Supplemental Information 1: Sequence data

Episodic sea level changes that repeatedly exposed and inundated the Sunda Shelf characterize the Pleistocene. Available evidence points to a more xeric central Sunda Shelf during periods of low sea levels, and despite the broad land connections that persisted during this time, some organisms are assumed to have faced barriers to dispersal between land-masses on the Sunda Shelf. Eutropis rugifera is a secretive, forest adapted scincid lizard that ranges across the Sunda Shelf. In this study, we sequenced one mitochondrial (ND2) and four nuclear (BRCA1, BRCA2, RAG1, and MC1R) markers and generated a time-calibrated phylogeny in BEAST to test whether divergence times between Sundaic populations of E. rugifera occurred during Pleistocene sea-level changes, or if they predate the Pleistocene. We find that E. rugifera shows pre-Pleistocene divergences between populations on different Sundaic land-masses. The earliest divergence within E. rugifera separates the Philippine samples from the Sundaic samples approximately 16 Ma; the Philippine populations thus cannot be considered conspecific with Sundaic congeners. Sundaic populations diverged approximately 6 Ma, and populations within Borneo from Sabah and Sarawak separated approximately 4.5 Ma in the early Pliocene, followed by further cladogenesis in Sarawak through the Pleistocene. Divergence of peninsular Malaysian populations from the Mentawai Archipelago occurred approximately 5 Ma. Separation among island populations from the Mentawai Archipelago likely dates to the Pliocene/Pleistocene boundary approximately 3.5 Ma, and our samples from peninsular Malaysia appear to coalesce in the middle Pleistocene, about 1 Ma. Coupled with the monophyly of these populations, these divergence times suggest that despite consistent land-connections between these regions throughout the Pleistocene E. rugifera still faced barriers to dispersal, which may be a result of environmental shifts that accompanied the sea-level changes

Diagonal conditions in ordered spaces

Abstract. For a space X and a regular uncountable cardinal κ ≤ |X| we say that then we say that X has a small diagonal, and if every regular uncountable κ ≤ |X| belongs to D(X) then we say that X has an H-diagonal. In this paper we investigate the interplay between D(X) and topological properties of X in the category of generalized ordered spaces. We obtain cardinal invariant theorems and metrization theorems for such spaces, proving, for example, that a Lindelöf linearly ordered space with a small diagonal is metrizable. We give examples showing that our results are the sharpest possible, e.g., that there is a first countable, perfect, paracompacť Cech-complete linearly ordered space with an H-diagonal that is not metrizable. Our example shows that a recent CH-result of Juhász and Szentmiklóssy on metrizability of compact Hausdorff spaces with small diagonals cannot be generalized beyond the class of locally compact spaces. We present examples showing the interplay of the above diagonal conditions with set theory in a natural extension of the Michael line construction

Using ancient DNA to unravel taxonomic puzzles: the identity of Deuterodon pedri (Ostariophysi: Characidae)

ABSTRACT Accurate identification is essential for any study exploring biodiversity. Unfortunately, museum type specimens preserved for more than a hundred years are often not informative enough for precise identification of the species represented by the name-bearing type. The use of ancient DNA can help solve taxonomic problems when name-bearing types no longer have diagnostic morphological features that allow for an accurate identification of the species involved. That is the case for Deuterodon pedri, an endemic species from a small drainage in the rio Doce basin in Minas Gerais, Brazil, for which the type material is in poor condition. Specimens of D. pedri were collected in 1865 by the Thayer Expedition to Brazil and fixed in spirits, enabling them to yield viable DNA. As the morphology alone of the type material does not allow for an accurate identification, we used both morphological and ancient DNA (aDNA) methods to decisively establish the identity of D. pedri. This identification allowed us to recognize the species among recently collected specimens and then, based on them, redescribe the species. A genetype for the lectotype of D. pedri is presented

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

Mitochondrial Genome Sequences Effectively Reveal the Phylogeny of Hylobates Gibbons

BACKGROUND: Uniquely among hominoids, gibbons exist as multiple geographically contiguous taxa exhibiting distinctive behavioral, morphological, and karyotypic characteristics. However, our understanding of the evolutionary relationships of the various gibbons, especially among Hylobates species, is still limited because previous studies used limited taxon sampling or short mitochondrial DNA (mtDNA) sequences. Here we use mtDNA genome sequences to reconstruct gibbon phylogenetic relationships and reveal the pattern and timing of divergence events in gibbon evolutionary history. METHODOLOGY/PRINCIPAL FINDINGS: We sequenced the mitochondrial genomes of 51 individuals representing 11 species belonging to three genera (Hylobates, Nomascus and Symphalangus) using the high-throughput 454 sequencing system with the parallel tagged sequencing approach. Three phylogenetic analyses (maximum likelihood, Bayesian analysis and neighbor-joining) depicted the gibbon phylogenetic relationships congruently and with strong support values. Most notably, we recover a well-supported phylogeny of the Hylobates gibbons. The estimation of divergence times using Bayesian analysis with relaxed clock model suggests a much more rapid speciation process in Hylobates than in Nomascus. CONCLUSIONS/SIGNIFICANCE: Use of more than 15 kb sequences of the mitochondrial genome provided more informative and robust data than previous studies of short mitochondrial segments (e.g., control region or cytochrome b) as shown by the reliable reconstruction of divergence patterns among Hylobates gibbons. Moreover, molecular dating of the mitogenomic divergence times implied that biogeographic change during the last five million years may be a factor promoting the speciation of Sundaland animals, including Hylobates species

Host selection by an insect herbivore with spatially variable density dependence

Many species of phytophagous insects do not oviposit preferentially on plants that yield high offspring performance. One proposed explanation is that negatively density-dependent offspring performance would select for females that disperse eggs among plants to minimize competition. Recent work showing larval density dependence often varies substantially among plants suggests that ovipositing females should not only respond to the density of competitors but also to traits predictive of the strength of density dependence mediated by plants. In this study, we used field and greenhouse experiments to examine oviposition behavior in an insect herbivore that experiences density-dependent larval performance and variability in the strength of that density dependence among host-plant individuals. We found females moved readily among plants in the field and had strong preferences for plants that mediate weak offspring density dependence. Females, however, did not avoid plants with high densities of competitors, despite the fact that offspring performance declines steeply with density on most plants in natural populations. This means females minimize the effects of density dependence on their offspring by choosing plants that mediate only weak larval density dependence, not by choosing plants with low densities of competitors. Our results suggest that explaining the lack of positive preference-performance correlations in many systems may not be as simple as invoking density dependence. Resource selection behavior may depend not just on the presence or absence of density-dependent offspring performance but also on variation in the strength of offspring density dependence among sites within populations

Review of Coronal Oscillations - An Observer's View

Recent observations show a variety of oscillation modes in the corona. Early non-imaging observations in radio wavelengths showed a number of fast-period oscillations in the order of seconds, which have been interpreted as fast sausage mode oscillations. TRACE observations from 1998 have for the first time revealed the lateral displacements of fast kink mode oscillations, with periods of ~3-5 minutes, apparently triggered by nearby flares and destabilizing filaments. Recently, SUMER discovered with Doppler shift measurements loop oscillations with longer periods (10-30 minutes) and relatively short damping times in hot (7 MK) loops, which seem to correspond to longitudinal slow magnetoacoustic waves. In addition, propagating longitudinal waves have also been detected with EIT and TRACE in the lowest density scale height of loops near sunspots. All these new observations seem to confirm the theoretically predicted oscillation modes and can now be used as a powerful tool for ``coronal seismology'' diagnostic.Comment: 5 Figure