Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas

Most individuals throughout the Americas are admixed descendants of Native American, European, and African ancestors. Complex historical factors have resulted in varying proportions of ancestral contributions between individuals within and among ethnic groups. We developed a panel of 446 ancestry informative markers (AIMs) optimized to estimate ancestral proportions in individuals and populations throughout Latin America. We used genome-wide data from 953 individuals from diverse African, European, and Native American populations to select AIMs optimized for each of the three main continental populations that form the basis of modern Latin American populations. We selected markers on the basis of locus-specific branch length to be informative, well distributed throughout the genome, capable of being genotyped on widely available commercial platforms, and applicable throughout the Americas by minimizing within-continent heterogeneity. We then validated the panel in samples from four admixed populations by comparing ancestry estimates based on the AIMs panel to estimates based on genome-wide association study (GWAS) data. The panel provided balanced discriminatory power among the three ancestral populations and accurate estimates of individual ancestry proportions (R2 > 0.9 for ancestral components with significant between-subject variance). Finally, we genotyped samples from 18 populations from Latin America using the AIMs panel and estimated variability in ancestry within and between these populations. This panel and its reference genotype information will be useful resources to explore population history of admixture in Latin America and to correct for the potential effects of population stratification in admixed samples in the region.     

Investigating the molecular basis of local adaptation to thermal stress: population differences in gene expression across the transcriptome of the copepod Tigriopus californicus

ABSTRACT: BACKGROUND: Geographic variation in the thermal environment impacts a broad range of biochemical and physiological processes and can be a major selective force leading to local population adaptation. In the intertidal copepod Tigriopus californicus, populations along the coast of California show differences in thermal tolerance that are consistent with adaptation, i.e., southern populations withstand thermal stresses that are lethal to northern populations. To understand the genetic basis of these physiological differences, we use an RNA-seq approach to compare genome-wide patterns of gene expression in two populations known to differ in thermal tolerance. RESULTS: Observed differences in gene expression between the southern (San Diego) and the northern (Santa Cruz) populations included both the number of affected loci as well as the identity of these loci. However, the most pronounced differences concerned the amplitude of upregulation of genes producing heat shock proteins (Hsps) and genes involved in ubiquitination and proteolysis. Among the hsp genes, orthologous pairs show markedly different thermal responses as the amplitude of hsp response was greatly elevated in the San Diego population, most notably in members of the hsp70 gene family. There was no evidence of accelerated evolution at the sequence level for hsp genes. Among other sets of genes, cuticle genes were up-regulated in SD but down-regulated in SC, and mitochondrial genes were down-regulated in both populations. CONCLUSIONS: Marked changes in gene expression were observed in response to acute sub-lethal thermal stress in the copepod T. californicus. Although some qualitative differences were observed between populations, the most pronounced differences involved the magnitude of induction of numerous hsp and ubiquitin genes. These differences in gene expression suggest that evolutionary divergence in the regulatory pathway(s) involved in acute temperature stress may offer at least a partial explanation of population differences in thermal tolerance observed in Tigriopus.     

Ecological role and historical trends of large pelagic predators in a subtropical marine ecosystem of the South Atlantic

Large pelagic predators occupy high positions in food webs and could control lower trophic level species by direct and indirect ecological interactions. In this study we aimed to test the hypotheses: (1) pelagic predators are keystone species, and their removals could trigger impacts on the food chain; (2) higher landings of pelagic predators could trigger fishing impacts with time leading to a drop in the mean trophic level of catches; and (3) recovery in the pelagic predators populations, especially for sharks, could be achieved with fishing effort reduction. We performed a food web approach using an Ecopath with Ecosim model to represent the Southeastern and Southern Brazil, a subtropical marine ecosystem, in 2001. We then calibrated the baseline model using catch and fishing effort time series from 2001 to 2012. Afterwards, we simulated the impact of fishing effort changes on species and assessed the ecological impacts on the pelagic community from 2012 to 2025. Results showed that the model was well fitted to landing data for the majority of groups. The pelagic predators species were classified as keystone species impacting mainly on pelagic community. The ecosystem was resilient and fisheries seem sustainable at that time. However, the temporal simulation, from 2001 to 2012, revealed declines in the biomass of three sharks, tuna and billfish groups. It was possible observe declines in the mean trophic level of the catch and in the mean total length of landings. Longline fisheries particularly affected the sharks, billfish and swordfish, while hammerhead sharks were mostly impacted by gillnet fishery. Model simulations showed that large sharks’ biomasses could be recovered or maintained only after strong fishing effort reduction.     

<Emphasis Type="Italic">Anemia tomentosa</Emphasis> var. <Emphasis Type="Italic">anthriscifolia</Emphasis> in vitro culture: sporophyte development and volatile compound profile of an aromatic fern

Anemia tomentosa var. anthriscifolia is an aromatic fern with a pleasant woody aroma and antimycobacterial activity. In this paper, we describe for the first time its spore-derived gametophyte development and the effect of indole-3-acetic acid and jasmonic acid on in vitro gametophyte/sporophyte development, as well as volatile compound production. Volatiles were obtained by simultaneous distillation and extraction (SDE) and analyzed by high resolution gas chromatography coupled with mass spectrometry. Spore-derived gametophytes were able to develop into sporophytes independently of the media culture composition, even when no plant growth regulator was added. Fifty different substances were detected in all in vitro A. tomentosa SDE extracts, while 20 were detected in the wild SDE plant extract. Monoterpenes were more prevalent (69.8–89.8%) than sesquiterpenes (9.4–28.7%) in in vitro plants, while sesquiterpenes represent 97.5% of the volatiles produced by the wild-grown plants. The major monoterpene components in in vitro plants were α-pinene (9.3–24.3%), trans-pinocarveol (20.6–27.9%), pinocarvone (15.4–25.1%) and myrtenyl acetate (6.4–12.3%). The triquinane sesquiterpenes silphiperfol-6-ene (0.6–2.9%), α-guaiene (0.5–2.5%), β-barbatene (1.1–3.9%) and 9-epi-presilphiperfolan-1-ol (2.5–5.6%) represent the most abundant sesquiterpenes. The changes in the monoterpene/sesquiterpene rates between micropropagated and wild plants are not related to the presence of JA or IAA in the media culture. Further studies are still needed to obtain a complete understanding of the factors leading to these results, which could be related to differences in the irradiance levels of in vitro plants versus those from a wild environment, as well as the developmental stage of the plants. This is the first report of the use of plant growth regulators on Anemia tomentosa in vitro culture development and their effects on volatile profiles.     

The structures of polysaccharides and glycolipids of Aspergillus fumigatus grown in the presence of human serum

A study was made of polysaccharides and glycosphingolipids isolated from Aspergillus fumigatus grown in media supplemented with human serum from healthy donors. Fractionation of Cetavlon-precipitated polysaccharides on Sephacryl S-400 gave rise to an excluded fraction (Fraction I) with molecular weight of >400 kDa and an included peak (Fraction II) with an average molecular weight of 30–80 kDa. Fraction I comprises about 5% of total polysaccharide and was identified as a glycogen-like molecule. Its structure was deduced from methylation data, treatment with amyloglucosidase, a red-brown coloration produced with an iodine solution and by ¹H and ¹³C-NMR spectroscopy. It was previously suggested that higher amounts of glycogen-like polysaccharide (20%) were present in A. fumigatus grown in serum-free medium. Fraction II was identified as a galactomannan and was the main polysaccharide of A. fumigatus grown in serum-supplemented medium. Its structure was elucidated mainly by ¹³C-NMR spectroscopy combined with partial acetolysis and methylation analysis. The ¹³C-NMR spectrum of the galactomannan showed a much greater complexity in the -d-galf and -d-manp C-1 regions, than was evident for galactomannan from serum-free cultures previously described, reflecting differences in the glycosylation pattern, stimulated in serum-supplemented medium.No differences in A. fumigatus glycosphingolipid could be detected between serum-containing and serum-free growth conditions.Our results demonstrate that the change in polysaccharide structure is a more specific response to the altered growth conditions and not merely a symptom of more general changes.This revised version was published online in October 2005 with corrections to the Cover Date.     

Age,Growth and Spatial Distribution of the Life Stages of the Shortfin Mako,Isurus oxyrinchus (Rafinesque, 1810) Caught in the Western and Central Atlantic

The shortfin mako (Isurus oxyrinchus) is a highly migratory pelagic shark that preferentially inhabits oceanic regions in practically all oceans. The wide distribution range of this species renders it susceptible to coastal and oceanic fishing operations. The International Union for Conservation of Nature (IUCN) and the International Commission for the Conservation of Atlantic Tunas (ICCAT) consider this species to be highly vulnerable, especially due to its biological parameters, which are different from those of other sharks that occupy the same niche (e.g., Prionace glauca). Consequently, considerable declines in abundance have been detected over various parts of its range, most of which are linked to oceanic longline fishing. The species has conflicting life history parameters in studies conducted in the last 30 years, especially with regard to age and growth. The main discrepancies regard the interpretation of the periodicity of the deposition of band pairs (BPs) on vertebrae and the possibility of ontogenetic variations in growth. Shortfin mako sharks (n = 1325) were sampled by onboard observers of the Brazilian chartered pelagic longline fleet based in northeast Brazil from 2005 to 2011. Lengths were 79 to 250 and 73 to 296 cm (fork length, FL) for males and females, respectively, with a statistically significant difference in size between sexes and differences in the proportion of individuals in each size class. The onboard observers collected a subsample of vertebrae (n = 467), only 234 of which were suitable for analyses. Reliability between readings was satisfactory. However, it was not possible to validate periodicity in the formation of age bands in the sample. Thus, the von Bertalanffy growth function was used to calculate growth rates for the species through the interpretation of BPs in different scenarios: one BP per year (s1), two BPs per year (s2) and two BPs per year until five years of life (s3). Growth parameters varied for both females (Linf = 309.7[s3] to 441.6[s1]; k = 0.04[s1] to 0.13[s3]; t0 = -7.08[s1] and -3.27[s3]) and males (Linf = 291.5[s3] to 340.2[s1]; k = 0.04[s1] to 0.13[s3]; t0 = -7.08[s1] and -3.27[s3]). To advance the understanding of the use of habitat, the first analysis of the spatial distribution of the life stages of the shortfin mako sharks caught by commercial longline fishing operations in the South Atlantic was performed. The findings indicate that the portion of the population exploited by the fleets is predominantly juvenile and future actions should take the following issues into account: improvements in the efficiency of data collection procedures, the reestablishment of the onboard observer program, emergency investments in studies that can contribute to a better understanding of habitat use and life history theory.