Colour pattern specification in the Mocker swallowtail Papilio dardanus: the transcription factor invected is a candidate for the mimicry locus H

The swallowtail butterfly, Papilio dardanus, is an iconic example of a polymorphic Batesian mimic. The expression of various female-limited colour forms is thought to be controlled by a single autosomal locus, termed H, whose function in determining the wing pattern remains elusive. As a step towards the physical mapping of H, we established a set of 272 polymorphic amplified fragment length polymorphism (AFLP) markers (EcoRI-MseI). Segregation patterns in a 'female-informative' brood (exploiting the absence of crossing over in female Lepidoptera) mapped these AFLPs to 30 linkage groups (putative chromosomes). The difference between the hippocoon and cenea female forms segregating in this family resides on a single one of these linkage groups, defined by 14 AFLPs. In a 'male-informative' cross (markers segregating within a linkage group), a pair of AFLPs co-segregated closely with the two female forms, except in four recombinants out of 19 female offspring. Linkage with these AFLP markers using four further female-informative families demonstrated that the genetic factor determining other morphs (poultoni, lamborni and trimeni) also maps to this same linkage group. The candidate gene invected, obtained in a screen for co-segregation of developmental genes with the colour forms, resides in a 13.9 cM interval flanked by the two AFLP markers. In the male-informative family invected co-segregated perfectly with the hippocoon/cenea factor, despite the four crossovers with the AFLPs. These findings make invected, and possibly its closely linked paralogue engrailed, strong candidates for H. This is supported by their known role in eyespot specification in nymphalid butterfly wings.     

A model for colour pattern formation in the butterfly wing of Papilio dardanus

The butterfly Papilio dardanus is well known for the spectacular phenotypic polymorphism in the female of the species. We show that numerical simulations of a reaction diffusion model on a geometrically accurate wing domain produce spatial patterns that are consistent with many of those observed on the butterfly. Our results suggest that the wing coloration is due to a simple underlying stripe-like pattern of some pigment-inducing morphogen. We focus on the effect of key factors such as parameter values for mode selection, threshold values which determine colour, wing shape and boundary conditions. The generality of our approach should allow us to investigate other butterfly species. The relationship between these key factors and gene activities is discussed in the context of recent biological advances.     

A molecular phylogenetic framework for the evolution of parasitic strategies in cymothoid isopods (Crustacea)

The parasitic isopods belonging to the family Cymothoidae attach under the scales, in the gills or on the tongue of their fish hosts, exhibiting distinctive life-histories and morphological modifications. According to conventional views, the three parasitic types (scale-, gill-, and mouth-dwellers) correspond to three distinct lineages. In this study, we have used fragments of two mitochondrial genes (large ribosomal DNA subunit, 16S rRNA, and cytochrome oxidase I) and two species for each of the three parasitic habits to present a preliminary hypothesis on the evolutionary history of the family. Our molecular data support the monophyly of the family but suggest that – contrary to what was previously believed – the more specialized mouth- and gill-inhabiting species are not necessarily derived from scale-dwelling ones.     

Natural selection for rare and mimetic colour pattern combinations in wild populations of the diadem butterfly, Hypolimnas misippus L

Mark recapture and morph frequency data, gathered during a population irruption of Hypolimnas misippus in southern Ghana, provide evidence for apostatic and mimetic selection. During a period of low adult survival, both the recapture rate and the frequency of the commonest morph ( misippus ) were significantly reduced. Selection against this form increased phenotypic diversity and generated significant disequilibrium in the combinations of unlinked fore- and hindwing phenotypes. There was also evidence for selection against those forms (weak alcippoides ) which most closely resemble misippus . Other morphs, including both good mimics of Danaus chrysippus and rare non-mimics, showed no reductions in recapture rate during the period of low survival, but only the good mimics increased significantly in frequency. The results provide a predictive ecological model for density-dependent selection by predators which is consistent with field data from previous studies of H. misippus in Ghana and Tanzania. Their evolutionary implications are discussed, and it is suggested that anomalies in the mimicry of this species may be partly due to lack of predation when it is scarce.     

Response of bee-flies to the shape and pattern of model flowers: implications for floral evolution in a Mediterranean herb

1. The functional significance of floral traits in Linum pubescens (Linaceae), a Mediterranean annual that is pollinated almost exclusively by the bee-fly Usia bicolor (Bombyliidae), was investigated. The flies feed on both pollen and nectar, and use the flowers as mating rendezvous sites in the afternoon.
2. Choice experiments with model flowers were used to determine the response of U. bicolor to visual cues, such as shape, size, colour and pattern.
3. Bee-flies strongly preferred models with a dissected outline over models with a simple outline. They also preferred pink models over other colours, and larger models over smaller models.
5. Flies landing on models with converging lines ('nectar guides') tended to follow the lines to the point where they meet in the centre of the model, while flies landing on plain models showed undirected behaviour, often moving to the edge of the model.
6. Flies were strongly attracted to flowers of L. pubescens which had a fly glued on to one of the petals, as well as flowers with a dark spot painted onto one of the petals. In addition, models with a dark spot were strongly preferred over plain models during the afternoon when flies exhibit mating behaviour. This evidence suggests that the dark centre of the L. pubescens flower may function as an attractant to mate-seeking bee-flies.     

A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock

Current understanding of the diversification of birds is hindered by their incomplete fossil record and uncertainty in phylogenetic relationships and phylogenetic rates of molecular evolution. Here we performed the first comprehensive analysis of mitogenomic data of 48 vertebrates, including 35 birds, to derive a Bayesian timescale for avian evolution and to estimate rates of DNA evolution. Our approach used multiple fossil time constraints scattered throughout the phylogenetic tree and accounts for uncertainties in time constraints, branch lengths, and heterogeneity of rates of DNA evolution. We estimated that the major vertebrate lineages originated in the Permian; the 95% credible intervals of our estimated ages of the origin of archosaurs (258 MYA), the amniote-amphibian split (356 MYA), and the archosaur-lizard divergence (278 MYA) bracket estimates from the fossil record. The origin of modern orders of birds was estimated to have occurred throughout the Cretaceous beginning about 139 MYA, arguing against a cataclysmic extinction of lineages at the Cretaceous/Tertiary boundary. We identified fossils that are useful as time constraints within vertebrates. Our timescale reveals that rates of molecular evolution vary across genes and among taxa through time, thereby refuting the widely used mitogenomic or cytochrome b molecular clock in birds. Moreover, the 5-Myr divergence time assumed between 2 genera of geese (Branta and Anser) to originally calibrate the standard mitochondrial clock rate of 0.01 substitutions per site per lineage per Myr (s/s/l/Myr) in birds was shown to be underestimated by about 9.5 Myr. Phylogenetic rates in birds vary between 0.0009 and 0.012 s/s/l/Myr, indicating that many phylogenetic splits among avian taxa also have been underestimated and need to be revised. We found no support for the hypothesis that the molecular clock in birds "ticks" according to a constant rate of substitution per unit of mass-specific metabolic energy rather than per unit of time, as recently suggested. Our analysis advances knowledge of rates of DNA evolution across birds and other vertebrates and will, therefore, aid comparative biology studies that seek to infer the origin and timing of major adaptive shifts in vertebrates.     

Molecular-based estimate of species number,phylogenetic relationships and divergence times for the genus Stenotaenia (Chilopoda,Geophilomorpha) in the Italian region

Stenotaenia is one of the largest and most widespread genera of geophilid centipedes in the Western Palearctic, with a very uniform morphology and about fifteen species provisionally recognized. For a better understanding of Stenotaenia species-level taxonomy, we have explored the possibility of using molecular data. As a preliminary assay, we sampled twelve populations, mainly from the Italian region, and analyzed partial sequences of the two genes COI and 28S. We employed a DNA-barcoding approach, complemented by a phylogenetic analysis coupled with divergence time estimation. Assuming a barcoding gap of 10–16% K2P pairwise distances, we found evidence for the presence of at least six Stenotaenia species in the Italian region, which started diverging about 50 million years ago, only partially matching with previously recognized species. We found that small-sized oligopodous species belong to a single clade that originated about 33 million years ago, and obtained some preliminary evidence of the related genus Tuoba being nested within Stenotaenia.     

A framework for the study of genetic variation in migratory behaviour

Evolutionary change results from selection acting on genetic variation. For migration to be successful, many different aspects of an animal’s physiology and behaviour need to function in a co-coordinated way. Changes in one migratory trait are therefore likely to be accompanied by changes in other migratory and life-history traits. At present, we have some knowledge of the pressures that operate at the various stages of migration, but we know very little about the extent of genetic variation in various aspects of the migratory syndrome. As a consequence, our ability to predict which species is capable of what kind of evolutionary change, and at which rate, is limited. Here, we review how our evolutionary understanding of migration may benefit from taking a quantitative-genetic approach and present a framework for studying the causes of phenotypic variation. We review past research, that has mainly studied single migratory traits in captive birds, and discuss how this work could be extended to study genetic variation in the wild and to account for genetic correlations and correlated selection. In the future, reaction-norm approaches may become very important, as they allow the study of genetic and environmental effects on phenotypic expression within a single framework, as well as of their interactions. We advocate making more use of repeated measurements on single individuals to study the causes of among-individual variation in the wild, as they are easier to obtain than data on relatives and can provide valuable information for identifying and selecting traits. This approach will be particularly informative if it involves systematic testing of individuals under different environmental conditions. We propose extending this research agenda by using optimality models to predict levels of variation and covariation among traits and constraints. This may help us to select traits in which we might expect genetic variation, and to identify the most informative environmental axes. We also recommend an expansion of the passerine model, as this model does not apply to birds, like geese, where cultural transmission of spatio-temporal information is an important determinant of migration patterns and their variation.     

Astronomically forced climate change in the Kenyan Rift Valley 2.7-2.55 Ma: implications for the evolution of early hominin ecosystems

Global climate change, linked to astronomical forcing factors, has been implicated in faunal evolutionary change in equatorial Africa, including the origin and diversification of hominin lineages. Empirical terrestrial data demonstrating that orbital forcing has a significant effect, or is detectable, at early hominin sites in equatorial continental interiors during the Pliocene, however, remain limited. Sedimentation patterns in the Baringo Basin within the Central Kenyan Rift Valley between ca. 2.7 and 2.55 Ma, controlled by climatic factors, provide a detailed paleoenvironmental record spanning 35 fossil vertebrate localities, including three hominin sites. The succession includes a sequence of diatomites that record rhythmic cycling of major freshwater lake systems consistent with approximately 23-kyr Milankovitch precessional periodicity. The temporal framework of shifting precipitation patterns, relative to Pliocene insolation curves, implicate African monsoonal climatic control and indicate that climatic fluctuations in Rift Valley ecosystems were paced by global climatic change documented in marine cores. These data provide direct evidence of orbitally mediated environmental change at Pliocene Rift Valley hominin fossil localities, providing a unique opportunity to assess the evolutionary effect of short-term climatic flux on late Pliocene East African terrestrial communities.     

Scrambled duplications in the feline leukemia virusgag gene: A putative pattern for molecular evolution

Summary The present study is a detailed computer-assisted analysis of the feline leukemia virus gag gene nucleotide sequence together wit its flanking sequences (ST-FeLV GAG) that is compared with the aligned sectors of the Moloney strain of murine leukemia virus (Mo-MuLV GAG) and of three strains of feline sarcoma virus. It shows that perfectly matched repeated oligomers up to 13 nucleotides long are overrepresented and scattered throughout both ST-FeLV GAG and Mo-MuLV GAG, in noncoding and coding sectors, with no stringent correlation to codon usage in ST-FeLV gPr80^gag. Many repeated oligomers share a core consensus that is intriguingly part of the inverted repeat at the termini of the long terminal repeat. Local scrambled repetitions of nucleotide subsequences have been found; they suggest a model of molecular evolution byslippage-like mechanisms. Thus, viral genomes could be subject to the same evolutionary mechanisms that are now known to be operating extensively in eukaryotic genomes. The data are discussed in light of putative patterns of molecular evolution.     

Evolutionarily conserved pressure for the existence of distinct G2/M cell cycle arrest and A3H inactivation functions in HIV-1 Vif

HIV-1 Vif assembles the Cul5-EloB/C E3 ubiquitin ligase to induce proteasomal degradation of the cellular antiviral APOBEC3 proteins. Detailed structural studies have confirmed critical functional domains in Vif that we have previously identified as important for the interaction of EloB/C, Cul5, and CBFβ. However, the mechanism by which Vif recognizes substrates remains poorly understood. Specific regions of Vif have been identified as being responsible for binding and depleting APOBEC3G and APOBEC3F. Interestingly, we have now identified distinct yet overlapping domains that are required for HIV-1 Vif-mediated G2/M-phase cell cycle arrest and APOBEC3H degradation, but not for the inactivation of APOBEC3G or APOBEC3F. Surprisingly, Vif molecules from primary HIV-1 variants that caused G2/M arrest were unable to inactivate APOBEC3H; on the other hand, HIV-1 Vif variants that could inactivate APOBEC3H were unable to induce G2/M arrest. All of these Vif variants still maintained the ability to inactivate APOBEC3G/F. Thus, primary HIV-1 variants have evolved to possess distinct functional activities that allow them to suppress APOBEC3H or cause G2 cell cycle arrest, using mutually exclusive interface domains. APOBEC3H depletion and G2 arrest are apparently evolutionary selected features that cannot co-exist on a single Vif molecule. The existence and persistence of both types of HIV-1 Vif variant suggests the importance of APOBEC3H suppression and cell cycle regulation for HIV-1''s survival in vivo.     

H9724, a Monoclonal Antibody to Borrelia burgdorferi's Flagellin, Binds to Heat Shock Protein 60 (HSP60) Within Live Neuroblastoma Cells: A Potential Role for HSP60 in Peptide Hormone Signaling and in an Autoimmune Pathogenesis of the Neuropathy of Lyme Disease

Although Borrelia burgdorferi, the causative agent of Lyme disease, is found at the site of many disease manifestations, local infection may not explain all its features. B. burgdorferi's flagellin cross-reacts with a component of human peripheral nerve axon, previously identified as heat shock protein 60 (HSP60). The cross-reacting epitopes are bound by a monoclonal antibody to B. burgdorferi's flagellin, H9724. Addition of H9724 to neuroblastoma cell cultures blocks in vitro spontaneous and peptide growth-factor–stimulated neuritogenesis. Withdrawal of H9724 allows return to normal growth and differentiation. Using electron microscopy, immunoprecipitation and immunoblotting, and FACS analysis we sought to identify the site of binding of H9724, with the starting hypotheses that the binding was intracellular and not identical to the binding site of II-13, a monoclonal anti-HSP60 antibody. The current studies show that H9724 binds to an intracellular target in cultured cells with negligible, if any, surface binding. We previously showed that sera from patients with neurological manifestations of Lyme disease bound to human axons in a pattern identical to H9724's binding; these same sera also bind to an intracellular neuroblastoma cell target. II-13 binds to a different HSP60 epitope than H9724; II-13 does not modify cellular function in vitro. As predicted, II-13 bound to mitochondria, in a pattern of cellular binding very different from H9724, which bound in a scattered cytoplasmic, nonorganelle-related pattern. H9724's effect is the first evidence that HSP60 may play a role in peptide-hormone–receptor function and demonstrates the modulatory potential of a monoclonal antibody on living cells.     

Quantifying the Hydroregime of a Temporary Pool Habitat: A Modelling Approach for Ephemeral Rock Pools in SE Botswana

Ecological and evolutionary processes in temporary rock pools operate within constraints imposed by their hydrologic regimes. These shallow pools flood when seasonal rains accumulate on impermeable substrates. Despite the ecological importance of hydrologic conditions for these ecosystems, we typically lack tools and empirical data required to understand the implications of hydrologic variability and climate change for biotic populations and communities in these habitats. In this study, we developed a hydrologic model to simulate rock pool hydrologic regimes based on rainfall, evapotranspiration, and basin geometry. The model was used to investigate long-term patterns of seasonal and inter-annual variation in hydroregime. In addition, hydrologic conditions associated with potential climate change scenarios were simulated and evaluated with respect to the biological requirements of the anostracan Branchipodopsis wolfi. The model’s output for daily inundation matched with field observations with an overall accuracy of 85% and correctly estimated complete hydroperiods with an overall accuracy of 70%. Simulations indicate large variation in individual hydroperiods (76–115%) as well as in the number of hydroperiods per year (19–23%). Furthermore, this study suggests that climate change may significantly alter the rock pool hydroregime. These findings confirm the hydrologic sensitivity of these ephemeral habitats to precipitation patterns, and their potential sensitivity to future climate change. Modelling indicates that the suitability of average inundation conditions for B. wolfi deteriorates significantly under future climate predictions. High levels of spatial and temporal variation in hydrologic conditions are dominant features of these habitats and an essential consideration for understanding population and community-level ecological processes.     

A 14C age calibration curve for the last 60 ka: the Greenland-Hulu U/Th timescale and its impact on understanding the Middle to Upper Paleolithic transition in Western Eurasia

This paper combines the data sets available today for ¹⁴C-age calibration of the last 60 ka. By stepwise synchronization of paleoclimate signatures, each of these sets of ¹⁴C-ages is compared with the U/Th-dated Chinese Hulu Cave speleothem records, which shows global paleoclimate change in high temporal resolution. By this synchronization we have established an absolute-dated Greenland-Hulu chronological framework, against which global paleoclimate data can be referenced, extending the ¹⁴C-age calibration curve back to the limits of the radiocarbon method. Based on this new, U/Th-based Greenland_Hulu chronology, we confirm that the radiocarbon timescale underestimates calendar ages by several thousand years during most of Oxygen Isotope Stage 3. Major atmospheric ¹⁴C variations are observed for the period of the Middle to Upper Paleolithic transition, which has significant implications for dating the demise of the last Neandertals. The early part of “the transition” (with ¹⁴C ages > 35.0 ka ¹⁴C BP) coincides with the Laschamp geomagnetic excursion. This period is characterized by highly-elevated atmospheric ¹⁴C levels. The following period ca. 35.0-32.5 ka ¹⁴C BP shows a series of distinct large-scale ¹⁴C age inversions and extended plateaus. In consequence, individual archaeological ¹⁴C dates older than 35.0 ka ¹⁴C BP can be age-calibrated with relatively high precision, while individual dates in the interval 35.0-32.5 ka ¹⁴C BP are subject to large systematic age-‘distortions,’ and chronologies based on large data sets will show apparent age-overlaps of up to ca. 5,000 cal years. Nevertheless, the observed variations in past ¹⁴C levels are not as extreme as previously proposed (“Middle to Upper Paleolithic dating anomaly”), and the new chronological framework leaves ample room for application of radiocarbon dating in the age-range 45.0-25.0 ka ¹⁴C BP at high temporal resolution.