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Gonzalez J.,Stanford University | Gonzalez J.,Institute of Evolutionary Biology | Petrov D.A.,Stanford University
Methods in Molecular Biology

Recent research is starting to shed light on the factors that influence the population and evolutionary dynamics of transposable elements (TEs) and TE life cycles. Genomes differ sharply in the number of TE copies, in the level of TE activity, in the diversity of TE families and types, and in the proportion of old and young TEs. In this chapter, we focus on two well-studied genomes with strikingly different architectures, humans and Drosophila, which represent two extremes in terms of TE diversity and population dynamics. We argue that some of the answers might lie in (1) the larger population size and consequently more effective selection against new TE insertions due to ectopic recombination in flies compared to humans; and (2) in the faster rate of DNA loss in flies compared to humans leading to much faster removal of fixed TE copies from the fly genome. © 2012 Springer Science+Business Media, LLC. Source

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

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. Source

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. Source

News Article
Site: https://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.

News Article
Site: http://www.nature.com/nature/current_issue/

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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