Thinking of Fish Population Discrimination: Population Average Phenotype vs. Population Phenotypes

The genetic polymorphism and phenotypic variation are key in ecology and evolution. The morphological variability of the contour of fish otoliths has been extensively used for the delimitation of stocks. These studies are conventionally based on average phenotype using elliptic Fourier analysis and lineal discriminant analysis as classifier. Considering new analytical options, such as the wavelet transform and non-parametric algorithms, we here analyzed the otolith shape of Trachurus picturatus (blue jack mackerel) from mainland Portugal, Madeira, and the Canaries. We explore the phenotypic variation throughout a latitudinal gradient, establish a hypothesis to explain this variability based on the reaction norms, and determine how the use of average phenotype and/or morphotypes influences in the delimitation of stocks. Four morphotypes were identified in all regions, with an increase of phenotypes in warmer waters. The findings demonstrated that stocks were clearly separated with classification rates over 90%. The use of morphotypes, revealed seasonal variations in their frequencies and per region. The presence of shared phenotypes in different proportions among fishing grounds may open new management approaches in migratory species. These results show the importance of the phenotypic diversity in fisheries management.

Biometric characteristics of the wild population of sea urchin Paracentrotus lividus (Lamarck, 1816) on the Tunisian coast

The present study was conducted to provide biometric data of the edible sea urchin Paracentrotus lividus along the Tunisian coastline where thirteen marine localities were selected randomly. A total of 653 individuals were collected and their metric and weight measurements were recorded. The size distribution of the different samples was determined and relative growth expressions were deduced. Data analysis showed that all localities’ samples of the wild population were dominated by one-size class, except Port Prince and Haouaria. Interestingly, only diameter-height relationships (D-H) were different between the geographical localities. Diameter-weight relationships (D-TW and D-TWTE) revealed a significant negative growth for all the localities, with the exception of Gammarth which showed positive growth for total weight (D-TW). Moreover, the multivariable analysis revealed divergences and/or similarities between metric and weight variables. Altogether, data highlights the inter-population discrimination with respect to geographic localization and clear segregation between the northern and the eastern localities demonstrated the plasticity of the species.

Microsatellite Marker Discovery in the Stingless Bee Uruçu-Amarela (Melipona rufiventris Group, Hymenoptera, Meliponini) for Population Genetic Analysis

The species Melipona rufiventris Lepeletier, 1836 is a Brazilian native stingless bee that is part of a species complex known as the ‘rufiventris group’, making it difficult to distinguish between the different species. Populations in this group are facing a severe decline, leading to the risk of local extinction, and therefore, their conservation should be treated as a major concern. This study describes the first set of tri- and tetranucleotide microsatellite markers, using next-generation sequencing technology for use in the identification of genetic diversity and population structure in the ‘rufiventris group’. A total of 16 microsatellite loci displayed polymorphism. Analysis of the whole data set (n = 50) detected 63 alleles in all loci, ranging from 2 to 7 with a mean of 3.9 alleles/locus. A genetic diversity analysis revealed high values for population differentiation estimates (FST = 0.252, RST = 0.317, and DEST = 0.284) between the Atlantic Forest, Cerrado, and Caatinga biomes. An additional evidence for genetic divergence among populations was also found in the ’rufiventris group’; these should be treated as separate conservation units or even as separate species. These microsatellite markers have demonstrated a strong potential for assessing population discrimination in this threatened stingless bee group.

Patterns of morphological variation in the Schlegel’s Japanese gecko (Gekko japonicus) across populations in China, Japan, and Korea

Background Studies of morphological variation within and among populations provide an opportunity to understand local adaptation and potential patterns of gene flow. To study the evolutionary divergence patterns of Schlegel’s Japanese gecko (Gekko japonicus) across its distribution, we analyzed data for 15 morphological characters of 324 individuals across 11 populations (2 in China, 4 in Japan, and 5 in Korea). Results Among-population morphological variation was smaller than within-population variation, which was primarily explained by variation in axilla-groin length, number of infralabials, number of scansors on toe IV, and head-related variables such as head height and width. The population discrimination power was 32.4% and in cluster analysis, populations from the three countries tended to intermix in two major groups. Conclusion Our results indicate that morphological differentiation among the studied populations is scarce, suggesting short history for some populations after their establishment, frequent migration of individuals among the populations, and/or local morphological differentiation in similar urban habitats. Nevertheless, we detected interesting phenetic patterns that may predict consistent linkage of particular populations that are independent of national borders. Additional sampling across the range and inclusion of genetic data could give further clue for the historical relationship among Chinese, Japanese, and Korean populations of G. japonicus.

High-Throughput Analysis of Clinical Flow Cytometry Data by Automated Gating

Advancements in flow cytometers with capability to measure 15 or more parameters have enabled us to characterize cell populations at unprecedented levels of detail. Beyond discovery research, there is now a growing demand to dive deeper into evaluating the immune response in clinical trials for immune modulating compounds. However, for high-volume, complex flow cytometry data generated in clinical trials, conventional manual gating remains the standard of practice. Traditional manual gating is resource intense and becomes a bottleneck and an impractical method to complete high volumes of flow cytometry data analysis. Current efforts to automate “manual gating” have shown that computational algorithms can facilitate the analysis of daunting multi-parameter data; however, a greater degree of precision in comparison with traditional manual gating is needed for wide-scale adoption of automated gating methods. In an effort to more closely follow the manual gating process, our automated gating pipeline was created to include negative controls (Fluorescence Minus One [FMO]) to enhance the reliability of gate placement. We demonstrate that use of an automated pipeline, heavily relying on FMO controls for population discrimination, can analyze multi-parameter, large-scale clinical datasets with comparable precision and accuracy to traditional manual gating.

Preliminary results of Turkish hazelnut (Corylus colurna L.) populations for testing the nut characteristics

This paper aims to identify the hazelnut characteristics of four different populations (A?l?-Tunuslar, A?l?-M?sellimler, Ara?-G?zl?k and Tosya-K???ksekiler) in the North Western Black Sea Region of Turkey, one of the most important areas of economic interest for this species. There, the Turkish hazel (Corylus colurna L.) grows in its optimal conditions and reveals relatively high inter-population and intra-population variation in terms of nut characteristics. With the purpose of assessing variation, measurements were performed in four populations in Kastamonu district on 14 different nut characteristics (number of nuts per cluster, nut length (mm), nut width (mm), nut thickness (mm), shell thickness (mm), nut size (mm), nut shape, compression index, nut weight (g), kernel length (mm), kernel width (mm), kernel thickness (mm), kernel weight (g) and kernel ratio (%) of representative samples of the populations. Significant differences were found out among populations with regard to all of nut characteristics (p<0.05). The four populations have created two groups, population of A?l?-Tunuslar and the others, according to cluster analysis. The closest populations have been Tosya-K???ksekiler and Ara?-G?zl?k in terms of nut characteristics. According to the results obtained either on population basis or without population discrimination; significant correlations were determined between the majorities of the nut characters. The Ara?-G?zl?k population showed nuts the biggest among those examined and it is the population which took the highest values in terms of nut size traits while the Tosya-K???ksekiler provenance showed the highest values with the average values of 5, 15.92 mm, 1.32 and 11.75 mm respectively for nuts per cluster, nut width, compression index and kernel width. The A?l?-Tunuslar population showed the highest kernel ratio with 38.2%.