Incongruences between nuclear and plastid phylogenies challenge the identification of correlates of diversification in Gentiana in the European Alpine System

Mountains are reservoirs for a tremendous biodiversity which was fostered by a suite of factors acting in concert throughout evolutionary times. These factors can be climatic, geological, or biotic, but the way they combine through time to generate diversity remains unknown. Here, we investigate these factors as correlates of diversification of three closely related sections of Gentiana in the European Alpine System. Based upon phylogenetic approaches coupled with divergence dating and ancestral state reconstructions, we attempted to identify the role of bedrock preferences, chromosome numbers coupled with relative genome sizes estimates, as well as morphological features through time. We also investigated extant climatic preferences using a heavily curated set of occurrence records individually selected for superior precision, and quantified rates of climatic niche evolution in each section. We found that a number of phylogenetic incongruences derail the identification of correlates of diversification, yet a number of patterns persist regardless of the topology considered. All the studied correlates are likely to have contributed to the diversification of Gentiana in Europe, however, their respective importance varied through time and across clades. Chromosomal variation and divergence of climatic preferences appear to correlate with diversification throughout the evolution of European Gentiana (Oligocene to present), whereas shifts in bedrock preferences appear to have been more defining during recent diversification (Pliocene). Overall, a complex interaction among climatic, geological and biotic attributes appear to have supported the diversification of Gentiana across the mountains of Europe, which based upon phylogenetic as well as other evidence, was probably also bolstered by hybridization.

Patterns of chromosomal variation in Mexican species of Aeschynomene (Fabaceae, Papilionoideae) and their evolutionary and taxonomic implications

A cytogenetic analysis of sixteen taxa of the genus Aeschynomene Linnaeus, 1753, which includes species belonging to both subgenera Aeschynomene (Léonard, 1954) and Ochopodium (Vogel, 1838) J. Léonard, 1954, was performed. All studied species had the same chromosome number (2n = 20) but exhibited karyotype diversity originating in different combinations of metacentric, submetacentric and subtelocentric chromosomes, chromosome size and number of SAT chromosomes. The plasticity of the genomes included the observation in a taxon belonging to the subgenus Aeschynomene of an isolated spherical structure similar in appearance to the extra chromosomal circular DNA observed in other plant genera. By superimposing the karyotypes in a recent phylogenetic tree, a correspondence between morphology, phylogeny and cytogenetic characteristics of the taxa included in the subgenus Aeschynomene is observed. Unlike subgenus Aeschynomene, the species of Ochopodium exhibit notable karyotype heterogeneity. However the limited cytogenetic information recorded prevents us from supporting the proposal of their taxonomic separation and raise it to the genus category. It is shown that karyotype information is useful in the taxonomic delimitation of Aeschynomene and that the diversity in the diploid level preceded the hybridization/polyploidization demonstrated in the genus. The systematic implications of our results and their value can be extended to other Dalbergieae genera as knowledge about the chromosomal structure and its evolution increases.

Chromosomal Differentiation in Genetically Isolated Populations of the Marsh-Specialist Crocidura suaveolens (Mammalia: Soricidae)

The genus Crocidura represents a remarkable model for the study of chromosome evolution. This is the case of the lesser white-toothed shrew (Crocidura suaveolens), a representative of the Palearctic group. Although continuously distributed from Siberia to Central Europe, C. suaveolens is a rare, habitat-specialist species in the southwesternmost limit of its distributional range, in the Gulf of Cádiz (Iberian Peninsula). In this area, C. suaveolens is restricted to genetically isolated populations associated to the tidal marches of five rivers (Guadiana, Piedras, Odiel, Tinto and Guadalquivir). This particular distributional range provides a unique opportunity to investigate whether genetic differentiation and habitat specialization was accompanied by chromosomal variation. In this context, the main objective of this study was to determinate the chromosomal characteristics of the habitat-specialist C. suaveolens in Southwestern Iberia, as a way to understand the evolutionary history of this species in the Iberian Peninsula. A total of 41 individuals from six different populations across the Gulf of Cádiz were collected and cytogenetically characterized. We detected four different karyotypes, with diploid numbers (2n) ranging from 2n = 40 to 2n = 43. Two of them (2n = 41 and 2n = 43) were characterized by the presence of B-chromosomes. The analysis of karyotype distribution across lineages and populations revealed an association between mtDNA population divergence and chromosomal differentiation. C. suaveolens populations in the Gulf of Cádiz provide a rare example of true karyotypic polymorphism potentially associated to genetic isolation and habitat specialization in which to investigate the evolutionary significance of chromosomal variation in mammals and their contribution to phenotypic and ecological divergence.

Interphase nuclear phenotype and chromosomal variation in Cynodon dactylon (L.) pers

Interphase nuclear phenotype in different accessions (Acc.) of Cynodon dactylon studied in the present experiment showed chromocentric nuclear organization and the chromocenters were found to be visible clearly. The chromocenter numbers were not same and sometimes it was found to be significantly less and never more than total number of chromosomes. Percentages of heterochromatin values were expressed per nuclear area and the values range from 19.759% (Acc. 16) to 66.022% (Acc.18). Nuclear volume as well as interphase chromosome volume was found to vary 0.674 μm3 (Acc.6) to 41.921 μm3 (Acc.10) and from 0.028 μm3 (Acc. 6) to 1.905 μm3 (Acc. 10), respectively. The somatic chromosome number found to vary from 12 to 40. 2n = 18 chromosomes were found in eight accessions of C. dactylon. Only one accession was found to be tetraploid and rest of them aneuploid whose chromosome numbers were 12, 14, 16, 22, 24, 26, 32, 40 etc. The availability of aneuploid shows great aspects of forage breeding programme. J. bio-sci. 27: 133-141, 2019

The role of recombination on genome-wide patterns of local ancestry exemplified by supplemented Brook Charr populations

Assessing the immediate and long-term evolutionary consequences of human-mediated hybridization is of major concern for conservation biology. Several studies have documented how selection in interaction with recombination modulates introgression at a genome-wide scale, but few have considered the dynamics of this process within and between chromosomes. Here, we used an exploited freshwater fish, the Brook Charr (Salvelinus fontinalis) for which decades of stocking practices have resulted in admixture between wild populations and an introduced domestic strain to assess both the temporal dynamics and local chromosomal variation in domestic ancestry. We provide a detailed picture of the domestic ancestry patterns across the genome using about 33,000 mapped SNPs genotyped in 611 individuals from 24 supplemented populations. For each lake, we distinguished early and late-generation hybrids using admixture tracts information. To assess the selective outcomes following admixture we then evaluated the relationship between recombination and admixture proportions at three different scales: the whole genome, chromosomes and within 2Mb windows. This allowed us to detect the signature of varied evolutionary mechanisms, as reflected by the finding of genomic regions where the introgression of domestic haplotypes are favored or disfavored. Among these, the main factor modulating local ancestry was likely the presence of deleterious recessive mutations in the wild populations, which can be efficiently hidden to selection in the presence of long admixture tracts. Overall, our results emphasize the relevance of taking into consideration local ancestry information to assess both the temporal and chromosomal variation in local ancestry toward better understanding post-hybridization evolutionary outcomes.

Omics-based comparative analysis of putative mobile genetic elements in Lactococcus lactis

ABSTRACT Lactococcus lactis is globally used in food fermentation. Genomics is useful to investigate speciation and differential occurrence of (un)desired gene functions, often related to mobile DNA. This study investigates L. lactis for putative chromosomal mobile genetic elements through comparative genomics, and analyses how they contribute to chromosomal variation at strain level. Our work identified 95 loci that may range over 10% of the chromosome size when including prophages, and the loci display a marked differential occurrence in the analysed strains. Analysis of differential transcriptomics data revealed how mobile genetic elements may impact the host physiology in response to conditional changes. This insight in the genetic variation of mobile genetic elements in L. lactis holds potential to further identify important functions related to food and biotechnology applications within this important species.