Journal of Phylogenetics & Evolutionary Biology

 A pre-requisite to any revegetation plan, as well as restoration of degraded land is the knowledge of physicochemical characterization, which is crucial for prediction of ecological succession for mine overburden spoil, including soil texture, hydrological regimes, pH, organic carbon, nitrogen and extractable phosphorous. Effects of mining activities are markedly adverse, because many of the beneficial soil characteristics may require a long span of time to develop through pedogenic processes, in order to reach the native forest soil condition, which evaluates the degree of functional microbial processes for ecosystem recovery, and used as an index of the progress of soil genesis in mine overburden spoil. Mine spoil samples collected from six different age series overburdens showed progressive increase in clay (%) (r=0.982, p<0.001), water holding capacity and organic carbon, which indicates the development of soil structural stability, aggregation with the increase in age of overburden spoil. The pH of spoil samples was noted to be in acidic range (6.11-6.87). Approximately, 93.7% variability in clay (%) among different mine spoils can be explained due to the variation in organic carbon. The organic carbon, nitrogen and phosphorous content showed an improvement of 2 mg C/g spoil, 161 µg N/g spoil and 8 µg P/g spoil, respectively, over a period of 10 years. Thus, the net annual  accumulation rate for carbon, nitrogen and phosphorous on hectare basis amounted to 255 kg C/ha/yr, 20 kg N/ha/yr and 1 kg P/ha/yr, respectively. Further, it was estimated that the mine overburden spoil to attain the soil features of nearby native forest soil, at study site through the process of reclamation, shall take approximately 28 years.

 In this present investigation, a total of 27 RAPD primers were used to elucidate the genetic relationships between cultivated Cajanus cajan cultivars and 10 allied species of primary, secondary and tertiary gene pool, including C. cajanifolius, C. scarabaeoides, C. platycarpus, C. albicans, C. volubilis, C. sericeus, C. acutifolius, C. lineatus, C. lanceolatus and C. reticulates. All primers showed polymorphism at species level and produced 215 unequivocal polymorphic bands, with an average of 7.96 bands per primer. These polymorphic primers exhibited variation with regard to average band informativeness, resolving power, and showed high polymorphism information content value. No single primer was able to distinguish between all the two cultivars of C. cajan and ten allied species of Cajanus, but several species specific amplified fragments were observed. The pair wise Jaccard’s similarity coefficient values revealed high level of inter-specific genetic variation in the genus Cajanus. Cluster analysis exhibited the grouping of two C. cajan accessions with C. cajanifolius in one cluster, while except C. platycarpus, all the nine wild Cajanus species belonging to the secondary and tertiary gene pool form another cluster. The present analysis more or less agreed with the sectional classification of the genus Cajanus, and it has been hypothesized that cultivated pigeonpea has evolved through multi-genomic interaction through C. cajanifolius, and it has experienced minor genomic reorganization during its divergence. Again, identification of species specific amplification pattern substantiated the utility of RAPD markers on selection of suitable species to transfer the desirable trait into cultivated C. cajan, through marker aided breeding for its genetic augmentation, and also for the effective management of genetic resources of C. cajan.

Self-recognition systems preventing chimera formation following somatic fusion between members of the same species have evolved only in certain phyla (e.g., fungi, cnidarians, poriferans, bryozoans, urochordates). We present here some of the biological features common to fungi and colonial marine invertebrates, which may have driven the evolution of such self-recognition systems. We conclude that the evolution of self-recognition mechanisms in fusible organisms is more likely to result from a complex trade-off between selection pressures linked with a gregariousness and sessile way of life. This trade-off also raises the question of how extrinsic interactions between a group of cooperative cells and its direct environment may have driven the evolution towards a form of individuality, via the emergence self-recognition systems in fusible organisms. Gregariousness and sessility being two features intrinsically associated emergence of multicellularity, somatic incompatibility systems could then be considered as one of the first expressions of individuality in early multicellular organisms.

 Biology education in the U.S. is under threat due to resistance to the principles of modern evolutionary theory. Although religious and cultural prejudices heavily influence this resistance, poor understanding of evolutionary theory itself is at least partly responsible. Thus, coherent and aggressive strategies are needed in order to rectify this poor understanding and properly educate the next generation of the electorate and its policy makers. Herein, we examine acceptance of evolutionary concepts among students in a majors-level introductory biology course and those in a gender studies course on sex, gender, and sexuality. Through pre- and post-course surveys, we measured the change in their acceptance. Surprisingly, students in the gender studies course consistently displayed greater improvement in their acceptance of evolutionary theory than the biology students, despite only tangential coverage of these topics in the gender studies course and substantial coverage of them in the biology course. These results provide evidence that one strategy for advancing the proper education of biology and natural history is through teaching of the biological basis of reproduction and sexuality, topicsthat exhibit a high level of student interest and uniquely convey the effects and consequence of evolutionary forces such as natural and sexual selection, adaptation, mutation, and genetic drift.

 Genetic and morphologic variation, haplotype relationships, and structuring of populations within Puntius denisonii and its close related species Puntius chalakkudiensis have been tested using molecular and biometric data, to infer phylogeographic patterns. Sequences of mitochondrial DNA ATPase 8 and 6 genes, and morphometric data, were used to find population structuring. Specimens were collected from 7 locations in the southern region of Western Ghats, a global biodiversity hotspot in India. Biometric analysis revealed apparent heterogeneity in the morphology and color pattern between the species at juvenile and adult stages, and among different geographically separated populations of these species. High values for mean pair wise distances and a high proportion of the total variance attributed to differences between the geographically isolated populations with AMOVA, indicated clear population structuring within these species. Extremely high values for Pair wise F_ST and significantly lower Nm values observed among the populations studied, suggested little or no effective gene flow among them. Constructed phylogenies further confirmed a high degree of population structuring within the species, showing local endemism with population specific haplotypes forming a species complex. The present study thus estimates the validity of subpopulations within P. denisonii and P. chalakkudiensis; clarifies the relationships of populations of P. denisonii with that of P. chalakkudiensis, and also indicates the presence of four different independent evolutionary lineages forming cryptic species within P. denisonii. The study further emphasizes the need for a conservation policy to be developed for each population of both species, separately based on MUs (Management Units).  

The Bardet-Biedl Syndrome (BBS) is a human developmental disorder that has been associated with fourteen BBS genes affecting the development of cilia. Three BBS genes are distant relatives of chaperonin proteins, a family of chaperones well known for the protein-folding role of their double-ringed complexes. Chaperonin-like BBS genes were originally thought to be vertebrate-specific, but related genes from different metazoan species have been identified as chaperonin-like BBS genes based on sequence similarity. Our phylogenetic analyses confirmed the classification of these genes in the chaperonin-like BBS gene family, and set the origin of the gene family earlier than the time of separation of Bilateria, Cnidaria, and Placozoa. By extensive searches of chaperonin-like genes in complete genomes representing several eukaryotic lineages, we discovered the presence of chaperonin-like BBS genes also in the genomes of Phytophthora and Pythium, belonging to the group of Oomycetes. This finding suggests that the chaperonin-like BBS gene family had already evolved before the origin of Metazoa, as early in eukaryote evolution as before separation of the lineages of Unikonts and Chromalveolates. The analysis of coding sequences indicated that chaperonin-like BBS proteins have evolved in all lineages under constraining selection. Furthermore, analysis of the predicted structural features suggested that, despite their high rate of divergence, chaperonin-like BBS proteins mostly conservea typical chaperonin-like three-dimensional structure, but question their ability to assemble and function as chaperonin-like double-ringed complexes.

A deeper understanding of positive selection is of fundamental importance. Evolutionary pressures acting on the genome as a whole and the specific role of environmental pressures on divergence shape the natural selection. However, despite the intense interest in genome-wide scans, a coherent study of recent human evolutionary history has yet to emerge due to the limitations of data, models, and analytical tools. Fast and cheaper Next Generation Sequencing (NGS) technologies will generate unprecedentedly massive and highly-dimensional genomic variation data. NGS will offer unprecedented opportunities for population genetic and natural selection studies, but also raise great challenges. In the conventional population genetics, most researches have primarily focused on natural selection acting on a single locus. Little attention has been paid to determining how the natural selection acts on multiple interacted genes in response to environmental perturbation. In addition, the current paradigm for analysis of natural selection on gene-expression is to use a single value of summarizing statistic to represent gene expression level and overlook all information on expression difference in exons, genomic position and alleles. To address these critical limitations, we develop a unified framework and statistical methods for genome-wide scans for natural selection and investigation of natural selection on pathways. To explore observed expression variation in exons or in genomic position across the genes, we extend one dimensional diffusion process to multidimensional diffusion process and a single variate stochastic differential equation to multivariate stochastic differential equations. We then use the extended multidimensional diffusion processes to model the evolution of gene-expression acted by natural selection. We hope that the present new development of natural selection analysis for NGS data will open a new avenue for natural selection analysis with NGS data.