Clock Method Research Articles

An updated phylogeny of Sordariomycetes based on phylogenetic and molecular clock evidence

The previous phylogenies of Sordariomycetes by M.E. Barr, O.E. Eriksson and D.L. Hawksworth, and T. Lumbsch and S. Huhndorf, were mainly based on morphology and thus were somewhat subjective. Later outlines by T. Lumbsch and S. Huhndorf, and Maharachchikumbura and co-authors, took into account phylogenetic evidence. However, even these phylogenetic driven arrangements for Sordariomycetes, were somewhat subjective, as the arrangements in trees depended on many variables, such as number of taxa, different gene regions and methods used in the analyses. What is needed is extra evidence to help standardize ranking in the fungi. Estimation of divergence times using molecular clock methods has been proposed for providing additional rational for higher ranking of taxa. Thus, in Sordariomycetes, a divergence period (i.e. 200–300 MYA) can be used as criteria to judge when a group of related taxa evolved and what rank they should be given. In this paper, we provide an updated classification of accepted subclasses, orders of Sordariomycetes and use divergence times to provide additional evidence to stabilize ranking of taxa in the class. We point out and discuss discrepancies where the phylogenetic tree conflicts with the molecular clock.

Into Africa: Molecular phylogenetics and historical biogeography of sub-Saharan African woodferns (Dryopteris).

Our goal was to infer the phylogenetic relationships and historical biogeography of the genus Dryopteris with a focus on taxa in sub-Saharan Africa and neighboring islands. In general, little is known about the relationships between African fern species and their congeners in other geographic regions, and our aim was to determine whether the sub-Saharan African species of Dryopteris are monophyletic and evolved within Africa or arrived there via repeated dispersals into Africa from other regions. We obtained sequence data for five chloroplast markers from 214 species of Dryopteris and 18 outgroups. We performed phylogenetic and molecular dating analyses using a Bayesian relaxed clock method in BEAST with fossil and secondary calibration points and estimated ancestral ranges for the genus globally by comparing multiple models in BioGeoBEARS. We found that 22 of 27 accessions of sub-Saharan African Dryopteris belong to a large clade of 31 accessions that also includes taxa from Indian and Atlantic Ocean islands. Additional accessions of taxa from our regions of interest have Asian, Hawaiian, European, or North American species as their closest relatives. The majority of sub-Saharan African Dryopteris species are descended from a shared common ancestor that dispersed to Africa from Asia approximately 10 Ma. There have been subsequent dispersal events from the African mainland to islands in the Atlantic and Indian Oceans, including Madagascar. Several additional species are estimated to have descended from ancestors that reached Africa via separate events over the last roughly 20 million years.

Similarities and differences of city-size distributions in three main urban agglomerations of China from 1992 to 2015: A comparative study based on nighttime light data

Comparing the city-size distribution at the urban agglomeration (UA) scale is important for understanding the processes of urban development. However, comparative studies of city-size distribution among China’s three largest UAs, the Beijing-Tianjin-Hebei agglomeration (BTHA), the Yangtze River Delta agglomeration (YRDA), and the Pearl River Delta agglomeration (PRDA), remain inadequate due to the limitation of data availability. Therefore, using urban data derived from time-series nighttime light data, the common characteristics and distinctive features of city-size distribution among the three UAs from 1992 to 2015 were compared by the Pareto regression and the rank clock method. We identified two common features. First, the city-size distribution became more even. The Pareto exponents increased by 0.17, 0.12, and 0.01 in the YRDA, BTHA, and PRDA, respectively. Second, the average ranks of small cities ascended, being 0.55, 0.08 and 0.04 in the three UAs, respectively. However, the average ranks of large and medium cities in the three UAs experienced different trajectories, which are closely related to the similarities and differences in the driving forces for the development of UAs. Place-based measures are encouraged to promote a coordinated development among cities of differing sizes in the three UAs.

Out of Africa: Biogeography and diversification of the pantropical pond skater genus Limnogonus Stål, 1868 (Hemiptera: Gerridae).

Gondwanan vicariance, long‐distance dispersal (LDD), and boreotropical migration have been proposed as alternative hypotheses explaining the pantropical distribution pattern of organisms. In this study, the historical biogeography of the pond skater genus Limnogonus was reconstructed to evaluate the impact of biogeographical scenarios in shaping their modern transoceanic disjunction. We sampled almost 65% of recognized Limnogonus species. Four DNA fragments including 69 sequences were used to reconstruct a phylogram. Divergence time was estimated using a Bayesian relaxed clock method and three fossil calibrations. Diversification dynamics and ancestral area reconstruction were investigated by using maximum likelihood and Bayesian approaches. Our results showed the crown group of Limnogonus originated and diversified in Africa in the early Eocene (49 Ma, HPD: 38–60 Ma), subsequently expanding into other regions via dispersal. The colonization of the New World originated from the Oriental Region probably via the Bering Land Bridge in the late Eocene. Two split events between the Old World and New World were identified: one between Neotropics and Oriental region around the middle Oligocene (30 Ma, HPD: 22–38 Ma), and the other between Neotropics and Africa during the middle Miocene (14 Ma, HPD: 8–21 Ma). The evolutionary history of Limnogonus involved two biogeographical processes. Gondwanan vicariance was not supported in our analyses. The diversification of Limnogonus among Africa, Oriental, and Neotropical regions corresponded with the age of land bridge connection and dispersed as a member associated with the broad boreotropical belt before local cooling (34 Ma). The current transoceanic disjunctions in Limnogonus could be better explained by the disruption of “mixed‐mesophytic” forest belt; however, the direct transoceanic LDD between the Neotropics and Africa could not be ruled out. In addition, the “LDD” model coupled with island hopping could be a reasonable explanation for the diversification of the Oriental and Australian regions during the Oligocene.

Estimation of phylogenetic divergence times in Panagrolaimidae and other nematodes using relaxed molecular clocks calibrated with insect and crustacean fossils

This study presents the use of relaxed molecular clock methods to infer the dates of divergence betweenPanagrolaimusspecies. Autocorrelated relaxed tree methods, combined with well characterised fossil calibration dates, yield estimates of nematode divergence dates in accordance with the palaeontological age of fossil ascarid eggs and with the previously estimated date of 18 Ma (range 11.6 to 29.9 Ma) for the divergence of theCaenorhabditislineage. Our data indicate thatPanagrolaimus davidifrom Antarctica separatedca21.98 Ma from its currently known, most closely related strain. Thus,P. davidimay have existed in Antarctica prior to the Last Glacial Maximum, although this seems unlikely as it shares physiological and life history traits with closely related nematodes from temperate climates. These traits may have facilitated colonisation of Antarctica byP. davidiafter the quaternary glaciation, analogous to the colonisation of Surtsey Island, Iceland, byP. superbusafter its volcanic formation. This study demonstrates that autocorrelated relaxed tree methods combined with well characterised fossil calibration dates may be used as a method to estimate the divergence dates within nematodes in order to gain insight into their evolutionary history.

Geographical structure, narrow species ranges, and Cenozoic diversification in a pantropical clade of epiphyllous leafy liverworts.

The evolutionary history and classification of epiphyllous cryptogams are still poorly known. Leptolejeunea is a largely epiphyllous pantropical liverwort genus with about 25 species characterized by deeply bilobed underleaves, elliptic to narrowly obovate leaf lobes, the presence of ocelli, and vegetative reproduction by cladia. Sequences of three chloroplast regions (rbcL, trnL‐F, psbA) and the nuclear ribosomal ITS region were obtained for 66 accessions of Leptolejeunea and six outgroup species to explore the phylogeny, divergence times, and ancestral areas of this genus. The phylogeny was estimated using maximum‐likelihood and Bayesian inference approaches, and divergence times were estimated with a Bayesian relaxed clock method. Leptolejeunea likely originated in Asia or the Neotropics within a time interval from the Early Eocene to the Late Cretaceous (67.9 Ma, 95% highest posterior density [HPD]: 47.9–93.7). Diversification of the crown group initiated in the Eocene or early Oligocene (38.4 Ma, 95% HPD: 27.2–52.6). Most species clades were established in the Miocene. Leptolejeunea epiphylla and L. schiffneri originated in Asia and colonized African islands during the Plio‐Pleistocene. Accessions of supposedly pantropical species are placed in different main clades. Several monophyletic morphospecies exhibit considerable sequence variation related to a geographical pattern. The clear geographic structure of the Leptolejeunea crown group points to evolutionary processes including rare long‐distance dispersal and subsequent speciation. Leptolejeunea may have benefitted from the large‐scale distribution of humid tropical angiosperm forests in the Eocene.

Measurement of combined glenoid and Hill-Sachs lesions in anterior shoulder instability.

Recurrent glenohumeral anterior instability (RGAI) frequently induces combined glenoid and Hill-Sachs bone lesions and is a risk factor for soft tissue repair failure. This cohort study describes a simple preoperative quantification method for bone loss, the Clock method, the first that combines glenoid and humeral lesions. Computed tomography scans of 34 shoulders with RGAI were twice reviewed by three independent observers, who measured bone lesions using the new Clock method and existing validated methods. Intra- and inter-observer reliability of the Clock method was evaluated (intraclass correlation coefficient). Pearson correlation was used to correlate Clock method with existing methods, and with function (Western Ontario Shoulder Instability, Quick-Disabilities of the Arm, Shoulder and Hand). Thirty-two patients met the inclusion criteria: three females and 29 males, mean age 28 years. The intra- and inter-observer reliability was excellent, with intraclass correlation coefficient ranging from 0.817 to 0.938 for the novel Clock method. Humeral Clock and Glenoid Clock strongly correlated with Humeral Ratio (r = 0.882, p < 0.001) and Glenoid Surface Area and Glenoid Ratio (r = 0.793 and 0.717, p < 0.001), respectively. The classic threshold of 25% of the glenoid diameter with the Glenoid Ratio method corresponds to 4 hours with the Glenoid Clock method. The Clock method is quick and reliable, with more studies being needed to investigate whether it is correlated with surgical outcomes.

Bayesian Morphological Clock Methods Resurrect Placoderm Monophyly and Reveal Rapid Early Evolution in Jawed Vertebrates

The phylogeny of early gnathostomes provides an important framework for understanding one of the most significant evolutionary events, the origin and diversification of jawed vertebrates. A series of recent cladistic analyses have suggested that the placoderms, an extinct group of armoured fish, form a paraphyletic group basal to all other jawed vertebrates. We revised and expanded this morphological data set, most notably by sampling autapomorphies in a similar way to parsimony-informative traits, thus ensuring this data (unlike most existing morphological data sets) satisfied an important assumption of Bayesian tip-dated morphological clock approaches. We also found problems with characters supporting placoderm paraphyly, including character correlation and incorrect codings. Analysis of this data set reveals that paraphyly and monophyly of core placoderms (excluding maxillate forms) are essentially equally parsimonious. The two alternative topologies have different root positions for the jawed vertebrates but are otherwise similar. However, analysis using tip-dated clock methods reveals strong support for placoderm monophyly, due to this analysis favoring trees with more balanced rates of evolution. Furthermore, enforcing placoderm paraphyly results in higher levels and unusual patterns of rate heterogeneity among branches, similar to that generated from simulated trees reconstructed with incorrect root positions. These simulations also show that Bayesian tip-dated clock methods outperform parsimony when the outgroup is largely uninformative (e.g., due to inapplicable characters), as might be the case here. The analysis also reveals that gnathostomes underwent a rapid burst of evolution during the Silurian period which declined during the Early Devonian. This rapid evolution during a period with few articulated fossils might partly explain the difficulty in ascertaining the root position of jawed vertebrates.

Surface Structure and Electron Transfer Dynamics of the Self-Assembly of Cyanide on Au{111}

A vibronic resonance between Au{111} surface states and adsorbed CN vibrations has been predicted, which we target for study. We have formed stable monolayers of cyanide on Au{111} and observe a hexagonal close-packed lattice with a nearest neighbor distance of 3.8 ± 0.5 A. Cyanide orients normal to the surface attached via a Au–C bond. We show that the substrate–molecule coupling is particularly strong, leading to ultrafast electron transfer from the cyanide molecules to the Au{111} substrate as measured by resonant Auger spectroscopy using the core–hole clock method. The CN/Au{111} system is a simple example of a strongly interacting adsorbate–substrate system and will be the subject of a number of further studies, as discussed.

Phylogeny and diversification of the cloud forest Morpho sulkowskyi group (Lepidoptera, Nymphalidae) in the evolving Andes

The monophyletic Morpho sulkowskyi butterfly group, endemic of Andean cloud forests, was studied to test the respective contributions of Mio‐Pliocene intense uplift period and Pleistocene glacial cycles on Andean biodiversity. We sampled nine taxa covering the whole geographical range of the group. Two mitochondrial and two nuclear genes were analysed using a Bayesian method. We established a dated phylogeny of the group using a relaxed clock method and a wide‐outgroup approach. To discriminate between two hypotheses, we used a biogeographical probabilistic method. Results suggest that the ancestor of the M. sulkowskyi group originated during the Middle–Late Miocene uplift of the Eastern Cordillera in northern Peru. Biogeographical inference suggests that the M. sulkowskyi and Morpho lympharis clades diverged in the northern Peruvian Andes. The subsequent divergences, from the Late Miocene to the Late Pliocene, should have resulted from a dispersal towards the Northern Andes (M. sulkowskyi clade), after the closure of the West Andean Portal separating the Central and Northern Andes, and a southwards dispersal along the Peruvian and Bolivian Eastern Cordilleras (M. lympharis clade). Only a few divergences occurred at the very end of the Pliocene or during the Pleistocene, a period when the more recent uplifts interfered with Pleistocene glacial cycles.

Increasing the safety of minimally invasive hallux surgery—An anatomical study introducing the clock method

BackgroundThe purpose of this study is to describe a simple and reproducible method to localize the neurological structures at risk and to describe a safe zone for hallux minimally invasive surgery (MIS) procedures. MethodsTen fresh-frozen cadaveric feet were dissected to identify the dorsomedial digital nerve (DMDN) and the dorsolateral digital nerve (DLDN) of the first toe. Axial sections were performed at the sites of metatarsal osteotomies. We documented the position of the nerves with respect to the extensor hallucis longus (EHL) tendon using a clock method superimposed on the axial section ResultsThe DMDN was found at an average of 26.2° medial to the medial border of the EHL tendon. (SD 11.26, range 14.5–45.5), whereas the average distance of the DLDN was 32.3° lateral to the medial border of the EHL tendon. (SD 6.29, range 13.5–40). ConclusionsUsing the clock method the DMDN and DLDN were found consistently between 10 o’clock and 2 o’clock in either right and left feet. The clock method may facilitate avoiding the area where these nerves are located serving as a valuable tool in minimally invasive foot surgery.

Plastid phylogenomic study of species within the genus Zea: rates and patterns of three classes of microstructural changes.

This project examines the relationships within the genus Zea using complete plastid genomes (plastomes). While Zea mays has been well studied, congeneric species have yet to be as thoroughly examined. For this study four complete plastomes and a fifth nearly complete plastome were sequenced in the five species (Zea diploperennis, Zea perennis, Zea luxurians, Zea nicaraguensis, and Zea mays subsp. huehuetenangensis) by Sanger or next-generation methods. An analysis of the microstructural changes, such as inversions, insertion or deletion mutations (indels) and determination of their frequencies were performed for the complete plastomes. It was determined that 193 indels and 15 inversions occurred across the examined plastomes of Zea. Tandem repeat indels were the most common type of microstructural change observed. Divergence times were estimated using a noncorrelated relaxed clock method. Divergence dates for specific nodes relative to Zea were calculated to fall between 38,000years before present (YBP) for the subspecies included in this study and 23,000 YBP for section Luxuriantes included in this study. The stem lineage of all Zea species was calculated to have diverged at 176,000 YBP. The calculated mutation rates for the genus fell within the range of 1.7E-8 to 3.5E-8 microstructural changes per site per year. These rates of change are not uniform, despite the close relationships of taxa in this study. Phylogenomic analyses using full plastome alignments were also conducted to compare tree topologies from different types of mutations. In most cases, the previous work examining Zea mitochondrial and nuclear data was confirmed.

Dating species divergences using rocks and clocks.

Knowledge of absolute species divergence times is not only fascinating to evolutionary biologists in establishing the age of a species group, but also critically important to addressing a variety of biological questions. Absolute times allow us to place speciation events (such as the diversification of the mammals relative to the demise of the dinosaurs) in the correct geological and environmental contexts and to gain a better understanding of speciation and dispersal mechanisms [1,2]. They also allow us to characterize species richness and species diversification rates over geological periods. Estimated molecular evolutionary rates can also be correlated with life-history traits and are important for interpretation of the fast-accumulating genomic sequence data. Molecular clock methods are also used widely in establishing the evolutionary history of viruses, including those related to human diseases.

Breeding system diversification and evolution in American Poa supersect. Homalopoa (Poaceae: Poeae: Poinae).

Background and Aims Poa subgenus Poa supersect. Homalopoa has diversified extensively in the Americas. Over half of the species in the supersection are diclinous; most of these are from the New World, while a few are from South-East Asia. Diclinism in Homalopoa can be divided into three main types: gynomonoecism, gynodioecism and dioecism. Here the sampling of species of New World Homalopoa is expanded to date its origin and diversification in North and South America and examine the evolution and origin of the breeding system diversity.Methods A total of 124 specimens were included in the matrix, of which 89 are species of Poa supersect. Homalopoa sections Acutifoliae, Anthochloa, Brizoides, Dasypoa, Dioicopoa, Dissanthelium, Homalopoa sensu lato (s.l.), Madropoa and Tovarochloa, and the informal Punapoa group. Bayesian and parsimony analyses were conducted on the data sets based on four markers: the nuclear ribosomal internal tanscribed spacer (ITS) and external transcribed spacer (ETS), and plastid trnT-L and trnL-F. Dating analyses were performed on a reduced Poa matrix and enlarged Poaceae outgroup to utilize fossils as calibration points. A relaxed Bayesian molecular clock method was used.Key Results Hermaphroditism appears to be pleisiomorphic in the monophyletic Poa supersect. Homalopoa, which is suggested to have originated in Eurasia 8·4–4·2 million years ago (Mya). The ancestor of Poa supersect. Homalopoa radiated throughout the New World in the Late Miocene–Early Pliocene, with major lineages originating during the Pliocene to Pleistocene (5–2 Mya). Breeding systems are linked to geographic areas, showing an evolutionary pattern associated with different habitats. At least three major pathways from hermaphroditism to diclinism are inferred in New World Homalopoa: two leading to dioecism, one via gynodioecism in South America and another directly from hermaphroditism in North America, a result that needs to be checked with a broader sampling of diclinous species in North America. A third pathway leads from hermaphroditism to gynomonoecism in Andean species of South America, with strictly pistillate species evolving in the highest altitudes.Conclusions Divergence dating provides a temporal context to the evolution of breeding systems in New World Poa supersect. Homalopoa. The results are consistent with the infrageneric classification in part; monophyletic sections are confirmed, it is proposed to reclassify species of sect. Acutifoliae, Dasypoa and Homalopoa s.l. and it is acknowledged that revision of the infrageneric taxonomy of the gynomonoecious species is needed.

Multiple transoceanic dispersals and geographical structure in the pantropical leafy liverwort Ceratolejeunea (Lejeuneaceae, Porellales)

AbstractAimHow disjunct distributions arise and why organisms differ in diversification patterns remain some of the most compelling fundamental questions in biogeography. We carry out phylogeographical analyses of the pantropical liverwort genus Ceratolejeunea to identify its geographical origin and the dispersal routes by which it gained its Neotropical‐African disjunction. Furthermore, we investigate whether there is geographical structure in Ceratolejeunea on islands and whether island diversity is a result of radiations or recurrent migration.LocationAmerica, Africa and Australasia.MethodsSequences of two chloroplast regions (trnL–F, rbcL) and the nuclear ribosomal ITS region were obtained for 55 accessions of 20 species to explore the phylogeny, divergence times and ancestral areas of Ceratolejeunea. The phylogeny was reconstructed using maximum likelihood and Bayesian inference approaches, and divergence times were estimated with a Bayesian relaxed clock method and fossil and secondary calibrations. Ancestral areas were estimated using BioGeoBEARS.ResultsCeratolejeunea likely originated in the Neotropics during the Palaeogene (42.2 Ma, 95% HPD: 22.2–64.8) and the initial diversification of its crown group took place between the Eocene and Miocene (25.5 Ma, 95% HPD: 16.6–35.8). Although boreotropical migration and subsequent extinction in northern regions cannot be rejected, the observed disjunctions are best explained by four transoceanic dispersal events from the Neotropics to Africa during the late Oligocene to Pleistocene. Geographical structure is prevalent on islands, particularly in the C. cornuta complex. Three species and the subgenus Ceratolejeunea are recovered as paraphyletic.Main conclusionsWidespread paraphyly and sister group relationships between disjunct taxa indicate an important role of cryptic speciation and transoceanic dispersal with subsequent genetic differentiation in the evolution of Ceratolejeunea. On islands, recurrent migration, rather than radiation, has shaped bryophyte diversity.

Occupied and unoccupied electronic structures of an L-cysteine film studied by core-absorption and resonant photoelectron spectroscopies

Unoccupied and occupied electronic structures of an L-cysteine film have been studied by absorption and resonant photoelectron spectroscopies. Core absorptions at S-L, C-K, N-K, and O-K levels indicate that the lower unoccupied states are predominantly composed of oxygen-2p, carbon-2p, and sulfur-4s+3d orbitals, while higher unoccupied states may be attributed dominantly to nitrogen-np (n ≥ 3), oxygen-np (n ≥ 3), and sulfur-ns+md (n ≥ 4, m ≥ 3) orbitals. Resonant photoelectron spectra at S-L23 and O-K levels indicate that the highest occupied state is originated from sulfur-3sp orbitals, while oxygen-2sp orbitals contribute to the deeper valence states. The delocalization lifetimes of the oxygen-1s and sulfur-2p excited states are estimated from a core-hole clock method to be about 9 ± 1 and 125 ± 25 fs, respectively.

Low Resource Fast Operation Using Register Scheduling In Mesochronous Design

In the process of making the system operating faster with low resource overhead, Mesochronous design approach has been suggested as an optimal solution. Such design performs a segregation of operational units in consideration to delay parameter. The delay units are considered towards common clocking system, to overcome the propagation delay in digital system operation. However, the delays are considered to be linearized w.r.to register alignment and common clocking method. The operation of a Mesochronous unit is performed via instruction and delay unit alignment. Here, the sequencing of instruction, however doesn’t consider the instruction redundancy property. In this paper, a new register re-alignment approach is suggested, which schedules the operation sequence by instruction property to achieve, low resource fast processing approach. The design model suggested, illustrates a higher processing efficiency in coding, as in comparison to conventional pipelined approach.

Phylogeny and historical biogeography of leafhopper subfamily Iassinae (Hemiptera: Cicadellidae) with a revised tribal classification based on morphological and molecular data

AbstractPhylogenetic relationships among major lineages of the leafhopper subfamily Iassinae were explored by analysing a dataset of 91 discrete morphological characters and DNA sequence data from nuclear 28S rDNA and histone H3 genes and mitochondrial 12S rDNA. Bayesian, maximum‐likelihood and maximum parsimony analyses yielded similar tree topologies that were well resolved with strong branch support except at the base of the tree, resulting in equivocal support for inclusion of Bythoniini as a tribe of Iassinae but strong support for the monophyly of Iassinae (excluding Bythoniini) and most previously recognized iassine tribes. Divergence times for recovered nodes were estimated using a Bayesian relaxed clock method with two fossil calibration points. The results suggest that the deepest divergences coincided with Gondwanan vicariant events but that more recent divergences resulted from long‐range dispersal and colonization. Biogeographical analyses suggest that the group most likely has a Neotropical origin. The following changes to the taxonomic classification are proposed: establishment of three new tribes, Batracomorphini trib.n. (based on type genus Batracomorphus Lewis), Hoplojassini trib.n. (based on type genus Hoplojassus Dietrich and including one other South American genus), Lipokrisnini trib.n. (based on type genus Lipokrisna Freytag and including two other endemic Caribbean genera); Krisnini is redefined to include only the Old World genera Krisna and Gessius; Iassini is redefined to include only the type genus and four endemic Afrotropical genera; Bascarrhinus Fowler and Platyhynna Berg, recently treated as genera incertae sedis, are placed in Hyalojassini; Thalattoscopus Kirkaldy is added to the previously monobasic tribe Trocnadini. Iassinae now includes 12 tribes, all of which appear to be monophyletic. Revised morphological diagnoses of the subfamily and each of the included tribes are provided and a key to tribes is also given.This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:41295B68‐2DAB‐4C4F‐B260‐F7C054922173.

Evolution of a Planktonic Foraminifer during Environmental Changes in the Tropical Oceans.

Ecological adaptation to environmental changes is a strong driver of evolution, enabling speciation of pelagic plankton in the open ocean without the presence of effective physical barriers to gene flow. The tropical ocean environment, which plays an important role in shaping marine biodiversity, has drastically and frequently changed since the Pliocene. Nevertheless, the evolutionary history of tropical pelagic plankton has been poorly understood, as phylogeographic investigations are still in the developing state and paleontological approaches are insufficient to obtain a sequential record from the deep-sea sediments. The planktonic foraminifer Pulleniatina obliquiloculata is widely distributed in the tropical area throughout the world’s oceans, and its phylogeography is well established. It is thus one of the best candidates to examine how past environmental changes may have shifted the spatial distribution and affected the diversification of tropical pelagic plankton. Such an examination requires the divergence history of the planktonic foraminifers, yet the gene marker (partial small subunit (SSU) rDNA) previously used for phylogeographic studies was not powerful enough to achieve a high accuracy in estimating the divergence times. The present study focuses on improving the precision of divergence time estimates for the splits between sibling species (genetic types) of planktonic foraminifers by increasing the number of genes as well as the number of nucleotide bases used for molecular clock estimates. We have amplified the entire coding regions of two ribosomal RNA genes (SSU rDNA and large subunit (LSU) rDNA) of three genetic types of P. obliquiloculata and two closely related species for the first time and applied them to the Bayesian relaxed clock method. The comparison of the credible intervals of the four datasets consisting either of sequences of the partial SSU rDNA, the complete SSU rDNA, LSU rDNA, or a combination of both genes (SSU+LSU) clearly demonstrated that the two-gene dataset improved the accuracy of divergence time estimates. The P. obliquiloculata lineage diverged twice, first at the end of the Pliocene (3.1 Ma) and again in the middle Pleistocene (1.4 Ma). Both timings coincided with the environmental changes, which indirectly involved geographic separation of populations. The habitat of P. obliquiloculata was expanded toward the higher latitudinal zones during the stable warm periods and subsequently placed on the steep environmental gradients following the global cooling. Different environmental conditions in the stable warm tropics and unstable higher latitudes may have triggered ecological divergence among the populations, leading to adaptive differentiation and eventually speciation. A comprehensive analysis of divergence time estimates combined with phylogeography enabled us to reveal the evolutionary history of the pelagic plankton and to find the potential paleoenvironmental events, which could have changed their biogeography and ecology.

Ultrafast Charge Transfer Pathways Through A Prototype Amino-Carboxylic Molecular Junction.

Charge transport properties of a vertically stacked organic heterojunction based on the amino-carboxylic (A-C) hydrogen bond coupling scheme are investigated by means of X-ray resonant photoemission and the core-hole clock method. We demonstrate that hydrogen bonding in molecular bilayers of benzoic acid/cysteamine (BA/CA) with an A-C coupling scheme opens a site selective pathway for ultrafast charge transport through the junction. Whereas charge transport from single BA layer directly coupled to the Au(111) is very fast and it is mediated by the phenyl group, the interposition of an anchoring layer of CA selectively hinders the delocalization of electrons from the BA phenyl group but opens a fast charge delocalization route through the BA orbitals close to the A-C bond. This evidences that hydrogen bonding established upon A-C recognition can be exploited to spatially/orbitally manipulate the charge transport properties of heteromolecular junctions.