Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross-specific and species-specific amplifications

Although whole-genome sequencing is becoming more accessible and feasible for nonmodel organisms, microsatellites have remained the markers of choice for various population and conservation genetic studies. However, the criteria for choosing microsatellites are still controversial due to ascertainment bias that may be introduced into the genetic inference. An empirical study of red deer (Cervus elaphus) populations, in which cross-specific and species-specific microsatellites developed through pyrosequencing of enriched libraries, was performed for this study. Two different strategies were used to select the species-specific panels: randomly vs. highly polymorphic markers. The results suggest that reliable and accurate estimations of genetic diversity can be obtained using random microsatellites distributed throughout the genome. In addition, the results reinforce previous evidence that selecting the most polymorphic markers leads to an ascertainment bias in estimates of genetic diversity, when compared with randomly selected microsatellites. Analyses of population differentiation and clustering seem less influenced by the approach of microsatellite selection, whereas assigning individuals to populations might be affected by a random selection of a small number of microsatellites. Individual multilocus heterozygosity measures produced various discordant results, which in turn had impacts on the heterozygosity-fitness correlation test. Finally, we argue that picking the appropriate microsatellite set should primarily take into account the ecological and evolutionary questions studied. Selecting the most polymorphic markers will generally overestimate genetic diversity parameters, leading to misinterpretations of the real genetic diversity, which is particularly important in managed and threatened populations.

Genealogy of the nuclear β-fibrinogen locus in a highly structured lizard species: comparison with mtDNA and evidence for intragenic recombination in the hybrid zone

The study of nuclear genealogies in natural populations of nonmodel organisms is expected to provide novel insights into the evolutionary history of populations, especially when developed in the framework of well-established mtDNA phylogeographical scenarios. In the Iberian Peninsula, the endemic Schreiber's green lizard Lacerta schreiberi exhibits two highly divergent and allopatric mtDNA lineages that started to split during the late Pliocene. In this work, we performed a fine-scale analysis of the putative mtDNA contact zone together with a global analysis of the patterns of variation observed at the nuclear beta-fibrinogen intron 7 (beta-fibint7). Using a combination of DNA sequencing with single-strand conformational polymorphism (SSCP) analysis, we show that the observed genealogy at the beta-fibint7 locus reveals extensive admixture between two formerly isolated lizard populations while the two mtDNA lineages remain essentially allopatric. In addition, a private beta-fibint7 haplotype detected in the single population where both mtDNA lineages were found in sympatry is probably the result of intragenic recombination between the two more common and divergent beta-fibint7 haplotypes. Our results suggest that the progressive incorporation of nuclear genealogies in investigating the ancient demography and admixture dynamics of divergent genomes will be necessary to obtain a more comprehensive picture of the evolutionary history of organisms.

Disentangling the photochemical salinity tolerance in Aster tripolium L.: connecting biophysical traits with changes in fatty acid composition

A profound analysis of A. tripolium photochemical traits under salinity exposure is lacking in the literature, with very few references focusing on its fatty acid profile role in photophysiology. To address this, the deep photochemical processes were evaluated by Pulse Amplitude Modulated (PAM) Fluorometry coupled with a discrimination of its leaf fatty acid profile. Plants exposed to 125-250 mm NaCl showed higher photochemical light harvesting efficiencies and lower energy dissipation rates. under higher NaCl exposure, there is evident damage of the oxygen evolving complexes (OECs). On the other hand, Reaction Centre (RC) closure net rate and density increased, improving the energy fluxes entering the PS II, in spite of the high amounts of energy dissipated and the loss of PS II antennae connectivity. Energy dissipation was mainly achieved through the auroxanthin pathway. Total fatty acid content displayed a similar trend, being also higher under 125-250 mm NaCl with high levels of omega-3 and omega-6 fatty acids. The increase in oleic acid and palmitic acid allows the maintenance of the good functioning of the PS II. Also relevant was the high concentration of chloroplastic C16:1t in the individuals subjected to 125-250 mm NaCl, related with a higher electron transport activity and with the organization of the Light Harvesting Complexes (LHC) and thus reducing the activation of energy dissipation mechanisms. All these new insights shed some light not only on the photophysiology of this potential cash-crop, but also highlight its important saline agriculture applications of this species as forage and potential source of essential fatty acids.

Genetic diversity at the hinge region of the unique immunoglobulin heavy gamma (IGHG) gene in leporids (Oryctolagus, Sylvilagus and Lepus)

Unlike other species, European rabbit (Oryctolagus cuniculus) possesses only one immunoglobulin gamma class. Allelic diversity at the Ig (immunoglobulin) gamma constant region encoded by the unique IGHG (immunoglobulin heavy gamma) gene is moreover much reduced. In the European rabbit, the genetic variation at IGGH hinge region is limited to a single nucleotide substitution, which causes a Met-Thr interchange at amino acid position 9 (IMGT hinge numbering). We have analysed the diversity at this region more in-depth by, (1) analysing the allelic variation in 11 breeds of domestic European rabbit (Oryctolagus cuniculus cuniculus), and (2) sequencing the gamma hinge exon in wild specimens of six species of rabbit (Oryctolagus and Sylvilagus) and hares (Lepus), including the two Oryctolagus subspecies (O. cuniculus cuniculus and O. cuniculus algirus). It appeared that among leporid species, amino acid changes occur exclusively at positions 8 and 9. However, while position 8 is occupied by either Pro or Ser residues, four different residues can occur at position 9 (Met, Thr, Pro and Leu). This variation concerns sites of potential O-glycosylation and/or proteolytic cleavage, suggesting that the underlying genetic diversity could be the outcome of selection. Preservation of the gamma hinge polymorphism in domestic stocks could therefore be important. We report here a polymerase chain reaction/restriction fragment length polymorphism protocol that has allowed the monitoring of the heterozygosity levels at the gamma hinge in 11 breeds of domestic European rabbit.

São Paulo aerosol characterization study

The São Paulo Metropolitan area (SPMA) is characterized as having one of the worst air pollution problems in Brazil, with frequent violations of air quality standards for particulate matter. This paper presents the results of a receptor model source apportionment study carried out to develop a quantitative database on which a control strategy could be developed. The study was conducted in four sites with distinct land uses. Fine, coarse (CP), and total suspended particles (TSP) samples were collected on Teflon and glass filters and analyzed by x-ray fluorescence (XRF), ion chromatography, and thermal evolution. The sources were characterized by similar methodology. Chemical mass balance (CMB) receptor modeling indicated that carbonaceous material plays an important role in the aerosol composition; that the three major source categories contributing to the fine particles are vehicles, secondary carbon, and sulfates; and that the main contributors to CP and TSP are road dust and vehicles. All sampling sites presented the same general pattern in terms of source contribution, although this contribution varied from site to site.

Spermatic cord liposarcoma: organ-sparing surgery

The authors report a case of a 53-year-old male patient who came to the urologic clinic with symptoms of a left-sided testicular mass with 4 years of evolution. A left inguinal approach was decided for scrotal exploration. High clamping of the spermatic cord was performed with complete excision of the lesion, which was sent for pathology, preserving the spermatic cord and the testicle. The peroperative result was a well-differentiated liposarcoma of the spermatic cord. We then chose to preserve the ipsilateral testis (organ-sparing surgery). Postoperatively, the final pathology confirmed a well-differentiated spermatic cord liposarcoma, revealing negative surgical margins and no signs of local invasion, namely of the underlying structures. The patient is currently doing well, with no signs of recurrence after one and a half year of follow-up.

Prior MRI-imaging impact of patients submitted to brachytherapy for prostate cancer

INTRODUCTION

Brachytherapy for the treatment of prostate cancer is a well-established option. Use of Multiparametric Magnetic Resonance Imaging (mpMRI) for staging and diagnosis of prostate cancer has come to change the current paradigm. In this study we aim to assess the impact of performing mpMRI to evaluate the presence of extracapsular lesions before brachytherapy in patients with prostate cancer concerning biochemical recurrence and time to nadir.

METHODS

Review data from 73 patients submitted to brachytherapy. The following factors were evaluated: age, initial PSA, MRI local staging results, ISUP, nadir, time to nadir, PSA at one-year, biochemical recurrence, and time to recurrence.

RESULTS

Median age was 68 years (51-72) and median follow-up 53 months (30-72). Concerning imaging modality 30,1% (n = 22) patients performed mpMRI. In the mpMRI group, 90.9% (n = 20) had at least one suspect lesion on mpMRI. Time to nadir was 27 months (3-64) in patients where mpMRI was not performed and 23.5 months (2-48) in patients submitted to mpMRI (P = .244). The median value of nadir was 0.42 ng/mL (<0.001-2) in patients submitted to mpMRI and vs 0.28 ng/mL (<0.001-4) in patients without MRI (P = .062) Recurrence utilizing Phoenix criteria was 9% (n = 2) in patients with MRI and 9.2% (n = 5) without mpMRI (P = .456), median follow-up of 43 months (12-72) for the MRI group with 58 months (30-78) for the non-mpMRI group. Both groups were statistically similar.

CONCLUSION

Our results allow us to conclude that in our series MRI did not influence biochemical recurrence, time to nadir, or nadir value.

Spatial genetic patterns in African wild dogs reveal signs of effective dispersal across southern Africa

Across much of Africa, decades of civil war, land reforms, and persecution by humans have decimated wildlife populations. African wild dogs (Lycaon pictus) have declined dramatically during the past decades, but have shown recent natural recolonisation of some areas. In Angola, they were rediscovered after almost five decades when no surveys were being conducted, and they have recolonised areas in southern Zimbabwe and northern South Africa. Wild dogs were also reintroduced to Mozambique, where only few individuals remained. Against this backdrop, understanding genetic structure and effective dispersal between fragmented populations is essential to ensure the best conservation approaches for the long-term survival of the species. Our study investigated population genetic diversity, differentiation and gene flow of wild dogs across southern Africa, to include areas where they have recently been rediscovered, reestablished or reintroduced. Our results point to four weakly differentiated genetic clusters, representing the lowveld of Zimbabwe/Limpopo, Kruger NP, Angola/KAZA-TFCA, and the managed metapopulation, counterbalanced by moderate levels of effective dispersal on a southern African scale. Our results suggest that if the human footprint and impact can be significantly minimized, natural dispersal of wild dogs could lead to the demographic recovery of the species in southern Africa.