Molecular phylogenetics and evolutionary analysis of body shape in the genus Cyrtonus (Coleoptera, Chrysomelidae)

Beyond fossil calibrations: realities of molecular clock practices in evolutionary biology

Molecular-based divergence dating methods, or molecular clocks, are the primary neontological tool for estimating the temporal origins of clades. While the appropriate use of vertebrate fossils as external clock calibrations has stimulated heated discussions in the paleontological community, less attention has been given to the quality and implementation of other calibration types. In lieu of appropriate fossils, many studies rely on alternative sources of age constraints based on geological events, substitution rates and heterochronous sampling, as well as dates secondarily derived from previous analyses. To illustrate the breadth and frequency of calibration types currently employed, we conducted a literature survey of over 600 articles published from 2007 to 2013. Over half of all analyses implemented one or more fossil dates as constraints, followed by geological events and secondary calibrations (15% each). Vertebrate taxa were subjects in nearly half of all studies, while invertebrates and plants together accounted for 43%, followed by viruses, protists and fungi (3% each). Current patterns in calibration practices were disproportionate to the number of discussions on their proper use, particularly regarding plants and secondarily derived dates, which are both relatively neglected in methodological evaluations. Based on our survey, we provide a comprehensive overview of the latest approaches in clock calibration, and outline strengths and weaknesses associated with each. This critique should serve as a call to action for researchers across multiple communities, particularly those working on clades for which fossil records are poor, to develop their own guidelines regarding selection and implementation of alternative calibration types. This issue is particularly relevant now, as time-calibrated phylogenies are used for more than dating evolutionary origins, but often serve as the backbone of investigations into biogeography, diversity dynamics and rates of phenotypic evolution.

Winding up the molecular clock in the genus Carabus (Coleoptera: Carabidae): assessment of methodological decisions on rate and node age estimation

BACKGROUND

Rates of molecular evolution are known to vary across taxa and among genes, and this requires rate calibration for each specific dataset based on external information. Calibration is sensitive to evolutionary model parameters, partitioning schemes and clock model. However, the way in which these and other analytical aspects affect both the rates and the resulting clade ages from calibrated phylogenies are not yet well understood. To investigate these aspects we have conducted calibration analyses for the genus Carabus (Coleoptera, Carabidae) on five mitochondrial and four nuclear DNA fragments with 7888 nt total length, testing different clock models and partitioning schemes to select the most suitable using Bayes Factors comparisons.

RESULTS

We used these data to investigate the effect of ambiguous character and outgroup inclusion on both the rates of molecular evolution and the TMRCA of Carabus. We found considerable variation in rates of molecular evolution depending on the fragment studied (ranging from 5.02% in cob to 0.26% divergence/My in LSU-A), but also on analytical conditions. Alternative choices of clock model, partitioning scheme, treatment of ambiguous characters, and outgroup inclusion resulted in rate increments ranging from 28% (HUWE1) to 1000% (LSU-B and ITS2) and increments in the TMRCA of Carabus ranging from 8.4% (cox1-A) to 540% (ITS2). Results support an origin of the genus Carabus during the Oligocene in the Eurasian continent followed by a Miocene differentiation that originated all main extant lineages.

CONCLUSIONS

The combination of several genes is proposed as the best strategy to minimise both the idiosyncratic behaviors of individual markers and the effect of analytical aspects in rate and age estimations. Our results highlight the importance of estimating rates of molecular evolution for each specific dataset, selecting for optimal clock and partitioning models as well as other methodological issues potentially affecting rate estimation.

Cytogenetics, cytotaxonomy and chromosomal evolution of Chrysomelinae revisited (Coleoptera, Chrysomelidae)

Nearly 260 taxa and chromosomal races of subfamily Chrysomelinae have been chromosomally analyzed showing a wide range of diploid numbers from 2n = 12 to 2n = 50, and four types of male sex-chromosome systems. with the parachute-like ones Xy(p) and XY(p) clearly prevailing (79.0%), but with the XO well represented too (19.75%). The modal haploid number for chrysomelines is n = 12 (34.2%) although it is not probably the presumed most plesiomorph for the whole subfamily, because in tribe Timarchini the modal number is n = 10 (53.6%) and in subtribe Chrysomelina n = 17 (65.7%). Some well sampled genera, such as Timarcha, Chrysolina and Cyrtonus, are variable in diploid numbers, whereas others, like Chrysomela, Paropsisterna, Oreina and Leptinotarsa, are conservative and these differences are discussed. The main shifts in the chromosomal evolution of Chrysomelinae seems to be centric fissions and pericentric inversions but other changes as centric fusions are also clearly demonstrated. The biarmed chromosome shape is the prevalent condition, as found in most Coleoptera, although a fair number of species hold a few uniarmed chromosomes at least. A significant negative correlation between the haploid numbers and the asymmetry in size of karyotypes (r = -0.74) has been found from a large sample of 63 checked species of ten different genera. Therefore, the increases in haploid number are generally associated with a higher karyotype symmetry.

A long-living species of the hydrophiloid beetles: Helophorus sibiricus from the early Miocene deposits of Kartashevo (Siberia, Russia)

The recent hydrophiloid species Helophorus (Gephelophorus) sibiricus (Motschulsky, 1860) is recorded from the early Miocene deposits of Kartashevo assigned to the Ombinsk Formation. A detailed comparison with recent specimens allowed a confident identification of the fossil specimen, which is therefore the oldest record of a recent species for the Hydrophiloidea. The paleodistribution as well as recent distribution of the species is summarized, and the relevance of the fossil is discussed. In addition, the complex geological settings of the Kartashevo area are briefly summarized.