Jessica A. Thomas

A generation time effect on the rate of molecular evolution in invertebrates

The rate of genome evolution varies significantly between species. Evidence is growing that at least some of this variation is associated with species characteristics, such as body size, diversification rate, or population size. One of the strongest correlates of the rate of molecular evolution in vertebrates is generation time (GT): Species with faster generation turnover tend to have higher rates of molecular evolution, presumably because their genomes are copied more frequently and therefore collect more DNA replication errors per unit time. But the GT effect has never been tested for nonvertebrate animals. Here, we present the first general test of the GT effect in invertebrates, using 15 genes from 143 species spread across the major eumetazoan superphyla (including arthropods, nematodes, molluscs, annelids, platyhelminthes, cnidarians, echinoderms, and urochordates). We find significant evidence that rates of molecular evolution are correlated with GT in invertebrates and that this effect applies consistently across genes and taxonomic groups. Furthermore, the GT effect is evident in nonsynonymous substitutions, whereas theory predicts (and most previous evidence has supported) a relationship only in synonymous changes. We discuss both the practical and theoretical implications of these findings.

The future of ancient DNA: Technical advances and conceptual shifts.

Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi‐fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7× coverage (mammoth) in 2008 to more than 50× coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics.

Metabolic rate does not calibrate the molecular clock

Rates of molecular evolution vary widely among lineages, but the causes of this variation remain poorly understood. It has been suggested that mass-specific metabolic rate may be one of the key factors determining the rate of molecular evolution, and that it can be used to derive “corrected” molecular clocks. However, previous studies have been hampered by a paucity of mass-specific metabolic rate data and have been largely limited to vertebrate taxa. Using mass-specific metabolic rate measurements and DNA sequence data for >300 metazoan species for 12 different genes, we find no evidence that mass-specific metabolic rate drives substitution rates. The mechanistic basis of the metabolic rate hypothesis is discussed in light of these findings.

Bayesian Estimation of Substitution Rates from Ancient DNA Sequences with Low Information Content

1Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia; 2School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia; 3School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK; 4Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA; and 5Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA; ∗Correspondence to be sent to: School of Biological Sciences, Macleay Building A12, University of Sydney, Sydney, NSW 2006, Australia; E-mail: simon.ho@sydney.edu.au.

Holarctic genetic structure and range dynamics in the woolly mammoth

Ancient DNA analyses have provided enhanced resolution of population histories in many Pleistocene taxa. However, most studies are spatially restricted, making inference of species-level biogeographic histories difficult. Here, we analyse mitochondrial DNA (mtDNA) variation in the woolly mammoth from across its Holarctic range to reconstruct its history over the last 200 thousand years (kyr). We identify a previously undocumented major mtDNA lineage in Europe, which was replaced by another major mtDNA lineage 32–34 kyr before present (BP). Coalescent simulations provide support for demographic expansions at approximately 121 kyr BP, suggesting that the previous interglacial was an important driver for demography and intraspecific genetic divergence. Furthermore, our results suggest an expansion into Eurasia from America around 66 kyr BP, coinciding with the first exposure of the Bering Land Bridge during the Late Pleistocene. Bayesian inference indicates Late Pleistocene demographic stability until 20–15 kyr BP, when a severe population size decline occurred.

Modern and ancient red fox (Vulpes vulpes) in Europe show an unusual lack of geographical and temporal structuring, and differing responses within the carnivores to historical climatic change

BackgroundDespite phylogeographical patterns being well characterised in a large number of species, and generalised patterns emerging, the carnivores do not all appear to show consistent trends. While some species tend to fit with standard theoretical phylogeographic expectations (e.g. bears), others show little obvious modern phylogeographic structure (e.g. wolves). In this study we briefly review these studies, and present a new phylogeographical study of the red fox (Vulpes vulpes) throughout Europe, using a combination of ancient DNA sequences obtained from museum specimens, and modern sequences collated from GenBank. We used cytochrome b (250 bp) and the mitochondrial control region (268 bp) to elucidate both current and historical phylogeographical patterning.ResultsWe found evidence for slight isolation by distance in modern populations, as well as differentiation associated with time, both of which can likely be attributed to random genetic drift. Despite high sequence diversity (11.2% cytochrome b, 16.4% control region), no evidence for spatial structure (from Bayesian trees) is found either in modern samples or ancient samples for either gene, and Bayesian skyline plots suggested little change in the effective population size over the past 40,000 years.ConclusionsIt is probable that the high dispersal ability and adaptability of the red fox has contributed to the lack of observable differentiation, which appears to have remained consistent over tens of thousands of years. Generalised patterns of how animals are thought to have responded to historical climatic change are not necessarily valid for all species, and so understanding the differences between species will be critical for predicting how species will be affected by future climatic change.

Relaxed Phylogenetics and the Palaeoptera Problem: Resolving Deep Ancestral Splits in the Insect Phylogeny

The order in which the 3 groups of winged insects (the Pterygota) diverged from their common ancestor has important implications for understanding the origin of insect flight. But despite this importance, the split between the Odonata (dragonflies and damselflies), Ephemeroptera (mayflies), and Neoptera (the other winged orders) remains very much unresolved. Indeed, previous studies have obtained strong apparent support for each of the 3 possible branching patterns. Here, we present a systematic reinvestigation of the basal pterygote split. Our results suggest that outgroup choice and limited taxon sampling have been major sources of systematic error, even for data sets with a large number of characters (e.g., in phylogenomic data sets). In particular, a data set of 113 taxa provides consistent support for the Palaeoptera hypothesis (the grouping of Odonata with Ephemeroptera), whereas results from data sets with fewer taxa give inconsistent results and are highly sensitive to minor changes in data and methods. We also focus on recent methods that exploit temporal information using fossil calibrations, combined with additional assumptions about the evolutionary process, and so reduce the influence of outgroup choice. These methods are shown to provide more consistent results, for example, supporting Palaeoptera, even for data sets that previously supported other hypotheses. Together, these results have implications for understanding insect origins and for resolving other problematic splits in the tree of life.

The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life.

DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of lifes species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between ‘Barcode Index Numbers’ (BINs) and ‘species’ that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description. This article is part of the themed issue ‘From DNA barcodes to biomes’.

Nanotechnology: Downsizing SQUIDs

Pull yourself togetherDeinococcus radiodurans, isolated in the 1950s from canned meat that had gone off despite being sterilized by high-dose radiation, can recover from radiation exposure even though the DNA damage caused completely fragments the genome. How does it achieve this remarkable feat? It is known to carry multiple copies of its genome and quick and effective DNA repair mechanisms. A new study now shows that first, DNA fragments with regions of complementary sequence find each other and initiate synthesis by a DNA polymerase to form long single-stranded ends on the fragments. Then, complementary single-strand tails pair, to regenerate long double-stranded DNA molecules that are processed into the original circular genome.