Special Issue "Cladistic Analysis and Molecular Evolution"

Guest Editor
Prof. Dr. Alan R. Templeton
Department of Biology, Washington University, St. Louis, Missouri 63130-4899, USA
Website: http://www.biology.wustl.edu/faculty/templeton/
E-Mail:

Dear Colleagues,

Cladistics comes from the Greek word clade, which means branch. In this case, the branches or clades are referring to parts of evolutionary trees. In modern systematics, cladistics refers to a method of inferring evolutionary trees based on character state data. However, cladistic analysis also connotes any type of analysis that uses branches of evolutionary trees as part of its statistical design. Increasingly, the evoltuionary trees used in cladistic analysis are the trees of genetic variation found in a DNA region with little to no recombination. This variation can be within species, between species, or a mixture of the two. A broad range of topics can be addressed by cladistic analysis. The analysis can focus on associations between clades and phenotypic variation at a candidate locus within a species, or look at differences between species or evolutionary lineages with respect to behavior, morphology or ecology. Cladistic analysis can be used to study associations between clades and geography within species in order to investigate its phylogeography, which in turn has applications in genetic epidemiology (such as identifying causes of population stratification), in conservation biology, and in inferring species status. Cladistic analysis can also be turned inward upon the gene region under study as a tool to investigate non-random patterns of mutation, recombination, and gene conversion. The common theme behind all these analyses is that many of the associations between genetic variation and other factors is influenced or even determined by evolutionary history. Therefore, the evolutionary history captured by the clades in an evolutionary tree can greatly increase our power to detect and understand associations observed at the present time.

Alan R. Templeton
Guest Editor

Related Journal

• Genes - an Open Access journal of genetics and genomics.

Submission

All papers should be submitted to ijms@mdpi.org. To be published continuously until the deadline and papers will be listed together at the special issue website.

Submitted papers should not have been published previously, nor be under consideration for publication elsewhere. All papers are refereed through a peer-review process. A guide for authors is available on the Instructions for Authors page. The International Journal of Molecular Sciences is an international peer-reviewed monthly journal published by Molecular Diversity Preservation International.

Open Access publication fees are 800 CHF per paper. English correction fees and/or formatting fees (250 CHF) will be added in certain cases (1050 CHF per paper for those papers that require extensive additional formatting and/or English corrections).

• cladistic analysis
• molecular evolution (evolution of the DNA, RNA and proteins, evolution of enzyme functions)
• molecular systematics
• taxonomy and classifications

Feature Papers

Type of Paper: Review
Title: The Diverse Applications of Cladistic Analysis of Molecular Evolution
Authors: Alan R. Templeton
Affiliations: Department of Biology, Washington University, St. Louis, Missouri 63130-4899, USA; E-mail: temple_a@wustl.edu
Abstract: The genetic variation found in small regions of the genomes of many species can be arranged into a haplotype tree that reflects the evolutionary genealogy of the DNA lineages found in that region and the accumulation of mutations on those lineages. This review demonstrates some of the many ways in which clades (branches) of haplotype trees have been applied in recent years, including the study of genotype/phenotype associations at candidate loci and in genome-wide association studies, the detection of non-random patterns of mutation and recombination in molecular evolution, the phylogeographic history of species, human evolution, the conservation of endangered species, and the identification of species.

Type of Paper: Article
Title: Comparison of Methods for Detecting Amino Acid Sites under the Influence of Positive Selection Using Empirical Data from HIV Drug Resistance Studies
Authors: Matthew L. Bendall, Jeffery Staples, Matthew Dyer and Keith A. Crandall
Affiliations: Department of Biology, Brigham Young University, Provo, UT 84602, USA
Abstract: There are several methods currently used for in silico detection of positive selection. These methods have been extensively verified through simulation and studies, yet the performance of these methods on empirical data has not been thoroughly investigated. In this study, we use data from HIV drug resistance studies to assess the performance of seven different models for detecting positive selection. All methods show low power (< 50%) when compared to sites responsible for the development of drug resistance. The dual rate REL model implemented in HyPhy, and the selection on amino acid properties method used in TreeSAAP proved to exhibit the greatest power, although type I error rates were high for both of these methods. We consider several reasons that might explain the lack of power and high false positive rates, and emphasize the need for better sampling procedures.

Type of Paper: Review
Title: Inference of Population Divergence History by Coupling Model-driven and Model-free Phylogeographic Analyses: Assessing Concordance and Integrating Outcomes
Authors: Ryan C. Garrick ¹ and Paul Sunnucks ²
Affiliations: ¹ Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA; E-mail: ryan.garrick@yale.edu
² Australian Centre for Biodiversity, School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia;
E-mail: paul.sunnucks@sci.monash.edu.au
Abstract: Understanding the nature, timing and geographic context of historical events and recurrent population processes that played key roles in shaping the spatial distribution of genetic diversity in extant species is critically important for addressing questions relating to speciation, selection, and applied conservation management. Cladistic analysis of gene trees is central to phylogeographic inference, but when coupled with approaches that make use of different components of the information carried by DNA sequences and their frequencies, the strength and resolution of these inferences can be improved. However, assessing concordance of inferences drawn using different analytical methods or genetic datasets, and integrating their outcomes, can be challenging. Here we overview practical approaches to exploiting the potentially synergistic interactions among widely used or emerging phylogeographic analyses.
Keywords: cladistic analysis; hypothesis testing; molecular markers; population structure; statistical phylogeography

Regular Papers

Type of Paper: Article
Title: Selective Pressure for Axial Stiffness Drives Tubulin Towards Anisotropy
Authors: Bradley E. Layton
Affiliations: Mechanical Engineering and Mechanics, Drexel University, 3141 Chestnut St, 151G Curtis Hall, Philadelphia, PA 19104-2884, USA
Abstract: Without a cytoskeletal structure such as microtubules, cell division, cell transport and thus life as we know it, would not exist. The prediction at the single-protein scale and observation at the microtubule scale that microtubules are mechanically anisotropic with an axial stiffness 50 to 100% greater than the circumferential direction raises the question of which sequences sustain the greatest selective pressure to maintain this anisotropy. Using a cladistic analysis across all known sequences in the three domains and within individual domains, we discuss trends in molecular morphology and sequence in conjunction with phylogeny.

Type of Paper: Article
Title: Molecular Clocks and Miocene Palaeogeography Enlighten the Evolutionary History of Dolichopoda Cave Crickets in the Mediterranean Area
Authors: Giuliana Allegrucci and Valerio Sbordoni
Affiliations: Department of Biology – University of Rome Tor Vergata- Rome, Italy
Abstract: Molecular phylogenetic divergence and historical biogeography of cave crickets belonging to the Mediterranean genus Dolichopoda (Orthoptera, Rhaphidophoridae) have been investigated by partly sequencing three mitochondrial (16S and 12S rRNA and COI) and one nuclear (28S) genes. A rather well resolved phylogeny was revealed, reflecting a phylogeographic pattern. Based on Bayesian analysis, we applied a relaxed molecular clock to estimate the divergence times between the lineages. The results revealed that the origins of eastern Mediterranean lineages are much older than those of western Mediterranean ones. Dispersal vicariance analysis showed that the centre of origin for the genus Dolichopoda is located in the east of the distribution’s range. Alternative biogeographic hypotheses were tested by comparing the degree of discordance between species trees and gene trees.

Type of Paper: Article
Title: A Comparative Analysis of the Phylogenetic Utility of Five Different Molecular Markers in Some Dermanyssoidea (Acari: Mesostigmata)
Authors: L. Roy¹, A. P. G. D. Dowling², C. Chauve¹ and T. Buronfosse¹
Affiliations: ¹ Université de Lyon, Ecole Nationale Vétérinaire de Lyon, Laboratoire de Parasitologie, Marcy-L'Etoile, France; E-mail:
l.roy@vet-lyon.fr (L.R.)
² Department of Entomology, University of Arkansas, Fayetteville, USA
Abstract: Molecular markers for cladistic analyses may perform differently according to the taxonomic group and taxonomic level under consideration. Here we evaluate the phylogenetic potential of five different markers including four traditionally used gene regions (mitochondrial and nuclear) as well as one less conventional nuclear marker for resolving phylogenetic relationships within Dermanyssus and between Dermanyssus and other dermanyssoid genera. By comparing the results of maximum parsimony, maximum likelihood and bayesian phylogenetic analyses, we explore the congruence between the five genes and discuss the valuable information provided by each during phylogeny reconstruction. We also discuss difficulties or inadequecies of these gene regions. Phylogenetic relationships revealed a derived clade of D. gallinae+D. apodis preceded by D. carpathicus and the most basal species D. hirundinis and D. longipes. The traditional split into hirsutus group and gallinae group is no longer supported, as D. hirsutus nests within the gallinae group. Additionally, D. longipes seems to be composed of two different entities, possibly representing cryptic species.