Publications by authors named "Giorgio Bertorelle"

53 Publications

Population structure, genomic diversity and demographic history of Komodo dragons inferred from whole-genome sequencing.

Mol Ecol 2021 Aug 14. Epub 2021 Aug 14.

Department of Biology, University of Florence, Firenze, Italy.

Population and conservation genetics studies have greatly benefited from the development of new techniques and bioinformatic tools associated with next-generation sequencing. Analysis of extensive data sets from whole-genome sequencing of even a few individuals allows the detection of patterns of fine-scale population structure and detailed reconstruction of demographic dynamics through time. In this study, we investigated the population structure, genomic diversity and demographic history of the Komodo dragon (Varanus komodoensis), the world's largest lizard, by sequencing the whole genomes of 24 individuals from the five main Indonesian islands comprising the entire range of the species. Three main genomic groups were observed. The populations of the Island of Komodo and the northern coast of Flores, in particular, were identified as two distinct conservation units. Degrees of genomic divergence among island populations were interpreted as a result of changes in sea level affecting connectivity across islands. Demographic inference suggested that Komodo dragons probably experienced a relatively steep population decline over the last million years, reaching a relatively stable N during the Saalian glacial cycle (400-150 thousand years ago) followed by a rapid N decrease. Genomic diversity of Komodo dragons was similar to that found in endangered or already extinct reptile species. Overall, this study provides an example of how whole-genome analysis of a few individuals per population can help define population structure and intraspecific demographic dynamics. This is particularly important when applying population genomics data to conservation of rare or elusive endangered species.
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http://dx.doi.org/10.1111/mec.16121DOI Listing
August 2021

Divergence and hybridization in sea turtles: Inferences from genome data show evidence of ancient gene flow between species.

Mol Ecol 2021 Aug 13. Epub 2021 Aug 13.

Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.

Reconstructing past events of hybridization and population size changes are required to understand speciation mechanisms and current patterns of genetic diversity, and ultimately contribute to species' conservation. Sea turtles are ancient species currently facing anthropogenic threats including climate change, fisheries, and illegal hunting. Five of the seven extant sea turtle species are known to currently hybridize, especially along the Brazilian coast where some populations can have ~32%-42% of hybrids. Although frequently observed today, it is not clear what role hybridization plays in the evolutionary diversification of this group of reptiles. In this study, we generated whole genome resequencing data of the five globally distributed sea turtle species to estimate a calibrated phylogeny and the population size dynamics, and to understand the role of hybridization in shaping the genomes of these ancient species. Our results reveal discordant species divergence dates between mitochondrial and nuclear genomes, with a high frequency of conflicting trees throughout the nuclear genome suggesting that some sea turtle species frequently hybridized in the past. The reconstruction of the species' demography showed a general decline in effective population sizes with no signs of recovery, except for the leatherback sea turtle. Furthermore, we discuss the influence of reference bias in our estimates. We show long-lasting ancestral gene flow events within Chelonioidea that continued for millions of years after initial divergence. Speciation with gene flow is a common pattern in marine species, and it raises questions whether current hybridization events should be considered as a part of these species' evolutionary history or a conservation issue.
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http://dx.doi.org/10.1111/mec.16113DOI Listing
August 2021

Ancient genomes reveal early Andean farmers selected common beans while preserving diversity.

Nat Plants 2021 02 8;7(2):123-128. Epub 2021 Feb 8.

Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.

All crops are the product of a domestication process that started less than 12,000 years ago from one or more wild populations. Farmers selected desirable phenotypic traits (such as improved energy accumulation, palatability of seeds and reduced natural shattering) while leading domesticated populations through several more or less gradual demographic contractions. As a consequence, the erosion of wild genetic variation is typical of modern cultivars, making them highly susceptible to pathogens, pests and environmental change. The loss of genetic diversity hampers further crop improvement programmes to increase food production in a changing world, posing serious threats to food security. Using both ancient and modern seeds, we analysed the temporal dynamics of genetic variation and selection during the domestication process of the common bean (Phaseolus vulgaris) in the southern Andes. Here, we show that most domestic traits were selected for before 2,500 years ago, with no or only minor loss of whole-genome heterozygosity. In fact, most of the changes at coding genes and linked regions that differentiate wild and domestic genomes are already present in the ancient genomes analysed here, and all ancient domestic genomes dated between 600 and 2,500 years ago are highly variable (at least as variable as modern genomes from the wild). Single seeds from modern cultivars show reduced variation when compared with ancient seeds, indicating that intensive selection within cultivars in the past few centuries probably partitioned ancestral variation within different genetically homogenous cultivars. When cultivars from different Andean regions are pooled, the genomic variation of the pool is higher than that observed in the pool of ancient seeds from north and central western Argentina. Considering that most desirable phenotypic traits are probably controlled by multiple polymorphic genes, a plausible explanation of this decoupling of selection and genetic erosion is that early farmers applied a relatively weak selection pressure by using many phenotypically similar but genetically diverse individuals as parents. Our results imply that selection strategies during the past few centuries, as compared with earlier times, more intensively reduced genetic variation within cultivars and produced further improvements by focusing on a few plants carrying the traits of interest, at the cost of marked genetic erosion within Andean landraces.
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http://dx.doi.org/10.1038/s41477-021-00848-7DOI Listing
February 2021

Mapping the geographic origin of captive and confiscated Hermann's tortoises: A genetic toolkit for conservation and forensic analyses.

Forensic Sci Int Genet 2021 03 25;51:102447. Epub 2020 Dec 25.

Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Largo dell'Università s.n.c., 01100, Viterbo, Italy.

The illegal trade has been threatening tortoise populations worldwide for decades. Nowadays, however, DNA typing and forensic genetic approaches allow us to investigate the geographic origin of confiscated animals and to relocate them into the wild, providing that suitable molecular tools and reference data are available. Here we assess the suitability of a small panel of microsatellite markers to investigate patterns of illegal translocations and to assist forensic genetic applications in the endangered Mediterranean land tortoise Testudo hermanni hermanni. Specific allelic ladders were created for each locus and tested on several reference samples. We used the microsatellite panel to (i) increase our understanding of the population genetic structure in wild populations with new data from previously unsampled geographic areas (overall 461 wild individuals from 28 sampling sites); (ii) detect the presence of non-native individuals in wild populations; and (iii) identify the most likely geographic area of origin of 458 confiscated individuals hosted in Italian seizure and recovery centers. Our analysis initially identified six major genetic clusters corresponding to different geographic macro-areas along the Mediterranean range. Long-distance migrants among wild populations, due to translocations, were found and removed from the reference database. Assignment tests allowed us to allocate approximately 70 % of confiscated individuals of unknown origin to one of the six Mediterranean macro-areas. Most of the assigned tortoises belonged to the genetic cluster corresponding to the area where the respective captivity center was located. However, we also found evidence of long-distance origins of confiscated individuals, especially in centers along the Adriatic coast and facing the Balkan regions, a well-known source of illegally traded individuals. Our results clearly show that the microsatellite panel and the reference dataset can play a beneficial role in reintroduction and repatriation projects when confiscated individuals need to be re-assigned to their respective macro-area of origin before release, and can assist future forensic genetic applications in detecting the illegal trade and possession of Testudo hermanni individuals.
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http://dx.doi.org/10.1016/j.fsigen.2020.102447DOI Listing
March 2021

Population Dynamics and Structural Effects at Short and Long Range Support the Hypothesis of the Selective Advantage of the G614 SARS-CoV-2 Spike Variant.

Mol Biol Evol 2021 05;38(5):1966-1979

Department of Life and Environmental Science, Marche Polytechnic University, Ancona, Italy.

SARS-CoV-2 epidemics quickly propagated worldwide, sorting virus genomic variants in newly established propagules of infections. Stochasticity in transmission within and between countries or an actual selective advantage could explain the global high frequency reached by some genomic variants. Using statistical analyses, demographic reconstructions, and molecular dynamics simulations, we show that the globally invasive G614 spike variant 1) underwent a significant demographic expansion in most countries explained neither by stochastic effects nor by overrepresentation in clinical samples, 2) increases the spike S1/S2 furin-like site conformational plasticity (short-range effect), and 3) modifies the internal motion of the receptor-binding domain affecting its cross-connection with other functional domains (long-range effect). Our results support the hypothesis of a selective advantage at the basis of the spread of the G614 variant, which we suggest may be due to structural modification of the spike protein at the S1/S2 proteolytic site, and provide structural information to guide the design of variant-specific drugs.
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http://dx.doi.org/10.1093/molbev/msaa337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7798934PMC
May 2021

Phylogenomic proof of Recurrent Demipolyploidization and Evolutionary Stalling of the "Triploid Bridge" in (Poaceae).

Int J Mol Sci 2020 Jul 24;21(15). Epub 2020 Jul 24.

Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all'Adige (TN), Italy.

Polyploidization is a frequent phenomenon in plants, which entails the increase from one generation to the next by multiples of the haploid number of chromosomes. While tetraploidization is arguably the most common and stable outcome of polyploidization, over evolutionary time triploids often constitute only a transient phase, or a "triploid bridge", between diploid and tetraploid levels. In this study, we reconstructed in a robust phylogenomic and statistical framework the evolutionary history of polyploidization in , a small genus from the Poaceae family with promising biomass, bioenergy and phytoremediation species. Through the obtainment of 10 novel leaf transcriptomes for and outgroup species, our results prove that recurrent demiduplication has likely been a major driver of evolution in this species-poor genus. Molecular dating further demonstrates that the species originating by demiduplication stalled in the "triploid bridge" for evolutionary times in the order of millions of years without undergoing tetratploidization. Nevertheless, we found signatures of molecular evolution highlighting some of the processes that accompanied the genus radiation. Our results clarify the complex nature of evolution and are valuable for future gene functional validation as well as reverse and comparative genomics efforts in the genus and other Arundinoideae.
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http://dx.doi.org/10.3390/ijms21155247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7432733PMC
July 2020

In silico identification and characterization of a diverse subset of conserved microRNAs in bioenergy crop Arundo donax L.

Sci Rep 2018 11 12;8(1):16667. Epub 2018 Nov 12.

Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.

MicroRNAs (miRNAs) are small non-coding RNA molecules involved in the post-transcriptional regulation of gene expression in plants. Arundo donax L. is a perennial C grass considered one of the most promising bioenergy crops. Despite its relevance, many fundamental aspects of its biology still remain to be elucidated. In the present study we carried out the first in silico mining and tissue-specific characterization of microRNAs and their putative targets in A. donax. We identified a total of 141 miRNAs belonging to 14 families along with the corresponding primary miRNAs, precursor miRNAs and a total of 462 high-confidence predicted targets and novel target sites were validated by 5'-race. Gene Ontology functional annotation showed that miRNA targets are constituted mainly by transcription factors, but three of the newly validated targets are enzymes involved in novel functions like RNA editing, acyl lipid metabolism and post-Golgi trafficking. Folding variability of pre-miRNA loops and phylogenetic analyses indicate variable selective pressure acting on the different miRNA families. The set of miRNAs identified in this study will pave the road to further miRNA research in Arundo donax and contribute towards a better understanding of miRNA-mediated gene regulatory processes in other bioenergy crops.
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http://dx.doi.org/10.1038/s41598-018-34982-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6232160PMC
November 2018

Partial genomic survival of cave bears in living brown bears.

Nat Ecol Evol 2018 10 27;2(10):1563-1570. Epub 2018 Aug 27.

Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.

Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.
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http://dx.doi.org/10.1038/s41559-018-0654-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6590514PMC
October 2018

Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers.

Proc Natl Acad Sci U S A 2017 11 24;114(45):E9589-E9597. Epub 2017 Oct 24.

Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy;

About 100 km east of Rome, in the central Apennine Mountains, a critically endangered population of ∼50 brown bears live in complete isolation. Mating outside this population is prevented by several 100 km of bear-free territories. We exploited this natural experiment to better understand the gene and genomic consequences of surviving at extremely small population size. We found that brown bear populations in Europe lost connectivity since Neolithic times, when farming communities expanded and forest burning was used for land clearance. In central Italy, this resulted in a 40-fold population decline. The overall genomic impact of this decline included the complete loss of variation in the mitochondrial genome and along long stretches of the nuclear genome. Several private and deleterious amino acid changes were fixed by random drift; predicted effects include energy deficit, muscle weakness, anomalies in cranial and skeletal development, and reduced aggressiveness. Despite this extreme loss of diversity, Apennine bear genomes show nonrandom peaks of high variation, possibly maintained by balancing selection, at genomic regions significantly enriched for genes associated with immune and olfactory systems. Challenging the paradigm of increased extinction risk in small populations, we suggest that random fixation of deleterious alleles () can be an important driver of divergence in isolation, () can be tolerated when balancing selection prevents random loss of variation at important genes, and () is followed by or results directly in favorable behavioral changes.
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http://dx.doi.org/10.1073/pnas.1707279114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5692547PMC
November 2017

High Level of Nonsynonymous Changes in Common Bean Suggests That Selection under Domestication Increased Functional Diversity at Target Traits.

Front Plant Sci 2016 6;7:2005. Epub 2017 Jan 6.

Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche Ancona, Italy.

Crop species have been deeply affected by the domestication process, and there have been many efforts to identify selection signatures at the genome level. This knowledge will help geneticists to better understand the evolution of organisms, and at the same time, help breeders to implement successful breeding strategies. Here, we focused on domestication in the Mesoamerican gene pool of by sequencing 49 gene fragments from a sample of 45 wild and domesticated accessions, and as controls, two accessions each of the closely related species and . An excess of nonsynonymous mutations within the domesticated germplasm was found. Our data suggest that the cost of domestication alone cannot explain fully this finding. Indeed, the significantly higher frequency of polymorphisms in the coding regions observed only in the domesticated plants (compared to noncoding regions), the fact that these mutations were mostly nonsynonymous and appear to be recently derived mutations, and the investigations into the functions of their relative genes (responses to biotic and abiotic stresses), support a scenario that involves new functional mutations selected for adaptation during domestication. Moreover, consistent with this hypothesis, selection analysis and the possibility to compare data obtained for the same genes in different studies of varying sizes, data types, and methodologies allowed us to identify four genes that were strongly selected during domestication. Each selection candidate is involved in plant resistance/tolerance to abiotic stresses, such as heat, drought, and salinity. Overall, our study suggests that domestication acted to increase functional diversity at target loci, which probably controlled traits related to expansion and adaptation to new agro-ecological growing conditions.
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http://dx.doi.org/10.3389/fpls.2016.02005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5216878PMC
January 2017

Full circumpolar migration ensures evolutionary unity in the Emperor penguin.

Nat Commun 2016 06 14;7:11842. Epub 2016 Jun 14.

Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postboks, Blindern, Oslo 1066, Norway.

Defining reliable demographic models is essential to understand the threats of ongoing environmental change. Yet, in the most remote and threatened areas, models are often based on the survey of a single population, assuming stationarity and independence in population responses. This is the case for the Emperor penguin Aptenodytes forsteri, a flagship Antarctic species that may be at high risk continent-wide before 2100. Here, using genome-wide data from the whole Antarctic continent, we reveal that this top-predator is organized as one single global population with a shared demography since the late Quaternary. We refute the view of the local population as a relevant demographic unit, and highlight that (i) robust extinction risk estimations are only possible by including dispersal rates and (ii) colony-scaled population size is rather indicative of local stochastic events, whereas the species' response to global environmental change is likely to follow a shared evolutionary trajectory.
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http://dx.doi.org/10.1038/ncomms11842DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4911614PMC
June 2016

The Biarzo case in northern Italy: is the temporal dynamic of swine mitochondrial DNA lineages in Europe related to domestication?

Sci Rep 2015 Nov 9;5:16514. Epub 2015 Nov 9.

Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italy.

Genetically-based reconstructions of the history of pig domestication in Europe are based on two major pillars: 1) the temporal changes of mitochondrial DNA lineages are related to domestication; 2) Near Eastern haplotypes which appeared and then disappeared in some sites across Europe are genetic markers of the first Near Eastern domestic pigs. We typed a small but informative fragment of the mitochondrial DNA in 23 Sus scrofa samples from a site in north eastern Italy (Biarzo shelter) which provides a continuous record across a ≈6,000 year time frame from the Upper Palaeolithic to the Neolithic. We additionally carried out several radiocarbon dating. We found that a rapid mitochondrial DNA turnover occurred during the Mesolithic, suggesting that substantial changes in the composition of pig mitochondrial lineages can occur naturally across few millennia independently of domestication processes. Moreover, so-called Near Eastern haplotypes were present here at least two millennia before the arrival of Neolithic package in the same area. Consequently, we recommend a re-evaluation of the previous idea that Neolithic farmers introduced pigs domesticated in the Near East, and that Mesolithic communities acquired domestic pigs via cultural exchanges, to include the possibility of a more parsimonious hypothesis of local domestication in Europe.
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http://dx.doi.org/10.1038/srep16514DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4637886PMC
November 2015

Population genetic structure of a centipede species with high levels of developmental instability.

PLoS One 2015 1;10(6):e0126245. Epub 2015 Jun 1.

Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy.

European populations of the geophilomorph centipede Haplophilus subterraneus show a high proportion of individuals with morphological anomalies, suggesting high levels of developmental instability. The broad geographic distribution of this phenomenon seems to exclude local environmental causes, but the source of instability is still to be identified. The goal of the present study was to collect quantitative data on the occurrence of phenodeviants in different populations, along with data on the patterns of genetic variation within and between populations, in order to investigate possible association between developmental instability and genetic features. In a sample of 11 populations of H. subterraneus, distributed in western and central Europe, we looked for phenodeviants, in particular with respect to trunk morphology, and studied genetic variation through the genotyping of microsatellite loci. Overall, no support was found to the idea that developmental instability in H. subterraneus is related to a specific patterns of genetic variation, including inbreeding estimates. We identified a major genetic partition that subdivides French populations from the others, and a low divergence among northwestern areas, which are possibly related to the post-glacial recolonization from southern refugia and/or to recent anthropogenic soil displacements. A weak correlation between individual number of leg bearing segments and the occurrence of trunk anomalies seems to support a trade-off between these two developmental traits. These results, complemented by preliminary data on developmental stability in two related species, suggest that the phenomenon has not a simple taxonomic distribution, while it exhibits an apparent localization in central and eastern Europe.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126245PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4452494PMC
February 2016

4P: fast computing of population genetics statistics from large DNA polymorphism panels.

Ecol Evol 2015 Jan 11;5(1):172-5. Epub 2014 Dec 11.

Department of Life Sciences and Biotechnology, University of Ferrara via L. Borsari, 46, 44100, Ferrara, Italy.

Massive DNA sequencing has significantly increased the amount of data available for population genetics and molecular ecology studies. However, the parallel computation of simple statistics within and between populations from large panels of polymorphic sites is not yet available, making the exploratory analyses of a set or subset of data a very laborious task. Here, we present 4P (parallel processing of polymorphism panels), a stand-alone software program for the rapid computation of genetic variation statistics (including the joint frequency spectrum) from millions of DNA variants in multiple individuals and multiple populations. It handles a standard input file format commonly used to store DNA variation from empirical or simulation experiments. The computational performance of 4P was evaluated using large SNP (single nucleotide polymorphism) datasets from human genomes or obtained by simulations. 4P was faster or much faster than other comparable programs, and the impact of parallel computing using multicore computers or servers was evident. 4P is a useful tool for biologists who need a simple and rapid computer program to run exploratory population genetics analyses in large panels of genomic data. It is also particularly suitable to analyze multiple data sets produced in simulation studies. Unix, Windows, and MacOs versions are provided, as well as the source code for easier pipeline implementations.
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http://dx.doi.org/10.1002/ece3.1261DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298444PMC
January 2015

Comparative evaluation of potential indicators and temporal sampling protocols for monitoring genetic erosion.

Evol Appl 2014 Nov 15;7(9):984-98. Epub 2014 Aug 15.

Department of Life Science, Università di Ferrara Ferrara, Italy.

Genetic biodiversity contributes to individual fitness, species' evolutionary potential, and ecosystem stability. Temporal monitoring of the genetic status and trends of wild populations' genetic diversity can provide vital data to inform policy decisions and management actions. However, there is a lack of knowledge regarding which genetic metrics, temporal sampling protocols, and genetic markers are sufficiently sensitive and robust, on conservation-relevant timescales. Here, we tested six genetic metrics and various sampling protocols (number and arrangement of temporal samples) for monitoring genetic erosion following demographic decline. To do so, we utilized individual-based simulations featuring an array of different initial population sizes, types and severity of demographic decline, and DNA markers [single nucleotide polymorphisms (SNPs) and microsatellites] as well as decline followed by recovery. Number of alleles markedly outperformed other indicators across all situations. The type and severity of demographic decline strongly affected power, while the number and arrangement of temporal samples had small effect. Sampling 50 individuals at as few as two time points with 20 microsatellites performed well (good power), and could detect genetic erosion while 80-90% of diversity remained. This sampling and genotyping effort should often be affordable. Power increased substantially with more samples or markers, and we observe that power of 2500 SNPs was nearly equivalent to 250 microsatellites, a result of theoretical and practical interest. Our results suggest high potential for using historic collections in monitoring programs, and demonstrate the need to monitor genetic as well as other levels of biodiversity.
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http://dx.doi.org/10.1111/eva.12197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4231590PMC
November 2014

Bayesian inferences suggest that Amazon Yunga Natives diverged from Andeans less than 5000 ybp: implications for South American prehistory.

BMC Evol Biol 2014 Sep 30;14:174. Epub 2014 Sep 30.

Background: Archaeology reports millenary cultural contacts between Peruvian Coast-Andes and the Amazon Yunga, a rainforest transitional region between Andes and Lower Amazonia. To clarify the relationships between cultural and biological evolution of these populations, in particular between Amazon Yungas and Andeans, we used DNA-sequence data, a model-based Bayesian approach and several statistical validations to infer a set of demographic parameters.

Results: We found that the genetic diversity of the Shimaa (an Amazon Yunga population) is a subset of that of Quechuas from Central-Andes. Using the Isolation-with-Migration population genetics model, we inferred that the Shimaa ancestors were a small subgroup that split less than 5300 years ago (after the development of complex societies) from an ancestral Andean population. After the split, the most plausible scenario compatible with our results is that the ancestors of Shimaas moved toward the Peruvian Amazon Yunga and incorporated the culture and language of some of their neighbors, but not a substantial amount of their genes. We validated our results using Approximate Bayesian Computations, posterior predictive tests and the analysis of pseudo-observed datasets.

Conclusions: We presented a case study in which model-based Bayesian approaches, combined with necessary statistical validations, shed light into the prehistoric demographic relationship between Andeans and a population from the Amazon Yunga. Our results offer a testable model for the peopling of this large transitional environmental region between the Andes and the Lower Amazonia. However, studies on larger samples and involving more populations of these regions are necessary to confirm if the predominant Andean biological origin of the Shimaas is the rule, and not the exception.
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http://dx.doi.org/10.1186/s12862-014-0174-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4189748PMC
September 2014

Geography has more influence than language on maternal genetic structure of various northeastern Thai ethnicities.

J Hum Genet 2014 Sep 31;59(9):512-20. Epub 2014 Jul 31.

Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.

Several literatures have shown the influence of geographic and linguistic factors in shaping genetic variation patterns, but their relative impact, if any, in the very heterogeneous northeastern region of Thailand has not yet been studied. This area, called Isan, is geographically structured in two wide basins, the Sakon Nakorn Basin and the Korat Basin, serving today as home to diverse ethnicities encompassing two different linguistic families, that is, the Austro-Asiatic; Suay (Kui), Mon, Chaobon (Nyahkur), So and Khmer, and the Tai-Kadai; Saek, Nyaw, Phu Tai, Kaleung and Lao Isan. In this study, we evaluated the relative role of geographic distance and barriers as well as linguistic differences as possible causes affecting the maternal genetic distances among northeastern Thai ethnicities. A 596-bp segment of the hypervariable region I mitochondrial DNA was utilized to elucidate the genetic structure and biological affinity from 433 individuals. Different statistical analyses agreed in suggesting that most ethnic groups in the Sakon Nakorn Basin are closely related. Mantel test revealed that genetic distances were highly associated to geographic (r = 0.445, P<0.01) but not to linguistic (r = 0.001, P>0.01) distances. Three evolutionary models were compared by Approximate Bayesian Computation. The posterior probability of the scenario, which assumed an initial population divergence possibly related to reduced gene flow among basins, was equal or higher than 0.87. All analyses exhibited concordant results supporting that geography was the most relevant factor in determining the maternal genetic structure of northeastern Thai populations.
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http://dx.doi.org/10.1038/jhg.2014.64DOI Listing
September 2014

Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean.

Plant Cell 2014 May 21;26(5):1901-1912. Epub 2014 May 21.

Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy Consiglio per la Ricerca e Sperimentazione in Agricoltura, Cereal Research Centre (CRA-CER), 71122 Foggia, Italy

Using RNA sequencing technology and de novo transcriptome assembly, we compared representative sets of wild and domesticated accessions of common bean (Phaseolus vulgaris) from Mesoamerica. RNA was extracted at the first true-leaf stage, and de novo assembly was used to develop a reference transcriptome; the final data set consists of ∼190,000 single nucleotide polymorphisms from 27,243 contigs in expressed genomic regions. A drastic reduction in nucleotide diversity (∼60%) is evident for the domesticated form, compared with the wild form, and almost 50% of the contigs that are polymorphic were brought to fixation by domestication. In parallel, the effects of domestication decreased the diversity of gene expression (18%). While the coexpression networks for the wild and domesticated accessions demonstrate similar seminal network properties, they show distinct community structures that are enriched for different molecular functions. After simulating the demographic dynamics during domestication, we found that 9% of the genes were actively selected during domestication. We also show that selection induced a further reduction in the diversity of gene expression (26%) and was associated with 5-fold enrichment of differentially expressed genes. While there is substantial evidence of positive selection associated with domestication, in a few cases, this selection has increased the nucleotide diversity in the domesticated pool at target loci associated with abiotic stress responses, flowering time, and morphology.
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http://dx.doi.org/10.1105/tpc.114.124040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079357PMC
May 2014

Genetic variation and population structure in the endangered Hermann's tortoise: the roles of geography and human-mediated processes.

J Hered 2014 Jan-Feb;105(1):70-81. Epub 2013 Oct 23.

Muséum National d'Histoire Naturelle, Département Systématique et Evolution, Université Pierre & Marie Curie, 75231 Paris cedex 05, France.

The Hermann's tortoise (Testudo hermanni) is an endangered land tortoise distributed in disjoint populations across Mediterranean Europe. We investigated its genetic variation by typing 1 mitochondrial locus and 9 nuclear microsatellites in approximately 300 individuals from 22 localities. Our goal was to understand the relative impact of natural and human-mediated processes in shaping the genetic structure and to identify the genetic priorities for the conservation of this species. We found that 1) all geographic areas are highly differentiated, mainly as a function of their distance but with a clear genetic discontinuity (F st values larger than 0.4) between the Eastern and the Western subspecies; 2) the contact zone between subspecies is located farthest to the west than previously believed, and it probably coincides with the delta of the largest Italian river; 3) extinction events due to climatic conditions in the Upper Palaeolithic and subsequent human-mediated translocations in the Neolithic possibly explain the unexpected similarity among Spain, Sicily, and Corsica. For conservation purposes, the large majority of genetic pools appears native although hybridization among subspecies, related to extensive 20th century trade of tortoises across Europe, is observed in Spain and some Italian samples. Most populations do not seem at immediate risk of low genetic variation, except the French population, which has very low nuclear genetic diversity (heterozygosity = 0.25) and where 50 out of 51 sampled animals shared the same mitochondrial sequence. In general, restocking and reintroduction plans should carefully consider the genetic background of the individuals.
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http://dx.doi.org/10.1093/jhered/est071DOI Listing
July 2014

High variance in reproductive success generates a false signature of a genetic bottleneck in populations of constant size: a simulation study.

BMC Bioinformatics 2013 Oct 16;14:309. Epub 2013 Oct 16.

Department of Life Sciences and Biotechnology, University of Ferrara, via Borsari 46, Ferrara I-44121, Italy.

Background: Demographic bottlenecks can severely reduce the genetic variation of a population or a species. Establishing whether low genetic variation is caused by a bottleneck or a constantly low effective number of individuals is important to understand a species' ecology and evolution, and it has implications for conservation management. Recent studies have evaluated the power of several statistical methods developed to identify bottlenecks. However, the false positive rate, i.e. the rate with which a bottleneck signal is misidentified in demographically stable populations, has received little attention. We analyse this type of error (type I) in forward computer simulations of stable populations having greater than Poisson variance in reproductive success (i.e., variance in family sizes). The assumption of Poisson variance underlies bottleneck tests, yet it is commonly violated in species with high fecundity.

Results: With large variance in reproductive success (Vk ≥ 40, corresponding to a ratio between effective and census size smaller than 0.1), tests based on allele frequencies, allelic sizes, and DNA sequence polymorphisms (heterozygosity excess, M-ratio, and Tajima's D test) tend to show erroneous signals of a bottleneck. Similarly, strong evidence of population decline is erroneously detected when ancestral and current population sizes are estimated with the model based method MSVAR.

Conclusions: Our results suggest caution when interpreting the results of bottleneck tests in species showing high variance in reproductive success. Particularly in species with high fecundity, computer simulations are recommended to confirm the occurrence of a population bottleneck.
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http://dx.doi.org/10.1186/1471-2105-14-309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852946PMC
October 2013

The number of markers and samples needed for detecting bottlenecks under realistic scenarios, with and without recovery: a simulation-based study.

Mol Ecol 2013 Jul;22(13):3444-50

Detecting bottlenecks is a common task in molecular ecology. While several bottleneck detection method sexist, evaluations of their power have focused only on severe bottlenecks (e.g. to Ne ~10). As a component of a recent review, Peery et al. (2012) analysed the power of two approaches, the M-ratio and heterozygote excess tests, to detect moderate bottlenecks (e.g. to Ne ~100),which is realistic for many conservation situations. In this Comment, we address three important points relevant to but not considered in Peery et al. Under moderate bottleneck scenarios, we test the (i) relative advantage of sampling more markers vs. more individuals, (ii) potential power to detect the bottleneck when utilizing dozens of microsatellites (a realistic possibility for contemporary studies) and (iii) reduction in power when post bottle neck recovery has occurred. For the realistic situations examined,we show that (i) doubling the number of loci shows equal or better power than tripling the number of individuals,(ii) increasing the number of markers (up to 100) results in continued additive gains in power, and (iii)recovery after a moderate amount of time or gradual change in size reduces power, by up to one-half. Our results provide a practical supplement to Peery et al. and encourage the continued use of bottleneck detection methods in the genomic age, but also emphasize that the power under different sampling schemes should be estimated,using simulation modelling, as a routine component of molecular ecology studies.
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http://dx.doi.org/10.1111/mec.12258DOI Listing
July 2013

A common ancestor more than 10,000 years old for patients with R854Q-related type 2N von Willebrand's disease in Italy.

Haematologica 2013 Jan 8;98(1):147-52. Epub 2012 Aug 8.

Department of Cardiologic, Thoracic and Vascular Sciences, University of Padua Medical School, Padua, France.

The impaired capacity of von Willebrand factor to carry factor VIII is identified as type 2N von Willebrand's disease. R854Q is the most common type 2N mutation, and almost the only one identified in Italy. This aim of this study was to ascertain whether R854Q mutations in a cohort of Italian patients with type 2N von Willebrand's disease originated from a single event or recurrent events. Thirteen unrelated Italian families were investigated, analyzing the von Willebrand factor gene haplotype associated with the R854Q mutation. A common haplotype emerged in all the families, extending from single nucleotide polymorphisms rs2166902 to rs216293 over 48.2 kb and including five intragenic markers. This haplotype is infrequent in the healthy Italian population (17% versus 100%, P<0.0001) and each genetic marker within the said haplotype is similarly rare. These data strongly suggest a founder effect, with a single R854Q mutation event being the cause of the type 2N von Willebrand's disease in our cohort of patients. Using DMLE+ software and the mathematical model of Bengtsson and Thomson, it was estimated that the R854Q mutation occurred from 10,000 to 40,000 years ago, which is consistent with the short dimension of the haplotype shared by our patients. Together with the fact that the R854Q mutation seems to be limited to Caucasian populations, these findings suggest that a single mutational event took place after human populations moved from Africa towards Europe.
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http://dx.doi.org/10.3324/haematol.2012.066019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3533677PMC
January 2013

Computer simulations: tools for population and evolutionary genetics.

Nat Rev Genet 2012 Jan 10;13(2):110-22. Epub 2012 Jan 10.

Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, BP 53, 38041 Grenoble, France.

Computer simulations are excellent tools for understanding the evolutionary and genetic consequences of complex processes whose interactions cannot be analytically predicted. Simulations have traditionally been used in population genetics by a fairly small community with programming expertise, but the recent availability of dozens of sophisticated, customizable software packages for simulation now makes simulation an accessible option for researchers in many fields. The in silico genetic data produced by simulations, along with greater availability of population-genomics data, are transforming genetic epidemiology, anthropology, evolutionary and population genetics and conservation. In this Review of the state-of-the-art of simulation software, we identify applications of simulations, evaluate simulator capabilities, provide a guide for their use and summarize future directions.
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http://dx.doi.org/10.1038/nrg3130DOI Listing
January 2012

Genetic structure of the Mon-Khmer speaking groups and their affinity to the neighbouring Tai populations in Northern Thailand.

BMC Genet 2011 Jun 15;12:56. Epub 2011 Jun 15.

Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.

Background: The Mon-Khmer speaking peoples inhabited northern Thailand before the arrival of the Tai speaking people from southern China in the thirteenth century A.D. Historical and anthropological evidence suggests a close relationship between the Mon-Khmer groups and the present day majority northern Thai groups. In this study, mitochondrial and Y-chromosomal DNA polymorphisms in more than 800 volunteers from eight Mon-Khmer and ten Tai speaking populations were investigated to estimate the degree of genetic divergence between these major linguistic groups and their internal structure.

Results: A large fraction of genetic variation is observed within populations (about 80% and 90% for mtDNA and the Y-chromosome, respectively). The genetic divergence between populations is much higher in Mon-Khmer than in Tai speaking groups, especially at the paternally inherited markers. The two major linguistic groups are genetically distinct, but only for a marginal fraction (1 to 2%) of the total genetic variation. Genetic distances between populations correlate with their linguistic differences, whereas the geographic distance does not explain the genetic divergence pattern.

Conclusions: The Mon-Khmer speaking populations in northern Thailand exhibited the genetic divergence among each other and also when compared to Tai speaking peoples. The different drift effects and the post-marital residence patterns between the two linguistic groups are the explanation for a small but significant fraction of the genetic variation pattern within and between them.
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http://dx.doi.org/10.1186/1471-2156-12-56DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3126721PMC
June 2011

Citizen science reveals unexpected continental-scale evolutionary change in a model organism.

PLoS One 2011 Apr 27;6(4):e18927. Epub 2011 Apr 27.

Department of Life Sciences, The Open University, Milton Keynes, United Kingdom.

Organisms provide some of the most sensitive indicators of climate change and evolutionary responses are becoming apparent in species with short generation times. Large datasets on genetic polymorphism that can provide an historical benchmark against which to test for recent evolutionary responses are very rare, but an exception is found in the brown-lipped banded snail (Cepaea nemoralis). This species is sensitive to its thermal environment and exhibits several polymorphisms of shell colour and banding pattern affecting shell albedo in the majority of populations within its native range in Europe. We tested for evolutionary changes in shell albedo that might have been driven by the warming of the climate in Europe over the last half century by compiling an historical dataset for 6,515 native populations of C. nemoralis and comparing this with new data on nearly 3,000 populations. The new data were sampled mainly in 2009 through the Evolution MegaLab, a citizen science project that engaged thousands of volunteers in 15 countries throughout Europe in the biggest such exercise ever undertaken. A known geographic cline in the frequency of the colour phenotype with the highest albedo (yellow) was shown to have persisted and a difference in colour frequency between woodland and more open habitats was confirmed, but there was no general increase in the frequency of yellow shells. This may have been because snails adapted to a warming climate through behavioural thermoregulation. By contrast, we detected an unexpected decrease in the frequency of Unbanded shells and an increase in the Mid-banded morph. Neither of these evolutionary changes appears to be a direct response to climate change, indicating that the influence of other selective agents, possibly related to changing predation pressure and habitat change with effects on micro-climate.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018927PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3083392PMC
April 2011

The complete mitochondrial genome of an 11,450-year-old aurochsen (Bos primigenius) from Central Italy.

BMC Evol Biol 2011 Jan 31;11:32. Epub 2011 Jan 31.

Dipartimento di Biologia ed Evoluzione, Università di Ferrara, Ferrara, Italy.

Background: Bos primigenius, the aurochs, is the wild ancestor of modern cattle breeds and was formerly widespread across Eurasia and northern Africa. After a progressive decline, the species became extinct in 1627. The origin of modern taurine breeds in Europe is debated. Archaeological and early genetic evidence point to a single Near Eastern origin and a subsequent spread during the diffusion of herding and farming. More recent genetic data are instead compatible with local domestication events or at least some level of local introgression from the aurochs. Here we present the analysis of the complete mitochondrial genome of a pre-Neolithic Italian aurochs.

Results: In this study, we applied a combined strategy employing both multiplex PCR amplifications and 454 pyrosequencing technology to sequence the complete mitochondrial genome of an 11,450-year-old aurochs specimen from Central Italy. Phylogenetic analysis of the aurochs mtDNA genome supports the conclusions from previous studies of short mtDNA fragments--namely that Italian aurochsen were genetically very similar to modern cattle breeds, but highly divergent from the North-Central European aurochsen.

Conclusions: Complete mitochondrial genome sequences are now available for several modern cattle and two pre-Neolithic mtDNA genomes from very different geographic areas. These data suggest that previously identified sub-groups within the widespread modern cattle mitochondrial T clade are polyphyletic, and they support the hypothesis that modern European breeds have multiple geographic origins.
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http://dx.doi.org/10.1186/1471-2148-11-32DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3039592PMC
January 2011

Genetic affinity and admixture of northern Thai people along their migration route in northern Thailand: evidence from autosomal STR loci.

J Hum Genet 2011 Feb 25;56(2):130-7. Epub 2010 Nov 25.

Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.

The Khon Mueang (KM) are the largest group of northern Thai people. Our previous mtDNA studies have suggested an admixture process among the KM with the earlier Mon-Khmer-speaking inhabitants of this region. In this study, we evaluate genetic affinities and admixture among 10 KM populations in northern Thailand lying along the historical Yuan migration route, and 10 neighboring populations belonging to 7 additional ethnic groups: Lawa, Mon (Mon-Khmer-speaking groups), Shan, Yuan, Lue, Khuen and Yong (Tai-speaking groups) by analyzing 15 hypervariable autosomal short tandem repeat loci. The KM exhibited close relationships with neighboring populations, especially the Tai-speaking groups, reflecting an admixed origin of the KM. Admixture proportions were observed in all KM populations, which had a higher contribution from the parental Tai than the Mon-Khmer groups. Different admixture patterns of the KM along the migration route might indicate high heterogeneity among the KM. These patterns were not directly associated with geographical proximity, suggesting other factors, like variation in the timing of admixture with the existing populations may have had an important role. More genetic data from different marker systems solely transmitted through the male or female lineages are needed to complete the description of genetic admixture and population history of the KM.
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http://dx.doi.org/10.1038/jhg.2010.135DOI Listing
February 2011

Evolution of detoxifying systems: the role of environment and population history in shaping genetic diversity at human CYP2D6 locus.

Pharmacogenet Genomics 2010 Aug;20(8):485-99

Department of Biology and Evolution, University of Ferrara, Ferrara, Italy.

Objective: The transition from food collection to food production (FP) modified the nature of selective pressures, and several studies illustrate that genetic adaptation to new lifestyle has occurred in humans since the agricultural revolution. Here we test the hypothesis that high levels of genetic variation at CYP2D6, a locus coding for a detoxifying enzyme of the cytochrome P450 complex, reflect this change.

Methods: We compared DNA sequences and predicted the levels of enzyme activity across 10 African, Asian and European populations, six of which currently rely on hunting and gathering (HG) while four on food production (FP).

Results And Conclusion: HG and FP showed similar levels of CYP2D6 diversity, but displayed different substitution patterns at coding DNA sites possibly related to selective differences. Comparison with variation at presumably neutral independent loci confirmed this finding, despite the confounding effects of population history, resulting in higher overall variation in Africans than in Eurasians. The differences between HG and FP populations suggest that new lifestyle and dietary habits acquired in the transition to agriculture affected the variation pattern at CYP2D6, leading to an increase in FP populations of the frequency of alleles that are associated with a slower rate of metabolism. These alleles reached a balanced co-existence with other important and previously selected variants. We suggest that the pronounced substrate-dependent activity of most of these enzymes expanded the spectrum of the metabolic response.
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http://dx.doi.org/10.1097/FPC.0b013e32833bba25DOI Listing
August 2010

[Origin and evolution of vasovagal syncope].

G Ital Cardiol (Rome) 2010 Jan;11(1):20-7

Divisione di Cardiologia, Ospedale Civile, Cento, FE.

Vasovagal syncope (VVS) is characterized by sudden hypotension and bradycardia, due to inhibition of the sympathetic system and activation of the vagal system, respectively. Major lines of evidence suggest that classical (emotional and orthostatic) VVS is not a disease, but a characteristic of the individual. It is, therefore, interesting to investigate the factors that can explain its origin and evolution and, to this purpose, we investigated the available literature data on the vasovagal reflex in animals, including humans. We found two processes in vertebrates, which appear relevant to the investigation of VVS evolution: fear and threat bradycardia in animals and vasovagal reflex during hemorrhagic shock, both in animals and humans. The trigger of the latter is thoracic hypovolemia, the same of the vasovagal reflex occurring in humans during orthostatic stress (prolonged standing, tilt testing). During thoracic hypovolemia, the vasovagal reflex in humans seems to share physiological mechanisms similar to those observed in other mammals, that is an activation of the vagal system and an inhibition of the sympathetic system, preceded by an activation of the same system. Even emotional VVS in humans seems to share physiological mechanisms similar to those observed in other vertebrates during fear/threat bradycardia. Therefore, the vasovagal reflex appears to be predisposed in humans and other vertebrates with the same mechanisms and this may indicate a common evolutionary root. If the vasovagal reflex persisted for millions of years along the vertebrates evolutionary history, we can reasonably assume that it has (or it maybe had in the past) a function. Also, since this reflex is sporadically displayed, a role as a "defense mechanism" appears likely. The most likely hypothesis is a defense mechanism of the heart during stressful and possible dangerous heart conditions. The slowing of heart rate induced by the vasovagal reflex may constitute a beneficial break of cardiac pump (thereby reducing myocardial oxygen consumption) and permit better diastolic filling and coronary perfusion.
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January 2010
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