Does Variation in Genome Sizes Reflect Adaptive or Neutral Processes? New Clues from Passiflora

One of the long-standing paradoxes in genomic evolution is the observation that much of the genome is composed of repetitive DNA which has been typically regarded as superfluous to the function of the genome in generating phenotypes. In this work, we used comparative phylogenetic approaches to investigate if the variations in genome sizes (GS) should be considered as adaptive or neutral processes by the comparison between GS and flower diameters (FD) of 50 Passiflora species, more specifically, within its two most species-rich subgenera, Passiflora and Decaloba. For this, we have constructed a phylogenetic tree of these species, estimated GS and FD of them, inferred the tempo and mode of evolution of these traits and their correlations, using both current and phylogenetically independent contrasted values. We found significant correlations among the traits, when considering the complete set of data or only the subgenus Passiflora, whereas no correlations were observed within Decaloba. Herein, we present convincing evidence of adaptive evolution of GS, as well as clues that this pattern is limited by a minimum genome size, which could reduce both the possibilities of changes in GS and the possibility of phenotypic responses to environment changes.     

Genetic diversity and ecological niche modelling of the restricted Recordia reitzii (Verbenaceae) from southern Brazilian Atlantic forest

Genetic diversity analyses, coupled with ecological niche modelling (ENM) of species with a restricted distribution, may provide valuable information for understanding diversification patterns in endangered areas. We analyzed the genetic diversity of Recordia reitzii, a tree restricted to the threatened and highly fragmented Brazilian Atlantic forest, using three intergenic cpDNA spacers and ten microsatellite (SSR) loci. To assess the historical processes that may have influenced the distribution of extant R. reitzii populations, the current potential distributions of R. reitzii and Recordia boliviana, a closely related species, were modelled and projected onto the Last Glacial Maximum (LGM) and Last Interglacial (LIG) periods. Niche divergence was quantified between these two. The cpDNA and SSR data showed a north–south pattern of the diversity distribution and structured populations, suggesting that gene flow is probably limited. According to our data, R. reitzii exhibits low genetic diversity, which may be a result of a founder or distribution‐reduction effect, narrow distribution or small population size. The ecological niche models showed a wider palaeodistribution during the LIG and a retraction during the LGM for both species. Tests of niche divergence and conservatism indicated that bioclimatic factors might have influenced the diversification of these Recordia species. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 332–348.     

Essential Oil of Thymus munbyanus subsp. coloratus from Algeria: Chemotypification and in vitro Biological Activities

Thymus munbyanus subsp. coloratus (Lamiaceae) is a small shrub endemic to Algeria and Morocco where is found in lawns, rockeries and mountainous regions. From a phytochemical point of view this taxon has never been characterized. In this work we have analysed the chemical compositions of the essential oils obtained from inflorescences and vegetative parts by GC/MS. A new chemotype, i.e. borneol‐chemotype, was characterized for the first time in the species. Furthermore, we assessed the biological activities of essential oils, namely the antioxidant, antimicrobial and cytotoxicity on tumor cells that were evaluated by the DPPH, ABTS, and FRAP, disc diffusion, and MTT methods, respectively. Biological assays highlighted a moderate inhibitory effect on Staphylococcus aureus, Escherichia coli and Candida albicans (inhibition zone diameter in the range 9 – 10 mm), and noteworthy cytotoxicity on A375 human melanoma cells (IC₅₀ of 46.95 μg/ml).     

Phylogeographic inferences concerning evolution of Brazilian Passiflora actinia and P. elegans (Passifloraceae) based on ITS (nrDNA) variation

BACKGROUND AND AIMS: Passiflora actinia and P. elegans, two markedly parapatric species, have their southern and northern distribution limits, respectively, in the most southern part of the Brazilian Atlantic Rain Forest. Despite the fact that they are classified in different taxonomic series, previous phylogenetic studies of this genus revealed a high genetic similarity between them. The aim of the present work was to analyse in more detail their geographical range in this region of overlap, to investigate intraspecific genetic variability and phylogeographic structure, and to search for possible hybrids. METHODS: Eighty-two localities were searched for these species, and nuclear internal transcribed spacer (ITS) sequences were investigated for 32 individuals of P. actinia, 20 of P. elegans and one putative interspecific hybrid. Plastid trnL-trnF and psbA-trnH were examined for 12 plants of each species and the putative hybrid. KEY RESULTS: Both species showed a high level of intraspecific and intra-individual ITS variability. Network analysis revealed a north-south geographic gradient in their intra and interspecific relationships. Mismatch analyses suggested a recent population expansion of P. elegans. The plastid markers showed restricted variability but, together with the nuclear data, they contributed to the identification of an interspecific hybrid of intermediate morphology at the border of the distribution of these two species. Both genetic and morphological data indicate the absence of an extensive hybridization zone between these species. CONCLUSIONS: Gene flow between lineages is the possible cause for the presence of different ITS sequences within a given plant, the absence of homogenization being due to the high degree of vegetative reproduction in the two species. Differentiation of P. actinia into geographic groups and the origin of P. elegans may have been influenced by the Atlantic Forest migration towards southern Brazil. The genetic pattern of the interspecific hybrid indicates that plastid inheritance in these species is at least sometimes paternal.     

Phylogeography and ecological niche modelling in Eugenia uniflora (Myrtaceae) suggest distinct vegetational responses to climate change between the southern and the northern Atlantic Forest

In this study, we evaluate phylogeographic patterns and predictions of ecological niche modelling (ENM) for Eugenia uniflora (Myrtaceae), a widely distributed taxon in the Atlantic forest domain, to understand the effect of past climatic oscillations on the demographic history of this species. An analysis of phylogeographic population structure and demography was conducted on E. uniflora from 46 localities in natural environments across the distribution range of the species based on three plastid markers. ENM was also performed to predict suitable environments and areas of dramatic decrease in future suitability for the species under distinct representative concentration pathways (RCPs). Eugenia uniflora exhibited higher haplotype and nucleotide diversity in the southern part of its distribution than in the northern part. Two divergent lineages were revealed in the phylogenetic analysis of haplotypes, with an estimated divergence at c. 4.9 Mya. The populations in the northern and central regions of the range probably experienced population growth, whereas populations in the southern region are marked by historical demographic stability. ENM results indicate that the distribution of E. uniflora was fragmented in cool periods and was broader and more connected during warm periods during Pleistocene. The results suggest distinct evolutionary histories in southern to northern populations, indicating region‐specific responses to changes.     

Characterization of a new <Emphasis Type="Italic">GmFAD3A</Emphasis> allele in Brazilian CS303TNKCA soybean cultivar

Key Message

We molecularly characterized a new mutation in the GmFAD3A gene associated with low linolenic content in the Brazilian soybean cultivar CS303TNKCA and developed a molecular marker to select this mutation.

Abstract

Soybean is one of the most important crops cultivated worldwide. Soybean oil has 13% palmitic acid, 4% stearic acid, 20% oleic acid, 55% linoleic acid and 8% linolenic acid. Breeding programs are developing varieties with high oleic and low polyunsaturated fatty acids (linoleic and linolenic) to improve the oil oxidative stability and make the varieties more attractive for the soy industry. The main goal of this study was to characterize the low linoleic acid trait in CS303TNKCA cultivar. We sequenced CS303TNKCA GmFAD3A, GmFAD3B and GmFAD3C genes and identified an adenine point deletion in the GmFAD3A exon 5 (delA). This alteration creates a premature stop codon, leading to a truncated protein with just 207 residues that result in a non-functional enzyme. Analysis of enzymatic activity by heterologous expression in yeast support delA as the cause of low linolenic acid content in CS303TNKCA. Thus, we developed a TaqMan genotyping assay to associate delA with low linolenic acid content in segregating populations. Lines homozygous for delA had a linolenic acid content of 3.3 to 4.4%, and the variation at this locus accounted for 50.83 to 73.70% of the phenotypic variation. This molecular marker is a new tool to introgress the low linolenic acid trait into elite soybean cultivars and can be used to combine with high oleic trait markers to produce soybean with enhanced economic value. The advantage of using CS303TNKCA compared to other lines available in the literature is that this cultivar has good agronomic characteristics and is adapted to Brazilian conditions.

     

Changes in the avifauna in a high Andean cloud forest in Colombia over a 24‐year period

The upper altitude ecosystems of the Andes are among the most threatened by climate change. Computer models suggest that a large percentage of species in these ecosystems will be at risk of extinction and that avian communities will suffer disruption and impoverishment. Studies in other Andean countries lend some support to these predictions, but there are no quantitative data from Colombia appropriate to test these models. In 1991–1992, we conducted a bird survey in a high Andean cloud forest to gather information about the species present and their abundance. We attempted to replicate this earlier study 24 yr later to detect any changes in the avifauna and determine possible causes for those changes. From June 2015 to May 2016, we made bimonthly trips to the study site and identified all birds detected either visually or by voice along a number of trails. We supplemented our observational data by also capturing birds in mist‐nets. Community species richness and composition as well as the overall abundance of birds changed little from 1991–1992 to 2015–2016, but nearly 30% of bird species changed in abundance. Changes in the presence or abundance of nine or 10 species reflected upward shifts in elevational limits potentially due to climate change. However, most changes in abundance appeared to reflect changes in the vegetation of the study area due to successional changes in forest and subparamo habitats and a large number of relatively recent treefalls of old canopy trees with heavy epiphyte loads and subsequent changes in the understory vegetation. Our results suggest that the effects of climate change on the avifauna in our study area at a high‐altitude site in Colombia are apparently occurring more slowly than predicted by recent computer models, although we conclude that the possible effects of climate change should definitely be considered in future studies. However, single‐site studies such as ours have limitations in documenting elevation shifts; the most conclusive and quantitative evidence for elevational shifts comes from long‐term studies conducted over a wide range of elevations. As such, we recommend establishment of such a monitoring program in Colombia because data obtained from such a program might be important in designing measures to mitigate the effects of climate change and conserve biodiversity.