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News Article | December 15, 2016
Site: www.eurekalert.org

Genomic analysis of the Iberian lynx confirms that it is one of the species with the least genetic diversity among individuals, which means that it has little margin for adaptation Spanish scientists have sequenced the genome of the Iberian lynx (Lynx pardinus), currently one of the world's most endangered felines. They have confirmed the "extreme erosion" suffered by its DNA. The Iberian lynx has one of the least genetically-diverse genomes. It is even less diverse than other endangered mammals, such as the cheetah or Tasmanian devil, or birds, like the crested ibis or osprey. The study, being published today in the scientific journal Genome Biology, has been coordinated by scientists from the Doñana Biological Station (CSIC). The Centre for Genomic Regulation (CRG) contributed to this research project from the very beginning including several groups and facilities. In particular, the laboratories of Roderic Guigó, Cedric Notredame, and Toni Gabaldón at the Bioinformatics and Genomics Programme as well as the CRG Bioinformatics unit. This is the first mammal genome of reference generated entirely in Spain. The project, financed by Banco Santander and managed by the Fundación General CSIC, has integrated the efforts of 50 scientists from research groups of 12 institutions, two of them from outside Spain, that cover a broad range of disciplines, including bioinformatics, genomics, oncology, evolution and conservation. The scientists have managed to read and organize 2.4 billion letters of DNA from Candiles, a male lynx born in the Sierra Morena lynx population, who now forms part of a program for breeding in captivity. To do so, they have used new sequencing techniques and developed innovative procedures to generate a high-quality draft genome on a limited budget. A total of 21,257 genes were identified, a number similar to that of human beings and other mammals, and they have been compared to those of cats, tigers, cheetahs and dogs. Specifically, Toni Gabaldón's group at the Centre for Genomic Regulation in Barcelona has compared the Iberian lynx genome with those of other species, attempting to identify genes that have lost their function because they have remained isolated and the existence of a small population of specimens of this species. Researchers have found evidence of modifications in genes related with the senses of hearing, sight and smell to facilitate the adaptation of the lynx to its environment, which have enabled them to become exceptional hunters specialized in rabbits as prey. History and diversity of the Iberian lynx With the aim of studying the history and genetic diversity of the species, analysis was conducted on the genomes of another ten Iberian lynxes from Doñana and Sierra Morena, the only two surviving populations on the Iberian Peninsula, which have been isolated from each other for decades. Researchers have also completed a comparative analysis with a European lynx, to discover the bonds between the two lynxes that inhabit Eurasia. The Iberian lynx began to diverge from its sister species, the Eurasian lynx (Lynx lynx) some 300,000 years ago, and the two species became completely separated some 2,500 years ago. Throughout that period, they continued to cross-breed and exchange genes, probably in the periods between glaciations, when the climatology allowed the species to spread and encounter each other on the Iberian Peninsula and in southern Europe. The demographic history of the Iberian lynx has been marked by three historic declines, the last of which took place some 300 years ago, decimating its population. In addition to this, there was a drastic drop in the number of specimens in the 20th century due to its persecution, the destruction of its habitat, and two major viral epidemics suffered by the rabbit, its main food source. Scientists have interpreted these demographic drops as the cause of the low levels of diversity observed, and warn that this could impair the lynx's capacity to adapt to changes in its environment (climate, disease, etc.). Furthermore, existence of multiple potentially harmful genetic variants has been confirmed, which could be contributing to the reduced survival and reproduction rates of the species. This genetic deterioration is especially marked in the Doñana population-smaller, and isolated for a longer period-which has half the genetic diversity of the Sierra Morena group. Nevertheless, the study reflects the situation before the exchange between the two relict populations and their inter-breeding in captivity were begun. These measures, taken within the Iberian lynx conservation program, have led to improvement of the species' genetic situation in recent years. The use of new genomic resources, within the framework of the project, will contribute to optimizing management aimed at preserving the greatest genetic diversity, in addition to diminishing these populations' genetic defects as much as possible. In addition to Doñana Biological Station (EBD-CSIC), also taking part in the project were the National Center for Genomic Analysis (CNAG-CRG); the Centre for Genomic Regulation (CRG); the Spanish National Cancer Research Center (CNIO); the Evolutionary Genomics Group of the Hospital del Mar Medical Research Institute (IMIM); the Institute of Evolutionary Biology (IBE, CSIC-UPF); the University Institute of Oncology of Asturias (IUOPA); the Institut de Biotecnologia i de Biomedicina and the Unit of Cell Culture of the Autonomous University of Barcelona (UAB); the Biological Research Center (CIB-CSIC) and the Catalan Institution for Research and Advanced Studies (ICREA). Furthermore, the project has received the cooperation of a team from College of Veterinary Medicine of Texas A&M University and the Bioinformatics Research Center of the University of Aarhus (Denmark).

News Article | December 14, 2016
Site: www.sciencenews.org

No paper or digital trails document ancient humans’ journey out of Africa to points around the globe. Fortunately, those intrepid travelers left a DNA trail. Genetic studies released in 2016 put a new molecular spin on humans’ long-ago migrations. These investigations also underscore the long trek ahead for scientists trying to reconstruct Stone Age road trips. “I’m beginning to suspect that the ancient out-of-Africa process was complex, involving several migrations and subsequent extinctions,” says evolutionary geneticist Carles Lalueza-Fox of the Institute of Evolutionary Biology in Barcelona. Untangling those comings, goings and dead ends increasingly looks like a collaborative job for related lines of evolutionary research — comparisons of DNA differences across populations of present-day people, DNA samples retrieved from the bones of ancient hominids, archaeological evidence, fossil finds and studies of ancient climates. It’s still hard to say when the clouds will part and a clear picture of humankind’s journey out of Africa will appear. Consider four papers published in October that featured intriguing and sometimes contradictory results. Three new studies expanded the list of present-day populations whose DNA has been analyzed. The results suggest that most non-Africans have inherited genes from people who left Africa in a single pulse between about 75,000 and 50,000 years ago (SN: 10/15/16, p. 6). One team, studying DNA from 142 distinct human populations, proposed that African migrants interbred with Neandertals in the Middle East before splitting into groups that headed into Europe or Asia. Other scientists whose dataset included 148 populations concluded that a big move out of Africa during that time period erased most genetic traces of a smaller exodus around 120,000 years ago. A third paper found that aboriginal Australians and New Guinea’s native Papuans descend from a distinctive mix of Eurasian populations that, like ancestors of other living non-Africans, trace back to Africans who left their homeland around 72,000 years ago. The timing of those migrations may be off, however. A fourth study, based on climate and sea level data, identified the period from 72,000 to 60,000 years ago as a time when deserts largely blocked travel out of Africa. Computer models suggested several favorable periods for intercontinental travel, including one starting around 59,000 years ago. But archaeological finds suggest that humans had already spread across Asia by that time. Clashing estimates of when ancient people left Africa should come as no surprise. To gauge the timing of these migrations, scientists have to choose a rate at which changes in DNA accumulate over time. Evolutionary geneticist Swapan Mallick of Harvard Medical School and the other authors of one of the new genetics papers say that the actual mutation rate could be 30 percent higher or lower than the mutation rate they used. Undetermined levels of interbreeding with now-extinct hominid species other than Neandertals may also complicate efforts to retrace humankind’s genetic history (SN: 10/15/16, p. 22), as would mating between Africans and populations that made return trips. “This can be clarified, to some extent, with genetic data from ancient people involved in out-of-Africa migrations,” says Lalueza-Fox. So far, though, no such data exist. The uncertainty highlights the need for more archaeological evidence. Though sites exist in Africa and Europe dating from more than 100,000 years ago to 10,000 years ago, little is known about human excursions into the Arabian Peninsula and the rest of Asia. Uncovering more bones, tools and cultural objects will help fill in the picture of how humans traveled, and what key evolutionary transitions occurred along the way. Mallick’s team has suggested, for example, that symbolic and ritual behavior mushroomed around 50,000 years ago, in the later part of the Stone Age, due to cultural changes rather than genetic changes. Some archaeologists have proposed that genetic changes must have enabled the flourishing of personal ornaments and artifacts that might have been used in rituals. But comparisons of present-day human DNA to that of Neandertals and extinct Asian hominids called Denisovans don’t support that idea. Instead, another camp argues, humans may have been capable of these behaviors some 200,000 years ago. Nicholas Conard, an archaeologist at the University of Tübingen in Germany, approaches the findings cautiously. “I do not assume that interpretations of the genetic data are right,” he says. Such reconstructions have been revised and corrected many times over the last couple of decades, which is how “a healthy scientific field moves forward,” Conard adds. Collaborations connecting DNA findings to archaeological discoveries are most likely to produce unexpected insights into where we come from and who we are.

News Article | March 14, 2016
Site: www.sciencenews.org

Neandertals hung out in what’s now northern Spain around 430,000 years ago, an analysis of ancient DNA suggests. That’s an earlier Neandertal presence in Europe, by at least 30,000 years, than many researchers had assumed. Fragments of nuclear DNA from a tooth and partial leg bone discovered at Sima de los Huesos, a chamber deep inside a Spanish cave, resemble corresponding parts of a previously reassembled Neandertal genome, researchers say in a study published online March 14 in Nature. Not much nuclear DNA survives in such ancient fossils, say paleogeneticist Matthias Meyer of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and his colleagues. Meyer’s group recovered DNA fragments covering a fraction of 1 percent of the newly recovered Neandertal tooth and leg genomes. Just enough DNA remained to enable comparisons with DNA of a Neandertal woman (SN: 1/25/14, p. 17) and a Denisovan woman (SN: 9/22/12, p. 5). Denisovans are considered close genetic cousins of Neandertals. The early age for the new genetic finds challenges the idea that fossils from Sima de los Huesos, or pit of bones, come from a species called Homo heidelbergensis. Some researchers have suspected that by around 400,000 years ago, H. heidelbergensis gave rise to evolutionary precursors of both Neandertals and Homo sapiens. An ancient genetic puzzle has also emerged at Sima de los Huesos. On one hand, nuclear DNA — which passes from both parents to their children — pegs the Spanish hominids as Neandertals. But mitochondrial DNA — typically inherited only from the mother — already extracted from one Sima de los Huesos fossil (SN: 12/28/13, p. 8) and described for a second fossil in the new study has more in common with Denisovans. Denisovans lived in East Asia at least 44,000 years ago, but their evolutionary history is unknown. If early Neandertals lived in northern Spain roughly 430,000 years ago, “we have to go back further in time to reach the common ancestor of Neandertals and Denisovans,” Meyer says. The new genetic data from Sima de los Huesos now suggest that Denisovans split from Neandertals perhaps 450,000 years ago, says paleoanthropologist Chris Stringer of the Natural History Museum in London. Genetic and fossil evidence point to Neandertals and H. sapiens diverging from a common ancestor around 650,000 years ago, he proposes. But it’s hard to say whether that common ancestor was H. heidelbergensis, Stringer adds. “Research must refocus on fossils from 400,000 to 800,000 years ago to determine which ones might lie on ancestral lineages of Neandertals, Denisovans and modern humans.” Hominids throughout Eurasia during that time may have shared a mitochondrial DNA pattern observed in Sima de los Huesos Neandertals and Asian Denisovans, Meyer suggests. If that was the case, Neandertals acquired a new form of mitochondrial DNA by interbreeding with modern humans or their direct ancestors from Africa sometime between 430,000 and 100,000 years ago (SN: 3/19/16, p. 6). Another possibility is that Neandertals traveled to Europe from Asia more than 430,000 years ago, carrying Denisovan mitochondrial DNA with them, says paleogeneticist Carles Lalueza-Fox of the Institute of Evolutionary Biology in Barcelona. Or hybrid descendants of early Neandertals and early Denisovans may have lived at Sima de los Huesos, carrying Denisovan mitochondrial DNA, he speculates. “We really need more genetic data from Sima de los Huesos, and other sites of that age, to narrow down these scenarios,” Meyer says.

Stone G.N.,Institute of Evolutionary Biology | Nee S.,Institute of Evolutionary Biology | Felsenstein J.,University of Washington
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2011

How do we quantify patterns (such as responses to local selection) sampled across multiple populations within a single species? Key to this question is the extent to which populations within species represent statistically independent data points in our analysis. Comparative analyses across species and higher taxa have long recognized the need to control for the non-independence of species data that arises through patterns of shared common ancestry among them (phylogenetic non-independence), as have quantitative genetic studies of individuals linked by a pedigree. Analyses across populations lacking pedigree information fall in the middle, and not only have to deal with shared common ancestry, but also the impact of exchange of migrants between populations (gene flow). As a result, phenotypes measured in one population are influenced by processes acting on others, and may not be a good guide to either the strength or direction of local selection. Although many studies examine patterns across populations within species, few consider such non-independence. Here, we discuss the sources of non-independence in comparative analysis, and show why the phylogeny-based approaches widely used in cross-species analyses are unlikely to be useful in analyses across populations within species. We outline the approaches (intraspecific contrasts, generalized least squares, generalized linear mixed models and autoregression) that have been used in this context, and explain their specific assumptions. We highlight the power of 'mixed models' in many contexts where problems of non-independence arise, and show that these allow incorporation of both shared common ancestry and gene flow. We suggest what can be done when ideal solutions are inaccessible, highlight the need for incorporation of a wider range of population models in intraspecific comparative methods and call for simulation studies of the error rates associated with alternative approaches. © 2011 The Royal Society.

Carranza S.,Institute of Evolutionary Biology | Arnold E.N.,Natural History Museum in London
Zootaxa | Year: 2012

The genus Hemidactylus is one of the most species-rich and widely distributed of all reptile genera, being found in the tropical and subtropical regions of the world and hundreds of continental and oceanic islands. Despite having already 111 species, the number of species described in recent years is very high. This has been facilitated, in part, by the use of molecular techniques, which in most cases have been employed to confirm the differentiation at the DNA level of some morphologically variable forms and to discover some cryptic lineages. Preliminary analyses indicate that some Hemidactylus species from Oman are quite variable in their morphology and may include more than one species. In order to test this hypothesis we inferred a molecular phylogeny including 131 Hemidactylus (20 species) using 1385 base pairs of mitochondrial DNA (353 bp 12S; 302 bp cytb; 588 bp nd4 and 142 bp tRNAs) and 1481 bp of nuclear DNA (403 bp c-mos; 668 bp mc1r and 410 bp rag2) and analyzed 226 specimens (15 species) for several meristic and pholidotic characters of which we took 3103 photographs that have been deposited in MorphoBank (project 483). Our results indicate the presence of eight new species of Hemidactylus geckos in Arabia: H. luqueorum sp. nov. and H. hajarensis sp. nov. from North Oman; H. masirahensis sp. nov. from Masirah Island; H. inexpectatus sp. nov. from one locality on coastal Central Oman; H. alkiyumii sp. nov., H. festivus sp. nov. and H. paucituberculatus sp. nov. from Dhofar, Southern Oman; and finally H. endophis sp. nov. probably from North Oman and described on the basis of morphology alone. An identification key to the genus Hemidactylus from Oman is also presented. With these descriptions, the number of Hemidactylus species found in Oman increases from 7 to 13 and the number of endemic Hemidactylus from 0 to 6. The description of three new species endemic to the Hajar Mountains in North Oman highlights the importance of this mountain range as a biodiversity hotspot that, up to now, includes 12 reptile species that are found nowhere else in the World. Another hotspot of Hemidactylus biodiversity is the Dhofar Mountain range, in the extreme Southwestern corner of Oman and East Yemen. As a result of its particular geographic situation, orography and the effect of the Southwest Monsoons, this mountain range presents a diverse variety of habitats with different species of Hemidactylus adapted to them. With the exception of H. flaviviridis and H. leschenaultii, which belong to the Tropical Asian clade of Hemidactylus, all Arabian Hemidactylus for which DNA sequence is available are members of the Arid clade of Hemidactylus. Relatively recent dispersal appears to have taken place within Arabia in the H. turcicus group, with the South Arabian H. lemurinus occurring far from other confirmed members of this assemblage. Hemidactylus flaviviridis and a clade of H. robustus are genetically uniform, widespread in Arabia and beyond and occur around human habitations, suggesting that much of their large distributions are anthropogenic, as appears to be so in several other Hemidactylus species outside Arabia. The way in which species of Arabian Hemidactylus separate ecologically is surprisingly varied. They may occur at similar altitudes but replace each other geographically, or if they are sympatric there may be altitudinal separation. Humidity may also be an important factor, and when animals exist within a few meters of each other, structural niche may be significant. While four native species occur close together in Dhofar, most Hemidactylus communities in Arabia consist of only one or two species, although climbing geckos belonging to other genera, such as Asaccus and Ptyodactylus, may also be present. © 2012 Magnolia Press.

Silva-Sousa R.,Institute of Evolutionary Biology | Lopez-Panades E.,Institute of Evolutionary Biology | Pineyro D.,Institute of Evolutionary Biology | Pineyro D.,Barcelona Institute for Research in Biomedicine | Casacuberta E.,Institute of Evolutionary Biology
PLoS Genetics | Year: 2012

Drosophila telomere maintenance depends on the transposition of the specialized retrotransposons HeT-A, TART, and TAHRE. Controlling the activation and silencing of these elements is crucial for a precise telomere function without compromising genomic integrity. Here we describe two chromosomal proteins, JIL-1 and Z4 (also known as Putzig), which are necessary for establishing a fine-tuned regulation of the transcription of the major component of Drosophila telomeres, the HeT-A retrotransposon, thus guaranteeing genome stability. We found that mutant alleles of JIL-1 have decreased HeT-A transcription, putting forward this kinase as the first positive regulator of telomere transcription in Drosophila described to date. We describe how the decrease in HeT-A transcription in JIL-1 alleles correlates with an increase in silencing chromatin marks such as H3K9me3 and HP1a at the HeT-A promoter. Moreover, we have detected that Z4 mutant alleles show moderate telomere instability, suggesting an important role of the JIL-1-Z4 complex in establishing and maintaining an appropriate chromatin environment at Drosophila telomeres. Interestingly, we have detected a biochemical interaction between Z4 and the HeT-A Gag protein, which could explain how the Z4-JIL-1 complex is targeted to the telomeres. Accordingly, we demonstrate that a phenotype of telomere instability similar to that observed for Z4 mutant alleles is found when the gene that encodes the HeT-A Gag protein is knocked down. We propose a model to explain the observed transcriptional and stability changes in relation to other heterochromatin components characteristic of Drosophila telomeres, such as HP1a. © 2012 Silva-Sousa et al.

Davey J.L.,Institute of Evolutionary Biology | Blaxter M.W.,University of Edinburgh
Briefings in Functional Genomics | Year: 2010

Next-generation sequencing technologies are making a substantial impact on many areas of biology, including the analysis of genetic diversity in populations. However, genome-scale population genetic studies have been accessible only to well-funded model systems. Restriction-site associated DNA sequencing, a method that samples at reduced complexity across target genomes, promises to deliver high resolution population genomic dataçthousands of sequenced markers across many individuals-for any organism at reasonable costs. It has found application in wild populations and non-traditional study species, and promises to become an important technology for ecological population genomics. © The Author 2011. Published by Oxford University Press. All rights reserved.

McTaggart S.J.,Institute of Evolutionary Biology | Obbard D.J.,Institute of Evolutionary Biology | Conlon C.,Institute of Evolutionary Biology | Little T.J.,Institute of Evolutionary Biology
BMC Evolutionary Biology | Year: 2012

Background: Understanding which parts of the genome have been most influenced by adaptive evolution remains an unsolved puzzle. Some evidence suggests that selection has the greatest impact on regions of the genome that interact with other evolving genomes, including loci that are involved in host-parasite co-evolutionary processes. In this study, we used a population genetic approach to test this hypothesis by comparing DNA sequences of 30 putative immune system genes in the crustacean Daphnia pulex with 24 non-immune system genes. Results: In support of the hypothesis, results from a multilocus extension of the McDonald-Kreitman (MK) test indicate that immune system genes as a class have experienced more adaptive evolution than non-immune system genes. However, not all immune system genes show evidence of adaptive evolution. Additionally, we apply single locus MK tests and calculate population genetic parameters at all loci in order to characterize the mode of selection (directional versus balancing) in the genes that show the greatest deviation from neutral evolution. Conclusions: Our data are consistent with the hypothesis that immune system genes undergo more adaptive evolution than non-immune system genes, possibly as a result of host-parasite arms races. The results of these analyses highlight several candidate loci undergoing adaptive evolution that could be targeted in future studies. © 2012 McTaggart et al.; licensee BioMed Central Ltd.

Harrison R.J.,Institute of Evolutionary Biology | Charlesworth B.,Institute of Evolutionary Biology
Molecular Biology and Evolution | Year: 2011

Patterns of synonymous codon usage vary between organisms and are controlled by neutral processes (such as drift and mutation) as well as by selection. Here we show that an additional neutral process, GC-biased gene conversion (gBGC), plays a part in shaping patterns of both synonymous codon usage and amino acid composition in a manner dependent upon the local recombination rate. We obtain estimates of the strength of gBGC acting on synonymous sites in five species of yeast, which we find to be a much weaker force than selection. We use this to correct estimates of the strength of selection on codon usage bias, which are normally confounded by the action of gBGC. Our estimate of the rate of gBGC agrees well with an experimentally determined value obtained from Saccharomyces cerevisiae. We also find that, contrary to expectation, codon usage bias is highest in areas of intermediate levels of recombination for GC-ending optimal codons. Possible reasons for this are discussed. © 2010 The Author.

News Article | October 28, 2015
Site: www.nature.com

The oldest ancestor of animal life used the same tricks that modern humans do to turn genes on and off. Alex de Mendoza at the Institute of Evolutionary Biology in Barcelona, Spain, and his colleagues studied gene regulation in the fungus-like single-celled organism Creolimax fragrantissima, which branched onto a separate evolutionary path before the evolution of multicellular organisms. To produce different cell types, multicellular organisms use three main gene-regulation processes: transcription factors, alternative splicing and non-coding RNAs. The authors found that C. fragrantissima uses the same processes to switch between life stages, meaning that these regulatory elements were likely to have been used by the last universal common ancestor of all animals, the authors say.

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