Spatial and temporal patterns of genetic diversity in Bombus terrestris populations of the Iberian Peninsula and their conservation implications

The bumblebee Bombus terrestris is used worldwide for crop pollination. Despite its positive impact on crop yield, it has become a widespread threat to biodiversity due to its interactions with local bumblebee populations. Commercial subspecies introduced to the Iberian Peninsula since the 1990s without any regulation have colonized the environment, with evidence of naturalization and introgression with the endemic subspecies Bombus terrestris lusitanicus. We have used mitochondrial and nuclear genetic data to describe the current genetic diversity of the Iberian population and to estimate the expansion of commercial bumblebees. Samples from the natural distribution range of the commercial subspecies, the natural intergradation area between the two subspecies and from a period prior to the use of commercial colonies (i.e., before the 1990s) have been used for comparison. Our results show that the mitochondrial haplotype of the commercial breeds has spread throughout the territory, which, together with subtle changes observed in the nuclear genetic diversity of the populations, indicates that hybridization and consequent introgression are occurring in most of the peninsula. It is, therefore, necessary to improve the existing legislation concerning the management and exportation of commercial bumblebees to conserve locally adapted populations.

Harbor porpoise losing its edges: genetic time series suggests a rapid population decline in Iberian waters over the last 30 years

Impact of climate changes on species is expected to be especially visible at the extremities of the species distribution, where they meet sub-optimal conditions. In Mauritania and Iberia, two genetically isolated populations of harbor porpoises form a distinct ecotype and are presumably locally adapted to the upwelling waters. By analyzing the evolution of mitochondrial genetic variation in the Iberian population between two temporal cohorts (1990-2002 vs. 2012-2015), we report a dramatic decrease in genetic diversity. Phylogenetic analyses including neighboring populations identified two porpoises in southern Iberia carrying a divergent haplotype close to the Mauritanian population, yet forming a distinctive lineage. This suggests that Iberian porpoises may not be as isolated as previously thought with immigration from Mauritania or an unknown population in between, but none from the northern ecotype. The rapid decline in the Iberian mitochondrial diversity may be driven by either genetic drift, or by a dramatic decline in census population size possibly resulting from environmental stochasticity, prey depletion, or acute fishery bycatches. These results illustrate the value of genetics time series to inform demographic trends and emphasize the urgent need for conservation measures to ensure the viability of this small harbor porpoise population in Iberia.

Minor Allele Frequencies and Molecular Pathways Differences for SNPs Associated with Amyotrophic Lateral Sclerosis in Subjects Participating in the UKBB and 1000 Genomes Project

Amyotrophic lateral sclerosis (ALS) is a complex disease with a late onset and is characterized by the progressive loss of muscular and respiratory functions. Although recent studies have partially elucidated ALS’s mechanisms, many questions remain such as what the most important molecular pathways involved in ALS are and why there is such a large difference in ALS onset among different populations. In this study, we addressed this issue with a bioinformatics approach, using the United Kingdom Biobank (UKBB) and the European 1000 Genomes Project (1KG) in order to analyze the most ALS-representative single nucleotide polymorphisms (SNPs) that differ for minor allele frequency (MAF) between the United Kingdom population and some European populations including Finnish in Finland, Iberian population in Spain, and Tuscans in Italy. We found 84 SNPs associated with 46 genes that are involved in different pathways including: “Ca2+ activated K+ channels”, “cGMP effects”, ”Nitric oxide stimulates guanylate cyclase”, “Proton/oligopeptide cotransporters”, and “Signaling by MAPK mutants”. In addition, we revealed that 83% of the 84 SNPs can alter transcription factor-motives binding sites of 224 genes implicated in “Regulation of beta-cell development”, “Transcription-al regulation by RUNX3”, “Transcriptional regulation of pluripotent stem cells”, and “FOXO-mediated transcription of cell death genes”. In conclusion, the genes and pathways analyzed could explain the cause of the difference of ALS onset.

GCAT|Panel, a comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing

The combined analysis of haplotype panels with phenotype clinical cohorts is a common approach to explore the genetic architecture of human diseases. However, genetic studies are mainly based on single nucleotide variants (SNVs) and small insertions and deletions (indels). Here, we contribute to fill this gap by generating a dense haplotype map focused on the identification, characterization and phasing of structural variants (SVs). By integrating multiple variant identification methods and Logistic Regression models, we present a catalogue of 35,431,441 variants, including 89,178 SVs (≥50bp), 30,325,064 SNVs and 5,017,199 indels, across 785 Illumina high coverage (30X) whole-genomes from the Iberian GCAT Cohort, containing 3.52M SNVs, 606,336 indels and 6,393 SVs in median per individual. The haplotype panel is able to impute up to 14,360,728 SNVs/indels and 23,179 SVs, showing a 2.7-fold increase for SVs compared with available genetic variation panels. The value of this panel for SVs analysis is shown through an imputed rare Alu element located in a new locus associated with mononeuritis of lower limb, a rare neuromuscular disease. This study represents the first deep characterization of genetic variation within the Iberian population and the first operational haplotype panel to systematically include the SVs into genome-wide genetic studies.

Out of Sight, Out of Mind: How Conservation Is Failing European Porpoises

The conservation of harbor porpoises (Phocoena phocoena) appears to be failing in Europe. There are particular concerns about this species in the Baltic Proper, Black, and Mediterranean Seas, as well as in the Northeast Atlantic, including the Iberian population, off the Spanish and Portuguese coasts. The Baltic Proper porpoise is “critically endangered,” with a population only in the low hundreds, and the Scientific Committee of the International Whaling Commission has repeatedly called for action to ensure its survival. In 2020, the Committee issued a series of recommendations relating to it and the Iberian population. Similarly, the Black Sea harbor porpoise, Phocoena phocoena ssp. relicta, is classified by the IUCN as endangered. Another population which may be genetically distinct is the West Greenland harbor porpoise, which is hunted without quotas or close seasons. European cetaceans and their habitats are covered by a number of international and regional conventions and agreements and, under European Union law, are “highly protected.” In practice, however, these legal protections have failed to generate effective conservation. For example, Special Areas of Conservation (SACs) are required for them and, although sites have been designated in some marine areas/countries, in the absence of appropriate management plans, SACs cannot be expected to help improve the harbor porpoise's conservation status. Compared to many other species, porpoises are relatively long-lived with low reproductive capacity and only poor public recognition. Conservation and management efforts are caught up in a complicated nexus of interactions involving a web of commitments under international conventions and agreements, European environmental laws, and European fisheries policy. However, public disinterest, lack of political will to implement conservation measures, and complicated fishing-related issues hinder any real progress. More positively, recent advice from the International Council for the Exploration of the Seas (ICES) provides a new scientific foundation for conservation action to address fisheries bycatch in the Baltic Proper harbor porpoise population. Populations of other porpoise species (family Phocoenidae) are also threatened, most notably the global population of the critically endangered vaquita, or Gulf of California porpoise (Phocoena sinus). The common threats and factors affecting porpoise populations are discussed and recommendations offered.

Origin, extinction and ancient DNA of a new fossil insular viper: molecular clues of overseas immigration

Viperinae is a subfamily of viperid snakes whose fossil record in the Mediterranean islands is, until now, restricted to 12 palaeontological deposits on seven islands. Revision of the material excavated 30 years ago from the Middle/Late Pleistocene–Holocene deposit of Es Pouàs [Eivissa (= Ibiza), Balearic Islands, western Mediterranean] revealed about 6000 bones of a small-sized viper across different stratigraphic levels. Its morphological characteristics are different enough to known species of Vipera to warrant the description of a new species, but the nearly complete mitochondrial genome obtained from this snake based on a sample dated to 16 130 ± 45 bp, suggested it belonged to a new insular population of Lataste’s viper (Vipera latastei), Vipera latastei ebusitana subsp. nov. Phylogenetic analysis indicates that the dispersal of the ancestors of V. l. ebusitana to Eivissa, most probably from a north-east Iberian population, occurred via overwater colonization < 1.5 Mya, well after the Messinian Salinity Crisis (5.97–5.32 Mya) when land bridges allowed terrestrial colonization of the Balearic Islands by mainland faunas. The morphological differences between V. l. ebusitana and the Iberian populations suggest that it is a new dwarf taxon resulting from insular evolutionary processes, becoming extinct shortly after the first human arrival to this island about 4000 years ago.

NUMERACY OF RELIGIOUS MINORITIES IN SPAIN AND PORTUGAL DURING THE INQUISITION ERA

ABSTRACTWe assess the numeracy (age heaping) of religious minorities, particularly Jews, and other defendants of the Spanish and Portuguese Inquisitions, and compare it with the general Iberian population. Our database includes 13,000 individuals who took part in Inquisition trials, and 17,000 individuals recorded in censuses and parish registers who serve as a control group. We thoroughly discuss the representativeness of our samples for the populations we aim to capture. Our results point at a substantial numeracy advantage of the Judaism-accused over the Catholic majority. Furthermore, Catholic priests and other groups of the religious elite who were occasional targets of the Inquisition had a similarly high level of numeracy.

P1770A MYBPC3 founder splicing mutation with high penetrance and early onset of Hypertrophic Cardiomyopathy in men

Introduction MYBPC3 is the most frequently affected gene in Hypertrophic Cardiomyopathy (HCM). This study aimed to analyze the founder origin and clinical phenotype of the MYBPC3 c.2149–1G>A pathogenic variant, which had been previously described in only one HCM proband. Methods HCM probands who underwent genetic test at our institution were reviewed. Clinical data from carriers were collected retrospectively. In order to identify the haplotypes sharing MYBPC3 c.2149–1G>A variant, six markers covering from 46 to 62 Mb of HSA11 were genotyped in 11 carriers and 6 non-carriers. Genotype information for those markers was extracted for Iberian population (n=107) from the 1000 Genomes Browser database. Haplotypes were reconstructed with Phase 2.1 software and phylogenetic analysis with MEGA7 software. Results MYBPC3 c.2149–1G>A was identified in 7 of 523 HCM probands and 23 family members. Penetrance in carriers older than 30 years was 80% (100% men, 55% women, p=0.03). Men were significantly younger at diagnoses, with larger left atrium. One patient had an aborted sudden death. The haplotype reconstruction showed the existence of 53 haplotypes. The most probable segregation for MYBPC3 c.2149–1G>A carriers was estimated in two haplotypes, H52 and H53. The phylogeny reconstruction estimated that both H52 and H53 haplotypes may come from common ancestor H16. In fact, H52 comes from one recombination event in H53 haplotype that has recently occurred in one of our families. Characteristics of affected carriers All (n=16) Men (n=11) Women (n=5) p Age at diagnoses (years) 44 (19) 38 (22) 48 (14.5) 0.036 Maximal LVWT (mm) 19 (4) 19 (3) 17 (6) 0.209 Ejection Fraction (%) 61 (5) 61 (4) 68 (17) 0.131 Left atrium (mm) 42 (13) 44 (15) 35 (11) 0.05 Outflow Tract Obstruction 2 (12.5%) 2 (18.2%) 0 (0%) 0.524 Late Gadolinium Enhancement† 13 (92.9%) 9 (90.0%) 4 (100%) 0.714 Dyspnea (NYHA ≥2) 4 (25%) 4 (36.4%) 0 (0%) 0.242 NSVT 6 (37.5%) 4 (36.4%) 2 (40%) 0.538 Atrial Fibrillation 4 (25%) 3 (27.3%) 1 (20%) 0.635 ICD primary/secondary prevention 7 (43.8%)/1 (6.3%) 5 (45.5%)/1 (9.1%) 2 (40%)/0 (0.0%) 0.750 Data are expressed as median (interquartile range) or number (%). LVWT: left ventricular wall thickness; NSVT: non sustained ventricular tachycardia. †14 man and 4 women underwent cardiac magnetic resonance. MYBPC3 haplotype tree. Conclusions MYBPC3 c.2149–1G>A is a founder pathogenic variant that shows a high penetrance and an early onset of HCM, specially in men.

Euphorbia duvalii (Euphorbiaceae) in the Iberian Peninsula

Euphorbia duvalii Lecoq & Lamotte is an endemic species from the Catalan-Occitan territory -western Mediterranean area- and is usually found in the south of France. Euphorbia duvalii has been cited from some localities of the Iberian Peninsula, but in later reviews all of these citations were finally identified as other species of Euphorbia L. One of these citations, from the Alt Empordà -Girona, Spain-, was of specific interest because not all the sources agreed on what the species was. To clarify whether or not this species is really present in the Iberian Peninsula, we examined new material from this population in order to establish whether the species is in fact E. duvalii. Once the morphology of the specimens from the Serra de Bac Grillera population had been analysed, we were able to confirm that they were indeed E. duvalii. This means that this is the only area on the Iberian Peninsula where this endemic species has been identified. The population is located in a rocky meadow that contains some scrub and is surrounded by pinewoods. Because this is the one and only Iberian population, a management and conservation plan needs to be drawn up to ensure its preservation.