Speciation dynamics in the SE Asian tropics: Putting a time perspective on the phylogeny and biogeography of Sundaland tree squirrels, Sundasciurus

Tropical rainforests are well known for their extraordinarily high levels of biodiversity. The origin of this species richness is still debated. For instance, the museum hypothesis states that over evolutionary time more and more species will accumulate with relatively few extinctions. In contrast, the Pleistocene diver- sification model argues that during the last 2 million years, climatic factors (glaciations) caused environ- mental changes that drove isolation and vicariant speciation events. In this study, we construct a molecular phylogeny of the Sundaland (Malay Peninsula, Sumata, Borneo, Palawan) and Greater Minda- nao (Mindanao, Samar, Leyte) tree squirrels (genus Sundasciurus). Our results show that most speciation events in this forest dependent taxon occurred before the Pleistocene and that even the timing of intra- specific splits among populations from different landmasses are relatively old. Additionally, we found unexpectedly high divergence within and between highland populations of S. tenuis on Sumatra and the Malay Peninsula, highlighting the importance of Pliocene events in both speciation and within species divergences in this regionPeer reviewe

Selective Enrichment and Sequencing of Whole Mitochondrial Genomes in the Presence of Nuclear Encoded Mitochondrial Pseudogenes (Numts)

Numts are an integral component of many eukaryote genomes offering a snapshot of the evolutionary process that led from the incorporation of an α-proteobacterium into a larger eukaryotic cell some 1.8 billion years ago. Although numt sequence can be harnessed as molecular marker, these sequences often remain unidentified and are mistaken for genuine mtDNA leading to erroneous interpretation of mtDNA data sets. It is therefore indispensable that during the process of amplifying and sequencing mitochondrial genes, preventive measures are taken to ensure the exclusion of numts to guarantee the recovery of genuine mtDNA. This applies to mtDNA analyses in general but especially to studies where mtDNAs are sequenced de novo as the launch pad for subsequent mtDNA-based research. By using a combination of dilution series and nested rolling circle amplification (RCA), we present a novel strategy to selectively amplify mtDNA and exclude the amplification of numt sequence. We have successfully applied this strategy to de novo sequence the mtDNA of the Black Field Cricket Teleogryllus commodus, a species known to contain numts. Aligning our assembled sequence to the reference genome of Teleogryllus emma (GenBank EU557269.1) led to the identification of a numt sequence in the reference sequence. This unexpected result further highlights the need of a reliable and accessible strategy to eliminate this source of error

Some preliminary results of petrological work in Galicia (N.W. Spain)

The Spanish region of Galicia is situated in the extreme north-western part of the country due North of Portugal and West of Asturias. It is bordered by the Atlantic Ocean to the West and by the Bay of Biscay to the North (see fig. 1). The area under investigation concerns the western provinces of La Coruña and Pontevedra mainly. Apart from early reconnaissance work by Schulz (1858), Barrois (1892), Sampelayo (1922), Lotze (1945), Carlé (1945), Navarro and del Valle (1959) the area is at present being investigated and mapped on a scale of 1:50.000 by López de Azcona, Parga Pondal and their associates for the Instituto Geológico y Minero de España. So far nine sheets and explanatory memoirs have been published between 1948 and 1956. Parga Pondal has also published a geological sketch map on a scale of 1:400.000 and an explanatory note of the province of La Coruña in 1956, and since 1931 he has contributed substantially to the knowledge of Galician geology in a series of papers concerning petrological, mineralogical, tectonic and sedimentological aspects of it. Between 1955 and 1959 de Sitter and Zwart conducted geological research by the Department of Structural and Applied Geology of the University of Leyden in the area between Lage and Malpica. Summaries of their results appeared in 1955 and 1957, while one of their associates, Insinger, published a short account of his work in the vicinity of Mugía in 1961

Tracing crustal evolution in the NW Iberian Peninsula through the Rb---Sr and U---Pb systematics of Palaeozoic granitoids: a review

The abundant granitoids in the Palaeozoic basement of the northwestern Iberian Peninsula include 470-440 Ma old suites (Early-Middle Ordovician, now present as orthogneisses) and several Variscan suites. The age data presently available suggest that the latter have been generated in three separate time intervals, ~ 330-320 Ma ago (Late Visean-Early Namurian), ~ 310-300 Ma ago (Westphalian)~ and 290-280 Ma ago (Late Stephanian-Autunian). Rb---Sr whole-rock and U---Pb zircon systematics, along with field and chemical evidence, testify to the generation of the Early and Late Palaeozoic granitoids from Lower Palaeozoic and Precambrian (maximum age ~ 1.7-1.6 Ga) sedimentary sequences, respectively. The source rocks contained zircons derived from a late Archaean-Early Proterozoic continental crust that probably underlies the whole of western Europe, although for the greater part modified beyond recognition by younger crustal reworking

Tracing crustal evolution in the NW Iberian Peninsula through the Rb---Sr and U---Pb systematics of Palaeozoic granitoids: a review

The abundant granitoids in the Palaeozoic basement of the northwestern Iberian Peninsula include 470-440 Ma old suites (Early-Middle Ordovician, now present as orthogneisses) and several Variscan suites. The age data presently available suggest that the latter have been generated in three separate time intervals, ~ 330-320 Ma ago (Late Visean-Early Namurian), ~ 310-300 Ma ago (Westphalian)~ and 290-280 Ma ago (Late Stephanian-Autunian). Rb---Sr whole-rock and U---Pb zircon systematics, along with field and chemical evidence, testify to the generation of the Early and Late Palaeozoic granitoids from Lower Palaeozoic and Precambrian (maximum age ~ 1.7-1.6 Ga) sedimentary sequences, respectively. The source rocks contained zircons derived from a late Archaean-Early Proterozoic continental crust that probably underlies the whole of western Europe, although for the greater part modified beyond recognition by younger crustal reworking

Nuclear copies of mitochondrial genes: another problem for ancient DNA

The application of ancient DNA techniques is subject to many problems caused primarily by low quality and by low quantity of DNA. For these reasons most studies employing ancient DNA rely on the characterization of mitochondrial DNA, which is present in many more copies per cell than nuclear DNA and hence more copies are likely to survive. We used universal and taxon specific mitochondrial primers to amplify DNA from museum specimens, and found many instances where the amplification of nuclear copies of the mitochondrial gene (numts) instead of the targeted mitochondrial fragment had occurred. Furthermore, the likelihood of amplifying numts increased dramatically when universal primers were utilized. Here we suggest that ancient DNA practitioners must consider the possibility that numts can be amplified at higher rates than previously thought. This is another complication for ancient DNA studies, but it also suggests that more extensive inclusion of nuclear markers in ancient DNA studies should be feasible. © 2010 Springer Science+Business Media B.V.Peer Reviewe