Late Diversification Research Articles

Out of the ocean: the timescale of molluscan evolution based on phylogenomics revealed the ages of mollusks’ evolutionary transitions into the novel environment

Being the phylum with the second largest biodiversity, mollusks are widely distributed in marine, freshwater, and land, conquered almost all habitats on the earth. Throughout geological time, several molluscan lineages independently colonized freshwater and land, evolving independently in new habitats. Resolving the timing of their colonization for novel environments is the basis of understanding the complex evolution of Mollusca. Herein, we obtained an elaborate single–copy orthologs set including 107 genes with a total length of 3,447,675 amino acid sites across 134 mollusks to reconstruct the phylogeny of Mollusca. The phylogenetic analysis recovered the “Aculifera+ Conchifera” topology with well–supported. By the divergence times estimation with fossil calibration, we revealed Cambrian rapid diversification of all molluscan classes. What’s more, our results provided the times of three major independent colonization of novel environments and consistent with previous studies. The freshwater mussels (Bivalvia: Unionida) colonized freshwater about 233 Mya, ancient origin and late diversification make this order to become the main represent of the freshwater bivalves. The orders Stylommatophora and Basommatophora (Gastropoda: Pulmonata) respectively colonized land and freshwater about 201 Mya, the Triassic–Jurassic mass extinction may have provided the opportunities for their colonization. Ampullariidae (Gastropoda) colonized freshwater about 156 Mya, their lungs may have contributed to the adaption of tropical freshwater environment and make them survive. Our results probably offer the most comprehensive time–scale of molluscan evolution, could provide some insights into the habitat transition and evolution of Mollusca.

Development of a cyclosporin A derivative with excellent anti-hepatitis C virus potency

Synthetic modification of cyclosporin A at P3-P4 positions led to the discovery of NIM258, a next generation cyclophilin inhibitor with excellent anti-hepatitis C virus potency, with decreased transporter inhibition, and pharmacokinetics suitable for coadministration with other drugs. Herein is disclosed the evolution of the synthetic strategy to from the original medicinal chemistry route, designed for late diversification, to a convergent and robust development synthesis. The chiral centers in the P4 fragment were constructed by an asymmetric chelated Claisen rearrangement in the presence of quinidine as the chiral ligand. Identification of advanced crystalline intermediates enabled practical supply of key intermediates. Finally, macrocyclization was carried out at 10% weight concentration by a general and unconventional “slow release” concept.

The spatial organization of intra-tumour heterogeneity and evolutionary trajectories of metastases in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) has one of the poorest survival rates among cancers. Using multi-regional sampling of nine resected HCC with different aetiologies, here we construct phylogenetic relationships of these sectors, showing diverse levels of genetic sharing, spanning early to late diversification. Unlike the variegated pattern found in colorectal cancers, a large proportion of HCC display a clear isolation-by-distance pattern where spatially closer sectors are genetically more similar. Two resected intra-hepatic metastases showed genetic divergence occurring before and after primary tumour diversification, respectively. Metastatic tumours had much higher variability than their primary tumours, suggesting that intra-hepatic metastasis is accompanied by rapid diversification at the distant location. The presence of co-existing mutations offers the possibility of drug repositioning for HCC treatment. Taken together, these insights into intra-tumour heterogeneity allow for a comprehensive understanding of the evolutionary trajectories of HCC and suggest novel avenues for personalized therapy.

Diversity partitioning in Jurassic level-bottom communities

The analysis of diversity partitioning is a potential tool for detecting the factors that control taxonomic diversification in a given ecological context. Previously proposed models provide a theoretical framework that is herein applied to three sets of level-bottom communities representing different phases of the Jurassic diversification of marine life. The analysis shows that mean alpha-diversity remained surprisingly constant through most of the Jurassic, whereas beta-diversity increased by a factor of 2.6 during the same time interval. Diversification that is primarily driven by increasing beta-diversity is indicative of late diversification phases in ecosystems with low interspecific competition and/or high predation, as typical for marine level-bottom communities. Although generality of this conclusion is not claimed because of data limitations, the example demonstrates that the study of diversity partitioning provides a promising approach to the basic question about the factors that control the diversification of life.

The Risks of Innovation in Health Care

Innovation in health care creates risks that are unevenly distributed. An evolutionary analogy using species to represent business models helps categorize innovation experiments and their risks. This classification reveals two qualitative categories: early and late diversification experiments. Early diversification has prolific innovations with high risk because they encounter a “decimation” stage, during which most experiments disappear. Participants face high risk. The few decimation survivors can be sustaining or disruptive according to Christensen’s criteria. Survivors enter late diversification, during which they again expand, but within a design range limited to variations of the previous surviving designs. Late diversifications carry lower risk. The exception is when disruptive survivors “diversify,” which amplifies their disruption. Health care and radiology will experience both early and late diversifications, often simultaneously. Although oversimplifying Christensen’s concepts, early diversifications are likely to deliver disruptive innovation, whereas late diversifications tend to produce sustaining innovations. Current health care consolidation is a manifestation of late diversification. Early diversifications will appear outside traditional care models and physical health care sites, as well as with new science such as molecular diagnostics. They warrant attention because decimation survivors will present both disruptive and sustaining opportunities to radiology. Radiology must participate in late diversification by incorporating sustaining innovations to its value chain. Given the likelihood of disruptive survivors, radiology should seriously consider disrupting itself rather than waiting for others to do so. Disruption entails significant modifications of its value chain, hence, its business model, for which lessons may become available from the pharmaceutical industry’s current simultaneous experience with early and late diversifications.

Pre-Cretaceous Agaricomycetes yet to be discovered: Reinvestigation of a putative Triassic bracket fungus from southern Germany

Agaricomycetes are major components of extant terrestrial ecosystems; however, their fruiting bodies are exceedingly rare as fossils. Reinvestigation of a peculiar fossil from Late Triassic sediments of southern Germany interpreted as a bracket fungus revealed that this fossil in fact represents a wood abnormality, resulting from injury to the cambium and subsequent callus growth in a <i>Baieroxylon</i> -like ginkgoalean wood. As a result, the fossil record of the Agaricomycetes does not yet pre-date the Early Cretaceous, suggesting a late diversification of basidiomycetes possessing large fruiting bodies. <br><br> doi:<a href="http://dx.doi.org/10.1002/mmng.201200006" target="_blank">10.1002/mmng.201200006</a>

Pre-Cretaceous Agaricomycetes yet to be discovered: Reinvestigation of a putative Triassic bracket fungus from southern Germany

Abstract. Agaricomycetes are major components of extant terrestrial ecosystems; however, their fruiting bodies are exceedingly rare as fossils. Reinvestigation of a peculiar fossil from Late Triassic sediments of southern Germany interpreted as a bracket fungus revealed that this fossil in fact represents a wood abnormality, resulting from injury to the cambium and subsequent callus growth in a Baieroxylon -like ginkgoalean wood. As a result, the fossil record of the Agaricomycetes does not yet pre-date the Early Cretaceous, suggesting a late diversification of basidiomycetes possessing large fruiting bodies. doi: 10.1002/mmng.201200006

Fine-scale biogeographical and temporal diversification processes of peacock swallowtails (Papilio subgenus Achillides) in the Indo-Australian Archipelago.

© The Willi Hennig Society 2012. ABSTRACT: Explanations for the high species diversity of the Indo-Australian Archipelago are often challenged by the region's complex climatic and geological histories. Here, we investigated the evolutionary history of swallowtail butterflies of the Papilio subgenus Achillides, comprising up to 25 recognized species and about 100 subspecies distributed across the Indo-Australian Archipelago. To estimate the relative contributions of factors influencing their biodiversity, we used DNA sequences to infer the phylogeny and species limits of 22 species including most of their subspecies. We recovered a highly resolved and well-supported phylogeny for the subgenus, and clarified some taxonomic ambiguities at the species level. The corresponding DNA-based species phylogeny was then employed to reconstruct their historical biogeography using relaxed-clock and parametric-based analyses. Molecular dating and biogeographical analyses showed that Achillides originated around 19 Ma in Sunda + Wallacea. Biogeographical reconstructions indicated that geological vicariance shaped the early evolutionary history of Achillides whereas dispersal influenced late diversification. Birth-death likelihood analyses allowed exploration of their tempo and mode of diversification. We detected several shifts in diversification rates that are attributable to past climate-induced biogeographical events. By assessing both regional and fine-scale biodiversity patterns, this study brings new findings to a biogeographical understanding of the Indo-Australian Archipelago.

Formulating a Historical and Demographic Model of Recent Human Evolution Based on Resequencing Data from Noncoding Regions

BackgroundEstimating the historical and demographic parameters that characterize modern human populations is a fundamental part of reconstructing the recent history of our species. In addition, the development of a model of human evolution that can best explain neutral genetic diversity is required to identify confidently regions of the human genome that have been targeted by natural selection.Methodology/Principal FindingsWe have resequenced 20 independent noncoding autosomal regions dispersed throughout the genome in 213 individuals from different continental populations, corresponding to a total of ∼6 Mb of diploid resequencing data. We used these data to explore and co-estimate an extensive range of historical and demographic parameters with a statistical framework that combines the evaluation of multiple models of human evolution via a best-fit approach, followed by an Approximate Bayesian Computation (ABC) analysis. From a methodological standpoint, evaluating the accuracy of the parameter co-estimation allowed us to identify the most accurate set of statistics to be used for the estimation of each of the different historical and demographic parameters characterizing recent human evolution.Conclusions/SignificanceOur results support a model in which modern humans left Africa through a single major dispersal event occurring ∼60,000 years ago, corresponding to a drastic reduction of ∼5 times the effective population size of the ancestral African population of ∼13,800 individuals. Subsequently, the ancestors of modern Europeans and East Asians diverged much later, ∼22,500 years ago, from the population of ancestral migrants. This late diversification of Eurasians after the African exodus points to the occurrence of a long maturation phase in which the ancestral Eurasian population was not yet diversified.

Historical biogeography and phenotype‐phylogeny ofChroodiscus(lichenized Ascomycota: Ostropales: Graphidaceae)

AbstractAim To analyse the historical biogeography of the lichen genusChroodiscususing a phenotype‐based phylogeny in the context of continental drift and evolution of tropical rain forest vegetation.Location All tropical regions (Central and South America, Africa, India, Southeast Asia, north‐east Australia).Methods We performed a phenotype‐based phylogenetic analysis and ancestral character state reconstruction of 14 species of the lichen genusChroodiscus, usingpaup* andmesquite; dispersal–vicariance analysis (DIVA) and dispersal–extinction–cladogenesis (DEC) modelling to trace the geographical origin of individual clades; and ordination and clustering by means ofpc‐ord, based on a novel similarity index, to visualize the biogeographical relationships of floristic regions in whichChroodiscusoccurs.Results The 14 species ofChroodiscusshow distinctive distribution patterns, with one pantropical and one amphi‐Pacific taxon and 12 species each restricted to a single continent. The genus comprises four clades. DIVA and DEC modelling suggest a South American origin ofChroodiscusin the mid to late Cretaceous (120–100 Ma), with subsequent expansion through a South American–African–Indian–Southeast Asian–Australian dispersal route and late diversification of theargillaceusclade in Southeast Asia. Based on the abundance of extant taxa, the probability of speciation events inChroodiscusis shown to be extremely low. Slow dispersal of foliicolous rain forest understorey lichens is consistent with estimated phylogenetic ages of individual species and with average lengths of biological species intervals in fungi (10–20 Myr).Main conclusions The present‐day distribution ofChroodiscuscan be explained by vicariance and mid‐distance dispersal through the interconnection or proximity of continental shelves, without the need for recent, trans‐oceanic long‐distance dispersal. Phylogenetic reconstruction and age estimation forChroodiscusare consistent with the ‘biotic ferry’ hypothesis: a South American origin and subsequent eastward expansion through Africa towards Southeast Asia and north‐eastern Australia via the Indian subcontinent. The present‐day pantropical distributions of many clades and species of foliicolous lichens might thus be explained by eastward expansion through continental drift, along with the evolution of modern rain forests starting 120 Ma, rather than by the existence of a hypothetical continuous area of pre‐modern rain forest spanning South America, Africa and Southeast Asia during the mid and late Cretaceous.

Synthesis and Diversification of Pyridone Dipeptide Chromophores

An improved synthetic protocol transforms D-alduronolactone via a bicyclic dipeptide lactam 2 into pyridone dipeptides with either Boc- or Fmoc-protecting groups 5 or 6. Regioselective bromination of 5 yields dipeptide 10 which is further diversified in Pd-catalyzed cross coupling reactions. This late diversification of a common peptide precursor makes a maximum number of rigid dipeptide chromophores accessible. The dipeptides 11, 12, and 13 exemplify a general strategy of accessing conformationally locked peptide chromophores as tools for chemical biology.

Late diversification in the clonal composition of human cytomegalovirus-specific CD8+ T cells following allogeneic hemopoietic stem cell transplantation

AbstractTo investigate the mechanisms of human T-cell reconstitution following allogeneic hemopoietic stem cell transplantation (alloSCT), we analyzed the clonal composition of human cytomegalovirus (HCMV)-specific or Epstein-Barr virus (EBV)-specific CD8+ T cells in 10 alloSC transplant recipients and their donors. All virus-specific CD8+ T-cell clones isolated from recipients after alloSCT contained DNA of donor origin. In all 6 D+/R+ sibling alloSCTs from seropositive donors into seropositive recipients, donor virus-specific clones transferred in the allograft underwent early expansion and were maintained long term in the recipient. In contrast, in 2 of 3 HCMV D+/R- alloSC transplant recipients in whom there was no detectable HCMV infection, donor HCMV-specific clones were undetectable, whereas donor EBV-specific clones were maintained in the same EBV-seropositive recipients, suggesting that transferred clones require antigen for their maintenance. Following D-/R+ transplantation from 3 seronegative donors into seropositive recipients, a delayed primary virus-specific CD8+ T-cell response was observed, in which the T cells contained donor DNA, suggesting that new antigen-specific T cells arose in the recipient from donor-derived progenitors. In 2 of 4 HCMV D+/R+ sibling allograft recipients the clonal composition underwent diversification as compared with their donors, with delayed persistent expansion of HCMV-specific clones that were undetectable in the donor or in the recipient during the early months after transplantation; this diversification may represent expansion of new clones generated from donor-derived progenitors. We conclude that, following alloSCT, late diversification of the HCMV-specific CD8+ T-cell clonal repertoire can occur in response to persistent viral antigen.

70 IRON DEFICIENCY ANEMIA IN INFANTS: WHO SHOULD WE SUPPLEMENT?

The authors evaluated the iron status of healthy infants at 9 months of age to determine the prevalence of iron deficiency anemia and to relate it with clinical, nutritional and socioeconomic factors. Of the first 300 infants born at São Macros Hospital in the last trimester of 1994 and invited for a consultation at 9 months of age, 220 attended and were evaluated for anthropometry, socioeconomic factors and nutrient intake using a questionnaire. Infant blood samples were also proposed to the parents for hemogram, serum iron, transferrin and serum ferritin. 27 parents refused. Five children with prematurity and intrauterine growth retardation were excluded. 188 infants were studied. Infants were labeled “anemic” if hemoglobin <11 g/dl, and with “iron deficiency anemia” (IDA) if, in addition, their ferritin was <12ng/ml [1]. Statistical analysis was made using chi-square and t tests and logistic regression. The mean (standard deviation) values for hemoglobin were 11,2g/dl (0,.9g/dl). The median (95% range) values for ferritin were 14,9g/ml (0,5-54,8ng/ml). 79 infants (43%) were considered to be anemic and 75 (41%) had a ferritin <12ng/ml. 37 (20%) met the criteria for IDA. Infants with IDA introduced solid food in average at 4,3 months compared with 3,9 months among those without IDA (p=0.03). Infants with IDA had had iron fortified formula for 2,3 months in average compared with 3,8 months among those without IDA (p<0.01). Finally, infants with IDA were breastfeeded for 4,8 months in average compared with 3,7 months among those without IDA (p=0.05). Age of introduction of cow's milk, vitamin C supplementation, social class, anthropometrics parameters were not significantly associated with IDA. In a stepwise logistic regression model which included all the above variables, only the number of months having iron fortified formula was significantly associated with IDA (OR=0.82, p=0.05). In conclusion, there was a high prevalence of iron deficiency anemia at 9 months of age and infants with prolonged breastfeeding and late diversification may iron supplementation.