Fully automatic multi-temporal land cover classification using Sentinel-2 image data

[Abstract] The analysis of remote sensing images represents a highly important issue to be performed in many relevant fields such as climate change studies or land cover mapping. Traditional proposals usually identify the land cover classes from general related groups such as different tree species or different crop varieties. Additionally, these proposals commonly use information from a precise time span or season, not accounting for the variability of the data over the entire year, specially in regions with several seasons. In this work, we propose a multi-temporal classification system to identify and represent diverse land cover classes over any period of the entire year by using Sentinel-2 satellite image data. To this end, 526 representative samples were labelled from 5 complex and variable different land cover types over the Special Area of Conservation (SAC) Betanzos-Mandeo in the northwest of the Iberian Peninsula. The method achieves a satisfactory mean accuracy value of 84.0% for the testing set using the best configuration with a radial Support Vector Machine classifier. This system will be used in the study of the population connectivity of two threatened herptiles, but it can be easily extended to other species of interest in the future.Xunta de Galicia; ED431G/01Xunta de Galicia; ED431C 2016-04

Karyological Characterization of the Endemic Iberian Rock Lizard, Iberolacerta Monticola (Squamata, Lacertidae): Insights into Sex Chromosome Evolution

[Abstract] Rock lizards of the genus Iberolacerta constitute a promising model to examine the process of sex chromosome evolution, as these closely related taxa exhibit remarkable diversity in the degree of sex chromosome differentiation with no clear phylogenetic segregation, ranging from cryptic to highly heteromorphic ZW chromosomes and even multiple chromosome systems (Z1Z1Z2Z2/Z1Z2W). To gain a deeper insight into the patterns of karyotype and sex chromosome evolution, we performed a cytogenetic analysis based on conventional staining, banding techniques and fluorescence in situ hybridization in the species I. monticola, for which previous cytogenetic investigations did not detect differentiated sex chromosomes. The karyotype is composed of 2n = 36 acrocentric chromosomes. NORs and the major ribosomal genes were located in the subtelomeric region of chromosome pair 6. Hybridization signals of the telomeric sequences (TTAGGG)n were visualized at the telomeres of all chromosomes and interstitially in 5 chromosome pairs. C-banding showed constitutive heterochromatin at the centromeres of all chromosomes, as well as clear pericentromeric and light telomeric C-bands in several chromosome pairs. These results highlight some chromosomal markers which can be useful to identify species specific diagnostic characters, although they may not accurately reflect the phylogenetic relationships among the taxa. In addition, C-banding revealed the presence of a heteromorphic ZW sex chromosome pair, where W is smaller than Z and almost completely heterochromatic. This finding sheds light on sex chromosome evolution in the genus Iberolacerta and suggests that further comparative cytogenetic analyses are needed to understand the processes underlying the origin, differentiation and plasticity of sex chromosome systems in lacertid lizards.Xunta de Galicia; PGIDIT03RFO10301PRXunta de Galicia; PGIDIT06RFO10301PRItalia. Ministero dell'istruzione, dell'università e della ricerca; PRIN 200

Evolutionary Dynamics of the Ty3/Gypsy LTR Retrotransposons in the Genome of Anopheles gambiae

Ty3/gypsy elements represent one of the most abundant and diverse LTR-retrotransposon (LTRr) groups in the Anopheles gambiae genome, but their evolutionary dynamics have not been explored in detail. Here, we conduct an in silico analysis of the distribution and abundance of the full complement of 1045 copies in the updated AgamP3 assembly. Chromosomal distribution of Ty3/gypsy elements is inversely related to arm length, with densities being greatest on the X, and greater on the short versus long arms of both autosomes. Taking into account the different heterochromatic and euchromatic compartments of the genome, our data suggest that the relative abundance of Ty3/gypsy LTRrs along each chromosome arm is determined mainly by the different proportions of heterochromatin, particularly pericentric heterochromatin, relative to total arm length. Additionally, the breakpoint regions of chromosomal inversion 2La appears to be a haven for LTRrs. These elements are underrepresented more than 7-fold in euchromatin, where 33% of the Ty3/gypsy copies are associated with genes. The euchromatin on chromosome 3R shows a faster turnover rate of Ty3/gypsy elements, characterized by a deficit of proviral sequences and the lowest average sequence divergence of any autosomal region analyzed in this study. This probably reflects a principal role of purifying selection against insertion for the preservation of longer conserved syntenyc blocks with adaptive importance located in 3R. Although some Ty3/gypsy LTRrs show evidence of recent activity, an important fraction are inactive remnants of relatively ancient insertions apparently subject to genetic drift. Consistent with these computational predictions, an analysis of the occupancy rate of putatively older insertions in natural populations suggested that the degenerate copies have been fixed across the species range in this mosquito, and also are shared with the sibling species Anopheles arabiensis

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics

Culex quinquefasciatus (the southern house mosquito) is an important mosquito vector of viruses such as West Nile virus and St. Louis encephalitis virus, as well as of nematodes that cause lymphatic filariasis. C. quinquefasciatus is one species within the Culex pipiens species complex and can be found throughout tropical and temperate climates of the world. The ability of C. quinquefasciatus to take blood meals from birds, livestock, and humans contributes to its ability to vector pathogens between species. Here, we describe the genomic sequence of C. quinquefasciatus: Its repertoire of 18,883 protein-coding genes is 22% larger than that of Aedes aegypti and 52% larger than that of Anopheles gambiae with multiple gene-family expansions, including olfactory and gustatory receptors, salivary gland genes, and genes associated with xenobiotic detoxification

Data from: A new mountain lizard from Montes de León (NW Iberian Peninsula): Iberolacerta monticola astur ssp. nov. (Squamata: Lacertidae)

Iberolacerta populations from the Northern Montes de León (NML) were studied by means of external morphology (scalation and biometry), osteology and genetics (mtDNA and microsatellites), searching for their homogeneity (“intrazonal analysis”) and, once verified, comparing them with Iberolacerta monticola s. str. (from Central Cantabrian Mountains) and I. galani (from Southern Montes de León) (“extrazonal analysis”) from neighboring areas

Paleogenomic Record of the Extinction of Human Endogenous Retrovirus ERV9

An outstanding question of genome evolution is what stops the invasion of a host genome by transposable elements (TEs). The human genome, harboring the remnants of many extinct TE families, offers an extraordinary opportunity to investigate this problem. ERV9 is an endogenous retrovirus repeatedly mobilized during primate evolution, 15 to 6 million years ago (MYA), which left a trace of over a hundred provirus-like copies and at least 4,000 solitary long terminal repeats (LTRs) in the human genome. Then, its proliferation ceased for unknown reasons, and the family went extinct. We have made a detailed reconstruction of its last active subfamily, ERV9_XII, by examining 115 solitary LTRs from it. These insertions were grouped into 11 sets according to shared nucleotide variants, which could be placed in a sequential order of 10 to 6 MYA. At least 75% of the subfamily was produced 8 to 6 MYA, during a stage of intense proliferation. With new analytical tools, we show that the youngest and most prolific sets may have been produced by effectively instantaneous expansions of corresponding single-sequence variants. The extinction of this family apparently was not a consequence of its slow gradual degeneration, but the outcome of the fixation of specific restrictive alleles in the human-chimpanzee ancestral population. Three species-specific insertions (two in humans and one in chimpanzees) were identified, further supporting that extinction took place when these two species were beginning to diverge. These are the only fixed differences of this kind so far observed between humans and chimpanzees, apart from those belonging to the human endogenous retrovirus K family

Census and contemporary effective population size of two populations of the protected Spanish Moon Moth (Graellsia isabellae)

International audienceGraellsia isabellae is a protected lepidopteran both in France and Spain; however, there has been considerable debate over its conservation status. Recent literature emphasised the need of monitoring population size in the different mountain ranges where this iconic species occurs. We used mark-capture-recapture and genotypes of nine molecular microsatellite markers to estimate the census (N) and contemporary effective population size (N-e) of two Spanish populations extending over similar size areas (10-15 km(2)): Puebla (Eastern Spain) and Ordesa (Western Pyrenees). Only adult males were captured and analysed, as sampling was based on the use of the synthesised female sex pheromone. Estimates of N were rather different in the two populations: 3398 males in Puebla (95% CI = 2875-4145) and 1500 in Ordesa (95% CI = 1229-1932), although the area occupied by the populations was larger and more densely forested in Ordesa than in Puebla. Several lines of evidence pointed to a moderate-large contemporary N-e at Puebla (173-178 individuals) and a one-order of magnitude lower N-e at Ordesa (27-49). Thus, N-e/N ratios were very low (0.026 and 0.01 respectively). We recommend G. isabellae to be classified as of Least Concern under the IUCN criteria; however, the high temporal fragmentation index and the very low values of the N-e/N ratios obtained for this species, as compared with those recorded for most others, are usually taken as indicators of actual threat for their conservation. As a cautionary measure, managers should aim at maintaining gene flow by ensuring connectivity of Pinus sylvestris in these areas

Data from: Causes and evolutionary consequences of population subdivision of an Iberian mountain lizard, Iberolacerta monticola

Aim: The study of the factors that influence population connectivity and spatial distribution of genetic variation is crucial for understanding speciation and for predicting the effects of landscape modification and habitat fragmentation, which are considered severe threats to global biodiversity. This dual perspective is obtained from analyses of subalpine mountain species, whose present distribution may have been shaped both by cyclical climate changes over ice ages and anthropogenic perturbations of their habitats. Here, we examine the phylogeography, population structure and genetic diversity of the lacertid lizard Iberolacerta monticola, an endemism considered to be facing a high risk of extinction in several populations. Location: Northwestern quadrant of the Iberian Peninsula. Methods: We analyzed the mtDNA variation at the control region (454 bp) and the cytochrome b (598 bp) loci, as well as at 10 nuclear microsatellite loci from 17 populations throughout the distribution range of the species. Results: According to nuclear markers, most sampling sites are defined as distinct, genetically differentiated populations, and many of them show traces of recent bottlenecks. Mitochondrial data identify a relatively old, geographically restricted lineage, and four to six younger geographically vicariant sister clades, whose origin may be traced back to the mid-Pleistocene revolution, with several subclades possibly associated to the mid-Bruhnes transition. Geographic range fragmentation of one of these clades, which includes lowland sites, is very recent, and most likely due to the accelerated loss of Atlantic forests by human intervention. Main Conclusions: Altogether, the data fit a “refugia within refugia” model, some lack of pattern uniformity notwithstanding, and suggest that these mountains might be the cradles of new species of Iberolacerta. However, the changes operated during the Holocene severely compromise the long-term survival of those genetic lineages more exposed to the anthropogenic perturbations of their habitats