide a valuable opportunity to gain insight into past evolutionary and demographic processes. Bayesian phylogenetic methods can estimate evolutionary rates and timescales from ancient DNA sequences, with the ages of the samples acting as calibrations for the molecular clock. Sample ages are often estimated using radiocarbon dating, but the associated measurement error is rarely taken into account. In addition, the total uncertainty quantified by converting radiocarbon dates to calendar dates is typically ignored. Here, we present a tool for incorporating both of these sources of uncertainty into Bayesian phylogenetic analyses of ancient DNA. This empirical calibrated radiocarbon sampler (ECRS) integrates the age uncertainty for each ancient sequence over the calibrated probability density function estimated for its radiocarbon date and associated error. We use the ECRS to analyse three ancient DNA data sets. Accounting for radiocarbon‐dating and calibration error appeared to have little impact on estimates of evolutionary rates and related parameters for these data sets. However, analyses of other data sets, particularly those with few or only very old radiocarbon dates, might be more sensitive to using artificially precise sample ages and should benefit from use of the ECRS.

Mitogenomic analysis of a 50-generation chicken pedigree reveals a rapid rate of mitochondrial evolution and evidence for paternal mtDNA inheritance

Mitochondrial genomes represent a valuable source of data for evolutionary research, but studies of their short-term evolution have typically been limited to invertebrates, humans and laboratory organisms. Here we present a detailed study of 12 mitochondrial genomes that span a total of 385 transmissions in a well-documented 50-generation pedigree in which two lineages of chickens were selected for low and high juvenile body weight. These data allowed us to test the hypothesis of time-dependent evolutionary rates and the assumption of strict maternal mitochondrial transmission, and to investigate the role of mitochondrial mutations in determining phenotype. The identification of a non-synonymous mutation in ND4L and a synonymous mutation in CYTB, both novel mutations in Gallus, allowed us to estimate a molecular rate of 3.13 × 10−7 mutations/site/year (95% confidence interval 3.75 × 10−8–1.12 × 10−6). This is substantially higher than avian rate estimates based upon fossil calibrations. Ascertaining which of the two novel mutations was present in an additional 49 individuals also revealed an instance of paternal inheritance of mtDNA. Lastly, an association analysis demonstrated that neither of the point mutations was strongly associated with the phenotypic differences between the two selection lines. Together, these observations reveal the highly dynamic nature of mitochondrial evolution over short time periods.

Locals, Resettlers, and Pilgrims: A Genetic Portrait of Three Pre-Columbian Andean Populations

The common practice of resettlement and the development of administrative and ceremonial systems shaped the population landscape of the Andean region under the Inca rule. The area surrounding Coropuna and Solimana volcanoes, in the Arequipa region (Peru), carried a high-density, multiethnic population. We studied the genetic variation among three pre-Columbian populations from three functionally diverse archaeological sites excavated in this region. By analyzing the genetic composition of a large ceremonial center (Acchaymarca), an isolated pastoral settlement (Tompullo 2), and an agricultural settlement characterized by architectural features rare in the region (Puca), we investigated the patterns of population movements and the distribution of genetic diversity. We obtained mitochondrial DNA sequences for 25 individuals and autosomal microsatellite profiles for 20 individuals from Acchaymarca and Puca sites. These were compared with previously published genetic data for Tompullo 2 and other pre-Columbian populations. We found differences among the genetic portraits of the three populations, congruent with the archaeologically described functions and characteristics of the sites. The Acchaymarca population had the highest genetic diversity and possessed the lowest number of unique mtDNA haplotypes. The Tompullo 2 population exhibited the lowest level of genetic diversity. The Puca population was distinct from the other two populations owing to a high frequency of haplogroup A haplotypes, what potentially explains the non-local character of the burial architecture. Our analyses of microsatellite data suggest that gene flow between sites was mostly mediated by females, which is consistent with ethnohistorical knowledge of the social organization of the pre-Columbian communities.

Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans.

Significance The majority of viral genomic sequences available today are fewer than 50 years old. Parvovirus B19 (B19V) is a ubiquitous human pathogen causing fifth disease in children, as well as other conditions. By isolating B19V DNA from human remains between ∼0.5 and 6.9 thousand years old, we show that B19V has been associated with humans for thousands of years, which is significantly longer than previously thought. We also show that the virus has been evolving at a rate an order of magnitude lower than estimated previously. Access to viral sequences isolated from individuals living thousands of years ago greatly improves our understanding of the timescales of virus evolution, spatiotemporal distribution, and their substitution rates, and can uncover genetic diversity that is now extinct. Human parvovirus B19 (B19V) is a ubiquitous human pathogen associated with a number of conditions, such as fifth disease in children and arthritis and arthralgias in adults. B19V is thought to evolve exceptionally rapidly among DNA viruses, with substitution rates previously estimated to be closer to those typical of RNA viruses. On the basis of genetic sequences up to ∼70 years of age, the most recent common ancestor of all B19V has been dated to the early 1800s, and it has been suggested that genotype 1, the most common B19V genotype, only started circulating in the 1960s. Here we present 10 genomes (63.9–99.7% genome coverage) of B19V from dental and skeletal remains of individuals who lived in Eurasia and Greenland from ∼0.5 to ∼6.9 thousand years ago (kya). In a phylogenetic analysis, five of the ancient B19V sequences fall within or basal to the modern genotype 1, and five fall basal to genotype 2, showing a long-term association of B19V with humans. The most recent common ancestor of all B19V is placed ∼12.6 kya, and we find a substitution rate that is an order of magnitude lower than inferred previously. Further, we are able to date the recombination event between genotypes 1 and 3 that formed genotype 2 to ∼5.0–6.8 kya. This study emphasizes the importance of ancient viral sequences for our understanding of virus evolution and phylogenetics.

Vertebrate palaeontology of Australasia into the twenty-first century

The 13th Conference on Australasian Vertebrate Evolution Palaeontology and Systematics (CAVEPS) took place in Perth, Western Australia, from 27 to 30 April 2011. This biennial meeting was jointly hosted by Curtin University, the Western Australian Museum, Murdoch University and the University of Western Australia. Researchers from diverse disciplines addressed many aspects of vertebrate evolution, including functional morphology, phylogeny, ecology and extinctions. New additions to the fossil record were reported, especially from hitherto under-represented ages and clades. Yet, application of new techniques in palaeobiological analyses dominated, such as dental microwear and geochronology, and technological advances, including computed tomography and ancient biomolecules. This signals a shift towards increased emphasis in interpreting broader evolutionary patterns and processes. Nonetheless, further field exploration for new fossils and systematic descriptions will continue to shape our understanding of vertebrate evolution in this little-studied, but most unusual, part of the globe.