http://www.mdpi.com/journal/ijms/special_issues/cladistic_analysis/ 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.com. 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 MDPI. 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). http://www.mdpi.com/1422-0067/11/5/2097/ Parsimony analysis of endemicity (PAE) was used to identify areas of endemism (AOEs) for Chinese birds at the subregional level. Four AOEs were identified based on a distribution database of 105 endemic species and using 18 avifaunal subregions as the operating geographical units (OGUs). The four AOEs are the Qinghai-Zangnan Subregion, the Southwest Mountainous Subregion, the Hainan Subregion and the Taiwan Subregion. Cladistic analysis of subregions generally supports the division of China’s avifauna into Palaearctic and Oriental realms. Two PAE area trees were produced from two different distribution datasets (year 1976 and 2007). The 1976 topology has four distinct subregional branches; however, the 2007 topology has three distinct branches. Moreover, three Palaearctic subregions in the 1976 tree clustered together with the Oriental subregions in the 2007 tree. Such topological differences may reflect changes in the distribution of bird species through circa three decades. http://www.mdpi.com/1422-0067/11/5/2097/ Mon, 10 May 2010 00:00:00 CEST International Journal of Molecular Sciences 2010-05-10 11 5 Article 2097 2108 1422-0067 Use of Parsimony Analysis to Identify Areas of Endemism of Chinese Birds: Implications for Conservation and Biogeography 2010-05-10 doi: 10.3390/ijms11052097 Huang Qiao Lei http://www.mdpi.com/1422-0067/11/4/1704/ Molecular markers for cladistic analyses may perform differently according to the taxonomic group considered and the historical level under investigation. Here we evaluate the phylogenetic potential of five different markers for resolving evolutionary relationships within the ectoparasitic genus Dermanyssus at the species level, and their ability to address questions about the evolution of specialization. COI provided 9–18% divergence between species (up to 9% within species), 16S rRNA 10–16% (up to 4% within species), ITS1 and 2 2–9% (up to 1% within species) and Tropomyosin intron n 8–20% (up to 6% within species). EF-1a revealed different non-orthologous copies withinindividuals of Dermanyssus and Ornithonyssus. Tropomyosin intron n was shown containing consistent phylogenetic signal at the specific level within Dermanyssus and represents a promising marker for future prospects in phylogenetics of Acari. Phylogenetic analyses revealed that the generalist condition is apomorphic and D. gallinae mightrepresent a complex of hybridized lineages. The split into hirsutus-group and gallinae-group in Dermanyssus does not seem to be appropriate based upon these results and D. longipes appears to be composed of two different entities. http://www.mdpi.com/1422-0067/11/4/1704/ Tue, 13 Apr 2010 00:00:00 CEST International Journal of Molecular Sciences 2010-04-13 11 4 Article 1704 1734 1422-0067 Diversity of Phylogenetic Information According to the Locus and the Taxonomic Level: An Example from a Parasitic Mesostigmatid Mite Genus 2010-04-13 doi: 10.3390/ijms11041704 Roy Dowling Chauve Buronfosse http://www.mdpi.com/1422-0067/11/4/1190/ Understanding the nature, timing and geographic context of historical events and population processes that shaped the spatial distribution of genetic diversity is critical for addressing questions relating to speciation, selection, and applied conservation management. Cladistic analysis of gene trees has been central to phylogeography, 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 the strengths and limitations of different types of genetic data, analysis methods, and approaches to historical inference. We then turn our attention to the potentially synergistic interactions among widely-used and emerging phylogeographic analyses, and discuss some of the ways that spatial and temporal concordance among inferences can be assessed. We close this review with a brief summary and outlook on future research directions. http://www.mdpi.com/1422-0067/11/4/1190/ Wed, 24 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-24 11 4 Review 1190 1227 1422-0067 Inference of Population History by Coupling Exploratory and Model-Driven Phylogeographic Analyses 2010-03-24 doi: 10.3390/ijms11041190 Garrick Caccone Sunnucks http://www.mdpi.com/1422-0067/11/3/1141/ A shortcoming of most correlation distance methods based on the composition vectors without alignment developed for phylogenetic analysis using complete genomes is that the “distances” are not proper distance metrics in the strict mathematical sense. In this paper we propose two new correlation-related distance metrics to replace the old one in our dynamical language approach. Four genome datasets are employed to evaluate the effects of this replacement from a biological point of view. We find that the two proper distance metrics yield trees with the same or similar topologies as/to those using the old “distance” and agree with the tree of life based on 16S rRNA in a majority of the basic branches. Hence the two proper correlation-related distance metrics proposed here improve our dynamical language approach for phylogenetic analysis. http://www.mdpi.com/1422-0067/11/3/1141/ Thu, 18 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-18 11 3 Article 1141 1154 1422-0067 Proper Distance Metrics for Phylogenetic Analysis Using Complete Genomes without Sequence Alignment 2010-03-18 doi: 10.3390/ijms11031141 Yu Zhan Han Wang Anh Chu http://www.mdpi.com/1422-0067/11/3/1090/ Catostomid fishes (suckers) have duplicate copies of the growth hormone gene and other nuclear genes, due to a genome duplication event early in the group’s history. Yet, paralogs of GH in suckers are more than 90% conserved in nucleotide (nt) and amino acid (aa) sequence. Within paralogs across species, variation in nt and aa sequence averages 3.33% and 4.46% for GHI, and 3.22% and 2.43% for GHII, respectively. Selection tests suggest that the two GH paralogs are under strong purifying selection. Consensus trees from phylogenetic analysis of GH coding region data for 23 species of suckers, other cypriniform fishes and outgroups resolved cypriniform relationships and relationships among GHI sequences of suckers more or less consistently with analyses based on other molecular data. However, the analysis failed to resolve all sucker GHI and GHII sequences as monophyletic sister groups. This unexpected topology did not differ significantly from topologies constrained to make all GH sequences monophyletic. We attribute this result either to limitations in our GHII data set or convergent adaptive changes in GHII of tribe Catostomini. http://www.mdpi.com/1422-0067/11/3/1090/ Tue, 16 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-16 11 3 Article 1090 1102 1422-0067 Evolutionary Divergence of Duplicate Copies of the Growth Hormone Gene in Suckers (Actinopterygii: Catostomidae) 2010-03-16 doi: 10.3390/ijms11031090 Henry L. Bart Paulette C. Reneau Michael H. Doosey Charles D. Bell http://www.mdpi.com/1422-0067/11/2/507/ A Gram-positive, facultatively anaerobic, endospore-forming and rod-shaped bacterium was isolated from soil samples and designated strain LQQ. This organism strongly quenches the acylhomoserine lactone quorum-sensing signal. The LQQ strain exhibits phenotypic characteristics consistent with its classification in the genus Bacillus. It is positive in catalase and no special growth factor is needed. It uses glucose as sole carbon source. The DNA G + C content is 39.8 mol %. The closest relatives based on the 16S rRNA gene sequence are Bacillus anthracis, Bacillus thuringiensis, and Brevibacillus brevis (syn. Bacillus brevis) with the similarity of 96.5%. The DNA–DNA hybridization data indicates a low level of genomic relatedness with the relative type strains of Bacillus thuringiensis (6.1%), Bacillus anthracis (10.5%) and Brevibacillus brevis (8.7%). On the basis of the phenotypic and phylogenetic data together with the genomic distinctiveness, the LQQ strain represents a novel species of the genus Bacillus, for which the name Bacillus marcorestinctum sp. nov. is proposed. The type strain is LQQT. http://www.mdpi.com/1422-0067/11/2/507/ Wed, 03 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-03 11 2 Article 507 520 1422-0067 Bacillus marcorestinctum sp. nov., a Novel Soil Acylhomoserine Lactone Quorum-Sensing Signal Quenching Bacterium 2010-02-03 doi: 10.3390/ijms11020507 Yan Han Fang Chen Nuo Li Bo Zhu Xianzhen Li http://www.mdpi.com/1422-0067/11/2/492/ Species delimitation has long been a difficult and controversial process, and different operational criteria often lead to different results. In particular, investigators using phenotypic vs. molecular data to delineate species may recognize different boundaries, especially if morphologically or ecologically differentiated populations have only recently diverged. Here we examine the genetic relationship between the widespread sunflower species Helianthus petiolaris and its narrowly distributed sand dune endemic sister species H. neglectus using sequence data from nine nuclear loci. The two species were initially described as distinct based on a number of minor morphological differences, somewhat different ecological tolerances, and at least one chromosomal rearrangement distinguishing them; but detailed molecular data has not been available until now. We find that, consistent with previous work, H. petiolaris is exceptionally genetically diverse. Surprisingly, H. neglectus harbors very similar levels of genetic diversity (average diversity across loci is actually slightly higher in H. neglectus). It is extremely unlikely that such a geographically restricted species could maintain these levels of genetic variation in isolation. In addition, the two species show very little evidence of any genetic divergence, and estimates of interspecific gene flow are comparable to gene flow estimates among regions within H. petiolaris. These results indicate that H. petiolaris and H. neglectus likely do not represent two distinct, isolated gene pools; H. neglectus is probably more accurately thought of as a geographically restricted, morphologically and ecologically distinct subspecies of H. petiolaris rather than a separate species. http://www.mdpi.com/1422-0067/11/2/492/ Tue, 02 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-02 11 2 Article 492 506 1422-0067 Effective Population Size, Gene Flow, and Species Status in a Narrow Endemic Sunflower, Helianthus neglectus, Compared to Its Widespread Sister Species, H. petiolaris 2010-02-02 doi: 10.3390/ijms11020492 Andrew R. Raduski Loren H. Rieseberg Jared L. Strasburg http://www.mdpi.com/1422-0067/11/2/407/ Collagens, or more precisely collagen-based extracellular matrices, are often considered as a metazoan hallmark. Among the collagens, fibrillar collagens are present from sponges to humans, and are involved in the formation of the well-known striated fibrils. In this review we discuss the different steps in the evolution of this protein family, from the formation of an ancestral fibrillar collagen gene to the formation of different clades. Genomic data from the choanoflagellate (sister group of Metazoa) Monosiga brevicollis, and from diploblast animals, have suggested that the formation of an ancestral α chain occurred before the metazoan radiation. Phylogenetic studies have suggested an early emergence of the three clades that were first described in mammals. Hence the duplication events leading to the formation of the A, B and C clades occurred before the eumetazoan radiation. Another important event has been the two rounds of “whole genome duplication” leading to the amplification of fibrillar collagen gene numbers, and the importance of this diversification in developmental processes. We will also discuss some other aspects of fibrillar collagen evolution such as the development of the molecular mechanisms involved in the formation of procollagen molecules and of striated fibrils. http://www.mdpi.com/1422-0067/11/2/407/ Thu, 28 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-28 11 2 Review 407 426 1422-0067 The Fibrillar Collagen Family 2010-01-28 doi: 10.3390/ijms11020407 Jean-Yves Exposito Ulrich Valcourt Caroline Cluzel Claire Lethias http://www.mdpi.com/1422-0067/11/1/370/ Genotype/phenotype association analyses (Treescan) with plasma lipid levels and functional site prediction methods (TreeSAAP and PolyPhen) were performed using sequence data for ANGPTL4 from 3,551 patients in the Dallas Heart Study. Biological assays of rare variants in phenotypic tails and results from a Treescan analysis were used as “known” variants to assess the site prediction abilities of PolyPhen and TreeSAAP. The E40K variant in European Americans and the R278Q variant in African Americans were significantly associated with multiple lipid phenotypes. Combining TreeSAAP and PolyPhen performed well to predict “known” functional variants while reducing noise from false positives. http://www.mdpi.com/1422-0067/11/1/370/ Mon, 25 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-25 11 1 Article 370 385 1422-0067 Phylogenetics Applied to Genotype/Phenotype Association and Selection Analyses with Sequence Data from Angptl4 in Humans 2010-01-25 doi: 10.3390/ijms11010370 Taylor J. Maxwell Matthew L. Bendall Jeffrey Staples Todd Jarvis Keith A. Crandall http://www.mdpi.com/1422-0067/11/1/124/ The genetic variation found in small regions of the genomes of many species can be arranged into haplotype trees that reflect 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 phylogeographic history of species, human evolution, the conservation of endangered species, and the identification of species. http://www.mdpi.com/1422-0067/11/1/124/ Fri, 08 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-08 11 1 Review 124 139 1422-0067 The Diverse Applications of Cladistic Analysis of Molecular Evolution, with Special Reference to Nested Clade Analysis 2010-01-08 doi: 10.3390/ijms11010124 Alan R. Templeton http://www.mdpi.com/1422-0067/10/12/5455/ Genealogical concordance is a critical overlay of all phylogenetic analyses, irrespective of taxonomic level. To assess such patterns of congruence we have compiled and derived sequence data for two mitochondrial (16S rRNA, COI) and two nuclear (ITS1, p26) markers in 14 American populations of the hypersaline branchiopod Artemia franciscana. Cladistic analysis revealed three reciprocally monophyletic mitochondrial clades. For nuclear DNA, incomplete lineage sorting was evident presumably as a result of slower coalescence or male-mediated dispersal. Our findings capture the genealogical interval between gene splitting and population divergence. In this sense, strong indications are provided in favour of a superspecies status and ongoing speciation in A. franciscana. http://www.mdpi.com/1422-0067/10/12/5455/ Fri, 18 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-18 10 12 Article 5455 5470 1422-0067 Sharp Phylogeographic Breaks and Patterns of Genealogical Concordance in the Brine Shrimp Artemia franciscana 2009-12-18 doi: 10.3390/ijms10125455 Stefania Maniatsi Ilias Kappas Athanasios D. Baxevanis Theodora Farmaki Theodore J. Abatzopoulos http://www.mdpi.com/1422-0067/10/11/4723/ The PD measure of phylogenetic diversity interprets branch lengths cladistically to make inferences about feature diversity. PD calculations extend conventional specieslevel ecological indices to the features level. The “phylogenetic beta diversity” framework developed by microbial ecologists calculates PD-dissimilarities between community localities. Interpretation of these PD-dissimilarities at the feature level explains the framework’s success in producing ordinations revealing environmental gradients. An example gradients space using PD-dissimilarities illustrates how evolutionary features form unimodal response patterns to gradients. This features model supports new application of existing species-level methods that are robust to unimodal responses, plus novel applications relating to climate change, commercial products discovery, and community assembly. http://www.mdpi.com/1422-0067/10/11/4723/ Tue, 03 Nov 2009 00:00:00 CET International Journal of Molecular Sciences 2009-11-03 10 11 Article 4723 4741 1422-0067 The Cladistic Basis for the Phylogenetic Diversity (PD) Measure Links Evolutionary Features to Environmental Gradients and Supports Broad Applications of Microbial Ecology’s “Phylogenetic Beta Diversity” Framework 2009-11-03 doi: 10.3390/ijms10114723 Daniel P. Faith Catherine A. Lozupone David Nipperess Rob Knight http://www.mdpi.com/1422-0067/10/9/3836/ The role that reticulate evolution (i.e., via lateral transfer, viral recombination and/or introgressive hybridization) has played in the origin and adaptation of individual taxa and even entire clades continues to be tested for all domains of life. Though falsified for some groups, the hypothesis of divergence in the face of gene flow is becoming accepted as a major facilitator of evolutionary change for many microorganisms, plants and animals. Yet, the effect of reticulate evolutionary change in certain assemblages has been doubted, either due to an actual dearth of genetic exchange among the lineages belonging to these clades or because of a lack of appropriate data to test alternative hypotheses. Marine organisms represent such an assemblage. In the past half-century, some evolutionary biologists interested in the origin and trajectory of marine organisms, particularly animals, have posited that horizontal transfer, introgression and hybrid speciation have been rare. In this review, we provide examples of such genetic exchange that have come to light largely as a result of analyses of molecular markers. Comparisons among these markers and between these loci and morphological characters have provided numerous examples of marine microorganisms, plants and animals that possess the signature of mosaic genomes. http://www.mdpi.com/1422-0067/10/9/3836/ Thu, 03 Sep 2009 00:00:00 CEST International Journal of Molecular Sciences 2009-09-03 10 9 Review 3836 3860 1422-0067 Reticulate Evolution and Marine Organisms: The Final Frontier? 2009-09-03 doi: 10.3390/ijms10093836 Michael L. Arnold Nicole D. Fogarty