Multi-GBS: A massively multiplexed GBS-based protocol optimized for large, repetitive conifer genomes

Reduced representation library approaches are still a valuable tool for breeding and population and ecological genomics, even with impressive increases in sequencing capacity in recent years. Unfortunately, current approaches only allow for multiplexing up to 384 samples. To take advantage of increased sequencing capacity, we present Multi-GBS, a massively multiplexable extension to Genotyping-by-Sequencing that is also optimized for large conifer genomes. In Norway Spruce, a highly repetitive 20Gbp diploid genome with high population genetic variation, we call over a million variants in 32 genotypes from three populations, two natural forest in the Alps and Bohemian Alps, and a managed population from southeastern Austria using the existing TASSEL GBSv2 pipeline. Metric MDS analysis of replicated genotypes shows that technical bias in resulting genotype calling is minimal and that populations cluster in biologically meaningful ways.

Extreme climatic events but not environmental heterogeneity shape within-population genetic variation in maritime pine

How evolutionary forces interact to maintain quantitative genetic variation within populations has been a matter of extensive theoretical debates. While mutation and migration increase genetic variation, natural selection and genetic drift are expected to deplete it. To date, levels of genetic variation observed in natural populations are hard to predict without accounting for other processes, such as balancing selection in heterogeneous environments. We aimed to empirically test three hypotheses: (i) admixed populations have higher quantitative genetic variation due to introgression from other gene pools, (ii) quantitative genetic variation is lower in populations from harsher environments (i.e. experiencing stronger selection), and (iii) quantitative genetic variation is higher in populations from spatially heterogeneous environments. We used phenotypic measurements of five growth, phenological and functional traits from three clonal common gardens, consisting of 523 clones from 33 populations of maritime pine (Pinus pinaster Aiton). Populations from harsher climates (mainly colder areas) showed lower genetic variation for height in the three common gardens. Surprisingly, we did not find any association between within-population genetic variation and environmental heterogeneity or population admixture for any trait. Our results suggest a predominant role of natural selection in driving within-population genetic variation, and therefore indirectly their adaptive potential.

Molecular Phylogenetics and Population Genetics of the Dengue Vector Aedes aegypti From the Arabian Peninsula

Aedes aegypti mosquito is the principal dengue vector in the Kingdom of Saudi Arabia (KSA); however, no study has addressed its ecology and population structure yet. Therefore, we report on Ae. aegypti phylo- and population genetics using three DNA markers: COI, ND4, and rDNA-ITS2. Sampling the immature stages of Ae. aegypti revealed that water storage tanks (34.3% of habitats) were the most productive and contained 33% of immatures stages. Other important habitats included containers for wastewater drainage (including air-conditioning and water cooler trays) and containers associated with ornamentation. Shallow water leakage spots (2.7% of habitats, 8% of immatures) can be considered rare-but-epidemiologically-important containers. Neighbor-joining (NJ) phylogenetic analysis of Ae. aegypti identified 8, 14, and 9 haplotypes of COI, ND4, and ITS2, respectively, and revealed high levels of genetic variation in Ae. aegypti populations of KSA. Global distribution of haplotypes also indicated multiple gene introductions into these populations, with high levels of intra-population genetic variation and continuous gene exchange. The neutrality values indicated a deficiency of alleles and suggested that the KSA Ae. aegypti loci tested did not follow a neutral model of molecular evolution. Fst values and AMOVA indicated that most of the genetic variation in the KSA Ae. aegypti populations is due to intra- rather than inter-population differences. This is the first comprehensive report on the phylo- and population genetics of Ae. aegypti from the Arabian Peninsula. This information expands our understanding of the ecology and population dynamics of this important arboviral vector for informed control efforts.

Multiple DNA marker-assisted diversity analysis of Indian mango (Mangifera indica L.) populations

Arbitrary (65 RAPD, 25 ISSR, 23 DAMD), gene-targeted (22 SCoT, 33 CBDP) and co-dominant sequence specific (40 SSR) markers were used individually, or in combinations, to examine the genetic variability within and among 70 selected Indian mango genotypes based on geographic origin (East India, West India, North India, South India) and fruit status (Selection, Hybrid, Landrace). The highest genetic variability was demonstrated by the East Indian populations, followed by those from South India, West India, and North India, when measured in terms of Na, Ne, H, I, PB%, Ht and Hs. Interestingly, the local genotypes of Odisha, which forms a part of East Indian populations, showed the highest diversity compared to hybrid or selection groups, suggesting that the indigenous genotypes hold a greater potential for exploiting the unique and favourable alleles. The maximum genetic variability was detected in geographical/fruit status populations with SSRs (Na—1.76/1.88, Ne—1.48/1.51, H—0.28/0.30, I—0.41/0.45, PB%—76.1/86.9, Ht—0.31/0.32 and Hs—0.28/0.30), followed by CBDPs and SCoTs, reflecting their preeminence for examining the level of genetic polymorphism and diversity. Outcome of AMOVA based analyses as well as low-to-moderate coefficient of genetic differentiation (Gst) and high gene flow (Nm) indicated a greater amount of intra-population genetic variation compared to heterogeneity at inter-population level. Information generated through this investigation could facilitate conservation and further exploitation of mango germplasm including genetic improvement through breeding.

Assessing the functional relevance of splice isoforms

Alternative splicing of messenger RNA can generate an array of mature transcripts, but it is not clear how many go on to produce functionally relevant protein isoforms. There is only limited evidence for alternative proteins in proteomics analyses and data from population genetic variation studies indicate that most alternative exons are evolving neutrally. Determining which transcripts produce biologically important isoforms is key to understanding isoform function and to interpreting the real impact of somatic mutations and germline variations. Here we have developed a method, TRIFID, to classify the functional importance of splice isoforms. TRIFID was trained on isoforms detected in large-scale proteomics analyses and distinguishes these biologically important splice isoforms with high confidence. Isoforms predicted as functionally important by the algorithm had measurable cross species conservation and significantly fewer broken functional domains. Additionally, exons that code for these functionally important protein isoforms are under purifying selection, while exons from low scoring transcripts largely appear to be evolving neutrally. TRIFID has been developed for the human genome, but it could in principle be applied to other well-annotated species. We believe that this method will generate valuable insights into the cellular importance of alternative splicing.

Population genetic structure of the Asian bush mosquito, Aedes japonicus (Diptera, Culicidae), in Belgium suggests multiple introductions

Background Aedes japonicus japonicus has expanded beyond its native range and has established in multiple European countries, including Belgium. In addition to the population located at Natoye, Belgium, locally established since 2002, specimens were recently collected along the Belgian border. The first objective of this study was therefore to investigate the origin of these new introductions, which were assumed to be related to the expansion of the nearby population in western Germany. Also, an intensive elimination campaign was undertaken at Natoye between 2012 and 2015, after which the species was declared to be eradicated. This species was re-detected in 2017, and thus the second objective was to investigate if these specimens resulted from a new introduction event and/or from a few undetected specimens that escaped the elimination campaign. Methods Population genetic variation at nad4 and seven microsatellite loci was surveyed in 224 and 68 specimens collected in Belgium and Germany, respectively. German samples were included as reference to investigate putative introduction source(s). At Natoye, 52 and 135 specimens were collected before and after the elimination campaign, respectively, to investigate temporal changes in the genetic composition and diversity. Results At Natoye, the genotypic microsatellite make-up showed a clear difference before and after the elimination campaign. Also, the population after 2017 displayed an increased allelic richness and number of private alleles, indicative of new introduction(s). However, the Natoye population present before the elimination programme is believed to have survived at low density. At the Belgian border, clustering results suggest a relation with the western German population. Whether the introduction(s) occur via passive human-mediated ground transport or, alternatively, by natural spread cannot be determined yet from the dataset. Conclusion Further introductions within Belgium are expected to occur in the near future, especially along the eastern Belgian border, which is at the front of the invasion of Ae. japonicus towards the west. Our results also point to the complexity of controlling invasive species, since 4 years of intense control measures were found to be not completely successful at eliminating this exotic at Natoye.

Genetic variation of Parapenaeopsis sculptilis (Decapoda, Penaeidae) and reassessment of the phylogenetic relationships within the genus Parapenaeopsis based on mitochondrial DNA variation

The genus Parapenaeopsis is an important group of marine shrimps for wild capture in the Indo-West Pacific region. Phylogenetics of penaeid shrimps is still a debatable issue. This study focuses on the phylogenetic relationships among seven species within the genus Parapenaeupsis, the population genetic variation of Parapenaeupsis sculptilis along Bangladesh coastline of the Bay of Bengal and the phylogeography of P. sculptilis in the Indian Ocean region by analysing cytochrome oxidase subunit 1 barcode (CO1) sequence. No population structure was detected in P. sculptilis collected from two sampling sites along the Bangladesh coastline (AMOVA and Φ ST = ‑0.014, p > 0.05; F ST = 0.061, p = 0.04), which expanded first around 73 (CI: 36‑119) kyr ago. The genealogical relationships in Bangladesh P. sculptilis population are shallow with haplotype diversity (h) of 0.58 and nucleotide diversity (π) of 0.0014. The different P. sculptilis samples from Bangladesh, India and Mozambique of the Indian Ocean revealed connectivity between western Indian Ocean and the Bay of Bengal. The phylogeny within the genus Parapenaeupsis showed a polyphyletic relationships for P. hardickwii and its taxonomy needs to be reevaluated. The study will help for genetic upgradation in aquaculture and monitoring of the population genetic diversity of P. sculptilis.