Complex fine‐scale phylogeographical patterns in a putative refugial region for Fagus sylvatica (Fagaceae)

Broad‐scale plastid (chloroplast) DNA studies of beech (Fagus sylvatica) populations suggest the existence of glacial refugia and introgression zones in south‐eastern Europe. We choose a possible refugium of beech in northern Greece, Mt. Paggeo, which hosts a private plastid haplotype for beech, to conduct a fine‐scale genetic study. We attempt to confirm or reject the hypothesis of the existence of a small‐scale refugium and to gain an understanding of the ecological and topographical factors affecting the spatial distribution of plastid haplotypes in the area. Our results reveal a high haplotype diversity on Mt. Paggeo, but the overall distribution of haplotypes shows no significant correlation with the ecological characteristics of the beech forests. However, the private haplotype is found at high frequencies in beech forests located in or near ravines, having a high spatial overlap with a relict vegetation type occurring in ecological conditions found mainly in ravines. This result emphasizes the importance of topography in the existence of glacial refugia in the wider area. Furthermore, haplotypes originating from two more widespread beech lineages in Greece are found on Mt. Paggeo, indicating a possible mixing of populations originating from a local refugium with populations from remote refugia that possibly migrated into the area after the last glaciation. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174 , 516–528.     

DyCoNet: A Gephi Plugin for Community Detection in Dynamic Complex Networks

Community structure detection has proven to be important in revealing the underlying organisation of complex networks. While most current analyses focus on static networks, the detection of communities in dynamic data is both challenging and timely. An analysis and visualisation procedure for dynamic networks is presented here, which identifies communities and sub-communities that persist across multiple network snapshots. An existing method for community detection in dynamic networks is adapted, extended, and implemented. We demonstrate the applicability of this method to detect communities in networks where individuals tend not to change their community affiliation very frequently. When stability of communities cannot be assumed, we show that the sub-community model may be a better alternative. This is illustrated through test cases of social and biological networks. A plugin for Gephi, an open-source software program used for graph visualisation and manipulation, named “DyCoNet”, was created to execute the algorithm and is freely available from https://github.com/juliemkauffman/DyCoNet.     

Evolution of the rate of biological aging using a phenotype based computational model

In this work I introduce a simple model to study how natural selection acts upon aging, which focuses on the viability of each individual. It is able to reproduce the Gompertz law of mortality and can make predictions about the relation between the level of mutation rates (beneficial/deleterious/neutral), age at reproductive maturity and the degree of biological aging. With no mutations, a population with low age at reproductive maturity R stabilizes at higher density values, while with mutations it reaches its maximum density, because even for large pre-reproductive periods each individual evolves to survive to maturity. Species with very short pre-reproductive periods can only tolerate a small number of detrimental mutations. The probabilities of detrimental (P_d) or beneficial (P_b) mutations are demonstrated to greatly affect the process. High absolute values produce peaks in the viability of the population over time. Mutations combined with low selection pressure move the system towards weaker phenotypes. For low values in the ratio P_d/P_b, the speed at which aging occurs is almost independent of R, while higher values favor significantly species with high R. The value of R is critical to whether the population survives or dies out. The aging rate is controlled by P_d and P_b and the amount of the viability of each individual is modified, with neutral mutations allowing the system more “room” to evolve. The process of aging in this simple model is revealed to be fairly complex, yielding a rich variety of results.     

Genetic diversity and population structure of the serpentine endemic Ni hyperaccumulator Alyssum lesbiacum

Alyssum lesbiacum is a well-established Ni hyperaccumulator, endemic to serpentine soils of Lesbos Island (Greece). A total of 95 individuals were collected from 17 plots encompassing the only four large populations of this species. ISSR (Inter-simple sequence repeat) markers were used to assess genetic diversity and population structure of A. lesbiacum to provide initial guidance for the development of successful management and conservation measures. A total of ten primers produced 82 bands, 96.34 % being polymorphic. The largest part of total diversity was found within populations, rather than among them. AMOVA analysis partitioned the largest part of diversity within plots (66 %), while 15 % contained among plots within populations and 19 % among populations. Principal coordinates analysis along with dendrogram based on genetic distances among populations showed a high degree of genetic differentiation of the isolated population Loutra. At a smaller scale, distance was not the most significant factor influencing the patterns of genetic diversity, but topography, ecosystem types and connectivity through streams. According to our results, conservation efforts should be organized at the level of watersheds and ecosystem types, considering them as management units. For ex situ conservation and restoration, seed samplings should be representative of the different habitats and watersheds as well as the patches of large and small populations while keeping the east population of Loutra separate from the other three central populations, to avoid any loss of genetic diversity and to preserve the character of the local adapted populations.     

Surface antigen-guided CRISPR screens identify regulators of myeloid leukemia differentiation

1. Download : Download high-res image (184KB)
2. Download : Download full-size image

     

Changeability of sperm chromatin structure during liquid storage of ovine semen in milk-egg yolk- and soybean lecithin-based extenders and their relationships to field-fertility

The aim of this experiment was to study the effect of semen extender on sperm chromatin structure and to correlate chromatin integrity with field-fertility of preserved ram semen. Ejaculates of at least 2 × 10⁹ sperm/ml and 70 % progressive motility were collected using an artificial vagina from Chios rams (n = 11, 4–6 years old), split-diluted to 1 × 10⁹ sperm/ml with milk-egg yolk- and soybean lecithin (Ovixcell^®)-based extenders, packaged in 0.5-ml straws and examined after 6, 24 and 48 h of storage at 5 ± 1 °C. Evaluation endpoints were computer-assisted sperm motion analysis, fluorescence-based analysis of chromatin structure by chromomycin A₃ and acridine orange assays, and 65-day pregnancy rate (PR) of 34- to 36-h preserved semen after intra-cervical insemination of ewes (n = 154) in progestagen-synchronized estrus. Neither extender nor storage time had any influence on incidence of decondensed chromatin. Unlike Ovixcell^® extender, deterioration of sperm motility (P < 0.01) and chromatin stability (P < 0.005) was detected after 48 h of storage in milk-egg yolk extender. Sperm motility accounted for 14.4–18.5 % of variations in chromatin integrity (P < 0.001). No significant difference was found in PR of Ovixcell^®- and milk-egg yolk-stored semen. Nevertheless, PR differed between rams (14.3–71.4 %; P < 0.025). Chromatin integrity explained 10.2–56.3 % of variations in PR (P < 0.05–0.01). A pronounced decline in PR (19.1 %) was observed when percentages of decondensed and destabilized chromatin have reached thresholds of 10.5–30 % and 4–9 %, respectively. In conclusion, Ovixcell^® is superior to milk-egg yolk extender in preserving chromatin stability and motility. Chromatin defects are negatively associated with sperm fertility.     

Changing social awareness of the illegal killing of migratory birds in the Ionian Islands,western Greece

ABSTRACT

The current study aims at monitoring, measuring and evaluating the ‘Safe havens for wild birds’ campaign, implemented within the framework of the LIFE programme, in Greece and more specifically in the Ionian Islands. The study detects attitude changes that occurred in three target groups (pupils, local hunters and residents) on three islands where the phenomenon of illegal spring killing is more intense. A questionnaire-based survey was conducted in two phases, just before the launch (2013) and after the completion of the campaign (2015), to enable a comparison of answers and data. The results show that pupils and to a lesser extent residents, enhanced their knowledge and awareness of poaching, the migration of avifauna and the consequences of illegal killing on migratory birds, while this aspect of attitude change was not observed in the hunting community which still believes that spring poaching should be treated as a legal activity and part of local culture.     

Comparative Benzofuran Chemistry of Enceliopsis

Enceliopsis (Asteraceae) is a small genus of herbaceous perennials from the Great Basin desert of the U.S.A. Phytochemical analysis revealed the presence of several benzofuran derivatives in Enceliopsis argophylla, E. covillei and E. nudicaulis. The compounds were either identical or very similar to benzofurans isolated from Encelia and Flourensia which supports the close affinity of these genera, as suggested previously, based on morphological, cytological and breeding studies.