Morphological species and discordant mtDNA: A genomic analysis of Phrynocephalus lizard lineages on the Qinghai-Tibetan Plateau.

Many species have been established on the basis of morphology, with markers such as mtDNA used to confirm the existence of independent historical lineages. Discordance between morphology and gene trees makes this less straightforward. Genotyping by sequencing (GBS) was used to analyse general genomic divergence across two recognized high altitude lizard species found in the eastern Qinghai-Tibetan Plateau. One of the species (Phyrnocephalus guinanensis) is found on a large area of sand dune habitat and distinguished from the other (P. putjatia) by morphology. We found that the primary pattern of genomic divergence is discordant with these morphological species: northern P. putjatia populations from around the large saline Qinghai lake are genomically distinct from P. putjatia and P. guinanensis populations located south of the Qinghai South and Riyue Mountains. Two competing historical scenarios were assessed using approximate Bayesian computation which unequivocally favoured a split between populations separated by the Qinghai South and Riyue mountains over a split between morphological species. The findings indicate that historical vicariance due to geographical features underpins the phylogenetic split rather than ecology-mediated divergence between sand dune and non-sand areas which i) is predicted by the mtDNA tree (showing the utility of this marker in species delimitation) and ii) demonstrates the unsuitability of the morphology-based taxonomy (indicating that large morphological differences do not always reflect historical lineages). In addition, we found a clear signal of isolation-by-distance around the periphery of Qinghai lake which suggests: i) a high level of resolution by GBS for detecting local divergence and ii) restricted gene flow over relatively short geographic distances. Overall, we show how morphological variation can mislead taxonomic conclusions and the utility of GBS for resolving these issues

Historical volcanism and within-island genetic divergence in the Tenerife skink (Squamata: Scincidae)

This study examines the genetic diversity of the Tenerife skink (Chalcides viridanus) within the context that Tenerife is now thought to have arisen as a single island as opposed to two/three precursor islands. DNA sequences were obtained from two mitochondrial regions and five nuclear loci. MtDNA divergence was substantial with four geographical clusters being detected. Two of these corresponded to two ancient areas that have undergone little recent eruptive activity (Anaga, Teno), while two further clusters were found within the more volcanically active central region. Nuclear divergence was low and revealed no strong geographical pattern. Estimated divergence of the Anaga group was 0.4-2.1 Ma ago (95% posterior interval), while the divergence time of the Teno cluster was 0.1-1.2 Ma ago. Phylogeographic distributions correspond well with ancient edifices, but divergence times postdate those expected under the previous ‘unification of ancient islands’ geological scenario. There is evidence of a major recent expansion of the central group following a decline in eruptive activity in this region, which also fits well with current geological hypotheses. Previously-described within-island evolutionary patterns in other Tenerife species also need to examined within this new geological context

Ecological divergence combined with ancient allopatry in lizard populations from a small volcanic island

Population divergence and speciation are often explained by geographical isolation, but may also be possible under high gene flow due to strong ecology-related differences in selection pressures. This study combines coalescent analyses of genetic data (11 microsatellite loci and 1 Kbp of mtDNA) and ecological modelling to examine the relative contributions of isolation and ecology to incipient speciation in the scincid lizard Chalcides sexlineatus within the volcanic island of Gran Canaria. Bayesian multispecies coalescent dating of within-island genetic divergence of northern and southern populations showed correspondence with the timing of volcanic activity in the north of the island 1.5–3.0 Ma ago. Coalescent estimates of demographic changes reveal historical size increases in northern populations, consistent with expansions from a volcanic refuge. Nevertheless, ecological divergence is also supported. First, the two morphs showed non-equivalence of ecological niches and species distribution modelling associated the northern morph with mesic habitat types and the southern morph with xeric habitat types. It seems likely that the colour morphs are associated with different antipredator strategies in the different habitats. Second, coalescent estimation of gene copy migration (based on microsatellites and mtDNA) suggest high rates from northern to southern morphs demonstrating the strength of ecology-mediated selection pressures that maintain the divergent southern morph. Together, these findings underline the complexity of the speciation process by providing evidence for the combined effects of ecological divergence and ancient divergence in allopatry

Geometric morphometric analyses of sexual dimorphism and allometry in two sympatric snakes: Natrix helvetica (Natricidae) and Vipera berus (Viperidae)

The non-venomous grass snake (Natrix helvetica) and the venomous adder (Vipera berus) are two native species that are often found in sympatry in Great Britain and Europe. They occupy partially overlapping ecological niches and prey on small vertebrates, but use different feeding strategies. Here, we investigated the morphologies of grass snakes and adders from Dorset (UK) using twodimensional geometric morphometrics to assess the degree of sexual dimorphism in size and shape together with the relative impact of allometry and general body dimensions on head shape. Both species showed significant sexual dimorphism in head size, but not in head shape. We found a clear allometric pattern in N. helvetica, whereas allometry in V. berus was generally less pronounced. Body dimensions were strongly correlated with head shape in the grass snake, but not in the adder. The fact that V. berus is venomous appears to explain the lack of allometric patterns and the lack of an association between body dimensions and head shape. The high degree of size dimorphism identified in both species could originate from the advantages of reduced intraspecific competition that are conveyed by a partial differentiation in feeding morphology

The legacy of translocations among populations of the Ibizan Wall Lizard, Podarcis pityusensis (Squamata: Lacertidae)

The Ibizan wall lizard, Podarcis pityusensis, was the subject of several documented 25 translocations by the German herpetologist Martin Eisentraut, in 1930. He aimed to initiate 26 long-term experiments into the evolution of melanism and other morphological traits and 27 accordingly reported introductions into five islets that (he believed) contained no lizards. In 28 this study, we analysed the genetics and morphological characteristics of individuals we found 29 there. We found no lizards on two of the islets, namely Escull de Tramuntana or Galera, but 30 for the first time, detected a large population on a third, Es Vaixell. Analyses of microsatellite 31 DNA placed individuals from a fourth islet, Dau Gran, with those from the islet of Escull 32 Vermell. They are also morphologically close to individuals from Escull Vermell. This 33 suggests that selection pressures could have favoured the Escull Vermell phenotype following 34 introduction. Eisentraut founded the Es Vaixell population with non- melanic Ibizan 35 specimens, but the present day population of Es Vaixell was found to be fully melanic. Genetic 36 markers support a strong similarity between Es Vaixell and Na Gorra, and indicate that, in all 37 likelihood, the individuals introduced by Eisentraut have left no descendants. It is likely that 38 Es Vaixell already contained lizards prior to this introduction. For reasons which we discuss, 39 the translocations have revealed less than Eisentraut would have originally hoped for, although 40 they do provide some potential insights into lizard morphological evolution following 41 colonization

Atmospheric effects of the emerging mainland Chinese transportation system at and beyond the regional scale

Local surface travel needs in the People's Republic of China (mainland China) have traditionally been met largely by nonpolluting bicycles. A major automobile manufacturing/importing effort has begun in the country over the last decade, and planning documents indicate that the Chinese may strive to acquire more than 100 million vehicles early in the next century. By analogy with large automotive fleets already existing in the western world, both regional and global scale pollution effects are to be expected from the increase. The present work adopts the latest projections of Chinese automobile manufacture and performs some quantitative assessments of the extent of pollution generation. Focus for the investigation is placed upon the oxidant ozone. Emissions of the precursor species nitrogen oxides and volatile organics are constructed based on data for the current automotive sector in the eastern portion of the United States. Ozone production is first estimated from measured values for continental/oceanic scale yields relative to precursor oxidation. The estimates are then corroborated through idealized two dimensional modeling of the photochemistry taking place in springtime air flow off the Asian land mass and toward the Pacific Ocean. The projected fleet sizes could increase coastal and remote oceanic ozone concentrations by tens of parts per billion (ppb) in the lower troposphere. Influences on the tropospheric aerosol system and on the major greenhouse gas carbon dioxide are treated peripherally. Nitrogen oxides created during the vehicular internal combustion process will contribute to nitrate pollution levels measured in the open Pacific. The potential for soot and fugitive dust increases should be considered as the automotive infrastructure develops. Since the emerging Chinese automotive transportation system will represent a substantial addition to the global fleet and all the carbon in gasoline is eventually oxidized completely, a significant rise in global carbon dioxide inputs will ensue as well. Some policy issues are treated preliminary. The assumption is made that alterations to regional oxidant/aerosol systems and to terrestrial climate are conceivable. The likelihood that the Chinese can achieve the latest vehicle fleet goals is discussed, from the points of view of new production, positive pollution feedbacks from a growing automobile industry, and known petroleum reserves. Vehicular fuel and maintenance options lying before the Chinese are outlines and compared. To provide some perspective on the magnitude of the environmental changes associated with an Asian automotive buildup, recent estimates of the effects of future air traffic over the Pacific Rim are described

Rate variation and estimation of divergence times using strict and relaxed clocks

Background Understanding causes of biological diversity may be greatly enhanced by knowledge of divergence times. Strict and relaxed clock models are used in Bayesian estimation of divergence times. We examined whether: i) strict clock models are generally more appropriate in shallow phylogenies where rate variation is expected to be low, ii) the likelihood ratio test of the clock (LRT) reliably informs which model is appropriate for dating divergence times. Strict and relaxed models were used to analyse sequences simulated under different levels of rate variation. Published shallow phylogenies (Black bass, Primate-sucking lice, Podarcis lizards, Gallotiinae lizards, and Caprinae mammals) were also analysed to determine natural levels of rate variation relative to the performance of the different models. Results Strict clock analyses performed well on data simulated under the independent rates model when the standard deviation of log rate on branches, σ, was low (≤0.1), but were inappropriate when σ>0.1 (95% of rates fall within 0.0082-0.0121 subs/site/Ma when σ = 0.1, for a mean rate of 0.01). The independent rates relaxed clock model performed well at all levels of rate variation, although posterior intervals on times were significantly wider than for the strict clock. The strict clock is therefore superior when rate variation is low. The performance of a correlated rates relaxed clock model was similar to the strict clock. Increased numbers of independent loci led to slightly narrower posteriors under the relaxed clock while older root ages provided proportionately narrower posteriors. The LRT had low power for σ = 0.01-0.1, but high power for σ = 0.5-2.0. Posterior means of σ2 were useful for assessing rate variation in published datasets. Estimates of natural levels of rate variation ranged from 0.05-3.38 for different partitions. Differences in divergence times between relaxed and strict clock analyses were greater in two datasets with higher σ2 for one or more partitions, supporting the simulation results. Conclusions The strict clock can be superior for trees with shallow roots because of low levels of rate variation between branches. The LRT allows robust assessment of suitability of the clock model as does examination of posteriors on σ2

Characterization of extrasolar terrestrial planets from diurnal photometric variability

The detection of massive planets orbiting nearby stars has become almost routine, but current techniques are as yet unable to detect terrestrial planets with masses comparable to the Earth's. Future space-based observatories to detect Earth-like planets are being planned. Terrestrial planets orbiting in the habitable zones of stars-where planetary surface conditions are compatible with the presence of liquid water-are of enormous interest because they might have global environments similar to Earth's and even harbor life. The light scattered by such a planet will vary in intensity and colour as the planet rotates; the resulting light curve will contain information about the planet's properties. Here we report a model that predicts features that should be discernible in light curves obtained by low-precision photometry. For extrasolar planets similar to Earth we expect daily flux variations up to hundreds of percent, depending sensitively on ice and cloud cover. Qualitative changes in surface or climate generate significant changes in the predicted light curves. This work suggests that the meteorological variability and the rotation period of an Earth-like planet could be derived from photometric observations. Other properties such as the composition of the surface (e.g., ocean versus land fraction), climate indicators (for example ice and cloud cover), and perhaps even signatures of Earth-like plant life could be constrained or possibly, with further study, even uniquely determined.Comment: Published in Nature. 9 pages including 3 figure

Evolutionary ecomorphology of the Falkland Islands wolf Dusicyon australis

The Falkland Islands wolf Dusicyon australis is an extinct canid that was once the only endemic terrestrial mammal to inhabit the Falkland Islands. There is still a puzzling picture of the morphological adaptations of this wolf that quickly evolved from its mainland fossil ancestor: Dusicyon avus. We employ a geometric morphometric approach to identify patterns of skull shape variation in extant canids and Dusicyon spp. The Falkland Islands wolf and its fossil ancestor show a more carnivorous feeding morphology than other South American foxes, and they cluster morphologically with jackals. This supports convergence in skull shape between Dusicyon and Old World canids, although the convergence is not as strong as that exhibited by their sister hyper- and hypocarnivorous taxa

A Conserved Ribosomal Protein Has Entirely Dissimilar Structures in Different Organisms

\ua9 The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. Ribosomes from different species can markedly differ in their composition by including dozens of ribosomal proteins that are unique to specific lineages but absent in others. However, it remains unknown how ribosomes acquire new proteins throughout evolution. Here, to help answer this question, we describe the evolution of the ribosomal protein msL1/msL2 that was recently found in ribosomes from the parasitic microorganism clade, microsporidia. We show that this protein has a conserved location in the ribosome but entirely dissimilar structures in different organisms: in each of the analyzed species, msL1/msL2 exhibits an altered secondary structure, an inverted orientation of the N-termini and C-termini on the ribosomal binding surface, and a completely transformed 3D fold. We then show that this fold switching is likely caused by changes in the ribosomal msL1/msL2-binding site, specifically, by variations in rRNA. These observations allow us to infer an evolutionary scenario in which a small, positively charged, de novo-born unfolded protein was first captured by rRNA to become part of the ribosome and subsequently underwent complete fold switching to optimize its binding to its evolving ribosomal binding site. Overall, our work provides a striking example of how a protein can switch its fold in the context of a complex biological assembly, while retaining its specificity for its molecular partner. This finding will help us better understand the origin and evolution of new protein components of complex molecular assemblies-thereby enhancing our ability to engineer biological molecules, identify protein homologs, and peer into the history of life on Earth