Comparative immunogenomics of molluscs.

PubMed

Schultz, Jonathan H; Adema, Coen M

2017-10-01

Comparative immunology, studying both vertebrates and invertebrates, provided the earliest descriptions of phagocytosis as a general immune mechanism. However, the large scale of animal diversity challenges all-inclusive investigations and the field of immunology has developed by mostly emphasizing study of a few vertebrate species. In addressing the lack of comprehensive understanding of animal immunity, especially that of invertebrates, comparative immunology helps toward management of invertebrates that are food sources, agricultural pests, pathogens, or transmit diseases, and helps interpret the evolution of animal immunity. Initial studies showed that the Mollusca (second largest animal phylum), and invertebrates in general, possess innate defenses but lack the lymphocytic immune system that characterizes vertebrate immunology. Recognizing the reality of both common and taxon-specific immune features, and applying up-to-date cell and molecular research capabilities, in-depth studies of a select number of bivalve and gastropod species continue to reveal novel aspects of molluscan immunity. The genomics era heralded a new stage of comparative immunology; large-scale efforts yielded an initial set of full molluscan genome sequences that is available for analyses of full complements of immune genes and regulatory sequences. Next-generation sequencing (NGS), due to lower cost and effort required, allows individual researchers to generate large sequence datasets for growing numbers of molluscs. RNAseq provides expression profiles that enable discovery of immune genes and genome sequences reveal distribution and diversity of immune factors across molluscan phylogeny. Although computational de novo sequence assembly will benefit from continued development and automated annotation may require some experimental validation, NGS is a powerful tool for comparative immunology, especially increasing coverage of the extensive molluscan diversity. To date, immunogenomics revealed new levels of complexity of molluscan defense by indicating sequence heterogeneity in individual snails and bivalves, and members of expanded immune gene families are expressed differentially to generate pathogen-specific defense responses. Copyright © 2017 Elsevier Ltd. All rights reserved.

Food Safety Impacts from Post-Harvest Processing Procedures of Molluscan Shellfish.

PubMed

Baker, George L

2016-04-18

Post-harvest Processing (PHP) methods are viable food processing methods employed to reduce human pathogens in molluscan shellfish that would normally be consumed raw, such as raw oysters on the half-shell. Efficacy of human pathogen reduction associated with PHP varies with respect to time, temperature, salinity, pressure, and process exposure. Regulatory requirements and PHP molluscan shellfish quality implications are major considerations for PHP usage. Food safety impacts associated with PHP of molluscan shellfish vary in their efficacy and may have synergistic outcomes when combined. Further research for many PHP methods are necessary and emerging PHP methods that result in minimal quality loss and effective human pathogen reduction should be explored.

The shell-forming proteome of Lottia gigantea reveals both deep conservations and lineage-specific novelties.

PubMed

Marie, Benjamin; Jackson, Daniel J; Ramos-Silva, Paula; Zanella-Cléon, Isabelle; Guichard, Nathalie; Marin, Frédéric

2013-01-01

Proteins that are occluded within the molluscan shell, the so-called shell matrix proteins (SMPs), are an assemblage of biomolecules attractive to study for several reasons. They increase the fracture resistance of the shell by several orders of magnitude, determine the polymorph of CaCO(3) deposited, and regulate crystal nucleation, growth initiation and termination. In addition, they are thought to control the shell microstructures. Understanding how these proteins have evolved is also likely to provide deep insight into events that supported the diversification and expansion of metazoan life during the Cambrian radiation 543 million years ago. Here, we present an analysis of SMPs isolated form the CaCO(3) shell of the limpet Lottia gigantea, a gastropod that constructs an aragonitic cross-lamellar shell. We identified 39 SMPs by combining proteomic analysis with genomic and transcriptomic database interrogations. Among these proteins are various low-complexity domain-containing proteins, enzymes such as peroxidases, carbonic anhydrases and chitinases, acidic calcium-binding proteins and protease inhibitors. This list is likely to contain the most abundant SMPs of the shell matrix. It reveals the presence of both highly conserved and lineage-specific biomineralizing proteins. This mosaic evolutionary pattern suggests that there may be an ancestral molluscan SMP set upon which different conchiferan lineages have elaborated to produce the diversity of shell microstructures we observe nowadays. © 2012 The Authors Journal compilation © 2012 FEBS.

Molluscan and Foraminiferan Paleoecological Reconstructions of Extreme Post-Glacial Seafloor Environments of the California Borderland

NASA Astrophysics Data System (ADS)

Moffitt, S. E.; Hill, T. M.; Kroeker, K.; Roopnarine, P. D.; Kennett, J.

2014-12-01

We have reconstructed paleoecological and climatic change in a Late Quaternary (16.1-3.4 ka) sediment core from the California margin (418 meters below sea level) of Santa Barbara Basin using quantitative analyses of Molluscan and Foraminiferan microfossils. This archive represents the first record of marine metazoan community ecology, and a comparison to a well-established biotic proxy (Foraminifera), through the climatic and oceanographic events of the most recent deglaciation. The high-resolution seafloor archive reveals strong coupling between orbital and millennial climatic episodes and the structure of shallow ocean ecosystems. Changes in the density and diversity of molluscs and foraminifera exhibit clear associations with climatic events that mark the deglacial episode, including rapid expansions and contractions of the Oxygen Minimum Zone and development of chemosynthetic bacterial mat communities. Molluscans occur discontinuously in only 28% of the sediment sequence, whereas foraminifera occur throughout. Multivariate statistical analyses of the community ecology assist with the interpretations of the multi-species paleoecological data and of processes that caused the variability. A surprising dominance of molluscan extremophiles (sulfidic Astrys permodesta and hypoxic Lucinoma aequizonatum) during cool, well oxygenated intervals reveals how such forms can thrive during inferred brief ephemeral extreme events. Hydrographic variability and bottom water flow, as well as the growth of benthic bacterial communities, determine where such extremophile communities dominate.

Production of biofuel using molluscan pseudofeces derived from algal cells

DOEpatents

Das, Keshav C.; Chinnasamy, Senthil; Shelton, James; Wilde, Susan B.; Haynie, Rebecca S.; Herrin, James A.

2012-08-28

Embodiments of the present disclosure provide for novel strategies to harvest algal lipids using mollusks which after feeding algae from the growth medium can convert algal lipids into their biomass or excrete lipids in their pseudofeces which makes algae harvesting energy efficient and cost effective. The bioconverter, filter-feeding mollusks and their pseudofeces can be harvested and converted to biocrude using an advanced thermochemical liquefaction technology. Methods, systems, and materials are disclosed for the harvest and isolation of algal lipids from the mollusks, molluscan feces and molluscan pseudofeces.

76 FR 65200 - Risk Assessment on Norovirus in Bivalve Molluscan Shellfish: Request for Comments and for...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-20

..., eaten raw and cooked, including method of cooking (e.g., steaming, frying, or baking); 2. Distribution...., steaming, frying, or baking) for bivalve molluscan shellfish, by species; 4. Experimental data and models...

The Cretaceous Tetori biota in Japan and its evolutionary significance for terrestrial ecosystems in Asia

USGS Publications Warehouse

Matsukawa, M.; Ito, M.; Nishida, N.; Koarai, K.; Lockley, M.G.; Nichols, D.J.

2006-01-01

Cretaceous nonmarine deposits are widely distributed on the Asian continent and include various kinds of zoo- and phyto-assemblages. The Tetori Group is one of the most important Mesozoic terrestrial deposits in East Asia, and for this reason its geology, stratigraphy, and biota have been studied intensively by our group for more than a decade. We present the main results herein. We confirm that formations as lithostratigraphic units are the best geological correlation tools for the Tetori Group and the best tools for a geological mapping of the group. Although subgroups have previously been used for correlation, proper designation and evaluation of subgroups is required if they are to be used effectively, and we show that previous geological correlation of the Tetori Group has been confused by inappropriate definition of these subgroups. We located fossil localities including reported zoo- and phyto-assemblages in the framework of formations correlated by our stratigraphy. The occurrence of zoo-assemblages was probably controlled by environments (i.e., most are in situ), but phyto-assemblages were mostly transported and rapidly buried by high-energy river systems. Although two distinct dinosaur faunas and four floras have been named for the zoo- and phyto-assemblages in the Tetori Group, in reality there is only one Tetori Dinosaur Fauna and one Tetori Flora, as proved by careful correlation. Two types of zoo-assemblages co-occur in the Tetori Group: vertebrate species whose ancestors flourished in the Jurassic (as found in China), and their descendants from the Late Cretaceous. As the latter modern type of assemblage is more abundant than the former, changeable environments at the continental margin probably accelerated evolution of more modern species. We can employ nonmarine molluscan species as geological correlation tools in some cases, i.e., when their taxon ranges are well-confirmed by independent evidence. However, because freshwater molluscan species and terrestrial vertebrate species had many opportunities to move to optimum habitat as environments changed through time on the Cretaceous Asian continent, their correlation potential is uncertain. Many nonmarine molluscan species from the Japanese and Chinese Cretaceous had their stratigraphic occurrences controlled by changing environments. ?? 2005 Elsevier Ltd. All rights reserved.

Mitogenomics does not resolve deep molluscan relationships (yet?).

PubMed

Stöger, I; Schrödl, M

2013-11-01

The origin of molluscs among lophotrochozoan metazoans is unresolved and interclass relationships are contradictory between morphology-based, multi-locus, and recent phylogenomic analyses. Within the "Deep Metazoan Phylogeny" framework, all available molluscan mitochondrial genomes were compiled, covering 6 of 8 classes. Genomes were reannotated, and 13 protein coding genes (PCGs) were analyzed in various taxon settings, under multiple masking and coding regimes. Maximum Likelihood based methods were used for phylogenetic reconstructions. In all cases, molluscs result mixed up with lophotrochozoan outgroups, and most molluscan classes with more than single representatives available are non-monophyletic. We discuss systematic errors such as long branch attraction to cause aberrant, basal positions of fast evolving ingroups such as scaphopods, patellogastropods and, in particular, the gastropod subgroup Heterobranchia. Mitochondrial sequences analyzed either as amino acids or nucleotides may perform well in some (Cephalopoda) but not in other palaeozoic molluscan groups; they are not suitable to reconstruct deep (Cambrian) molluscan evolution. Supposedly "rare" mitochondrial genome level features have long been promoted as phylogenetically informative. In our newly annotated data set, features such as genome size, transcription on one or both strands, and certain coupled pairs of PCGs show a homoplastic, but obviously non-random distribution. Apparently congruent (but not unambiguous) signal for non-trivial subclades, e.g. for a clade composed of pteriomorph and heterodont bivalves, needs confirmation from a more comprehensive bivalve sampling. We found that larger clusters not only of PCGs but also of rRNAs and even tRNAs can bear local phylogenetic signal; adding trnG-trnE to the end of the ancestral cluster trnM-trnC-trnY-trnW-trnQ might be synapomorphic for Mollusca. Mitochondrial gene arrangement and other genome level features explored and reviewed herein thus failed as golden bullets, but are promising as additional characters or evidence supporting deep molluscan clades revealed by other data sets. A representative and dense sampling of molluscan subgroups may contribute to resolve contentious interclass relationships in the future, and is vital for exploring the evolution of especially diverse mitochondrial genomes in molluscs. Copyright © 2012 Elsevier Inc. All rights reserved.

21 CFR 1240.60 - Molluscan shellfish.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Molluscan shellfish. 1240.60 Section 1240.60 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) REGULATIONS UNDER CERTAIN OTHER ACTS ADMINISTERED BY THE FOOD AND DRUG ADMINISTRATION CONTROL OF COMMUNICABLE...

21 CFR 1240.60 - Molluscan shellfish.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Molluscan shellfish. 1240.60 Section 1240.60 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) REGULATIONS UNDER CERTAIN OTHER ACTS ADMINISTERED BY THE FOOD AND DRUG ADMINISTRATION CONTROL OF COMMUNICABLE...

The biology of mass extinction: a palaeontological view

NASA Technical Reports Server (NTRS)

Jablonski, D.; Raup, D. M. (Principal Investigator)

1989-01-01

Extinctions are not biologically random: certain taxa or functional/ecological groups are more extinction-prone than others. Analysis of molluscan survivorship patterns for the end-Cretaceous mass extinctions suggests that some traits that tend to confer extinction resistance during times of normal ('background') levels of extinction are ineffectual during mass extinction. For genera, high species-richness and possession of widespread individual species imparted extinction-resistance during background times but not during the mass extinction, when overall distribution of the genus was an important factor. Reanalysis of Hoffman's (1986) data (Neues Jb. Geol. Palaont. Abh. 172, 219) on European bivalves, and preliminary analysis of a new northern European data set, reveals a similar change in survivorship rules, as do data scattered among other taxa and extinction events. Thus taxa and adaptations can be lost not because they were poorly adapted by the standards of the background processes that constitute the bulk of geological time, but because they lacked--or were not linked to--the organismic, species-level or clade-level traits favoured under mass-extinction conditions. Mass extinctions can break the hegemony of species-rich, well-adapted clades and thereby permit radiation of taxa that had previously been minor faunal elements; no net increase in the adaptation of the biota need ensue. Although some large-scale evolutionary trends transcend mass extinctions, post extinction evolutionary pathways are often channelled in directions not predictable from evolutionary patters during background times.

21 CFR 123.28 - Source controls.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 2 2013-04-01 2013-04-01 false Source controls. 123.28 Section 123.28 Food and... CONSUMPTION FISH AND FISHERY PRODUCTS Raw Molluscan Shellfish § 123.28 Source controls. (a) In order to meet... molluscan shellfish harvested from growing waters approved for harvesting by a shellfish control authority...

21 CFR 123.28 - Source controls.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 2 2011-04-01 2011-04-01 false Source controls. 123.28 Section 123.28 Food and... CONSUMPTION FISH AND FISHERY PRODUCTS Raw Molluscan Shellfish § 123.28 Source controls. (a) In order to meet... molluscan shellfish harvested from growing waters approved for harvesting by a shellfish control authority...

21 CFR 123.28 - Source controls.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 2 2012-04-01 2012-04-01 false Source controls. 123.28 Section 123.28 Food and... CONSUMPTION FISH AND FISHERY PRODUCTS Raw Molluscan Shellfish § 123.28 Source controls. (a) In order to meet... molluscan shellfish harvested from growing waters approved for harvesting by a shellfish control authority...

21 CFR 123.28 - Source controls.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 2 2014-04-01 2014-04-01 false Source controls. 123.28 Section 123.28 Food and... CONSUMPTION FISH AND FISHERY PRODUCTS Raw Molluscan Shellfish § 123.28 Source controls. (a) In order to meet... molluscan shellfish harvested from growing waters approved for harvesting by a shellfish control authority...

Persistent ecological shifts in marine molluscan assemblages across the end-Cretaceous mass extinction.

PubMed

Aberhan, Martin; Kiessling, Wolfgang

2015-06-09

Contemporary biodiversity loss and population declines threaten to push the biosphere toward a tipping point with irreversible effects on ecosystem composition and function. As a potential example of a global-scale regime shift in the geological past, we assessed ecological changes across the end-Cretaceous mass extinction based on molluscan assemblages at four well-studied sites. By contrasting preextinction and postextinction rank abundance and numerical abundance in 19 molluscan modes of life--each defined as a unique combination of mobility level, feeding mode, and position relative to the substrate--we find distinct shifts in ecospace utilization, which significantly exceed predictions from null models. The magnitude of change in functional traits relative to normal temporal fluctuations at far-flung sites indicates that molluscan assemblages shifted to differently structured systems and faunal response was global. The strengths of temporal ecological shifts, however, are mostly within the range of preextinction site-to-site variability, demonstrating that local ecological turnover was similar to geographic variation over a broad latitudinal range. In conjunction with varied site-specific temporal patterns of individual modes of life, these spatial and temporal heterogeneities argue against a concerted phase shift of molluscan assemblages from one well-defined regime to another. At a broader ecological level, by contrast, congruent tendencies emerge and suggest deterministic processes. These patterns comprise the well-known increase of deposit-feeding mollusks in postextinction assemblages and increases in predators and predator-resistant modes of life, i.e., those characterized by elevated mobility and infaunal life habits.

The Continuing Debate on Deep Molluscan Phylogeny: Evidence for Serialia (Mollusca, Monoplacophora + Polyplacophora)

PubMed Central

Stöger, I.; Sigwart, J. D.; Kano, Y.; Knebelsberger, T.; Marshall, B. A.; Schwabe, E.; Schrödl, M.

2013-01-01

Molluscs are a diverse animal phylum with a formidable fossil record. Although there is little doubt about the monophyly of the eight extant classes, relationships between these groups are controversial. We analysed a comprehensive multilocus molecular data set for molluscs, the first to include multiple species from all classes, including five monoplacophorans in both extant families. Our analyses of five markers resolve two major clades: the first includes gastropods and bivalves sister to Serialia (monoplacophorans and chitons), and the second comprises scaphopods sister to aplacophorans and cephalopods. Traditional groupings such as Testaria, Aculifera, and Conchifera are rejected by our data with significant Approximately Unbiased (AU) test values. A new molecular clock indicates that molluscs had a terminal Precambrian origin with rapid divergence of all eight extant classes in the Cambrian. The recovery of Serialia as a derived, Late Cambrian clade is potentially in line with the stratigraphic chronology of morphologically heterogeneous early mollusc fossils. Serialia is in conflict with traditional molluscan classifications and recent phylogenomic data. Yet our hypothesis, as others from molecular data, implies frequent molluscan shell and body transformations by heterochronic shifts in development and multiple convergent adaptations, leading to the variable shells and body plans in extant lineages. PMID:24350268

An overview of paleogene molluscan biostratigraphy and paleoecology of the Gulf of Alaska region

USGS Publications Warehouse

Marincovich, L.; McCoy, S.

1984-01-01

Paleogene marine strata in the Gulf of Alaska region occur in three geographic areas and may be characterized by their molluscan faunal composition and paleoecology: a western area consisting of the Alaska Peninsula, Kodiak Island, and adjacent islands; a central area encompassing Prince William Sound; and an eastern area extending from the mouth of the Copper River to Icy Point in the Lituya district. Strata in the western area include the Ghost Rocks, Narrow Cape (in part), Sitkalidak, Stepovak, Belkofski, and Tolstoi Formations; in the central area Paleogene strata are assigned entirely to the Orca Group; Paleogene strata in the eastern area include the Kulthieth and Poul Creek Formations and several coeval units. Environments ranging from marginal marine to bathyal and from subtropical to cool-temperate are inferred for the various molluscan faunas. Sediments range from interbedded coal and marine sands to deep-water turbidites. The known Paleogene molluscan faunas of these three southern Alaskan areas permit recognition of biostratigraphic schemes within each area, preliminary correlations between faunas of the three areas, and more general correlations with faunas of the Pacific Northwest, the Far Eastern U.S.S.R., and northern Japan. ?? 1984.

Invertebrate shells (mollusca, foraminifera) as pollution indicators, Red Sea Coast, Egypt

NASA Astrophysics Data System (ADS)

Youssef, Mohamed; Madkour, Hashem; Mansour, Abbas; Alharbi, Wedad; El-Taher, Atef

2017-09-01

To assess the degree of pollution and its impact on the environment along the Red Sea Coast, the most abundant nine species of recent benthic foraminifera and three species of molluscan shells have been selected for the analysis of Fe, Mn, Zn, Cu, Pb, Ni, Co, and Cd concentrations. The selected foraminiferal species are: Textularia agglutinans, Amphispsorus hemprichii, Sorites marginalis, Peneroplis planatus, Borelis schlumbergeri, Amphistegina lessonii, Ammonia beccarii, Operculina gaimairdi, and Operculinella cumingii. The selected molluscan shells are: Lambis truncata and Strombus tricornis (gastropods) and Tridacana gigas (bivalves). The inorganic material analysis of foraminifera and molluscs from the Quseir and Safaga harbors indicates that foraminifera tests include higher concentrations of heavy metals such as Fe and Mn than molluscan shells. These results are supported by the black tests of porcelaneous foraminifera and reflect iron selectivity. The Cd and Pb concentrations in molluscan shells are high in the El Esh Area because of oil pollution at this site. The Cu, Zn, and Ni concentrations in the studied invertebrates are high at Quseir Harbor and in the El Esh Area because of the strong influence of terrigenous materials that are rich in these metals. The heavy metal contamination is mostly attributed to anthropogenic sources.

Molluscan extinction patterns across the Cenomanian-Turonian stage boundary in the western interior of the United States

USGS Publications Warehouse

Elder, W.P.

1989-01-01

High-resolution stratigraphic analysis of 18 sections spanning the Cenomanian-Turonian Stage boundary in the western interior of the United States has allowed determination of the magnitude and pattern of molluscan extinction and disruption. Composite range data from all sections show that the faunal turnover across the stage boundary occurs in a series of narrow stratigraphic zones, defined by multiple first and last occurrences, separated by intervals displaying little or no taxonomic turnover. Two of the apparent extinction steps (bottom and top of the Neocardioceras juddii Zone) may be intercontinentally developed. The additional steps apparently reflect cyclic changes in water mass and substrate characteristics in the western interior basin produced in response to orbital forcing of climate. The most affected mollusks were those having intercontinental distributions. -Author

Relationship Between Metabolic Rate and Sea Depth in Bivalves and Gastropods

NASA Astrophysics Data System (ADS)

Ruiz, B. R.; Shih, B.; Heim, N.; Payne, J.

2016-12-01

The purpose of this study was to find and observe trends in the metabolic rate of bivalves and gastropod in regards to sea depth in order to see if all organisms follow a general trend for metabolism and to provide data to help future conservation efforts of these keystone organisms. Using geographic data produced by McClain et. al (2012) and body size data from Heim et. al (2015), the metabolic rate and sea depth data were plotted using the `R statistical software'. The Pearson correlation test was performed on each respective graph. Deep sea mollusks were considered those that resided at a water depth of 500 meters or deeper while shallow mollusks resided at a depth less than 500 meters. The gastropods showed positive correlations in the relationship between metabolic rate and ocean depth while bivalves showed a negative trend. When the metabolic rate versus minimum ocean depth was graphed, the graphs for deep bivalves and shallow gastropods returned bad p-values. From this data, it can be seen that water depth and metabolic rate have relationships, although different molluscan classes are adapted to their environments in different ways, as seen by the differences in the relationships between metabolic rates and ocean depth of the gastropods and bivalves. The results indicated that there is a general negative trend between metabolic rate and ocean depth of bivalves, and a positive relationship for gastropods. The difference in relationship in gastropods is thought to be attributed to the size trends of gastropods as they live in deeper waters, which is that gastropods increase in size across the bathyal region, and decrease as gastropods approach the extremely deep water. As displayed by the two different metabolic trends, this study shows the different ways molluscan classes have adapted to different evolutionary selection pressures.

De Novo Assembly and Characterization of Two Transcriptomes Reveal Multiple Light-Mediated Functions in the Scallop Eye (Bivalvia: Pectinidae)

PubMed Central

Pairett, Autum N.; Serb, Jeanne M.

2013-01-01

Background The eye has evolved across 13 separate lineages of molluscs. Yet, there have been very few studies examining the molecular machinary underlying eye function of this group, which is due, in part, to a lack of genomic resources. The scallop (Bivalvia: Pectinidae) represents a compeling molluscan model to study photoreception due to its morphologically novel and separately evolved mirror-type eye. We sequenced the adult eye transcriptome of two scallop species to: 1) identify the phototransduction pathway components; 2) identify any additional light detection functions; and 3) test the hypothesis that molluscs possess genes not found in other animal lineages. Results A total of 3,039 contigs from the bay scallop, Argopecten irradians and 26,395 contigs from the sea scallop, Placopecten magellanicus were produced by 454 sequencing. Targeted BLAST searches and functional annotation using Gene Ontology (GO) terms and KEGG pathways identified transcripts from three light detection systems: two phototransduction pathways and the circadian clock, a previously unrecognized function of the scallop eye. By comparing the scallop transcriptomes to molluscan and non-molluscan genomes, we discovered that a large proportion of the transcripts (7,776 sequences) may be specific to the scallop lineage. Nearly one-third of these contain transmembrane protein domains, suggesting these unannotated transcripts may be sensory receptors. Conclusions Our data provide the most comprehensive transcriptomic resource currently available from a single molluscan eye type. Candidate genes potentially involved in sensory reception were identified, and are worthy of further investigation. This resource, combined with recent phylogenetic and genomic data, provides a strong foundation for future investigations of the function and evolution of molluscan photosensory systems in this morphologically and taxonomically diverse phylum. PMID:23922823

Latitudinal gradients in tertiary molluscan faunas of the Pacific coast

USGS Publications Warehouse

Addicott, W.O.

1970-01-01

Tertiary molluscan faunas of the middle latitudes of the marginal eastern North Pacific are characterized by warm-water taxa whose descendants now live in more southerly latitudes. A series of profiles in which cumulative percentages of warm-water faunal elements are plotted against latitude show progressive northward decreases in the percentage of these elements in the faunas of Pacific coast Tertiary stages. Systematic changes in the relative position of these latitudinal gradients during the Middle and Late Tertiary are related to climatic change in the Pacific Basin. Widespread tropical marine climate in the middle latitudes of the eastern North Pacific during the Eocene is indicated by widespread faunal units characterized by high levels of taxonomic diversity. Succeeding Early Oligocene faunas are less diverse, suggesting cooler climatic conditions. Unusually low representations of warm-water genera characterize the molluscan faunas of the Acila shumardi Zone in central California (latitude 34??-37??N). The anomalously cool-water aspect of these faunas may record the occurrence of upwelling along a bold linear segment of the Pacific coast. During the Late Oligocene or the Early Miocene, they are replaced by faunas of unusually warm-water aspect resulting in positive anomalies in Miocene latitudinal faunal gradients in central California. The Miocene anomalies seem to result from the development of an irregular Neogene coastline with extensive, newly established shallow-water embayments. ?? 1970.

A quantitative analysis of naiad mollusks from the Prairie du Chien, Wisconsin dredge material site on the Mississippi River

USGS Publications Warehouse

Havlik, M.E.; Marking, L.L.

1980-01-01

The Prairie du Chien dredge material site contains about 100,000 cubic meters of material dredged from the East Channel of the Mississippi Riverin1976. Previous studies in that area suggested a rich molluscan fauna, but most studies were only qualitative or simply observations. Our study of this material was designed to determine the density and diversity of molluscan fauna, to assess changes in the fauna, to identify endemic species previously unreported, and to evaluate the status of the endangered Lampsilis higginsi. Ten cubic meters of dredge material were sieved to recover shells. Molluscan fauna at the site contained38 species of naiades and up to 1,737 identifiable valves per cubic meter. The endangered L. higginsi ranked18th In occurrence, accounted for only 0.52% of the identifiable shells, and averaged about three valves per cubic meter. From a total of 813 kg of naiades and gastropods, 6,339 naiad valves were identified. Five naiad species were collected at the site for the first time, and Eploblasma triquetra had not been reported previously in the Prairie du Chien area. Although the molluscan fauna has changed, the East Channel at Prairie du Chien is obviously suitable for L. higginsi.

Detection, isolation, and persistence of viruses within bivalve mollusks

USDA-ARS?s Scientific Manuscript database

Norovirus (NV), hepatitis A virus (HAV), and other virus transmission by molluscan shellfish is a significant issue. Research at the ARS-Dover DE laboratory has led to the development of improved methods for detecting these viruses. To identify pathogenic viruses within mollusks, a rapid highly-se...

76 FR 37815 - Cooperative Agreement To Support Shellfish Safety Assistance Project

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-28

...; funding support to research the influence of water and air temperature, dissolved oxygen, and nutrients on... controls to reduce the risk of illness associated with molluscan shellfish consumption, including Vibrio... professionals concerning Vibrio illness and shellfish consumption; 9. Development and maintenance of a World...

Data on Molluscan Shells in parts of Nellore Coast, southeast coast of India.

PubMed

Lakshmanna, B; Jayaraju, N; Prasad, T Lakshmi; Sreenivasulu, G; Nagalakshmi, K; Kumar, M Pramod; Madakka, M

2018-02-01

X-ray diffraction (XRD), Scanning Electron Microscope-Energy Dispersive Spectroscopy (SEM-EDS), and Fourier Transform Infrared Spectroscopy (FT-IR), were applied to analyze the organic matrix of two Molluscan shells . The Mollusca shells are mineral structure and calcium carbonate crystallized as aragonite. The FT-IR spectra showed Alkyl Halide, Alkanes, Alcohols, Amides, Aromatic, and Hydroxyl groups in the organic matrix of the whole (organic and mineral) Molluscan shells. SEM images of particles of the two Molluscan shells at different magnifications were taken. The morphologies of the samples show a flake like structures with irregular grains, their sizes are at micrometric scale and the chemical analysis of EDS indicated that the major elements of Cardita and Gastropoda were C, O, and Ca, consistent with the results of XRD analysis. The results of the analysis of the EDS spectra of the shells showed that the content of most of the powder composition of shells is the element carbon, calcium oxygen, aluminium, and lead peaks that appear on the Cardita and Gastropoda and shells powders tap EDS spectra. The present work examined organic matrix of the selected shells of the heavily polluted and light polluted sites, along Nellore Coast, South East Coast of India. The heavily polluted sites have significantly thickened shells. The data demonstrated the sensitivity of this abundant and widely distributed intertidal fragile environment.

A Holocene molluscan succession from floodplain sediments of the upper Lena River (Lake Baikal region), Siberia

NASA Astrophysics Data System (ADS)

White, Dustin; Preece, Richard C.; Shchetnikov, Alexander A.; Parfitt, Simon A.; Dlussky, Konstantin G.

2008-05-01

Floodplain sediments of the upper Lena River near Basovo in south-central Siberia have yielded the most detailed Holocene molluscan succession yet reported from the entire eastern Palaearctic. Over 72,500 shells from at least 28 species of terrestrial and 23 species of freshwater mollusc have been recovered, an abundance and diversity far higher than previously reported from the region. The molluscan assemblages are dominated by land snails, especially members of the genus Vallonia, represented by five species including Vallonia tenuilabris and two poorly known species Vallonia kamtschatica and Vallonia cf. chinensis. Other noteworthy species recovered include Gastrocopta theeli, Carychium pessimum, Vertigo extima (southernmost record), Vertigo microsphaera and the first Asian records of three other taxa ( Vertigo geyeri, Vertigo genesii and Vertigo parcedentata). Illustrations are provided for the critical species, since opinions differ about the status of various taxa and the correct names that should be used. The molluscan assemblages show clear successional trends during the early to mid-Holocene, reflecting episodes of dryness/wetness on the floodplain. Drier conditions at ca 6350 14C yr BP coincide with major changes in the archaeological record seen at other sites in the region but it remains unclear whether the two are linked. A prominent charcoal-rich horizon dated to ca 2800 14C yr BP marks a burning event in the catchment, which resulted in a two-fold increase in sediment accumulation rate. Remains of small mammals occurred throughout the sequence including a tooth of Microtus cf. maximowiczii, possibly the first occurrence of Ungar vole west of Lake Baikal. The faunal analyses have been integrated with a detailed pedological study of the sedimentary profile and a chronology was obtained by means of 12 AMS radiocarbon dates. This study provides the first detailed palaeoecological information relating to Holocene molluscan assemblages from the Cis-Baikal region and lays the foundation for future work in the eastern Palaearctic.

Development of rapid hemocyte-based extraction methods for detection of hepatitis A virus and murine norovirus in contaminated oysters

USDA-ARS?s Scientific Manuscript database

The human enteric pathogens, hepatitis A virus and human norovirus, have been shown to contaminate molluscan shellfish and cause foodborne disease in consumers. Rapid viral extraction methods are needed to replace current time consuming methods, which use whole oysters or dissected tissues. In our ...

Crystal Structure of the 3.8-MDa Respiratory Supermolecule Hemocyanin at 3.0 Å Resolution.

PubMed

Gai, Zuoqi; Matsuno, Asuka; Kato, Koji; Kato, Sanae; Khan, Md Rafiqul Islam; Shimizu, Takeshi; Yoshioka, Takeya; Kato, Yuki; Kishimura, Hideki; Kanno, Gaku; Miyabe, Yoshikatsu; Terada, Tohru; Tanaka, Yoshikazu; Yao, Min

2015-12-01

Molluscan hemocyanin, a copper-containing oxygen transporter, is one of the largest known proteins. Although molluscan hemocyanins are currently applied as immunotherapeutic agents, their precise structure has not been determined because of their enormous size. Here, we have determined the first X-ray crystal structure of intact molluscan hemocyanin. The structure unveiled the architecture of the 3.8-MDa supermolecule composed of homologous functional units (FUs), wherein the dimers of FUs hierarchically associated to form the entire cylindrical decamer. Most of the specific inter-FU interactions were localized at narrow regions in the FU dimers, suggesting that rigid FU dimers formed by specific interactions assemble with flexibility. Furthermore, the roles of carbohydrates in assembly and allosteric effect, and conserved sulfur-containing residues in copper incorporation, were revealed. The precise structural information obtained in this study will accelerate our understanding of the molecular basis of hemocyanin and its future applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

Transient and Big Are Key Features of an Invertebrate T-type Channel (LCav3) from the Central Nervous System of Lymnaea stagnalis*

PubMed Central

Senatore, Adriano; Spafford, J. David

2010-01-01

Here we describe features of the first non-mammalian T-type calcium channel (LCav3) expressed in vitro. This molluscan channel possesses combined biophysical properties that are reminiscent of all mammalian T-type channels. It exhibits T-type features such as “transient” kinetics, but the “tiny” label, usually associated with Ba2+ conductance, is hard to reconcile with the “bigness” of this channel in many respects. LCav3 is 25% larger than any voltage-gated ion channel expressed to date. It codes for a massive, 322-kDa protein that conducts large macroscopic currents in vitro. LCav3 is also the most abundant Ca2+ channel transcript in the snail nervous system. A window current at typical resting potentials appears to be at least as large as that reported for mammalian channels. This distant gene provides a unique perspective to analyze the structural, functional, drug binding, and evolutionary aspects of T-type channels. PMID:20056611

Prolonged Permian Triassic ecological crisis recorded by molluscan dominance in Late Permian offshore assemblages.

PubMed

Clapham, Matthew E; Bottjer, David J

2007-08-07

The end-Permian mass extinction was the largest biotic crisis in the history of animal life, eliminating as many as 95% of all species and dramatically altering the ecological structure of marine communities. Although the causes of this pronounced ecosystem shift have been widely debated, the broad consensus based on inferences from global taxonomic diversity patterns suggests that the shift from abundant brachiopods to dominant molluscs was abrupt and largely driven by the catastrophic effects of the end-Permian mass extinction. Here we analyze relative abundance counts of >33,000 fossil individuals from 24 silicified Middle and Late Permian paleocommunities, documenting a substantial ecological shift to numerical dominance by molluscs in the Late Permian, before the major taxonomic shift at the end-Permian mass extinction. This ecological change was coincident with the development of fluctuating anoxic conditions in deep marine basins, suggesting that numerical dominance by more tolerant molluscs may have been driven by variably stressful environmental conditions. Recognition of substantial ecological deterioration in the Late Permian also implies that the end-Permian extinction was the climax of a protracted environmental crisis. Although the Late Permian shift to molluscan dominance was a pronounced ecological change, quantitative counts of 847 Carboniferous-Cretaceous collections from the Paleobiology Database indicate that it was only the first stage in a stepwise transition that culminated with the final shift to molluscan dominance in the Late Jurassic. Therefore, the ecological transition from brachiopods to bivalves was more protracted and complex than their simple Permian-Triassic switch in diversity.

Prolonged Permian–Triassic ecological crisis recorded by molluscan dominance in Late Permian offshore assemblages

PubMed Central

Clapham, Matthew E.; Bottjer, David J.

2007-01-01

The end-Permian mass extinction was the largest biotic crisis in the history of animal life, eliminating as many as 95% of all species and dramatically altering the ecological structure of marine communities. Although the causes of this pronounced ecosystem shift have been widely debated, the broad consensus based on inferences from global taxonomic diversity patterns suggests that the shift from abundant brachiopods to dominant molluscs was abrupt and largely driven by the catastrophic effects of the end-Permian mass extinction. Here we analyze relative abundance counts of >33,000 fossil individuals from 24 silicified Middle and Late Permian paleocommunities, documenting a substantial ecological shift to numerical dominance by molluscs in the Late Permian, before the major taxonomic shift at the end-Permian mass extinction. This ecological change was coincident with the development of fluctuating anoxic conditions in deep marine basins, suggesting that numerical dominance by more tolerant molluscs may have been driven by variably stressful environmental conditions. Recognition of substantial ecological deterioration in the Late Permian also implies that the end-Permian extinction was the climax of a protracted environmental crisis. Although the Late Permian shift to molluscan dominance was a pronounced ecological change, quantitative counts of 847 Carboniferous–Cretaceous collections from the Paleobiology Database indicate that it was only the first stage in a stepwise transition that culminated with the final shift to molluscan dominance in the Late Jurassic. Therefore, the ecological transition from brachiopods to bivalves was more protracted and complex than their simple Permian–Triassic switch in diversity. PMID:17664426

Diel and seasonal variation of a molluscan taxocoenosis associated with a Zostera marina bed in southern Spain (Alboran Sea)

NASA Astrophysics Data System (ADS)

Rueda, Jose L.; Urra, Javier; Salas, Carmen

2008-09-01

The diel and seasonal variation of molluscs living in a Zostera marina bed (12-14 m depth) from southern Spain have been studied for one year using a small Agassiz trawl for collecting the samples (222 m2). The frequent and dominant species were very similar in both diurnal and nocturnal samples, including mainly gastropods such as Jujubinus striatus, Nassarius pygmaeus, Mitrella minor, Calliostoma planatum, Rissoa membranacea or Smaragdia viridis. Nevertheless, a significant increase of abundance of scavengers (e.g. Nassarius spp.) and carnivores (e.g. cephalopods) was registered in nocturnal samples. The abundance was maximal in spring and summer in diurnal and nocturnal samples and also in autumn for nocturnal ones, displaying significantly higher values in nocturnal samples. The species richness, diversity and evenness displayed a similar seasonal trend for diurnal and nocturnal samples, with maximum values during summer months. Monthly variation of the molluscan composition (species presence-absence data) was more acute than diel variation, according to the Cluster, MDS and ANOSIM results. Nevertheless, both monthly and diel changes in the structure (species abundance data) of the molluscan taxocoenosis were important throughout the year. Diel changes in the structure of the molluscan fauna are related to an increase of abundance of some species at nighttime due to vertical movements from the sediment to the shoots or along them (e.g. J. striatus, Nassarius spp.) or due to horizontal movements from adjacent habitats (e.g. cephalopods). Nevertheless, some species such as Rissoa spp. or Bittium spp. stay on the leaves of Z. marina during day as well as nighttime.

Effect of Hurricane Hugo on molluscan skeletal distributions,Salt River Bay, St. Croix, U.S. Virgin Islands

NASA Astrophysics Data System (ADS)

Miller, Arnold I.; Llewellyn, Ghislaine; Parsons, Karla M.; Cummins, Hays; Boardman, Mark R.; Greenstein, Benjamin J.; Jacobs, David K.

1992-01-01

Just prior to the passage of Hurricane Hugo over St. Croix, U.S. Virgin Islands, 35 molluscan skeletal samples were collected at 30 m intervals along a sampling transect in Salt River Bay, on the north-central coast. Three months after the hurricane, the transect was resampled to permit direct assessment of storm effects on skeletal distributions. Results indicate that spatial zonation of molluscan accumulations, associated with environmental transitions along the transect, was maintained in the wake of the hurricane. However, limited transport was diagnosed by comparing the compositions of prestorm and poststorm samples from the deepest, mud-rich subenvironment on the transect. In aggregate, the species richness of samples from the southern half of this zone increased from 16 to 40, and the abundance of species that were not among the characteristic molluscs of this subenvironment increased from 11% to 26%. These storm effects could probably not have been recognized, and attributed directly to Hugo, had there been no prestorm samples with which to compare directly the poststorm samples.

Changes in the northern Adriatic molluscan community from the Holocene transgression up to the present

NASA Astrophysics Data System (ADS)

Gallmetzer, Ivo; Haselmair, Alexandra; Tomasovych, Adam; Stachowitsch, Michael; Zuschin, Martin

2016-04-01

The northern Adriatic Sea is one of the few modern, epicontinental seas comparable to typical Palaeozoic shelf environments. It has a shallow average water depth (<50 m) and was formed at the end of the last glaciation when the sea level rose. Since historical times this part of the Adriatic has been strongly influenced by human activities through multiple direct or indirect impacts (e.g. fishing, coastal building development, pollution, eutrophication, increased sedimentation), making it one of the most degraded marine ecosystems worldwide. Our study was designed to reconstruct major environmental changes here since the onset of the Holocene transgression using down-core changes in death assemblages of molluscs as indicators for ecological shifts. The sediment cores were taken at three different stations (Brijuni Islands, Croatia, off Piran, Slovenia, and off Venice, Italy), each representative of specific sediment and nutrient conditions and degrees of habitat exploitation. The cores were 1.5 m long and had diameters of 90 or 160 mm. For the molluscan shell analyses, sediment subsamples were examined for species composition, abundance, taxonomic similarity and ecological interactions (e.g. frequencies of drilling predation). In total, 98,700 valves and shells were investigated and 113 bivalve and 178 gastropod species recorded. Sedimentation rates derived from 210Pb dating are very low, between 0.15 cm/yr at Brijuni and 0.25 cm/yr at Piran. The dating of Lucinella divaricata, Timoclea ovata and Gouldia minima shells with 14C calibrated amino-acid racemisation (AAR) revealed that the cores at all three stations cover at least 6000 to 8000 years, i.e. the whole Holocene transgression period. Time averaging is high, especially in the lower core layers of Piran station, probably due to strong bioturbation. Surface mixed-layer assemblages tend to show right-skewed postmortem age-frequency distributions, whereas subsurface assemblages show unimodal or uniform shapes. Molluscan assemblages show significant interregional differences that correlate with sedimentation rate, grain size, and the occurrence of organic pollutants and heavy metals. Down-core changes in molluscan communities are also conspicuous in all cores. They partly reflect long-term changes in water depth, vegetation cover or grain size distribution caused by natural fluctuations of environmental conditions over the past millennia. In the uppermost core layers, however, these changes can be interpreted as indicators of anthropogenic impacts.

Structural Changes in Molluscan Community over a 15-Year Period before and after the 2011 Great East Japan Earthquake and Subsequent Tsunami around Matsushima Bay, Miyagi Prefecture, Northeastern Japan.

PubMed

Sato, Shin'ichi; Chiba, Tomoki

2016-01-01

We examined structural changes in the molluscan community for ten years (2001-2010) before and five years (2011-2015) after the 2011 Great East Japan Earthquake and subsequent tsunami around Matsushima Bay, Miyagi Prefecture, northeastern Japan. Before the earthquake and tsunami, Ruditapes philippinarum, Macoma incongrua, Pillucina pisidium, and Batillaria cumingii were dominant, and an alien predator Laguncula pulchella appeared in 2002 and increased in number. After the tsunami, R. philippinarum and M. incongrua populations quickly recovered in 2012, but P. pisidium and B. cumingii populations did not recover until 2015. By contrast, Musculista senhousia, Mya arenaria, Retusa sp., and Solen strictus were found in low densities before the tsunami, but they rapidly increased in abundance/number over five years after the tsunami. These results suggest that the molluscan community on the Tona Coast was drastically changed by the earthquake and tsunami, and some species mainly inhabiting the intertidal-subtidal zone may have increased in number because of land subsidence. We also emphasize that the seawall delayed recovery of the intertidal community after the earthquake and tsunami.

Structural Changes in Molluscan Community over a 15-Year Period before and after the 2011 Great East Japan Earthquake and Subsequent Tsunami around Matsushima Bay, Miyagi Prefecture, Northeastern Japan

PubMed Central

Chiba, Tomoki

2016-01-01

We examined structural changes in the molluscan community for ten years (2001–2010) before and five years (2011–2015) after the 2011 Great East Japan Earthquake and subsequent tsunami around Matsushima Bay, Miyagi Prefecture, northeastern Japan. Before the earthquake and tsunami, Ruditapes philippinarum, Macoma incongrua, Pillucina pisidium, and Batillaria cumingii were dominant, and an alien predator Laguncula pulchella appeared in 2002 and increased in number. After the tsunami, R. philippinarum and M. incongrua populations quickly recovered in 2012, but P. pisidium and B. cumingii populations did not recover until 2015. By contrast, Musculista senhousia, Mya arenaria, Retusa sp., and Solen strictus were found in low densities before the tsunami, but they rapidly increased in abundance/number over five years after the tsunami. These results suggest that the molluscan community on the Tona Coast was drastically changed by the earthquake and tsunami, and some species mainly inhabiting the intertidal—subtidal zone may have increased in number because of land subsidence. We also emphasize that the seawall delayed recovery of the intertidal community after the earthquake and tsunami. PMID:27936182

Molluscan cells in culture: primary cell cultures and cell lines

PubMed Central

Yoshino, T. P.; Bickham, U.; Bayne, C. J.

2013-01-01

In vitro cell culture systems from molluscs have significantly contributed to our basic understanding of complex physiological processes occurring within or between tissue-specific cells, yielding information unattainable using intact animal models. In vitro cultures of neuronal cells from gastropods show how simplified cell models can inform our understanding of complex networks in intact organisms. Primary cell cultures from marine and freshwater bivalve and gastropod species are used as biomonitors for environmental contaminants, as models for gene transfer technologies, and for studies of innate immunity and neoplastic disease. Despite efforts to isolate proliferative cell lines from molluscs, the snail Biomphalaria glabrata Say, 1818 embryonic (Bge) cell line is the only existing cell line originating from any molluscan species. Taking an organ systems approach, this review summarizes efforts to establish molluscan cell cultures and describes the varied applications of primary cell cultures in research. Because of the unique status of the Bge cell line, an account is presented of the establishment of this cell line, and of how these cells have contributed to our understanding of snail host-parasite interactions. Finally, we detail the difficulties commonly encountered in efforts to establish cell lines from molluscs and discuss how these difficulties might be overcome. PMID:24198436

Crystallization and preliminary X-ray crystallographic study of a 3.8-MDa respiratory supermolecule hemocyanin.

PubMed

Matsuno, Asuka; Gai, Zuoqi; Tanaka, Miyuki; Kato, Koji; Kato, Sanae; Katoh, Tsuyoshi; Shimizu, Takeshi; Yoshioka, Takeya; Kishimura, Hideki; Tanaka, Yoshikazu; Yao, Min

2015-06-01

Many molluscs transport oxygen using a very large cylindrical multimeric copper-containing protein named hemocyanin. The molluscan hemocyanin forms a decamer (cephalopods) or multidecamer (gastropods) of approximately 330-450kDa subunits, resulting in a molecular mass >3.3MDa. Therefore, molluscan hemocyanin is one of the largest proteins. The reason why these organisms use such a large supermolecule for oxygen transport remains unclear. Atomic-resolution X-ray crystallographic analysis is necessary to unveil the detailed molecular structure of this mysterious large molecule. However, its propensity to dissociate in solution has hampered the crystallization of its intact form. In the present study, we successfully obtained the first crystals of an intact decameric molluscan hemocyanin. The diffraction dataset at 3.0-Å resolution was collected by merging the datasets of two isomorphic crystals. Electron microscopy analysis of the dissolved crystals revealed cylindrical particles. Furthermore, self-rotation function analysis clearly showed the presence of a fivefold symmetry with several twofold symmetries perpendicular to the fivefold axis. The absorption spectrum of the crystals showed an absorption peak around 345nm. These results indicated that the crystals contain intact hemocyanin decamers in the oxygen-bound form. Copyright © 2015 Elsevier Inc. All rights reserved.

Molecular Evolution of the Oxygen-Binding Hemerythrin Domain

PubMed Central

Alvarez-Carreño, Claudia; Becerra, Arturo; Lazcano, Antonio

2016-01-01

Background The evolution of oxygenic photosynthesis during Precambrian times entailed the diversification of strategies minimizing reactive oxygen species-associated damage. Four families of oxygen-carrier proteins (hemoglobin, hemerythrin and the two non-homologous families of arthropodan and molluscan hemocyanins) are known to have evolved independently the capacity to bind oxygen reversibly, providing cells with strategies to cope with the evolutionary pressure of oxygen accumulation. Oxygen-binding hemerythrin was first studied in marine invertebrates but further research has made it clear that it is present in the three domains of life, strongly suggesting that its origin predated the emergence of eukaryotes. Results Oxygen-binding hemerythrins are a monophyletic sub-group of the hemerythrin/HHE (histidine, histidine, glutamic acid) cation-binding domain. Oxygen-binding hemerythrin homologs were unambiguously identified in 367/2236 bacterial, 21/150 archaeal and 4/135 eukaryotic genomes. Overall, oxygen-binding hemerythrin homologues were found in the same proportion as single-domain and as long protein sequences. The associated functions of protein domains in long hemerythrin sequences can be classified in three major groups: signal transduction, phosphorelay response regulation, and protein binding. This suggests that in many organisms the reversible oxygen-binding capacity was incorporated in signaling pathways. A maximum-likelihood tree of oxygen-binding hemerythrin homologues revealed a complex evolutionary history in which lateral gene transfer, duplications and gene losses appear to have played an important role. Conclusions Hemerythrin is an ancient protein domain with a complex evolutionary history. The distinctive iron-binding coordination site of oxygen-binding hemerythrins evolved first in prokaryotes, very likely prior to the divergence of Firmicutes and Proteobacteria, and spread into many bacterial, archaeal and eukaryotic species. The later evolution of the oxygen-binding hemerythrin domain in both prokaryotes and eukaryotes led to a wide variety of functions, ranging from protection against oxidative damage in anaerobic and microaerophilic organisms, to oxygen supplying to particular enzymes and pathways in aerobic and facultative species. PMID:27336621

Responses of molluscan communities to centuries of human impact in the northern Adriatic Sea

PubMed Central

Haselmair, Alexandra; Tomašových, Adam; Stachowitsch, Michael; Zuschin, Martin

2017-01-01

In sediment cores spanning ~500 years of history in the Gulf of Trieste, down-core changes in molluscan community structure are characterized by marked shifts in species and functional composition. Between the 16th and 19th century, a strong heavy metal contamination of the sediments, most notably by Hg, together with the effects of natural climatic oscillations (increased sedimentation and organic enrichment) drive community changes. Since the early 20th century up to 2013, the combined impacts of cultural eutrophication, frequent hypoxic events and intensifying bottom trawling replace heavy metal contamination and climatic factors as the main drivers. The pollution-tolerant and opportunistic bivalve Corbula gibba and the scavenging gastropod Nassarius pygmaeus significantly increase in abundance during the 20th century, while species more sensitive to disturbances and hypoxia such as Turritella communis and Kurtiella bidentata become rare or absent. An infaunal life habit and scavenging emerge as the dominant life strategies during the late 20th century. Down-core shifts in the proportional abundances of molluscan species and functional groups represent a sensitive proxy for past ecological changes and reveal a century-long anthropogenic impact as the main driver behind these processes in the northern Adriatic Sea, offering also a unique perspective for other shallow marine ecosystems worldwide. PMID:28723935

New Vibrio species associated to molluscan microbiota: a review

PubMed Central

Romalde, Jesús L.; Dieguez, Ana L.; Lasa, Aide; Balboa, Sabela

2014-01-01

The genus Vibrio consists of more than 100 species grouped in 14 clades that are widely distributed in aquatic environments such as estuarine, coastal waters, and sediments. A large number of species of this genus are associated with marine organisms like fish, molluscs and crustaceans, in commensal or pathogenic relations. In the last decade, more than 50 new species have been described in the genus Vibrio, due to the introduction of new molecular techniques in bacterial taxonomy, such as multilocus sequence analysis or fluorescent amplified fragment length polymorphism. On the other hand, the increasing number of environmental studies has contributed to improve the knowledge about the family Vibrionaceae and its phylogeny. Vibrio crassostreae, V. breoganii, V. celticus are some of the new Vibrio species described as forming part of the molluscan microbiota. Some of them have been associated with mortalities of different molluscan species, seriously affecting their culture and causing high losses in hatcheries as well as in natural beds. For other species, ecological importance has been demonstrated being highly abundant in different marine habitats and geographical regions. The present work provides an updated overview of the recently characterized Vibrio species isolated from molluscs. In addition, their pathogenic potential and/or environmental importance is discussed. PMID:24427157

Patterns of parasite transmission in polar seas: Daily rhythms of cercarial emergence from intertidal snails

NASA Astrophysics Data System (ADS)

Prokofiev, Vladimir V.; Galaktionov, Kirill V.; Levakin, Ivan A.

2016-07-01

Trematodes are common parasites in intertidal ecosystems. Cercariae, their dispersive larvae, ensure transmission of infection from the first intermediate molluscan host to the second intermediate (invertebrates and fishes) or the final (fishes, marine birds and mammals) host. Trematode transmission in polar seas, while interesting in many respects, is poorly studied. This study aimed to elucidate the patterns of cercarial emergence from intertidal snails at the White Sea and Barents Sea. The study, involving cercariae of 12 species, has provided the most extensive material obtained so far in high latitude seas (66-69° N). The experiments were conducted in situ. Multichannel singular spectral analysis (MSSA) used for processing primary data made it possible to estimate the relative contribution of different oscillations into the analysed time series and to separate the daily component from the other oscillatory components and the noise. Cercarial emergence had pronounced daily rhythms, which did not depend on the daily tidal schedule but were regulated by thermo- and photoperiod. Daily emergence maximums coincided with periods favourable for infecting the second intermediate hosts. Cercarial daily emergence rhythms differed in species using the same molluscan hosts which can be explained by cercarial host searching behaviour. Daily cercarial output (DCO) correlated negatively with larval volume and positively with that of the molluscan host except in cercariae using ambuscade behaviour. In the Barents Sea cercariae emerged from their molluscan hosts at lower temperatures than in the warmer White Sea but the daily emergence period was prolonged. Thus, DCO of related species were similar in these two seas and comparable with DCO values reported for boreal seas. Local temperature adaptations in cercarial emergence suggests that in case of Arctic climate warming trematode transmission in coastal ecosystems is likely to be intensified not because of the increased summer temperature but because of the prolongation of the warm season favouring cercarial emergence (transmission window).

Sea shell diversity and rapidly evolving secretomes: insights into the evolution of biomineralization.

PubMed

Kocot, Kevin M; Aguilera, Felipe; McDougall, Carmel; Jackson, Daniel J; Degnan, Bernard M

2016-01-01

An external skeleton is an essential part of the body plan of many animals and is thought to be one of the key factors that enabled the great expansion in animal diversity and disparity during the Cambrian explosion. Molluscs are considered ideal to study the evolution of biomineralization because of their diversity of highly complex, robust and patterned shells. The molluscan shell forms externally at the interface of animal and environment, and involves controlled deposition of calcium carbonate within a framework of macromolecules that are secreted from the dorsal mantle epithelium. Despite its deep conservation within Mollusca, the mantle is capable of producing an incredible diversity of shell patterns, and macro- and micro-architectures. Here we review recent developments within the field of molluscan biomineralization, focusing on the genes expressed in the mantle that encode secreted proteins. The so-called mantle secretome appears to regulate shell deposition and patterning and in some cases becomes part of the shell matrix. Recent transcriptomic and proteomic studies have revealed marked differences in the mantle secretomes of even closely-related molluscs; these typically exceed expected differences based on characteristics of the external shell. All mantle secretomes surveyed to date include novel genes encoding lineage-restricted proteins and unique combinations of co-opted ancient genes. A surprisingly large proportion of both ancient and novel secreted proteins containing simple repetitive motifs or domains that are often modular in construction. These repetitive low complexity domains (RLCDs) appear to further promote the evolvability of the mantle secretome, resulting in domain shuffling, expansion and loss. RLCD families further evolve via slippage and other mechanisms associated with repetitive sequences. As analogous types of secreted proteins are expressed in biomineralizing tissues in other animals, insights into the evolution of the genes underlying molluscan shell formation may be applied more broadly to understanding the evolution of metazoan biomineralization.

Application of molluscan analyses to the reconstruction of past environmental conditions in estuaries: Chapter 15

USGS Publications Warehouse

Wingard, G. Lynn; Surge, Donna

2017-01-01

Molluscs possess a number of attributes that make them an excellent source of past environmental conditions in estuaries: they are common in estuarine environments; they typically have hard shells and are usually well preserved in sediments; they are relatively easy to detect in the environment; they have limited mobility as adults; they grow by incremental addition of layers to their shells; and they are found in all the major environments surrounding estuaries—terrestrial, freshwater, brackish, and marine waters. Analysis of molluscan assemblages can contribute information about past changes in sea level, climate, land use patterns, anthropogenic alterations, salinity, and other parameters of the benthic habitat and water chemistry within the estuary. High-resolution (from less than a day to annual) records of changes in environmental parameters can be obtained by analyzing the incremental growth layers in mollusc shells (sclerochronology). The shell layers retain information on changes in water temperature, salinity, seasonality, climate, river discharge, productivity, pollution and human activity. Isotopic analyses of mollusc shell growth layers can be problematic in estuaries where water temperatures and isotopic ratios can vary simultaneously; however, methods are being developed to overcome these problems. In addition to sclerochronology, molluscs are important to Holocene and Pleistocene estuarine palaeoenvironmental studies because of their use in the development of age models through radiocarbon dating, amino acid racemization, uranium-thorium series dating, and electron spin resonance (ESR) dating.

Complex Responses of Intertidal Molluscan Embryos to a Warming and Acidifying Ocean in the Presence of UV Radiation

PubMed Central

Davis, Andrew R.; Coleman, Daniel; Broad, Allison; Byrne, Maria; Dworjanyn, Symon A.; Przeslawski, Rachel

2013-01-01

Climate change and ocean acidification will expose marine organisms to synchronous multiple stressors, with early life stages being potentially most vulnerable to changing environmental conditions. We simultaneously exposed encapsulated molluscan embryos to three abiotic stressors—acidified conditions, elevated temperate, and solar UV radiation in large outdoor water tables in a multifactorial design. Solar UV radiation was modified with plastic filters, while levels of the other factors reflected IPCC predictions for near-future change. We quantified mortality and the rate of embryonic development for a mid-shore littorinid, Bembicium nanum, and low-shore opisthobranch, Dolabrifera brazieri. Outcomes were consistent for these model species with embryos faring significantly better at 26°C than 22°C. Mortality sharply increased at the lowest temperature (22°C) and lowest pH (7.6) examined, producing a significant interaction. Under these conditions mortality approached 100% for each species, representing a 2- to 4-fold increase in mortality relative to warm (26°C) non-acidified conditions. Predictably, development was more rapid at the highest temperature but this again interacted with acidified conditions. Development was slowed under acidified conditions at the lowest temperature. The presence of UV radiation had minimal impact on the outcomes, only slowing development for the littorinid and not interacting with the other factors. Our findings suggest that a warming ocean, at least to a threshold, may compensate for the effects of decreasing pH for some species. It also appears that stressors will interact in complex and unpredictable ways in a changing climate. PMID:23405238

21 CFR 1240.3 - General definitions.

Code of Federal Regulations, 2011 CFR

2011-04-01

... characteristics of milk, cream, or whey by using enzymes, solvents, heat, pressure, cooling, vacuum, genetic... that includes activities such as classification of molluscan shellfish growing areas, enforcement of...

Characterisation of Reproduction-Associated Genes and Peptides in the Pest Land Snail, Theba pisana.

PubMed

Stewart, Michael J; Wang, Tianfang; Harding, Bradley I; Bose, U; Wyeth, Russell C; Storey, Kenneth B; Cummins, Scott F

2016-01-01

Increased understanding of the molecular components involved in reproduction may assist in understanding the evolutionary adaptations used by animals, including hermaphrodites, to produce offspring and retain a continuation of their lineage. In this study, we focus on the Mediterranean snail, Theba pisana, a hermaphroditic land snail that has become a highly invasive pest species within agricultural areas throughout the world. Our analysis of T. pisana CNS tissue has revealed gene transcripts encoding molluscan reproduction-associated proteins including APGWamide, gonadotropin-releasing hormone (GnRH) and an egg-laying hormone (ELH). ELH isoform 1 (ELH1) is known to be a potent reproductive peptide hormone involved in ovulation and egg-laying in some aquatic molluscs. Two other non-CNS ELH isoforms were also present in T. pisana (Tpi-ELH2 and Tpi-ELH3) within the snail dart sac and mucous glands. Bioactivity of a synthetic ELH1 on sexually mature T. pisana was confirmed through bioassay, with snails showing ELH1-induced egg-laying behaviours, including soil burrowing and oviposition. In summary, this study presents a detailed molecular analysis of reproductive neuropeptide genes in a land snail and provides a foundation for understanding ELH function.

Down-core changes in molluscan death assemblages at Panzano Bay, an impacted area in the northern Adriatic Sea

NASA Astrophysics Data System (ADS)

Haselmair, Alexandra; Gallmetzer, Ivo; Stachowitsch, Michael; Tomasovych, Adam; Zuschin, Martin

2016-04-01

We use a historical ecology approach to shed light on the environmental history of the northern Adriatic Sea over the last hundreds to thousands of years. We focus on down-core changes in molluscan death assemblages, which serve as proxies for ecological shifts over time. The northern Adriatic Sea is particularly suited to study ecosystem modification under human pressure because it is among the most degraded marine ecosystems worldwide. We chose a sampling station in Panzano Bay, close the Isonzo River mouth and not far from the major industrial harbours of Trieste (Italy) and Koper (Slovenia), and traced down-core changes in molluscan community structure in correlation to major anthropogenic impacts that occurred here during the last centuries. Five sediment cores (1.5 m in length and diameters of 90 and 160 mm) were taken at a water depth of 12 m. We analysed grain size composition, the concentration of heavy metals and organic pollutants, and radiometrically dated the sediment using 210Pb. Furthermore, we dated shells of the abundant bivalve species Corbula gibba using 14C calibrated amino acid-racemisation (AAR). The whole molluscan community in the cores was analysed for species composition, abundance, taxonomic similarity, evidence for ecological interactions (i.e., frequencies of drilling predation) and taphonomic conditions of shells. The granulometric analysis shows that silt and clay dominate equally throughout the cores. Radiometric sediment dating revealed an average sedimentation rate of 2.5 mm/yr during the last 120 years. Shell dating points to a comparable overall core age, with only a few shell specimens being older than 500 years in the deepest core layer. In total, 10,452 mollusc individuals were analysed and 104 species identified. The most abundant bivalve species are Kurtiella bidentata, Corbula gibba and Abra nitida. Turritella communis and Nassarius pygmaeus are the most frequent gastropod species. Down-core changes in species composition and molluscan abundance are conspicuous, with a high peak in abundance between 20 and 50 cm depth and another peak in the lower part of the core. These trends in community composition correlate with the concentration curves of several heavy metals (Pb, Zn, Hg) and polycyclic aromatic hydrocarbons. In the deeper core horizons, a high mercury peak signals a massive and century-long contamination caused be the Idrija mercury mine located up the Isonzo River. In the uppermost 20 cm of sediment, Pb, Zn and PAHs display high concentrations and are accompanied by a decrease of formerly abundant species (e.g. Kurtiella bidentata) and an increase of a few opportunists. Our study shows how pollution, among other factors, affects individual mollusc species and leads to marked and long-lasting changes on the community level.

Discordance between living and death assemblages as evidence for anthropogenic ecological change

PubMed Central

Kidwell, Susan M.

2007-01-01

Mismatches between the composition of a time-averaged death assemblage (dead remains sieved from the upper mixed-zone of the sedimentary column) and the local living community are typically attributed to natural postmortem processes. However, statistical analysis of 73 molluscan data sets from estuaries and lagoons reveals significantly poorer average “live-dead agreement” in settings of documented anthropogenic eutrophication (AE) than in areas where AE and other human impacts are negligible. Taxonomic similarity of paired live and dead species lists declines steadily among areas as a function of AE severity, and, for data sets comprising only adults, rank-order agreement in species abundance drops where AE is suspected. The observed live-dead differences in composition are consistent with eutrophication (anomalous abundance of seagrass-dwellers and/or scarcity of organic-loving species in the death assemblage), suggesting compositional inertia of death assemblages to recent environmental change. Molluscan data sets from open shelf settings (n = 34) also show higher average live-dead discordance in areas of AE. These results indicate that (i) live-dead discordance in surficial grab samples provides valuable evidence for strong anthropogenic modification of benthic communities, (ii) actualistic estimates of the ecological fidelity of molluscan death assemblages tend to be erroneously pessimistic when conducted in nonpristine settings, and (iii) based on their high fidelity in pristine study areas, death assemblages are a promising means of reconstructing otherwise elusive preimpact ecological baselines from sedimentary records. PMID:17965231

Molluscan successions from the Holocene tufa of St Germain-le-Vasson, Normandy (France) and their biogeographical significance

NASA Astrophysics Data System (ADS)

Limondin-Lozouet, Nicole; Preece, Richard C.

2004-01-01

A detailed molluscan succession from a 10 m thick deposit of Holocene tufa at St Germain-le-Vasson, Normandy, provides the most complete record from northern France and has shed new light on the historical biogeography of several species of land snail. The succession has been reconstructed from four profiles and a chronology provided by accelerator mass spectrometry radiocarbon dating of charcoal, wood and shell. The onset of tufa formation occurred after 9700+/-90 yr BP and persisted until 4213+/-77 yr BP. The tufa appears to have accumulated at a remarkably constant rate (14.4-16.5 cm 100 yr-1), except for the upper levels, where the rate increases fourfold. The succession has been divided into six local molluscan zones. An early assemblage consisting of ecologically tolerant species and those indicative of marshy grassland is replaced by a sequence of shade-demanding taxa, reflecting the encroachment of woodland. Shaded conditions persist until the end of the sequence but the most hygrophilous elements decline after 5422+/-60 yr BP (zone 5), a change also reflected in the tufa lithology by the development of silty grey horizons. Notable species recovered from the tufa include Acicula fusca, Vertigo substriata, V. alpestris, V. moulinsiana (all rare or unknown living in northern France). Hygromia limbata, a twentieth century introduction to Britain, was previously thought to be a relatively recent arrival in northern France, but its record at St Germain shows that it has been present in Normandy since 6500 yr BP. Azeca goodalli, another shade-demanding species, appeared at St Germain much later, just after 4420+/-65 yr BP. Several other species present in the tufa, such as Pomatias elegans, no longer live on the site, adding to the evidence for a distributional decline in Normandy and elsewhere. Perhaps the most noteworthy record is that of Leiostyla anglica, between about 8500 yr BP and 5000 yr BP, because this constitutes its only Holocene occurrence from mainland Europe. Following this discovery it seems likely that further Holocene sites with L. anglica may be found along the western seaboard of Europe connecting populations in Iberia with those of the British Isles. Copyright

A multi-gene phylogeny of Cephalopoda supports convergent morphological evolution in association with multiple habitat shifts in the marine environment

PubMed Central

2012-01-01

Background The marine environment is comprised of numerous divergent organisms living under similar selective pressures, often resulting in the evolution of convergent structures such as the fusiform body shape of pelagic squids, fishes, and some marine mammals. However, little is known about the frequency of, and circumstances leading to, convergent evolution in the open ocean. Here, we present a comparative study of the molluscan class Cephalopoda, a marine group known to occupy habitats from the intertidal to the deep sea. Several lineages bear features that may coincide with a benthic or pelagic existence, making this a valuable group for testing hypotheses of correlated evolution. To test for convergence and correlation, we generate the most taxonomically comprehensive multi-gene phylogeny of cephalopods to date. We then create a character matrix of habitat type and morphological characters, which we use to infer ancestral character states and test for correlation between habitat and morphology. Results Our study utilizes a taxonomically well-sampled phylogeny to show convergent evolution in all six morphological characters we analyzed. Three of these characters also correlate with habitat. The presence of an autogenic photophore (those relying upon autonomous enzymatic light reactions) is correlated with a pelagic habitat, while the cornea and accessory nidamental gland correlate with a benthic lifestyle. Here, we present the first statistical tests for correlation between convergent traits and habitat in cephalopods to better understand the evolutionary history of characters that are adaptive in benthic or pelagic environments, respectively. Discussion Our study supports the hypothesis that habitat has influenced convergent evolution in the marine environment: benthic organisms tend to exhibit similar characteristics that confer protection from invasion by other benthic taxa, while pelagic organisms possess features that facilitate crypsis and communication in an environment lacking physical refuges. Features that have originated multiple times in distantly related lineages are likely adaptive for the organisms inhabiting a particular environment: studying the frequency and evolutionary history of such convergent characters can increase understanding of the underlying forces driving ecological and evolutionary transitions in the marine environment. PMID:22839506

Austropeplea ollula (Pulmonata: Lymnaeidae): A new molluscan intermediate host of a human intestinal fluke, Echinostoma cinetorchis (Trematoda: Echinostomatidae) in Korea

PubMed Central

Jung, Younghun; Park, Yun-Kyu; Hwang, Myung-Ki

2001-01-01

Three freshwater snail species of the family Lymnaeidae have been reported from Korea, Radix auricularia coreana, Austropeplea ollula and Fossaria truncatula. Out of 3 lymnaeid snail species, A. ollula was naturally infected with the Echinostoma cinetorchis cercariae (infection rate = 0.7%). In the experiments with the laboratory-bred snails, F. truncatula as well as A. ollula was also susceptible to the E. cinetorchis miracidia with infection rates of 25% and 40%, respectively. All of three lymnaeid snail species exposed to the E. cinetorchis cercariae were infected with the E. cinetorchis metacercariae. It is evident that A. ollula acts as the first molluscan intermediate host of E. cinetorchis in Korea, and F. truncatula may be a possible candidate for the first intermediate host of this intestinal fluke. Also, three lymnaeid snail species targeted were experimentally infected with E. cinetorchis metacercariae. PMID:11590915

Spatial distribution of epibenthic molluscs on a sandstone reef in the Northeast of Brazil.

PubMed

Martinez, A S; Mendes, L F; Leite, T S

2012-05-01

The present study investigated the distribution and abundance of epibenthic molluscs and their feeding habits associated to substrate features (coverage and rugosity) in a sandstone reef system in the Northeast of Brazil. Rugosity, low coral cover and high coverage of zoanthids and fleshy alga were the variables that influenced a low richness and high abundance of a few molluscan species in the reef habitat. The most abundant species were generalist carnivores, probably associated to a lesser offer and variability of resources in this type of reef system, when compared to the coral reefs. The results found in this study could reflect a normal characteristic of the molluscan community distribution in sandstone reefs, with low coral cover, or could indicate a degradation state of this habitat if it is compared to coral reefs, once that the significantly high coverage of fleshy alga has been recognized as a negative indicator of reef ecosystems health.

Comparative molecular analysis of evolutionarily distant glyceraldehyde-3-phosphate dehydrogenase from Sardina pilchardus and Octopus vulgaris.

PubMed

Baibai, Tarik; Oukhattar, Laila; Mountassif, Driss; Assobhei, Omar; Serrano, Aurelio; Soukri, Abdelaziz

2010-12-01

The NAD(+)-dependent cytosolic glyceraldehyde-3-phosphate dehydrogenase (GAPDH, EC 1.2.1.12), which is recognized as a key to central carbon metabolism in glycolysis and gluconeogenesis and as an important allozymic polymorphic biomarker, was purified from muscles of two marine species: the skeletal muscle of Sardina pilchardus Walbaum (Teleost, Clupeida) and the incompressible arm muscle of Octopus vulgaris (Mollusca, Cephalopoda). Comparative biochemical studies have revealed that they differ in their subunit molecular masses and in pI values. Partial cDNA sequences corresponding to an internal region of the GapC genes from Sardina and Octopus were obtained by polymerase chain reaction using degenerate primers designed from highly conserved protein motifs. Alignments of the deduced amino acid sequences were used to establish the 3D structures of the active site of two enzymes as well as the phylogenetic relationships of the sardine and octopus enzymes. These two enzymes are the first two GAPDHs characterized so far from teleost fish and cephalopod, respectively. Interestingly, phylogenetic analyses indicated that the sardina GAPDH is in a cluster with the archetypical enzymes from other vertebrates, while the octopus GAPDH comes together with other molluscan sequences in a distant basal assembly closer to bacterial and fungal orthologs, thus suggesting their different evolutionary scenarios.

Distribution of heavy metals in internal organs and tissues of Korean molluscan shellfish and potential risk to human health.

PubMed

Mok, Jong Soo; Kwon, Ji Young; Son, Kwang Tae; Choi, Woo Seok; Kim, Poong Ho; Lee, Tae Seek; Kim, Ji Hoe

2015-09-01

Molluscan shellfish (gastropods and bivalves) were collected from major fish markets on the Korean coast and analyzed for mercury by direct Hg analyzer and for other metals, such as cadmium, lead, chromium, silver, nickel, copper and zinc, using inductively coupled plasma mass spectrometry. Distribution of heavy metals in muscles, internal organs and whole tissues were determined and a potential risk assessment was conducted to evaluate their hazard for human consumption. Heavy metals were accumulated significantly higher (P < 0.05) in internal organs than in muscles for all species. The mean Cd level, which had the highest level of three hazardous metals (Cd, Pb, and Hg) in all internal-organ samples were above the regulatory limit of Korea and the mean level in whole tissue samples of the selected gastropod species, bay scallop and comb pen shell, exceeded the limit (except in a few cases). The sum of the estimated dietary intake of Cd, Pb and Hg for each part of all tested species accounted for 1.59-16.94, 0.02-0.36, and 0.07-0.16% respectively, of the provisional tolerable daily intake adopted by the Joint FAO/WHO Expert Committee on Food Additives. The hazard index for each part of gastropods and bivalves was below 1.0, however, the maximum HI for internal organs of all analysed species was quite high (0.71). These results suggest that consumption of flesh after removing the internal organs of some molluscan shellfish (all gastropod species, bay scallop and comb pen shell) is a suitable way for reducing Cd exposure.

Mechanisms of Anesthetic Action and Neurotoxicity: Lessons from Molluscs

PubMed Central

Armstrong, Ryden; Riaz, Saba; Hasan, Sean; Iqbal, Fahad; Rice, Tiffany; Syed, Naweed

2018-01-01

Anesthesia is a prerequisite for most surgical procedures in both animals and humans. Significant strides have been made in search of effective and safer compounds that elicit rapid induction and recovery from anesthesia. However, recent studies have highlighted possible negative effects of several anesthetic agents on the developing brain. The precise nature of this cytotoxicity remains to be determined mainly due to the complexity and the intricacies of the mammalian brain. Various invertebrates have contributed significantly toward our understanding of how both local and general anesthetics affect intrinsic membrane and synaptic properties. Moreover, the ability to reconstruct in vitro synapses between individually identifiable pre- and postsynaptic neurons is a unique characteristic of molluscan neurons allowing us to ask fundamental questions vis-à-vis the long-term effects of anesthetics on neuronal viability and synaptic connectivity. Here, we highlight some of the salient aspects of various molluscan organisms and their contributions toward our understanding of the fundamental mechanisms underlying the actions of anesthetic agents as well as their potential detrimental effects on neuronal growth and synaptic connectivity. We also present some novel preliminary data regarding a newer anesthetic agent, dexmedetomidine, and its effects on synaptic transmission between Lymnaea neurons. The findings presented here underscore the importance of invertebrates for research in the field of anesthesiology while highlighting their relevance to both vertebrates and humans. PMID:29410627

Enteric virus and vibrio contamination of shellfish: intervention strategies

USDA-ARS?s Scientific Manuscript database

INTRODUCTION. Molluscan shellfish include oysters, clams, mussels, and cockles, which can cause illnesses from a variety of human pathogens. Enteric viruses, like norovirus and hepatitis A virus, are generally transmitted to shellfish through fecal contamination of shellfish harvesting areas, alth...

Identification and qualification of 500 nuclear, single-copy, orthologous genes for the Eupulmonata (Gastropoda) using transcriptome sequencing and exon capture.

PubMed

Teasdale, Luisa C; Köhler, Frank; Murray, Kevin D; O'Hara, Tim; Moussalli, Adnan

2016-09-01

The qualification of orthology is a significant challenge when developing large, multiloci phylogenetic data sets from assembled transcripts. Transcriptome assemblies have various attributes, such as fragmentation, frameshifts and mis-indexing, which pose problems to automated methods of orthology assessment. Here, we identify a set of orthologous single-copy genes from transcriptome assemblies for the land snails and slugs (Eupulmonata) using a thorough approach to orthology determination involving manual alignment curation, gene tree assessment and sequencing from genomic DNA. We qualified the orthology of 500 nuclear, protein-coding genes from the transcriptome assemblies of 21 eupulmonate species to produce the most complete phylogenetic data matrix for a major molluscan lineage to date, both in terms of taxon and character completeness. Exon capture targeting 490 of the 500 genes (those with at least one exon >120 bp) from 22 species of Australian Camaenidae successfully captured sequences of 2825 exons (representing all targeted genes), with only a 3.7% reduction in the data matrix due to the presence of putative paralogs or pseudogenes. The automated pipeline Agalma retrieved the majority of the manually qualified 500 single-copy gene set and identified a further 375 putative single-copy genes, although it failed to account for fragmented transcripts resulting in lower data matrix completeness when considering the original 500 genes. This could potentially explain the minor inconsistencies we observed in the supported topologies for the 21 eupulmonate species between the manually curated and 'Agalma-equivalent' data set (sharing 458 genes). Overall, our study confirms the utility of the 500 gene set to resolve phylogenetic relationships at a range of evolutionary depths and highlights the importance of addressing fragmentation at the homolog alignment stage for probe design. © 2016 John Wiley & Sons Ltd.

Functional hypervariability and gene diversity of cardioactive neuropeptides.

PubMed

Möller, Carolina; Melaun, Christian; Castillo, Cecilia; Díaz, Mary E; Renzelman, Chad M; Estrada, Omar; Kuch, Ulrich; Lokey, Scott; Marí, Frank

2010-12-24

Crustacean cardioactive peptide (CCAP) and related peptides are multifunctional regulatory neurohormones found in invertebrates. We isolated a CCAP-related peptide (conoCAP-a, for cone snail CardioActive Peptide) and cloned the cDNA of its precursor from venom of Conus villepinii. The precursor of conoCAP-a encodes for two additional CCAP-like peptides: conoCAP-b and conoCAP-c. This multi-peptide precursor organization is analogous to recently predicted molluscan CCAP-like preprohormones, and suggests a mechanism for the generation of biological diversification without gene amplification. While arthropod CCAP is a cardio-accelerator, we found that conoCAP-a decreases the heart frequency in Drosophila larvae, demonstrating that conoCAP-a and CCAP have opposite effects. Intravenous injection of conoCAP-a in rats caused decreased heart frequency and blood pressure in contrast to the injection of CCAP, which did not elicit any cardiac effect. Perfusion of rat ventricular cardiac myocytes with conoCAP-a decreased systolic calcium, indicating that conoCAP-a cardiac negative inotropic effects might be mediated via impairment of intracellular calcium trafficking. The contrasting cardiac effects of conoCAP-a and CCAP indicate that molluscan CCAP-like peptides have functions that differ from those of their arthropod counterparts. Molluscan CCAP-like peptides sequences, while homologous, differ between taxa and have unique sequences within a species. This relates to the functional hypervariability of these peptides as structure activity relationship studies demonstrate that single amino acids variations strongly affect cardiac activity. The discovery of conoCAPs in cone snail venom emphasizes the significance of their gene plasticity to have mutations as an adaptive evolution in terms of structure, cellular site of expression, and physiological functions.

Fidelity of life and death molluscan assemblages from carbonate tidal flats in the Persian (Arabian) Gulf

NASA Astrophysics Data System (ADS)

García-Ramos, Diego A.; Albano, Paolo G.; Harzhauser, Mathias; Piller, Werner E.; Zuschin, Martin

2016-04-01

Live-dead (LD) studies aim to help understand how faithfully fossil assemblages can be used to quantitatively infer the structure of the original living communities that generated them. To this purpose, LD comparisons have been conducted in different terrestrial and aquatic environments to assess how environment-specific differences in quality and intensity of taphonomic factors affect LD fidelity. In sub-tropical and tropical settings, most LD studies have focused on hard substrates or seagrass bottoms. Here we present results on molluscan assemblages from soft carbonate sediments in tidal flats of the Persian (Arabian) Gulf (Indo-West Pacific biogeographic province). We analyzed a total of 7193 mollusks collected from six sites comprising time-averaged death assemblages (DAs) and snapshot living assemblages (LAs). All analyses were performed at site and at habitat scales after correcting for sample-size differences. We found a good match in proportional abundance and a notable mismatch in species composition. In fact, species richness in DAs is 6 times larger than in LAs at site scale, and 4 times at habitat scale. Additionally, we found a good fidelity of evenness, and rank abundance of feeding guilds. Other studies have shown that molluscan DAs from subtidal carbonate environments can display lower time-averaging than those from siliciclastic environments due to high rates of shell loss to bioerosion and dissolution. For our case study of tidal flat carbonate settings, we interpret that despite temporal autocorrelation (good fidelity of proportional abundance), substantial differences in species richness and composition can be explained by early cementation, lateral mixing, intense bioturbation and moderate sedimentation rates. Our results suggest that tidal flat carbonate environments can potentially lead to a wider window of time-averaging in comparison with subtidal carbonate settings.

Diversity of macrofaunal Mollusca of the abyssal Vema Fracture Zone and hadal Puerto Rico Trench, Tropical North Atlantic

NASA Astrophysics Data System (ADS)

Linse, Katrin; Schwabe, Enrico

2018-02-01

While biodiversity patterns of Atlantic deep-sea bivalves and gastropods have served as model taxa for setting global latitudinal and bathymetric hypotheses, less is known on abyssal, amphi-Atlantic molluscan assemblage compositions. The Vema-TRANSIT expedition sampled 17 stations in the Vema Fracture Zone (VFZ) and the Puerto Rico Trench (PRT) by epibenthic sledge. These samples comprised a total of 1333 specimens and 64 morphospecies of the classes Caudofoveata (7 species), Solenogastres (7 spp.), Bivalvia (22 spp.), Gastropoda (24 spp.), and Scaphopoda (4 spp.) while Cephalopoda, Monoplacophora and Polyplacophora were absent. The majority of species was rare with 21 uniques (32.8% of all species) and 10 duplicates (15.6% of all species) and of these 15 (48% of rare/23.4% of all species) morphospecies were singletons and 8 (25.8% of rare/12.5% of all species) morphospecies were doubletons. Overall bivalves (686 specimens) were most abundant, followed by scaphopods (314 spec.), while solenogastres (180 spec.), caudofoveates (86 spec.) and gastropods (67 spec.) were less abundant. The abyssal macro-molluscan species composition did not vary significantly between the eastern and western Atlantic sides of the VFZ while abundances standardized to 1000 m2 trawled area were higher on the eastern side. The abyssal PRT stations resembled the VFZ ones in species composition and abundances, in the latter the eastern VFZ. The hadal PRT differed in species composition from the abyssal VFZ and PRT and abundances were similarly low like the western VFZ. The Mid-Atlantic Ridge appeared not to be a barrier for the dispersal of the mostly lecitotrophic or plankotrophic larval stages of the reported molluscan species in this study.

Molluscan assemblages on coral reefs and associated hard substrata in the northern Red Sea

NASA Astrophysics Data System (ADS)

Zuschin, M.; Hohenegger, J.; Steininger, F.

2001-09-01

Information on spatial variability and distribution patterns of organisms in coral reef environments is necessary to evaluate the increasing anthropogenic disturbance of marine environments (Richmond 1993; Wilkinson 1993; Dayton 1994). Therefore different types of subtidal, reef-associated hard substrata (reef flats, reef slopes, coral carpets, coral patches, rock grounds), each with different coral associations, were investigated to determine the distribution pattern of molluscs and their life habits (feeding strategies and substrate relations). The molluscs were strongly dominated by taxa with distinct relations to corals, and five assemblages were differentiated. The Dendropoma maxima assemblage on reef flats is a discrete entity, strongly dominated by this encrusting and suspension-feeding gastropod. All other assemblages are arranged along a substrate gradient of changing coral associations and potential molluscan habitats. The Coralliophila neritoidea- Barbatia foliata assemblage depends on the presence of Porites and shows a dominance of gastropods feeding on corals and of bivalves associated with living corals. The Chamoidea- Cerithium spp. assemblage on rock grounds is strongly dominated by encrusting bivalves. The Drupella cornus-Pteriidae assemblage occurs on Millepora- Acropora reef slopes and is strongly dominated by bivalves associated with living corals. The Barbatia setigera- Ctenoides annulata assemblage includes a broad variety of taxa, molluscan life habits and bottom types, but occurs mainly on faviid carpets and is transitional among the other three assemblages. A predicted degradation of coral coverage to rock bottoms due to increasing eutrophication and physical damage in the study area (Riegl and Piller 2000) will result in a loss of coral-associated molluscs in favor of bivalve crevice dwellers in dead coral heads and of encrusters on dead hard substrata.

Identification and Functional Characterization of a Novel Acetylcholine-binding Protein from the Marine Annelid Capitella teleta

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCormack, T.; Petrovich,; Mercier, K

2010-01-01

We identified a homologue of the molluscan acetylcholine-binding protein (AChBP) in the marine polychaete Capitella teleta, from the annelid phylum. The amino acid sequence of C. teleta AChBP (ct-AChBP) is 21-30% identical with those of known molluscan AChBPs. Sequence alignments indicate that ct-AChBP has a shortened Cys loop compared to other Cys loop receptors, and a variation on a conserved Cys loop triad, which is associated with ligand binding in other AChBPs and nicotinic ACh receptor (nAChR) {alpha} subunits. Within the D loop of ct-AChBP, a conserved aromatic residue (Tyr or Trp) in nAChRs and molluscan AChBPs, which has beenmore » implicated directly in ligand binding, is substituted with an isoleucine. Mass spectrometry results indicate that Asn122 and Asn216 of ct-AChBP are glycosylated when expressed using HEK293 cells. Small-angle X-ray scattering data suggest that the overall shape of ct-AChBP in the apo or unliganded state is similar to that of homologues with known pentameric crystal structures. NMR experiments show that acetylcholine, nicotine, and {alpha}-bungarotoxin bind to ct-AChBP with high affinity, with KD values of 28.7 {micro}M, 209 nM, and 110 nM, respectively. Choline bound with a lower affinity (K{sub D} = 163 {micro}M). Our finding of a functional AChBP in a marine annelid demonstrates that AChBPs may exhibit variations in hallmark motifs such as ligand-binding residues and Cys loop length and shows conclusively that this neurotransmitter binding protein is not limited to the phylum Mollusca.« less

Functional Hypervariability and Gene Diversity of Cardioactive Neuropeptides*

PubMed Central

Möller, Carolina; Melaun, Christian; Castillo, Cecilia; Díaz, Mary E.; Renzelman, Chad M.; Estrada, Omar; Kuch, Ulrich; Lokey, Scott; Marí, Frank

2010-01-01

Crustacean cardioactive peptide (CCAP) and related peptides are multifunctional regulatory neurohormones found in invertebrates. We isolated a CCAP-related peptide (conoCAP-a, for cone snail CardioActive Peptide) and cloned the cDNA of its precursor from venom of Conus villepinii. The precursor of conoCAP-a encodes for two additional CCAP-like peptides: conoCAP-b and conoCAP-c. This multi-peptide precursor organization is analogous to recently predicted molluscan CCAP-like preprohormones, and suggests a mechanism for the generation of biological diversification without gene amplification. While arthropod CCAP is a cardio-accelerator, we found that conoCAP-a decreases the heart frequency in Drosophila larvae, demonstrating that conoCAP-a and CCAP have opposite effects. Intravenous injection of conoCAP-a in rats caused decreased heart frequency and blood pressure in contrast to the injection of CCAP, which did not elicit any cardiac effect. Perfusion of rat ventricular cardiac myocytes with conoCAP-a decreased systolic calcium, indicating that conoCAP-a cardiac negative inotropic effects might be mediated via impairment of intracellular calcium trafficking. The contrasting cardiac effects of conoCAP-a and CCAP indicate that molluscan CCAP-like peptides have functions that differ from those of their arthropod counterparts. Molluscan CCAP-like peptides sequences, while homologous, differ between taxa and have unique sequences within a species. This relates to the functional hypervariability of these peptides as structure activity relationship studies demonstrate that single amino acids variations strongly affect cardiac activity. The discovery of conoCAPs in cone snail venom emphasizes the significance of their gene plasticity to have mutations as an adaptive evolution in terms of structure, cellular site of expression, and physiological functions. PMID:20923766

Molluscan shell communities: a window into the ecological history of the northern Adriatic Sea

NASA Astrophysics Data System (ADS)

Gallmetzer, Ivo; Haselmair, Alexandra; Tomasovych, Adam; Stachowitsch, Michael; Zuschin, Martin

2015-04-01

The historical ecology approach used in the present study sheds light on the younger ecological history of the northern Adriatic Sea, targeting the period of the last 500 to 1500 years. We focus on down-core changes in molluscan death assemblages, where differences between community structures serve as a proxy for ecological shifts over time. The northern Adriatic Sea, with its densely populated shoreline, is among the most degraded marine ecosystems worldwide and is therefore particularly suited to study ecosystem modification under human pressure. Multiple cores of 1.5 m length and diameters of 90 and 160 mm were taken at seven sampling stations throughout the northern Adriatic Sea, covering different sediment types, nutrient conditions and degrees of exploitation. For the mollusc analyses, the cores were sliced into smaller subsamples and analysed for species composition, abundance, taxonomic similarity, evidence for ecological interactions (i.e., frequencies of drilling predation) and taphonomic condition of shells. Sediment analyses include granulometry and radiometric sediment dating using Pb 210. Sediment age analysis revealed one-order-of-magnitude differences in sedimentation rates between stations (34 mm/yr at the Po delta, Italy, 1.5 mm/yr at Brijuni islands, Croatia). In total, 114 bivalve and 112 gastropod species were recorded. Bivalve assemblages showed significant interregional differences that are strongly correlated with sedimentation rates and sediment composition. Down-core changes in molluscan communities are conspicuous in all cores, particularly in the uppermost core sections. This information, together with radiometric shell dating for selected species, helps to specify the timing of major ecological changes in the past and define pristine benthic communities as references for future conservation and management efforts.

High pressure processing of bivalve shellfish and HPP's potential use as a virus intervention

USDA-ARS?s Scientific Manuscript database

Bivalve shellfish readily bioconcentrate pathogenic microbes and substance, such as algal and dinoflagulate toxins, fecal viruses and bacteria, and naturally present vibrio bacteria. High pressure processing (HPP) is currently used as an intervention for Vibrio vulnificus bacteria within molluscan ...

The Regulation of Catch in Molluscan Muscle

PubMed Central

Twarog, Betty M.

1967-01-01

Molluscan catch muscles are smooth muscles. As with mammalian smooth muscles, there is no transverse ordering of filaments or dense bodies. In contrast to mammalian smooth muscles, two size ranges of filaments are present. The thick filaments are long as well as large in diameter and contain paramyosin. The thin filaments contain actin and appear to run into and join the dense bodies. Vesicles are present which may be part of a sarcoplasmic reticulum. Neural activation of contraction in Mytilus muscle is similar to that observed in mammalian smooth muscles, and in some respects to frog striated muscle. The relaxing nerves, which reduce catch, are unique to catch muscles. 5-Hydroxytryptamine, which appears to mediate relaxation, specifically blocks catch tension but increases the ability of the muscle to fire spikes. It is speculated that Mytilus muscle actomyosin is activated by a Ca++-releasing mechanism, and that 5-hydroxytryptamine may reduce catch and increase excitability by influencing the rate of removal of intracellular free Ca++. PMID:6050594

Application of polymerase chain reaction for detection of Vibrio parahaemolyticus associated with tropical seafoods and coastal environment.

PubMed

Dileep, V; Kumar, H S; Kumar, Y; Nishibuchi, M; Karunasagar, Indrani; Karunasagar, Iddya

2003-01-01

To study the incidence of Vibrio parahaemolyticus in seafoods, water and sediment by molecular techniques vs conventional microbiological methods. Of 86 samples analysed, 28 recorded positive for V. parahaemolyticus by conventional microbiological method, while 53 were positive by the toxR-targeted PCR, performed directly on enrichment broth lysates. While one sample of molluscan shellfish was positive for tdh gene, trh gene was detected in three enrichment broths of molluscan shellfish. Direct application of PCR to enrichment broths will be useful for the rapid and sensitive detection of potentially pathogenic strains of V. parahemolyticus in seafoods. Vibrio parahaemolyticus is an important human pathogen responsible for food-borne gastroenteritis world-wide. As, both pathogenic and non-pathogenic strains of V. parahaemolyticus exist in the seafood, application of PCR specific for the virulence genes (tdh & trh) will help in detection of pathogenic strains of V. parahaemolyticus and consequently reduce the risk of food-borne illness.

Sedimentology, palaeoecology and geochronology of Last Interglacial deposits from Deeping St James, Lincolnshire, England

NASA Astrophysics Data System (ADS)

Keen, D. H.; Bateman, M. D.; Coope, G. R.; Field, M. H.; Langford, H. E.; Merry, J. S.; Mighall, T. M.

1999-08-01

Pollen, plant macrofossil, molluscan and coleopteran data from organic muds below the low terrace of the River Welland at Deeping St James, Lincolnshire indicate deposition in the mixed oak forest phase of a Late Pleistocene interglacial. Coleopteran and molluscan data suggest summer temperatures up to 4°C warmer than at present in eastern England, and plant macrofossil material suggests a climate more continental than that of Britain in the Holocene. No direct analogue of this biota, however, exists currently in Europe. Biostratigraphical indications from the pollen coleoptera and Mollusca suggest an age in the Ipswichian Interglacial. Thermoluminescence dates between 120 ka and 75 ka and amino-acid ratios with a mean of 0.11 show that deposition of the sediments took place during Oxygen Isotope Stage 5. This accurate dating of a partial Ipswichian succession allows discussion of the ages of a number of other interglacial sites in eastern England of assumed Ipswichian age.

Evaluation of the efficacy of twelve mitochondrial protein-coding genes as barcodes for mollusk DNA barcoding.

PubMed

Yu, Hong; Kong, Lingfeng; Li, Qi

2016-01-01

In this study, we evaluated the efficacy of 12 mitochondrial protein-coding genes from 238 mitochondrial genomes of 140 molluscan species as potential DNA barcodes for mollusks. Three barcoding methods (distance, monophyly and character-based methods) were used in species identification. The species recovery rates based on genetic distances for the 12 genes ranged from 70.83 to 83.33%. There were no significant differences in intra- or interspecific variability among the 12 genes. The monophyly and character-based methods provided higher resolution than the distance-based method in species delimitation. Especially in closely related taxa, the character-based method showed some advantages. The results suggested that besides the standard COI barcode, other 11 mitochondrial protein-coding genes could also be potentially used as a molecular diagnostic for molluscan species discrimination. Our results also showed that the combination of mitochondrial genes did not enhance the efficacy for species identification and a single mitochondrial gene would be fully competent.

Comparison of live and dead molluscan assemblages suggests recent human-driven decline in benthic diversity in Phetchaburi (NW Gulf of Thailand)

NASA Astrophysics Data System (ADS)

Negri, Mauro Pietro; Sanfilippo, Rossana; Basso, Daniela; Rosso, Antonietta

2015-12-01

Dead and live molluscan assemblages from the coastal area of Phetchaburi (NW Gulf of Thailand) were compared by means of multivariate analysis. Seven thanatofacies were recognized, thriving in the area after the 1960s. Five of them, scattered along the tidal flat, represent oligotypic intertidal biotopes linked to a variety of environmental factors; the remaining two mirror high-diversity infralittoral associations. Conversely, only two poor, ill-defined biofacies thrive at present between the intertidal and the shallow infralittoral zones, somewhat resembling two of the thanatofacies. Diversity indexes reveal a dramatic biodiversity decline occurred from the 1960s onwards, far beyond the effects of time-averaging and accumulation. The responsibility for this reduction is largely attributable to the high impact of human activities, such as the intensive sea bottom trawling, the wastewaters from aquaculture (shrimp and fish ponds) and dense coastal villages, and, at a minor extent, the digging of edible molluscs from the tidal flat.

Developing tools for the study of molluscan immunity: The sequencing of the genome of the eastern oyster, Crassostrea virginica.

PubMed

Gómez-Chiarri, Marta; Warren, Wesley C; Guo, Ximing; Proestou, Dina

2015-09-01

The eastern oyster, Crassostrea virginica, provides important ecological and economical services, making it the target of restoration projects and supporting a significant fishery/aquaculture industry with landings valued at more than $100 million in 2012 in the United States of America. Due to the impact of infectious diseases on wild, restored, and cultured populations, the eastern oyster has been the focus of studies on host-pathogen interactions and immunity, as well as the target of selective breeding efforts for disease resistant oyster lines. Despite these efforts, relatively little is known about the genetic basis of resistance to diseases or environmental stress, not only in eastern oyster, but also in other molluscan species of commercial interest worldwide. In order to develop tools and resources to assist in the elucidation of the genomic basis of traits of commercial, biological, and ecological interest in oysters, a team of genome and bioinformatics experts, in collaboration with the oyster research community, is sequencing, assembling, and annotating the first reference genome for the eastern oyster and producing an exhaustive transcriptome from a variety of oyster developmental stages and tissues in response to a diverse set of environmentally-relevant stimuli. These transcriptomes and reference genome for the eastern oyster, added to the already available genome and transcriptomes for the Pacific oyster (Crassostrea gigas) and other bivalve species, will be an essential resource for the discovery of candidate genes and markers associated with traits of commercial, biological, and ecologic importance in bivalve molluscs, including those related to host-pathogen interactions and immunity. Copyright © 2015 Elsevier Ltd. All rights reserved.

Selective suppression of the slow-inactivating potassium currents by nootropics in molluscan neurons.

PubMed

Bukanova, Julia V; Solntseva, Elena I; Skrebitsky, Vladimir G

2002-09-01

The role of the voltage-gated K+ channels in the effect of some nootropics was investigated. Earlier, the multiple effect of high concentrations of two nootropics, piracetam and its peptide analogue GVS-111 [Seredenin et al. (1995), US Patent No. 5,439,930], on Ca2+ and K+ currents of molluscan neurons was shown [Solntseva et al. (1997), General Pharmacology 29, 85-89]. In the present work, we describe the selective effect of low concentrations of these nootropics as well as vinpocetine on certain types of K+ current. The experiments were performed on isolated neurons of the land snail Helix pomatia using a two-microelectrode voltage-clamp method. The inward voltage-gated Ca2+ current (ICa) and three subtypes of the outward voltage-gated K+ current were recorded: Ca2+-dependent K+ current (IK(Ca)), delayed rectifying current (IKD), and fast-inactivating K+ current (IA). It has been found that I Ca was not changed in the presence of 30 microM vinpocetine, 100 microM piracetam or 10 nM GVS-111, while slow-inactivating, TEA-sensitive IK(Ca) and IKD were inhibited (IK(Ca) more strongly than IKD). In contrast, the fast-inactivating, 4-AP-sensitive K+ current (IA) was not diminished by low concentrations of piracetam and GVS-111, while vinpocetine even augmented it. A possible role of slow-inactivating subtypes of the K+ channels in the development of different forms of dementia is discussed.

Potential virus detection and intervention methods for molluscan shellfish

USDA-ARS?s Scientific Manuscript database

Norovirus is the number one cause of foodborne illness in the Unites States, causing an estimated 9 million cases/yr. Hepatitis A is uncommon in the US but can result in serious illness. Bivalve shellfish are efficient bioconcentrators of these viruses from contaminated growing waters. Consequentl...

Mitogen-activated protein kinase 1 from disk abalone (Haliotis discus discus): Roles in early development and immunity-related transcriptional responses.

PubMed

Perera, N C N; Godahewa, G I; Lee, Jehee

2016-12-01

Mitogen-activated protein kinase (MAPK) is involved in the regulation of cellular events by mediating signal transduction pathways. MAPK1 is a member of the extracellular-signal regulated kinases (ERKs), playing roles in cell proliferation, differentiation, and development. This is mainly in response to growth factors, mitogens, and many environmental stresses. In the current study, we have characterized the structural features of a homolog of MAPK1 from disk abalone (AbMAPK1). Further, we have unraveled its expressional kinetics against different experimental pathogenic infections or related chemical stimulants. AbMAPK1 harbors a 5' untranslated region (UTR) of 23 bps, a coding sequence of 1104 bps, and a 3' UTR of 448 bp. The putative peptide comprises a predicted molecular mass of 42.2 kDa, with a theoretical pI of 6.28. Based on the in silico analysis, AbMAPK1 possesses two N-glycosylation sites, one S_TK catalytic domain, and a conserved His-Arg-Asp domain (HRD). In addition, a conservative glycine rich ATP-phosphate-binding loop and a threonine-x-tyrosine motif (TEY) important for the autophosphorylation were also identified in the protein. Homology assessment of AbMAPK1 showed several conserved regions, and ark clam (Aplysia californica) showed the highest sequence identity (87.9%). The phylogenetic analysis supported close evolutionary kinship with molluscan orthologs. Constitutive expression of AbMAPK1 was observed in six different tissues of disk abalone, with the highest expression in the digestive tract, followed by the gills and hemocytes. Highest AbMAPK1 mRNA expression level was detected at the trochophore developmental stage, suggesting its role in abalone cell differentiation and proliferation. Significant modulation of AbMAPK1 expression under pathogenic stress suggested its putative involvement in the immune defense mechanism. Copyright © 2016 Elsevier Ltd. All rights reserved.

Epigenetic modification in neurons of the mollusc Pomacea canaliculata after immune challenge.

PubMed

Ottaviani, Enzo; Accorsi, Alice; Rigillo, Giovanna; Malagoli, Davide; Blom, Joan M C; Tascedda, Fabio

2013-11-06

In human and rodents, the transcriptional response of neurons to stress is related to epigenetic modifications of both DNA and histone proteins. To assess the suitability of simple invertebrate models in studying the basic mechanisms of stress-related epigenetic modifications, we analyzed epigenetic modifications in neurons of the freshwater snail Pomacea canaliculata after the injection of Escherichia coli-derived lipopolysaccharide (LPS). The phospho-acetylation of histone H3, together with the induction of stress-related factors, c-Fos and HSP70, were evaluated in large and small neurons of the pedal ganglia of sham- and LPS-injected snails. Immunocytochemical investigations showed that after LPS injection, the immunopositivity towards phospho (Ser10)-acetyl (Lys14)-histone H3 and c-Fos increases in the nuclei of small gangliar neurons. Western blot analysis confirmed a significant increase of phospho (Ser10)-acetyl (Lys14)-histone H3 in nuclear extracts from 2h LPS-injected animals. c-Fos protein levels were significantly augmented 6h after LPS injection. Immunocytochemistry and western blot indicated that no changes occurred in HSP70 distribution and protein levels. To our knowledge this is the first demonstration of epigenetic changes in molluscan neurons after an immune challenge and indicate the gastropod P. canaliculata as a suitable model for evolutionary and translational studies on stress-related epigenetic modifications. © 2013 Published by Elsevier B.V.

21 CFR 123.20 - General.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 2 2010-04-01 2010-04-01 false General. 123.20 Section 123.20 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN CONSUMPTION FISH AND FISHERY PRODUCTS Raw Molluscan Shellfish § 123.20 General. This subpart augments subpart...

21 CFR 123.20 - General.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 2 2011-04-01 2011-04-01 false General. 123.20 Section 123.20 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN CONSUMPTION FISH AND FISHERY PRODUCTS Raw Molluscan Shellfish § 123.20 General. This subpart augments subpart...

Rapid detection of hepatitis A virus and murine norovirus in hemocytes of contaminated oysters

USDA-ARS?s Scientific Manuscript database

The human enteric pathogens, hepatitis A virus and human norovirus, have been shown to contaminate molluscan shellfish and cause foodborne disease in consumers. Rapid viral extraction methods are needed to replace current time consuming methods, which use whole oysters or dissected tissues. In our ...

21 CFR 123.28 - Source controls.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 2 2010-04-01 2010-04-01 false Source controls. 123.28 Section 123.28 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN CONSUMPTION FISH AND FISHERY PRODUCTS Raw Molluscan Shellfish § 123.28 Source controls. (a) In order to meet...

Polyplacophora (Mollusca) from the San Diego Formation: A remarkable assemblage of fossil chitons from the Pliocene of southern Califoria

USGS Publications Warehouse

Vendrasco, Michael J.; Eernisse, Douglas J.; Powell, Charles L.; Fernandez, Christine Z.

2012-01-01

taphonomic factors bias valve ratios long after valves are disarticulated. New foraminiferan and molluscan data indicate a middle or late Pliocene age of deposition for these beds, between 3.3 to 2.5 million years ago (Ma), and possibly about 3.0 Ma.

PARASITIC AND SYMBIOTIC FAUNA IN OYSTERS (CRASSOSTREA VIRGINICA) AND MUD CRABS (PANOPEUS SPP.) FROM THE CALOOSAHATCHEE ESTUARY, FLORIDA, USA.

EPA Science Inventory

Volety, Aswani K., S. Greg Tolley and James T. Winstead. 2002. Parasitic and Symbiotic Fauna in Oysters (Crassostrea virginica) and Mud Crabs (Panopeus spp.) from the Caloosahatchee Estuary, Florida, USA (Abstract). Presented at the 4th International Conference on Molluscan Shell...

Multivariate Analysis of Remains of Molluscan Foods Consumed by Latest Pleistocene and Holocene Humans in Nerja Cave, Málaga, Spain

NASA Astrophysics Data System (ADS)

Serrano, Francisco; Guerra-Merchán, Antonio; Lozano-Francisco, Carmen; Vera-Peláez, José Luis

1997-09-01

Nerja Cave is a karstic cavity used by humans from Late Paleolithic to post-Chalcolithic times. Remains of molluscan foods in the uppermost Pleistocene and Holocene sediments were studied with cluster analysis and principal components analysis, in both Qand Rmodes. The results from cluster analysis distinguished interval groups mainly in accordance with chronology and distinguished assemblages of species mainly according to habitat. Significant changes in the shellfish diet through time were revealed. In the Late Magdalenian, most molluscs consumed consisted of pulmonate gastropods and species from sandy sea bottoms. The Epipaleolithic diet was more varied and included species from rocky shorelines. From the Neolithic onward most molluscs consumed were from rocky shorelines. From the principal components analysis in Qmode, the first factor reflected mainly changes in the predominant capture environment, probably because of major paleogeographic changes. The second factor may reflect selective capture along rocky coastlines during certain times. The third factor correlated well with the sea-surface temperature curve in the western Mediterranean (Alboran Sea) during the late Quaternary.

The goldfish nervus terminalis: a luteinizing hormone-releasing hormone and molluscan cardioexcitatory peptide immunoreactive olfactoretinal pathway.

PubMed

Stell, W K; Walker, S E; Chohan, K S; Ball, A K

1984-02-01

Antisera to two putative neurotransmitters, luteinizing hormone-releasing hormone (LHRH) and molluscan cardioexcitatory tetrapeptide (H-Phe-Met-Arg-Phe-NH2; FMRF-amide), bind specifically to neurites in the inner nuclear and inner plexiform layers of the goldfish retina. Retrograde labeling showed that intraocular axon terminals originate from the nervus terminalis, whose cell bodies are located in the olfactory nerves. Double immunocytochemical and retrograde labeling showed that some terminalis neurons project to the retina; others may project only within the brain. All terminalis neurons having proven retinal projections were both LHRH- and FMRF-amide-immunoreactive. The activity of retinal ganglion cells was recorded with microelectrodes in isolated superfused goldfish retinas. In ON- and OFF-center double-color-opponent cells, micromolar FMRF-amide and salmon brain gonadotropin-releasing factor ( [Trp7, Leu8] LHRH) caused increased spontaneous activity in the dark, loss of light-induced inhibition, and increased incidence of light-entrained pulsatile response. The nervus terminalis is therefore a putatively peptidergic retinopetal projection. Sex-related olfactory stimuli may act through it, thereby modulating the output of ganglion cells responsive to color contrast.

Paleo­geographic implications of molluscan assemblages in the Upper Cretaceous (Campanian) Pigeon Point Formation, California

USGS Publications Warehouse

Elder, William P.; Saul, LouElla

1993-01-01

The Pigeon Point Formation crops out along the San Mateo County coastline in a northern and southern sequence of folded and faulted strata. Correlation of the two sequences remains somewhat equivocal, although on the basis of biostratigraphy and a reversed magnetic interval both appear to have been deposited during the early to middle Campanian. Sedimentary structures suggest that the northern sequence was deposited by turbidity currents in a continental rise setting, whereas the southern sequence primarily reflects deposition in shelf and slope environments . Right-lateral offset on the San Andreas and subsidiary faults to the east of the Pigeon Point Formation can account for 100's of km of northward transport since its deposition. However, Champion and others (1984) suggested 2500 km of northward transport from a tropical setting of about 21°N. Molluscan assemblages in the formation argue strongly for a less tropical site of deposition. Relative abundances of warm and temperate taxa and the presence or absence of key species are similar to those of the Santa Ana Mountains Cretaceous section, and are indicative of a war

Late Paleocene Arctic Ocean shallow-marine temperatures from mollusc stable isotopes

USGS Publications Warehouse

Bice, Karen L.; Arthur, Michael A.; Marincovich, Louie

1996-01-01

Late Paleocene high-latitude (80°N) Arctic Ocean shallow-marine temperatures are estimated from molluscan δ18O time series. Sampling of individual growth increments of two specimens of the bivalve Camptochlamys alaskensis provides a high-resolution record of shell stable isotope composition. The heavy carbon isotopic values of the specimens support a late Paleocene age for the youngest marine beds of the Prince Creek Formation exposed near Ocean Point, Alaska. The oxygen isotopic composition of regional freshwater runoff is estimated from the mean δ18O value of two freshwater bivalves collected from approximately coeval fluviatile beds. Over a 30 – 34‰ range of salinity, values assumed to represent the tolerance of C. alaskensis, the mean annual shallow-marine temperature recorded by these individuals is between 11° and 22°C. These values could represent maximum estimates of the mean annual temperature because of a possible warm-month bias imposed on the average δ18O value by slowing or cessation of growth in winter months. The amplitude of the molluscan δ18O time series probably records most of the seasonality in shallow-marine temperature. The annual temperature range indicated is approximately 6°C, suggesting very moderate high-latitude marine temperature seasonality during the late Paleocene. On the basis of analogy with modern Chlamys species, C. alaskensis probably inhabited water depths of 30–50 m. The seasonal temperature range derived from δ18O is therefore likely to be damped relative to the full range of annual sea surface temperatures. High-resolution sampling of molluscan shell material across inferred growth bands represents an important proxy record of seasonality of marine and freshwater conditions applicable at any latitude. If applied to other regions and time periods, the approach used here would contribute substantially to the paleoclimate record of seasonality.

Phylogenetic patterns and phenotypic plasticity of molluscan sexual systems.

PubMed

Collin, Rachel

2013-10-01

Molluscs show a wide diversity of sexual systems and strategies. There are both gastropod and bivalve families that are each primarily dioecious, simultaneous hermaphrodites, or sequential hermaphrodites, and other families in which almost every sexual strategy occurs. The multiple evolutionary transitions of sexual systems within molluscs would allow comparative analyses of the associated ecological factors, but data on all but a few groups are too sparse to draw many solid conclusions. The phylogenetic distribution of sexual systems in the Mollusca shows that gastropods and bivalves demonstrate different patterns, possibly associated with the presence/absence of copulation. The distribution of change of sex suggests that, in gastropods, sequential hermaphrodites do not evolve from simultaneous hermaphrodites, and that sex reversal (flip-flopping) occurs in free-spawners but not in copulators. Three well-studied protandrous gastropod groups (calyptraeids, coralliophilids, and patellogastropods) show similar responses to environmental conditions and associations with conspecifics. They all have the following attributes: (1) they are sedentary, (2) they live in groups, patches, or aggregates, and (3) size at sex change varies among sites and among aggregates. In addition the available experimental evidence suggests that (4) the presence of females or large individuals represses growth and sex change of males, and (5) behavior seems to mediate the repressive influence of large females. Available data from other species tend to support these patterns. Finally, the repression of growth of males by females in protandry likely facilitates the evolution of dwarf males.

Tertiary climatic change in the marginal northeastern Pacific Ocean

USGS Publications Warehouse

Addicott, W.O.

1969-01-01

Analysis of distributional patterns of shallow-water molluscan faunas of the middle latitudes of the marginal northeastern Pacific Ocean discloses a sharp reversal during the Miocene of the progressive climatic deterioration. A low point in the Tertiary cooling trend during the Oligocene was followed by climatic warming that culminated during the middle Miocene, as illustrated by a series of zoogeographic profiles.

Tertiary climatic change in the marginal northeastern pacific ocean.

PubMed

Addicott, W O

1969-08-08

Analysis of distributional patterns of shallow-water molluscan faunas of the middle latitudes of the marginal northeastern Pacific Ocean discloses a sharp reversal during the Miocene of the progressive climatic deterioration. A low point in the Tertiary cooling trend during the Oligocene was followed by climatic warming that culminated during the middle Miocene, as illustrated by a series of zoogeographic profiles.

Anatomy of a Natural Composite Material

DTIC Science & Technology

1989-11-01

from the vitellaria of the liver fluke, Fasciola hepatica. Biochemistry 28, 6104-6110. 2. Waite, J.H., Hansen, D.C., & Little, K.T. (1989) The glue...certainly belong to distinct genera and inhabit distinct ecological niches. Adhesive protein sequences from two non-molluscan species, Fasciola hepatica...choros), Gd (Geukensia demissa), Fh ( Fasciola hepatica), Me (Mytilus edulis), Mg (Mytella guyanensis), Mms (Modiolus modiolus squamosus), Pc

Robust cross-links in molluscan adhesive gels: Testing for contributions from hydrophobic and electrostatic interactions

PubMed Central

Smith, A.M.; Robinson, T. M.; Salt, M. D.; Hamilton, K. S.; Silvia, B. E.; Blasiak, R.

2009-01-01

The cross-linking interactions that provide cohesive strength to molluscan adhesive gels were investigated. Metal-based interactions have been shown to play an important role in the glue of the slug Arion subfuscus (Draparnaud), but other types of interactions may also contribute to the glue's strength and their role has not been investigated. This study shows that treatments that normally disrupt hydrophobic or electrostatic interactions have little to no effect on the slug glue. High salt concentrations and non-ionic detergent do not affect the solubility of the proteins in the glue or the ability of the glue proteins to stiffen gels. In contrast, metal chelation markedly disrupts the gel. Experiments with gel filtration chromatography identify a 40 kDa protein that is a central component of the cross-links in the glue. This 40 kDa protein forms robust macromolecular aggregations that are stable even in the presence of high concentrations of salt, non-ionic detergent, urea or metal chelators. Metal chelation during glue secretion, however, may block some of these cross-links. Such robust, non-specific interactions in an aqueous environment are highly unusual for hydrogels and reflect an intriguing cross-linking mechanism. PMID:18952190

Rediscovery of Leptoxis compacta (Anthony, 1854) (Gastropoda: Cerithioidea: Pleuroceridae)

PubMed Central

Whelan, Nathan V.; Johnson, Paul D.; Harris, Phil M.

2012-01-01

The Mobile River Basin is a hotspot of molluscan endemism, but anthropogenic activities have caused at least 47 molluscan extinctions, 37 of which were gastropods, in the last century. Nine of these suspected extinctions were in the freshwater gastropod genus Leptoxis (Cerithioidea: Pleuroceridae). Leptoxis compacta, a Cahaba River endemic, has not been collected for >70 years and was formally declared extinct in 2000. Such gastropod extinctions underscore the imperilment of freshwater resources and the current biodiversity crisis in the Mobile River Basin. During a May 2011 gastropod survey of the Cahaba River in central Alabama, USA, L. compacta was rediscovered. The identification of snails collected was confirmed through conchological comparisons to the L. compacta lectotype, museum records, and radulae morphology of historically collected L. compacta. Through observations of L. compacta in captivity, we document for the first time that the species lays eggs in short, single lines. Leptoxis compacta is restricted to a single location in the Cahaba River, and is highly susceptible to a single catastrophic extinction event. As such, the species deserves immediate conservation attention. Artificial propagation and reintroduction of L. compacta into its native range may be a viable recovery strategy to prevent extinction from a single perturbation event. PMID:22905139

Twin density of aragonite in molluscan shells characterized using X-ray diffraction and transmission electron microscopy

NASA Astrophysics Data System (ADS)

Kogure, Toshihiro; Suzuki, Michio; Kim, Hyejin; Mukai, Hiroki; Checa, Antonio G.; Sasaki, Takenori; Nagasawa, Hiromichi

2014-07-01

{110} twin density in aragonites constituting various microstructures of molluscan shells has been characterized using X-ray diffraction (XRD) and transmission electron microscopy (TEM), to find the factors that determine the density in the shells. Several aragonite crystals of geological origin were also investigated for comparison. The twin density is strongly dependent on the microstructures and species of the shells. The nacreous structure has a very low twin density regardless of the shell classes. On the other hand, the twin density in the crossed-lamellar (CL) structure has large variation among classes or subclasses, which is mainly related to the crystallographic direction of the constituting aragonite fibers. TEM observation suggests two types of twin structures in aragonite crystals with dense {110} twins: rather regulated polysynthetic twins with parallel twin planes, and unregulated polycyclic ones with two or three directions for the twin planes. The former is probably characteristic in the CL structures of specific subclasses of Gastropoda. The latter type is probably related to the crystal boundaries dominated by (hk0) interfaces in the microstructures with preferred orientation of the c-axis, and the twin density is mainly correlated to the crystal size in the microstructures.

Effects of productivity, consumers, competitors, and El Nino events on food chain patterns in a rocky intertidal community

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wootton, J.T.; Pfister, C.A.; Paine, R.T.

We experimentally manipulated nutrient input to a rocky intertidal community, using nutrient-diffusing flowerpots, to determine (i) whether nutrients limited intertidal productivity, (ii) how a large-scale oceanographic disturbance (an El Nino event) affected patterns of nutrient limitation, (iii) the relative impacts of molluscan grazers and nutrient limitation, and (iv) if responses to experimental nutrient addition among trophic levels were more consistent with prey-dependent or ratio-dependent food chain models. Nutrients measurably increased the abundance of micrograzers (amphipods and chironomid larvae), but not algal biomass, during the summer of an El Nino years and during the autumn of an El Nino year. Addingmore » nutrients did not affect food chain stability as assessed by temporal variation in algal biomass and micrograzer abundance. Large molluscan grazers caused large reductions in micrograzers and smaller reductions in algae, indicating consistent consumer effects. The results demonstrate that in this intertidal community, nutrient limitation can occur under conditions of nutrient stress, that top-down grazing effects are typically stronger than bottom-up nutrient effects, and that prey-dependent models are more appropriate than ratio-dependent models. 40 refs., 1 fig., 1 tab.« less

The goldfish nervus terminalis: a luteinizing hormone-releasing hormone and molluscan cardioexcitatory peptide immunoreactive olfactoretinal pathway.

PubMed Central

Stell, W K; Walker, S E; Chohan, K S; Ball, A K

1984-01-01

Antisera to two putative neurotransmitters, luteinizing hormone-releasing hormone (LHRH) and molluscan cardioexcitatory tetrapeptide (H-Phe-Met-Arg-Phe-NH2; FMRF-amide), bind specifically to neurites in the inner nuclear and inner plexiform layers of the goldfish retina. Retrograde labeling showed that intraocular axon terminals originate from the nervus terminalis, whose cell bodies are located in the olfactory nerves. Double immunocytochemical and retrograde labeling showed that some terminalis neurons project to the retina; others may project only within the brain. All terminalis neurons having proven retinal projections were both LHRH- and FMRF-amide-immunoreactive. The activity of retinal ganglion cells was recorded with microelectrodes in isolated superfused goldfish retinas. In ON- and OFF-center double-color-opponent cells, micromolar FMRF-amide and salmon brain gonadotropin-releasing factor ( [Trp7, Leu8] LHRH) caused increased spontaneous activity in the dark, loss of light-induced inhibition, and increased incidence of light-entrained pulsatile response. The nervus terminalis is therefore a putatively peptidergic retinopetal projection. Sex-related olfactory stimuli may act through it, thereby modulating the output of ganglion cells responsive to color contrast. Images PMID:6199789

Robust cross-links in molluscan adhesive gels: testing for contributions from hydrophobic and electrostatic interactions.

PubMed

Smith, A M; Robinson, T M; Salt, M D; Hamilton, K S; Silvia, B E; Blasiak, R

2009-02-01

The cross-linking interactions that provide cohesive strength to molluscan adhesive gels were investigated. Metal-based interactions have been shown to play an important role in the glue of the slug Arion subfuscus (Draparnaud), but other types of interactions may also contribute to the glue's strength and their role has not been investigated. This study shows that treatments that normally disrupt hydrophobic or electrostatic interactions have little to no effect on the slug glue. High salt concentrations and non-ionic detergent do not affect the solubility of the proteins in the glue or the ability of the glue proteins to stiffen gels. In contrast, metal chelation markedly disrupts the gel. Experiments with gel filtration chromatography identify a 40 kDa protein that is a central component of the cross-links in the glue. This 40 kDa protein forms robust macromolecular aggregations that are stable even in the presence of high concentrations of salt, non-ionic detergent, urea or metal chelators. Metal chelation during glue secretion, however, may block some of these cross-links. Such robust, non-specific interactions in an aqueous environment are highly unusual for hydrogels and reflect an intriguing cross-linking mechanism.

A cysteine protease (cathepsin Z) from disk abalone, Haliotis discus discus: Genomic characterization and transcriptional profiling during bacterial infections.

PubMed

Godahewa, G I; Perera, N C N; Lee, Sukkyoung; Kim, Myoung-Jin; Lee, Jehee

2017-09-05

Cathepsin Z (CTSZ) is lysosomal cysteine protease of the papain superfamily. It participates in the host immune defense via phagocytosis, signal transduction, cell-cell communication, proliferation, and migration of immune cells such as monocytes, macrophages, and dendritic cells. Hence, CTSZ is also acknowledged as an acute-phase protein in host immunity. In this study, we sought to identify the CTSZ homolog from disk abalone (AbCTSZ) and characterize it at the molecular, genomic, and transcriptional levels. AbCTSZ encodes a protein with 318 amino acids and a molecular mass of 36kDa. The structure of AbCTSZ reveals amino acid sequences that are characteristic of the signal sequence, pro-peptide, peptidase-C1 papain family cysteine protease domain, mini-loop, HIP motif, N-linked glycosylation sites, active sites, and conserved Cys residues. A pairwise comparison revealed that AbCTSZ shared the highest amino acid homology with its molluscan counterpart from Crassostrea gigas. A multiple alignment analysis revealed the conservation of functionally crucial elements of AbCTSZ, and a phylogenetic study further confirmed a proximal evolutionary relationship with its invertebrate counterparts. Further, an analysis of AbCTSZ genomic structure revealed seven exons separated by six introns, which differs from that of its vertebrate counterparts. Quantitative real time PCR (qPCR) detected the transcripts of AbCTSZ in early developmental stages and in eight different tissues. Higher levels of AbCTSZ transcripts were found in trochophore, gill, and hemocytes, highlighting its importance in the early development and immunity of disk abalone. In addition, we found that viable bacteria (Vibrio parahaemolyticus and Listeria monocytogenes) and bacterial lipopolysaccharides significantly modulated AbCTSZ transcription. Collectively, these lines of evidences suggest that AbCTSZ plays an indispensable role in the innate immunity of disk abalone. Copyright © 2017. Published by Elsevier B.V.

Cloning retinoid and peroxisome proliferator-activated nuclear receptors of the Pacific oyster and in silico binding to environmental chemicals

PubMed Central

Vogeler, Susanne; Galloway, Tamara S.; Isupov, Michail

2017-01-01

Disruption of nuclear receptors, a transcription factor superfamily regulating gene expression in animals, is one proposed mechanism through which pollution causes effects in aquatic invertebrates. Environmental pollutants have the ability to interfere with the receptor’s functions through direct binding and inducing incorrect signals. Limited knowledge of invertebrate endocrinology and molecular regulatory mechanisms, however, impede the understanding of endocrine disruptive effects in many aquatic invertebrate species. Here, we isolated three nuclear receptors of the Pacific oyster, Crassostrea gigas: two isoforms of the retinoid X receptor, CgRXR-1 and CgRXR-2, a retinoic acid receptor ortholog CgRAR, and a peroxisome proliferator-activated receptor ortholog CgPPAR. Computer modelling of the receptors based on 3D crystal structures of human proteins was used to predict each receptor’s ability to bind to different ligands in silico. CgRXR showed high potential to bind and be activated by 9-cis retinoic acid and the organotin tributyltin (TBT). Computer modelling of CgRAR revealed six residues in the ligand binding domain, which prevent the successful interaction with natural and synthetic retinoid ligands. This supports an existing theory of loss of retinoid binding in molluscan RARs. Modelling of CgPPAR was less reliable due to high discrepancies in sequence to its human ortholog. Yet, there are suggestions of binding to TBT, but not to rosiglitazone. The effect of potential receptor ligands on early oyster development was assessed after 24h of chemical exposure. TBT oxide (0.2μg/l), all-trans retinoic acid (ATRA) (0.06 mg/L) and perfluorooctanoic acid (20 mg/L) showed high effects on development (>74% abnormal developed D-shelled larvae), while rosiglitazone (40 mg/L) showed no effect. The results are discussed in relation to a putative direct (TBT) disruption effect on nuclear receptors. The inability of direct binding of ATRA to CgRAR suggests either a disruptive effect through a pathway excluding nuclear receptors or an indirect interaction. Our findings provide valuable information on potential mechanisms of molluscan nuclear receptors and the effects of environmental pollution on aquatic invertebrates. PMID:28426724

On the identities of the molluscan names described in A Short Zoology of Tahiti in the Society Islands by Anthony Curtiss in 1938 (Mollusca: Cephalopoda, Gastropoda).

PubMed

Low, Martyn E Y; Tan, Siong Kiat

2014-02-11

Anthony Curtiss described two species of cephalopod and nine species of gastropod molluscs from Tahiti. Herein, we discuss and determine the identities of these eleven names. Ten of these names are considered to be junior subjective synonyms of well-known taxa, and one an unavailable name.

Irradiation in the production, processing, and handling of food. Final rule.

PubMed

2005-08-16

The Food and Drug Administration (FDA) is amending the food additive regulations to provide for the safe use of ionizing radiation for control of Vibrio species and other foodborne pathogens in fresh or frozen molluscan shellfish (e.g., oysters, mussels, clams, etc.). This action is in response to a petition filed by the National Fisheries Institute and the Louisiana Department of Agriculture and Forestry.

[Principal stages in the Cenozoic diversification of shallow-water molluscan faunas in the North Pacific].

PubMed

Kafanov, A I

2006-01-01

Cluster analysis of bivalve species recorded in Cenozoic deposits in Sakhalin Island, western Kamchatka, Hokkaido, and California was used to determine geological age of the modem North Pacific biogeographic region and its constituent subregions (Japan-Mandchurian, Beringian, and Oregon-Sitkan). The North Pacific region developed during the Paleogene-Neogene transition due to Drake Passage opening to deep-water movement, formation of the deep-water Antarctic Circumpolar Current, and the change in climate from greenhouse to psychospheric. Differentiation of the three subregions within the North Pacific Region seems to have occurred in late Miocene-early Pliocene, about 5.6 millions years ago and was probably due to the flooding of the Bering Land Bridge and development of the present configuration of circulation in the North Pacific. In the Northwest Pacific, during Paleogene and early Neogene, the faunal diversification occurred more rapidly and was more extensive than in the Northeast Pacific.

Functional Characterization and Expression of Molluscan Detoxification Enzymes and Transporters Involved in Dietary Allelochemical Resistance

DTIC Science & Technology

2008-06-01

gastropod Cvphoma gibbosum feeding on a variety of chemically defended gorgonian corals, and to identify those dietary natural products that act as...detoxification and transport-mediated resistance to dietary allelochemicals. The ovulid gastropod Cyphoma gibbosum is considered a trophic generalist, feeding...enzymatic activity of glutathione S-transferases from the generalist marine gastropod , Cyphoma gibbosum Abstract 74 Introduction 75 Methods 78 Results 86

Multi-species collapses at the warm edge of a warming sea

PubMed Central

Rilov, Gil

2016-01-01

Even during the current biodiversity crisis, reports on population collapses of highly abundant, non-harvested marine species were rare until very recently. This is starting to change, especially at the warm edge of species’ distributions where populations are more vulnerable to stress. The Levant basin is the southeastern edge of distribution of most Mediterranean species. Coastal water conditions are naturally extreme, and are fast warming, making it a potential hotspot for species collapses. Using multiple data sources, I found strong evidence for major, sustained, population collapses of two urchins, one large predatory gastropod and a reef-building gastropod. Furthermore, of 59 molluscan species once-described in the taxonomic literature as common on Levant reefs, 38 were not found in the present-day surveys, and there was a total domination of non-indigenous species in molluscan assemblages. Temperature trends indicate an exceptional warming of the coastal waters in the past three decades. Though speculative at this stage, the fast rise in SST may have helped pushing these invertebrates beyond their physiological tolerance limits leading to population collapses and possible extirpations. If so, these collapses may indicate the initiation of a multi-species range contraction at the Mediterranean southeastern edge that may spread westward with additional warming. PMID:27853237

Bivalve immunity and response to infections: Are we looking at the right place?

PubMed

Allam, Bassem; Pales Espinosa, Emmanuelle

2016-06-01

Significant progress has been made in the understanding of cellular and molecular mediators of immunity in invertebrates in general and bivalve mollusks in particular. Despite this information, there is a lack of understanding of factors affecting animal resistance and specific responses to infections. This in part results from limited consideration of the spatial (and to some extent temporal) heterogeneity of immune responses and very limited information on host-pathogen (and microbes in general) interactions at initial encounter/colonization sites. Of great concern is the fact that most studies on molluscan immunity focus on the circulating hemocytes and the humoral defense factors in the plasma while most relevant host-microbe interactions occur at mucosal interfaces. This paper summarizes information available on the contrasting value of information available on focal and systemic immune responses in infected bivalves, and highlights the role of mucosal immune factors in host-pathogen interactions. Available information underlines the diversity of immune effectors at molluscan mucosal interfaces and highlights the tailored immune response to pathogen stimuli. This context raises fascinating basic research questions around host-microbe crosstalk and feedback controls of these interactions and may lead to novel disease mitigation strategies and improve the assessment of resistant crops or the screening of probiotic candidates. Copyright © 2016 Elsevier Ltd. All rights reserved.

Proteomic analysis of the organic matrix of the abalone Haliotis asinina calcified shell

PubMed Central

2010-01-01

Background The formation of the molluscan shell is regulated to a large extent by a matrix of extracellular macromolecules that are secreted by the shell forming tissue, the mantle. This so called "calcifying matrix" is a complex mixture of proteins and glycoproteins that is assembled and occluded within the mineral phase during the calcification process. While the importance of the calcifying matrix to shell formation has long been appreciated, most of its protein components remain uncharacterised. Results Recent expressed sequence tag (EST) investigations of the mantle tissue from the tropical abalone (Haliotis asinina) provide an opportunity to further characterise the proteins in the shell by a proteomic approach. In this study, we have identified a total of 14 proteins from distinct calcified layers of the shell. Only two of these proteins have been previously characterised from abalone shells. Among the novel proteins are several glutamine- and methionine-rich motifs and hydrophobic glycine-, alanine- and acidic aspartate-rich domains. In addition, two of the new proteins contained Kunitz-like and WAP (whey acidic protein) protease inhibitor domains. Conclusion This is one of the first comprehensive proteomic study of a molluscan shell, and should provide a platform for further characterization of matrix protein functions and interactions. PMID:21050442

Mini-titins in striated and smooth molluscan muscles: structure, location and immunological crossreactivity.

PubMed

Vibert, P; Edelstein, S M; Castellani, L; Elliott, B W

1993-12-01

Invertebrate mini-titins are members of a class of myosin-binding proteins belonging to the immunoglobulin superfamily that may have structural and/or regulatory properties. We have isolated mini-titins from three molluscan sources: the striated and smooth adductor muscles of the scallop, and the smooth catch muscles of the mussel. Electron microscopy reveals flexible rod-like molecules about 0.2 micron long and 30 A wide with a distinctive polarity. Antibodies to scallop mini-titin label the A-band and especially the A/I junction of scallop striated muscle myofibrils by indirect immunofluorescence and immuno-electron microscopy. This antibody crossreacts with mini-titins in scallop smooth and Mytilus catch muscles, as well as with proteins in striated muscles from Limulus, Lethocerus (asynchronous flight muscle), and crayfish. It labels the A/I junction (I-region in Lethocerus) in these striated muscles as well as in chicken skeletal muscle. Antibodies to the repetitive immunoglobulin-like regions and also to the kinase domain of nematode twitchin crossreact with scallop mini-titin and label the A-band of scallop myofibrils. Electron microscopy of single molecules shows that antibodies to twitchin kinase bind to scallop mini-titin near one end of the molecule, suggesting how the scallop structure might be aligned with the sequence of nematode twitchin.

Salicylic acid, a plant defense hormone, is specifically secreted by a molluscan herbivore.

PubMed

Kästner, Julia; von Knorre, Dietrich; Himanshu, Himanshu; Erb, Matthias; Baldwin, Ian T; Meldau, Stefan

2014-01-01

Slugs and snails are important herbivores in many ecosystems. They differ from other herbivores by their characteristic mucus trail. As the mucus is secreted at the interface between the plants and the herbivores, its chemical composition may play an essential role in plant responses to slug and snail attack. Based on our current knowledge about host-manipulation strategies employed by pathogens and insects, we hypothesized that mollusks may excrete phytohormone-like substances into their mucus. We therefore screened locomotion mucus from thirteen molluscan herbivores for the presence of the plant defense hormones jasmonic acid (JA), salicylic acid (SA) and abscisic acid (ABA). We found that the locomotion mucus of one slug, Deroceras reticulatum, contained significant amounts of SA, a plant hormone that is known to induce resistance to pathogens and to suppress plant immunity against herbivores. None of the other slugs and snails contained SA or any other hormone in their locomotion mucus. When the mucus of D. reticulatum was applied to wounded leaves of A. thaliana, the promotor of the SA-responsive gene pathogenesis related 1 (PR1) was activated, demonstrating the potential of the mucus to regulate plant defenses. We discuss the potential ecological, agricultural and medical implications of this finding.

Salicylic Acid, a Plant Defense Hormone, Is Specifically Secreted by a Molluscan Herbivore

PubMed Central

Kästner, Julia; von Knorre, Dietrich; Himanshu, Himanshu; Erb, Matthias; Baldwin, Ian T.; Meldau, Stefan

2014-01-01

Slugs and snails are important herbivores in many ecosystems. They differ from other herbivores by their characteristic mucus trail. As the mucus is secreted at the interface between the plants and the herbivores, its chemical composition may play an essential role in plant responses to slug and snail attack. Based on our current knowledge about host-manipulation strategies employed by pathogens and insects, we hypothesized that mollusks may excrete phytohormone-like substances into their mucus. We therefore screened locomotion mucus from thirteen molluscan herbivores for the presence of the plant defense hormones jasmonic acid (JA), salicylic acid (SA) and abscisic acid (ABA). We found that the locomotion mucus of one slug, Deroceras reticulatum, contained significant amounts of SA, a plant hormone that is known to induce resistance to pathogens and to suppress plant immunity against herbivores. None of the other slugs and snails contained SA or any other hormone in their locomotion mucus. When the mucus of D. reticulatum was applied to wounded leaves of A. thaliana, the promotor of the SA-responsive gene pathogenesis related 1 (PR1) was activated, demonstrating the potential of the mucus to regulate plant defenses. We discuss the potential ecological, agricultural and medical implications of this finding. PMID:24466122

Malacological and palynological evidence of the Lower Pleistocene cold phase at the Carpathian Foothills (Southern Poland)

NASA Astrophysics Data System (ADS)

Stworzewicz, Ewa; Granoszewski, Wojciech; Wójcik, Antoni

2012-05-01

Early Pleistocene sediments bearing gastropod shells and pollen flora were found during coring at Jawornik (South Poland) at a depth interval of 54.30-39.00 m, beneath the oldest till of the Carpathians. Thirteen land-snail taxa identified in 55 samples of the core formed two molluscan assemblages. In the bottom part, typical cold-loving snails were found (e.g. Vallonia tenuilabris, Pupilla loessica, Vertigo genesii, Columella columella), whereas in the upper part only Semilimax kotulae was present. The succession of molluscan assemblages may suggest that at the site of deposition, after a phase of tundra, steppe-tundra or forest-steppe landscape with patches of wet habitats in cold climate, the climate became slightly milder but still cool, favourable to the spreading of boreal (coniferous) woodlands. Pollen analysis was performed only for the upper part of the profile. The pollen spectra, besides the Tertiary (Miocene) elements, contained sporomorphs common to the Tertiary and Quaternary floras. Among them, the highest percentages were noted for Pinus haploxylon t., P. diploxylon t., Picea, Quercus, Ericaceae, Betula, and Ulmus. The fact that the sediments with organic remains underlie the oldest Scandinavian till suggests that they are older than the oldest glacial unit of the South-Polish Complex (Narevian = Menapian, ~ 1.2 Ma).

National collaborative shellfish pollution-indicator study: Site selection. Phase 1. Rept. for 1987-88

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leonard, D.L.; Broutman, M.A.; Caverly, K.E.

1988-07-01

Each year approximately 16 million acres of estuarine waters are classified for the harvest of molluscan shellfish as open or limited to harvest according to microbiological 'indicator' standards and pollution survey guidelines established by the National Shellfish Sanitation Program. The program was developed in the 1920's in response to typhoid fever outbreaks and may no longer protect the consumer from the most prevalent shellfish-borne diseases: hepatitis and gastroenteritis. Today, 1/3 of productive or potentially productive shellfish-growing waters are closed to harvest at some time during the year. In response to these problems, the industry has initiated a national cooperative effortmore » to re-evaluate the standard and establish a classification system directly related to public health implications.« less

The Scourge of Tropical Water Resources, Schistosomiasis,

DTIC Science & Technology

1980-12-13

penetrate into a suitable gastropod host. The miracidia locate their molluscan hosts by first being brought into range as a result natural taxes and...3). Upon entering a compatible gastropod host, the ciliated epithelium of the miracidium is sloughed and the parasite metamorphoses into a first...particular strain of snail to which the worm is adapted . Soon the infected snail swarms with progeny of the single larva that entered it; in a few weeks

Common and scientific names of aquatic invertebrates from the United States and Canada: Mollusks

USGS Publications Warehouse

Turgeon, D. D.; Quinn, J.F.; Bogan, A.E.; Coan, E. V.; Hochberg, F.G.; Lyons, W.G.; Mikkelsen, P. M.; Neves, R.J.; Roper, C. F. E.; Rosenberg, G.; Roth, B.; Scheltema, A.; Thompson, F.G.; Vecchione, M.; Williams, J.D.

1998-01-01

This edition of Common and Scientific Names of Invertebrates from the United States and Canada: Mollusks represents the efforts of 15 molluscan taxonomic specialists in compiling a comprehensive checklist of the mollusks found in North America and Canada and their vernacular names. Built upon the success of the first edition, the authors have updated the nomenclature to reflect recent phylogenetic analyses and have included more than 300 new species.

Fouling and Boring of Glass Reinforced Plastic - Balsa Blocks in a Tropical Marine Environment,

DTIC Science & Technology

1983-03-01

borers had decomposed prior to examination of the blocks but eight molluscan species were identified from hard parts (pallets and shells ) found in the...or bivalve molluscs and these differ in their boring habit and subsequently the type of damage they cause. Crustacean borers excavate tunnels several...or teredo, excavate tunnels lined with calcium carbonate to accomodate their elongate bodies which, in some species, can be up to 2m long. They feed

Endolithic algae and micrite envelope formation in Bahamian oolites as revealed by scanning electron microscopy.

NASA Technical Reports Server (NTRS)

Margolis, S.; Rex, R. W.

1971-01-01

Examination of Holocene Bahamian ooelites by scanning electron and light microscopy has revealed the morphology and orientation of aragonite crystals in the lamellar ooelitic envelope, and their modification by the boring activities of endolithic algae. The voids produced by these algae are found in progressive stages of being lined and filled with precipitated microcrystalline aragonite, which is similar to the process of micrite envelope formation in molluscan and other skeletal carbonate grains.

Eutrophication and Dreissena invasion as drivers of biodiversity: a century of change in the mollusc community of Oneida Lake.

PubMed

Karatayev, Vadim A; Karatayev, Alexander Y; Burlakova, Lyubov E; Rudstam, Lars G

2014-01-01

Changes in nutrient loading and invasive species are among the strongest human-driven disturbances in freshwater ecosystems, but our knowledge on how they affect the biodiversity of lakes is still limited. We conducted a detailed historical analysis of the mollusc community of Oneida Lake based on our comprehensive lakewide study in 2012 and previous surveys dating back to 1915. In the early 20th century, the lake had a high water clarity, with abundant macrophytes and benthic algae, and hosted the most diverse molluscan community in New York State, including 32 gastropod and 9 unionid species. By the 1960s, lake turbidity increased during a period of anthropogenic eutrophication, resulting in a 38% decline in species richness and a 95% reduction in abundance of native gastropods grazing on benthic algae. Following the invasion of Dreissena spp. in 1991 and subsequent increases in water clarity, native gastropod species richness expanded by 37% and abundance increased 20-fold by 2012. In contrast, filter-feeding unionids were unaffected by increased turbidity during the period of eutrophication but were extirpated by dreissenids. Through contrasting effects on turbidity, eutrophication and Dreissena spp. have likely driven the observed changes in native grazing gastropods by affecting the abundance of light-limited benthic algae. Given the high species richness and ecological importance of benthic grazers, monitoring and managing turbidity is important in preserving molluscan diversity.

An evolutionary medicine approach to understanding factors that contribute to chronic obstructive pulmonary disease.

PubMed

Aoshiba, Kazutetsu; Tsuji, Takao; Itoh, Masayuki; Yamaguchi, Kazuhiro; Nakamura, Hiroyuki

2015-01-01

Although many studies have been published on the causes and mechanisms of chronic obstructive pulmonary disease (COPD), the reason for the existence of COPD and the reasons why COPD develops in humans have hardly been studied. Evolutionary medical approaches are required to explain not only the proximate factors, such as the causes and mechanisms of a disease, but the ultimate (evolutionary) factors as well, such as why the disease is present and why the disease develops in humans. According to the concepts of evolutionary medicine, disease susceptibility is acquired as a result of natural selection during the evolutionary process of traits linked to the genes involved in disease susceptibility. In this paper, we discuss the following six reasons why COPD develops in humans based on current evolutionary medical theories: (1) evolutionary constraints; (2) mismatch between environmental changes and evolution; (3) co-evolution with pathogenic microorganisms; (4) life history trade-off; (5) defenses and their costs, and (6) reproductive success at the expense of health. Our perspective pursues evolutionary answers to the fundamental question, 'Why are humans susceptible to this common disease, COPD, despite their long evolutionary history?' We believe that the perspectives offered by evolutionary medicine are essential for researchers to better understand the significance of their work.

The nervus terminalis in the chick: a FMRFamide-immunoreactive and AChE-positive nerve.

PubMed

Wirsig-Wiechmann, C R

1990-07-16

The chick terminal nerve (TN) was examined by immunocytochemical and histochemical methods. Molluscan cardioexcitatory peptide-immunoreactive (FMRFamide-ir) and acetylcholinesterase (AChE)-positive TN perikarya and fibers were distributed along olfactory and trigeminal nerves. FMRFamide-ir TN fibers terminated in the olfactory lamina propria and epithelium and in ganglia along the rostroventral nasal septum. This initial description of several populations of avian TN neurons should provide the foundation for future developmental studies of this system.

Evolutionary Perspectives on the Development of Social Exchanges.

ERIC Educational Resources Information Center

Sheese, Brad E.; Graziano, William G.

2002-01-01

Argues that apparent incompatibilities between social exchange and developmental perspectives can be resolved by using evolutionary theories to extend the logic of social exchange. Discusses the implications of an expanded evolutionary perspective on social exchange and development, proposing that developmental context and genetic relatedness may…

Measurement of Selected Enzymatic Activities in Solanum nigrum-Treated Biomphalaria arabica Snails

NASA Astrophysics Data System (ADS)

Al-Daihan, Sooad

In the present study, glucose, acid and alkaline phosphatases (ACP and ALP), α-amylase and lipase were measured for the first time in tissue homogenates of Biomphalaria arabica snails, molluscan intermediate host for Schistosoma mansoni in Saudi Arabia. Also, the effect of sublethal concentrations (LC25) of dry powdered Solanum nigrum leaf was tested as plant molluscicide against this snail species. The tested enzymes were altered in molluscicide-treated snails compared to control. While ALP and amylase were slightly affected, ACP and lipase were significantly altered. Glucose as an important energy source for a successful schistosome-snail relationship was significantly reduced in molluscicide-treated snails. In conclusion, sublethal concentration of the molluscicide showed potent effect in disturbing snail biochemistry which may render them physiologically unsuitable for the developing of schistosome parasite. This could be considered as a promising strategy to control the disease.

Application of a weighted-averaging method for determining paleosalinity: a tool for restoration of south Florida's estuaries

USGS Publications Warehouse

Wingard, G.L.; Hudley, J.W.

2012-01-01

A molluscan analogue dataset is presented in conjunction with a weighted-averaging technique as a tool for estimating past salinity patterns in south Florida’s estuaries and developing targets for restoration based on these reconstructions. The method, here referred to as cumulative weighted percent (CWP), was tested using modern surficial samples collected in Florida Bay from sites located near fixed water monitoring stations that record salinity. The results were calibrated using species weighting factors derived from examining species occurrence patterns. A comparison of the resulting calibrated species-weighted CWP (SW-CWP) to the observed salinity at the water monitoring stations averaged over a 3-year time period indicates, on average, the SW-CWP comes within less than two salinity units of estimating the observed salinity. The SW-CWP reconstructions were conducted on a core from near the mouth of Taylor Slough to illustrate the application of the method.

Ocean Acidification Causes Increased Calcium Carbonate Turnover during Larval Shell Formation

NASA Astrophysics Data System (ADS)

Frieder, C.; Pan, F.; Applebaum, S.; Manahan, D. T.

2016-02-01

Mollusca is a major taxon for studies of the evolution and mechanisms of calcification. Under current and future ocean change scenarios, decreases in shell size have been observed in many molluscan species during early development. The mechanistic basis for these decreases are of significant interest. In this study, Pacific oyster larvae (Crassostrea gigas) reared at aragonite undersaturation (Ω < 1) accreted just a third of shell mass relative to control (Ω >> 1). Coupling radioisotope tracer assays with mineral mass measurements allowed calculation of calcification budgets for first shell formation in veliger stage larvae. Three primary mechanisms (in order of increasing effect) contributed to the change in shell mass at undersaturation: delayed onset of calcification, increased dissolution rates, and decreased net calcification rates. The observation of dissolution indicates turnover of the newly formed shell, and physicochemical constraints of undersaturation provide a mechanistic basis for decreased calcification.

Statoconia formation in molluscan statocysts

NASA Technical Reports Server (NTRS)

Wiederhold, M. L.; Sheridan, C. E.; Smith, N. K.

1986-01-01

The gravity sensors of all molluscs phylogenetically below the cephalopods are spherical organs called statocysts. The wall of the sphere contains mechanosensory cells whose sensory cilia project into the lumen of the cyst. The lumen is filled with fluid and dense "stones", the statoconia or statoliths, which sink under the influence of gravity to load, and stimulate, those receptor cells which are at the bottom. The statoconia of Aplysia californica are shown to be calcified about a lamellar arrangement of membranes. Similar lamellar membrane arrangements are seen within the receptor cells, and their possible role in the formation of the statoconia is discussed. SEM of unfixed statoconia reveals plate-like crystallization on their surface. Elemental analysis shows a relatively high Sr content, which is of interest, since others have recently reported that Sr is required in the culture medium of several laboratory reared molluscs in order for the statoconia to develop.

Microcell parasites of molluscs: introduction to DAO Special 7.

PubMed

Carnegie, Ryan B; Engelsma, Marc Y

2014-07-24

First discovered decades ago, microcell protistan parasites of the genera Bonamia and Mikrocytos remain relevant today for their economic impacts on growing molluscan aquaculture industries and fisheries. Bonamia parasites have received more attention over the years in part because they are more widespread and thus of wider concern, but there has been renewed interest in Mikrocytos recently with the generation of important new findings. Among these has been the surprising observation that Mikrocytos has phylogenetic affinities to the Rhizaria, which includes the haplosporidian protists and the genus Bonamia. This Diseases of Aquatic Organisms Special, emerging from the 5th Meeting of the Microcell Working Group held at the Central Veterinary Institute, Lelystad, the Netherlands, in February 2012, presents new insights into Mikrocytos and Bonamia diversity, distributions, diagnostics, ultrastructure, and infection dynamics, and captures major developments in the field since the last review of these genera in 2004.

Articulated Wiwaxia from the Cambrian Stage 3 Xiaoshiba lagerstätte.

PubMed

Yang, Jie; Smith, Martin R; Lan, Tian; Hou, Jin-bo; Zhang, Xi-guang

2014-04-10

Wiwaxia is a bizarre metazoan that has been interpreted as a primitive mollusc and as a polychaete annelid worm. Extensive material from the Burgess Shale provides a detailed picture of its morphology and ontogeny, but the fossil record outside this lagerstätte is scarce, and complete wiwaxiids are particularly rare. Here we report small articulated specimens of Wiwaxia foliosa sp. nov. from the Xiaoshiba fauna (Cambrian Stage 3, Hongjingshao Formation, Kunming, south China). Although spines are absent, the fossils' sclerites - like those of W. corrugata - are symmetrically arranged in five distinct zones. They form rows across the body, and were individually added and shed throughout growth to retain an approximately symmetrical body shape. Their development pattern suggests a molluscan affinity. The basic body plan of wiwaxiids is fundamentally conserved across two continents through Cambrian Stages 3-5 - revealing morphological stasis in the wake of the Cambrian explosion.

Development of X-TOOLSS: Preliminary Design of Space Systems Using Evolutionary Computation

NASA Technical Reports Server (NTRS)

Schnell, Andrew R.; Hull, Patrick V.; Turner, Mike L.; Dozier, Gerry; Alverson, Lauren; Garrett, Aaron; Reneau, Jarred

2008-01-01

Evolutionary computational (EC) techniques such as genetic algorithms (GA) have been identified as promising methods to explore the design space of mechanical and electrical systems at the earliest stages of design. In this paper the authors summarize their research in the use of evolutionary computation to develop preliminary designs for various space systems. An evolutionary computational solver developed over the course of the research, X-TOOLSS (Exploration Toolset for the Optimization of Launch and Space Systems) is discussed. With the success of early, low-fidelity example problems, an outline of work involving more computationally complex models is discussed.

A paleoecologic reconstruction of the history of Featherbed Bank, Biscayne National Park, Biscayne Bay, Florida

USGS Publications Warehouse

Stone, Jeffery R.; Cronin, T. M.; Brewster-Wingard, G. L.; Ishman, S.E.; Wardlaw, B.R.; Holmes, C.W.

2000-01-01

Using multiple-proxy biological indicators, a paleoecological history of the past 550 years of Featherbed Bank, Biscayne Bay, has been reconstructed from a short (2.26 m) sediment core. Paleoecological changes in ostracode, mollusc, and foraminifer assemblages show that core SEI297-FB-1 can be divided into three distinctly different zones, which together provide evidence for distinct changes in historical environmental conditions at Featherbed Bank. Assemblages from fossil biotic communities within zone 1, representing approximately 1440 to 1550 AD, are characterized by open-marine biota with relatively limited numbers of epiphytic biota. Molluscan faunal indicators suggest the sediment was capable of supporting infaunal organisms and that faunal richness was relatively limited during this time period. A change in the biotic community occurred around 1550 AD and continued until the late 1800's distinguishing zone 2. Fossil biotic indicators from zone 2 show a strong dominance of epiphytic organisms within all of the biotic communities examined. Foraminifers, molluscs, and ostracodes capable of subsisting in salinities slightly lower than normal marine begin to flourish in this time period, and there is a marked decline in infaunal molluscs. Zone 2 assemblages are replaced around 1900 AD by increased numbers of organisms that typify open-marine conditions and a return to decreased epiphytic assemblages, similar to zone 1. Zone 3 assemblages, however, show some strong dissimilarities from zone 1, including limited infaunal molluscs, increased abundances of the ostracode Malzella floridana, and a significant increase in molluscan faunal richness.

Daily oscillation of gene expression associated with nacreous layer formation

NASA Astrophysics Data System (ADS)

Miyazaki, Yoko; Usui, Tomomi; Kajikawa, Aya; Hishiyama, Hajime; Matsuzawa, Norifumi; Nishida, Takuma; Machii, Akira; Samata, Tetsuro

2008-06-01

Three major organic matrix components, nacrein, MSI60 and N16 have been reported from the nacreous layer of Japanese pearl oyster, Pinctada fucata. Though several in vitro experiments have been carried out to elucidate the functions of these molecules details have not yet been clarified. In this report, we tempt to clarify the gene expression levels encoding the above three proteins between samples of 1) summer and winter seasons and 2) ocean and aquarium environments by using real-time polymerase chain reaction (PCR). It was confirmed that the biomineralization process of P. fucata is mainly influenced by the circatidal rhythm of the ocean environment. The gene expressions coding for N16 and MSI60 increased at the time of high tide, while that of nacrein increased at the time of low tide. The similar tendency observed in N16 and MSI60 showed the possibility that both components are secreted simultaneously, supporting a hypothesis that N16 forms cross-linkage with MSI60 to form the membrane. The expressions of MSI60, N16 and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes were remarkable in winter season, while no variation was found in the expression level of the nacrein gene in summer and winter season. The study is the first attempt regarding the seasonal and circadian rhythms observed on gene expressions incorporated into molluscan shell formation. The results will give a new insight into the relationship between molluscan physiology and the mechanism of shell formation.

Eutrophication and Dreissena Invasion as Drivers of Biodiversity: A Century of Change in the Mollusc Community of Oneida Lake

PubMed Central

Karatayev, Vadim A.; Karatayev, Alexander Y.; Burlakova, Lyubov E.; Rudstam, Lars G.

2014-01-01

Changes in nutrient loading and invasive species are among the strongest human-driven disturbances in freshwater ecosystems, but our knowledge on how they affect the biodiversity of lakes is still limited. We conducted a detailed historical analysis of the mollusc community of Oneida Lake based on our comprehensive lakewide study in 2012 and previous surveys dating back to 1915. In the early 20th century, the lake had a high water clarity, with abundant macrophytes and benthic algae, and hosted the most diverse molluscan community in New York State, including 32 gastropod and 9 unionid species. By the 1960s, lake turbidity increased during a period of anthropogenic eutrophication, resulting in a 38% decline in species richness and a 95% reduction in abundance of native gastropods grazing on benthic algae. Following the invasion of Dreissena spp. in 1991 and subsequent increases in water clarity, native gastropod species richness expanded by 37% and abundance increased 20-fold by 2012. In contrast, filter-feeding unionids were unaffected by increased turbidity during the period of eutrophication but were extirpated by dreissenids. Through contrasting effects on turbidity, eutrophication and Dreissena spp. have likely driven the observed changes in native grazing gastropods by affecting the abundance of light-limited benthic algae. Given the high species richness and ecological importance of benthic grazers, monitoring and managing turbidity is important in preserving molluscan diversity. PMID:25010705

Cyclic nucleotides induce long-term augmentation of glutamate-activated chloride current in molluscan neurons.

PubMed

Bukanova, Julia V; Solntseva, Elena I; Skrebitsky, Vladimir G

2005-12-01

1. Literature data indicate that serotonin induces the long-term potentiation of glutamate (Glu) response in molluscan neurons. The aim of present work was to elucidate whether cyclic nucleotides can cause the same effect. 2. Experiments were carried out on isolated neurons of the edible snail (Helix pomatia) using a two-microelectrode voltage-clamp method. 3. In the majority of the cells examined, the application of Glu elicited a Cl- -current. The reversal potential (Er) of this current lied between -35 and -55 mV in different cells. 4. Picrotoxin, a blocker of Cl- -channels, suppressed this current equally on both sides of Er. Furosemide, an antagonist of both Cl- -channels and the Na+/K+/Cl- -cotransporter, had a dual effect on Glu-response: decrease in conductance, and shift of Er to negative potentials. 5. A short-term (2 min) cell treatment with 8-Br-cAMP or 8-Br-cGMP caused long-term (up to 30 min) change in Glu-response. At a holding potential of -60 mV, which was close to the resting level, an increase in Glu-activated inward current was observed. This potentiation seems to be related to the right shift of Er of Glu-activated Cl- -current rather than to the increase in conductance of Cl- -channels. The blocking effect of picrotoxin rested after 8-Br-cAMP treatment. 6. The change in the Cl- -homeostasis as a possible mechanism for the observed effect of cyclic nucleotides is discussed.

Using Evolutionary Data in Developing Phylogenetic Trees: A Scaffolded Approach with Authentic Data

ERIC Educational Resources Information Center

Davenport, K. D.; Milks, Kirstin Jane; Van Tassell, Rebecca

2015-01-01

Analyzing evolutionary relationships requires that students have a thorough understanding of evidence and of how scientists use evidence to develop these relationships. In this lesson sequence, students work in groups to process many different lines of evidence of evolutionary relationships between ungulates, then construct a scientific argument…

The complete sequences and gene organisation of the mitochondrial genomes of the heterodont bivalves Acanthocardia tuberculata and Hiatella arctica – and the first record for a putative Atpase subunit 8 gene in marine bivalves

PubMed Central

Dreyer, Hermann; Steiner, Gerhard

2006-01-01

Background Mitochondrial (mt) gene arrangement is highly variable among molluscs and especially among bivalves. Of the 30 complete molluscan mt-genomes published to date, only one is of a heterodont bivalve, although this is the most diverse taxon in terms of species numbers. We determined the complete sequence of the mitochondrial genomes of Acanthocardia tuberculata and Hiatella arctica, (Mollusca, Bivalvia, Heterodonta) and describe their gene contents and genome organisations to assess the variability of these features among the Bivalvia and their value for phylogenetic inference. Results The size of the mt-genome in Acanthocardia tuberculata is 16.104 basepairs (bp), and in Hiatella arctica 18.244 bp. The Acanthocardia mt-genome contains 12 of the typical protein coding genes, lacking the Atpase subunit 8 (atp8) gene, as all published marine bivalves. In contrast, a complete atp8 gene is present in Hiatella arctica. In addition, we found a putative truncated atp8 gene when re-annotating the mt-genome of Venerupis philippinarum. Both mt-genomes reported here encode all genes on the same strand and have an additional trnM. In Acanthocardia several large non-coding regions are present. One of these contains 3.5 nearly identical copies of a 167 bp motive. In Hiatella, the 3' end of the NADH dehydrogenase subunit (nad)6 gene is duplicated together with the adjacent non-coding region. The gene arrangement of Hiatella is markedly different from all other known molluscan mt-genomes, that of Acanthocardia shows few identities with the Venerupis philippinarum. Phylogenetic analyses on amino acid and nucleotide levels robustly support the Heterodonta and the sister group relationship of Acanthocardia and Venerupis. Monophyletic Bivalvia are resolved only by a Bayesian inference of the nucleotide data set. In all other analyses the two unionid species, being to only ones with genes located on both strands, do not group with the remaining bivalves. Conclusion The two mt-genomes reported here add to and underline the high variability of gene order and presence of duplications in bivalve and molluscan taxa. Some genomic traits like the loss of the atp8 gene or the encoding of all genes on the same strand are homoplastic among the Bivalvia. These characters, gene order, and the nucleotide sequence data show considerable potential of resolving phylogenetic patterns at lower taxonomic levels. PMID:16948842

Stable carbon and oxygen isotope signatures in molluscan shells under ocean acidification

NASA Astrophysics Data System (ADS)

Nishida, K.; Hayashi, M.; Suzuki, A.; Sato, M.; Nojiri, Y.

2017-12-01

Stable carbon and oxygen isotope compositions (δ13C, δ18O) of biogenic carbonate have been widely used for many paleoclimate, paleoecological, and biomineralization studies. δ13C of molluscan shells reflects the mixing of δ13C of dissolved inorganic carbon (DIC) of seawater and respiratory carbon. Previous studies reported physiological effects on molluscs by ocean acidification, and thus the metabolic changes could potentially appear in shell δ13C as changes in a fraction of two carbon sources. In addition, shell δ18O, a commonly used proxy of seawater temperature and seawater δ18O, is also affected by seawater carbonate chemistry. As changes in the marine carbonate system, such as pH and pCO2, have occurred in the past 300 million years, to estimate pH effect on paleotemperature reconstruction is important. Here, we experimentally examined acidification effects on shell δ13C and δ18O of two species of clams for understanding of environmental and physiological proxies. Juvenile specimens of bloody clam Scapharca broughtonii and Japanese surf clam Pseudocardium sachalinense were cultured at five (400, 600, 800, 1000, and 1200 µatm, P. sachalinense) or six (280, 400, 600, 800, 1000, and 1200 µatm, S. broughtonii) different pCO2 levels using CO2 control system of the Demonstration Laboratory, MERI, Japan. Significant negative correlations between shell δ13C and pH appeared in S. broughtonii, which showed non-significant pH effects on calcification, and the slope of the relationship of shell carbonate was lower than that of seawater DIC. On the other hand, in P. sachalinense which showed a decrease in calcification at low-pH treatment, the slopes of the relationship between shell δ13C and pH was roughly the same as that of seawater DIC. Thus, the extrapallial fluid of P. sachalinense might more strongly affected by acidified seawater than S. broughtonii. The results of two species might be attributable to differences in physiological responses to acidified seawater. δ18O of S. broughtonii had a significant negative correlation with pH (-0.48‰ /pH, at 17°C). These of P. sachalinense showed a significant positive relationship with pH (+1.05‰ /pH, at 17°C). As two species showed different trends of shell δ18O, further experimental studies are needed for the understanding of pH dependency on molluscan shell δ18O.

Modelling the influence of parental effects on gene-network evolution.

PubMed

Odorico, Andreas; Rünneburger, Estelle; Le Rouzic, Arnaud

2018-05-01

Understanding the importance of nongenetic heredity in the evolutionary process is a major topic in modern evolutionary biology. We modified a classical gene-network model by allowing parental transmission of gene expression and studied its evolutionary properties through individual-based simulations. We identified ontogenetic time (i.e. the time gene networks have to stabilize before being submitted to natural selection) as a crucial factor in determining the evolutionary impact of this phenotypic inheritance. Indeed, fast-developing organisms display enhanced adaptation and greater robustness to mutations when evolving in presence of nongenetic inheritance (NGI). In contrast, in our model, long development reduces the influence of the inherited state of the gene network. NGI thus had a negligible effect on the evolution of gene networks when the speed at which transcription levels reach equilibrium is not constrained. Nevertheless, simulations show that intergenerational transmission of the gene-network state negatively affects the evolution of robustness to environmental disturbances for either fast- or slow-developing organisms. Therefore, these results suggest that the evolutionary consequences of NGI might not be sought only in the way species respond to selection, but also on the evolution of emergent properties (such as environmental and genetic canalization) in complex genetic architectures. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Biology Needs Evolutionary Software Tools: Let’s Build Them Right

PubMed Central

Team, Galaxy; Goecks, Jeremy; Taylor, James

2018-01-01

Abstract Research in population genetics and evolutionary biology has always provided a computational backbone for life sciences as a whole. Today evolutionary and population biology reasoning are essential for interpretation of large complex datasets that are characteristic of all domains of today’s life sciences ranging from cancer biology to microbial ecology. This situation makes algorithms and software tools developed by our community more important than ever before. This means that we, developers of software tool for molecular evolutionary analyses, now have a shared responsibility to make these tools accessible using modern technological developments as well as provide adequate documentation and training. PMID:29688462

Ancestral assumptions and the clinical uncertainty of evolutionary medicine.

PubMed

Cournoyea, Michael

2013-01-01

Evolutionary medicine is an emerging field of medical studies that uses evolutionary theory to explain the ultimate causes of health and disease. Educational tools, online courses, and medical school modules are being developed to help clinicians and students reconceptualize health and illness in light of our evolutionary past. Yet clinical guidelines based on our ancient life histories are epistemically weak, relying on the controversial assumptions of adaptationism and advocating a strictly biophysical account of health. To fulfill the interventionist goals of clinical practice, it seems that proximate explanations are all we need to develop successful diagnostic and therapeutic guidelines. Considering these epistemic concerns, this article argues that the clinical relevance of evolutionary medicine remains uncertain at best.

New Indo-Pacific species of the genus Teretia Norman, 1888 (Gastropoda: Raphitomidae).

PubMed

Morassi, Mauro; Bonfitto, Antonio

2015-01-21

Four new species are assigned to the genus Teretia Norman, 1888 in the family Raphitomidae Bellardi, 1875 and herein described: Teretia neocaledonica sp. nov., T. sysoevi sp. nov., T. tongaensis sp. nov. from the southeastern Pacific and Teretia tavianii sp. nov. from the Gulf of Aden. The new species represent the first Indo-Pacific record of a genus previously known in the recent molluscan fauna by only two species from the Atlantic Ocean-Mediterranean Sea and Southern Africa. A possible Tethyan origin for the genus Teretia is suggested. 

Non-native molluscan colonizers on deliberately placed shipwrecks in the Florida Keys, with description of a new species of potentially invasive worm-snail (Gastropoda: Vermetidae).

PubMed

Bieler, Rüdiger; Granados-Cifuentes, Camila; Rawlings, Timothy A; Sierwald, Petra; Collins, Timothy M

2017-01-01

Artificial reefs created by deliberately sinking ships off the coast of the Florida Keys island chain are providing new habitat for marine invertebrates. This newly developing fouling community includes the previously reported invasive orange tube coral Tubastraea coccinea and the non-native giant foam oyster Hyotissa hyotis . New SCUBA-based surveys involving five shipwrecks spanning the upper, middle, and lower Florida Keys, show T. coccinea now also established in the lower Keys and H. hyotis likewise extending to new sites. Two additional mollusks found on the artificial reefs, the amathinid gastropod Cyclothyca pacei and gryphaeid oyster Hyotissa mcgintyi , the latter also common in the natural reef areas, are discussed as potentially non-native. A new species of sessile, suspension-feeding, worm-snail, Thylacodes vandyensi s Bieler, Rawlings & Collins n. sp. (Vermetidae), is described from the wreck of the USNS Vandenberg off Key West and discussed as potentially invasive. This new species is compared morphologically and by DNA barcode markers to other known members of the genus, and may be a recent arrival from the Pacific Ocean. Thylacodes vandyensis is polychromatic, with individuals varying in both overall head-foot coloration and mantle margin color pattern. Females brood stalked egg capsules attached to their shell within the confines of their mantle cavity, and give rise to crawl-away juveniles. Such direct-developing species have the demonstrated capacity for colonizing habitats isolated far from their native ranges and establishing rapidly growing founder populations. Vermetid gastropods are common components of the marine fouling community in warm temperate and tropical waters and, as such, have been tagged as potentially invasive or with a high potential to be invasive in the Pacific Ocean. As vermetids can influence coral growth/composition in the Pacific and have been reported serving as intermediate hosts for blood flukes of loggerhead turtles, such new arrivals in the Florida Keys National Marine Sanctuary are of concern. Growing evidence indicates that artificial reefs can act as permanent way-stations for arriving non-natives, providing nurseries within which populations may grow in an environment with reduced competition compared to native habitats. Consequently, artificial reefs can act as sentinels for the appearance of new species. Ongoing monitoring of the developing molluscan fauna on the artificial reefs of the Florida Keys is necessary to recognize new invasions and identify potential eradication targets, thereby assuring the health of the nearby natural barrier reef.

Non-native molluscan colonizers on deliberately placed shipwrecks in the Florida Keys, with description of a new species of potentially invasive worm-snail (Gastropoda: Vermetidae)

PubMed Central

Granados-Cifuentes, Camila; Rawlings, Timothy A.; Sierwald, Petra; Collins, Timothy M.

2017-01-01

Artificial reefs created by deliberately sinking ships off the coast of the Florida Keys island chain are providing new habitat for marine invertebrates. This newly developing fouling community includes the previously reported invasive orange tube coral Tubastraea coccinea and the non-native giant foam oyster Hyotissa hyotis. New SCUBA-based surveys involving five shipwrecks spanning the upper, middle, and lower Florida Keys, show T. coccinea now also established in the lower Keys and H. hyotis likewise extending to new sites. Two additional mollusks found on the artificial reefs, the amathinid gastropod Cyclothyca pacei and gryphaeid oyster Hyotissa mcgintyi, the latter also common in the natural reef areas, are discussed as potentially non-native. A new species of sessile, suspension-feeding, worm-snail, Thylacodes vandyensis Bieler, Rawlings & Collins n. sp. (Vermetidae), is described from the wreck of the USNS Vandenberg off Key West and discussed as potentially invasive. This new species is compared morphologically and by DNA barcode markers to other known members of the genus, and may be a recent arrival from the Pacific Ocean. Thylacodes vandyensis is polychromatic, with individuals varying in both overall head-foot coloration and mantle margin color pattern. Females brood stalked egg capsules attached to their shell within the confines of their mantle cavity, and give rise to crawl-away juveniles. Such direct-developing species have the demonstrated capacity for colonizing habitats isolated far from their native ranges and establishing rapidly growing founder populations. Vermetid gastropods are common components of the marine fouling community in warm temperate and tropical waters and, as such, have been tagged as potentially invasive or with a high potential to be invasive in the Pacific Ocean. As vermetids can influence coral growth/composition in the Pacific and have been reported serving as intermediate hosts for blood flukes of loggerhead turtles, such new arrivals in the Florida Keys National Marine Sanctuary are of concern. Growing evidence indicates that artificial reefs can act as permanent way-stations for arriving non-natives, providing nurseries within which populations may grow in an environment with reduced competition compared to native habitats. Consequently, artificial reefs can act as sentinels for the appearance of new species. Ongoing monitoring of the developing molluscan fauna on the artificial reefs of the Florida Keys is necessary to recognize new invasions and identify potential eradication targets, thereby assuring the health of the nearby natural barrier reef. PMID:28392984

Evolutionary molecular medicine.

PubMed

Nesse, Randolph M; Ganten, Detlev; Gregory, T Ryan; Omenn, Gilbert S

2012-05-01

Evolution has long provided a foundation for population genetics, but some major advances in evolutionary biology from the twentieth century that provide foundations for evolutionary medicine are only now being applied in molecular medicine. They include the need for both proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, competition between alleles, co-evolution, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are transforming evolutionary biology in ways that create even more opportunities for progress at its interfaces with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and related principles to speed the development of evolutionary molecular medicine.

Taxonomic and numerical sufficiency in a Lower and Middle Miocene molluscan metacommunity of the Central Paratethys

NASA Astrophysics Data System (ADS)

Zuschin, Martin; Nawrot, Rafal; Harzhauser, Mathias; Mandic, Oleg

2015-04-01

Among the most important questions in quantitative palaeoecology is how taxonomic and numerical resolution affect the analysis of community and metacommunity patterns. A species-abundance data set (10 localities, 213 bulk samples, 478 species, > 49,000 shells) from Burdigalian, Langhian and Serravallian benthic marine molluscan assemblages of the Central Paratethys was studied for this purpose. Assemblages are from two nearshore habitats (estuarine and marine intertidal) and three subtidal habitats (estuarine, fully marine sandy, and fully marine pelitic), which represent four biozones and four 3rd order depositional sequences over more than three million years, and are developed along the same depth-related environmental gradient. Double-standardized data subsampled to 19 samples per habitat, each with a minimum of 50 specimens, were used to calculate R²-values from PERMANOVA as a measure of differences between habitats at three taxonomic levels (species, genera and families) and at five levels of data transformation (raw abundances, percentages, square-root transformed percentages, fourth-root transformed percentages, presence-absence data). Species discriminate better between habitats than genera and families, but the differences between taxonomic levels are much stronger in the subtidal, where genera and families have more species than than in the intertidal. When all habitats are compared percentages and square-root transformed percentages discriminate equally well and perform better than higher levels of data transformation. Among nearshore and among subtidal habitats, however, the ability to discriminate between habitats increases with the level of data transformation (i.e., it is best for fourth-root transformed percentages and presence-absence data). The impact of decreasing taxonomic resolution is of minor importance in nearshore habitats, which are characterized by similar assemblages showing strong dominance of few widely distributed species, and many families represented by only one species (77.9%). Consequently, the differentiation between nearshore habitats is much weaker compared to subtidal assemblages. The latter are characterized by more distinct, relatively even assemblages with comparatively few families represented by only one species (64.2%) and many rare taxa, whose importance is emphasized by higher levels of data transformation.

EVOLUTIONARY FOUNDATIONS FOR MOLECULAR MEDICINE

PubMed Central

Nesse, Randolph M.; Ganten, Detlev; Gregory, T. Ryan; Omenn, Gilbert S.

2015-01-01

Evolution has long provided a foundation for population genetics, but many major advances in evolutionary biology from the 20th century are only now being applied in molecular medicine. They include the distinction between proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are further transforming evolutionary biology and creating yet more opportunities for progress at the interface of evolution with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and others to speed the development of evolutionary molecular medicine. PMID:22544168

[The history of development of evolutionary methods in St. Petersburg school of computer simulation in biology].

PubMed

Menshutkin, V V; Kazanskiĭ, A B; Levchenko, V F

2010-01-01

The history of rise and development of evolutionary methods in Saint Petersburg school of biological modelling is traced and analyzed. Some pioneering works in simulation of ecological and evolutionary processes, performed in St.-Petersburg school became an exemplary ones for many followers in Russia and abroad. The individual-based approach became the crucial point in the history of the school as an adequate instrument for construction of models of biological evolution. This approach is natural for simulation of the evolution of life-history parameters and adaptive processes in populations and communities. In some cases simulated evolutionary process was used for solving a reverse problem, i. e., for estimation of uncertain life-history parameters of population. Evolutionary computations is one more aspect of this approach application in great many fields. The problems and vistas of ecological and evolutionary modelling in general are discussed.

Individual Development and Evolution: Experiential Canalization of Self-Regulation

ERIC Educational Resources Information Center

Blair, Clancy; Raver, C. Cybele

2012-01-01

In this article, we contrast evolutionary and psychobiological models of individual development to address the idea that individual development occurring in prototypically risky and unsupportive environments can be understood as adaptation. We question traditional evolutionary explanations of individual development, calling on the principle of…

Developmental Transcriptome of Aplysia californica

PubMed Central

HEYLAND, ANDREAS; VUE, ZER; VOOLSTRA, CHRISTIAN R.; MEDINA, MÓNICA; MOROZ, LEONID L.

2014-01-01

Genome-wide transcriptional changes in development provide important insight into mechanisms underlying growth, differentiation, and patterning. However, such large-scale developmental studies have been limited to a few representatives of Ecdysozoans and Chordates. Here, we characterize transcriptomes of embryonic, larval, and metamorphic development in the marine mollusc Aplysia californica and reveal novel molecular components associated with life history transitions. Specifically, we identify more than 20 signal peptides, putative hormones, and transcription factors in association with early development and metamorphic stages—many of which seem to be evolutionarily conserved elements of signal transduction pathways. We also characterize genes related to biomineralization—a critical process of molluscan development. In summary, our experiment provides the first large-scale survey of gene expression in mollusc development, and complements previous studies on the regulatory mechanisms underlying body plan patterning and the formation of larval and juvenile structures. This study serves as a resource for further functional annotation of transcripts and genes in Aplysia, specifically and molluscs in general. A comparison of the Aplysia developmental transcriptome with similar studies in the zebra fish Danio rerio, the fruit fly Drosophila melanogaster, the nematode Caenorhabditis elegans, and other studies on molluscs suggests an overall highly divergent pattern of gene regulatory mechanisms that are likely a consequence of the different developmental modes of these organisms. PMID:21328528

Evolutionary psychology and evolutionary developmental psychology: understanding the evolution of human behavior and development.

PubMed

Hernández Blasi, Carlos; Causey, Kayla

2010-02-01

This is an introduction to this special issue on evolutionary psychology (EP) and evolutionary developmental psychology (EDP). We suggest here that, contrary to some common assumptions, mainstream psychology continues to be essentially non Darwinian and that EP and EDP are new approaches that can potentially help us to change this situation. We then present the organization of the special issue (composed of six papers). We conclude that evolution is certainly not the final consideration in psychology, but emphasize its importance as the basis upon which all modern behaviors and development are built.

An evolutionary critique of cultural analysis in sociology.

PubMed

Crippen, T

1992-12-01

A noteworthy development that has transpired in American sociology in the past quarter century has been the increasingly sophisticated interest in the analysis of human cultural systems. Sadly, however, these analyses reveal that social scientists rarely appreciate the profoundly evolutionary aspects of human culture. The chief purpose of this essay is to address this shortcoming and to offer some tentative suggestions toward its rectification. The essay begins by briefly reviewing recent developments in the analysis of cultural systems, primarily by reference to the influential work of Wuthnow. Second, a common flaw in these approaches is addressed-namely, the absence of any recognition of the value of grounding sociocultural theory in an informed evolutionary framework-and the case is made that this shortcoming is avoidable, even within the context of the intellectual traditions of the social sciences. Third, the evolutionary foundations of human cultural behavior are explored in terms of an analysis of relevant theoretical and empirical developments in the evolutionary neurosciences. Fourth, the value of these insights is illustrated by reference to an evolutionary critique of a recent and thought-provoking contribution to the study of modern political culture-Douglas and Wildavsky's analysis ofRisk and Culture. Finally, the article concludes by emphasizing the value of and the necessity for incorporating evolutionary reasoning into the domain of sociocultural theory.

Rediscovery of type locality of Turritella andersoni and its geologic age implications for Eocene strata in northeast Pacific

DOE Office of Scientific and Technical Information (OSTI.GOV)

Squires, R.L.

1988-03-01

Turritella andersoni is one of the most important index fossils from the early Eocene in the northeast Pacific region. Its geographic range is from Baja Sur, Mexico, to Victoria, British Columbia. Its holotype locality is in Urruttia Canyon, 26 km (16 mi) north of Coalinga, central California, but the exact topographic and stratigraphic positions of this locality have been a source of confusion and uncertainty for the past 76 years. The holotype locality has been rediscovered, based on consultation of museum records, original field notes of early workers, and field checking. Numerous specimens were found only in the upper partmore » of the Cerros Shale Member of the Lodo Formation in the center of Sec. 15, T18S, R14E, (1969, Joaquin Rocks, 7.5' quadrangle, California). The Cerros Shale Member is 26 m thick in this area. Microfossil samples were taken from greenish-gray siltstone in the immediate area of the holotype locality. Calcareous nannofossils (especially Discoaster lodoensis) from these strata indicate an early Eocene (CP10 Biozone) age, which would be equivalent to the provincial molluscan Capay Stage in the restricted sense of modern workers. Previously the molluscan stage of T. andersoni had been Meganos . (earliest Eocene) through Capay, because of the possibility that the holotype locality (when eventually rediscovered) might be of Meganos age. This present study negates the Meganos age possibility, and T. andersoni can now be shown to be confined to the Capay Stage. This age refinement will be a valuable asset to future biostratigraphic, paleogeographic, and paleobiogeographic work.« less

Neuropeptides encoded by the genomes of the Akoya pearl oyster Pinctata fucata and Pacific oyster Crassostrea gigas: a bioinformatic and peptidomic survey.

PubMed

Stewart, Michael J; Favrel, Pascal; Rotgans, Bronwyn A; Wang, Tianfang; Zhao, Min; Sohail, Manzar; O'Connor, Wayne A; Elizur, Abigail; Henry, Joel; Cummins, Scott F

2014-10-02

Oysters impart significant socio-ecological benefits from primary production of food supply, to estuarine ecosystems via reduction of water column nutrients, plankton and seston biomass. Little though is known at the molecular level of what genes are responsible for how oysters reproduce, filter nutrients, survive stressful physiological events and form reef communities. Neuropeptides represent a diverse class of chemical messengers, instrumental in orchestrating these complex physiological events in other species. By a combination of in silico data mining and peptide analysis of ganglia, 74 putative neuropeptide genes were identified from genome and transcriptome databases of the Akoya pearl oyster, Pinctata fucata and the Pacific oyster, Crassostrea gigas, encoding precursors for over 300 predicted bioactive peptide products, including three newly identified neuropeptide precursors PFGx8amide, RxIamide and Wx3Yamide. Our findings also include a gene for the gonadotropin-releasing hormone (GnRH) and two egg-laying hormones (ELH) which were identified from both oysters. Multiple sequence alignments and phylogenetic analysis supports similar global organization of these mature peptides. Computer-based peptide modeling of the molecular tertiary structures of ELH highlights the structural homologies within ELH family, which may facilitate ELH activity leading to the release of gametes. Our analysis demonstrates that oysters possess conserved molluscan neuropeptide domains and overall precursor organization whilst highlighting many previously unrecognized bivalve idiosyncrasies. This genomic analysis provides a solid foundation from which further studies aimed at the functional characterization of these molluscan neuropeptides can be conducted to further stimulate advances in understanding the ecology and cultivation of oysters.

Structure-based function prediction of the expanding mollusk tyrosinase family

NASA Astrophysics Data System (ADS)

Huang, Ronglian; Li, Li; Zhang, Guofan

2017-11-01

Tyrosinase (Ty) is a common enzyme found in many different animal groups. In our previous study, genome sequencing revealed that the Ty family is expanded in the Pacific oyster ( Crassostrea gigas). Here, we examine the larger number of Ty family members in the Pacific oyster by high-level structure prediction to obtain more information about their function and evolution, especially the unknown role in biomineralization. We verified 12 Ty gene sequences from Crassostrea gigas genome and Pinctada fucata martensii transcriptome. By using phylogenetic analysis of these Tys with functionally known Tys from other molluscan species, eight subgroups were identified (CgTy_s1, CgTy_s2, MolTy_s1, MolTy-s2, MolTy-s3, PinTy-s1, PinTy-s2 and PviTy). Structural data and surface pockets of the dinuclear copper center in the eight subgroups of molluscan Ty were obtained using the latest versions of prediction online servers. Structural comparison with other Ty proteins from the protein databank revealed functionally important residues (HA1, HA2, HA3, HB1, HB2, HB3, Z1-Z9) and their location within these protein structures. The structural and chemical features of these pockets which may related to the substrate binding showed considerable variability among mollusks, which undoubtedly defines Ty substrate binding. Finally, we discuss the potential driving forces of Ty family evolution in mollusks. Based on these observations, we conclude that the Ty family has rapidly evolved as a consequence of substrate adaptation in mollusks.

Density of total and pathogenic (tdh+) Vibrio parahaemolyticus in Atlantic and Gulf coast molluscan shellfish at harvest.

PubMed

Cook, David W; Bowers, John C; DePaola, Angelo

2002-12-01

The densities of total and pathogenic Vibrio parahaemolyticus in 671 samples of molluscan shellfish harvested in 1999 and 2000 from 14 sites in seven Gulf and Atlantic coast states were determined at 2-week intervals over a period of 12 to 16 months in each state. Changes in V. parahaemolyticus densities in shellfish between harvest and sample analysis were minimized with time and temperature controls. Densities were measured by direct plating techniques, and gene probes were used for identification. Total and pathogenic V. parahaemolyticus organisms were identified with probes for the thermolabile direct hemolysin (tlh) gene and the thermostable direct hemolysin (tdh) gene, respectively. An enrichment procedure involving 25 g of shellfish was also used for the recovery of pathogenic V. parahaemolyticus. The densities of V. parahaemolyticus in shellfish from all harvest sites were positively correlated with water temperature. Shellfish from the Gulf Coast typically had higher densities of V. parahaemolyticus than did shellfish harvested from the North Atlantic or mid-Atlantic coast. Vibrio parahaemolyticus counts exceeded 1,000 CFU/g for only 5% of all samples. Pathogenic (tdh+) V. parahaemolyticus was detected in approximately 6% of all samples by both procedures, and 61.5% of populations in the positive samples from the direct plating procedure were at the lower limit of detection (10 CFU/g). The frequency of detection of pathogenic V. parahaemolyticus was significantly related to water temperature and to the density of total V. parahaemolyticus. The failure to detect pathogenic V. parahaemolyticus in shellfish more frequently was attributed to the low numbers and uneven distribution of the organism.

Molecular confirmation of oysters as the vector for hepatitis A in a 2005 multistate outbreak.

PubMed

Shieh, Y C; Khudyakov, Y E; Xia, G; Ganova-Raeva, L M; Khambaty, F M; Woods, J W; Veazey, J E; Motes, M L; Glatzer, M B; Bialek, S R; Fiore, A E

2007-01-01

Numerous hepatitis A outbreaks were linked to the consumption of raw molluscan shellfish in the United States between 1960 and 1989. However, there had been no major molluscan shellfish-associated hepatitis A outbreaks reported in the United States for more than a decade (1989 to 2004). Beginning in late August 2005, at least 10 clusters of hepatitis A illnesses, totaling 39 persons, occurred in four states among restaurant patrons who ate oysters. Epidemiologic data indicated that oysters were the source of the outbreak. Traceback information showed that the implicated oysters were harvested from specific Gulf Coast areas. A voluntary recall of oysters was initiated in September. Hepatitis A virus (HAV) was detected in multiple 25-g portions in one of two recalled samples, indicating that as many as 1 of every 15 oysters from this source was contaminated. Comparing 315 nucleotides within the HAV VPl-2B region, 100% homology was found among four amplicons recovered from a total of six independent experiments of the implicated oysters, and an identical HAV sequence was detected in sera from all 28 patient serum specimens tested. Ten percent heterogeneity over 315 nucleotides (31 variants) was observed between the outbreak strain (subgenotype 1A) and an HM-175 strain (subgenotype 1B) used in the laboratory where the oysters were processed. To our knowledge, this investigation is the first in the United States to identify an HAV-identical strain in persons with hepatitis A as well as in the food that was implicated as the source of their infections.

Reconstructing evolutionary trees in parallel for massive sequences.

PubMed

Zou, Quan; Wan, Shixiang; Zeng, Xiangxiang; Ma, Zhanshan Sam

2017-12-14

Building the evolutionary trees for massive unaligned DNA sequences is challenging and crucial. However, reconstructing evolutionary tree for ultra-large sequences is hard. Massive multiple sequence alignment is also challenging and time/space consuming. Hadoop and Spark are developed recently, which bring spring light for the classical computational biology problems. In this paper, we tried to solve the multiple sequence alignment and evolutionary reconstruction in parallel. HPTree, which is developed in this paper, can deal with big DNA sequence files quickly. It works well on the >1GB files, and gets better performance than other evolutionary reconstruction tools. Users could use HPTree for reonstructing evolutioanry trees on the computer clusters or cloud platform (eg. Amazon Cloud). HPTree could help on population evolution research and metagenomics analysis. In this paper, we employ the Hadoop and Spark platform and design an evolutionary tree reconstruction software tool for unaligned massive DNA sequences. Clustering and multiple sequence alignment are done in parallel. Neighbour-joining model was employed for the evolutionary tree building. We opened our software together with source codes via http://lab.malab.cn/soft/HPtree/ .

The Growth of Developmental Thought: Implications for a New Evolutionary Psychology

PubMed Central

Lickliter, Robert

2009-01-01

Evolution has come to be increasingly discussed in terms of changes in developmental processes rather than simply in terms of changes in gene frequencies. This shift is based in large part on the recognition that since all phenotypic traits arise during ontogeny as products of individual development, a primary basis for evolutionary change must be variations in the patterns and processes of development. Further, the products of development are epigenetic, not just genetic, and this is the case even when considering the evolutionary process. These insights have led investigators to reconsider the established notion of genes as the primary cause of development, opening the door to research programs focused on identifying how genetic and non-genetic factors coact to guide and constrain the process of development and its outcomes. I explore this growth of developmental thought and its implications for the achievement of a unified theory of heredity, development, and evolution and consider its implications for the realization of a new, developmentally-based evolutionary psychology. PMID:19956346

Threat-detection in child development: an evolutionary perspective.

PubMed

Boyer, Pascal; Bergstrom, Brian

2011-03-01

Evidence for developmental aspects of fear-targets and anxiety suggests a complex but stable pattern whereby specific kinds of fears emerge at different periods of development. This developmental schedule seems appropriate to dangers encountered repeatedly during human evolution. Also consistent with evolutionary perspective, the threat-detection systems are domain-specific, comprising different kinds of cues to do with predation, intraspecific violence, contamination-contagion and status loss. Proper evolutionary models may also be relevant to outstanding issues in the domain, notably the connections between typical development and pathology. Copyright © 2010 Elsevier Ltd. All rights reserved.

An Evolutionary Framework for Understanding the Origin of Eukaryotes.

PubMed

Blackstone, Neil W

2016-04-27

Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real-the endosymbiosis that led to the mitochondrion is often described as "non-Darwinian" because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious-all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes.

Functional genomic characterization of neoblast-like stem cells in larval Schistosoma mansoni

PubMed Central

Wang, Bo; Collins, James J; Newmark, Phillip A

2013-01-01

Schistosomes infect hundreds of millions of people in the developing world. Transmission of these parasites relies on a stem cell-driven, clonal expansion of larvae inside a molluscan intermediate host. How this novel asexual reproductive strategy relates to current models of stem cell maintenance and germline specification is unclear. Here, we demonstrate that this proliferative larval cell population (germinal cells) shares some molecular signatures with stem cells from diverse organisms, in particular neoblasts of planarians (free-living relatives of schistosomes). We identify two distinct germinal cell lineages that differ in their proliferation kinetics and expression of a nanos ortholog. We show that a vasa/PL10 homolog is required for proliferation and maintenance of both populations, whereas argonaute2 and a fibroblast growth factor receptor-encoding gene are required only for nanos-negative cells. Our results suggest that an ancient stem cell-based developmental program may have enabled the evolution of the complex life cycle of parasitic flatworms. DOI: http://dx.doi.org/10.7554/eLife.00768.001 PMID:23908765

National collaborative shellfish pollution-indicator study: Site selection. Phase 2. Rept. for 1988-89

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leonard, D.L.; Slaughter, E.A.; Corning, B.C.

1990-07-01

Each year, about 16 million areas of estuarine waters are classified for the harvest of molluscan shellfish as open or limited to harvest according to microbiological 'indicator' standards and pollution survey guidelines established by the National Shellfish Sanitation Program. The program was developed in the 1920s in response to typhoid fever outbreaks associated with shellfish consumption. Current microbiological indicator standards in shellfish and shellfish-growing waters are extrpolated from standards set in the 1920s. Results from studies in the last decade have indicated that these microbiological indicator standards and thus classification of shellfish-growing waters may no longer be valid. The Nationalmore » Collaborative Shellfish Pollution Indicator Study is proposed as a four-year study to evaluate the current relationships between indicators of human enteric pathogens and the incidence of shellfish-borne diseases. Tasks forces were established to address specific issues, including site selection, shoreline surveys, and laboratory methodologies.« less

A PDGF/VEGF homologue provides new insights into the nucleus grafting operation and immune response in the pearl oyster Pinctada fucata.

PubMed

Huang, Xian-De; Zhang, Hua; He, Mao-Xian

2017-12-30

The platelet-derived growth factor/vascular endothelial growth factor (PDGF/VEGF, PVF) family of proteins have been implicated in a wide range of biological functions in vertebrates, including cell proliferation, cell differentiation, cell migration, neural development and especially angiogenesis/vasculogenesis. In this study, a PVF gene, belonging to the PDGF/VEGF family, was cloned and characterized from Pinctada fucata. It contained an ORF of 1110bp encoding a putative protein of 369 amino acids. The deduced amino acid sequence presented the typical structural features of PDGF family members and the N-terminal signal peptide for secretion. Comparative phylogenetic analysis revealed that PfPVF shows relatively high identity with other invertebrate PVF homologues. Furthermore, gene expression analysis revealed that PfPVF is involved in not only the nucleus grafting operation and but also the response to immune stimulation. The study may help to increase understanding of the functions of molluscan PVF. Copyright © 2017 Elsevier B.V. All rights reserved.

Some aspects of snail ecology in South Africa

PubMed Central

de Meillon, B.; Frank, G. H.; Allanson, B. R.

1958-01-01

In this paper, the authors present the preliminary results of a recent ecological survey of some rivers in the Transvaal, Union of South Africa. Representative samples of the molluscan fauna of the rivers were collected and chemical analyses of the river waters were carried out. In addition, such characteristics as current speed, temperature, turbidity, biochemical oxygen demand, and amount of oxygen absorbed from potassium permanganate were determined. No evidence was obtained to show that the chemical composition of natural, unpolluted waters plays any part in determining vector snail habitats. Current speed was found to have some effect, bilharzia vector snails not being found in fast-flowing waters. Of the other factors, turbidity was shown to be of some importance, probably because it affects the growth of the algae on which certain snails seem to depend for their proper development, and severe pollution with sewage and industrial wastes also appeared to have an adverse affect on the snail population. PMID:13573112

A new species of Pulvinites (Mollusca: Bivalvia) from the upper Paleocene Paspotansa Member of the Aquia Formation in Virginia ( USA).

USGS Publications Warehouse

Ward, L.W.; Waller, T.R.

1988-01-01

Pulvinites lawrencei n.sp. is described from the upper Paleocene (Landenian Stage) Paspotansa Member of the Aquia Formation in Stafford County, Virginia. This is the first report of a member of the pteriacean family Pulvinitidae in the Tertiary on either side of the Atlantic, the only other post-Mesozoic records of Pulvinites being in the Paleocene of California and the present-day Pacific off southeast Australia. The stratigraphic setting and co-occurring molluscan assemblage of the new species indicate shallow-shelf, open-marine conditions with near normal salinities. -Authors

Catalog of taxa introduced by Luitfried Salvini-Plawen (1939-2014).

PubMed

Affenzeller, Susanne; Steiner, Gerhard

2017-10-17

Luitfried Salvini-Plawen was one of the most distinguished researchers for molluscan phylogenetic systematics of the last decades. In his publications he described a total of 193 species: 134 Solenogastres, 34 Caudofoveata, 14 interstitial Gastropoda, one polyplacophoran and the remaining comprising Cnidaria, Priapulida, Kamptozoa, and Echinodermata. In addition, he introduced 47 genus-group names and 54 names for family-level and higher taxa. This catalog comprises lists of all taxon names published by Luitfried Salvini-Plawen. The catalog entries contain taxonomic information, original citations, type localities and type collections. It aims to facilitate further research on these and related taxa.

First Record of Porpita porpita (Cnidaria: Hydrozoa) from the coral reef ecosystem, Bangladesh

NASA Astrophysics Data System (ADS)

Chowdhury, M. Shah Nawaz; Sharifuzzaman, S. M.; Chowdhury, Sayedur Rahman; Rashed-Un-Nabi, Md.; Hossain, M. Shahadat

2016-03-01

The occurrence of Porpita porpita is reported, for the first time, in the coral island of St. Martin's located in the southeastern coastal region of Bangladesh. P. porpita was found to occur in the lower littoral zone and beach rock pools, together with molluscan species, and collected during the pre-monsoon season when both water temperature (> 30°C) and salinity (> 30‰) tend to reach a maximum. This study recounts some details on the discovery and description of the species, and thus extends the global distribution and range limits of the genus Porpita.

Inference of Evolutionary Jumps in Large Phylogenies using Lévy Processes

PubMed Central

Duchen, Pablo; Leuenberger, Christoph; Szilágyi, Sándor M.; Harmon, Luke; Eastman, Jonathan; Schweizer, Manuel

2017-01-01

Abstract Although it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so-called new adaptive zones, for instance after dispersal into a new geographic area, after rapid climatic changes, or following the appearance of an evolutionary novelty. Only recently, large, accurate and well calibrated phylogenies have become available that allow testing this hypothesis directly, yet inferring evolutionary jumps remains computationally very challenging. Here, we develop a computationally highly efficient algorithm to accurately infer the rate and strength of evolutionary jumps as well as their phylogenetic location. Following previous work we model evolutionary jumps as a compound process, but introduce a novel approach to sample jump configurations that does not require matrix inversions and thus naturally scales to large trees. We then make use of this development to infer evolutionary jumps in Anolis lizards and Loriinii parrots where we find strong signal for such jumps at the basis of clades that transitioned into new adaptive zones, just as postulated by Simpson’s hypothesis. [evolutionary jump; Lévy process; phenotypic evolution; punctuated equilibrium; quantitative traits. PMID:28204787

Some assembly required: evolutionary and systems perspectives on the mammalian reproductive system.

PubMed

Mordhorst, Bethany R; Wilson, Miranda L; Conant, Gavin C

2016-01-01

In this review, we discuss the way that insights from evolutionary theory and systems biology shed light on form and function in mammalian reproductive systems. In the first part of the review, we contrast the rapid evolution seen in some reproductive genes with the generally conservative nature of development. We discuss directional selection and coevolution as potential drivers of rapid evolution in sperm and egg proteins. Such rapid change is very different from the highly conservative nature of later embryo development. However, it is not unique, as some regions of the sex chromosomes also show elevated rates of evolutionary change. To explain these contradictory trends, we argue that it is not reproductive functions per se that induce rapid evolution. Rather, it is the fact that biotic interactions, such as speciation events and sexual conflict, have no evolutionary endpoint and hence can drive continuous evolutionary changes. Returning to the question of sex chromosome evolution, we discuss the way that recent advances in evolutionary genomics and systems biology and, in particular, the development of a theory of gene balance provide a better understanding of the evolutionary patterns seen on these chromosomes. We end the review with a discussion of a surprising and incompletely understood phenomenon observed in early embryos: namely the Warburg effect, whereby glucose is fermented to lactate and alanine rather than respired to carbon dioxide. We argue that evolutionary insights, from both yeasts and tumor cells, help to explain the Warburg effect, and that new metabolic modeling approaches are useful in assessing the potential sources of the effect.

Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family.

PubMed

Song, Jia; Zheng, Sisi; Nguyen, Nhung; Wang, Youjun; Zhou, Yubin; Lin, Kui

2017-10-03

Because phylogenetic inference is an important basis for answering many evolutionary problems, a large number of algorithms have been developed. Some of these algorithms have been improved by integrating gene evolution models with the expectation of accommodating the hierarchy of evolutionary processes. To the best of our knowledge, however, there still is no single unifying model or algorithm that can take all evolutionary processes into account through a stepwise or simultaneous method. On the basis of three existing phylogenetic inference algorithms, we built an integrated pipeline for inferring the evolutionary history of a given gene family; this pipeline can model gene sequence evolution, gene duplication-loss, gene transfer and multispecies coalescent processes. As a case study, we applied this pipeline to the STIMATE (TMEM110) gene family, which has recently been reported to play an important role in store-operated Ca 2+ entry (SOCE) mediated by ORAI and STIM proteins. We inferred their phylogenetic trees in 69 sequenced chordate genomes. By integrating three tree reconstruction algorithms with diverse evolutionary models, a pipeline for inferring the evolutionary history of a gene family was developed, and its application was demonstrated.

Evolutionary domestication in Drosophila subobscura.

PubMed

Simões, P; Rose, M R; Duarte, A; Gonçalves, R; Matos, M

2007-03-01

The domestication of plants and animals is historically one of the most important topics in evolutionary biology. The evolutionary genetic changes arising from human cultivation are complex because of the effects of such varied processes as continuing natural selection, artificial selection, deliberate inbreeding, genetic drift and hybridization of different lineages. Despite the interest of domestication as an evolutionary process, few studies of multicellular sexual species have approached this topic using well-replicated experiments. Here we present a comprehensive study in which replicated evolutionary trajectories from several Drosophila subobscura populations provide a detailed view of the evolutionary dynamics of domestication in an outbreeding animal species. Our results show a clear evolutionary response in fecundity traits, but no clear pattern for adult starvation resistance and juvenile traits such as development time and viability. These results supply new perspectives on the confounding of adaptation with other evolutionary mechanisms in the process of domestication.

Anthropomorphizing Science: How Does It Affect the Development of Evolutionary Concepts?

ERIC Educational Resources Information Center

Legare, Cristine H.; Lane, Jonathan D.; Evans, E. Margaret

2013-01-01

Despite the ubiquitous use of anthropomorphic language to describe biological change in both educational settings and popular science, little is known about how anthropomorphic language influences children's understanding of evolutionary concepts. In an experimental study, we assessed whether the language used to convey evolutionary concepts…

Transforming Biology Assessment with Machine Learning: Automated Scoring of Written Evolutionary Explanations

ERIC Educational Resources Information Center

Nehm, Ross H.; Ha, Minsu; Mayfield, Elijah

2012-01-01

This study explored the use of machine learning to automatically evaluate the accuracy of students' written explanations of evolutionary change. Performance of the Summarization Integrated Development Environment (SIDE) program was compared to human expert scoring using a corpus of 2,260 evolutionary explanations written by 565 undergraduate…

The Experimental Study of Bacterial Evolution and Its Implications for the Modern Synthesis of Evolutionary Biology.

PubMed

O'Malley, Maureen A

2018-06-01

Since the 1940s, microbiologists, biochemists and population geneticists have experimented with the genetic mechanisms of microorganisms in order to investigate evolutionary processes. These evolutionary studies of bacteria and other microorganisms gained some recognition from the standard-bearers of the modern synthesis of evolutionary biology, especially Theodosius Dobzhansky and Ledyard Stebbins. A further period of post-synthesis bacterial evolutionary research occurred between the 1950s and 1980s. These experimental analyses focused on the evolution of population and genetic structure, the adaptive gain of new functions, and the evolutionary consequences of competition dynamics. This large body of research aimed to make evolutionary theory testable and predictive, by giving it mechanistic underpinnings. Although evolutionary microbiologists promoted bacterial experiments as methodologically advantageous and a source of general insight into evolution, they also acknowledged the biological differences of bacteria. My historical overview concludes with reflections on what bacterial evolutionary research achieved in this period, and its implications for the still-developing modern synthesis.

Evolutionary psychology in the modern world: applications, perspectives, and strategies.

PubMed

Roberts, S Craig; van Vugt, Mark; Dunbar, Robin I M

2012-12-20

An evolutionary approach is a powerful framework which can bring new perspectives on any aspect of human behavior, to inform and complement those from other disciplines, from psychology and anthropology to economics and politics. Here we argue that insights from evolutionary psychology may be increasingly applied to address practical issues and help alleviate social problems. We outline the promise of this endeavor, and some of the challenges it faces. In doing so, we draw parallels between an applied evolutionary psychology and recent developments in Darwinian medicine, which similarly has the potential to complement conventional approaches. Finally, we describe some promising new directions which are developed in the associated papers accompanying this article.

An Evolutionary Framework for Understanding the Origin of Eukaryotes

PubMed Central

Blackstone, Neil W.

2016-01-01

Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real—the endosymbiosis that led to the mitochondrion is often described as “non-Darwinian” because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious—all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes. PMID:27128953

Role of protein kinase C in light adaptation of molluscan microvillar photoreceptors

PubMed Central

Piccoli, Giuseppe; del Pilar Gomez, Maria; Nasi, Enrico

2002-01-01

The mechanisms by which Ca2+ regulates light adaptation in microvillar photoreceptors remain poorly understood. Protein kinase C (PKC) is a likely candidate, both because some sub-types are activated by Ca2+ and because of its association with the macromolecular ‘light-transduction complex’ in Drosophila. We investigated the possible role of PKC in the modulation of the light response in molluscan photoreceptors. Western blot analysis with isoform-specific antibodies revealed the presence of PKCα in retinal homogenates. Immunocytochemistry in isolated cell preparations confirmed PKCα localization in microvillar photoreceptors, preferentially confined to the light-sensing lobe. Light stimulation induced translocation of PKCα immunofluorescence to the photosensitive membrane, an effect that provides independent evidence for PKC activation by illumination; a similar outcome was observed after incubation with the phorbol ester PMA. Several chemically distinct activators of PKC, such as phorbol-12-myristate-13-acetate (PMA), (-)indolactam V and 1,2,-dioctanoyl-sn-glycerol (DOG) inhibited the light response of voltage-clamped microvillar photoreceptors, but were ineffective in ciliary photoreceptors, in which light does not activate the Gq/PLC cascade, nor elevates intracellular Ca2+. Pharmacological inhibition of PKC antagonized the desensitization produced by adapting lights and also caused a small, but consistent enhancement of basal sensitivity. These results strongly support the involvement of PKC activation in the light-dependent regulation of response sensitivity. However, unlike adapting background light or elevation of [Ca2+]i, PKC activators did not speed up the photoresponse, nor did PKC inhibitors antagonize the accelerating effects of background adaptation, suggesting that modulation of photoresponse time course may involve a separate Ca2+-dependent signal. PMID:12205183

Book review of Littler DM. Littler MM (2000) Caribbean Reef Plants An Identification Guide to the Reef Plants of the Caribbean, Bahamas, Florida and Gulf of Mexico

NASA Astrophysics Data System (ADS)

Zuschin, M.; Hohenegger, J.; Steininger, F.

2001-09-01

Information on spatial variability and distribution patterns of organisms in coral reef environments is necessary to evaluate the increasing anthropogenic disturbance of marine environments (Richmond 1993; Wilkinson 1993; Dayton 1994). Therefore different types of subtidal, reef-associated hard substrata (reef flats, reef slopes, coral carpets, coral patches, rock grounds), each with different coral associations, were investigated to determine the distribution pattern of molluscs and their life habits (feeding strategies and substrate relations). The molluscs were strongly dominated by taxa with distinct relations to corals, and five assemblages were differentiated. The Dendropoma maxima assemblage on reef flats is a discrete entity, strongly dominated by this encrusting and suspension-feeding gastropod. All other assemblages are arranged along a substrate gradient of changing coral associations and potential molluscan habitats. The Coralliophila neritoidea- Barbatia foliata assemblage depends on the presence of Porites and shows a dominance of gastropods feeding on corals and of bivalves associated with living corals. The Chamoidea- Cerithium spp. assemblage on rock grounds is strongly dominated by encrusting bivalves. The Drupella cornus-Pteriidae assemblage occurs on Millepora- Acropora reef slopes and is strongly dominated by bivalves associated with living corals. The Barbatia setigera- Ctenoides annulata assemblage includes a broad variety of taxa, molluscan life habits and bottom types, but occurs mainly on faviid carpets and is transitional among the other three assemblages. A predicted degradation of coral coverage to rock bottoms due to increasing eutrophication and physical damage in the study area (Riegl and Piller 2000) will result in a loss of coral-associated molluscs in favor of bivalve crevice dwellers in dead coral heads and of encrusters on dead hard substrata.

Innovative application of classic and newer techniques for the characterization of haemocytes in the New Zealand black-footed abalone (Haliotis iris).

PubMed

Grandiosa, Roffi; Mérien, Fabrice; Pillay, Krish; Alfaro, Andrea

2016-01-01

Haemocytes play an important role in innate immune responses within invertebrate organisms. However, identification and quantification of different types of haemocytes can be extremely challenging, and has led to numerous inconsistencies and misinterpretations within the literature. As a step to rectify this issue, we present a comprehensive and detailed approach to characterize haemocytes using a combination of classical (cytochemical and phagocytosis assays with optical microscopy) and novel (flow cytometry with Sysmex XN-1000 and Muse(®) Cell analyser) techniques. The Sysmex XN-1000 is an innovative fluorescent flow cytometric analyser that can effectively detect, identify and count haemocytes, while the Muse(®) Cell analyser provides accurate and rapid haemocyte cell counts and viability. To illustrate this approach, we present the first report on morphological and functional features of New Zealand black-footed abalone (Haliotis iris) haemocyte cells. Two types of haemocytes were identified in this study, including type I (monocyte-like) and type II (lymphocyte-like) cells. Granular cells, which have been reported in other molluscan species, were not detected in H. iris. Cell types were categorized based on shape, size, internal structures and function. The lymphocyte-like haemocytes were the most abundant hemocytes in the haemolymph samples, and they had large nuclei and basic cytoplasms. Monocyte-like cells generally were larger cells compared to lymphocyte-like cells, and had low nucleus-cytoplasm ratios. Monocyte-like cells showed higher phagocytic activity when encountering Zymosan A particles compared to lymphocyte-like cells. The present study provides a comprehensive and accurate new approach to identify and quantify haemocyte cells for future comparative studies on the immune system of abalone and other molluscan species. Copyright © 2015 Elsevier Ltd. All rights reserved.

Hemocyanin of the molluscan Concholepas concholepas exhibits an unusual heterodecameric array of subunits.

PubMed

De Ioannes, Pablo; Moltedo, Bruno; Oliva, Harold; Pacheco, Rodrigo; Faunes, Fernando; De Ioannes, Alfredo E; Becker, María Inés

2004-06-18

We describe here the structure of the hemocyanin from the Chilean gastropod Concholepas concholepas (CCH), emphasizing some attributes that make it interesting among molluscan hemocyanins. CCH exhibits a predominant didecameric structure as revealed by electron microscopy and a size of 8 MDa by gel filtration, and, in contrast with other mollusc hemocyanins, its stabilization does not require additional Ca(2+) and/or Mg(2+) in the medium. Polyacrylamide gel electrophoresis studies, analyses by a MonoQ FPLC column, and Western blots with specific monoclonal antibodies showed that CCH is made by two subunits noncovalently linked, named CCH-A and CCH-B, with molecular masses of 405 and 350 kDa, respectively. Interestingly, one of the subunits undergoes changes within the macromolecule; we demonstrated that CCH-A has an autocleavage site that under reducing conditions is cleaved to yield two polypeptides, CCH-A1 (300 kDa) and CCH-A2 (108 kDa), whereas CCH-B remains unchanged. The CCH-A nick occurs at 4 degrees C, increases at 37 degrees C, and is not inhibited by the addition of protease inhibitors and/or divalent cations. Since the CCH structure is a heterodimer, we investigated whether subunits would be either intermingled, forming heterodecamers, or assembled as two homogeneous decamers. Light scattering and electron microscope studies of the in vitro reassociation of purified CCH subunits demonstrated that the sole addition of Mg(2+) is needed for its reassembly into the native decameric molecule; no homodecamer reorganization was found with either CCH-A or CCH-B subunits alone. Our evidence showed that C. concholepas hemocyanin is an unusual example of heterodecameric organization.

Antifungal and antiviral products of marine organisms

PubMed Central

Cheung, Randy Chi Fai; Pan, Wen Liang; Chan, Yau Sang; Yin, Cui Ming; Dan, Xiu Li; Wang, He Xiang; Fang, Evandro Fei; Lam, Sze Kwan; Ngai, Patrick Hung Kui; Xia, Li Xin; Liu, Fang; Ye, Xiu Yun; Zhang, Guo Qing; Liu, Qing Hong; Sha, Ou; Lin, Peng; Ki, Chan; Bekhit, Adnan A; Bekhit, Alaa El-Din; Wan, David Chi Cheong

2017-01-01

Marine organisms including bacteria, fungi, algae, sponges, echinoderms, mollusks, and cephalochordates produce a variety of products with antifungal activity including bacterial chitinases, lipopeptides, and lactones; fungal (−)-sclerotiorin and peptaibols, purpurides B and C, berkedrimane B and purpuride; algal gambieric acids A and B, phlorotannins; 3,5-dibromo-2-(3,5-dibromo-2-methoxyphenoxy)phenol, spongistatin 1, eurysterols A and B, nortetillapyrone, bromotyrosine alkaloids, bis-indole alkaloid, ageloxime B and (−)-ageloxime D, haliscosamine, hamigeran G, hippolachnin A from sponges; echinoderm triterpene glycosides and alkene sulfates; molluscan kahalalide F and a 1485-Da peptide with a sequence SRSELIVHQR; and cepalochordate chitotriosidase and a 5026.9-Da antifungal peptide. The antiviral compounds from marine organisms include bacterial polysaccharide and furan-2-yl acetate; fungal macrolide, purpurester A, purpurquinone B, isoindolone derivatives, alterporriol Q, tetrahydroaltersolanol C and asperterrestide A, algal diterpenes, xylogalactofucan, alginic acid, glycolipid sulfoquinovosyldiacylglycerol, sulfated polysaccharide p-KG03, meroditerpenoids, methyl ester derivative of vatomaric acid, lectins, polysaccharides, tannins, cnidarian zoanthoxanthin alkaloids, norditerpenoid and capilloquinol; crustacean antilipopolysaccharide factors, molluscan hemocyanin; echinoderm triterpenoid glycosides; tunicate didemnin B, tamandarins A and B and; tilapia hepcidin 1–5 (TH 1–5), seabream SauMx1, SauMx2, and SauMx3, and orange-spotted grouper β-defensin. Although the mechanisms of antifungal and antiviral activities of only some of the afore-mentioned compounds have been elucidated, the possibility to use those known to have distinctly different mechanisms, good bioavailability, and minimal toxicity in combination therapy remains to be investigated. It is also worthwhile to test the marine antimicrobials for possible synergism with existing drugs. The prospects of employing them in clinical practice are promising in view of the wealth of these compounds from marine organisms. The compounds may also be used in agriculture and the food industry. PMID:24562325

Macrobenthic molluscs from a marine - lagoonal environmental transition in Lesvos Island (Greece).

PubMed

Evagelopoulos, Athanasios; Koutsoubas, Drosos; Gerovasileiou, Vasilis; Katsiaras, Nikolaos

2016-01-01

This paper describes an occurence dataset, also including numerical abundance and biomass data, pertaining to the macrobenthic molluscan assemblages from a marine - lagoonal environmental transition. The study system was the soft-substrate benthoscape of the area of the Kalloni solar saltworks (Lesvos Island, Greece). Specifically, the study area extended from the infralittoral zone of the inner Kalloni Gulf (marine habitat) to the bottoms of the first two evaporation ponds of the Kalloni solar saltworks (lagoonal habitat). Bottom sediment samples (3 replicates) were collected with a Van Veen grab sampler (0.1 m 2 ) at four sampling sites, along a 1.5 km long line transect that spanned the marine - lagoonal environmental transition. A total of four surveys were carried out seasonally in 2004.  A total of 39,345 molluscan individuals were sorted out of the sediment samples and were identified to 71 species, belonging to the Gastropoda (36), Bivalvia (34) and Scaphopoda (1) classes. Numerical abundance and wet biomass (with shells) data are included in the dataset. The dataset described in the present paper partially fills a significant gap in the scientific literature: Because ecological research of coastal lagoons has seldom explicitly considered the marine - lagoonal habitats interface, there are no openly accessible datasets pertaining to the particular structural component of the transitional waters benthoscapes of the Mediterranean Sea. Such datasets could prove valuable in the research of the structure and functioning of transitional waters benthoscapes. The present dataset is available as a supplementary file (Suppl. material 1) and can also be accessed at http://ipt.medobis.eu/resource?r=kalloni_saltworks_phd.

Human norovirus RNA persists in seawater under simulated winter conditions but does not bioaccumulate efficiently in Pacific Oysters (Crassostrea gigas).

PubMed

Dancer, D; Rangdale, R E; Lowther, J A; Lees, D N

2010-11-01

Norovirus (NoV) is the principal agent of bivalve molluscan shellfish-associated gastroenteric illness worldwide. Currently, noncultivable human NoVs can be detected in bivalve molluscan shellfish by using molecular methods such as real-time reverse transcription PCR assays (qRT-PCR). In addition to infectious viruses, this methodology may also detect noninfectious NoV, including fragments of the NoV genome. This study addresses, in part, the implications of qRT-PCR results for the detection of NoV in shellfish in the absence of an infectivity assay. To evaluate environmental persistence, the stability of a short fragment of the NoV genome, spanning the qRT-PCR target in the open reading frame 1/2 junction, was assessed in seawater under artificial environmental conditions simulating winter in the United Kingdom (1 mW/cm² UV irradiation, 8°C) during a 4-week period. Detectable RNA levels decreased exponentially (T₉₀ of approximately 141 h); however, sequences were still detectable for up to 2 weeks. The ability of Pacific oysters (Crassostrea gigas) to bioaccumulate NoV particles (from human feces) and RNA fragments was also compared using qRT-PCR. Oysters exposed to NoV particles subsequently were positive for NoV by qRT-PCR at levels several orders of magnitude in excess of the theoretical limit of detection, whereas oysters exposed to similar quantities of NoV RNA were either negative or positive at significantly lower levels. Therefore, although noninfectious fragments of NoV RNA may persist in the environment under winter conditions, this type of material will not be efficiently bioaccumulated by Pacific oysters and should not significantly contribute to positive qRT-PCR results.

Inference of Evolutionary Jumps in Large Phylogenies using Lévy Processes.

PubMed

Duchen, Pablo; Leuenberger, Christoph; Szilágyi, Sándor M; Harmon, Luke; Eastman, Jonathan; Schweizer, Manuel; Wegmann, Daniel

2017-11-01

Although it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so-called new adaptive zones, for instance after dispersal into a new geographic area, after rapid climatic changes, or following the appearance of an evolutionary novelty. Only recently, large, accurate and well calibrated phylogenies have become available that allow testing this hypothesis directly, yet inferring evolutionary jumps remains computationally very challenging. Here, we develop a computationally highly efficient algorithm to accurately infer the rate and strength of evolutionary jumps as well as their phylogenetic location. Following previous work we model evolutionary jumps as a compound process, but introduce a novel approach to sample jump configurations that does not require matrix inversions and thus naturally scales to large trees. We then make use of this development to infer evolutionary jumps in Anolis lizards and Loriinii parrots where we find strong signal for such jumps at the basis of clades that transitioned into new adaptive zones, just as postulated by Simpson's hypothesis. [evolutionary jump; Lévy process; phenotypic evolution; punctuated equilibrium; quantitative traits. The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

How Cultural Evolutionary Theory Can Inform Social Psychology and Vice Versa

ERIC Educational Resources Information Center

Mesoudi, Alex

2009-01-01

Cultural evolutionary theory is an interdisciplinary field in which human culture is viewed as a Darwinian process of variation, competition, and inheritance, and the tools, methods, and theories developed by evolutionary biologists to study genetic evolution are adapted to study cultural change. It is argued here that an integration of the…

Match Fitness: Development, Evolution, and Behavior--Comment on Frankenhuis and Del Giudice (2012)

ERIC Educational Resources Information Center

Gluckman, Peter D.; Beedle, Alan S.

2012-01-01

The application of evolutionary thinking to human physical and psychological medicine suggests several pathways through which evolutionary processes affect risk of disease. Among these is the concept of mismatch between an individual and its environment, either because the environment has changed for the whole species ("evolutionary novelty") or…

Evolutionary Explanations for Antibiotic Resistance in Daily Press, Online Websites and Biology Textbooks in Sweden

ERIC Educational Resources Information Center

Bohlin, Gustav; Höst, Gunnar E.

2015-01-01

The present study explores the extent and precision of evolutionary explanations for antibiotic resistance in communication directed toward the Swedish public. Bacterial resistance develops through evolutionary mechanisms and knowledge of these helps to explain causes underlying the growing prevalence of resistant strains, as well as important…

The Implications of the Cognitive Sciences for the Relation Between Religion and Science Education: The Case of Evolutionary Theory

NASA Astrophysics Data System (ADS)

Blancke, Stefaan; De Smedt, Johan; De Cruz, Helen; Boudry, Maarten; Braeckman, Johan

2012-08-01

This paper discusses the relationship between religion and science education in the light of the cognitive sciences. We challenge the popular view that science and religion are compatible, a view that suggests that learning and understanding evolutionary theory has no effect on students' religious beliefs and vice versa. We develop a cognitive perspective on how students manage to reconcile evolutionary theory with their religious beliefs. We underwrite the claim developed by cognitive scientists and anthropologists that religion is natural because it taps into people's intuitive understanding of the natural world which is constrained by essentialist, teleological and intentional biases. After contrasting the naturalness of religion with the unnaturalness of science, we discuss the difficulties cognitive and developmental scientists have identified in learning and accepting evolutionary theory. We indicate how religious beliefs impede students' understanding and acceptance of evolutionary theory. We explore a number of options available to students for reconciling an informed understanding of evolutionary theory with their religious beliefs. To conclude, we discuss the implications of our account for science and biology teachers.

Replaying evolutionary transitions from the dental fossil record

PubMed Central

Harjunmaa, Enni; Seidel, Kerstin; Häkkinen, Teemu; Renvoisé, Elodie; Corfe, Ian J.; Kallonen, Aki; Zhang, Zhao-Qun; Evans, Alistair R.; Mikkola, Marja L.; Salazar-Ciudad, Isaac; Klein, Ophir D.; Jernvall, Jukka

2014-01-01

The evolutionary relationships of extinct species are ascertained primarily through the analysis of morphological characters. Character inter-dependencies can have a substantial effect on evolutionary interpretations, but the developmental underpinnings of character inter-dependence remain obscure because experiments frequently do not provide detailed resolution of morphological characters. Here we show experimentally and computationally how gradual modification of development differentially affects characters in the mouse dentition. We found that intermediate phenotypes could be produced by gradually adding ectodysplasin A (EDA) protein in culture to tooth explants carrying a null mutation in the tooth-patterning gene Eda. By identifying development-based character interdependencies, we show how to predict morphological patterns of teeth among mammalian species. Finally, in vivo inhibition of sonic hedgehog signalling in Eda null teeth enabled us to reproduce characters deep in the rodent ancestry. Taken together, evolutionarily informative transitions can be experimentally reproduced, thereby providing development-based expectations for character state transitions used in evolutionary studies. PMID:25079326

Evolutionary Medicine: The Ongoing Evolution of Human Physiology and Metabolism.

PubMed

Rühli, Frank; van Schaik, Katherine; Henneberg, Maciej

2016-11-01

The field of evolutionary medicine uses evolutionary principles to understand changes in human anatomy and physiology that have occurred over time in response to environmental changes. Through this evolutionary-based approach, we can understand disease as a consequence of anatomical and physiological "trade-offs" that develop to facilitate survival and reproduction. We demonstrate how diachronic study of human anatomy and physiology is fundamental for an increased understanding of human health and disease. ©2016 Int. Union Physiol. Sci./Am. Physiol. Soc.

Evolutionary cell biology: two origins, one objective.

PubMed

Lynch, Michael; Field, Mark C; Goodson, Holly V; Malik, Harmit S; Pereira-Leal, José B; Roos, David S; Turkewitz, Aaron P; Sazer, Shelley

2014-12-02

All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within- and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology.

Evolutionary cell biology: Two origins, one objective

PubMed Central

Lynch, Michael; Field, Mark C.; Goodson, Holly V.; Malik, Harmit S.; Pereira-Leal, José B.; Roos, David S.; Turkewitz, Aaron P.; Sazer, Shelley

2014-01-01

All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within- and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology. PMID:25404324

A Metatheory for Cognitive Development (or "Piaget is Dead" Revisited).

PubMed

Bjorklund, David F

2018-01-16

In 1997, I argued that with the loss of Piaget's theory as an overarching guide, cognitive development had become disjointed and a new metatheory was needed to unify the field. I suggested developmental biology, particularly evolutionary theory, as a candidate. Here, I examine the increasing emphasis of biology in cognitive development research over the past 2 decades. I describe briefly the emergence of evolutionary developmental psychology and examine areas in which proximal and distal biological causation have been particularly influential. I argue that developmental biology will continue to increasingly influence research and theory in cognitive development and that evolutionary theory is well on its way to becoming a metatheory, not just for cognitive development, but for developmental psychology generally. © 2018 The Authors. Child Development © 2018 Society for Research in Child Development, Inc.

Toward a unifying framework for evolutionary processes.

PubMed

Paixão, Tiago; Badkobeh, Golnaz; Barton, Nick; Çörüş, Doğan; Dang, Duc-Cuong; Friedrich, Tobias; Lehre, Per Kristian; Sudholt, Dirk; Sutton, Andrew M; Trubenová, Barbora

2015-10-21

The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Theoretical Approaches in Evolutionary Ecology: Environmental Feedback as a Unifying Perspective.

PubMed

Lion, Sébastien

2018-01-01

Evolutionary biology and ecology have a strong theoretical underpinning, and this has fostered a variety of modeling approaches. A major challenge of this theoretical work has been to unravel the tangled feedback loop between ecology and evolution. This has prompted the development of two main classes of models. While quantitative genetics models jointly consider the ecological and evolutionary dynamics of a focal population, a separation of timescales between ecology and evolution is assumed by evolutionary game theory, adaptive dynamics, and inclusive fitness theory. As a result, theoretical evolutionary ecology tends to be divided among different schools of thought, with different toolboxes and motivations. My aim in this synthesis is to highlight the connections between these different approaches and clarify the current state of theory in evolutionary ecology. Central to this approach is to make explicit the dependence on environmental dynamics of the population and evolutionary dynamics, thereby materializing the eco-evolutionary feedback loop. This perspective sheds light on the interplay between environmental feedback and the timescales of ecological and evolutionary processes. I conclude by discussing some potential extensions and challenges to our current theoretical understanding of eco-evolutionary dynamics.

EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data.

PubMed

Linard, Benjamin; Nguyen, Ngoc Hoan; Prosdocimi, Francisco; Poch, Olivier; Thompson, Julie D

2012-01-01

Evolutionary systems biology aims to uncover the general trends and principles governing the evolution of biological networks. An essential part of this process is the reconstruction and analysis of the evolutionary histories of these complex, dynamic networks. Unfortunately, the methodologies for representing and exploiting such complex evolutionary histories in large scale studies are currently limited. Here, we propose a new formalism, called EvoluCode (Evolutionary barCode), which allows the integration of different evolutionary parameters (eg, sequence conservation, orthology, synteny …) in a unifying format and facilitates the multilevel analysis and visualization of complex evolutionary histories at the genome scale. The advantages of the approach are demonstrated by constructing barcodes representing the evolution of the complete human proteome. Two large-scale studies are then described: (i) the mapping and visualization of the barcodes on the human chromosomes and (ii) automatic clustering of the barcodes to highlight protein subsets sharing similar evolutionary histories and their functional analysis. The methodologies developed here open the way to the efficient application of other data mining and knowledge extraction techniques in evolutionary systems biology studies. A database containing all EvoluCode data is available at: http://lbgi.igbmc.fr/barcodes.

The Importance of Evolutionary Theory for Developmental Science--And Vice Versa: The Case of Developmental Psychology

ERIC Educational Resources Information Center

Greve, Werner

2012-01-01

The empirical and conceptual interrelations of phylogeny (evolution) and ontogeny (development) may prove to be more important than previously acknowledged. It is argued that this holds particularly for evolutionary psychology. For instance, an evolutionary point of view will add to the explanation of (the shape of) pre- and post-reductive phases…

The evolutionary history of the development of the pelvic fin/hindlimb

PubMed Central

Don, Emily K; Currie, Peter D; Cole, Nicholas J

2013-01-01

The arms and legs of man are evolutionarily derived from the paired fins of primitive jawed fish. Few evolutionary changes have attracted as much attention as the origin of tetrapod limbs from the paired fins of ancestral fish. The hindlimbs of tetrapods are derived from the pelvic fins of ancestral fish. These evolutionary origins can be seen in the examination of shared gene and protein expression patterns during the development of pelvic fins and tetrapod hindlimbs. The pelvic fins of fish express key limb positioning, limb bud induction and limb outgrowth genes in a similar manner to that seen in hindlimb development of higher vertebrates. We are now at a point where many of the key players in the development of pelvic fins and vertebrate hindlimbs have been identified and we can now readily examine and compare mechanisms between species. This is yielding fascinating insights into how the developmental programme has altered during evolution and how that relates to anatomical change. The role of pelvic fins has also drastically changed over evolutionary history, from playing a minor role during swimming to developing into robust weight-bearing limbs. In addition, the pelvic fins/hindlimbs have been lost repeatedly in diverse species over evolutionary time. Here we review the evolution of pelvic fins and hindlimbs within the context of the changes in anatomical structure and the molecular mechanisms involved. PMID:22913749

Core principles of evolutionary medicine

PubMed Central

Grunspan, Daniel Z; Nesse, Randolph M; Barnes, M Elizabeth; Brownell, Sara E

2018-01-01

Abstract Background and objectives Evolutionary medicine is a rapidly growing field that uses the principles of evolutionary biology to better understand, prevent and treat disease, and that uses studies of disease to advance basic knowledge in evolutionary biology. Over-arching principles of evolutionary medicine have been described in publications, but our study is the first to systematically elicit core principles from a diverse panel of experts in evolutionary medicine. These principles should be useful to advance recent recommendations made by The Association of American Medical Colleges and the Howard Hughes Medical Institute to make evolutionary thinking a core competency for pre-medical education. Methodology The Delphi method was used to elicit and validate a list of core principles for evolutionary medicine. The study included four surveys administered in sequence to 56 expert panelists. The initial open-ended survey created a list of possible core principles; the three subsequent surveys winnowed the list and assessed the accuracy and importance of each principle. Results Fourteen core principles elicited at least 80% of the panelists to agree or strongly agree that they were important core principles for evolutionary medicine. These principles over-lapped with concepts discussed in other articles discussing key concepts in evolutionary medicine. Conclusions and implications This set of core principles will be helpful for researchers and instructors in evolutionary medicine. We recommend that evolutionary medicine instructors use the list of core principles to construct learning goals. Evolutionary medicine is a young field, so this list of core principles will likely change as the field develops further. PMID:29493660

Core principles of evolutionary medicine: A Delphi study.

PubMed

Grunspan, Daniel Z; Nesse, Randolph M; Barnes, M Elizabeth; Brownell, Sara E

2018-01-01

Evolutionary medicine is a rapidly growing field that uses the principles of evolutionary biology to better understand, prevent and treat disease, and that uses studies of disease to advance basic knowledge in evolutionary biology. Over-arching principles of evolutionary medicine have been described in publications, but our study is the first to systematically elicit core principles from a diverse panel of experts in evolutionary medicine. These principles should be useful to advance recent recommendations made by The Association of American Medical Colleges and the Howard Hughes Medical Institute to make evolutionary thinking a core competency for pre-medical education. The Delphi method was used to elicit and validate a list of core principles for evolutionary medicine. The study included four surveys administered in sequence to 56 expert panelists. The initial open-ended survey created a list of possible core principles; the three subsequent surveys winnowed the list and assessed the accuracy and importance of each principle. Fourteen core principles elicited at least 80% of the panelists to agree or strongly agree that they were important core principles for evolutionary medicine. These principles over-lapped with concepts discussed in other articles discussing key concepts in evolutionary medicine. This set of core principles will be helpful for researchers and instructors in evolutionary medicine. We recommend that evolutionary medicine instructors use the list of core principles to construct learning goals. Evolutionary medicine is a young field, so this list of core principles will likely change as the field develops further.

Hybrid Co-Evolutionary Motion Planning via Visibility-Based Repair

NASA Technical Reports Server (NTRS)

Dozier, Gerry; McCullough, Shaun; Brown, Edward, Jr.; Homaifar, Abdollah; Bikdash, Mar-wan

1997-01-01

This paper introduces a hybrid co-evolutionary system for global motion planning within unstructured environments. This system combines the concept of co-evolutionary search along with a concept that we refer to as the visibility-based repair to form a hybrid which quickly transforms infeasible motions into feasible ones. Also, this system makes use of a novel representation scheme for the obstacles within an environment. Our hybrid evolutionary system differs from other evolutionary motion planners in that (1) more emphasis is placed on repairing infeasible motions to develop feasible motions rather than using simulated evolution exclusively as a means of discovering feasible motions, (2) a continuous map of the environment is used rather than a discretized map, and (3) it develops global motion plans for multiple mobile destinations by co-evolving populations of sub-global motion plans. In this paper, we demonstrate the effectiveness of this system by using it to solve two challenging motion planning problems where multiple targets try to move away from a point robot.

Manager’s Guide to Technology Transition in an Evolutionary Acquisition Environment

DTIC Science & Technology

2005-06-01

program managers, product managers, staffs, and organizations that manage the development , procurement, production, and fielding of systems...rapidly advancing technologies. Technology transitions can occur during the development of systems, or even after a system has been in the field ...Documentation Evolutionary acquisition is an acquisition strategy that defines, develops , produces or acquires, and fields an initial hardware or software

Tools for Accurate and Efficient Analysis of Complex Evolutionary Mechanisms in Microbial Genomes. Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakhleh, Luay

I proposed to develop computationally efficient tools for accurate detection and reconstruction of microbes' complex evolutionary mechanisms, thus enabling rapid and accurate annotation, analysis and understanding of their genomes. To achieve this goal, I proposed to address three aspects. (1) Mathematical modeling. A major challenge facing the accurate detection of HGT is that of distinguishing between these two events on the one hand and other events that have similar "effects." I proposed to develop a novel mathematical approach for distinguishing among these events. Further, I proposed to develop a set of novel optimization criteria for the evolutionary analysis of microbialmore » genomes in the presence of these complex evolutionary events. (2) Algorithm design. In this aspect of the project, I proposed to develop an array of e cient and accurate algorithms for analyzing microbial genomes based on the formulated optimization criteria. Further, I proposed to test the viability of the criteria and the accuracy of the algorithms in an experimental setting using both synthetic as well as biological data. (3) Software development. I proposed the nal outcome to be a suite of software tools which implements the mathematical models as well as the algorithms developed.« less

Natural Selection as Coarsening

NASA Astrophysics Data System (ADS)

Smerlak, Matteo

2017-11-01

Analogies between evolutionary dynamics and statistical mechanics, such as Fisher's second-law-like "fundamental theorem of natural selection" and Wright's "fitness landscapes", have had a deep and fruitful influence on the development of evolutionary theory. Here I discuss a new conceptual link between evolution and statistical physics. I argue that natural selection can be viewed as a coarsening phenomenon, similar to the growth of domain size in quenched magnets or to Ostwald ripening in alloys and emulsions. In particular, I show that the most remarkable features of coarsening—scaling and self-similarity—have strict equivalents in evolutionary dynamics. This analogy has three main virtues: it brings a set of well-developed mathematical tools to bear on evolutionary dynamics; it suggests new problems in theoretical evolution; and it provides coarsening physics with a new exactly soluble model.

Natural Selection as Coarsening

NASA Astrophysics Data System (ADS)

Smerlak, Matteo

2018-07-01

Analogies between evolutionary dynamics and statistical mechanics, such as Fisher's second-law-like "fundamental theorem of natural selection" and Wright's "fitness landscapes", have had a deep and fruitful influence on the development of evolutionary theory. Here I discuss a new conceptual link between evolution and statistical physics. I argue that natural selection can be viewed as a coarsening phenomenon, similar to the growth of domain size in quenched magnets or to Ostwald ripening in alloys and emulsions. In particular, I show that the most remarkable features of coarsening—scaling and self-similarity—have strict equivalents in evolutionary dynamics. This analogy has three main virtues: it brings a set of well-developed mathematical tools to bear on evolutionary dynamics; it suggests new problems in theoretical evolution; and it provides coarsening physics with a new exactly soluble model.

From the "Modern Synthesis" to cybernetics: Ivan Ivanovich Schmalhausen (1884-1963) and his research program for a synthesis of evolutionary and developmental biology.

PubMed

Levit, Georgy S; Hossfeld, Uwe; Olsson, Lennart

2006-03-15

Ivan I. Schmalhausen was one of the central figures in the Russian development of the "Modern Synthesis" in evolutionary biology. He is widely cited internationally even today. Schmalhausen developed the main principles of his theory facing the danger of death in the totalitarian Soviet Union. His great services to evolutionary and theoretical biology are indisputable. However, the received view of Schmalhausen's contributions to evolutionary biology makes an unbiased reading of his texts difficult. Here we show that taking all of his works into consideration (including those only available in Russian) paints a much more dynamic and exciting picture of what he tried to achieve. Schmalhausen pioneered the integration of a developmental perspective into evolutionary thinking. A main tool for achieving this was his approach to living objects as complex multi-level self-regulating systems. Schmalhausen put enormous effort into bringing this idea into fruition during the final stages of his career by combining evolutionary theory with cybernetics. His results and ideas remain thought-provoking, and his texts are of more than just historical interest. Copyright 2006 Wiley-Liss, Inc.

Integrating genomics into evolutionary medicine.

PubMed

Rodríguez, Juan Antonio; Marigorta, Urko M; Navarro, Arcadi

2014-12-01

The application of the principles of evolutionary biology into medicine was suggested long ago and is already providing insight into the ultimate causes of disease. However, a full systematic integration of medical genomics and evolutionary medicine is still missing. Here, we briefly review some cases where the combination of the two fields has proven profitable and highlight two of the main issues hindering the development of evolutionary genomic medicine as a mature field, namely the dissociation between fitness and health and the still considerable difficulties in predicting phenotypes from genotypes. We use publicly available data to illustrate both problems and conclude that new approaches are needed for evolutionary genomic medicine to overcome these obstacles. Copyright © 2014 Elsevier Ltd. All rights reserved.

Why don’t you use Evolutionary Algorithms in Big Data?

NASA Astrophysics Data System (ADS)

Stanovov, Vladimir; Brester, Christina; Kolehmainen, Mikko; Semenkina, Olga

2017-02-01

In this paper we raise the question of using evolutionary algorithms in the area of Big Data processing. We show that evolutionary algorithms provide evident advantages due to their high scalability and flexibility, their ability to solve global optimization problems and optimize several criteria at the same time for feature selection, instance selection and other data reduction problems. In particular, we consider the usage of evolutionary algorithms with all kinds of machine learning tools, such as neural networks and fuzzy systems. All our examples prove that Evolutionary Machine Learning is becoming more and more important in data analysis and we expect to see the further development of this field especially in respect to Big Data.

Why an extended evolutionary synthesis is necessary

PubMed Central

2017-01-01

Since the last major theoretical integration in evolutionary biology—the modern synthesis (MS) of the 1940s—the biosciences have made significant advances. The rise of molecular biology and evolutionary developmental biology, the recognition of ecological development, niche construction and multiple inheritance systems, the ‘-omics’ revolution and the science of systems biology, among other developments, have provided a wealth of new knowledge about the factors responsible for evolutionary change. Some of these results are in agreement with the standard theory and others reveal different properties of the evolutionary process. A renewed and extended theoretical synthesis, advocated by several authors in this issue, aims to unite pertinent concepts that emerge from the novel fields with elements of the standard theory. The resulting theoretical framework differs from the latter in its core logic and predictive capacities. Whereas the MS theory and its various amendments concentrate on genetic and adaptive variation in populations, the extended framework emphasizes the role of constructive processes, ecological interactions and systems dynamics in the evolution of organismal complexity as well as its social and cultural conditions. Single-level and unilinear causation is replaced by multilevel and reciprocal causation. Among other consequences, the extended framework overcomes many of the limitations of traditional gene-centric explanation and entails a revised understanding of the role of natural selection in the evolutionary process. All these features stimulate research into new areas of evolutionary biology. PMID:28839929

Agency, Values, and Well-Being: A Human Development Model

ERIC Educational Resources Information Center

Welzel, Christian; Inglehart, Ronald

2010-01-01

This paper argues that feelings of agency are linked to human well-being through a sequence of adaptive mechanisms that promote human development, once existential conditions become permissive. In the first part, we elaborate on the evolutionary logic of this model and outline why an evolutionary perspective is helpful to understand changes in…

Terminal addition in a cellular world.

PubMed

Torday, J S; Miller, William B

2018-07-01

Recent advances in our understanding of evolutionary development permit a reframed appraisal of Terminal Addition as a continuous historical process of cellular-environmental complementarity. Within this frame of reference, evolutionary terminal additions can be identified as environmental induction of episodic adjustments to cell-cell signaling patterns that yield the cellular-molecular pathways that lead to differing developmental forms. Phenotypes derive, thereby, through cellular mutualistic/competitive niche constructions in reciprocating responsiveness to environmental stresses and epigenetic impacts. In such terms, Terminal Addition flows according to a logic of cellular needs confronting environmental challenges over space-time. A reconciliation of evolutionary development and Terminal Addition can be achieved through a combined focus on cell-cell signaling, molecular phylogenies and a broader understanding of epigenetic phenomena among eukaryotic organisms. When understood in this manner, Terminal Addition has an important role in evolutionary development, and chronic disease might be considered as a form of 'reverse evolution' of the self-same processes. Copyright © 2017. Published by Elsevier Ltd.

Development of a population of cancer cells: Observation and modeling by a Mixed Spatial Evolutionary Games approach.

PubMed

Świerniak, Andrzej; Krześlak, Michał; Student, Sebastian; Rzeszowska-Wolny, Joanna

2016-09-21

Living cells, like whole living organisms during evolution, communicate with their neighbors, interact with the environment, divide, change their phenotypes, and eventually die. The development of specific ways of communication (through signaling molecules and receptors) allows some cellular subpopulations to survive better, to coordinate their physiological status, and during embryonal development to create tissues and organs or in some conditions to become tumors. Populations of cells cultured in vitro interact similarly, also competing for space and nutrients and stimulating each other to better survive or to die. The results of these intercellular interactions of different types seem to be good examples of biological evolutionary games, and have been the subjects of simulations by the methods of evolutionary game theory where individual cells are treated as players. Here we present examples of intercellular contacts in a population of living human cancer HeLa cells cultured in vitro and propose an evolutionary game theory approach to model the development of such populations. We propose a new technique termed Mixed Spatial Evolutionary Games (MSEG) which are played on multiple lattices corresponding to the possible cellular phenotypes which gives the possibility of simulating and investigating the effects of heterogeneity at the cellular level in addition to the population level. Analyses performed with MSEG suggested different ways in which cellular populations develop in the case of cells communicating directly and through factors released to the environment. Copyright © 2016 Elsevier Ltd. All rights reserved.

Using Evolutionary Theory to Guide Mental Health Research.

PubMed

Durisko, Zachary; Mulsant, Benoit H; McKenzie, Kwame; Andrews, Paul W

2016-03-01

Evolutionary approaches to medicine can shed light on the origins and etiology of disease. Such an approach may be especially useful in psychiatry, which frequently addresses conditions with heterogeneous presentation and unknown causes. We review several previous applications of evolutionary theory that highlight the ways in which psychiatric conditions may persist despite and because of natural selection. One lesson from the evolutionary approach is that some conditions currently classified as disorders (because they cause distress and impairment) may actually be caused by functioning adaptations operating "normally" (as designed by natural selection). Such conditions suggest an alternative illness model that may generate alternative intervention strategies. Thus, the evolutionary approach suggests that psychiatry should sometimes think differently about distress and impairment. The complexity of the human brain, including normal functioning and potential for dysfunctions, has developed over evolutionary time and has been shaped by natural selection. Understanding the evolutionary origins of psychiatric conditions is therefore a crucial component to a complete understanding of etiology. © The Author(s) 2016.

Using Evolutionary Theory to Guide Mental Health Research

PubMed Central

Mulsant, Benoit H.; McKenzie, Kwame; Andrews, Paul W.

2016-01-01

Evolutionary approaches to medicine can shed light on the origins and etiology of disease. Such an approach may be especially useful in psychiatry, which frequently addresses conditions with heterogeneous presentation and unknown causes. We review several previous applications of evolutionary theory that highlight the ways in which psychiatric conditions may persist despite and because of natural selection. One lesson from the evolutionary approach is that some conditions currently classified as disorders (because they cause distress and impairment) may actually be caused by functioning adaptations operating “normally” (as designed by natural selection). Such conditions suggest an alternative illness model that may generate alternative intervention strategies. Thus, the evolutionary approach suggests that psychiatry should sometimes think differently about distress and impairment. The complexity of the human brain, including normal functioning and potential for dysfunctions, has developed over evolutionary time and has been shaped by natural selection. Understanding the evolutionary origins of psychiatric conditions is therefore a crucial component to a complete understanding of etiology. PMID:27254091

Evo-devo of human adolescence: beyond disease models of early puberty

PubMed Central

2013-01-01

Despite substantial heritability in pubertal development, much variation remains to be explained, leaving room for the influence of environmental factors to adjust its phenotypic trajectory in the service of fitness goals. Utilizing evolutionary development biology (evo-devo), we examine adolescence as an evolutionary life-history stage in its developmental context. We show that the transition from the preceding stage of juvenility entails adaptive plasticity in response to energy resources, other environmental cues, social needs of adolescence and maturation toward youth and adulthood. Using the evolutionary theory of socialization, we show that familial psychosocial stress fosters a fast life history and reproductive strategy rather than early maturation being just a risk factor for aggression and delinquency. Here we explore implications of an evolutionary-developmental-endocrinological-anthropological framework for theory building, while illuminating new directions for research. PMID:23627891

Sociality in Parasitic Flatworms: When Do Soldiers Matter?

NASA Astrophysics Data System (ADS)

Garcia-Vedrenne, A. E.

2016-02-01

Although not traditionally recognized as such, trematode infections in molluscan first intermediate hosts comprise colonies. When two trematode species simultaneously infect a snail host, one generally kills the other. Thus, there can be strong selective pressure for established trematode colonies to protect and defend against new infections. Recent findings demonstrate that some trematode species have a reproductive division of labor involving a reproductive and a soldier caste. Reproductives are larger and filled with offspring, while soldiers lack developing embryos, and are specialized for inter-trematode antagonism. This reproductive division of labor has now been documented for intramolluscan stages of fourteen trematode species from different geographic regions and host species. Further, literature descriptions of the life history of several species suggest that this phenomenon is widespread, although there are important intra- and inter-specific differences in colony structure. It has been predicted that trematode soldier castes would most likely evolve in taxa that are typically dominant in interspecific hierarchies, in situations of invasion risk, and among trematodes that infect longer lived hosts. Here I address these hypotheses and present the extent of evidence for trematode social organization.

Molecular context of Schistosoma mansoni transmission in the molluscan environments: A mini-review.

PubMed

Famakinde, Damilare Olatunji

2017-12-01

Schistosoma mansoni, being transmitted by some freshwater Biomphalaria snails, is a major causative agent of human schistosomiasis. In the absence of effective vaccine and alternative drug designs to fight against the disease, and with the limitations of molluscicide application, developing more efficient strategies to interrupt the snail-mediated parasite transmission is being emphasized as potentially instrumental in the efforts toward schistosomiasis elimination, hence, necessitating thorough and comprehensive understanding of the fundamental mechanisms involved in the transmission process. Based on the current advances, this paper presents a concise exposition of the cellular, biochemical, genetic and immunological dynamics of the complex and statge-by-stage interactions between the parasite and its vector in their aquatic environment. It also highlights the possible crosstalk between the parasite's intracellular cyclic adenosine monophosphate (cAMP) and p38 mitogen-activated protein kinase (p38 MAPK) during the intramolluscan stage. Undoubtedly, decades of intensive investigation have untangled many S. mansoni-B. glabrata complexities, yet many aspects of the parasite-vector cycle which can help define potential control clues await further elucidation. Copyright © 2017 Elsevier B.V. All rights reserved.

Cancer Evolution: Mathematical Models and Computational Inference

PubMed Central

Beerenwinkel, Niko; Schwarz, Roland F.; Gerstung, Moritz; Markowetz, Florian

2015-01-01

Cancer is a somatic evolutionary process characterized by the accumulation of mutations, which contribute to tumor growth, clinical progression, immune escape, and drug resistance development. Evolutionary theory can be used to analyze the dynamics of tumor cell populations and to make inference about the evolutionary history of a tumor from molecular data. We review recent approaches to modeling the evolution of cancer, including population dynamics models of tumor initiation and progression, phylogenetic methods to model the evolutionary relationship between tumor subclones, and probabilistic graphical models to describe dependencies among mutations. Evolutionary modeling helps to understand how tumors arise and will also play an increasingly important prognostic role in predicting disease progression and the outcome of medical interventions, such as targeted therapy. PMID:25293804

[Charles Darwin and the problem of evolutionary progress].

PubMed

Iordanskiĭ, N N

2010-01-01

According to Ch. Darwin's evolutionary theory, evolutionary progress (interpreted as morpho-physiological progress or arogenesis in recent terminology) is one of logical results of natural selection. At the same time, natural selection does not hold any factors especially promoting evolutionary progress. Darwin emphasized that the pattern of evolutionary changes depends on organism nature more than on the pattern of environment changes. Arogenesis specificity is determined by organization of rigorous biological systems - integral organisms. Onward progressive development is determined by fundamental features of living organisms: metabolism and homeostasis. The concept of social Darwinism differs fundamentally from Darwin's ideas about the most important role of social instincts in progress of mankind. Competition and selection play secondary role in socio-cultural progress of human society.

Evolutionary biology: a basic science for medicine in the 21st century.

PubMed

Perlman, Robert L

2011-01-01

Evolutionary biology was a poorly developed discipline at the time of the Flexner Report and was not included in Flexner's recommendations for premedical or medical education. Since that time, however, the value of an evolutionary approach to medicine has become increasingly recognized. There are several ways in which an evolutionary perspective can enrich medical education and improve medical practice. Evolutionary considerations rationalize our continued susceptibility or vulnerability to disease; they call attention to the idea that the signs and symptoms of disease may be adaptations that prevent or limit the severity of disease; they help us understand the ways in which our interventions may affect the evolution of microbial pathogens and of cancer cells; and they provide a framework for thinking about population variation and risk factors for disease. Evolutionary biology should become a foundational science for the medical education of the future.

Michael Akam and the rise of evolutionary developmental biology

PubMed Central

Stern, David L.; Dawes-Hoang, Rachel E.

2010-01-01

Michael Akam has been awarded the 2007 Kowalevsky medal for his many research accomplishments in the area of evolutionary developmental biology. We highlight three tributaries of Michael’s contribution to evolutionary developmental biology. First, he has made major contributions to our understanding of development of the fruit fly, Drosophila melanogaster. Second, he has maintained a consistent focus on several key problems in evolutionary developmental biology, including the evolving role of Hox genes in arthropods and, more recently, the evolution of segmentation mechanisms. Third, Michael has written a series of influential reviews that have integrated progress in developmental biology into an evolutionary perspective. Michael has also made a large impact on the field through his effective mentorship style, his selfless promotion of younger colleagues, and his leadership of the University Museum of Zoology at Cambridge and the European community of evolutionary developmental biologists. PMID:20209429

Adult Education and Social Sustainability: Harnessing the "Red Queen Effect"

ERIC Educational Resources Information Center

Easton, Peter

2007-01-01

In 1973, the evolutionary biologist Leigh Van Valen of the University of Chicago devised what he called the "Red Queen Effect" to describe the growth and development of species. It stipulated that an evolutionary system must continue to develop just to maintain its fitness relative to others evolving in its environment. The literary reference is…

A Course in Evolutionary Biology: Engaging Students in the "Practice" of Evolution. Research Report.

ERIC Educational Resources Information Center

Passmore, Cynthia; Stewart, James

Recent education reform documents emphasize the need for students to develop a rich understanding of evolution's power to integrate knowledge of the natural world. This paper describes a nine-week high school course designed to help students understand evolutionary biology by engaging them in developing, elaborating, and using Charles Darwin's…

War, Trauma and Children's Development: Observations from a Modern Evolutionary Perspective

ERIC Educational Resources Information Center

Belsky, Jay

2008-01-01

Lethal intergroup conflict has been part of the human experience ever since our species emerged on the African savannah. Modern evolutionary thinking suggests that children's development could have evolved a variety of responses to it, some of which are highlighted upon considering, from the field of behavioural ecology, life-history theory and,…

From evolutionary computation to the evolution of things.

PubMed

Eiben, Agoston E; Smith, Jim

2015-05-28

Evolution has provided a source of inspiration for algorithm designers since the birth of computers. The resulting field, evolutionary computation, has been successful in solving engineering tasks ranging in outlook from the molecular to the astronomical. Today, the field is entering a new phase as evolutionary algorithms that take place in hardware are developed, opening up new avenues towards autonomous machines that can adapt to their environment. We discuss how evolutionary computation compares with natural evolution and what its benefits are relative to other computing approaches, and we introduce the emerging area of artificial evolution in physical systems.

Left-right asymmetry of the gnathostome skull: its evolutionary, developmental, and functional aspects.

PubMed

Compagnucci, Claudia; Fish, Jennifer; Depew, Michael J

2014-06-01

Much of the gnathostome (jawed vertebrate) evolutionary radiation was dependent on the ability to sense and interpret the environment and subsequently act upon this information through utilization of a specialized mode of feeding involving the jaws. While the gnathostome skull, reflective of the vertebrate baüplan, typically is bilaterally symmetric with right (dextral) and left (sinistral) halves essentially representing mirror images along the midline, both adaptive and abnormal asymmetries have appeared. Herein we provide a basic primer on studies of the asymmetric development of the gnathostome skull, touching briefly on asymmetry as a field of study, then describing the nature of cranial development and finally underscoring evolutionary and functional aspects of left-right asymmetric cephalic development. © 2014 Wiley Periodicals, Inc.

System Design under Uncertainty: Evolutionary Optimization of the Gravity Probe-B Spacecraft

NASA Technical Reports Server (NTRS)

Pullen, Samuel P.; Parkinson, Bradford W.

1994-01-01

This paper discusses the application of evolutionary random-search algorithms (Simulated Annealing and Genetic Algorithms) to the problem of spacecraft design under performance uncertainty. Traditionally, spacecraft performance uncertainty has been measured by reliability. Published algorithms for reliability optimization are seldom used in practice because they oversimplify reality. The algorithm developed here uses random-search optimization to allow us to model the problem more realistically. Monte Carlo simulations are used to evaluate the objective function for each trial design solution. These methods have been applied to the Gravity Probe-B (GP-B) spacecraft being developed at Stanford University for launch in 1999, Results of the algorithm developed here for GP-13 are shown, and their implications for design optimization by evolutionary algorithms are discussed.

Protaeolidiella atra Baba, 1955 versus Pleurolidia juliae Burn, 1966: One or two species?

NASA Astrophysics Data System (ADS)

Carmona, Leila; Pola, Marta; Gosliner, Terrence M.; Cervera, Juan Lucas

2015-06-01

Protaeolidiella atra Baba, 1955 and Pleurolidia juliae Burn, 1966 are two species traditionally regarded as the members of Aeolidiidae but recently attributed to Facelinidae. Because of their apparent similarities, Rudman (J Molluscan Stud 56:505-514, 1990) rendered P. juliae as a junior synonym of P. atra. In this paper, we conducted a review of both species and completed their descriptions with new data regarding the anatomy of the reproductive system . P. atra and P. juliae have differences in their colouration, number of cerata and characteristics of their reproductive system. Based on these differences, we conclude that these species are not conspecific and should be regarded as distinct taxa.

Evolutionary stability concepts in a stochastic environment

NASA Astrophysics Data System (ADS)

Zheng, Xiu-Deng; Li, Cong; Lessard, Sabin; Tao, Yi

2017-09-01

Over the past 30 years, evolutionary game theory and the concept of an evolutionarily stable strategy have been not only extensively developed and successfully applied to explain the evolution of animal behaviors, but also widely used in economics and social sciences. Nonetheless, the stochastic dynamical properties of evolutionary games in randomly fluctuating environments are still unclear. In this study, we investigate conditions for stochastic local stability of fixation states and constant interior equilibria in a two-phenotype model with random payoffs following pairwise interactions. Based on this model, we develop the concepts of stochastic evolutionary stability (SES) and stochastic convergence stability (SCS). We show that the condition for a pure strategy to be SES and SCS is more stringent than in a constant environment, while the condition for a constant mixed strategy to be SES is less stringent than the condition to be SCS, which is less stringent than the condition in a constant environment.

Social defense: an evolutionary-developmental model of children's strategies for coping with threat in the peer group.

PubMed

Martin, Meredith J; Davies, Patrick T; MacNeill, Leigha A

2014-04-29

Navigating the ubiquitous conflict, competition, and complex group dynamics of the peer group is a pivotal developmental task of childhood. Difficulty negotiating these challenges represents a substantial source of risk for psychopathology. Evolutionary developmental psychology offers a unique perspective with the potential to reorganize the way we think about the role of peer relationships in shaping how children cope with the everyday challenges of establishing a social niche. To address this gap, we utilize the ethological reformulation of the emotional security theory as a guide to developing an evolutionary framework for advancing an understanding of the defense strategies children use to manage antagonistic peer relationships and protect themselves from interpersonal threat (Davies and Sturge-Apple, 2007). In this way, we hope to illustrate the value of an evolutionary developmental lens in generating unique theoretical insight and novel research directions into the role of peer relationships in the development of psychopathology.

Evolutionary and mechanistic theories of aging.

PubMed

Hughes, Kimberly A; Reynolds, Rose M

2005-01-01

Senescence (aging) is defined as a decline in performance and fitness with advancing age. Senescence is a nearly universal feature of multicellular organisms, and understanding why it occurs is a long-standing problem in biology. Here we present a concise review of both evolutionary and mechanistic theories of aging. We describe the development of the general evolutionary theory, along with the mutation accumulation, antagonistic pleiotropy, and disposable soma versions of the evolutionary model. The review of the mechanistic theories focuses on the oxidative stress resistance, cellular signaling, and dietary control mechanisms of life span extension. We close with a discussion of how an approach that makes use of both evolutionary and molecular analyses can address a critical question: Which of the mechanisms that can cause variation in aging actually do cause variation in natural populations?

Selecting the Best: Evolutionary Engineering of Chemical Production in Microbes.

PubMed

Shepelin, Denis; Hansen, Anne Sofie Lærke; Lennen, Rebecca; Luo, Hao; Herrgård, Markus J

2018-05-11

Microbial cell factories have proven to be an economical means of production for many bulk, specialty, and fine chemical products. However, we still lack both a holistic understanding of organism physiology and the ability to predictively tune enzyme activities in vivo, thus slowing down rational engineering of industrially relevant strains. An alternative concept to rational engineering is to use evolution as the driving force to select for desired changes, an approach often described as evolutionary engineering. In evolutionary engineering, in vivo selections for a desired phenotype are combined with either generation of spontaneous mutations or some form of targeted or random mutagenesis. Evolutionary engineering has been used to successfully engineer easily selectable phenotypes, such as utilization of a suboptimal nutrient source or tolerance to inhibitory substrates or products. In this review, we focus primarily on a more challenging problem-the use of evolutionary engineering for improving the production of chemicals in microbes directly. We describe recent developments in evolutionary engineering strategies, in general, and discuss, in detail, case studies where production of a chemical has been successfully achieved through evolutionary engineering by coupling production to cellular growth.

Evolutionary adaptations: theoretical and practical implications for visual ergonomics.

PubMed

Fostervold, Knut Inge; Watten, Reidulf G; Volden, Frode

2014-01-01

The literature discussing visual ergonomics often mention that human vision is adapted to light emitted by the sun. However, theoretical and practical implications of this viewpoint is seldom discussed or taken into account. The paper discusses some of the main theoretical implications of an evolutionary approach to visual ergonomics. Based on interactional theory and ideas from ecological psychology an evolutionary stress model is proposed as a theoretical framework for future research in ergonomics and human factors. The model stresses the importance of developing work environments that fits with our evolutionary adaptations. In accordance with evolutionary psychology, the environment of evolutionary adaptedness (EEA) and evolutionarily-novel environments (EN) are used as key concepts. Using work with visual display units (VDU) as an example, the paper discusses how this knowledge can be utilized in an ergonomic analysis of risk factors in the work environment. The paper emphasises the importance of incorporating evolutionary theory in the field of ergonomics. Further, the paper encourages scientific practices that further our understanding of any phenomena beyond the borders of traditional proximal explanations.

Characterizing behavioural ‘characters’: an evolutionary framework

PubMed Central

Araya-Ajoy, Yimen G.; Dingemanse, Niels J.

2014-01-01

Biologists often study phenotypic evolution assuming that phenotypes consist of a set of quasi-independent units that have been shaped by selection to accomplish a particular function. In the evolutionary literature, such quasi-independent functional units are called ‘evolutionary characters’, and a framework based on evolutionary principles has been developed to characterize them. This framework mainly focuses on ‘fixed’ characters, i.e. those that vary exclusively between individuals. In this paper, we introduce multi-level variation and thereby expand the framework to labile characters, focusing on behaviour as a worked example. We first propose a concept of ‘behavioural characters’ based on the original evolutionary character concept. We then detail how integration of variation between individuals (cf. ‘personality’) and within individuals (cf. ‘individual plasticity’) into the framework gives rise to a whole suite of novel testable predictions about the evolutionary character concept. We further propose a corresponding statistical methodology to test whether observed behaviours should be considered expressions of a hypothesized evolutionary character. We illustrate the application of our framework by characterizing the behavioural character ‘aggressiveness’ in wild great tits, Parus major. PMID:24335984

The development of terrestrial mollusc faunas in the ?Rheinland region? (western Germany and Luxembourg) during the Lateglacial and Holocene

NASA Astrophysics Data System (ADS)

Meyrick, R. A.

2001-10-01

A composite faunal history, covering the last ˜13,000 radiocarbon years, has been reconstructed from the few molluscan successions available from the 'Rheinland' region. The region, centred on the German Land of Rheinland-Pfalz (but including the Principality of Luxembourg) does not form a discrete biogeographical province but does represent an important link between the better known faunas of central Europe and those of north-west Europe. Open-ground assemblages dominated by Vallonia and Trichia, with few shade-demanding elements, occur throughout the Lateglacial and early Holocene. The Lateglacial is characterised by the presence of Vertigo genesii and Abida secale, depending on whether the depositional environment is wet or dry, respectively. Catholic elements became increasingly important at the start of the Holocene. The establishment of woodland, from approximately 9700 yr BP, is indicated by the expansion of shade-demanding taxa, most notably Carychium tridentatum. Deciduous forest optimum faunas developed by about 7500 yr BP and are characterised by Platyla polita, Perforatella incarnata and Sphyradium doliolum. The modern ranges of these species suggest that during the Holocene Platyla polita, Perforatella incarnata (and possibly Sphyradium doliolum also) colonised northwestern Europe from refugia further east. The reappearance of open-ground faunas from ˜5000 yr BP reflects widespread anthropogenic clearance.

Does playing pay? The fitness-effect of free play during childhood.

PubMed

Greve, Werner; Thomsen, Tamara; Dehio, Cornelia

2014-04-29

Evolutionary developmental psychology claims that the sequences and processes of human development, in fact the mere fact of ontogeny itself, have to be viewed as evolutionary products. However, although the functional benefits of childish behavior (child playing) for cognitive and emotional development have been shown repeatedly, claiming evolutionary adaptiveness of playing in childhood suggests that childish play supports evolutionary success in mature stages of development. This hypothesis is tested in a study with N=134 adults (93 females; age range 20-66 years). Participants were asked to recollect their play experiences during childhood in detail, and to report their current developmental status with respect to several aspects of social success. Results show that the opportunity for and the promotion of free play in childhood significantly predict some indicators of social success. Additional analyses strive to explore mediating processes for this relationship. In particular, the mediating role of individual adaptivity (flexibility of goal adjustment) is investigated. Results suggest that freely playing in childhood promotes developmental resources, in particular individual adaptivity in adulthood, which, in turn, promote developmental success.

EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A

PubMed Central

Ndhlovu, Andrew; Durand, Pierre M.; Hazelhurst, Scott

2015-01-01

The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry. EvoDB contains 98.83% of the gapped nucleotide sequence alignments and 97.1% of the evolutionary rate profiles for the corresponding information in PFAM-A. As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after information for molecular evolutionary biologists, evolutionary rate profiles were determined under the M2a model using the CODEML algorithm in the PAML (Phylogenetic Analysis by Maximum Likelihood) suite of software. Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality. EvoDB is a catalogue of the evolutionary rate profiles and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identifier data. In addition, the database can be explored and queried using known evolutionary rate profiles to identify domains under similar evolutionary constraints and pressures. EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases. Database URL: http://www.bioinf.wits.ac.za/software/fire/evodb PMID:26140928

EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A.

PubMed

Ndhlovu, Andrew; Durand, Pierre M; Hazelhurst, Scott

2015-01-01

The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry. EvoDB contains 98.83% of the gapped nucleotide sequence alignments and 97.1% of the evolutionary rate profiles for the corresponding information in PFAM-A. As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after information for molecular evolutionary biologists, evolutionary rate profiles were determined under the M2a model using the CODEML algorithm in the PAML (Phylogenetic Analysis by Maximum Likelihood) suite of software. Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality. EvoDB is a catalogue of the evolutionary rate profiles and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identifier data. In addition, the database can be explored and queried using known evolutionary rate profiles to identify domains under similar evolutionary constraints and pressures. EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases. © The Author(s) 2015. Published by Oxford University Press.

An Interdisciplinary Model for Teaching Evolutionary Ecology.

ERIC Educational Resources Information Center

Coletta, John

1992-01-01

Describes a general systems evolutionary model and demonstrates how a previously established ecological model is a function of its past development based on the evolution of the rock, nutrient, and water cycles. Discusses the applications of the model in environmental education. (MDH)

Do coastal fronts influence bioerosion patterns along Patagonia? Late Quaternary ichnological tools from Golfo San Jorge

NASA Astrophysics Data System (ADS)

Richiano, Sebastián; Aguirre, Marina; Castellanos, Ignacio; Davies, Karen; Farinati, Ester

2017-12-01

Late Quaternary marine molluscan skeletal concentrations from Argentina constitute a remarkable record of variations in palaeoceanographical conditions during interglacial times (mainly ca. 125 ka to present). Particularly, the Golfo San Jorge coastal area represents an extraordinary geographical zone to target from different points of view, mainly due to its linkage between northern and southern Patagonia, characterized by particular and contrasting physico-chemical conditions with direct consequences for littoral marine communities, determining their composition and structure. Among varied biological activities controlled by different environmental factors (i.e., substrate nature, sedimentation rates, water depth, sea surface temperature, salinity, nutrients-productivity), bioerosion traces can provide palaeoenvironmental evidence with important implications for palaeoclimate interpretations. In addition, the application of bioerosion patterns regionally and through time is a recent valuable worthy palaeoenvironmental tool not as yet developed for Patagonia. We attempted to characterize, qualitatively/semiquantitatively, the ichnotaxonomic composition of the coastal area of northern Golfo San Jorge since the Late Pleistocene; to compare results with those obtained for other geographical areas along Patagonia and the Bonaerensian coastal sectors; lastly, to evaluate its palaeoenvironmental/palaeoclimatic significance in a clue area in terms of circulation patterns near the Southern Ocean climatic pump. At Bustamante (Northern Patagonia Frontal System) Domichnia traces were dominant during the Late Pleistocene while Praedichnia in the mid-Holocene. Bustamante exhibits the highest ichnodiversity for the whole Argentinean coastal area. Ichnodiversity is not strongly different between Late Pleistocene and mid-Holocene interglacials and compared to present; however, the relative abundance of some ichnotaxa (e.g., Oichnus, Iramena, Pennatichnus, at Camarones; Oichnus, Iramena, Pinaceocladichnus, at Bustamante) differs across time. These variations, particularly the highest abundance in the Late Pleistocene (mainly Last Interglacial) of traces made by bryozoans- associated at present with modern enhanced productivity levels and coastal fronts in the Argentine continental shelf- point to higher productivity and more intensified northern Patagonia Front, as a result of a different palaeocirculation pattern, reinforcing previous independent sources of evidence based on molluscan palaeobiogeographical analyses. Supplementary Appendix 2 List of ichnotaxa recorded in gastropod and bivalve taxa as observed in shells from the Quaternary deposits sampled, authors and corresponding ethological classification. Abbreviations are those used along the text. Full references in Richiano et al. (2012, 2015). Supplementary Appendix 3 General biogenic composition of the beach ridge systems (Marine Terraces) at Camarones and Bustamante coastal areas and along the adjacent modern littoral. List of molluscan species and other invertebrates recovered from the deposits sampled. Modified from Aguirre et al. (2005, 2006). See also Table 1 of this paper, Aguirre et al. (2008, 2011a), Richiano et al. (2012, 2015). Supplementary Appendix 4 Independent palaeobiogeographical evidence for lower SST during the Late Pleistocene against higher during the Mid-Holocene. Geographical patterns of relationships between areas through time. PCO (Principal Coordinate analyses), CA (Cluster Analysis) and PAE (Parsimony Analysis of Endemicity) (modified from Aguirre et al., 2011a, 2013). (A1): PCO (top) and (A2): CA (middle) for Late Pleistocene, Holocene and modern molluscs. (A3): PAE showing patterns between localities for the Pleistocene (only time interval with records of Tegula atra) compared to the present. __: Areas of endemism. Note the isolation of SAO (SMCF) relative to the remaining Patagonian localities at present and during the mid-Holocene vs. its linkage to the remaining Patagonian sites during the Late Pleistocene (especially MIS5e). Tegula atra characterizes (and is dominant within) the marine Pleistocene of Patagonia, especially south of SAO (San Antonio Oeste) along ca. 1000 km during MIS5e. Modified from Aguirre et al. (2011a, 2013).

Salinity and Temperature Tolerance Experiments on Selected Florida Bay Mollusks

USGS Publications Warehouse

Murray, James B.; Wingard, G. Lynn

2006-01-01

The ultimate goal of the Comprehensive Everglades Restoration Plan (CERP) is to restore and preserve the unique ecosystems of South Florida, including the estuaries. Understanding the effect of salinity and temperature changes, beyond typical oscillations, on the biota of South Florida's estuaries is a necessary component of achieving the goal of restoring the estuaries. The U.S. Geological Survey has been actively involved in researching the history of the South Florida Ecosystem, to provide targets, performance measures, and baseline data for restoration managers. These experiments addressed two aspects of ecosystem history research: 1) determining the utility of using molluscan shells as recorders of change in water chemistry parameters, primarily salinity, and 2) enhancing our in situ observations on modern assemblages by exceeding typically observed aquatic conditions. This set of experiments expanded our understanding of the effects of salinity, temperature and other water chemistry parameters on the reproduction, growth and overall survivability of key species of mollusks used in interpreting sediment core data. Observations on mollusks, plants and microbes made as part of these experiments have further refined our knowledge and understanding of the effects of ecosystem feedback and the role salinity and temperature play in ecosystem stability. The results have demonstrated the viability of several molluscan species as indicators of atypical salinity, and possibly temperature, modulations. For example Cerithium muscarum and Bulla striata demonstrated an ability to withstand a broad salinity and temperature range, with reproduction occurring in atypically high salinities and temperatures. These experiments also provided calibration data for the shell biogeochemistry of Chione cancellata and the possible use of this species as a water chemistry recorder. Observations made in the mesocosms, on a scale not normally observable in the field, have led to new questions about the influence of salinity on the localized ecosystem. The next phase of these experiments; to calibrate growth rate and reproductive viability in atypical salinities is currently underway.

Phylogeography and connectivity of molluscan parasites: Perkinsus spp. in Panama and beyond.

PubMed

Pagenkopp Lohan, Katrina M; Hill-Spanik, Kristina M; Torchin, Mark E; Fleischer, Robert C; Carnegie, Ryan B; Reece, Kimberly S; Ruiz, Gregory M

2018-02-01

Panama is a major hub for commercial shipping between two oceans, making it an ideal location to examine parasite biogeography, potential invasions, and the spread of infectious agents. Our goals were to (i) characterise the diversity and genetic connectivity of Perkinsus spp. haplotypes across the Panamanian Isthmus and (ii) combine these data with sequences from around the world to evaluate the current phylogeography and genetic connectivity of these widespread molluscan parasites. We collected 752 bivalves from 12 locations along the coast of Panama including locations around the Bocas del Toro archipelago and the Caribbean and Pacific entrances to the Panama Canal, from December 2012 to February 2013. We used molecular genetic methods to screen for Perkinsus spp. and obtained internal transcribed spacer region (ITS) ribosomal DNA (rDNA) sequences for all positive samples. Our sequence data were used to evaluate regional haplotype diversity and distribution across both coasts of Panama, and were then combined with publicly available sequences to create global haplotype networks. We found 26 ITS haplotypes from four Perkinsus spp. (1-12 haplotypes per species) in Panama. Perkinsus beihaiensis haplotypes had the highest genetic diversity, were the most regionally widespread, and were associated with the greatest number of hosts. On a global scale, network analyses demonstrated that some haplotypes found in Panama were cosmopolitan (Perkinsus chesapeaki, Perkinsus marinus), while others were more geographically restricted (Perkinsus olseni, P. beihaiensis), indicating different levels of genetic connectivity and dispersal. We found some Perkinsus haplotypes were shared across the Isthmus of Panama and several regions around the world, including across ocean basins. We also found that haplotype diversity is currently underestimated and directly related to the number of sequences. Nevertheless, our results demonstrate long-range dispersal and global connectivity for many haplotypes, suggesting that dispersal through shipping probably contributes to these biogeographical patterns. Published by Elsevier Ltd.

Local diversity hot spots in the Middle Miocene of the Central Paratethys: influence of environment and sampling

NASA Astrophysics Data System (ADS)

Nawrot, Rafal; Zuschin, Martin; Harzhauser, Mathias; Kroh, Andreas; Mandic, Oleg

2015-04-01

Species richness captured by historical fossil inventories is a complex function of true local diversity, degree of outcrop-scale heterogeneity in species composition and sampling intensity. Disentangling these factors is hindered by the fact that the 'systematists follow the fossils' (Raup, 1977) and thus non-uniform research effort may both drive apparent diversity patterns and follow the actual presence of highly fossiliferous strata. The molluscan fauna of Lapugiu de Sus (Hunedoara District, Romania) constitutes one of the most diverse Early Badenian (Langhian) assemblages of the Paratethys Sea, with almost one thousand species reported during 170 years of extensive studies. We evaluate whether this exceptional richness reflects the actual diversity hot spot or just a long history of fossil-collecting by comparing the fauna of Lapugiu with other Paratethyan molluscan lagerstätten of similar age. The literature-derived species lists for each section were contrasted with independent abundance data based on a standardized sampling protocol (42 samples, 24,000 specimens, and 530 species from six localities). Although individual samples from other localities can exhibit comparable diversity levels, richness estimates for samples from Lapugiu are all consistently high, reflecting increasing evenness in more offshore depositional settings. This translates to the highest diversity at the outcrop scale when all samples are pooled. In contrast to other localities, however, for which data from historical inventories corresponds well to our quantitative estimates of total richness, the number of species described from Lapugiu is much higher than expected. This excessive richness likely reflects the 'Bonanza Effect' (sensu Dunhill et al., 2012), where uniformly species-rich deposits were attracting intensive taxonomic studies. The strong positive feedback between palaeontological sampling effort and fossil diversity may thus greatly overestimate the true differences in species richness between the most diverse faunas and more typical, background, fossil assemblages. References Raup, D.M., 1977. Paleobiology, 3: 328-329. Dunhill, A.M. et al., 2012. Palaeontology, 55: 1155-1175.

Commentary: An Exciting Evolutionary Framework for New Bridges between Social-Emotional and Cognitive Development--A Reflection on Suor et al. (2017)

ERIC Educational Resources Information Center

Kochanska, Grazyna; Goffin, Kathryn C.

2017-01-01

Suor et al. (2017) present a compelling new evolutionary framework that offers an alternative interpretation of the well-established findings of cognitive deficits in children raised in harsh early environments. They argue that such findings do not convey a complete picture of those children's cognitive development, because children's cognition…

Applying Evolutionary Anthropology

PubMed Central

Gibson, Mhairi A; Lawson, David W

2015-01-01

Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution. PMID:25684561

Applying evolutionary anthropology.

PubMed

Gibson, Mhairi A; Lawson, David W

2015-01-01

Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution. © 2015 Wiley Periodicals, Inc.

Applying evolutionary biology to address global challenges

PubMed Central

Carroll, Scott P.; Jørgensen, Peter Søgaard; Kinnison, Michael T.; Bergstrom, Carl T.; Denison, R. Ford; Gluckman, Peter; Smith, Thomas B.; Strauss, Sharon Y.; Tabashnik, Bruce E.

2014-01-01

Two categories of evolutionary challenges result from escalating human impacts on the planet. The first arises from cancers, pathogens and pests that evolve too quickly, and the second from the inability of many valued species to adapt quickly enough. Applied evolutionary biology provides a suite of strategies to address these global challenges that threaten human health, food security, and biodiversity. This review highlights both progress and gaps in genetic, developmental and environmental manipulations across the life sciences that either target the rate and direction of evolution, or reduce the mismatch between organisms and human-altered environments. Increased development and application of these underused tools will be vital in meeting current and future targets for sustainable development. PMID:25213376

Cancer evolution: mathematical models and computational inference.

PubMed

Beerenwinkel, Niko; Schwarz, Roland F; Gerstung, Moritz; Markowetz, Florian

2015-01-01

Cancer is a somatic evolutionary process characterized by the accumulation of mutations, which contribute to tumor growth, clinical progression, immune escape, and drug resistance development. Evolutionary theory can be used to analyze the dynamics of tumor cell populations and to make inference about the evolutionary history of a tumor from molecular data. We review recent approaches to modeling the evolution of cancer, including population dynamics models of tumor initiation and progression, phylogenetic methods to model the evolutionary relationship between tumor subclones, and probabilistic graphical models to describe dependencies among mutations. Evolutionary modeling helps to understand how tumors arise and will also play an increasingly important prognostic role in predicting disease progression and the outcome of medical interventions, such as targeted therapy. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society of Systematic Biologists.

Scheduling Earth Observing Satellites with Evolutionary Algorithms

NASA Technical Reports Server (NTRS)

Globus, Al; Crawford, James; Lohn, Jason; Pryor, Anna

2003-01-01

We hypothesize that evolutionary algorithms can effectively schedule coordinated fleets of Earth observing satellites. The constraints are complex and the bottlenecks are not well understood, a condition where evolutionary algorithms are often effective. This is, in part, because evolutionary algorithms require only that one can represent solutions, modify solutions, and evaluate solution fitness. To test the hypothesis we have developed a representative set of problems, produced optimization software (in Java) to solve them, and run experiments comparing techniques. This paper presents initial results of a comparison of several evolutionary and other optimization techniques; namely the genetic algorithm, simulated annealing, squeaky wheel optimization, and stochastic hill climbing. We also compare separate satellite vs. integrated scheduling of a two satellite constellation. While the results are not definitive, tests to date suggest that simulated annealing is the best search technique and integrated scheduling is superior.

Life is determined by its environment

NASA Astrophysics Data System (ADS)

Torday, John S.; Miller, William B.

2016-10-01

A well-developed theory of evolutionary biology requires understanding of the origins of life on Earth. However, the initial conditions (ontology) and causal (epistemology) bases on which physiology proceeded have more recently been called into question, given the teleologic nature of Darwinian evolutionary thinking. When evolutionary development is focused on cellular communication, a distinctly different perspective unfolds. The cellular communicative-molecular approach affords a logical progression for the evolutionary narrative based on the basic physiologic properties of the cell. Critical to this appraisal is recognition of the cell as a fundamental reiterative unit of reciprocating communication that receives information from and reacts to epiphenomena to solve problems. Following the course of vertebrate physiology from its unicellular origins instead of its overt phenotypic appearances and functional associations provides a robust, predictive picture for the means by which complex physiology evolved from unicellular organisms. With this foreknowledge of physiologic principles, we can determine the fundamentals of Physiology based on cellular first principles using a logical, predictable method. Thus, evolutionary creativity on our planet can be viewed as a paradoxical product of boundary conditions that permit homeostatic moments of varying length and amplitude that can productively absorb a variety of epigenetic impacts to meet environmental challenges.

Development of antibiotic regimens using graph based evolutionary algorithms.

PubMed

Corns, Steven M; Ashlock, Daniel A; Bryden, Kenneth M

2013-12-01

This paper examines the use of evolutionary algorithms in the development of antibiotic regimens given to production animals. A model is constructed that combines the lifespan of the animal and the bacteria living in the animal's gastro-intestinal tract from the early finishing stage until the animal reaches market weight. This model is used as the fitness evaluation for a set of graph based evolutionary algorithms to assess the impact of diversity control on the evolving antibiotic regimens. The graph based evolutionary algorithms have two objectives: to find an antibiotic treatment regimen that maintains the weight gain and health benefits of antibiotic use and to reduce the risk of spreading antibiotic resistant bacteria. This study examines different regimens of tylosin phosphate use on bacteria populations divided into Gram positive and Gram negative types, with a focus on Campylobacter spp. Treatment regimens were found that provided decreased antibiotic resistance relative to conventional methods while providing nearly the same benefits as conventional antibiotic regimes. By using a graph to control the information flow in the evolutionary algorithm, a variety of solutions along the Pareto front can be found automatically for this and other multi-objective problems. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Life is determined by its environment

PubMed Central

Torday, John S.; Miller, William B.

2016-01-01

A well-developed theory of evolutionary biology requires understanding of the origins of life on Earth. However, the initial conditions (ontology) and causal (epistemology) bases on which physiology proceeded have more recently been called into question, given the teleologic nature of Darwinian evolutionary thinking. When evolutionary development is focused on cellular communication, a distinctly different perspective unfolds. The cellular communicative-molecular approach affords a logical progression for the evolutionary narrative based on the basic physiologic properties of the cell. Critical to this appraisal is recognition of the cell as a fundamental reiterative unit of reciprocating communication that receives information from and reacts to epiphenomena to solve problems. Following the course of vertebrate physiology from its unicellular origins instead of its overt phenotypic appearances and functional associations provides a robust, predictive picture for the means by which complex physiology evolved from unicellular organisms. With this foreknowledge of physiologic principles, we can determine the fundamentals of Physiology based on cellular first principles using a logical, predictable method. Thus, evolutionary creativity on our planet can be viewed as a paradoxical product of boundary conditions that permit homeostatic moments of varying length and amplitude that can productively absorb a variety of epigenetic impacts to meet environmental challenges. PMID:27708547

Adaptive evolution of Mediterranean pines.

PubMed

Grivet, Delphine; Climent, José; Zabal-Aguirre, Mario; Neale, David B; Vendramin, Giovanni G; González-Martínez, Santiago C

2013-09-01

Mediterranean pines represent an extremely heterogeneous assembly. Although they have evolved under similar environmental conditions, they diversified long ago, ca. 10 Mya, and present distinct biogeographic and demographic histories. Therefore, it is of special interest to understand whether and to what extent they have developed specific strategies of adaptive evolution through time and space. To explore evolutionary patterns, the Mediterranean pines' phylogeny was first reconstructed analyzing a new set of 21 low-copy nuclear genes with multilocus Bayesian tree reconstruction methods. Secondly, a phylogenetic approach was used to search for footprints of natural selection and to examine the evolution of multiple phenotypic traits. We identified two genes (involved in pines' defense and stress responses) that have likely played a role in the adaptation of Mediterranean pines to their environment. Moreover, few life-history traits showed historical or evolutionary adaptive convergence in Mediterranean lineages, while patterns of character evolution revealed various evolutionary trade-offs linking growth-development, reproduction and fire-related traits. Assessing the evolutionary path of important life-history traits, as well as the genomic basis of adaptive variation is central to understanding the past evolutionary success of Mediterranean pines and their future response to environmental changes. Copyright © 2013 Elsevier Inc. All rights reserved.

The roles of ecological fitting, phylogeny and physiological equivalence in understanding realized and fundamental host ranges in endoparasitoid wasps.

PubMed

Harvey, J A; Ximénez de Embún, M G; Bukovinszky, T; Gols, R

2012-10-01

Co-evolutionary theory underpins our understanding of interactions in nature involving plant-herbivore and host-parasite interactions. However, many studies that are published in the empirical literature that have explored life history and development strategies between endoparasitoid wasps and their hosts are based on species that have no evolutionary history with one another. Here, we investigated novel associations involving two closely related solitary endoparasitoids that originate from Europe and North America and several of their natural and factitious hosts from both continents. The natural hosts of both species are also closely related, all being members of the same family. We compared development and survival of both parasitoids on the four host species and predicted that parasitoid performance is better on their own natural hosts. In contrast with this expectation, survival, adult size and development time of both parasitoids were similar on all (with one exception) hosts, irrespective as to their geographic origin. Our results show that phylogenetic affinity among the natural and factitious hosts plays an important role in their nutritional suitability for related parasitoids. Evolved traits in parasitoids, such as immune suppression and development, thus enable them to successfully develop in novel host species with which they have no evolutionary history. Our results show that host suitability for specialized organisms like endoparasitoids is closely linked with phylogenetic history and macro-evolution as well as local adaptation and micro-evolution. We argue that the importance of novel interactions and 'ecological fitting' based on phylogeny is a greatly underappreciated concept in many resource-consumer studies. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

There must be a prokaryote somewhere: microbiology's search for itself

NASA Technical Reports Server (NTRS)

Woese, C. R.

1994-01-01

While early microbiologists showed considerable interest in the problem of the natural (evolutionary) relationships among prokaryotes, by the middle of this century that problem had largely been discarded as being unsolvable. In other words, the science of microbiology developed without an evolutionary framework, the lack of which kept it a weak discipline, defined largely by external forces. Modern technology has allowed microbiology finally to develop the needed evolutionary framework, and with this comes a sense of coherence, a sense of identity. Not only is this development radically changing microbiology itself, but also it will change microbiology's relationship to the other biological disciplines. Microbiology of the future will become the primary biological science, the base upon which our future understanding of the living world rests, and the font from which new understanding of it flows.

Segmenting healthcare terminology users: a strategic approach to large scale evolutionary development.

PubMed

Price, C; Briggs, K; Brown, P J

1999-01-01

Healthcare terminologies have become larger and more complex, aiming to support a diverse range of functions across the whole spectrum of healthcare activity. Prioritization of development, implementation and evaluation can be achieved by regarding the "terminology" as an integrated system of content-based and functional components. Matching these components to target segments within the healthcare community, supports a strategic approach to evolutionary development and provides essential product differentiation to enable terminology providers and systems suppliers to focus on end-user requirements.

Humanism and multiculturalism: an evolutionary alliance.

PubMed

Comas-Diaz, Lillian

2012-12-01

Humanism and multiculturalism are partners in an evolutionary alliance. Humanistic and multicultural psychotherapies have historically influenced each other. Humanism represents the third force in psychotherapy, while multiculturalism embodies the fourth developmental stage. Multiculturalism embraces humanistic values grounded in collective and social justice contexts. Examples of multicultural humanistic constructs include contextualism, holism, and liberation. Certainly, the multicultural-humanistic connection is a necessary shift in the evolution of psychotherapy. Humanism and multiculturalism participate in the development of an inclusive and evolutionary psychotherapy. (c) 2012 APA, all rights reserved.

A Bright Future for Evolutionary Methods in Drug Design.

PubMed

Le, Tu C; Winkler, David A

2015-08-01

Most medicinal chemists understand that chemical space is extremely large, essentially infinite. Although high-throughput experimental methods allow exploration of drug-like space more rapidly, they are still insufficient to fully exploit the opportunities that such large chemical space offers. Evolutionary methods can synergistically blend automated synthesis and characterization methods with computational design to identify promising regions of chemical space more efficiently. We describe how evolutionary methods are implemented, and provide examples of published drug development research in which these methods have generated molecules with increased efficacy. We anticipate that evolutionary methods will play an important role in future drug discovery. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Misrepresentations of evolutionary psychology in sex and gender textbooks.

PubMed

Winegard, Benjamin M; Winegard, Bo M; Deaner, Robert O

2014-05-20

Evolutionary psychology has provoked controversy, especially when applied to human sex differences. We hypothesize that this is partly due to misunderstandings of evolutionary psychology that are perpetuated by undergraduate sex and gender textbooks. As an initial test of this hypothesis, we develop a catalog of eight types of errors and document their occurrence in 15 widely used sex and gender textbooks. Consistent with our hypothesis, of the 12 textbooks that discussed evolutionary psychology, all contained at least one error, and the median number of errors was five. The most common types of errors were "Straw Man," "Biological Determinism," and "Species Selection." We conclude by suggesting improvements to undergraduate sex and gender textbooks.

Applying Evolutionary Prototyping In Developing LMIS: A Spatial Web-Based System For Land Management

NASA Astrophysics Data System (ADS)

Agustiono, W.

2018-01-01

Software development project is a difficult task. Especially for software designed to comply with regulations that are constantly being introduced or changed, it is almost impossible to make just one change during the development process. Even if it is possible, nonetheless, the developers may take bulk of works to fix the design to meet specified needs. This iterative work also means that it takes additional time and potentially leads to failing to meet the original schedule and budget. In such inevitable changes, it is essential for developers to carefully consider and use an appropriate method which will help them carry out software project development. This research aims to examine the implementation of a software development method called evolutionary prototyping for developing software for complying regulation. It investigates the development of Land Management Information System (pseudonym), initiated by the Australian government, for use by farmers to meet regulatory demand requested by Soil and Land Conservation Act. By doing so, it sought to provide understanding the efficacy of evolutionary prototyping in helping developers address frequent changing requirements and iterative works but still within schedule. The findings also offer useful practical insights for other developers who seek to build similar regulatory compliance software.

The significance and scope of evolutionary developmental biology: a vision for the 21st century.

PubMed

Moczek, Armin P; Sears, Karen E; Stollewerk, Angelika; Wittkopp, Patricia J; Diggle, Pamela; Dworkin, Ian; Ledon-Rettig, Cristina; Matus, David Q; Roth, Siegfried; Abouheif, Ehab; Brown, Federico D; Chiu, Chi-Hua; Cohen, C Sarah; Tomaso, Anthony W De; Gilbert, Scott F; Hall, Brian; Love, Alan C; Lyons, Deirdre C; Sanger, Thomas J; Smith, Joel; Specht, Chelsea; Vallejo-Marin, Mario; Extavour, Cassandra G

2015-01-01

Evolutionary developmental biology (evo-devo) has undergone dramatic transformations since its emergence as a distinct discipline. This paper aims to highlight the scope, power, and future promise of evo-devo to transform and unify diverse aspects of biology. We articulate key questions at the core of eleven biological disciplines-from Evolution, Development, Paleontology, and Neurobiology to Cellular and Molecular Biology, Quantitative Genetics, Human Diseases, Ecology, Agriculture and Science Education, and lastly, Evolutionary Developmental Biology itself-and discuss why evo-devo is uniquely situated to substantially improve our ability to find meaningful answers to these fundamental questions. We posit that the tools, concepts, and ways of thinking developed by evo-devo have profound potential to advance, integrate, and unify biological sciences as well as inform policy decisions and illuminate science education. We look to the next generation of evolutionary developmental biologists to help shape this process as we confront the scientific challenges of the 21st century. © 2015 Wiley Periodicals, Inc.

Test of Von Baer's law of the conservation of early development.

PubMed

Poe, Steven

2006-11-01

One of the oldest and most pervasive ideas in comparative embryology is the perceived evolutionary conservation of early ontogeny relative to late ontogeny. Karl Von Baer first noted the similarity of early ontogeny across taxa, and Ernst Haeckel and Charles Darwin gave evolutionary interpretation to this phenomenon. In spite of a resurgence of interest in comparative embryology and the development of mechanistic explanations for Von Baer's law, the pattern itself has been largely untested. Here, I use statistical phylogenetic approaches to show that Von Baer's law is an unnecessarily complex explanation of the patterns of ontogenetic timing in several clades of vertebrates. Von Baer's law suggests a positive correlation between ontogenetic time and amount of evolutionary change. I compare ranked position in ontogeny to frequency of evolutionary change in rank for developmental events and find that these measures are not correlated, thus failing to support Von Baer's model. An alternative model that postulates that small changes in ontogenetic rank are evolutionarily easier than large changes is tentatively supported.

The study on knowledge transferring incentive for information system requirement development

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Yang

2015-03-10

Information system requirement development is a process of users’ knowledge sharing and transferring. However the tacit requirements developing is a main problem during requirement development process, for the reason of difficult to encoding, express, and communicate. Knowledge fusion and corporate effort is needed to finding tacit requirements. Under this background, our paper try to find out the rule of effort dynamic evolutionary of software developer and user by building an evolutionary game model on the condition of incentive system. And in addition this paper provides an in depth discussion at the end of this paper.

Helminth parasites of bighorn sheep in Oregon.

PubMed

Kistner, T P; Matlock, S M; Wyse, D; Mason, G E

1977-04-01

The lungs and gastrointestinal tracts from 18 hunter-killed bighorn rams (Ovis canadensis californiana) were examined in total or in part for helminth parasites during a two-year study of three separate herds in Eastern Oregon. Prevalence was 100% with the lungworm Protostrongylus stilesi. The gastrointestinal fauna from 11 rams comprised Cooperia oncophora, Marshallagia marshalli, Nematodirus oiratianus, Oesophagostomum spp., Ostertagia occidentalis, O. ostertagi, Skrjabinema ovis, Trichostrongylus axei and Trichuris spp. Adult Wyominia tetoni and cysticerci of Taenia hydatigena were recovered from two of six livers examined. Additionally, searches for potential molluscan intermediate hosts for P. stilesi were conducted on one bighorn range. Snails identified as belonging to the genera Euconulus, Pupilla and Vallonia were found on both the summer and winter ranges.

Catalogue of the type specimens deposited in the Mollusca Collection of the Museu Nacional / UFRJ, Rio de Janeiro, Brazil.

PubMed

Pimenta, Alexandre Dias; Monteiro, Júlio César; Barbosa, André Favaretto; Salgado, Norma Campos; Coelho, Arnaldo Campos Dos Santos

2014-03-20

A curatorial revision of the type specimens deposited in the Mollusca Collection of the Museu Nacional / UFRJ, Rio de Janeiro, Brazil (MNRJ) revealed the existence of 518 lots of type specimens (holotypes, neotypes, syntypes and paratypes) for 285 names of molluscan taxa from 88 families, including 247 gastropods, 30 bivalves, three cephalopods and five scaphopods. A total of 106 holotypes and one neotype are deposited in the MNRJ. Type material for ten nominal taxa described as being deposited in the MNRJ was not located; the probable reasons are discussed. Some previously published erroneous information about types in the MNRJ is rectified. A total of 37 type specimens are illustrated.

First columbellid species (Gastropoda: Buccinoidea) from deep-sea hydrothermal vents, discovered in Okinawa Trough, Japan.

PubMed

Chen, Chong; Watanabe, Hiromi Kayama; Araya, Juan Francisco

2017-12-12

The molluscan diversity of deep-sea chemosynthetic ecosystems in Japan has been in general well documented with about 80 described species, of which over half are gastropods (Sasaki et al. 2005; Fujikura et al. 2012; Sasaki et al. 2016). Recently, however, a number of novel hydrothermal vent sites were discovered in the area using multibeam echo-sounding (Nakamura et al. 2015), providing opportunities for new discoveries. As a part of ongoing studies documenting the biodiversity of such sites, we present the first record of Columbellidae from hydrothermal vents, with a new species recovered from Natsu and Aki sites, in the Iheya North hydrothermal field (for map and background on the vent field see Nakamura et al. 2015).

Chemical taxonomy of the hinge-ligament proteins of bivalves according to their amino acid compositions.

PubMed Central

Kikuchi, Y; Tamiya, N

1987-01-01

The proteins in the hinge ligaments of molluscan bivalves were subjected to chemotaxonomic studies according to their amino acid compositions. The hinge-ligament protein is a new class of structure proteins, and this is the first attempt to introduce chemical taxonomy into the systematics of bivalves. The hinge-ligament proteins from morphologically close species, namely mactra (superfamily Mactracea) or scallop (family Pectinidae) species, showed high intraspecific homology in their compositions. On the other hand, inconsistent results were obtained with two types of ligament proteins in pearl oyster species (genus Pinctada). The results of our chemotaxonomic analyses were sometimes in good agreement with the morphological classifications and sometimes inconsistent, implying a complicated phylogenetic relationship among the species. PMID:3593265

Applying ecological and evolutionary theory to cancer: a long and winding road.

PubMed

Thomas, Frédéric; Fisher, Daniel; Fort, Philippe; Marie, Jean-Pierre; Daoust, Simon; Roche, Benjamin; Grunau, Christoph; Cosseau, Céline; Mitta, Guillaume; Baghdiguian, Stephen; Rousset, François; Lassus, Patrice; Assenat, Eric; Grégoire, Damien; Missé, Dorothée; Lorz, Alexander; Billy, Frédérique; Vainchenker, William; Delhommeau, François; Koscielny, Serge; Itzykson, Raphael; Tang, Ruoping; Fava, Fanny; Ballesta, Annabelle; Lepoutre, Thomas; Krasinska, Liliana; Dulic, Vjekoslav; Raynaud, Peggy; Blache, Philippe; Quittau-Prevostel, Corinne; Vignal, Emmanuel; Trauchessec, Hélène; Perthame, Benoit; Clairambault, Jean; Volpert, Vitali; Solary, Eric; Hibner, Urszula; Hochberg, Michael E

2013-01-01

Since the mid 1970s, cancer has been described as a process of Darwinian evolution, with somatic cellular selection and evolution being the fundamental processes leading to malignancy and its many manifestations (neoangiogenesis, evasion of the immune system, metastasis, and resistance to therapies). Historically, little attention has been placed on applications of evolutionary biology to understanding and controlling neoplastic progression and to prevent therapeutic failures. This is now beginning to change, and there is a growing international interest in the interface between cancer and evolutionary biology. The objective of this introduction is first to describe the basic ideas and concepts linking evolutionary biology to cancer. We then present four major fronts where the evolutionary perspective is most developed, namely laboratory and clinical models, mathematical models, databases, and techniques and assays. Finally, we discuss several of the most promising challenges and future prospects in this interdisciplinary research direction in the war against cancer.

Universality and predictability in molecular quantitative genetics.

PubMed

Nourmohammad, Armita; Held, Torsten; Lässig, Michael

2013-12-01

Molecular traits, such as gene expression levels or protein binding affinities, are increasingly accessible to quantitative measurement by modern high-throughput techniques. Such traits measure molecular functions and, from an evolutionary point of view, are important as targets of natural selection. We review recent developments in evolutionary theory and experiments that are expected to become building blocks of a quantitative genetics of molecular traits. We focus on universal evolutionary characteristics: these are largely independent of a trait's genetic basis, which is often at least partially unknown. We show that universal measurements can be used to infer selection on a quantitative trait, which determines its evolutionary mode of conservation or adaptation. Furthermore, universality is closely linked to predictability of trait evolution across lineages. We argue that universal trait statistics extends over a range of cellular scales and opens new avenues of quantitative evolutionary systems biology. Copyright © 2013. Published by Elsevier Ltd.

A Philosophical Perspective on Evolutionary Systems Biology

PubMed Central

Soyer, Orkun S.; Siegal, Mark L.

2015-01-01

Evolutionary systems biology (ESB) is an emerging hybrid approach that integrates methods, models, and data from evolutionary and systems biology. Drawing on themes that arose at a cross-disciplinary meeting on ESB in 2013, we discuss in detail some of the explanatory friction that arises in the interaction between evolutionary and systems biology. These tensions appear because of different modeling approaches, diverse explanatory aims and strategies, and divergent views about the scope of the evolutionary synthesis. We locate these discussions in the context of long-running philosophical deliberations on explanation, modeling, and theoretical synthesis. We show how many of the issues central to ESB’s progress can be understood as general philosophical problems. The benefits of addressing these philosophical issues feed back into philosophy too, because ESB provides excellent examples of scientific practice for the development of philosophy of science and philosophy of biology. PMID:26085823

A phylogeny for the pomatiopsidae (Gastropoda: Rissooidea): a resource for taxonomic, parasitological and biodiversity studies.

PubMed

Liu, Liang; Huo, Guan-Nan; He, Hong-Bin; Zhou, Benjiang; Attwood, Stephen W

2014-02-18

The Pomatiopsidae are reported from northern India into southern China and Southeast Asia, with two sub-families, the Pomatiopsinae (which include freshwater, amphibious, terrestrial and marine species) and the freshwater Triculinae. Both include species acting as intermediate host for species of the blood-fluke Schistosoma which cause a public health problem in East Asia. Also, with around 120 species, triculine biodiversity exceeds that of any other endemic freshwater molluscan fauna. Nevertheless, the origins of the Pomatiopsidae, the factors driving such a diverse radiation and aspects of their co-evolution with Schistosoma are not fully understood. Many taxonomic questions remain; there are problems identifying medically relevant species. The predicted range is mostly unsurveyed and the true biodiversity of the family is underestimated. Consequently, the aim of the study was to collect DNA-sequence data for as many pomatiopsid taxa as possible, as a first step in providing a resource for identification of epidemiologically significant species (by non-malacologists), for use in resolving taxonomic confusion and for testing phylogeographical hypotheses. The evolutionary radiation of the Triculinae was shown to have been rapid and mostly post late Miocene. Molecular dating indicated that the radiation of these snails was driven first by the uplift of the Himalaya and onset of a monsoon system, and then by late-Pliocene global warming. The status of Erhaia as Anmicolidae is supported. The genera Tricula and Neotricula are shown to be non-monophyletic and the tribe Jullieniini may be polyphyletic (based on convergent characters). Triculinae from northern Vietnam could be derived from Gammatricula of Fujian/Yunnan, China. The molecular dates and phylogenetic estimates in this study are consistent with an Australasian origin for the Pomatiopsidae and an East to West radiation via Oligocene Borneo-Philippines island hopping to Japan and then China (Triculinae arising mid-Miocene in Southeast China), and less so with a triculine origin in Tibet. The lack of monophyly in the medically important genera and indications of taxonomic inaccuracies, call for further work to identify epidemiologically significant taxa (e.g., Halewisia may be potential hosts for Schistosoma mekongi) and highlight the need for surveys to determine the true biodiversity of the Triculinae.

phyloXML: XML for evolutionary biology and comparative genomics

PubMed Central

Han, Mira V; Zmasek, Christian M

2009-01-01

Background Evolutionary trees are central to a wide range of biological studies. In many of these studies, tree nodes and branches need to be associated (or annotated) with various attributes. For example, in studies concerned with organismal relationships, tree nodes are associated with taxonomic names, whereas tree branches have lengths and oftentimes support values. Gene trees used in comparative genomics or phylogenomics are usually annotated with taxonomic information, genome-related data, such as gene names and functional annotations, as well as events such as gene duplications, speciations, or exon shufflings, combined with information related to the evolutionary tree itself. The data standards currently used for evolutionary trees have limited capacities to incorporate such annotations of different data types. Results We developed a XML language, named phyloXML, for describing evolutionary trees, as well as various associated data items. PhyloXML provides elements for commonly used items, such as branch lengths, support values, taxonomic names, and gene names and identifiers. By using "property" elements, phyloXML can be adapted to novel and unforeseen use cases. We also developed various software tools for reading, writing, conversion, and visualization of phyloXML formatted data. Conclusion PhyloXML is an XML language defined by a complete schema in XSD that allows storing and exchanging the structures of evolutionary trees as well as associated data. More information about phyloXML itself, the XSD schema, as well as tools implementing and supporting phyloXML, is available at . PMID:19860910

Evolutionary Connectionism: Algorithmic Principles Underlying the Evolution of Biological Organisation in Evo-Devo, Evo-Eco and Evolutionary Transitions.

PubMed

Watson, Richard A; Mills, Rob; Buckley, C L; Kouvaris, Kostas; Jackson, Adam; Powers, Simon T; Cox, Chris; Tudge, Simon; Davies, Adam; Kounios, Loizos; Power, Daniel

2016-01-01

The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term "evolutionary connectionism" to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary systems and modify the adaptive capabilities of natural selection over time. We review the evidence supporting the functional equivalences between the domains of learning and of evolution, and discuss the potential for this to resolve conceptual problems in our understanding of the evolution of developmental, ecological and reproductive organisations and, in particular, the major evolutionary transitions.

How cancer shapes evolution, and how evolution shapes cancer

PubMed Central

Casás-Selves, Matias; DeGregori, James

2013-01-01

Evolutionary theories are critical for understanding cancer development at the level of species as well as at the level of cells and tissues, and for developing effective therapies. Animals have evolved potent tumor suppressive mechanisms to prevent cancer development. These mechanisms were initially necessary for the evolution of multi-cellular organisms, and became even more important as animals evolved large bodies and long lives. Indeed, the development and architecture of our tissues were evolutionarily constrained by the need to limit cancer. Cancer development within an individual is also an evolutionary process, which in many respects mirrors species evolution. Species evolve by mutation and selection acting on individuals in a population; tumors evolve by mutation and selection acting on cells in a tissue. The processes of mutation and selection are integral to the evolution of cancer at every step of multistage carcinogenesis, from tumor genesis to metastasis. Factors associated with cancer development, such as aging and carcinogens, have been shown to promote cancer evolution by impacting both mutation and selection processes. While there are therapies that can decimate a cancer cell population, unfortunately, cancers can also evolve resistance to these therapies, leading to the resurgence of treatment-refractory disease. Understanding cancer from an evolutionary perspective can allow us to appreciate better why cancers predominantly occur in the elderly, and why other conditions, from radiation exposure to smoking, are associated with increased cancers. Importantly, the application of evolutionary theory to cancer should engender new treatment strategies that could better control this dreaded disease. PMID:23705033

Development of an evolutionary simulator and an overall control system for intelligent wheelchair

NASA Astrophysics Data System (ADS)

Imai, Makoto; Kawato, Koji; Hamagami, Tomoki; Hirata, Hironori

The goal of this research is to develop an intelligent wheelchair (IWC) system which aids an indoor safe mobility for elderly and disabled people with a new conceptual architecture which realizes autonomy, cooperativeness, and a collaboration behavior. In order to develop the IWC system in real environment, we need design-tools and flexible architecture. In particular, as more significant ones, this paper describes two key techniques which are an evolutionary simulation and an overall control mechanism. The evolutionary simulation technique corrects the error between the virtual environment in a simulator and real one in during the learning of an IWC agent, and coevolves with the agent. The overall control mechanism is implemented with subsumption architecture which is employed in an autonomous robot controller. By using these techniques in both simulations and experiments, we confirm that our IWC system acquires autonomy, cooperativeness, and a collaboration behavior efficiently.

The current status of REH theory. [Random Evolutionary Hits in biological molecular evolution

NASA Technical Reports Server (NTRS)

Holmquist, R.; Jukes, T. H.

1981-01-01

A response is made to the evaluation of Fitch (1980) of REH (random evolutionary hits) theory for the evolutionary divergence of proteins and nucleic acids. Correct calculations for the beta hemoglobin mRNAs of the human, mouse and rabbit in the absence and presence of selective constraints are summarized, and it is shown that the alternative evolutionary analysis of Fitch underestimates the total fixed mutations. It is further shown that the model used by Fitch to test for the completeness of the count of total base substitutions is in fact a variant of REH theory. Considerations of the variance inherent in evolutionary estimations are also presented which show the REH model to produce no more variance than other evolutionary models. In the reply, it is argued that, despite the objections raised, REH theory applied to proteins gives inaccurate estimates of total gene substitutions. It is further contended that REH theory developed for nucleic sequences suffers from problems relating to the frequency of nucleotide substitutions, the identity of the codons accepting silent and amino acid-changing substitutions, and estimate uncertainties.

A Study of Driver's Route Choice Behavior Based on Evolutionary Game Theory

PubMed Central

Jiang, Xiaowei; Ji, Yanjie; Deng, Wei

2014-01-01

This paper proposes a route choice analytic method that embeds cumulative prospect theory in evolutionary game theory to analyze how the drivers adjust their route choice behaviors under the influence of the traffic information. A simulated network with two alternative routes and one variable message sign is built to illustrate the analytic method. We assume that the drivers in the transportation system are bounded rational, and the traffic information they receive is incomplete. An evolutionary game model is constructed to describe the evolutionary process of the drivers' route choice decision-making behaviors. Here we conclude that the traffic information plays an important role in the route choice behavior. The driver's route decision-making process develops towards different evolutionary stable states in accordance with different transportation situations. The analysis results also demonstrate that employing cumulative prospect theory and evolutionary game theory to study the driver's route choice behavior is effective. This analytic method provides an academic support and suggestion for the traffic guidance system, and may optimize the travel efficiency to a certain extent. PMID:25610455

Evolutionary accounts of human behavioural diversity

PubMed Central

Brown, Gillian R.; Dickins, Thomas E.; Sear, Rebecca; Laland, Kevin N.

2011-01-01

Human beings persist in an extraordinary range of ecological settings, in the process exhibiting enormous behavioural diversity, both within and between populations. People vary in their social, mating and parental behaviour and have diverse and elaborate beliefs, traditions, norms and institutions. The aim of this theme issue is to ask whether, and how, evolutionary theory can help us to understand this diversity. In this introductory article, we provide a background to the debate surrounding how best to understand behavioural diversity using evolutionary models of human behaviour. In particular, we examine how diversity has been viewed by the main subdisciplines within the human evolutionary behavioural sciences, focusing in particular on the human behavioural ecology, evolutionary psychology and cultural evolution approaches. In addition to differences in focus and methodology, these subdisciplines have traditionally varied in the emphasis placed on human universals, ecological factors and socially learned behaviour, and on how they have addressed the issue of genetic variation. We reaffirm that evolutionary theory provides an essential framework for understanding behavioural diversity within and between human populations, but argue that greater integration between the subfields is critical to developing a satisfactory understanding of diversity. PMID:21199836

A study of driver's route choice behavior based on evolutionary game theory.

PubMed

Jiang, Xiaowei; Ji, Yanjie; Du, Muqing; Deng, Wei

2014-01-01

This paper proposes a route choice analytic method that embeds cumulative prospect theory in evolutionary game theory to analyze how the drivers adjust their route choice behaviors under the influence of the traffic information. A simulated network with two alternative routes and one variable message sign is built to illustrate the analytic method. We assume that the drivers in the transportation system are bounded rational, and the traffic information they receive is incomplete. An evolutionary game model is constructed to describe the evolutionary process of the drivers' route choice decision-making behaviors. Here we conclude that the traffic information plays an important role in the route choice behavior. The driver's route decision-making process develops towards different evolutionary stable states in accordance with different transportation situations. The analysis results also demonstrate that employing cumulative prospect theory and evolutionary game theory to study the driver's route choice behavior is effective. This analytic method provides an academic support and suggestion for the traffic guidance system, and may optimize the travel efficiency to a certain extent.

Making the case for orthogenesis: the popularization of definitely directed evolution (1890-1926).

PubMed

Ulett, Mark A

2014-03-01

Throughout the history of evolutionary theory a number of scientists have argued that evolution proceeds along a limited number of definite trajectories, a concept and group of theories known as "orthogenesis". Beginning in the 1880s, influential evolutionists including Theodor Eimer, Edward Drinker Cope, and Leo Berg argued that a fully causal explanation of evolution must take into account the origin and nature of variation, an idea that implied orthogenesis in their views. This paper argues that these orthogenesis developed theories that were more than highly technical and theoretically dubious hypotheses accessible only to elite specialists, as certain histories of these ideas might suggest. Some orthogenesists made their case to a non-specialist audience to gain support for their ideas in the face of widespread controversy over evolutionary theory. Through a case study analysis of three major books by Eimer, Cope, and Berg, this paper contends that they sought to re-orient the central tenets of the science of evolution to include the causal impact of variation on evolutionary outcomes. These orthogenesists developed novel and synthetic evolutionary theories in a publishing platform suited for non-specialist audiences in an effort to impact the debates over evolutionary causation prevalent in the late-19th and early 20th centuries. Copyright © 2013 Elsevier Ltd. All rights reserved.

Bullying and Evolutionary Psychology: The Dominance Hierarchy among Students and Implications for School Personnel

ERIC Educational Resources Information Center

Kolbert, Jered B.; Crothers, Laura M.

2003-01-01

The phenomenon of childhood bullying is conceptualized from an evolutionary psychological perspective. In this manuscript, the research literature is examined regarding the role of the relationship between aggression, testosterone, and social status in the development and maintenance of dominance hierarchies, which involve a reciprocal…

Education, Evolution, and the Future.

ERIC Educational Resources Information Center

Ogilvy, James

1981-01-01

This paper explores some implications of applying evolutionary theory to education. New developments in evolutionary theory provide insights on both the macro- and micro-levels of learning: for trends in the educational system, and for a better understanding of individual cases. (Part of a theme issue on educational futures.) (Author/SJL)

Theories of Evolution, Science (Experimental): 5315.42.

ERIC Educational Resources Information Center

Adams, Joseph P.

This is an in-depth course of study of the historical attempts to explain the evolutionary process and of recent developments pertinent to the study of biomedical evolution. Topics included in the module are: (1) ancient concepts of the evolutionary process; (2) various aspects of Lamarckism, Darwinism and neo-Darwinism, including substantiating…

Stimulating Scientific Reasoning with Drawing-Based Modeling

ERIC Educational Resources Information Center

Heijnes, Dewi; van Joolingen, Wouter; Leenaars, Frank

2018-01-01

We investigate the way students' reasoning about evolution can be supported by drawing-based modeling. We modified the drawing-based modeling tool SimSketch to allow for modeling evolutionary processes. In three iterations of development and testing, students in lower secondary education worked on creating an evolutionary model. After each…

Attachment in Middle Childhood: An Evolutionary-Developmental Perspective

ERIC Educational Resources Information Center

Del Giudice, Marco

2015-01-01

Middle childhood is a key transitional stage in the development of attachment processes and representations. Here I discuss the middle childhood transition from an evolutionary-developmental perspective and show how this approach offers fresh insight into the function and organization of attachment in this life stage. I begin by presenting an…

Evolutionary Developmental Psychology: Contributions from Comparative Research with Nonhuman Primates

ERIC Educational Resources Information Center

Maestripieri, Dario; Roney, James R.

2006-01-01

Evolutionary developmental psychology is a discipline that has the potential to integrate conceptual approaches to the study of behavioral development derived from psychology and biology as well as empirical data from humans and animals. Comparative research with animals, and especially with nonhuman primates, can provide evidence of adaptation in…

The evolutionary development of high specific impulse electric thruster technology

NASA Technical Reports Server (NTRS)

Sovey, James S.; Hamley, John A.; Patterson, Michael J.; Rawlin, Vincent K.; Myers, Roger M.

1992-01-01

Electric propulsion flight and technology demonstrations conducted primarily by Europe, Japan, China, the U.S., and the USSR are reviewed. Evolutionary mission applications for high specific impulse electric thruster systems are discussed, and the status of arcjet, ion, and magnetoplasmadynamic thrusters and associated power processor technologies are summarized.

Space, time and thrips: biogeographic issues in the evolutionary ecology of Thysanoptera

Treesearch

John R. Grehan

1991-01-01

Most participants of this symposium will be concerned with understanding thrips ecology primarily in order to develop practical and effective control strategies. Questions dealing with historical aspects (evolution) may seem of only isolated "theoretical" interest with little significance for everyday pragmatic concerns. Evolutionary theory is widely...

The Evolution of Personality Variation in Humans and Other Animals

ERIC Educational Resources Information Center

Nettle, Daniel

2006-01-01

A comprehensive evolutionary framework for understanding the maintenance of heritable behavioral variation in humans is yet to be developed. Some evolutionary psychologists have argued that heritable variation will not be found in important, fitness-relevant characteristics because of the winnowing effect of natural selection. This article…

NASA's Evolutionary Xenon Thruster (NEXT) Ion Propulsion System Information Summary

NASA Technical Reports Server (NTRS)

Pencil, Eirc S.; Benson, Scott W.

2008-01-01

This document is a guide to New Frontiers mission proposal teams. The document describes the development and status of the NASA's Evolutionary Xenon Thruster (NEXT) ion propulsion system (IPS) technology, its application to planetary missions, and the process anticipated to transition NEXT to the first flight mission.

Selfish genetic elements, genetic conflict, and evolutionary innovation.

PubMed

Werren, John H

2011-06-28

Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual's genome but are neutral or harmful to the individual as a whole. As a result, genetic conflict occurs between SGEs and other genetic elements in the genome. There is growing evidence that SGEs, and the resulting genetic conflict, are an important motor for evolutionary change and innovation. In this review, the kinds of SGEs and their evolutionary consequences are described, including how these elements shape basic biological features, such as genome structure and gene regulation, evolution of new genes, origin of new species, and mechanisms of sex determination and development. The dynamics of SGEs are also considered, including possible "evolutionary functions" of SGEs.

Selfish genetic elements, genetic conflict, and evolutionary innovation

PubMed Central

Werren, John H.

2011-01-01

Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual's genome but are neutral or harmful to the individual as a whole. As a result, genetic conflict occurs between SGEs and other genetic elements in the genome. There is growing evidence that SGEs, and the resulting genetic conflict, are an important motor for evolutionary change and innovation. In this review, the kinds of SGEs and their evolutionary consequences are described, including how these elements shape basic biological features, such as genome structure and gene regulation, evolution of new genes, origin of new species, and mechanisms of sex determination and development. The dynamics of SGEs are also considered, including possible “evolutionary functions” of SGEs. PMID:21690392

Achieving sustainable plant disease management through evolutionary principles.

PubMed

Zhan, Jiasui; Thrall, Peter H; Burdon, Jeremy J

2014-09-01

Plants and their pathogens are engaged in continuous evolutionary battles and sustainable disease management requires novel systems to create environments conducive for short-term and long-term disease control. In this opinion article, we argue that knowledge of the fundamental factors that drive host-pathogen coevolution in wild systems can provide new insights into disease development in agriculture. Such evolutionary principles can be used to guide the formulation of sustainable disease management strategies which can minimize disease epidemics while simultaneously reducing pressure on pathogens to evolve increased infectivity and aggressiveness. To ensure agricultural sustainability, disease management programs that reflect the dynamism of pathogen population structure are essential and evolutionary biologists should play an increasing role in their design. Copyright © 2014 Elsevier Ltd. All rights reserved.

Using concepts from biology to improve problem-solving methods

NASA Astrophysics Data System (ADS)

Goodman, Erik D.; Rothwell, Edward J.; Averill, Ronald C.

2011-06-01

Observing nature has been a cornerstone of engineering design. Today, engineers look not only at finished products, but imitate the evolutionary process by which highly optimized artifacts have appeared in nature. Evolutionary computation began by capturing only the simplest ideas of evolution, but today, researchers study natural evolution and incorporate an increasing number of concepts in order to evolve solutions to complex engineering problems. At the new BEACON Center for the Study of Evolution in Action, studies in the lab and field and in silico are laying the groundwork for new tools for evolutionary engineering design. This paper, which accompanies a keynote address, describes various steps in development and application of evolutionary computation, particularly as regards sensor design, and sets the stage for future advances.

Aligning science and policy to achieve evolutionarily enlightened conservation.

PubMed

Cook, Carly N; Sgrò, Carla M

2017-06-01

There is increasing recognition among conservation scientists that long-term conservation outcomes could be improved through better integration of evolutionary theory into management practices. Despite concerns that the importance of key concepts emerging from evolutionary theory (i.e., evolutionary principles and processes) are not being recognized by managers, there has been little effort to determine the level of integration of evolutionary theory into conservation policy and practice. We assessed conservation policy at 3 scales (international, national, and provincial) on 3 continents to quantify the degree to which key evolutionary concepts, such as genetic diversity and gene flow, are being incorporated into conservation practice. We also evaluated the availability of clear guidance within the applied evolutionary biology literature as to how managers can change their management practices to achieve better conservation outcomes. Despite widespread recognition of the importance of maintaining genetic diversity, conservation policies provide little guidance about how this can be achieved in practice and other relevant evolutionary concepts, such as inbreeding depression, are mentioned rarely. In some cases the poor integration of evolutionary concepts into management reflects a lack of decision-support tools in the literature. Where these tools are available, such as risk-assessment frameworks, they are not being adopted by conservation policy makers, suggesting that the availability of a strong evidence base is not the only barrier to evolutionarily enlightened management. We believe there is a clear need for more engagement by evolutionary biologists with policy makers to develop practical guidelines that will help managers make changes to conservation practice. There is also an urgent need for more research to better understand the barriers to and opportunities for incorporating evolutionary theory into conservation practice. © 2016 Society for Conservation Biology.

Epigenetic game theory and its application in plants. Comment on: ;Epigenetic game theory: How to compute the epigenetic control of maternal-to-zygotic transition; by Qian Wang et al.

NASA Astrophysics Data System (ADS)

Zhang, Yuan-Ming; Zhang, Yinghao; Guo, Mingyue

2017-03-01

Wang's et al. article [1] is the first to integrate game theory (especially evolutionary game theory) with epigenetic modification of zygotic genomes. They described and assessed a modeling framework based on evolutionary game theory to quantify, how sperms and oocytes interact through epigenetic processes, to determine embryo development. They also studied the internal mechanisms for normal embryo development: 1) evolutionary interactions between DNA methylation of the paternal and maternal genomes, and 2) the application of game theory to formulate and quantify how different genes compete or cooperate to regulate embryogenesis through methylation. Although it is not very comprehensive and profound regarding game theory modeling, this article bridges the gap between evolutionary game theory and the epigenetic control of embryo development by powerful ordinary differential equations (ODEs). The epiGame framework includes four aspects: 1) characterizing how epigenetic game theory works by the strategy matrix, in which the pattern and relative magnitude of the methylation effects on embryogenesis, are described by the cooperation and competition mechanisms, 2) quantifying the game that the direction and degree of P-M interactions over embryo development can be explained by the sign and magnitude of interaction parameters in model (2), 3) modeling epigenetic interactions within the morula, especially for two coupled nonlinear ODEs, with explicit functions in model (4), which provide a good fit to the observed data for the two sexes (adjusted R2 = 0.956), and 4) revealing multifactorial interactions in embryogenesis from the coupled ODEs in model (2) to triplet ODEs in model (6). Clearly, this article extends game theory from evolutionary game theory to epigenetic game theory.

Monitoring the evolutionary aspect of the Gene Ontology to enhance predictability and usability.

PubMed

Park, Jong C; Kim, Tak-eun; Park, Jinah

2008-04-11

Much effort is currently made to develop the Gene Ontology (GO). Due to the dynamic nature of information it addresses, GO undergoes constant updates whose results are released at regular intervals as separate versions. Although there are a large number of computational tools to aid the development of GO, they are operating on a particular version of GO, making it difficult for GO curators to anticipate the full impact of particular changes along the time axis on a larger scale. We present a method for tapping into such an evolutionary aspect of GO, by making it possible to keep track of important temporal changes to any of the terms and relations of GO and by consequently making it possible to recognize associated trends. We have developed visualization methods for viewing the changes between two different versions of GO by constructing a colour-coded layered graph. The graph shows both versions of GO with highlights to those GO terms that are added, removed and modified between the two versions. Focusing on a specific GO term or terms of interest over a period, we demonstrate the utility of our system that can be used to make useful hypotheses about the cause of the evolution and to provide new insights into more complex changes. GO undergoes fast evolutionary changes. A snapshot of GO, as presented by each version of GO alone, overlooks such evolutionary aspects, and consequently limits the utilities of GO. The method that highlights the differences of consecutive versions or two different versions of an evolving ontology with colour-coding enhances the utility of GO for users as well as for developers. To the best of our knowledge, this is the first proposal to visualize the evolutionary aspect of GO.

The developmental basis of an evolutionary diversification of female gametophyte structure in Piper and Piperaceae

PubMed Central

Madrid, Eric N.; Friedman, William E.

2009-01-01

Background and Aims Fritillaria-type female gametophyte development is a complex, yet homoplasious developmental pattern that is interesting from both evolutionary and developmental perspectives. Piper (Piperaceae) was chosen for this study of Fritillaria-type female gametophyte development because Piperales represent a ‘hotspot’ of female gametophyte developmental evolution and have been the subject of several recent molecular phylogenetic analyses. This wealth of phylogenetic and descriptive data make Piper an excellent candidate for inferring the evolutionary developmental basis for the origin of Fritillaria-type female gametophytes. Methods Developing ovules of Piper peltatum were taken from greenhouse collections, embedded in glycol methacrylate, and serially sectioned. Light microscopy and laser scanning confocal microscopy were combined to produce three-dimensional computer reconstructions of developing female gametophytes. The ploidies of the developing embryos and endosperms were calculated using microspectrofluorometry. Key Results The data describe female gametophyte development in Piper with highly detailed three-dimensional models, and document two previously unknown arrangements of megaspore nuclei during early development. Also collected were microspectrofluorometric data that indicate that Fritillaria-type female gametophyte development in Piper results in pentaploid endosperm. Conclusions The three-dimensional models resolve previous ambiguities in developmental interpretations of Fritillaria-type female gametophytes in Piper. The newly discovered arrangements of megaspore nuclei that are described allow for the construction of explicit hypotheses of female gametophyte developmental evolution within Piperaceae, and more broadly throughout Piperales. These detailed hypotheses indicate that the common ancestor of Piperaceae minus Verhuellia had a Drusa-type female gametophyte, and that evolutionary transitions to derived tetrasporic female gametophyte ontogenies in Piperaceae, including Fritillaria-type female gametophyte development, are the consequence of key nuclear migration and patterning events at the end of megasporogenesis. PMID:19202137

An evolutionary solution to anesthesia automated record keeping.

PubMed

Bicker, A A; Gage, J S; Poppers, P J

1998-08-01

In the course of five years the development of an automated anesthesia record keeper has evolved through nearly a dozen stages, each marked by new features and sophistication. Commodity PC hardware and software minimized development costs. Object oriented analysis, programming and design supported the process of change. In addition, we developed an evolutionary strategy that optimized motivation, risk management, and maximized return on investment. Besides providing record keeping services, the system supports educational and research activities and through a flexible plotting paradigm, supports each anesthesiologist's focus on physiological data during and after anesthesia.

The role of evolutionary biology in research and control of liver flukes in Southeast Asia.

PubMed

Echaubard, Pierre; Sripa, Banchob; Mallory, Frank F; Wilcox, Bruce A

2016-09-01

Stimulated largely by the availability of new technology, biomedical research at the molecular-level and chemical-based control approaches arguably dominate the field of infectious diseases. Along with this, the proximate view of disease etiology predominates to the exclusion of the ultimate, evolutionary biology-based, causation perspective. Yet, historically and up to today, research in evolutionary biology has provided much of the foundation for understanding the mechanisms underlying disease transmission dynamics, virulence, and the design of effective integrated control strategies. Here we review the state of knowledge regarding the biology of Asian liver Fluke-host relationship, parasitology, phylodynamics, drug-based interventions and liver Fluke-related cancer etiology from an evolutionary biology perspective. We consider how evolutionary principles, mechanisms and research methods could help refine our understanding of clinical disease associated with infection by Liver Flukes as well as their transmission dynamics. We identify a series of questions for an evolutionary biology research agenda for the liver Fluke that should contribute to an increased understanding of liver Fluke-associated diseases. Finally, we describe an integrative evolutionary medicine approach to liver Fluke prevention and control highlighting the need to better contextualize interventions within a broader human health and sustainable development framework. Copyright © 2016 Elsevier B.V. All rights reserved.

The Role of Evolutionary Biology in Research and Control of Liver Flukes in Southeast Asia

PubMed Central

Echaubard, Pierre; Sripa, Banchob; Mallory, Frank F.; Wilcox, Bruce A.

2016-01-01

Stimulated largely by the availability of new technology, biomedical research at the molecular-level and chemical-based control approaches arguably dominate the field of infectious diseases. Along with this, the proximate view of disease etiology predominates to the exclusion of the ultimate, evolutionary biology-based, causation perspective. Yet, historically and up to today, research in evolutionary biology has provided much of the foundation for understanding the mechanisms underlying disease transmission dynamics, virulence, and the design of effective integrated control strategies. Here we review the state of knowledge regarding the biology of Asian liver Fluke-host relationship, parasitology, phylodynamics, drug-based interventions and liver Fluke-related cancer etiology from an evolutionary biology perspective. We consider how evolutionary principles, mechanisms and research methods could help refine our understanding of clinical disease associated with infection by Liver Flukes as well as their transmission dynamics. We identify a series of questions for an evolutionary biology research agenda for the liver Fluke that should contribute to an increased understanding of liver Fluke-associated diseases. Finally, we describe an integrative evolutionary medicine approach to liver Fluke prevention and control highlighting the need to better contextualize interventions within a broader human health and sustainable development framework. PMID:27197053

Neptunism and Transformism: Robert Jameson and other Evolutionary Theorists in Early Nineteenth-Century Scotland.

PubMed

Jenkins, Bill

2016-08-01

This paper sheds new light on the prevalence of evolutionary ideas in Scotland in the early nineteenth century and establish what connections existed between the espousal of evolutionary theories and adherence to the directional history of the earth proposed by Abraham Gottlob Werner and his Scottish disciples. A possible connection between Wernerian geology and theories of the transmutation of species in Edinburgh in the period when Charles Darwin was a medical student in the city was suggested in an important 1991 paper by James Secord. This study aims to deepen our knowledge of this important episode in the history of evolutionary ideas and explore the relationship between these geological and evolutionary discourses. To do this it focuses on the circle of natural historians around Robert Jameson, Wernerian geologist and professor of natural history at the University of Edinburgh from 1804 to 1854. From the evidence gathered here there emerges a clear confirmation that the Wernerian model of geohistory facilitated the acceptance of evolutionary explanations of the history of life in early nineteenth-century Scotland. As Edinburgh was at this time the most important center of medical education in the English-speaking world, this almost certainly influenced the reception and development of evolutionary ideas in the decades that followed.

Scientific Change as AN Evolutionary, Information Process: its Structural, Conceptual and Cultural Elements.

NASA Astrophysics Data System (ADS)

Al-Bustany, Fatin Khalil Ismail

1989-09-01

My aim in this dissertation is to develop an evolutionary conception of science based on recent studies in evolution theory, the thermodynamics of non-equilibrium and information theory, as exemplified in the works of Prigogine, Jantsch, Wicken and Gatlin. The nature of scientific change is of interest to philosophers and historians of science. Some construe it after a revolutionary model (e.g. Kuhn), others adopt an evolutionary view (e.g. Toulmin). It appears to me that it is possible to construct an evolutionary model encompassing the revolutionary mode as well. The following strategies are employed: (1) A distinction is made between two types of growth: one represents gradual change, the other designates radical transformations, and two principles underlying the process of change, one of conservation, the other of innovation. (2) Science in general, and scientific theories in particular, are looked upon as dissipative structures. These are characterised by openness, irreversibility and self-organisation. In terms of these, one may identify a state of "normal" growth and another of violent fluctuations leading to a new order (revolutionary phase). These fluctuations are generated by the flow of information coming from the observable world. The chief merits of this evolutionary model of the development of science lie in the emphasis it puts on the relation of science to its environment, in the description of scientific change as a process of interaction between internal and external elements (structural, conceptual, and cultural), in the enhancement of our understanding progress and rationality in science, and in the post Neo -Darwinian conception of evolution, stressing self-organisation, the innovativeness of the evolutionary process and the trend toward complexification. These features are also manifested in the process of discovery, which is a fundamental part of the scientific enterprise. In addition, a distinction is made between two types of discovery which serves as a criterion for delineating various episodes in the development of science. The evolutionary model further displays a complementarity mode of description on several levels: between science and its milieu, stability and instability, discovery and confirmation.

On the origins of anticipation as an evolutionary framework: functional systems perspective

NASA Astrophysics Data System (ADS)

Kurismaa, Andres

2015-08-01

This paper discusses the problem of anticipation from an evolutionary and systems-theoretical perspective, developed in the context of Russian/Soviet evolutionary biological and neurophysiological schools in the early and mid-twentieth century. On this background, an outline is given of the epigenetic interpretation of anticipatory capacities formulated and substantiated by the eminent Russian neurophysiologist academician Peter K. Anokhin in the framework of functional systems theory. It is considered that several key positions of this theory are well confirmed by recent evidence on anticipation as an evolutionarily basic adaptive capacity, possibly inherent to the organization of life. In the field of neuroscience, the theory of functional systems may potentially facilitate future studies at the intersection of learning, development and evolution by representing an integrative approach to the problem of anticipation.

Evolutionary thinking: "A conversation with Carter Phipps about the role of evolutionary thinking in modern culture".

PubMed

Hunt, Tam

2014-12-01

Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution-both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place-has been sustained and heated. A growing share of this debate is now devoted to examining how evolutionary thinking affects areas outside of biology. How do our lives change when we recognize that all is in flux? What can we learn about life more generally if we study change instead of stasis? Carter Phipps' book, Evolutionaries: Unlocking the Spiritual and Cultural Potential of Science's Greatest Idea, delves deep into this relatively new development. Phipps generally takes as a given the validity of the Modern Synthesis of evolutionary biology. His story takes us into, as the subtitle suggests, the spiritual and cultural implications of evolutionary thinking. Can religion and evolution be reconciled? Can evolutionary thinking lead to a new type of spirituality? Is our culture already being changed in ways that we don't realize by evolutionary thinking? These are all important questions and Phipps book is a great introduction to this discussion. Phipps is an author, journalist, and contributor to the emerging "integral" or "evolutionary" cultural movement that combines the insights of Integral Philosophy, evolutionary science, developmental psychology, and the social sciences. He has served as the Executive Editor of EnlightenNext magazine (no longer published) and more recently is the co-founder of the Institute for Cultural Evolution, a public policy think tank addressing the cultural roots of America's political challenges. What follows is an email interview with Phipps.

Evolutionary Stability in the Traveler's Dilemma

ERIC Educational Resources Information Center

Barker, Andrew T.

2009-01-01

The traveler's dilemma is a generalization of the prisoner's dilemma which shows clearly a paradox of game theory. In the traveler's dilemma, the strategy chosen by analysis and theory seems obviously wrong intuitively. Here we develop a measure of evolutionary stability and show that the evolutionarily stable equilibrium is in some sense not very…

A Tale of Four Stories: Soil Ecology, Theory, Evolution and the Publication System

PubMed Central

Barot, Sébastien; Blouin, Manuel; Fontaine, Sébastien; Jouquet, Pascal; Lata, Jean-Christophe; Mathieu, Jérôme

2007-01-01

Background Soil ecology has produced a huge corpus of results on relations between soil organisms, ecosystem processes controlled by these organisms and links between belowground and aboveground processes. However, some soil scientists think that soil ecology is short of modelling and evolutionary approaches and has developed too independently from general ecology. We have tested quantitatively these hypotheses through a bibliographic study (about 23000 articles) comparing soil ecology journals, generalist ecology journals, evolutionary ecology journals and theoretical ecology journals. Findings We have shown that soil ecology is not well represented in generalist ecology journals and that soil ecologists poorly use modelling and evolutionary approaches. Moreover, the articles published by a typical soil ecology journal (Soil Biology and Biochemistry) are cited by and cite low percentages of articles published in generalist ecology journals, evolutionary ecology journals and theoretical ecology journals. Conclusion This confirms our hypotheses and suggests that soil ecology would benefit from an effort towards modelling and evolutionary approaches. This effort should promote the building of a general conceptual framework for soil ecology and bridges between soil ecology and general ecology. We give some historical reasons for the parsimonious use of modelling and evolutionary approaches by soil ecologists. We finally suggest that a publication system that classifies journals according to their Impact Factors and their level of generality is probably inadequate to integrate “particularity” (empirical observations) and “generality” (general theories), which is the goal of all natural sciences. Such a system might also be particularly detrimental to the development of a science such as ecology that is intrinsically multidisciplinary. PMID:18043755

A Bell-Curved Based Algorithm for Mixed Continuous and Discrete Structural Optimization

NASA Technical Reports Server (NTRS)

Kincaid, Rex K.; Weber, Michael; Sobieszczanski-Sobieski, Jaroslaw

2001-01-01

An evolutionary based strategy utilizing two normal distributions to generate children is developed to solve mixed integer nonlinear programming problems. This Bell-Curve Based (BCB) evolutionary algorithm is similar in spirit to (mu + mu) evolutionary strategies and evolutionary programs but with fewer parameters to adjust and no mechanism for self adaptation. First, a new version of BCB to solve purely discrete optimization problems is described and its performance tested against a tabu search code for an actuator placement problem. Next, the performance of a combined version of discrete and continuous BCB is tested on 2-dimensional shape problems and on a minimum weight hub design problem. In the latter case the discrete portion is the choice of the underlying beam shape (I, triangular, circular, rectangular, or U).

Beyond the EDGE with EDAM: Prioritising British Plant Species According to Evolutionary Distinctiveness, and Accuracy and Magnitude of Decline

PubMed Central

Pearse, William D.; Chase, Mark W.; Crawley, Michael J.; Dolphin, Konrad; Fay, Michael F.; Joseph, Jeffrey A.; Powney, Gary; Preston, Chris D.; Rapacciuolo, Giovanni; Roy, David B.; Purvis, Andy

2015-01-01

Conservation biologists have only finite resources, and so must prioritise some species over others. The EDGE-listing approach ranks species according to their combined evolutionary distinctiveness and degree of threat, but ignores the uncertainty surrounding both threat and evolutionary distinctiveness. We develop a new family of measures for species, which we name EDAM, that incorporates evolutionary distinctiveness, the magnitude of decline, and the accuracy with which decline can be predicted. Further, we show how the method can be extended to explore phyogenetic uncertainty. Using the vascular plants of Britain as a case study, we find that the various EDAM measures emphasise different species and parts of Britain, and that phylogenetic uncertainty can strongly affect the prioritisation scores of some species. PMID:26018568

Open Reading Frame Phylogenetic Analysis on the Cloud

PubMed Central

2013-01-01

Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus. PMID:23671843

The presence of abalone egg-laying hormone-like peptide in the central nervous system and ovary of the Spotted Babylon, Babylonia areolata.

PubMed

Saetan, Jirawat; Boonyoung, Piyakorn; Vongvatcharanon, Uraporn; Kruangkum, Thanapong; Khornchatri, Kanjana; Thaweethamsewee, Pinij; Sobhon, Prasert; Sretarugsa, Prapee

2017-09-01

Recently, the neuronal classification of the ivory shell Spotted Babylon, Babylonia areolata, was readily demonstrated. Regarding its importance as marine economic molluscan species, the attempt to understand the neuroendocrine regulation is necessary. This study firstly demonstrated the neurosecretory cells as well as the existence and distribution of the egg-laying hormone (ELH)-like peptide in the central nervous system (CNS) and ovary of the B. areolata. The neurosecretory cell was characterized by the cytoplasmic purple dot-like structure as stained by the Gomori's paraldehyde fuchsin. Using the anti-abalone (a) ELH, we detected the aELH-like-peptide in neurons (Nr) and neurosecretory cells (Ns) of all ganglia including the cerebral, pleural, parietal, pedal and buccal ganglia. The aELH-like peptide was also present in the neuropil of each. It was noted that not all Ns presented the aELH-like peptide. In the ovary, the aELH-like peptide was slightly detected in early developing oocytes and strongly detected in late developing oocytes and follicular cells. This study firstly reported the evidence of ELH-like peptide in the CNS and ovary of the B. areolata. The molecular cloning as well as to investigate the function of ELH in this species is needed as it will be beneficial for future applications in aquaculture. Copyright © 2017 Elsevier GmbH. All rights reserved.

Quantifying the Evolutionary Conservation of Genes Encoding Multidrug Efflux Pumps in the ESKAPE Pathogens To Identify Antimicrobial Drug Targets.

PubMed

Brooks, Lauren E; Ul-Hasan, Sabah; Chan, Benjamin K; Sistrom, Mark J

2018-01-01

Increasing rates of antibiotic-resistant bacterial infection are one of the most pressing contemporary global health concerns. The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) have been identified as the leading global cause of multidrug-resistant bacterial infections, and overexpression of multidrug efflux (MEX) transport systems has been identified as one of the most critical mechanisms facilitating the evolution of multidrug resistance in ESKAPE pathogens. Despite efforts to develop efflux pump inhibitors to combat antibiotic resistance, the need persists to identify additional targets for future investigations. We evaluated evolutionary pressures on 110 MEX-encoding genes from all annotated ESKAPE organism genomes. We identify several MEX genes under stabilizing selection-representing targets which can facilitate broad-spectrum treatments with evolutionary constraints limiting the potential emergence of escape mutants. We also examine MEX systems being evaluated as drug targets, demonstrating that divergent selection may underlie some of the problems encountered in the development of effective treatments-specifically in relation to the NorA system in S. aureus. This study provides a comprehensive evolutionary context to efflux in the ESKAPE pathogens, which will provide critical context to the evaluation of efflux systems as antibiotic targets. IMPORTANCE Increasing rates of antibiotic-resistant bacterial infection are one of the most pressing contemporary global health concerns. The ESKAPE pathogen group represents the leading cause of these infections, and upregulation of efflux pump expression is a significant mechanism of resistance in these pathogens. This has resulted in substantial interest in the development of efflux pump inhibitors to combat antibiotic-resistant infections; however, no widespread treatments have been developed to date. Our study evaluates an often-underappreciated aspect of resistance-the impact of evolutionary selection. We evaluate selection on all annotated efflux genes in all sequenced ESKAPE pathogens, providing critical context for and insight into current and future development of efflux-targeting treatments for resistant bacterial infections.

Quantifying the Evolutionary Conservation of Genes Encoding Multidrug Efflux Pumps in the ESKAPE Pathogens To Identify Antimicrobial Drug Targets

PubMed Central

Ul-Hasan, Sabah; Chan, Benjamin K.; Sistrom, Mark J.

2018-01-01

ABSTRACT Increasing rates of antibiotic-resistant bacterial infection are one of the most pressing contemporary global health concerns. The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) have been identified as the leading global cause of multidrug-resistant bacterial infections, and overexpression of multidrug efflux (MEX) transport systems has been identified as one of the most critical mechanisms facilitating the evolution of multidrug resistance in ESKAPE pathogens. Despite efforts to develop efflux pump inhibitors to combat antibiotic resistance, the need persists to identify additional targets for future investigations. We evaluated evolutionary pressures on 110 MEX-encoding genes from all annotated ESKAPE organism genomes. We identify several MEX genes under stabilizing selection—representing targets which can facilitate broad-spectrum treatments with evolutionary constraints limiting the potential emergence of escape mutants. We also examine MEX systems being evaluated as drug targets, demonstrating that divergent selection may underlie some of the problems encountered in the development of effective treatments—specifically in relation to the NorA system in S. aureus. This study provides a comprehensive evolutionary context to efflux in the ESKAPE pathogens, which will provide critical context to the evaluation of efflux systems as antibiotic targets. IMPORTANCE Increasing rates of antibiotic-resistant bacterial infection are one of the most pressing contemporary global health concerns. The ESKAPE pathogen group represents the leading cause of these infections, and upregulation of efflux pump expression is a significant mechanism of resistance in these pathogens. This has resulted in substantial interest in the development of efflux pump inhibitors to combat antibiotic-resistant infections; however, no widespread treatments have been developed to date. Our study evaluates an often-underappreciated aspect of resistance—the impact of evolutionary selection. We evaluate selection on all annotated efflux genes in all sequenced ESKAPE pathogens, providing critical context for and insight into current and future development of efflux-targeting treatments for resistant bacterial infections. PMID:29719870

The scope and strength of sex-specific selection in genome evolution.

PubMed

Wright, A E; Mank, J E

2013-09-01

Males and females share the vast majority of their genomes and yet are often subject to different, even conflicting, selection. Genomic and transcriptomic developments have made it possible to assess sex-specific selection at the molecular level, and it is clear that sex-specific selection shapes the evolutionary properties of several genomic characteristics, including transcription, post-transcriptional regulation, imprinting, genome structure and gene sequence. Sex-specific selection is strongly influenced by mating system, which also causes neutral evolutionary changes that affect different regions of the genome in different ways. Here, we synthesize theoretical and molecular work in order to provide a cohesive view of the role of sex-specific selection and mating system in genome evolution. We also highlight the need for a combined approach, incorporating both genomic data and experimental phenotypic studies, in order to understand precisely how sex-specific selection drives evolutionary change across the genome. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Treatment resistance in urothelial carcinoma: an evolutionary perspective.

PubMed

Vlachostergios, Panagiotis J; Faltas, Bishoy M

2018-05-02

The emergence of treatment-resistant clones is a critical barrier to cure in patients with urothelial carcinoma. Setting the stage for the evolution of resistance, urothelial carcinoma is characterized by extensive mutational heterogeneity, which is detectable even in patients with early stage disease. Chemotherapy and immunotherapy both act as selective pressures that shape the evolutionary trajectory of urothelial carcinoma throughout the course of the disease. A detailed understanding of the dynamics of evolutionary drivers is required for the rational development of curative therapies. Herein, we describe the molecular basis of the clonal evolution of urothelial carcinomas and the use of genomic approaches to predict treatment responses. We discuss various mechanisms of resistance to chemotherapy with a focus on the mutagenic effects of the DNA dC->dU-editing enzymes APOBEC3 family of proteins. We also review the evolutionary mechanisms underlying resistance to immunotherapy, such as the loss of clonal tumour neoantigens. By dissecting treatment resistance through an evolutionary lens, the field will advance towards true precision medicine for urothelial carcinoma.

First steps in experimental cancer evolution

PubMed Central

Taylor, Tiffany B; Johnson, Louise J; Jackson, Robert W; Brockhurst, Michael A; Dash, Philip R

2013-01-01

Evolutionary processes play a central role in the development, progression and response to treatment of cancers. The current challenge facing researchers is to harness evolutionary theory to further our understanding of the clinical progression of cancers. Central to this endeavour will be the development of experimental systems and approaches by which theories of cancer evolution can be effectively tested. We argue here that the experimental evolution approach – whereby evolution is observed in real time and which has typically employed microorganisms – can be usefully applied to cancer. This approach allows us to disentangle the ecological causes of natural selection, identify the genetic basis of evolutionary changes and determine their repeatability. Cell cultures used in cancer research share many of the desirable traits that make microorganisms ideal for studying evolution. As such, experimental cancer evolution is feasible and likely to give great insight into the selective pressures driving the evolution of clinically destructive cancer traits. We highlight three areas of evolutionary theory with importance to cancer biology that are amenable to experimental evolution: drug resistance, social evolution and resource competition. Understanding the diversity, persistence and evolution of cancers is vital for treatment and drug development, and an experimental evolution approach could provide strategic directions and focus for future research. PMID:23745144

Evolution of the Plant Reproduction Master Regulators LFY and the MADS Transcription Factors: The Role of Protein Structure in the Evolutionary Development of the Flower.

PubMed

Silva, Catarina S; Puranik, Sriharsha; Round, Adam; Brennich, Martha; Jourdain, Agnès; Parcy, François; Hugouvieux, Veronique; Zubieta, Chloe

2015-01-01

Understanding the evolutionary leap from non-flowering (gymnosperms) to flowering (angiosperms) plants and the origin and vast diversification of the floral form has been one of the focuses of plant evolutionary developmental biology. The evolving diversity and increasing complexity of organisms is often due to relatively small changes in genes that direct development. These "developmental control genes" and the transcription factors (TFs) they encode, are at the origin of most morphological changes. TFs such as LEAFY (LFY) and the MADS-domain TFs act as central regulators in key developmental processes of plant reproduction including the floral transition in angiosperms and the specification of the male and female organs in both gymnosperms and angiosperms. In addition to advances in genome wide profiling and forward and reverse genetic screening, structural techniques are becoming important tools in unraveling TF function by providing atomic and molecular level information that was lacking in purely genetic approaches. Here, we summarize previous structural work and present additional biophysical and biochemical studies of the key master regulators of plant reproduction - LEAFY and the MADS-domain TFs SEPALLATA3 and AGAMOUS. We discuss the impact of structural biology on our understanding of the complex evolutionary process leading to the development of the bisexual flower.

Possible steps in the evolutionary development of bird navigation

NASA Technical Reports Server (NTRS)

Bellrose, F. C.

1972-01-01

Hypotheses are presented to explain the evolutionary development of navigational ability in migratory birds. Areas of discussion to describe the possible techniques are: (1) sun compass, (2) bicoordinate navigation, (3) star compass, (4) wind cues, (5) earth magnetic field, and (6) landscape features. It is concluded that landscape is the single most important cue for orientation of nonmigratory birds. The long range migratory birds appear to use a combination of cues with the relative importance of the cue dependent upon the species of the bird involved.

Evolutionary medicine: update on the relevance to family practice.

PubMed

Naugler, Christopher T

2008-09-01

To review the relevance of evolutionary medicine to family practice and family physician training. Articles were located through a MEDLINE search, using the key words evolution, Darwin, and adaptation. Most references presented level III evidence (expert opinion), while a minority provided level II evidence (epidemiologic studies). Evolutionary medicine deals with the interplay of biology and the environment in the understanding of human disease. Yet medical schools have virtually ignored the need for family physicians to have more than a cursory knowledge of this topic. A review of the main trends in this field most relevant to family practice revealed that a basic knowledge of evolutionary medicine might help in explaining the causation of diseases to patients. Evolutionary medicine has also proven key to explaining the reasons for the development of antibiotic resistance and has the potential to explain cancer pathogenesis. As an organizing principle, this field also has potential in the teaching of family medicine. Evolutionary medicine should be studied further and incorporated into medical training and practice. Its practical utility will be proven through the generation of testable hypotheses and their application in relation to disease causation and possible prevention.

The Generation of Variation and The Developmental Basis for Evolutionary Novelty

PubMed Central

Hallgrímsson, Benedikt; Jamniczky, Heather A.; Young, Nathan M.; Rolian, Campbell; Schmidt-Ott, Urs; Marcucio, Ralph S.

2013-01-01

Organisms exhibit an incredible diversity of form, a fact that makes the evolution of novelty seemingly self-evident. However, despite the “obvious” case for novelty, defining this concept in evolutionary terms is highly problematic, so much so that some have suggested discarding it altogether. Approaches to this problem tend to take either an adaptation or development-based perspective, but we argue here that an exclusive focus on either of these misses the original intent of the novelty concept and undermines its practical utility. We instead propose that for a feature to be novel it must have evolved both by a transition between adaptive peaks on the fitness landscape and that this transition must have overcome a previous developmental constraint. This definition focuses novelty on the explanation of apparently difficult or low probability evolutionary transitions and highlights how the integration of developmental and functional considerations is necessary to evolutionary explanation. It further reinforces that novelty is a central concern not just of evolutionary developmental biology (i.e., “evo-devo”) but of evolutionary biology more generally. We explore this definition of novelty in light of four examples that range from the obvious to subtle. PMID:22649039

Evolution and the Growth Process: Natural Selection of Entrepreneurial Traits.

PubMed

Galor, Oded; Michalopoulos, Stelios

2012-03-01

This research suggests that a Darwinian evolution of entrepreneurial spirit played a significant role in the process of economic development and the dynamics of inequality within and across societies. The study argues that entrepreneurial spirit evolved non-monotonically in the course of human history. In early stages of development, risk-tolerant, growth promoting traits generated an evolutionary advantage and their increased representation accelerated the pace of technological progress and the process of economic development. In mature stages of development, however, risk-averse traits gained an evolutionary advantage, diminishing the growth potential of advanced economies and contributing to convergence in economic growth across countries.

Evolution and the Growth Process: Natural Selection of Entrepreneurial Traits*

PubMed Central

Galor, Oded; Michalopoulos, Stelios

2013-01-01

This research suggests that a Darwinian evolution of entrepreneurial spirit played a significant role in the process of economic development and the dynamics of inequality within and across societies. The study argues that entrepreneurial spirit evolved non-monotonically in the course of human history. In early stages of development, risk-tolerant, growth promoting traits generated an evolutionary advantage and their increased representation accelerated the pace of technological progress and the process of economic development. In mature stages of development, however, risk-averse traits gained an evolutionary advantage, diminishing the growth potential of advanced economies and contributing to convergence in economic growth across countries. PMID:25089059

NEXT Ion Propulsion System Development Status and Capabilities

NASA Technical Reports Server (NTRS)

Patterson, Michael J.; Benson, Scott W.

2008-01-01

NASA s Evolutionary Xenon Thruster (NEXT) project is developing next generation ion propulsion technologies to provide future NASA science missions with enhanced mission performance benefit at a low total development cost. The objective of the NEXT project is to advance next generation ion propulsion technology by producing engineering model system components, validating these through qualification-level and integrated system testing, and ensuring preparedness for transitioning to flight system development. As NASA s Evolutionary Xenon Thruster technology program completes advanced development activities, it is advantageous to review the existing technology capabilities of the system under development. This paper describes the NEXT ion propulsion system development status, characteristics and performance. A review of mission analyses results conducted to date using the NEXT system is also provided.

The fossil land and freshwater snails of Gündlkofen (Middle Miocene, Germany).

PubMed

Salvador, Rodrigo B

2014-04-03

The molluscan fauna from the Middle Miocene (MN 5-6) fossil site of Gündlkofen in southern Germany was first reported by Gall (1980: Mitt. Bayer. Staatssaml. Paläont. hist. Geol., 20, 51-77). He listed 34 continental gastropod species, which were neither figured nor properly described in many cases. Here a revision of his identifications is presented, with a full description of the material and illustration of the best preserved specimens. Following this revision, 20 species are listed for Gündlkofen. Unfortunately, part of the original material was missing and the record of a few species could not be confirmed. The depositional environment seems to have been a temporary water body, like an oxbow lake, surrounded by a humid and warm forest and scrubland.

The impact of depuration on mussel hepatopancreas bacteriome composition and predicted metagenome.

PubMed

Rubiolo, J A; Lozano-Leon, A; Rodriguez-Souto, R; Fol Rodríguez, N; Vieytes, M R; Botana, L M

2018-07-01

Due to the rapid elimination of bacteria through normal behaviour of filter feeding and excretion, the decontamination of hazardous contaminating bacteria from shellfish is performed by depuration. This process, under conditions that maximize shellfish filtering activity, is a useful method to eliminate microorganisms from bivalves. The microbiota composition in bivalves reflects that of the environment of harvesting waters, so quite different bacteriomes would be expected in shellfish collected in different locations. Bacterial accumulation within molluscan shellfish occurs primarily in the hepatopancreas. In order to assess the effect of the depuration process on these different bacteriomes, in this work we used 16S RNA pyrosequencing and metagenome prediction to assess the impact of 15 h of depuration on the whole hepatopancreas bacteriome of mussels collected in three different locations.

Conformational States of the Rapana thomasiana Hemocyanin and Its Substructures Studied by Dynamic Light Scattering and Time-Resolved Fluorescence Spectroscopy

PubMed Central

Georgieva, Dessislava; Schwark, Daniel; Nikolov, Peter; Idakieva, Krassimira; Parvanova, Katja; Dierks, Karsten; Genov, Nicolay; Betzel, Christian

2005-01-01

Hemocyanins are dioxygen-transporting proteins freely dissolved in the hemolymph of mollusks and arthropods. Dynamic light scattering and time-resolved fluorescence measurements show that the oxygenated and apo-forms of the Rapana thomasiana hemocyanin, its structural subunits RtH1 and RtH2, and those of the functional unit RtH2e, exist in different conformations. The oxygenated respiratory proteins are less compact and more asymmetric than the respective apo-forms. Different conformational states were also observed for the R. thomasiana hemocyanin in the absence and presence of an allosteric regulator. The results are in agreement with a molecular mechanism for cooperative dioxygen binding in molluscan hemocyanins including transfer of conformational changes from one functional unit to another. PMID:15533921

EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity

PubMed Central

Nahum, Laila A; Reynolds, Matthew T; Wang, Zhengyuan O; Faith, Jeremiah J; Jonna, Rahul; Jiang, Zhi J; Meyer, Thomas J; Pollock, David D

2006-01-01

Background Evolutionary genomics requires management and filtering of large numbers of diverse genomic sequences for accurate analysis and inference on evolutionary processes of genomic and functional change. We developed Evolutionary Genomics and Biodiversity (EGenBio; ) to begin to address this. Description EGenBio is a system for manipulation and filtering of large numbers of sequences, integrating curated sequence alignments and phylogenetic trees, managing evolutionary analyses, and visualizing their output. EGenBio is organized into three conceptual divisions, Evolution, Genomics, and Biodiversity. The Genomics division includes tools for selecting pre-aligned sequences from different genes and species, and for modifying and filtering these alignments for further analysis. Species searches are handled through queries that can be modified based on a tree-based navigation system and saved. The Biodiversity division contains tools for analyzing individual sequences or sequence alignments, whereas the Evolution division contains tools involving phylogenetic trees. Alignments are annotated with analytical results and modification history using our PRAED format. A miscellaneous Tools section and Help framework are also available. EGenBio was developed around our comparative genomic research and a prototype database of mtDNA genomes. It utilizes MySQL-relational databases and dynamic page generation, and calls numerous custom programs. Conclusion EGenBio was designed to serve as a platform for tools and resources to ease combined analysis in evolution, genomics, and biodiversity. PMID:17118150

Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection

PubMed Central

Sheng, Zizhang; Schramm, Chaim A.; Connors, Mark; Morris, Lynn; Mascola, John R.; Kwong, Peter D.; Shapiro, Lawrence

2016-01-01

Accumulation of somatic mutations in antibody variable regions is critical for antibody affinity maturation, with HIV-1 broadly neutralizing antibodies (bnAbs) generally requiring years to develop. We recently found that the rate at which mutations accumulate decreases over time, but the mechanism governing this slowing is unclear. In this study, we investigated whether natural selection and/or mutability of the antibody variable region contributed significantly to observed decrease in rate. We used longitudinally sampled sequences of immunoglobulin transcripts of single lineages from each of 3 donors, as determined by next generation sequencing. We estimated the evolutionary rates of the complementarity determining regions (CDRs), which are most significant for functional selection, and found they evolved about 1.5- to 2- fold faster than the framework regions. We also analyzed the presence of AID hotspots and coldspots at different points in lineage development and observed an average decrease in mutability of less than 10 percent over time. Altogether, the correlation between Darwinian selection strength and evolutionary rate trended toward significance, especially for CDRs, but cannot fully explain the observed changes in evolutionary rate. The mutability modulated by AID hotspots and coldspots changes correlated only weakly with evolutionary rates. The combined effects of Darwinian selection and mutability contribute substantially to, but do not fully explain, evolutionary rate change for HIV-1-targeting bnAb lineages. PMID:27191167

Evolutionary thinking

PubMed Central

Hunt, Tam

2014-01-01

Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution—both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place—has been sustained and heated. A growing share of this debate is now devoted to examining how evolutionary thinking affects areas outside of biology. How do our lives change when we recognize that all is in flux? What can we learn about life more generally if we study change instead of stasis? Carter Phipps’ book, Evolutionaries: Unlocking the Spiritual and Cultural Potential of Science's Greatest Idea, delves deep into this relatively new development. Phipps generally takes as a given the validity of the Modern Synthesis of evolutionary biology. His story takes us into, as the subtitle suggests, the spiritual and cultural implications of evolutionary thinking. Can religion and evolution be reconciled? Can evolutionary thinking lead to a new type of spirituality? Is our culture already being changed in ways that we don't realize by evolutionary thinking? These are all important questions and Phipps book is a great introduction to this discussion. Phipps is an author, journalist, and contributor to the emerging “integral” or “evolutionary” cultural movement that combines the insights of Integral Philosophy, evolutionary science, developmental psychology, and the social sciences. He has served as the Executive Editor of EnlightenNext magazine (no longer published) and more recently is the co-founder of the Institute for Cultural Evolution, a public policy think tank addressing the cultural roots of America's political challenges. What follows is an email interview with Phipps. PMID:26478766

[To the 80-anniversary of cholinesterase. The cholinesterase club in Sechenov Institute of Evolutionary Physiology and Biochemistry].

PubMed

Rozengart, E V; Basova, N E; Moralev, S N

2012-01-01

For the second half of the XX century, Sechenov Institute of Evolutionary Physiology and Biochemistry of the Russian Academy of Sciences was the center of the Russian cholinesterase investigations ("the Russian cholinesterase club"). The close cooperation with chemists-syntheticians of different scientific schools provided success and fruitfulness of this scientific search. All these years, there was preserved dualism of this investigation: a study of the mechanism of functioning and kinetics of cholinesterase catalysis as well as the comparative-enzymological character of studies of cholinesterases of the animals being at different levels of evolutionary development.

External and internal shell formation in the ramshorn snail Marisa cornuarietis are extremes in a continuum of gradual variation in development

PubMed Central

2013-01-01

Background Toxic substances like heavy metals can inhibit and disrupt the normal embryonic development of organisms. Exposure to platinum during embryogenesis has been shown to lead to a “one fell swoop” internalization of the shell in the ramshorn snail Marisa cornuarietis, an event which has been discussed to be possibly indicative of processes in evolution which may result in dramatic changes in body plans. Results Whereas at usual cultivation temperature, 26°C, platinum inhibits the growth of both shell gland and mantle edge during embryogenesis leading to an internalization of the mantle and, thus, also of the shell, higher temperatures induce a re-start of the differential growth of the mantle edge and the shell gland after a period of inactivity. Here, developing embryos exhibit a broad spectrum of shell forms: in some individuals only the ventral part of the visceral sac is covered while others develop almost “normal” shells. Histological studies and scanning electron microscopy images revealed platinum to inhibit the differential growth of the shell gland and the mantle edge, and elevated temperature (28 - 30°C) to mitigate this platinum effect with varying efficiency. Conclusion We could show that the formation of internal, external, and intermediate shells is realized within the continuum of a developmental gradient defined by the degree of differential growth of the embryonic mantle edge and shell gland. The artificially induced internal and intermediate shells are first external and then partly internalized, similar to internal shells found in other molluscan groups. PMID:23682742

Microbial multicellular development: mechanical forces in action.

PubMed

Rivera-Yoshida, Natsuko; Arias Del Angel, Juan A; Benítez, Mariana

2018-06-06

Multicellular development occurs in diverse microbial lineages and involves the complex interaction among biochemical, physical and ecological factors. We focus on the mechanical forces that appear to be relevant for the scale and material qualities of individual cells and small cellular conglomerates. We review the effects of such forces on the development of some paradigmatic microorganisms, as well as their overall consequences in multicellular structures. Microbes exhibiting multicellular development have been considered models for the evolutionary transition to multicellularity. Therefore, we discuss how comparative, integrative and dynamic approaches to the mechanical effects involved in microbial development can provide valuable insights into some of the principles behind the evolutionary transition to multicellularity. Copyright © 2018 Elsevier Ltd. All rights reserved.

In search of a metatheory for cognitive development (or, Piaget is dead and I don't feel so good myself).

PubMed

Bjorklund, D F

1997-02-01

With the waning of influence of Piaget's theory and the shortcomings of information-processing perspectives of cognitive growth, cognitive developmentalists lack a common set of broad, overarching principles and assumptions--a metatheory--to guide their research. Developmental biology is suggested as metatheory for cognitive development. Although it is important for developmentalists to understand proximal biological causes (e.g., brain development), most important for such a metatheory is an evolutionary perspective. Some basic principles of evolutionary psychology are introduced, and examples of contemporary research and theory consistent with these ideas are provided.

An evolutionary morphological approach for software development cost estimation.

PubMed

Araújo, Ricardo de A; Oliveira, Adriano L I; Soares, Sergio; Meira, Silvio

2012-08-01

In this work we present an evolutionary morphological approach to solve the software development cost estimation (SDCE) problem. The proposed approach consists of a hybrid artificial neuron based on framework of mathematical morphology (MM) with algebraic foundations in the complete lattice theory (CLT), referred to as dilation-erosion perceptron (DEP). Also, we present an evolutionary learning process, called DEP(MGA), using a modified genetic algorithm (MGA) to design the DEP model, because a drawback arises from the gradient estimation of morphological operators in the classical learning process of the DEP, since they are not differentiable in the usual way. Furthermore, an experimental analysis is conducted with the proposed model using five complex SDCE problems and three well-known performance metrics, demonstrating good performance of the DEP model to solve SDCE problems. Copyright © 2012 Elsevier Ltd. All rights reserved.

Evo-devo of infantile and childhood growth.

PubMed

Hochberg, Ze'ev; Albertsson-Wikland, Kerstin

2008-07-01

Human size is a tradeoff between the evolutionary advantages and disadvantages of being small or big. We now propose that adult size is determined to an important extent during transition from infancy to childhood. This transition is marked by a growth spurt. A delay in the transition has a lifelong impact on stature and is responsible for 44% of children with short stature in developed countries and many more in developing countries. Here, we present the data and theory of an evolutionary adaptive strategy of plasticity in the timing of transition from infancy into childhood to match the prevailing energy supply. We propose that humans have evolved to withstand energy crises by decreasing their body size, and that evolutionary short-term adaptations to energy crises trigger a predictive adaptive response that modify the transition into childhood, culminating in short stature.

Developing of the future: scaffolded Darwinism in societal evolution.

PubMed

Andersson, Claes; Törnberg, Anton; Törnberg, Petter

2014-08-01

We sympathize with the project of a synthetic approach for devising a "theory of intentional change" and agree that Darwinism should be central in such a theory. But Darwinism is not the only process of evolution that needs to be included. Evolutionary biology itself has taken such a turn recently, with the emergence of developmental evolutionary approaches.

The Sound Patterns of Camuno: Description and Explanation in Evolutionary Phonology

ERIC Educational Resources Information Center

Cresci, Michela

2014-01-01

This dissertation presents a linguistic study of the sound patterns of Camuno framed within Evolutionary Phonology (Blevins, 2004, 2006, to appear). Camuno is a variety of Eastern Lombard, a Romance language of northern Italy, spoken in Valcamonica. Camuno is not a local variety of Italian, but a sister of Italian, a local divergent development of…

Overcoming obstacles to interspecies hybridization of ash

Treesearch

Jennifer L. Koch; David W. Carey; Mary E. Mason; M. Nurul Islam-Faridi

2010-01-01

Tree species that share a long co-evolutionary history with insects and pathogens are likely to have developed mechanisms of resistance that allow them to coexist. When insects and pathogens are introduced to different parts of the world, high levels of susceptibility can be observed, presumably in part due to the lack of co-evolutionary history between the insect (or...

EvoluZion: A Computer Simulator for Teaching Genetic and Evolutionary Concepts

ERIC Educational Resources Information Center

Zurita, Adolfo R.

2017-01-01

EvoluZion is a forward-in-time genetic simulator developed in Java and designed to perform real time simulations on the evolutionary history of virtual organisms. These model organisms harbour a set of 13 genes that codify an equal number of phenotypic features. These genes change randomly during replication, and mutant genes can have null,…

Evolutionary Maps: A New Model for the Analysis of Conceptual Development, with Application to the Diurnal Cycle

ERIC Educational Resources Information Center

Navarro, Manuel

2014-01-01

This paper presents a model of how children generate concrete concepts from perception through processes of differentiation and integration. The model informs the design of a novel methodology ("evolutionary maps" or "emaps"), whose implementation on certain domains unfolds the web of itineraries that children may follow in the…

Biology Teachers' Conceptions of the Diversity of Life and the Historical Development of Evolutionary Concepts

ERIC Educational Resources Information Center

da Silva, Paloma Rodrigues; de Andrade, Mariana A. Bologna Soares; de Andrade Caldeira, Ana Maria

2015-01-01

Biology is a science that involves study of the diversity of living organisms. This diversity has always generated questions and has motivated cultures to seek plausible explanations for the differences and similarities between types of organisms. In biology teaching, these issues are addressed by adopting an evolutionary approach. The aim of this…

The Nestor Effect: Extending Evolutionary Developmental Psychology to a Lifespan Perspective

ERIC Educational Resources Information Center

Greve, Werner; Bjorklund, David F.

2009-01-01

We extend an evolutionary perspective of development to the lifespan, proposing that human longevity may be related to the experience, knowledge, and wisdom provided by older members of human groups. In addition to the assistance in childcare provided by grandmothers to their daughters, the experience of wise elders could have served to benefit…

The ABCs of an evolutionary education science: The academic, behavioral, and cultural implications of an evolutionary approach to education theory and practice

NASA Astrophysics Data System (ADS)

Kauffman, Rick, Jr.

Calls for improving research-informed policy in education are everywhere. Yet, while there is an increasing trend towards science-based practice, there remains little agreement over which of the sciences to consult and how to organize a collective effort between them. What Education lacks is a general theoretical framework through which policies can be constructed, implemented, and assessed. This dissertation submits that evolutionary theory can provide a suitable framework for coordinating educational policies and practice, and can provide the entire field of education with a clearer sense of how to better manage the learning environment. This dissertation explores two broad paths that outline the conceptual foundations for an Evolutionary Education Science: "Teaching Evolution" and "Using Evolution to Teach." Chapter 1 introduces both of these themes. After describing why evolutionary science is best suited for organizing education research and practice, Chapter 1 proceeds to "teach" an overview of the "evolutionary toolkit"---the mechanisms and principles that underlie the modern evolutionary perspective. The chapter then employs the "toolkit" in examining education from an evolutionary perspective, outlining the evolutionary precepts that can guide theorizing and research in education, describing how educators can "use evolution to teach.". Chapters 2-4 expand on this second theme. Chapters 2 and 3 describe an education program for at-risk 9th and 10th grade students, the Regents Academy, designed entirely with evolutionary principles in mind. The program was rigorously assessed in a randomized control design and has demonstrated success at improving students' academic performance (Chapter 2) and social & behavioral development (Chapter 3). Chapter 4 examines current teaching strategies that underlie effective curriculum-instruction-assessment practices and proposes a framework for organizing successful, evidence-based strategies for neural-/cognitive-focused learning goals. Chapter 5 explores the cognitive effects that "teaching evolution" has on the learner. This chapter examines the effects that a course on evolutionary theory has on university undergraduate students in understanding and applying evolution and how learning the evolutionary toolkit affects critical thinking skills and domain transfer of knowledge. The results demonstrate that a single course on evolutionary theory increases students' acceptance and understanding of evolution and science, and, in effect, increases critical thinking performance.

The evolution of ecosystem ascendency in a complex systems based model.

PubMed

Brinck, Katharina; Jensen, Henrik Jeldtoft

2017-09-07

General patterns in ecosystem development can shed light on driving forces behind ecosystem formation and recovery and have been of long interest. In recent years, the need for integrative and process oriented approaches to capture ecosystem growth, development and organisation, as well as the scope of information theory as a descriptive tool has been addressed from various sides. However data collection of ecological network flows is difficult and tedious and comprehensive models are lacking. We use a hierarchical version of the Tangled Nature Model of evolutionary ecology to study the relationship between structure, flow and organisation in model ecosystems, their development over evolutionary time scales and their relation to ecosystem stability. Our findings support the validity of ecosystem ascendency as a meaningful measure of ecosystem organisation, which increases over evolutionary time scales and significantly drops during periods of disturbance. The results suggest a general trend towards both higher integrity and increased stability driven by functional and structural ecosystem coadaptation. Copyright © 2017 Elsevier Ltd. All rights reserved.

A systems approach to physiologic evolution: From micelles to consciousness.

PubMed

Torday, John S; Miller, William B

2018-01-01

A systems approach to evolutionary biology offers the promise of an improved understanding of the fundamental principles of life through the effective integration of many biologic disciplines. It is presented that any critical integrative approach to evolutionary development involves a paradigmatic shift in perspective, more than just the engagement of a large number of disciplines. Critical to this differing viewpoint is the recognition that all biological processes originate from the unicellular state and remain permanently anchored to that phase throughout evolutionary development despite their macroscopic appearances. Multicellular eukaryotic development can, therefore, be viewed as a series of connected responses to epiphenomena that proceeds from that base in continuous iterative maintenance of collective cellular homeostatic equipoise juxtaposed against an ever-changing and challenging environment. By following this trajectory of multicellular eukaryotic evolution from within unicellular First Principles of Physiology forward, the mechanistic nature of complex physiology can be identified through a step-wise analysis of a continuous arc of vertebrate evolution based upon serial exaptations. © 2017 Wiley Periodicals, Inc.

Smartphones in ecology and evolution: a guide for the app-rehensive.

PubMed

Teacher, Amber G F; Griffiths, David J; Hodgson, David J; Inger, Richard

2013-12-01

Smartphones and their apps (application software) are now used by millions of people worldwide and represent a powerful combination of sensors, information transfer, and computing power that deserves better exploitation by ecological and evolutionary researchers. We outline the development process for research apps, provide contrasting case studies for two new research apps, and scan the research horizon to suggest how apps can contribute to the rapid collection, interpretation, and dissemination of data in ecology and evolutionary biology. We emphasize that the usefulness of an app relies heavily on the development process, recommend that app developers are engaged with the process at the earliest possible stage, and commend efforts to create open-source software scaffolds on which customized apps can be built by nonexperts. We conclude that smartphones and their apps could replace many traditional handheld sensors, calculators, and data storage devices in ecological and evolutionary research. We identify their potential use in the high-throughput collection, analysis, and storage of complex ecological information.

Darwin in Mind: New Opportunities for Evolutionary Psychology

PubMed Central

Bolhuis, Johan J.; Brown, Gillian R.; Richardson, Robert C.; Laland, Kevin N.

2011-01-01

Evolutionary Psychology (EP) views the human mind as organized into many modules, each underpinned by psychological adaptations designed to solve problems faced by our Pleistocene ancestors. We argue that the key tenets of the established EP paradigm require modification in the light of recent findings from a number of disciplines, including human genetics, evolutionary biology, cognitive neuroscience, developmental psychology, and paleoecology. For instance, many human genes have been subject to recent selective sweeps; humans play an active, constructive role in co-directing their own development and evolution; and experimental evidence often favours a general process, rather than a modular account, of cognition. A redefined EP could use the theoretical insights of modern evolutionary biology as a rich source of hypotheses concerning the human mind, and could exploit novel methods from a variety of adjacent research fields. PMID:21811401

The great struggles of life: Darwin and the emergence of evolutionary psychology.

PubMed

Buss, David M

2009-01-01

Darwin envisioned a scientific revolution for psychology. His theories of natural and sexual selection identified two classes of struggles--the struggle for existence and the struggle for mates. The emergence of evolutionary psychology and related disciplines signals the fulfillment of Darwin's vision. Natural selection theory guides scientists to discover adaptations for survival. Sexual selection theory illuminates the sexual struggle, highlighting mate choice and same-sex competition adaptations. Theoretical developments since publication of On the Origin of Species identify important struggles unknown to Darwin, notably, within-families conflicts and conflict between the sexes. Evolutionary psychology synthesizes modern evolutionary biology and psychology to penetrate some of life's deep mysteries: Why do many struggles center around sex? Why is social conflict pervasive? And what are the mechanisms of mind that define human nature? 2009 APA, all rights reserved

On the Evolution of the Cardiac Pacemaker

PubMed Central

Burkhard, Silja; van Eif, Vincent; Garric, Laurence; Christoffels, Vincent M.; Bakkers, Jeroen

2017-01-01

The rhythmic contraction of the heart is initiated and controlled by an intrinsic pacemaker system. Cardiac contractions commence at very early embryonic stages and coordination remains crucial for survival. The underlying molecular mechanisms of pacemaker cell development and function are still not fully understood. Heart form and function show high evolutionary conservation. Even in simple contractile cardiac tubes in primitive invertebrates, cardiac function is controlled by intrinsic, autonomous pacemaker cells. Understanding the evolutionary origin and development of cardiac pacemaker cells will help us outline the important pathways and factors involved. Key patterning factors, such as the homeodomain transcription factors Nkx2.5 and Shox2, and the LIM-homeodomain transcription factor Islet-1, components of the T-box (Tbx), and bone morphogenic protein (Bmp) families are well conserved. Here we compare the dominant pacemaking systems in various organisms with respect to the underlying molecular regulation. Comparative analysis of the pathways involved in patterning the pacemaker domain in an evolutionary context might help us outline a common fundamental pacemaker cell gene programme. Special focus is given to pacemaker development in zebrafish, an extensively used model for vertebrate development. Finally, we conclude with a summary of highly conserved key factors in pacemaker cell development and function. PMID:29367536

Mechanistic insights into induction of vitellogenin gene expression by estrogens in Sydney rock oysters, Saccostrea glomerata.

PubMed

Tran, Thi Kim Anh; MacFarlane, Geoff R; Kong, Richard Yuen Chong; O'Connor, Wayne A; Yu, Richard Man Kit

2016-05-01

Marine molluscs, such as oysters, respond to estrogenic compounds with the induction of the egg yolk protein precursor, vitellogenin (Vtg), availing a biomarker for estrogenic pollution. Despite this application, the precise molecular mechanism through which estrogens exert their action to induce molluscan vitellogenesis is unknown. As a first step to address this question, we cloned a gene encoding Vtg from the Sydney rock oyster Saccostrea glomerata (sgVtg). Using primers designed from a partial sgVtg cDNA sequence available in Genbank, a full-length sgVtg cDNA of 8498bp was obtained by 5'- and 3'-RACE. The open reading frame (ORF) of sgVtg was determined to be 7980bp, which is substantially longer than the orthologs of other oyster species. Its deduced protein sequence shares the highest homology at the N- and C-terminal regions with other molluscan Vtgs. The full-length genomic DNA sequence of sgVtg was obtained by genomic PCR and genome walking targeting the gene body and flanking regions, respectively. The genomic sequence spans 20kb and consists of 30 exons and 29 introns. Computer analysis identified three closely spaced half-estrogen responsive elements (EREs) in the promoter region and a 210-bp CpG island 62bp downstream of the transcription start site. Upregulation of sgVtg mRNA expression was observed in the ovaries following in vitro (explants) and in vivo (tank) exposure to 17β-estradiol (E2). Notably, treatment with an estrogen receptor (ER) antagonist in vitro abolished the upregulation, suggesting a requirement for an estrogen-dependent receptor for transcriptional activation. DNA methylation of the 5' CpG island was analysed using bisulfite genomic sequencing of the in vivo exposed ovaries. The CpG island was found to be hypomethylated (with 0-3% methylcytosines) in both control and E2-exposed oysters. However, no significant differential methylation or any correlation between methylation and sgVtg expression levels was observed. Overall, the results support the possible involvement of an ERE-containing promoter and an estrogen-activated receptor in estrogen signalling in marine molluscs. Copyright © 2016 Elsevier B.V. All rights reserved.

Ionic mechanisms and receptor properties underlying the responses of molluscan neurones to 5-hydroxytryptamine

PubMed Central

Gerschenfeld, H. M.; Tritsch, Danièle Paupardin

1974-01-01

1. Molluscan neurones have been found to show six different types of response (three excitatory and three inhibitory) to the iontophoretic application of 5-hydroxytryptamine (5-HT). The pharmacological properties of the receptors and the ionic mechanisms associated with these responses have been analysed. 2. Four of the responses to 5-HT (named A, A′, B and C) are consequent upon an increase in membrane conductance whereas the other two (named α and β) are caused by a decrease in membrane conductance. 3. The A-response to 5-HT consists of a `fast' depolarization due to an increase mainly in Na+-conductance; the A′-response is a `slow' depolarization also associated with a Na+-conductance increase. Receptors mediating the A- and A′-depolarizations have different pharmacological properties and may exist side by side on the same neurone. 4. Both the B- and C-responses are inhibitory. The B-response is a `slow' hyperpolarization due to an increase in K+-conductance, the C-response is a fast hyperpolarization associated with an increase in Cl--conductance. 5. The α-response to 5-HT is a depolarization which becomes reduced in amplitude with cell hyperpolarization and reverses at -75 mV; it is caused by a decrease in K+-conductance. The β-response is an hyperpolarization which increases in amplitude with cell hyperpolarization and reverses at -20/-30 mV. It results from a decrease in conductance to both Na+ and K+ ions. 6. The receptors involved in the 5-HT responses associated with a conductance increase may be recognized by the action of specific antagonists: 7-methyltryptamine blocks only the A-receptors, 5-methoxygramine only the B-receptors and neostigmine only the C-receptors. Curare blocks the A- and C-receptors and bufotenine, the A-, A′- and B-receptors. No specific antagonists have yet been found for the 5-HT responses caused by a conductance decrease. 7. The significance of the multiplicity of receptors is discussed. Their functional significance at synapses is analysed in the following paper. PMID:4155767

Upper Cretaceous molluscan record along a transect from Virden, New Mexico, to Del Rio, Texas

USGS Publications Warehouse

Cobban, W.A.; Hook, S.C.; McKinney, K.C.

2008-01-01

Updated age assignments and new collections of molluscan fossils from lower Cenomanian through upper Campanian strata in Texas permit a much refined biostratigraphic correlation with the rocks of New Mexico and the Western Interior. Generic names of many Late Cretaceous ammonites and inoceramid bivalves from Texas are updated to permit this correlation. Strata correlated in the west-to-east transect include the lower Cenomanian Beartooth Quartzite and Sarten Sandstone of southwest New Mexico, and the Eagle Mountains Formation, Del Rio Clay, Buda Limestone, and. basal beds of the Chispa Summit, Ojinaga, and Boquillas Formations of the Texas-Mexico border area. Middle Cenomanian strata are lacking in southwestern New Mexico but are present in the lower parts of the Chispa Summit and Boquillas Formations in southwest Texas. Upper Cenomanian and lower Turonian rocks are present at many localities in New Mexico and Texas in the Mancos Shale and Chispa Summit, Ojinaga, and Boquillas Formations. Middle Turonian and younger rocks seem to be entirely nonmarine in southwestern New Mexico, but they are marine in the Rio Grande area in the Chispa. Summit, Ojinaga, and Boquillas Formations. The upper part of the Chispa Summit and Boquillas contain late Turonian fossils. Rocks of Coniacian and Santonian age are present high in the Chispa Summit, Ojinaga, and Boquillas Formations, and in the lower part of the Austin. The San Carlos, Aguja, Pen, and Austin Formations contain fossils of Campanian age. Fossils representing at least 38 Upper Cretaceous ammonite zones are present along the transect. Collections made in recent years in southwestern New Mexico and at Sierra de Cristo Rey just west of downtown El Paso, Texas, have been well treated and do not need revision. Taxonomic names and zonations published in the pre-1970 literature on the Rio Grande area of Texas have been updated. New fossil collections from the Big Bend National Park, Texas, allow for a much refined correlation in the central part of the transect in Texas. Middle Turonian-Campanian zonation in southwest Texas is based mainly on ammonites of the Family Collignoniceratidae, as opposed to the scaphitid and baculitid ammonites that are especially abundant farther north in the Western Interior.

Development links psychological causes to evolutionary explanations.

PubMed

Fedyk, Mark; Kushnir, Tamar

2014-04-01

Our conscious abilities are learned in environments that have evolved to support them. This insight provides an alternative way of framing Huang & Bargh's (H&B's) provocative hypothesis. To understand the conflict between unconscious goals and consciousness, we can study the emergence of conscious thought and control in childhood. These developmental processes are also central to the best available current evolutionary theories.

The Implications of the Cognitive Sciences for the Relation between Religion and Science Education: The Case of Evolutionary Theory

ERIC Educational Resources Information Center

Blancke, Stefaan; De Smedt, Johan; De Cruz, Helen; Boudry, Maarten; Braeckman, Johan

2012-01-01

This paper discusses the relationship between religion and science education in the light of the cognitive sciences. We challenge the popular view that science and religion are compatible, a view that suggests that learning and understanding evolutionary theory has no effect on students' religious beliefs and vice versa. We develop a cognitive…

Survival of the Fittest and the Sexiest: Evolutionary Origins of Adolescent Bullying.

PubMed

Koh, Jun-Bin; Wong, Jennifer S

2015-07-09

The central idea of evolutionary psychology theory (EPT) is that species evolve to carry or exhibit certain traits/behaviors because these characteristics increase their ability to survive and reproduce. Proponents of EPT propose that bullying emerges from evolutionary development, providing an adaptive edge for gaining better sexual opportunities and physical protection, and promoting mental health. This study examines adolescent bullying behaviors via the lens of EPT. Questionnaires were administered to 135 adolescents, ages 13 to 16, from one secondary school in metro Vancouver, British Columbia. Participants were categorized into one of four groups (bullies, victims, bully/victims, or bystanders) according to their involvement in bullying interactions as measured by the Olweus Bully/Victim Questionnaire. Four dependent variables were examined: depression, self-esteem, social status, and social anxiety. Results indicate that bullies had the most positive scores on mental health measures and held the highest social rank in the school environment, with significant differences limited to comparisons between bullies and bully/victims. These results lend support to the hypothesis that youth bullying is derived from evolutionary development. Implications for approaching anti-bullying strategies in schools and directions for future studies are discussed. © The Author(s) 2015.

Evolutionary rescue: an emerging focus at the intersection between ecology and evolution.

PubMed

Gonzalez, Andrew; Ronce, Ophélie; Ferriere, Regis; Hochberg, Michael E

2013-01-19

There is concern that the rate of environmental change is now exceeding the capacity of many populations to adapt. Mitigation of biodiversity loss requires science that integrates both ecological and evolutionary responses of populations and communities to rapid environmental change, and can identify the conditions that allow the recovery of declining populations. This special issue focuses on evolutionary rescue (ER), the idea that evolution might occur sufficiently fast to arrest population decline and allow population recovery before extinction ensues. ER emphasizes a shift to a perspective on evolutionary dynamics that focuses on short time-scales, genetic variants of large effects and absolute rather than relative fitness. The contributions in this issue reflect the state of field; the articles address the latest conceptual developments, and report novel theoretical and experimental results. The examples in this issue demonstrate that this burgeoning area of research can inform problems of direct practical concern, such as the conservation of biodiversity, adaptation to climate change and the emergence of infectious disease. The continued development of research on ER will be necessary if we are to understand the extent to which anthropogenic global change will reduce the Earth's biodiversity.

Evolution of SH2 domains and phosphotyrosine signalling networks

PubMed Central

Liu, Bernard A.; Nash, Piers D.

2012-01-01

Src homology 2 (SH2) domains mediate selective protein–protein interactions with tyrosine phosphorylated proteins, and in doing so define specificity of phosphotyrosine (pTyr) signalling networks. SH2 domains and protein-tyrosine phosphatases expand alongside protein-tyrosine kinases (PTKs) to coordinate cellular and organismal complexity in the evolution of the unikont branch of the eukaryotes. Examination of conserved families of PTKs and SH2 domain proteins provides fiduciary marks that trace the evolutionary landscape for the development of complex cellular systems in the proto-metazoan and metazoan lineages. The evolutionary provenance of conserved SH2 and PTK families reveals the mechanisms by which diversity is achieved through adaptations in tissue-specific gene transcription, altered ligand binding, insertions of linear motifs and the gain or loss of domains following gene duplication. We discuss mechanisms by which pTyr-mediated signalling networks evolve through the development of novel and expanded families of SH2 domain proteins and the elaboration of connections between pTyr-signalling proteins. These changes underlie the variety of general and specific signalling networks that give rise to tissue-specific functions and increasingly complex developmental programmes. Examination of SH2 domains from an evolutionary perspective provides insight into the process by which evolutionary expansion and modification of molecular protein interaction domain proteins permits the development of novel protein-interaction networks and accommodates adaptation of signalling networks. PMID:22889907

Evolution of the Plant Reproduction Master Regulators LFY and the MADS Transcription Factors: The Role of Protein Structure in the Evolutionary Development of the Flower

PubMed Central

Silva, Catarina S.; Puranik, Sriharsha; Round, Adam; Brennich, Martha; Jourdain, Agnès; Parcy, François; Hugouvieux, Veronique; Zubieta, Chloe

2016-01-01

Understanding the evolutionary leap from non-flowering (gymnosperms) to flowering (angiosperms) plants and the origin and vast diversification of the floral form has been one of the focuses of plant evolutionary developmental biology. The evolving diversity and increasing complexity of organisms is often due to relatively small changes in genes that direct development. These “developmental control genes” and the transcription factors (TFs) they encode, are at the origin of most morphological changes. TFs such as LEAFY (LFY) and the MADS-domain TFs act as central regulators in key developmental processes of plant reproduction including the floral transition in angiosperms and the specification of the male and female organs in both gymnosperms and angiosperms. In addition to advances in genome wide profiling and forward and reverse genetic screening, structural techniques are becoming important tools in unraveling TF function by providing atomic and molecular level information that was lacking in purely genetic approaches. Here, we summarize previous structural work and present additional biophysical and biochemical studies of the key master regulators of plant reproduction – LEAFY and the MADS-domain TFs SEPALLATA3 and AGAMOUS. We discuss the impact of structural biology on our understanding of the complex evolutionary process leading to the development of the bisexual flower. PMID:26779227

From experimental systems to evolutionary biology: an impossible journey?

PubMed

Morange, Michel

2013-01-01

The historical approach to the sciences has undergone a sea change during recent decades. Maybe the major contribution of Hans-Jörg Rheinberger to this movement was his demonstration of the importance of experimental systems, and of their transformations, in the development of the sciences. To describe these transformations, Hans-Jörg borrows metaphors from evolutionary biology. I want to argue that evolutionary biologists can find in these recent historical studies plenty of models and concepts to address unresolved issues in their discipline. At a time when transdisciplinarity is highly praised, it is useful to provide a precise description of the obstacles that have so far prevented this exchange.

Performance comparison of some evolutionary algorithms on job shop scheduling problems

NASA Astrophysics Data System (ADS)

Mishra, S. K.; Rao, C. S. P.

2016-09-01

Job Shop Scheduling as a state space search problem belonging to NP-hard category due to its complexity and combinational explosion of states. Several naturally inspire evolutionary methods have been developed to solve Job Shop Scheduling Problems. In this paper the evolutionary methods namely Particles Swarm Optimization, Artificial Intelligence, Invasive Weed Optimization, Bacterial Foraging Optimization, Music Based Harmony Search Algorithms are applied and find tuned to model and solve Job Shop Scheduling Problems. To compare about 250 Bench Mark instances have been used to evaluate the performance of these algorithms. The capabilities of each these algorithms in solving Job Shop Scheduling Problems are outlined.

Bio-inspired algorithms applied to molecular docking simulations.

PubMed

Heberlé, G; de Azevedo, W F

2011-01-01

Nature as a source of inspiration has been shown to have a great beneficial impact on the development of new computational methodologies. In this scenario, analyses of the interactions between a protein target and a ligand can be simulated by biologically inspired algorithms (BIAs). These algorithms mimic biological systems to create new paradigms for computation, such as neural networks, evolutionary computing, and swarm intelligence. This review provides a description of the main concepts behind BIAs applied to molecular docking simulations. Special attention is devoted to evolutionary algorithms, guided-directed evolutionary algorithms, and Lamarckian genetic algorithms. Recent applications of these methodologies to protein targets identified in the Mycobacterium tuberculosis genome are described.

Langley's CSI evolutionary model: Phase O

NASA Technical Reports Server (NTRS)

Belvin, W. Keith; Elliott, Kenny B.; Horta, Lucas G.; Bailey, Jim P.; Bruner, Anne M.; Sulla, Jeffrey L.; Won, John; Ugoletti, Roberto M.

1991-01-01

A testbed for the development of Controls Structures Interaction (CSI) technology to improve space science platform pointing is described. The evolutionary nature of the testbed will permit the study of global line-of-sight pointing in phases 0 and 1, whereas, multipayload pointing systems will be studied beginning with phase 2. The design, capabilities, and typical dynamic behavior of the phase 0 version of the CSI evolutionary model (CEM) is documented for investigator both internal and external to NASA. The model description includes line-of-sight pointing measurement, testbed structure, actuators, sensors, and real time computers, as well as finite element and state space models of major components.

From wide to close binaries?

NASA Astrophysics Data System (ADS)

Eggleton, Peter P.

The mechanisms by which the periods of wide binaries (mass 8 solar mass or less and period 10-3000 d) are lengthened or shortened are discussed, synthesizing the results of recent theoretical investigations. A system of nomenclature involving seven evolutionary states, three geometrical states, and 10 types of orbital-period evolution is developed and applied; classifications of 71 binaries are presented in a table along with the basic observational parameters. Evolutionary processes in wide binaries (single-star-type winds, magnetic braking with tidal friction, and companion-reinforced attrition), late case B systems, low-mass X-ray binaries, and triple systems are examined in detail, and possible evolutionary paths are shown in diagrams.

Human Germline Mutation and the Erratic Evolutionary Clock

PubMed Central

Przeworski, Molly

2016-01-01

Our understanding of the chronology of human evolution relies on the “molecular clock” provided by the steady accumulation of substitutions on an evolutionary lineage. Recent analyses of human pedigrees have called this understanding into question by revealing unexpectedly low germline mutation rates, which imply that substitutions accrue more slowly than previously believed. Translating mutation rates estimated from pedigrees into substitution rates is not as straightforward as it may seem, however. We dissect the steps involved, emphasizing that dating evolutionary events requires not “a mutation rate” but a precise characterization of how mutations accumulate in development in males and females—knowledge that remains elusive. PMID:27760127

Teaching Tree-Thinking to Undergraduate Biology Students.

PubMed

Meisel, Richard P

2010-07-27

Evolution is the unifying principle of all biology, and understanding how evolutionary relationships are represented is critical for a complete understanding of evolution. Phylogenetic trees are the most conventional tool for displaying evolutionary relationships, and "tree-thinking" has been coined as a term to describe the ability to conceptualize evolutionary relationships. Students often lack tree-thinking skills, and developing those skills should be a priority of biology curricula. Many common student misconceptions have been described, and a successful instructor needs a suite of tools for correcting those misconceptions. I review the literature on teaching tree-thinking to undergraduate students and suggest how this material can be presented within an inquiry-based framework.

Quantifying rates of evolutionary adaptation in response to ocean acidification.

PubMed

Sunday, Jennifer M; Crim, Ryan N; Harley, Christopher D G; Hart, Michael W

2011-01-01

The global acidification of the earth's oceans is predicted to impact biodiversity via physiological effects impacting growth, survival, reproduction, and immunology, leading to changes in species abundances and global distributions. However, the degree to which these changes will play out critically depends on the evolutionary rate at which populations will respond to natural selection imposed by ocean acidification, which remains largely unquantified. Here we measure the potential for an evolutionary response to ocean acidification in larval development rate in two coastal invertebrates using a full-factorial breeding design. We show that the sea urchin species Strongylocentrotus franciscanus has vastly greater levels of phenotypic and genetic variation for larval size in future CO(2) conditions compared to the mussel species Mytilus trossulus. Using these measures we demonstrate that S. franciscanus may have faster evolutionary responses within 50 years of the onset of predicted year-2100 CO(2) conditions despite having lower population turnover rates. Our comparisons suggest that information on genetic variation, phenotypic variation, and key demographic parameters, may lend valuable insight into relative evolutionary potentials across a large number of species.

Understanding plant reproductive diversity.

PubMed

Barrett, Spencer C H

2010-01-12

Flowering plants display spectacular floral diversity and a bewildering array of reproductive adaptations that promote mating, particularly outbreeding. A striking feature of this diversity is that related species often differ in pollination and mating systems, and intraspecific variation in sexual traits is not unusual, especially among herbaceous plants. This variation provides opportunities for evolutionary biologists to link micro-evolutionary processes to the macro-evolutionary patterns that are evident within lineages. Here, I provide some personal reflections on recent progress in our understanding of the ecology and evolution of plant reproductive diversity. I begin with a brief historical sketch of the major developments in this field and then focus on three of the most significant evolutionary transitions in the reproductive biology of flowering plants: the pathway from outcrossing to predominant self-fertilization, the origin of separate sexes (females and males) from hermaphroditism and the shift from animal pollination to wind pollination. For each evolutionary transition, I consider what we have discovered and some of the problems that still remain unsolved. I conclude by discussing how new approaches might influence future research in plant reproductive biology.

Evolutionary genetics of the Drosophila alcohol dehydrogenase gene-enzyme system.

PubMed

Heinstra, P W

1993-01-01

Evolutionary genetics embodies a broad research area that ranges from the DNA level to studies of genetic aspects in populations. In all cases the purpose is to determine the impact of genetic variation on evolutionary change. The broad range of evolutionary genetics requires the involvement of a diverse group of researchers: molecular biologists, (population) geneticists, biochemists, physiologists, ecologists, ethologists and theorists, each of which has its own insights and interests. For example, biochemists are often not concerned with the physiological function of a protein (with respect to pH, substrates, temperature, etc.), while ecologists, in turn, are often not interested in the biochemical-physiological aspects underlying the traits they study. This review deals with several evolutionary aspects of the Drosophila alcohol dehydrogenase gene-enzyme system, and includes my own personal viewpoints. I have tried to condense and integrate the current knowledge in this field as it has developed since the comprehensive review by van Delden (1982). Details on specific issues may be gained from Sofer and Martin (1987), Sullivan, Atkinson and Starmer (1990); Chambers (1988, 1991); Geer, Miller and Heinstra (1991); and Winberg and McKinley-McKee (1992).

Physical characteristics and evolutionary trends of continental rifts

NASA Technical Reports Server (NTRS)

Ramberg, I. B.; Morgan, P.

1984-01-01

Rifts may be defined as zones beneath which the entire lithosphere has ruptured in extension. They are widespread and occur in a variety of tectonic settings, and range up to 2,600 m.y. in age. The object of this review is to highlight characteristic features of modern and ancient rifts, to emphasize differences and similarities in order to help characterize evolutionary trends, to identify physical conditions favorable for initiation as well as termination of rifting, and to provide constraints for future modeling studies of rifting. Rifts are characterized on the basis of their structural, geomorphic, magmatic and geophysical features and the diverse character of these features and their evolutionary trends through time are discussed. Mechanisms of rifting are critically examined in terms of the physical characteristics and evolutionary trends of rifts, and it is concluded that while simple models can give valuable insight into specific processes of rifting, individual rifts can rarely, if ever, be characterized by well defined trends predicted by these models. More data are required to clearly define evolutionary trends, and the models require development to incorporate the effects of lithospheric heterogeneities and complex geologic histories.

A molecular signaling approach to linking intraspecific variation and macro-evolutionary patterns.

PubMed

Swanson, Eli M; Snell-Rood, Emilie C

2014-11-01

Macro-evolutionary comparisons are a valued tool in evolutionary biology. Nevertheless, our understanding of how systems involved in molecular signaling change in concert with phenotypic diversification has lagged. We argue that integrating our understanding of the evolution of molecular signaling systems with phylogenetic comparative methods is an important step toward understanding the processes linking variation among individuals with variation among species. Focusing mostly on the endocrine system, we discuss how the complexity and mechanistic nature of molecular signaling systems may influence the application and interpretation of macro-evolutionary comparisons. We also detail five hypotheses concerning the role that physiological mechanisms can play in shaping macro-evolutionary patterns, and discuss ways in which these hypotheses could influence phenotypic diversification. Finally, we review a series of tools able to analyze the complexity of physiological systems and the way they change in concert with the phenotypes for which they coordinate development. © The Author 2014. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Indoor Thermal Comfort, an Evolutionary Biology Perspective

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stoops, John L.

2006-04-15

As is becoming increasingly clear, the human species evolvedin the East African savannah. Details of the precise evolutionary chainremain unresolved however it appears that the process lasted severalmillion years, culminating with the emergence of modern Homo sapiensroughly 200,000 years ago. Following that final evolutionary developmentmodern Homo sapiens relatively quickly populated the entire world.Clearly modern Homo sapiens is a successful, resourceful and adaptablespecies. In the developed societies, modern humans live an existence farremoved from our evolutionary ancestors. As we have learned over the lastcentury, this "new" lifestyle can often result in unintendedconsequences. Clearly, our modern access to food, shelter, transportationand healthcaremore » has resulted in greatly expanded expected lifespan butthis new lifestyle can also result in the emergence of different kinds ofdiseases and health problems. The environment in modern buildings haslittle resemblance to the environment of the savannah. We strive tocreate environments with little temperature, air movement and lightvariation. Building occupants often express great dissatisfaction withthese modern created environments and a significant fraction even developsomething akin to allergies to specific buildings (sick buildingsyndrome). Are the indoor environments we are creating fundamentallyunhealthy -- when examined from an evolutionary perspective?« less

Progress in life's history: Linking Darwinism and palaeontology in Britain, 1860-1914.

PubMed

Manias, Chris

2017-12-01

This paper examines the tension between Darwinian evolution and palaeontological research in Britain in the 1860-1914 period, looking at how three key promoters of Darwinian thinking - Thomas Henry Huxley, Edwin Ray Lankester and Alfred Russell Wallace - integrated palaeontological ideas and narratives of life's history into their public presentations of evolutionary theory. It shows how engagement with palaeontological science was an important part of the promotion of evolutionary ideas in Britain, which often bolstered notions that evolution depended upon progress and development along a wider plan. While often critical of some of the non-Darwinian concepts of evolution professed by many contemporary palaeontologists, and frequently citing the 'imperfection' of the fossil record itself, Darwinian thinkers nevertheless engaged extensively with palaeontology to develop evolutionary narratives informed by notions of improvement and progress within the natural world. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Neuroscience and the fallacies of functionalism.

PubMed

Reddy, William M

2010-01-01

Smail's "On Deep History and the Brain" is rightly critical of the functionalist fallacies that have plagued evolutionary theory, sociobiology, and evolutionary psychology. However, his attempt to improve on these efforts relies on functional explanations that themselves oversimplify the lessons of neuroscience. In addition, like explanations in evolutionary psychology, they are highly speculative and cannot be confirmed or disproved by evidence. Neuroscience research is too diverse to yield a single picture of brain functioning. Some recent developments in neuroscience research, however, do suggest that cognitive processing provides a kind of “operating system” that can support a great diversity of cultural material. These developments include evidence of “top-down” processing in motor control, in visual processing, in speech recognition, and in “emotion regulation.” The constraints that such a system may place on cultural learning and transmission are worth investigating. At the same time, historians are well advised to remain wary of the pitfalls of functionalism.

A teleofunctional account of evolutionary mismatch.

PubMed

Cofnas, Nathan

When the environment in which an organism lives deviates in some essential way from that to which it is adapted, this is described as "evolutionary mismatch," or "evolutionary novelty." The notion of mismatch plays an important role, explicitly or implicitly, in evolution-informed cognitive psychology, clinical psychology, and medicine. The evolutionary novelty of our contemporary environment is thought to have significant implications for our health and well-being. However, scientists have generally been working without a clear definition of mismatch. This paper defines mismatch as deviations in the environment that render biological traits unable, or impaired in their ability, to produce their selected effects (i.e., to perform their proper functions in Neander's sense). The machinery developed by Millikan in connection with her account of proper function, and with her related teleosemantic account of representation, is used to identify four major types, and several subtypes, of evolutionary mismatch. While the taxonomy offered here does not in itself resolve any scientific debates, the hope is that it can be used to better formulate empirical hypotheses concerning the effects of mismatch. To illustrate, it is used to show that the controversial hypothesis that general intelligence evolved as an adaptation to handle evolutionary novelty can, contra some critics, be formulated in a conceptually coherent way.

Applying Evolutionary Genetics to Developmental Toxicology and Risk Assessment

PubMed Central

Leung, Maxwell C. K.; Procter, Andrew C.; Goldstone, Jared V.; Foox, Jonathan; DeSalle, Robert; Mattingly, Carolyn J.; Siddall, Mark E.; Timme-Laragy, Alicia R.

2018-01-01

Evolutionary thinking continues to challenge our views on health and disease. Yet, there is a communication gap between evolutionary biologists and toxicologists in recognizing the connections among developmental pathways, high-throughput screening, and birth defects in humans. To increase our capability in identifying potential developmental toxicants in humans, we propose to apply evolutionary genetics to improve the experimental design and data interpretation with various in vitro and whole-organism models. We review five molecular systems of stress response and update 18 consensual cell-cell signaling pathways that are the hallmark for early development, organogenesis, and differentiation; and revisit the principles of teratology in light of recent advances in high-throughput screening, big data techniques, and systems toxicology. Multiscale systems modeling plays an integral role in the evolutionary approach to cross-species extrapolation. Phylogenetic analysis and comparative bioinformatics are both valuable tools in identifying and validating the molecular initiating events that account for adverse developmental outcomes in humans. The discordance of susceptibility between test species and humans (ontogeny) reflects their differences in evolutionary history (phylogeny). This synthesis not only can lead to novel applications in developmental toxicity and risk assessment, but also can pave the way for applying an evo-devo perspective to the study of developmental origins of health and disease. PMID:28267574

Evolutionary model selection and parameter estimation for protein-protein interaction network based on differential evolution algorithm

PubMed Central

Huang, Lei; Liao, Li; Wu, Cathy H.

2016-01-01

Revealing the underlying evolutionary mechanism plays an important role in understanding protein interaction networks in the cell. While many evolutionary models have been proposed, the problem about applying these models to real network data, especially for differentiating which model can better describe evolutionary process for the observed network urgently remains as a challenge. The traditional way is to use a model with presumed parameters to generate a network, and then evaluate the fitness by summary statistics, which however cannot capture the complete network structures information and estimate parameter distribution. In this work we developed a novel method based on Approximate Bayesian Computation and modified Differential Evolution (ABC-DEP) that is capable of conducting model selection and parameter estimation simultaneously and detecting the underlying evolutionary mechanisms more accurately. We tested our method for its power in differentiating models and estimating parameters on the simulated data and found significant improvement in performance benchmark, as compared with a previous method. We further applied our method to real data of protein interaction networks in human and yeast. Our results show Duplication Attachment model as the predominant evolutionary mechanism for human PPI networks and Scale-Free model as the predominant mechanism for yeast PPI networks. PMID:26357273

Evolutionary perspectives on learning: conceptual and methodological issues in the study of adaptive specializations.

PubMed

Krause, Mark A

2015-07-01

Inquiry into evolutionary adaptations has flourished since the modern synthesis of evolutionary biology. Comparative methods, genetic techniques, and various experimental and modeling approaches are used to test adaptive hypotheses. In psychology, the concept of adaptation is broadly applied and is central to comparative psychology and cognition. The concept of an adaptive specialization of learning is a proposed account for exceptions to general learning processes, as seen in studies of Pavlovian conditioning of taste aversions, sexual responses, and fear. The evidence generally consists of selective associations forming between biologically relevant conditioned and unconditioned stimuli, with conditioned responses differing in magnitude, persistence, or other measures relative to non-biologically relevant stimuli. Selective associations for biologically relevant stimuli may suggest adaptive specializations of learning, but do not necessarily confirm adaptive hypotheses as conceived of in evolutionary biology. Exceptions to general learning processes do not necessarily default to an adaptive specialization explanation, even if experimental results "make biological sense". This paper examines the degree to which hypotheses of adaptive specializations of learning in sexual and fear response systems have been tested using methodologies developed in evolutionary biology (e.g., comparative methods, quantitative and molecular genetics, survival experiments). A broader aim is to offer perspectives from evolutionary biology for testing adaptive hypotheses in psychological science.

Genetic Regulatory Networks in Embryogenesis and Evolution

NASA Technical Reports Server (NTRS)

1998-01-01

The article introduces a series of papers that were originally presented at a workshop titled Genetic Regulatory Network in Embryogenesis and Evaluation. Contents include the following: evolution of cleavage programs in relationship to axial specification and body plan evolution, changes in cell lineage specification elucidate evolutionary relations in spiralia, axial patterning in the leech: developmental mechanisms and evolutionary implications, hox genes in arthropod development and evolution, heterochronic genes in development and evolution, a common theme for LIM homeobox gene function across phylogeny, and mechanisms of specification in ascidian embryos.

Multidimensional extended spatial evolutionary games.

PubMed

Krześlak, Michał; Świerniak, Andrzej

2016-02-01

The goal of this paper is to study the classical hawk-dove model using mixed spatial evolutionary games (MSEG). In these games, played on a lattice, an additional spatial layer is introduced for dependence on more complex parameters and simulation of changes in the environment. Furthermore, diverse polymorphic equilibrium points dependent on cell reproduction, model parameters, and their simulation are discussed. Our analysis demonstrates the sensitivity properties of MSEGs and possibilities for further development. We discuss applications of MSEGs, particularly algorithms for modelling cell interactions during the development of tumours. Copyright © 2015 Elsevier Ltd. All rights reserved.

Intelligent monitoring and diagnosis systems for the Space Station Freedom ECLSS

NASA Technical Reports Server (NTRS)

Dewberry, Brandon S.; Carnes, James R.

1991-01-01

Specific activities in NASA's environmental control and life support system (ECLSS) advanced automation project that is designed to minimize the crew and ground manpower needed for operations are discussed. Various analyses and the development of intelligent software for the initial and evolutionary Space Station Freedom (SSF) ECLSS are described. The following are also discussed: (1) intelligent monitoring and diagnostics applications under development for the ECLSS domain; (2) integration into the MSFC ECLSS hardware testbed; and (3) an evolutionary path from the baseline ECLSS automation to the more advanced ECLSS automation processes.

Using Nonlinear Stochastic Evolutionary Game Strategy to Model an Evolutionary Biological Network of Organ Carcinogenesis Under a Natural Selection Scheme

PubMed Central

Chen, Bor-Sen; Tsai, Kun-Wei; Li, Cheng-Wei

2015-01-01

Molecular biologists have long recognized carcinogenesis as an evolutionary process that involves natural selection. Cancer is driven by the somatic evolution of cell lineages. In this study, the evolution of somatic cancer cell lineages during carcinogenesis was modeled as an equilibrium point (ie, phenotype of attractor) shifting, the process of a nonlinear stochastic evolutionary biological network. This process is subject to intrinsic random fluctuations because of somatic genetic and epigenetic variations, as well as extrinsic disturbances because of carcinogens and stressors. In order to maintain the normal function (ie, phenotype) of an evolutionary biological network subjected to random intrinsic fluctuations and extrinsic disturbances, a network robustness scheme that incorporates natural selection needs to be developed. This can be accomplished by selecting certain genetic and epigenetic variations to modify the network structure to attenuate intrinsic fluctuations efficiently and to resist extrinsic disturbances in order to maintain the phenotype of the evolutionary biological network at an equilibrium point (attractor). However, during carcinogenesis, the remaining (or neutral) genetic and epigenetic variations accumulate, and the extrinsic disturbances become too large to maintain the normal phenotype at the desired equilibrium point for the nonlinear evolutionary biological network. Thus, the network is shifted to a cancer phenotype at a new equilibrium point that begins a new evolutionary process. In this study, the natural selection scheme of an evolutionary biological network of carcinogenesis was derived from a robust negative feedback scheme based on the nonlinear stochastic Nash game strategy. The evolvability and phenotypic robustness criteria of the evolutionary cancer network were also estimated by solving a Hamilton–Jacobi inequality – constrained optimization problem. The simulation revealed that the phenotypic shift of the lung cancer-associated cell network takes 54.5 years from a normal state to stage I cancer, 1.5 years from stage I to stage II cancer, and 2.5 years from stage II to stage III cancer, with a reasonable match for the statistical result of the average age of lung cancer. These results suggest that a robust negative feedback scheme, based on a stochastic evolutionary game strategy, plays a critical role in an evolutionary biological network of carcinogenesis under a natural selection scheme. PMID:26244004

Evolutionary Development of the Simulation by Logical Modeling System (SIBYL)

NASA Technical Reports Server (NTRS)

Wu, Helen

1995-01-01

Through the evolutionary development of the Simulation by Logical Modeling System (SIBYL) we have re-engineered the expensive and complex IBM mainframe based Long-term Hardware Projection Model (LHPM) to a robust cost-effective computer based mode that is easy to use. We achieved significant cost reductions and improved productivity in preparing long-term forecasts of Space Shuttle Main Engine (SSME) hardware. The LHPM for the SSME is a stochastic simulation model that projects the hardware requirements over 10 years. SIBYL is now the primary modeling tool for developing SSME logistics proposals and Program Operating Plan (POP) for NASA and divisional marketing studies.

ECOD: An Evolutionary Classification of Protein Domains

PubMed Central

Kinch, Lisa N.; Pei, Jimin; Shi, Shuoyong; Kim, Bong-Hyun; Grishin, Nick V.

2014-01-01

Understanding the evolution of a protein, including both close and distant relationships, often reveals insight into its structure and function. Fast and easy access to such up-to-date information facilitates research. We have developed a hierarchical evolutionary classification of all proteins with experimentally determined spatial structures, and presented it as an interactive and updatable online database. ECOD (Evolutionary Classification of protein Domains) is distinct from other structural classifications in that it groups domains primarily by evolutionary relationships (homology), rather than topology (or “fold”). This distinction highlights cases of homology between domains of differing topology to aid in understanding of protein structure evolution. ECOD uniquely emphasizes distantly related homologs that are difficult to detect, and thus catalogs the largest number of evolutionary links among structural domain classifications. Placing distant homologs together underscores the ancestral similarities of these proteins and draws attention to the most important regions of sequence and structure, as well as conserved functional sites. ECOD also recognizes closer sequence-based relationships between protein domains. Currently, approximately 100,000 protein structures are classified in ECOD into 9,000 sequence families clustered into close to 2,000 evolutionary groups. The classification is assisted by an automated pipeline that quickly and consistently classifies weekly releases of PDB structures and allows for continual updates. This synchronization with PDB uniquely distinguishes ECOD among all protein classifications. Finally, we present several case studies of homologous proteins not recorded in other classifications, illustrating the potential of how ECOD can be used to further biological and evolutionary studies. PMID:25474468

ECOD: an evolutionary classification of protein domains.

PubMed

Cheng, Hua; Schaeffer, R Dustin; Liao, Yuxing; Kinch, Lisa N; Pei, Jimin; Shi, Shuoyong; Kim, Bong-Hyun; Grishin, Nick V

2014-12-01

Understanding the evolution of a protein, including both close and distant relationships, often reveals insight into its structure and function. Fast and easy access to such up-to-date information facilitates research. We have developed a hierarchical evolutionary classification of all proteins with experimentally determined spatial structures, and presented it as an interactive and updatable online database. ECOD (Evolutionary Classification of protein Domains) is distinct from other structural classifications in that it groups domains primarily by evolutionary relationships (homology), rather than topology (or "fold"). This distinction highlights cases of homology between domains of differing topology to aid in understanding of protein structure evolution. ECOD uniquely emphasizes distantly related homologs that are difficult to detect, and thus catalogs the largest number of evolutionary links among structural domain classifications. Placing distant homologs together underscores the ancestral similarities of these proteins and draws attention to the most important regions of sequence and structure, as well as conserved functional sites. ECOD also recognizes closer sequence-based relationships between protein domains. Currently, approximately 100,000 protein structures are classified in ECOD into 9,000 sequence families clustered into close to 2,000 evolutionary groups. The classification is assisted by an automated pipeline that quickly and consistently classifies weekly releases of PDB structures and allows for continual updates. This synchronization with PDB uniquely distinguishes ECOD among all protein classifications. Finally, we present several case studies of homologous proteins not recorded in other classifications, illustrating the potential of how ECOD can be used to further biological and evolutionary studies.

Evolutionary branching under multi-dimensional evolutionary constraints.

PubMed

Ito, Hiroshi; Sasaki, Akira

2016-10-21

The fitness of an existing phenotype and of a potential mutant should generally depend on the frequencies of other existing phenotypes. Adaptive evolution driven by such frequency-dependent fitness functions can be analyzed effectively using adaptive dynamics theory, assuming rare mutation and asexual reproduction. When possible mutations are restricted to certain directions due to developmental, physiological, or physical constraints, the resulting adaptive evolution may be restricted to subspaces (constraint surfaces) with fewer dimensionalities than the original trait spaces. To analyze such dynamics along constraint surfaces efficiently, we develop a Lagrange multiplier method in the framework of adaptive dynamics theory. On constraint surfaces of arbitrary dimensionalities described with equality constraints, our method efficiently finds local evolutionarily stable strategies, convergence stable points, and evolutionary branching points. We also derive the conditions for the existence of evolutionary branching points on constraint surfaces when the shapes of the surfaces can be chosen freely. Copyright © 2016 Elsevier Ltd. All rights reserved.

Asymmetric Evolutionary Games.

PubMed

McAvoy, Alex; Hauert, Christoph

2015-08-01

Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner's Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games.

Analysis of convergence of an evolutionary algorithm with self-adaptation using a stochastic Lyapunov function.

PubMed

Semenov, Mikhail A; Terkel, Dmitri A

2003-01-01

This paper analyses the convergence of evolutionary algorithms using a technique which is based on a stochastic Lyapunov function and developed within the martingale theory. This technique is used to investigate the convergence of a simple evolutionary algorithm with self-adaptation, which contains two types of parameters: fitness parameters, belonging to the domain of the objective function; and control parameters, responsible for the variation of fitness parameters. Although both parameters mutate randomly and independently, they converge to the "optimum" due to the direct (for fitness parameters) and indirect (for control parameters) selection. We show that the convergence velocity of the evolutionary algorithm with self-adaptation is asymptotically exponential, similar to the velocity of the optimal deterministic algorithm on the class of unimodal functions. Although some martingale inequalities have not be proved analytically, they have been numerically validated with 0.999 confidence using Monte-Carlo simulations.

Under pressure: evolutionary engineering of yeast strains for improved performance in fuels and chemicals production.

PubMed

Mans, Robert; Daran, Jean-Marc G; Pronk, Jack T

2018-04-01

Evolutionary engineering, which uses laboratory evolution to select for industrially relevant traits, is a popular strategy in the development of high-performing yeast strains for industrial production of fuels and chemicals. By integrating whole-genome sequencing, bioinformatics, classical genetics and genome-editing techniques, evolutionary engineering has also become a powerful approach for identification and reverse engineering of molecular mechanisms that underlie industrially relevant traits. New techniques enable acceleration of in vivo mutation rates, both across yeast genomes and at specific loci. Recent studies indicate that phenotypic trade-offs, which are often observed after evolution under constant conditions, can be mitigated by using dynamic cultivation regimes. Advances in research on synthetic regulatory circuits offer exciting possibilities to extend the applicability of evolutionary engineering to products of yeasts whose synthesis requires a net input of cellular energy. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Fitness costs and benefits of novel herbicide tolerance in a noxious weed

PubMed Central

Baucom, Regina S.; Mauricio, Rodney

2004-01-01

Glyphosate, the active ingredient in the herbicide RoundUp, has increased dramatically in use over the past decade and constitutes a potent anthropogenic source of selection. In the southeastern United States, weedy morning glories have begun to develop tolerance to glyphosate, representing a unique opportunity to examine the evolutionary genetics of a novel trait. We found genetic variation for tolerance, indicating the potential for the population to respond to selection by glyphosate. However, the following significant evolutionary constraint exists: in the absence of glyphosate, tolerant genotypes produced fewer seeds than susceptible genotypes. The combination of strong positive directional selection in the presence of glyphosate and strong negative directional selection in its absence may indicate that the selective landscape of land use could drive the evolutionary trajectory of glyphosate tolerance. Understanding these evolutionary forces is imperative for devising comprehensive management strategies to help slow the rate of the evolution of tolerance. PMID:15326309

Selection on Network Dynamics Drives Differential Rates of Protein Domain Evolution

PubMed Central

Mannakee, Brian K.; Gutenkunst, Ryan N.

2016-01-01

The long-held principle that functionally important proteins evolve slowly has recently been challenged by studies in mice and yeast showing that the severity of a protein knockout only weakly predicts that protein’s rate of evolution. However, the relevance of these studies to evolutionary changes within proteins is unknown, because amino acid substitutions, unlike knockouts, often only slightly perturb protein activity. To quantify the phenotypic effect of small biochemical perturbations, we developed an approach to use computational systems biology models to measure the influence of individual reaction rate constants on network dynamics. We show that this dynamical influence is predictive of protein domain evolutionary rate within networks in vertebrates and yeast, even after controlling for expression level and breadth, network topology, and knockout effect. Thus, our results not only demonstrate the importance of protein domain function in determining evolutionary rate, but also the power of systems biology modeling to uncover unanticipated evolutionary forces. PMID:27380265

Incorporating evolutionary processes into population viability models.

PubMed

Pierson, Jennifer C; Beissinger, Steven R; Bragg, Jason G; Coates, David J; Oostermeijer, J Gerard B; Sunnucks, Paul; Schumaker, Nathan H; Trotter, Meredith V; Young, Andrew G

2015-06-01

We examined how ecological and evolutionary (eco-evo) processes in population dynamics could be better integrated into population viability analysis (PVA). Complementary advances in computation and population genomics can be combined into an eco-evo PVA to offer powerful new approaches to understand the influence of evolutionary processes on population persistence. We developed the mechanistic basis of an eco-evo PVA using individual-based models with individual-level genotype tracking and dynamic genotype-phenotype mapping to model emergent population-level effects, such as local adaptation and genetic rescue. We then outline how genomics can allow or improve parameter estimation for PVA models by providing genotypic information at large numbers of loci for neutral and functional genome regions. As climate change and other threatening processes increase in rate and scale, eco-evo PVAs will become essential research tools to evaluate the effects of adaptive potential, evolutionary rescue, and locally adapted traits on persistence. © 2014 Society for Conservation Biology.

Evolving political science. Biological adaptation, rational action, and symbolism.

PubMed

Tingley, Dustin

2006-01-01

Political science, as a discipline, has been reluctant to adopt theories and methodologies developed in fields studying human behavior from an evolutionary standpoint. I ask whether evolutionary concepts are reconcilable with standard political-science theories and whether those concepts help solve puzzles to which these theories classically are applied. I find that evolutionary concepts readily and simultaneously accommodate theories of rational choice, symbolism, interpretation, and acculturation. Moreover, phenomena perennially hard to explain in standard political science become clearer when human interactions are understood in light of natural selection and evolutionary psychology. These phenomena include the political and economic effects of emotion, status, personal attractiveness, and variations in information-processing and decision-making under uncertainty; exemplary is the use of "focal points" in multiple-equilibrium games. I conclude with an overview of recent research by, and ongoing debates among, scholars analyzing politics in evolutionarily sophisticated terms.

Evolutionary ethics from Darwin to Moore.

PubMed

Allhoff, Fritz

2003-01-01

Evolutionary ethics has a long history, dating all the way back to Charles Darwin. Almost immediately after the publication of the Origin, an immense interest arose in the moral implications of Darwinism and whether the truth of Darwinism would undermine traditional ethics. Though the biological thesis was certainly exciting, nobody suspected that the impact of the Origin would be confined to the scientific arena. As one historian wrote, 'whether or not ancient populations of armadillos were transformed into the species that currently inhabit the new world was certainly a topic about which zoologists could disagree. But it was in discussing the broader implications of the theory...that tempers flared and statements were made which could transform what otherwise would have been a quiet scholarly meeting into a social scandal' (Farber 1994, 22). Some resistance to the biological thesis of Darwinism sprung from the thought that it was incompatible with traditional morality and, since one of them had to go, many thought that Darwinism should be rejected. However, some people did realize that a secular ethics was possible so, even if Darwinism did undermine traditional religious beliefs, it need not have any effects on moral thought. Before I begin my discussion of evolutionary ethics from Darwin to Moore, I would like to make some more general remarks about its development. There are three key events during this history of evolutionary ethics. First, Charles Darwin published On the Origin of the Species (Darwin 1859). Since one did not have a fully developed theory of evolution until 1859, there exists little work on evolutionary ethics until then. Shortly thereafter, Herbert Spencer (1898) penned the first systematic theory of evolutionary ethics, which was promptly attacked by T.H. Huxley (Huxley 1894). Second, at about the turn of the century, moral philosophers entered the fray and attempted to demonstrate logical errors in Spencer's work; such errors were alluded to but never fully brought to the fore by Huxley. These philosophers were the well known moralists from Cambridge: Henry Sidgwick (Sidgwick 1902, 1907) and G.E. Moore (Moore 1903), though their ideas hearkened back to David Hume (Hume 1960). These criticisms were so strong that the industry of evolutionary ethics was largely abandoned (though with some exceptions) for many years. Third, E.O. Wilson, a Harvard entomologist, published Sociobiology: The New Synthesis in 1975 (Wilson E.O. 1975), which sparked renewed interest in evolutionary ethics and offered new directions of investigation. These events suggest the following stages for the history of evolutionary ethics: development, criticism and abandonment, revival. In this paper, I shall focus on the first two stages, since those are the ones on which the philosophical merits have already been largely decided. The revival stage is still in progress and we shall eventually find out whether it was a success.

Transmissible cancers in an evolutionary context.

PubMed

Ujvari, Beata; Papenfuss, Anthony T; Belov, Katherine

2016-07-01

Cancer is an evolutionary and ecological process in which complex interactions between tumour cells and their environment share many similarities with organismal evolution. Tumour cells with highest adaptive potential have a selective advantage over less fit cells. Naturally occurring transmissible cancers provide an ideal model system for investigating the evolutionary arms race between cancer cells and their surrounding micro-environment and macro-environment. However, the evolutionary landscapes in which contagious cancers reside have not been subjected to comprehensive investigation. Here, we provide a multifocal analysis of transmissible tumour progression and discuss the selection forces that shape it. We demonstrate that transmissible cancers adapt to both their micro-environment and macro-environment, and evolutionary theories applied to organisms are also relevant to these unique diseases. The three naturally occurring transmissible cancers, canine transmissible venereal tumour (CTVT) and Tasmanian devil facial tumour disease (DFTD) and the recently discovered clam leukaemia, exhibit different evolutionary phases: (i) CTVT, the oldest naturally occurring cell line is remarkably stable; (ii) DFTD exhibits the signs of stepwise cancer evolution; and (iii) clam leukaemia shows genetic instability. While all three contagious cancers carry the signature of ongoing and fairly recent adaptations to selective forces, CTVT appears to have reached an evolutionary stalemate with its host, while DFTD and the clam leukaemia appear to be still at a more dynamic phase of their evolution. Parallel investigation of contagious cancer genomes and transcriptomes and of their micro-environment and macro-environment could shed light on the selective forces shaping tumour development at different time points: during the progressive phase and at the endpoint. A greater understanding of transmissible cancers from an evolutionary ecology perspective will provide novel avenues for the prevention and treatment of both contagious and non-communicable cancers. © 2016 The Authors. BioEssays published by WILEY Periodicals, Inc.

Sex-Specific Pathways to Early Puberty, Sexual Debut, and Sexual Risk Taking: Tests of an Integrated Evolutionary-Developmental Model

ERIC Educational Resources Information Center

James, Jenee; Ellis, Bruce J.; Schlomer, Gabriel L.; Garber, Judy

2012-01-01

The current study tested sex-specific pathways to early puberty, sexual debut, and sexual risk taking, as specified by an integrated evolutionary-developmental model of adolescent sexual development and behavior. In a prospective study of 238 adolescents (n = 129 girls and n = 109 boys) followed from approximately 12-18 years of age, we tested for…

[Participation of insulin in regulating the metabolism of marine bivalve mollusks].

PubMed

Plisetskaia, E M; Soltitskaia, L P; Leĭbson, L G

1979-01-01

Marine bivalve molluscs, the mussel Mytilus galloprovincialis aud the scallop Chlamys (Flexopecten) glaber ponticus, have been injected (intramuscularly or in the haemolymph) with glucose, mammalian insulin, insulin (or insulin-like substance) from molluscs, and anti-insulin serum, checking changes in glucose and fatty acid content of the haemolymph as well as in the content of glycogen and the activity of glycogen synthetase in muscles. After glucose injections, studies were also made on the level of IRI in the haemolymph. Comparison of the data obtained in the present work with those reported earlier for freshwater bivalve molluscs suggests that: 1) metabolic shifts induced by anti-insulin serum are more rapid in vigorous scallops than in sedentary mussels; 2) molluscan insulin (or insulin-like substance) exerts the same effect on metabolic parameters of the molluscs, as mammalian insulin exerts in vertebrates.

Geologic and molluscan evidence for a previously misunderstood late pleistocene, cool water, open coast terrace at Newport Bay, Southern California

USGS Publications Warehouse

Powell, C.L.

2001-01-01

A macro-invertebrate fauna from a 7 m elevation terrace remnant on the front of the Newport Mesa contains 63 mollusks, 58 specifically identified. These taxa represent a mixed death assemblage similar to that seen on rocky terrace platforms at intertidal depths in southern to central California today. The extralimital northern bivalve Macoma inquinala (Carpenter) and gastropods Tectura sp., cf. T. persona (Rathke), and Tegula montereyi (Kiener) suggest slightly cooler water temperatures than present today. These extralimital cool-water taxa, along with the terrace's geomorphic position in the palisades along the front of Newport Mesa, below other mapped terraces, separate it from the well known first terrace and its associated warm-water fauna recognized by previous authors, and suggest a younger age than the first terrace around Newport Bay.

Two new turrid species (Gastropoda: Pseudomelatomidae) from the Palawan region, the Philippines.

PubMed

Stahlschmidt, Peter; Fraussen, Koen

2014-03-26

Species richness of tropical marine molluscs is considerably underestimated (Bouchet et al. 2002). Indeed, the molluscan faunas of some regions, such as Palawan in the western Pacific, have received little attention and some hyper-diverse groups, such as the turrids (a parapyhletic group of Conoidea, formerly known as Turridae), are barely documented. For example, apart from original descriptions of two turrid taxa that have their type locations in Palawan (Comitas aequatorialis palawanica Powell, 1969 and Mangilia quadrasi Boettger, 1895 = Gingicithara notabilis (E. A. Smith, 1888)), there are no published records of turrids from this region. We have been fortunate to have access to recent collections of turrids from different parts of Palawan. Examination of these materials has revealed existence of several undescribed and potentially endemic species. In the present paper two new Pseudomelatomidae species are described.

The Brain in its Body: Motor Control and Sensing in a Biomechanical Context

PubMed Central

Chiel, Hillel J.; Ting, Lena H.; Ekeberg, Orjan; Hartmann, Mitra J. Z.

2009-01-01

Although it is widely recognized that adaptive behavior emerges from the ongoing interactions among the nervous system, the body, and the environment, it has only become possible in recent years to experimentally study and to simulate these interacting systems. We briefly review work on molluscan feeding, maintenance of postural control in cats and humans, simulations of locomotion in lamprey, insect, cat and salamander, and active vibrissal sensing in rats to illustrate the insights that can be derived from studies of neural control and sensing within a biomechanical context. These studies illustrate that control may be shared between the nervous system and the periphery, that neural activity organizes degrees of freedom into biomechanically meaningful subsets, that mechanics alone may play crucial roles in enforcing gait patterns, and that mechanics of sensors is crucial for their function. PMID:19828793

Pliocene Invertebrates From the Travertine Point Outcrop of the Imperial Formation, Imperial County, California

USGS Publications Warehouse

Powell, Charles L.

2008-01-01

Forty-four invertebrate taxa, including one coral, 40 mollusks (30 bivalves and 10 gastropods), and three echinoids are recognized from a thin marine interval of the Imperial Formation near Travertine Point, Imperial County, California. The Travertine Point outcrop lies about midway between exposures of the Imperial Formation around Palm Springs, Riverside County, and exposures centered at Coyote Mountain in Imperial and San Diego Counties. Based on faunal comparisons, the Travertine Point outcrop corresponds to the Imperial and San Diego outcrops. The Travertine Point fauna is inferred to have lived in subtropical to tropical waters at littoral to inner sublittorial (<50 m) water depths. Coral and molluscan species from the Travertine Point outcrop indicate a Pliocene age. Two extant bivalve mollusks present have not previously been reported as fossils Anadara reinharti and forms questionably referred to Dosinia semiobliterata.

Zinc treatment of the digestive gland of the slug Arion ater L. 1. Cellular distribution of zinc and calcium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Recio, A.; Marigomez, J.A.; Angulo, E.

1988-12-01

Extensive literature has been published on the molluscan capability for metal bioaccumulation. As a consequence, a variety of species have been proposed for environmental pollution biomonitoring. The knowledge of biological mechanisms of accumulation and elimination of environmental pollutants is essential to get a proper use of bioindicator species. Histological procedures may indicate (a) the events involved in the metabolic regulation of pollutant bioavailability and release and (b) their specific toxic effects. The relevance of the digestive gland as a major site for Zn accumulation has been reported. The Zn distribution in this organ might indicate the level of environmental bioavailablemore » Zn. The present study is a histochemical investigation of the distribution and release of zinc by the different cell types of the digestive gland of A. ater.« less

The Stochastic Evolutionary Game for a Population of Biological Networks Under Natural Selection

PubMed Central

Chen, Bor-Sen; Ho, Shih-Ju

2014-01-01

In this study, a population of evolutionary biological networks is described by a stochastic dynamic system with intrinsic random parameter fluctuations due to genetic variations and external disturbances caused by environmental changes in the evolutionary process. Since information on environmental changes is unavailable and their occurrence is unpredictable, they can be considered as a game player with the potential to destroy phenotypic stability. The biological network needs to develop an evolutionary strategy to improve phenotypic stability as much as possible, so it can be considered as another game player in the evolutionary process, ie, a stochastic Nash game of minimizing the maximum network evolution level caused by the worst environmental disturbances. Based on the nonlinear stochastic evolutionary game strategy, we find that some genetic variations can be used in natural selection to construct negative feedback loops, efficiently improving network robustness. This provides larger genetic robustness as a buffer against neutral genetic variations, as well as larger environmental robustness to resist environmental disturbances and maintain a network phenotypic traits in the evolutionary process. In this situation, the robust phenotypic traits of stochastic biological networks can be more frequently selected by natural selection in evolution. However, if the harbored neutral genetic variations are accumulated to a sufficiently large degree, and environmental disturbances are strong enough that the network robustness can no longer confer enough genetic robustness and environmental robustness, then the phenotype robustness might break down. In this case, a network phenotypic trait may be pushed from one equilibrium point to another, changing the phenotypic trait and starting a new phase of network evolution through the hidden neutral genetic variations harbored in network robustness by adaptive evolution. Further, the proposed evolutionary game is extended to an n-tuple evolutionary game of stochastic biological networks with m players (competitive populations) and k environmental dynamics. PMID:24558296

Maternal source of variability in the embryo development of an annual killifish.

PubMed

Polačik, M; Smith, C; Reichard, M

2017-04-01

Organisms inhabiting unpredictable environments often evolve diversified reproductive bet-hedging strategies, expressed as production of multiple offspring phenotypes, thereby avoiding complete reproductive failure. To cope with unpredictable rainfall, African annual killifish from temporary savannah pools lay drought-resistant eggs that vary widely in the duration of embryo development. We examined the sources of variability in the duration of individual embryo development, egg production and fertilization rate in Nothobranchius furzeri. Using a quantitative genetics approach (North Carolina type II design), we found support for maternal effects rather than polyandrous mating as the primary source of the variability in the duration of embryo development. The number of previously laid eggs appeared to serve as an internal physiological cue initiating a shift from rapid-to-slow embryo developmental mode. In annual killifish, extensive phenotypic variability in progeny traits is adaptive, as the conditions experienced by parents have limited relevance to the offspring generation. In contrast to genetic control, with high phenotypic expression and heritability, maternal control of traits under natural selection prevents standing genetic diversity from potentially detrimental effects of selection in fluctuating environments. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Development of a sensitive and selective liquid chromatography-mass spectrometry method for high throughput analysis of paralytic shellfish toxins using graphitised carbon solid phase extraction.

PubMed

Boundy, Michael J; Selwood, Andrew I; Harwood, D Tim; McNabb, Paul S; Turner, Andrew D

2015-03-27

Routine regulatory monitoring of paralytic shellfish toxins (PST) commonly employs oxidative derivitisation and complex liquid chromatography fluorescence detection methods (LC-FL). The pre-column oxidation LC-FL method is currently implemented in New Zealand and the United Kingdom. When using this method positive samples are fractionated and two different oxidations are required to confirm the identity and quantity of each PST analogue present. There is a need for alternative methods that are simpler, provide faster turnaround times and have improved detection limits. Hydrophilic interaction liquid chromatography (HILIC) HPLC-MS/MS analysis of PST has been used for research purposes, but high detection limits and substantial sample matrix issues have prevented it from becoming a viable alternative for routine monitoring purposes. We have developed a HILIC UPLC-MS/MS method for paralytic shellfish toxins with an optimised desalting clean-up procedure on inexpensive carbon solid phase extraction cartridges for reduction of matrix interferences. This represents a major technical breakthrough and allows sensitive, selective and rapid analysis of paralytic shellfish toxins from a variety of sample types, including many commercially produced bivalve molluscan shellfish species. Additionally, this analytical approach avoids the need for complex calculations to determine sample toxicity, as unlike other methods each PST analogue is able to be quantified as a single resolved peak. This article presents the method development and optimisation information. A thorough single laboratory validation study has subsequently been performed and this data will be presented elsewhere. Copyright © 2015 Elsevier B.V. All rights reserved.

A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel, Limnoperna fortunei

PubMed Central

Uliano-Silva, Marcela; Dondero, Francesco; Dan Otto, Thomas; Costa, Igor; Lima, Nicholas Costa Barroso; Americo, Juliana Alves; Mazzoni, Camila Junqueira; Prosdocimi, Francisco; Rebelo, Mauro de Freitas

2018-01-01

Abstract Background For more than 25 years, the golden mussel, Limnoperna fortunei, has aggressively invaded South American freshwaters, having travelled more than 5000 km upstream across 5 countries. Along the way, the golden mussel has outcompeted native species and economically harmed aquaculture, hydroelectric powers, and ship transit. We have sequenced the complete genome of the golden mussel to understand the molecular basis of its invasiveness and search for ways to control it. Findings We assembled the 1.6-Gb genome into 20 548 scaffolds with an N50 length of 312 Kb using a hybrid and hierarchical assembly strategy from short and long DNA reads and transcriptomes. A total of 60 717 coding genes were inferred from a customized transcriptome-trained AUGUSTUS run. We also compared predicted protein sets with those of complete molluscan genomes, revealing an exacerbation of protein-binding domains in L. fortunei. Conclusions We built one of the best bivalve genome assemblies available using a cost-effective approach using Illumina paired-end, mate-paired, and PacBio long reads. We expect that the continuous and careful annotation of L. fortunei’s genome will contribute to the investigation of bivalve genetics, evolution, and invasiveness, as well as to the development of biotechnological tools for aquatic pest control. PMID:29267857

Managing marine mollusc diseases in the context of regional and international commerce: policy issues and emerging concerns.

PubMed

Carnegie, Ryan B; Arzul, Isabelle; Bushek, David

2016-03-05

Marine mollusc production contributes to food and economic security worldwide and provides valuable ecological services, yet diseases threaten these industries and wild populations. Although the infrastructure for mollusc aquaculture health management is well characterized, its foundations are not without flaws. Use of notifiable pathogen lists can leave blind spots with regard to detection of unlisted and emerging pathogens. Increased reliance on molecular tools has come without similar attention to diagnostic validation, raising questions about assay performance, and has been accompanied by a reduced emphasis on microscopic diagnostic expertise that could weaken pathogen detection capabilities. Persistent questions concerning pathogen biology and ecology promote regulatory paralysis that impedes trade and which could weaken biosecurity by driving commerce to surreptitious channels. Solutions that might be pursued to improve shellfish aquaculture health management include the establishment of more broad-based surveillance programmes, wider training and use of general methods like histopathology to ensure alertness to emerging diseases, an increased focus on assay assessment and validation as fundamental to assay development, investment in basic research, and application of risk analyses to improve regulation. A continual sharpening of diagnostic tools and approaches and deepening of scientific knowledge is necessary to manage diseases and promote sustainable molluscan shellfish industries. © 2016 The Author(s).

Ultrastructure developments during spermiogenesis in Polydora ciliata (Annelida: Spionidae), a parasite of mollusca

NASA Astrophysics Data System (ADS)

Gao, Yan; Zhang, Tao; Zhang, Libin; Qiu, Tianlong; Xue, Dongxiu; Yang, Hongsheng

2014-12-01

Spionid worms of Polydora ciliata inhabit the shells of many commercially important bivalves and cause disease in molluscan aquaculture. Their sperm structure is closely related to their fertilization method. To give an insight into the sperm structure and spermatogenesis, ultrastructure details of the subcellular components of germ cells during spermiogenesis of Polydora ciliata are detected by transmission electron microscopy (TEM). In P. ciliata, during spermiogenesis, chromatin is regularly arranged as dense fibrils and becomes more condensed when the nucleus elongates. Microtubules do not surround the nucleus during its elongation. The Golgi phase is characterized by the formation of proacrosomal granules within the Golgi apparatus. The proacrosomal granules fuse to form a single, spherical acrosomal vesicle that migrates to the anterior pole of the cell. At the time of nuclear condensation, mitochondria become reduced in number but increased in size, causing deep indentation at the base of the nucleus. The mid-piece has a few mitochondria. The cap phase includes the spreading of the acrosomal granule over the surface of the nucleus of the differentiating spermatid. The acrosomal phase of spermiogenesis is typically associated with changes in the shape of the nucleus, acrosome and tail. The relationship of sperm ultrastructure to spermiogenesis in spionidae species was discussed.

Managing marine mollusc diseases in the context of regional and international commerce: policy issues and emerging concerns

PubMed Central

Carnegie, Ryan B.; Arzul, Isabelle; Bushek, David

2016-01-01

Marine mollusc production contributes to food and economic security worldwide and provides valuable ecological services, yet diseases threaten these industries and wild populations. Although the infrastructure for mollusc aquaculture health management is well characterized, its foundations are not without flaws. Use of notifiable pathogen lists can leave blind spots with regard to detection of unlisted and emerging pathogens. Increased reliance on molecular tools has come without similar attention to diagnostic validation, raising questions about assay performance, and has been accompanied by a reduced emphasis on microscopic diagnostic expertise that could weaken pathogen detection capabilities. Persistent questions concerning pathogen biology and ecology promote regulatory paralysis that impedes trade and which could weaken biosecurity by driving commerce to surreptitious channels. Solutions that might be pursued to improve shellfish aquaculture health management include the establishment of more broad-based surveillance programmes, wider training and use of general methods like histopathology to ensure alertness to emerging diseases, an increased focus on assay assessment and validation as fundamental to assay development, investment in basic research, and application of risk analyses to improve regulation. A continual sharpening of diagnostic tools and approaches and deepening of scientific knowledge is necessary to manage diseases and promote sustainable molluscan shellfish industries. PMID:26880834

A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel, Limnoperna fortunei.

PubMed

Uliano-Silva, Marcela; Dondero, Francesco; Dan Otto, Thomas; Costa, Igor; Lima, Nicholas Costa Barroso; Americo, Juliana Alves; Mazzoni, Camila Junqueira; Prosdocimi, Francisco; Rebelo, Mauro de Freitas

2018-02-01

For more than 25 years, the golden mussel, Limnoperna fortunei, has aggressively invaded South American freshwaters, having travelled more than 5000 km upstream across 5 countries. Along the way, the golden mussel has outcompeted native species and economically harmed aquaculture, hydroelectric powers, and ship transit. We have sequenced the complete genome of the golden mussel to understand the molecular basis of its invasiveness and search for ways to control it. We assembled the 1.6-Gb genome into 20 548 scaffolds with an N50 length of 312 Kb using a hybrid and hierarchical assembly strategy from short and long DNA reads and transcriptomes. A total of 60 717 coding genes were inferred from a customized transcriptome-trained AUGUSTUS run. We also compared predicted protein sets with those of complete molluscan genomes, revealing an exacerbation of protein-binding domains in L. fortunei. We built one of the best bivalve genome assemblies available using a cost-effective approach using Illumina paired-end, mate-paired, and PacBio long reads. We expect that the continuous and careful annotation of L. fortunei's genome will contribute to the investigation of bivalve genetics, evolution, and invasiveness, as well as to the development of biotechnological tools for aquatic pest control.

How evolutionary crystal structure prediction works--and why.

PubMed

Oganov, Artem R; Lyakhov, Andriy O; Valle, Mario

2011-03-15

Once the crystal structure of a chemical substance is known, many properties can be predicted reliably and routinely. Therefore if researchers could predict the crystal structure of a material before it is synthesized, they could significantly accelerate the discovery of new materials. In addition, the ability to predict crystal structures at arbitrary conditions of pressure and temperature is invaluable for the study of matter at extreme conditions, where experiments are difficult. Crystal structure prediction (CSP), the problem of finding the most stable arrangement of atoms given only the chemical composition, has long remained a major unsolved scientific problem. Two problems are entangled here: search, the efficient exploration of the multidimensional energy landscape, and ranking, the correct calculation of relative energies. For organic crystals, which contain a few molecules in the unit cell, search can be quite simple as long as a researcher does not need to include many possible isomers or conformations of the molecules; therefore ranking becomes the main challenge. For inorganic crystals, quantum mechanical methods often provide correct relative energies, making search the most critical problem. Recent developments provide useful practical methods for solving the search problem to a considerable extent. One can use simulated annealing, metadynamics, random sampling, basin hopping, minima hopping, and data mining. Genetic algorithms have been applied to crystals since 1995, but with limited success, which necessitated the development of a very different evolutionary algorithm. This Account reviews CSP using one of the major techniques, the hybrid evolutionary algorithm USPEX (Universal Structure Predictor: Evolutionary Xtallography). Using recent developments in the theory of energy landscapes, we unravel the reasons evolutionary techniques work for CSP and point out their limitations. We demonstrate that the energy landscapes of chemical systems have an overall shape and explore their intrinsic dimensionalities. Because of the inverse relationships between order and energy and between the dimensionality and diversity of an ensemble of crystal structures, the chances that a random search will find the ground state decrease exponentially with increasing system size. A well-designed evolutionary algorithm allows for much greater computational efficiency. We illustrate the power of evolutionary CSP through applications that examine matter at high pressure, where new, unexpected phenomena take place. Evolutionary CSP has allowed researchers to make unexpected discoveries such as a transparent phase of sodium, a partially ionic form of boron, complex superconducting forms of calcium, a novel superhard allotrope of carbon, polymeric modifications of nitrogen, and a new class of compounds, perhydrides. These methods have also led to the discovery of novel hydride superconductors including the "impossible" LiH(n) (n=2, 6, 8) compounds, and CaLi(2). We discuss extensions of the method to molecular crystals, systems of variable composition, and the targeted optimization of specific physical properties. © 2011 American Chemical Society

Comparative Transcriptomes and EVO-DEVO Studies Depending on Next Generation Sequencing.

PubMed

Liu, Tiancheng; Yu, Lin; Liu, Lei; Li, Hong; Li, Yixue

2015-01-01

High throughput technology has prompted the progressive omics studies, including genomics and transcriptomics. We have reviewed the improvement of comparative omic studies, which are attributed to the high throughput measurement of next generation sequencing technology. Comparative genomics have been successfully applied to evolution analysis while comparative transcriptomics are adopted in comparison of expression profile from two subjects by differential expression or differential coexpression, which enables their application in evolutionary developmental biology (EVO-DEVO) studies. EVO-DEVO studies focus on the evolutionary pressure affecting the morphogenesis of development and previous works have been conducted to illustrate the most conserved stages during embryonic development. Old measurements of these studies are based on the morphological similarity from macro view and new technology enables the micro detection of similarity in molecular mechanism. Evolutionary model of embryo development, which includes the "funnel-like" model and the "hourglass" model, has been evaluated by combination of these new comparative transcriptomic methods with prior comparative genomic information. Although the technology has promoted the EVO-DEVO studies into a new era, technological and material limitation still exist and further investigations require more subtle study design and procedure.

On evolutionary systems.

PubMed

Alvarez de Lorenzana, J M; Ward, L M

1987-01-01

This paper develops a metatheoretical framework for understanding evolutionary systems (systems that develop in ways that increase their own variety). The framework addresses shortcomings seen in other popular systems theories. It concerns both living and nonliving systems, and proposes a metahierarchy of hierarchical systems. Thus, it potentially addresses systems at all descriptive levels. We restrict our definition of system to that of a core system whose parts have a different ontological status than the system, and characterize the core system in terms of five global properties: minimal length interval, minimal time interval, system cycle, total receptive capacity, and system potential. We propose two principles through the interaction of which evolutionary systems develop. The Principle of Combinatorial Expansion describes how a core system realizes its developmental potential through a process of progressive differentiation of the single primal state up to a limit stage. The Principle of Generative Condensation describes how the components of the last stage of combinatorial expansion condense and become the environment for and components of new, enriched systems. The early evolution of the Universe after the "big bang" is discussed in light of these ideas as an example of the application of the framework.

The Ancient Evolutionary History of Polyomaviruses

PubMed Central

Buck, Christopher B.; Van Doorslaer, Koenraad; Peretti, Alberto; Geoghegan, Eileen M.; Tisza, Michael J.; An, Ping; Katz, Joshua P.; Pipas, James M.; McBride, Alison A.; Camus, Alvin C.; McDermott, Alexa J.; Dill, Jennifer A.; Delwart, Eric; Ng, Terry F. F.; Farkas, Kata; Austin, Charlotte; Kraberger, Simona; Davison, William; Pastrana, Diana V.; Varsani, Arvind

2016-01-01

Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae. PMID:27093155

Phylogenetics.

PubMed

Sleator, Roy D

2011-04-01

The recent rapid expansion in the DNA and protein databases, arising from large-scale genomic and metagenomic sequence projects, has forced significant development in the field of phylogenetics: the study of the evolutionary relatedness of the planet's inhabitants. Advances in phylogenetic analysis have greatly transformed our view of the landscape of evolutionary biology, transcending the view of the tree of life that has shaped evolutionary theory since Darwinian times. Indeed, modern phylogenetic analysis no longer focuses on the restricted Darwinian-Mendelian model of vertical gene transfer, but must also consider the significant degree of lateral gene transfer, which connects and shapes almost all living things. Herein, I review the major tree-building methods, their strengths, weaknesses and future prospects.

The contribution of statistical physics to evolutionary biology.

PubMed

de Vladar, Harold P; Barton, Nicholas H

2011-08-01

Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and independent development, as with stochastic methods in population genetics. Here, we discuss aspects of population genetics that have embraced methods from physics: non-equilibrium statistical mechanics, travelling waves and Monte-Carlo methods, among others, have been used to study polygenic evolution, rates of adaptation and range expansions. These applications indicate that evolutionary biology can further benefit from interactions with other areas of statistical physics; for example, by following the distribution of paths taken by a population through time. Copyright © 2011 Elsevier Ltd. All rights reserved.

Teaching Tree-Thinking to Undergraduate Biology Students

PubMed Central

2011-01-01

Evolution is the unifying principle of all biology, and understanding how evolutionary relationships are represented is critical for a complete understanding of evolution. Phylogenetic trees are the most conventional tool for displaying evolutionary relationships, and “tree-thinking” has been coined as a term to describe the ability to conceptualize evolutionary relationships. Students often lack tree-thinking skills, and developing those skills should be a priority of biology curricula. Many common student misconceptions have been described, and a successful instructor needs a suite of tools for correcting those misconceptions. I review the literature on teaching tree-thinking to undergraduate students and suggest how this material can be presented within an inquiry-based framework. PMID:21572571

Evolutionary grinding model for nanometric control of surface roughness for aspheric optical surfaces.

PubMed

Han, Jeong-Yeol; Kim, Sug-Whan; Han, Inwoo; Kim, Geon-Hee

2008-03-17

A new evolutionary grinding process model has been developed for nanometric control of material removal from an aspheric surface of Zerodur substrate. The model incorporates novel control features such as i) a growing database; ii) an evolving, multi-variable regression equation; and iii) an adaptive correction factor for target surface roughness (Ra) for the next machine run. This process model demonstrated a unique evolutionary controllability of machining performance resulting in the final grinding accuracy (i.e. averaged difference between target and measured surface roughness) of -0.2+/-2.3(sigma) nm Ra over seven trial machine runs for the target surface roughness ranging from 115 nm to 64 nm Ra.

Progress in faunal correlation of Late Cenozoic fluvial sequences 2000 4: the report of the IGCP 449 biostratigraphy subgroup

NASA Astrophysics Data System (ADS)

Schreve, D. C.; Keen, D. H.; Limondin-Lozouet, N.; Auguste, P.; Santisteban, Juan I.; Ubilla, M.; Matoshko, A.; Bridgland, D. R.; Westaway, R.

2007-11-01

Vertebrate and invertebrate faunal biostratigraphy is a well-tested method for establishing relative chronologies for fluviatile sequences that has proved useful in many parts of the world. The robust bones and teeth of large mammals are commonly found in fluviatile deposits, whereas small vertebrates can be readily recovered through systematic sieving of calcareous sediments, as can molluscs, the other major faunal group that has been used for biostratigraphical analysis of fluvial sequences. Because of their rapid and quantifiable rates of evolution, extinction, body mass change and dispersal during the Late Cenozoic, mammals are especially useful for ordering the fragmentary terrestrial sequence of interglacials and glacials, and proposing correlation with the global marine climatostratigraphic record. Other groups (e.g. reptiles and amphibians, ostracods) are as yet only in the initial stages of development as a dating tool, whereas some (e.g. fish, birds) still require substantial development in order to fully explore their utility. As part of IGCP 449, vertebrate and molluscan assemblages have made important contributions to datasets from a number of areas, notably northern France, central Germany, the Czech Republic and the Ukraine. Further south, mammalian assemblages have proved useful in separating discrete periods of climatic change in Iberia and Syria. At greater distances from the core area of fluvial biostratigraphical archives, significant contributions have come from South America (Uruguay River), South Africa (Vaal) and Australia (Riverine Plain and Lake Eyre drainage basin).

Initial implementation of a comparative data analysis ontology.

PubMed

Prosdocimi, Francisco; Chisham, Brandon; Pontelli, Enrico; Thompson, Julie D; Stoltzfus, Arlin

2009-07-03

Comparative analysis is used throughout biology. When entities under comparison (e.g. proteins, genomes, species) are related by descent, evolutionary theory provides a framework that, in principle, allows N-ary comparisons of entities, while controlling for non-independence due to relatedness. Powerful software tools exist for specialized applications of this approach, yet it remains under-utilized in the absence of a unifying informatics infrastructure. A key step in developing such an infrastructure is the definition of a formal ontology. The analysis of use cases and existing formalisms suggests that a significant component of evolutionary analysis involves a core problem of inferring a character history, relying on key concepts: "Operational Taxonomic Units" (OTUs), representing the entities to be compared; "character-state data" representing the observations compared among OTUs; "phylogenetic tree", representing the historical path of evolution among the entities; and "transitions", the inferred evolutionary changes in states of characters that account for observations. Using the Web Ontology Language (OWL), we have defined these and other fundamental concepts in a Comparative Data Analysis Ontology (CDAO). CDAO has been evaluated for its ability to represent token data sets and to support simple forms of reasoning. With further development, CDAO will provide a basis for tools (for semantic transformation, data retrieval, validation, integration, etc.) that make it easier for software developers and biomedical researchers to apply evolutionary methods of inference to diverse types of data, so as to integrate this powerful framework for reasoning into their research.

The extended evolutionary synthesis: its structure, assumptions and predictions

PubMed Central

Laland, Kevin N.; Uller, Tobias; Feldman, Marcus W.; Sterelny, Kim; Müller, Gerd B.; Moczek, Armin; Jablonka, Eva; Odling-Smee, John

2015-01-01

Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the ‘extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism–environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology. PMID:26246559

True-Triaxial Experimental Study of the Evolutionary Features of the Acoustic Emissions and Sounds of Rockburst Processes

NASA Astrophysics Data System (ADS)

Su, Guoshao; Shi, Yanjiong; Feng, Xiating; Jiang, Jianqing; Zhang, Jie; Jiang, Quan

2018-02-01

Rockbursts are markedly characterized by the ejection of rock fragments from host rocks at certain speeds. The rockburst process is always accompanied by acoustic signals that include acoustic emissions (AE) and sounds. A deep insight into the evolutionary features of AE and sound signals is important to improve the accuracy of rockburst prediction. To investigate the evolutionary features of AE and sound signals, rockburst tests on granite rock specimens under true-triaxial loading conditions were performed using an improved rockburst testing system, and the AE and sounds during rockburst development were recorded and analyzed. The results show that the evolutionary features of the AE and sound signals were obvious and similar. On the eve of a rockburst, a `quiescent period' could be observed in both the evolutionary process of the AE hits and the sound waveform. Furthermore, the time-dependent fractal dimensions of the AE hits and sound amplitude both showed a tendency to continuously decrease on the eve of the rockbursts. In addition, on the eve of the rockbursts, the main frequency of the AE and sound signals both showed decreasing trends, and the frequency spectrum distributions were both characterized by low amplitudes, wide frequency bands and multiple peak shapes. Thus, the evolutionary features of sound signals on the eve of rockbursts, as well as that of AE signals, can be used as beneficial information for rockburst prediction.

Imprinting, latchment and displacement: a mini review of early instinctual behaviour in newborn infants influencing breastfeeding success.

PubMed

Mobbs, Elsie J; Mobbs, George A; Mobbs, Anthony E D

2016-01-01

Instinctive behaviours have evolved favouring the mother-infant dyad based on fundamental processes of neurological development, including oral tactile imprinting and latchment. Latchment is the first stage of emotional development based on the successful achievement of biological imprinting. The mechanisms underpinning imprinting are identified and the evolutionary benefits discussed. It is proposed that the oral tactile imprint to the breast is a keystone for optimal latchment and breastfeeding, promoting evolutionary success. ©2015 The Authors. Acta Paediatrica published by John Wiley & Sons Ltd on behalf of Foundation Acta Paediatrica.

Development of Gravity-Sensing Organs in Altered Gravity Conditions: Opposite Conclusions From an Amphibian and a Molluscan Preparation

NASA Technical Reports Server (NTRS)

Wiederhold, Michael L.; Pedrozo, Hugo A.; Harrison, Jeffrey L.; Hejl, Robert; Gao, Wenyuan

1997-01-01

Several components of the systems animals use to orient to gravity might develop differently in micrograms. If the growth of the "test masses" on which gravity acts (otoliths, in vertebrates, statoliths or statoconia in most invertebrates) is controlled on the basis of their weight, larger otoliths (or their analogs) would be expected to develop in micrograms. The vestibular systems in animals reared in altered gravity have been studied in several species, with varied results being reported. Early Russian reports of Xenopus larvae reared in space indicated no qualitative differences in the vestibular organs, compared to ground-reared controls. A similar lack of differences in Xenopus were reported. The ultricular otolith was 30% larger in space-reared Xenopus. No differences in saccular otolith volume between centrifuged and control adult rats were found. A delay in otoconial development in chick embryos reared at 2 grams on a centrifuge was reported but in a later report, no differences in otolith weight between 2 grams and control chicks were found. Increased optokinetic responses in flight-reared Xenopus tadpoles, suggesting that the animals reared in the absence of gravity made greater relative use of their visual system, rather than the vestibular system, in orienting to a moving stimulus was reported. To test early Japanese newt, CYnops pyrrhogaster, were maintained in orbit for 15 days on the IML-2 mission in 1994. All specimens reached orbit before any otoconia were formed and all major components of the inner ear were formed by the end of the flight. In ground-based studies of he Aplysia statocyst, the volume of the statolith in embryos and the number statoconia in post-metamorphic animals were compared between 1-gram controls and specimens reared at 2 to 5.7 grams.

Evolvable Hardware for Space Applications

NASA Technical Reports Server (NTRS)

Lohn, Jason; Globus, Al; Hornby, Gregory; Larchev, Gregory; Kraus, William

2004-01-01

This article surveys the research of the Evolvable Systems Group at NASA Ames Research Center. Over the past few years, our group has developed the ability to use evolutionary algorithms in a variety of NASA applications ranging from spacecraft antenna design, fault tolerance for programmable logic chips, atomic force field parameter fitting, analog circuit design, and earth observing satellite scheduling. In some of these applications, evolutionary algorithms match or improve on human performance.

Computability, Gödel's incompleteness theorem, and an inherent limit on the predictability of evolution

PubMed Central

Day, Troy

2012-01-01

The process of evolutionary diversification unfolds in a vast genotypic space of potential outcomes. During the past century, there have been remarkable advances in the development of theory for this diversification, and the theory's success rests, in part, on the scope of its applicability. A great deal of this theory focuses on a relatively small subset of the space of potential genotypes, chosen largely based on historical or contemporary patterns, and then predicts the evolutionary dynamics within this pre-defined set. To what extent can such an approach be pushed to a broader perspective that accounts for the potential open-endedness of evolutionary diversification? There have been a number of significant theoretical developments along these lines but the question of how far such theory can be pushed has not been addressed. Here a theorem is proven demonstrating that, because of the digital nature of inheritance, there are inherent limits on the kinds of questions that can be answered using such an approach. In particular, even in extremely simple evolutionary systems, a complete theory accounting for the potential open-endedness of evolution is unattainable unless evolution is progressive. The theorem is closely related to Gödel's incompleteness theorem, and to the halting problem from computability theory. PMID:21849390

Evolutionary analyses of hedgehog and Hoxd-10 genes in fish species closely related to the zebrafish

PubMed Central

Zardoya, Rafael; Abouheif, Ehab; Meyer, Axel

1996-01-01

The study of development has relied primarily on the isolation of mutations in genes with specific functions in development and on the comparison of their expression patterns in normal and mutant phenotypes. Comparative evolutionary analyses can complement these approaches. Phylogenetic analyses of Sonic hedgehog (Shh) and Hoxd-10 genes from 18 cyprinid fish species closely related to the zebrafish provide novel insights into the functional constraints acting on Shh. Our results confirm and extend those gained from expression and crystalline structure analyses of this gene. Unexpectedly, exon 1 of Shh is found to be almost invariant even in third codon positions among these morphologically divergent species suggesting that this exon encodes for a functionally important domain of the hedgehog protein. This is surprising because the main functional domain of Shh had been thought to be that encoded by exon 2. Comparisons of Shh and Hoxd-10 gene sequences and of resulting gene trees document higher evolutionary constraints on the former than on the latter. This might be indicative of more general evolutionary patterns in networks of developmental regulatory genes interacting in a hierarchical fashion. The presence of four members of the hedgehog gene family in cyprinid fishes was documented and their homologies to known hedgehog genes in other vertebrates were established. PMID:8917540

Evolutionary analyses of hedgehog and Hoxd-10 genes in fish species closely related to the zebrafish.

PubMed

Zardoya, R; Abouheif, E; Meyer, A

1996-11-12

The study of development has relied primarily on the isolation of mutations in genes with specific functions in development and on the comparison of their expression patterns in normal and mutant phenotypes. Comparative evolutionary analyses can complement these approaches. Phylogenetic analyses of Sonic hedgehog (Shh) and Hoxd-10 genes from 18 cyprinid fish species closely related to the zebrafish provide novel insights into the functional constraints acting on Shh. Our results confirm and extend those gained from expression and crystalline structure analyses of this gene. Unexpectedly, exon 1 of Shh is found to be almost invariant even in third codon positions among these morphologically divergent species suggesting that this exon encodes for a functionally important domain of the hedgehog protein. This is surprising because the main functional domain of Shh had been thought to be that encoded by exon 2. Comparisons of Shh and Hoxd-10 gene sequences and of resulting gene trees document higher evolutionary constraints on the former than on the latter. This might be indicative of more general evolutionary patterns in networks of developmental regulatory genes interacting in a hierarchical fashion. The presence of four members of the hedgehog gene family in cyprinid fishes was documented and their homologies to known hedgehog genes in other vertebrates were established.

Evolution in health and medicine Sackler colloquium: Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease.

PubMed

Feinberg, Andrew P; Irizarry, Rafael A

2010-01-26

Neo-Darwinian evolutionary theory is based on exquisite selection of phenotypes caused by small genetic variations, which is the basis of quantitative trait contribution to phenotype and disease. Epigenetics is the study of nonsequence-based changes, such as DNA methylation, heritable during cell division. Previous attempts to incorporate epigenetics into evolutionary thinking have focused on Lamarckian inheritance, that is, environmentally directed epigenetic changes. Here, we propose a new non-Lamarckian theory for a role of epigenetics in evolution. We suggest that genetic variants that do not change the mean phenotype could change the variability of phenotype; and this could be mediated epigenetically. This inherited stochastic variation model would provide a mechanism to explain an epigenetic role of developmental biology in selectable phenotypic variation, as well as the largely unexplained heritable genetic variation underlying common complex disease. We provide two experimental results as proof of principle. The first result is direct evidence for stochastic epigenetic variation, identifying highly variably DNA-methylated regions in mouse and human liver and mouse brain, associated with development and morphogenesis. The second is a heritable genetic mechanism for variable methylation, namely the loss or gain of CpG dinucleotides over evolutionary time. Finally, we model genetically inherited stochastic variation in evolution, showing that it provides a powerful mechanism for evolutionary adaptation in changing environments that can be mediated epigenetically. These data suggest that genetically inherited propensity to phenotypic variability, even with no change in the mean phenotype, substantially increases fitness while increasing the disease susceptibility of a population with a changing environment.

Longevity and ageing: appraising the evolutionary consequences of growing old

PubMed Central

Bonsall, Michael B

2005-01-01

Senescence or ageing is an increase in mortality and/or decline in fertility with increasing age. Evolutionary theories predict that ageing or longevity evolves in response to patterns of extrinsic mortality or intrinsic damage. If ageing is viewed as the outcome of the processes of behaviour, growth and reproduction then it should be possible to predict mortality rate. Recent developments have shown that it is now possible to integrate these ecological and physiological processes and predict the shape of mortality trajectories. By drawing on the key exciting developments in the cellular, physiological and ecological process of longevity the evolutionary consequences of ageing are reviewed. In presenting these ideas an evolutionary demographic framework is used to argue how trade-offs in life-history strategies are important in the maintenance of variation in longevity within and between species. Evolutionary processes associated with longevity have an important role in explaining levels of biological diversity and speciation. In particular, the effects of life-history trait trade-offs in maintaining and promoting species diversity are explored. Such trade-offs can alleviate the effects of intense competition between species and promote species coexistence and diversification. These results have important implications for understanding a number of core ecological processes such as how species are divided among niches, how closely related species co-occur and the rules by which species assemble into food-webs. Theoretical work reveals that the proximate physiological processes are as important as the ecological factors in explaining the variation in the evolution of longevity. Possible future research challenges integrating work on the evolution and mechanisms of growing old are briefly discussed. PMID:16553312

The semaphorontic view of homology.

PubMed

Havstad, Joyce C; Assis, Leandro C S; Rieppel, Olivier

2015-11-01

The relation of homology is generally characterized as an identity relation, or alternatively as a correspondence relation, both of which are transitive. We use the example of the ontogenetic development and evolutionary origin of the gnathostome jaw to discuss identity and transitivity of the homology relation under the transformationist and emergentist paradigms respectively. Token identity and consequent transitivity of homology relations are shown to be requirements that are too strong to allow the origin of genuine evolutionary novelties. We consequently introduce the concept of compositional identity that is grounded in relations prevailing between parts (organs and organ systems) of a whole (organism). We recognize an ontogenetic identity of parts within a whole throughout the sequence of successive developmental stages of those parts: this is an intra-organismal character identity maintained throughout developmental trajectory. Correspondingly, we recognize a phylogenetic identity of homologous parts within two or more organisms of different species: this is an inter-species character identity maintained throughout evolutionary trajectory. These different dimensions of character identity--ontogenetic (through development) and phylogenetic (via shared evolutionary history)--break the transitivity of homology relations. Under the transformationist paradigm, the relation of homology reigns over the entire character (-state) transformation series, and thus encompasses the plesiomorphic as well as the apomorphic condition of form. In contrast, genuine evolutionary novelties originate not through transformation of ancestral characters (-states), but instead through deviating developmental trajectories that result in alternate characters. Under the emergentist paradigm, homology is thus synonymous with synapomorphy. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution Published by Wiley Periodicals, Inc.

Using evolutionary computations to understand the design and evolution of gene and cell regulatory networks.

PubMed

Spirov, Alexander; Holloway, David

2013-07-15

This paper surveys modeling approaches for studying the evolution of gene regulatory networks (GRNs). Modeling of the design or 'wiring' of GRNs has become increasingly common in developmental and medical biology, as a means of quantifying gene-gene interactions, the response to perturbations, and the overall dynamic motifs of networks. Drawing from developments in GRN 'design' modeling, a number of groups are now using simulations to study how GRNs evolve, both for comparative genomics and to uncover general principles of evolutionary processes. Such work can generally be termed evolution in silico. Complementary to these biologically-focused approaches, a now well-established field of computer science is Evolutionary Computations (ECs), in which highly efficient optimization techniques are inspired from evolutionary principles. In surveying biological simulation approaches, we discuss the considerations that must be taken with respect to: (a) the precision and completeness of the data (e.g. are the simulations for very close matches to anatomical data, or are they for more general exploration of evolutionary principles); (b) the level of detail to model (we proceed from 'coarse-grained' evolution of simple gene-gene interactions to 'fine-grained' evolution at the DNA sequence level); (c) to what degree is it important to include the genome's cellular context; and (d) the efficiency of computation. With respect to the latter, we argue that developments in computer science EC offer the means to perform more complete simulation searches, and will lead to more comprehensive biological predictions. Copyright © 2013 Elsevier Inc. All rights reserved.

Why evolutionary biologists should get seriously involved in ecological monitoring and applied biodiversity assessment programs

PubMed Central

Brodersen, Jakob; Seehausen, Ole

2014-01-01

While ecological monitoring and biodiversity assessment programs are widely implemented and relatively well developed to survey and monitor the structure and dynamics of populations and communities in many ecosystems, quantitative assessment and monitoring of genetic and phenotypic diversity that is important to understand evolutionary dynamics is only rarely integrated. As a consequence, monitoring programs often fail to detect changes in these key components of biodiversity until after major loss of diversity has occurred. The extensive efforts in ecological monitoring have generated large data sets of unique value to macro-scale and long-term ecological research, but the insights gained from such data sets could be multiplied by the inclusion of evolutionary biological approaches. We argue that the lack of process-based evolutionary thinking in ecological monitoring means a significant loss of opportunity for research and conservation. Assessment of genetic and phenotypic variation within and between species needs to be fully integrated to safeguard biodiversity and the ecological and evolutionary dynamics in natural ecosystems. We illustrate our case with examples from fishes and conclude with examples of ongoing monitoring programs and provide suggestions on how to improve future quantitative diversity surveys. PMID:25553061

Evolutionary medicine and its implications for endocrinological issues (e.g. menopause).

PubMed

Kirchengast, Sylvia; Rühli, Frank

2013-06-01

Evolutionary medicine, which was formalized in the early 1990s, investigates evolutionary causes of recent human disease, disorders and malfunctions but also the influence of changing living conditions and modernization on health and disease. Evolutionary medicine can also provide insights into endocrinological disorders and in particular in the process of female reproductive senescence. Female reproductive senescence, i.e. menopausal transition is physiologically caused by the decline of estrogen secretion, which is associated with various somatic and psychic discomforts making this stage of life extremely uncomfortable. From the viewpoint of evolutionary medicine, these menopausal symptoms are the result from the sudden decrease of very high lifetime estrogen levels to zero during postmenopause, a situation which is quite new in our evolution and history. While women in recent developed countries experience menarche early, menopause late, few pregnancies, short periods of lactation and consequently low life time estrogen levels. The opposite is true of women living in traditional societies, whose living conditions may be interpreted as a mirror of the situation in our history. From this viewpoint we can conclude that menopausal symptoms may are the result of a mismatch between female reproductive physiology and recent living conditions. Copyright © 2013 Elsevier Inc. All rights reserved.

Evolutionary systems biology: historical and philosophical perspectives on an emerging synthesis.

PubMed

O'Malley, Maureen A

2012-01-01

Systems biology (SB) is at least a decade old now and maturing rapidly. A more recent field, evolutionary systems biology (ESB), is in the process of further developing system-level approaches through the expansion of their explanatory and potentially predictive scope. This chapter will outline the varieties of ESB existing today by tracing the diverse roots and fusions that make up this integrative project. My approach is philosophical and historical. As well as examining the recent origins of ESB, I will reflect on its central features and the different clusters of research it comprises. In its broadest interpretation, ESB consists of five overlapping approaches: comparative and correlational ESB; network architecture ESB; network property ESB; population genetics ESB; and finally, standard evolutionary questions answered with SB methods. After outlining each approach with examples, I will examine some strong general claims about ESB, particularly that it can be viewed as the next step toward a fuller modern synthesis of evolutionary biology (EB), and that it is also the way forward for evolutionary and systems medicine. I will conclude with a discussion of whether the emerging field of ESB has the capacity to combine an even broader scope of research aims and efforts than it presently does.

The evolutionary origins of Syngnathidae: pipefishes and seahorses.

PubMed

Wilson, A B; Orr, J W

2011-06-01

Despite their importance as evolutionary and ecological model systems, the phylogenetic relationships among gasterosteiforms remain poorly understood, complicating efforts to understand the evolutionary origins of the exceptional morphological and behavioural diversity of this group. The present review summarizes current knowledge on the origin and evolution of syngnathids, a gasterosteiform family with a highly developed form of male parental care, combining inferences based on morphological and molecular data with paleontological evidence documenting the evolutionary history of the group. Molecular methods have provided new tools for the study of syngnathid relationships and have played an important role in recent conservation efforts. Despite recent insights into syngnathid evolution, however, a survey of the literature reveals a strong taxonomic bias towards studies on the species-rich genera Hippocampus and Syngnathus, with a lack of data for many morphologically unique members of the family. The study of the evolutionary pressures responsible for generating the high diversity of syngnathids would benefit from a wider perspective, providing a comparative framework in which to investigate the evolution of the genetic, morphological and behavioural traits of the group as a whole. © 2011 The Authors. Journal of Fish Biology © 2011 The Fisheries Society of the British Isles.

SLiM 2: Flexible, Interactive Forward Genetic Simulations.

PubMed

Haller, Benjamin C; Messer, Philipp W

2017-01-01

Modern population genomic datasets hold immense promise for revealing the evolutionary processes operating in natural populations, but a crucial prerequisite for this goal is the ability to model realistic evolutionary scenarios and predict their expected patterns in genomic data. To that end, we present SLiM 2: an evolutionary simulation framework that combines a powerful, fast engine for forward population genetic simulations with the capability of modeling a wide variety of complex evolutionary scenarios. SLiM achieves this flexibility through scriptability, which provides control over most aspects of the simulated evolutionary scenarios with a simple R-like scripting language called Eidos. An example SLiM simulation is presented to illustrate the power of this approach. SLiM 2 also includes a graphical user interface for simulation construction, interactive runtime control, and dynamic visualization of simulation output, facilitating easy and fast model development with quick prototyping and visual debugging. We conclude with a performance comparison between SLiM and two other popular forward genetic simulation packages. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Neoplastic growth: the consequence of evolutionary malignant resistance to chronic damage for survival of cells (review of a new theory of the origin of cancer).

PubMed

Monceviciūte-Eringiene, E

2005-01-01

In the present review, a new theory that the mechanisms of general evolutionary persistent resistance to damaging factors are closely related to the development of tumour cells is introduced. Evolutionary resistance and its variability have an immense power to drive and control the process of carcinogenesis and the success of microbial and antitumour chemotherapy. First, this phenomenon of adaptation is characteristic of microbial cells whose resistance to antibiotics and other chemotherapeutic drugs is manifested through ATP-dependent transmembrane transporters. The structure and function of some multidrug transporters of resistance are conserved from microorganisms to mammals. When somatic cells are exposed to carcinogens and develop into tumour cells, they also acquire resistance to the toxic effects of carcinogens through these same transmembrane transporters (P-glycoprotein, glutathione S-transferases and other products of evolutionary resistance-related genes arisen for detoxification and exportation of cytotoxic xenobiotics and drugs). Cancerous cells acquire a persistent evolutionary resistance to chemotherapy drugs or irradiation through the same ATP-dependent transporters encountered in prokaryotic and eukaryotic cells. The mechanism of acquired resistance of cells to damaging factors, which becomes manifested during tumorigenic process formation, is a general biological law of primary significance in carcinogenesis. This resistance can be called malignant as, once formed, it does not disappear, as does also a clone of malignant cells. In tumorous cells, the mutagenic processes, morphological and functional modifications are a mechanism of secondary significance in carcinogenesis, contributing to formation of damage-resistant cells. This mechanism characterizes the processes of simplification arising in damage-resistant cells. Such cells acquire parasitic features. To survive under unfavourable conditions, they get adapted as if returning down the evolutionary stairs back to a more primitive stage of atavistic regression, which is characteristic of primitive forms of existence. Therefore they cease obeying the growth-regulating mechanisms in the organism and acquire the potential of unlimited division and accelerated growth (metastases) as do unicellular organisms or their forms resistant to damaging factors in the environment and in the host organism. Thus, cancer is a natural self-protective response of the damaged cells to the biological, physical and chemical damage and oxidative stress. This response has been developed in the process of evolution under the impact of the general biological Darwinian law of nature--to survive through variability and adaptation to the changed environmental conditions. Thus, malignization is the consequence of an evolutionary variety of the general biological resistance of cells to damage and stress in order to survive.

Holistic Darwinism: the new evolutionary paradigm and some implications for political science.

PubMed

Corning, Peter A

2008-03-01

Holistic Darwinism is a candidate name for a major paradigm shift that is currently underway in evolutionary biology and related disciplines. Important developments include (1) a growing appreciation for the fact that evolution is a multilevel process, from genes to ecosystems, and that interdependent coevolution is a ubiquitous phenomenon in nature; (2) a revitalization of group selection theory, which was banned (prematurely) from evolutionary biology over 30 years ago (groups may in fact be important evolutionary units); (3) a growing respect for the fact that the genome is not a "bean bag" (in biologist Ernst Mayr's caricature), much less a gladiatorial arena for competing selfish genes, but a complex, interdependent, cooperating system; (4) an increased recognition that symbiosis is an important phenomenon in nature and that symbiogenesis is a major source of innovation in evolution; (5) an array of new, more advanced game theory models, which support the growing evidence that cooperation is commonplace in nature and not a rare exception; (6) new research and theoretical work that stresses the role of nurture in evolution, including developmental processes, phenotypic plasticity, social information transfer (culture), and especially the role of behavioral innovations as pacemakers of evolutionary change (e.g., niche construction theory, which is concerned with the active role of organisms in shaping the evolutionary process, and gene-culture coevolution theory, which relates especially to the dynamics of human evolution); (7) and, not least, a broad effort to account for the evolution of biological complexity--from major transition theory to the "Synergism Hypothesis." Here I will briefly review these developments and will present a case for the proposition that this paradigm shift has profound implications for the social sciences, including specifically political theory, economic theory, and political science as a discipline. Interdependent superorganisms, it turns out, have played a major role in evolution--from eukaryotes to complex human societies.

A phylogeny for the pomatiopsidae (Gastropoda: Rissooidea): a resource for taxonomic, parasitological and biodiversity studies

PubMed Central

2014-01-01

Background The Pomatiopsidae are reported from northern India into southern China and Southeast Asia, with two sub-families, the Pomatiopsinae (which include freshwater, amphibious, terrestrial and marine species) and the freshwater Triculinae. Both include species acting as intermediate host for species of the blood-fluke Schistosoma which cause a public health problem in East Asia. Also, with around 120 species, triculine biodiversity exceeds that of any other endemic freshwater molluscan fauna. Nevertheless, the origins of the Pomatiopsidae, the factors driving such a diverse radiation and aspects of their co-evolution with Schistosoma are not fully understood. Many taxonomic questions remain; there are problems identifying medically relevant species. The predicted range is mostly unsurveyed and the true biodiversity of the family is underestimated. Consequently, the aim of the study was to collect DNA-sequence data for as many pomatiopsid taxa as possible, as a first step in providing a resource for identification of epidemiologically significant species (by non-malacologists), for use in resolving taxonomic confusion and for testing phylogeographical hypotheses. Results The evolutionary radiation of the Triculinae was shown to have been rapid and mostly post late Miocene. Molecular dating indicated that the radiation of these snails was driven first by the uplift of the Himalaya and onset of a monsoon system, and then by late-Pliocene global warming. The status of Erhaia as Anmicolidae is supported. The genera Tricula and Neotricula are shown to be non-monophyletic and the tribe Jullieniini may be polyphyletic (based on convergent characters). Triculinae from northern Vietnam could be derived from Gammatricula of Fujian/Yunnan, China. Conclusions The molecular dates and phylogenetic estimates in this study are consistent with an Australasian origin for the Pomatiopsidae and an East to West radiation via Oligocene Borneo-Philippines island hopping to Japan and then China (Triculinae arising mid-Miocene in Southeast China), and less so with a triculine origin in Tibet. The lack of monophyly in the medically important genera and indications of taxonomic inaccuracies, call for further work to identify epidemiologically significant taxa (e.g., Halewisia may be potential hosts for Schistosoma mekongi) and highlight the need for surveys to determine the true biodiversity of the Triculinae. PMID:24548800

A median third eye: pineal gland retraces evolution of vertebrate photoreceptive organs.

PubMed

Mano, Hiroaki; Fukada, Yoshitaka

2007-01-01

In many vertebrates, the pineal gland serves as a photoreceptive neuroendocrine organ. Morphological and functional similarities between the pineal and retinal photoreceptor cells indicate their close evolutionary relationship, and hence the comparative studies on the pineal gland and the retina are the keys to deciphering the evolutionary traces of the vertebrate photoreceptive organs. Several studies have suggested common genetic and molecular mechanisms responsible for their similarities, but largely unknown are those underlying pineal-specific development and physiological functions. Recent studies have identified several cis-acting DNA elements that participate in transcriptional control of the pineal-specific genes. Genetic approaches in the zebrafish have also contributed to elucidating the genetic network regulating the pineal development and neurogenesis. These efforts toward elucidating the molecular instrumentation intrinsic to the pineal gland, back to back with those to the retina, should lead to a comprehensive understanding of the evolutionary history of the vertebrate photoreceptive structures. This article summarizes the current status of research on these topics.

Automated discovery of local search heuristics for satisfiability testing.

PubMed

Fukunaga, Alex S

2008-01-01

The development of successful metaheuristic algorithms such as local search for a difficult problem such as satisfiability testing (SAT) is a challenging task. We investigate an evolutionary approach to automating the discovery of new local search heuristics for SAT. We show that several well-known SAT local search algorithms such as Walksat and Novelty are composite heuristics that are derived from novel combinations of a set of building blocks. Based on this observation, we developed CLASS, a genetic programming system that uses a simple composition operator to automatically discover SAT local search heuristics. New heuristics discovered by CLASS are shown to be competitive with the best Walksat variants, including Novelty+. Evolutionary algorithms have previously been applied to directly evolve a solution for a particular SAT instance. We show that the heuristics discovered by CLASS are also competitive with these previous, direct evolutionary approaches for SAT. We also analyze the local search behavior of the learned heuristics using the depth, mobility, and coverage metrics proposed by Schuurmans and Southey.

Facultative parthenogenesis in vertebrates: reproductive error or chance?

PubMed

Lampert, K P

2008-01-01

Parthenogenesis, the development of an embryo from a female gamete without any contribution of a male gamete, is very rare in vertebrates. Parthenogenetically reproducing species have, so far, only been found in the Squamate reptiles (lizards and snakes). Facultative parthenogenesis, switching between sexual and clonal reproduction, although quite common in invertebrates, e.g. Daphnia and aphids, seems to be even rarer in vertebrates. However, isolated cases of parthenogenetic development have been reported in all vertebrate groups. Facultative parthenogenesis in vertebrates has only been found in captive animals but might simply have been overlooked in natural populations. Even though its evolutionary impact is hard to determine and very likely varies depending on the ploidy restoration mechanisms and sex-determining mechanisms involved, facultative parthenogenesis is already discussed in conservation biology and medical research. To raise interest for facultative parthenogenesis especially in evolutionary biology, I summarize the current knowledge about facultative parthenogenesis in the different vertebrate groups, introduce mechanisms of diploid oocyte formation and discuss the genetic consequences and potential evolutionary impact of facultative parthenogenesis in vertebrates.

Dilemma strength as a framework for advancing evolutionary game theory. Reply to comments on "Universal scaling for the dilemma strength in evolutionary games"

NASA Astrophysics Data System (ADS)

Wang, Zhen; Kokubo, Satoshi; Jusup, Marko; Tanimoto, Jun

2015-09-01

While comprehensive reviews of the literature, by gathering in one place most of the relevant information, undoubtedly steer the development of every scientific field, we found that the comments in response to a review article can be as informative as the review itself, if not more. Namely, reading through the comments on the ideas expressed in Ref. [1], we could identify a number of pressing problems for evolutionary game theory, indicating just how much space there still is for major advances and breakthroughs. In an attempt to bring a sense of order to a multitude of opinions, we roughly classified the comments into three categories, i.e. those concerned with: (i) the universality of scaling in heterogeneous topologies, including empirical dynamic networks [2-8], (ii) the universality of scaling for more general game setups, such as the inclusion of multiple strategies and external features [4,9-11], and (iii) experimental confirmations of the theoretical developments [2,12,13].

Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs.

PubMed

Lopez-Rios, Javier; Duchesne, Amandine; Speziale, Dario; Andrey, Guillaume; Peterson, Kevin A; Germann, Philipp; Unal, Erkan; Liu, Jing; Floriot, Sandrine; Barbey, Sarah; Gallard, Yves; Müller-Gerbl, Magdalena; Courtney, Andrew D; Klopp, Christophe; Rodriguez, Sabrina; Ivanek, Robert; Beisel, Christian; Wicking, Carol; Iber, Dagmar; Robert, Benoit; McMahon, Andrew P; Duboule, Denis; Zeller, Rolf

2014-07-03

The large spectrum of limb morphologies reflects the wide evolutionary diversification of the basic pentadactyl pattern in tetrapods. In even-toed ungulates (artiodactyls, including cattle), limbs are adapted for running as a consequence of progressive reduction of their distal skeleton to symmetrical and elongated middle digits with hoofed phalanges. Here we analyse bovine embryos to establish that polarized gene expression is progressively lost during limb development in comparison to the mouse. Notably, the transcriptional upregulation of the Ptch1 gene, which encodes a Sonic hedgehog (SHH) receptor, is disrupted specifically in the bovine limb bud mesenchyme. This is due to evolutionary alteration of a Ptch1 cis-regulatory module, which no longer responds to graded SHH signalling during bovine handplate development. Our study provides a molecular explanation for the loss of digit asymmetry in bovine limb buds and suggests that modifications affecting the Ptch1 cis-regulatory landscape have contributed to evolutionary diversification of artiodactyl limbs.

Optimizing a realistic large-scale frequency assignment problem using a new parallel evolutionary approach

NASA Astrophysics Data System (ADS)

Chaves-González, José M.; Vega-Rodríguez, Miguel A.; Gómez-Pulido, Juan A.; Sánchez-Pérez, Juan M.

2011-08-01

This article analyses the use of a novel parallel evolutionary strategy to solve complex optimization problems. The work developed here has been focused on a relevant real-world problem from the telecommunication domain to verify the effectiveness of the approach. The problem, known as frequency assignment problem (FAP), basically consists of assigning a very small number of frequencies to a very large set of transceivers used in a cellular phone network. Real data FAP instances are very difficult to solve due to the NP-hard nature of the problem, therefore using an efficient parallel approach which makes the most of different evolutionary strategies can be considered as a good way to obtain high-quality solutions in short periods of time. Specifically, a parallel hyper-heuristic based on several meta-heuristics has been developed. After a complete experimental evaluation, results prove that the proposed approach obtains very high-quality solutions for the FAP and beats any other result published.

Investigating the evolutionary history of irrigated agricultural technology in the Heihe River Basin, China

NASA Astrophysics Data System (ADS)

Wu, S.; Wei, Y.; Zhao, Y.; Zheng, H.

2017-12-01

Human's innovative abilities do not only enable rapid expansion of civilization, but also lead to enormous modifications on the natural environment. Technology, while a key factor embedded in socioeconomic developments, its impacts have been rarely appropriately considered in river basin management. This research aims to examine the evolutionary history of irrigated agricultural technology in the Heihe River Basin, China, and how its characteristics interacted with the river basin environment. It adopts a content analysis approach to collect and summarize quantitative technological information in the Heihe River Basin across a time span of more than 2000 years from the Han Dynasty (206 BC) to 2015. Two Chinese academic research databases: Wan Fang Data and China National Knowledge Infrastructure (CNKI) were chosen as data sources. The results show that irrigated agricultural technologies in Heihe River Basin have shifted from focusing on developing new farming tools and cultivation methods to adapting modernized, water-saving irrigation methods and water diversion infrastructures. In additions, the center of irrigated agricultural technology in the Heihe river basin has moved from downstream to middle stream since the Ming Dynasty (1368AD) as a result of degraded natural environment. The developing trend of technology in the Heihe River Basin thus coincides with the change of societal focus from agricultural production efficiency to the human-water balance and environmental remediation. This research demonstrates that irrigated agricultural technologies had a twisted evolutionary history in the Heihe River Basin, influenced by a diverse range of environmental and socioeconomic factors. It provides insights into the fact that technology exhibits a co-evolutionary characteristic with the social development history in the region, pointing towards the urgent need to maintain the balance between human and environment.

Simulation of the evolution of root water foraging strategies in dry and shallow soils.

PubMed

Renton, Michael; Poot, Pieter

2014-09-01

The dynamic structural development of plants can be seen as a strategy for exploiting the limited resources available within their environment, and we would expect that evolution would lead to efficient strategies that reduce costs while maximizing resource acquisition. In particular, perennial species endemic to habitats with shallow soils in seasonally dry environments have been shown to have a specialized root system morphology that may enhance access to water resources in the underlying rock. This study aimed to explore these hypotheses by applying evolutionary algorithms to a functional-structural root growth model. A simulation model of a plant's root system was developed, which represents the dynamics of water uptake and structural growth. The model is simple enough for evolutionary optimization to be computationally feasible, yet flexible enough to allow a range of structural development strategies to be explored. The model was combined with an evolutionary algorithm in order to investigate a case study habitat with a highly heterogeneous distribution of resources, both spatially and temporally--the situation of perennial plants occurring on shallow soils in seasonally dry environments. Evolution was simulated under two contrasting fitness criteria: (1) the ability to find wet cracks in underlying rock, and (2) maximizing above-ground biomass. The novel approach successfully resulted in the evolution of more efficient structural development strategies for both fitness criteria. Different rooting strategies evolved when different criteria were applied, and each evolved strategy made ecological sense in terms of the corresponding fitness criterion. Evolution selected for root system morphologies which matched those of real species from corresponding habitats. Specialized root morphology with deeper rather than shallower lateral branching enhances access to water resources in underlying rock. More generally, the approach provides insights into both evolutionary processes and ecological costs and benefits of different plant growth strategies.

Despotism, democracy, and the evolutionary dynamics of leadership and followership.

PubMed

Van Vugt, Mark

2009-01-01

Responds to comments made by George B. Graen and Stephen J. Guastello on the current author's article Leadership, followership, and evolution: Some lessons from the past by Van Vugt, Hogan, and Kaiser. In the original article my co-authors and I proposed a new way of thinking about leadership, informed by evolutionary (neo-Darwinian) theory. In the first commentary, Graen noted that we ignored a number of recently developed psychological theories of leadership that take into account the leader-follower relationship, most notably LMX theory. LMX theory asserts that leadership effectiveness and team performance are affected by the quality of working relationships between superior and subordinates. Because the original article primarily dealt with questions about the origins of leadership--the phylogenetic and evolutionary causes--we had to be concise in our review of proximate psychological theories of leadership. In the second commentary, Guastello concurred with the importance of an evolutionary game analysis for studying leadership but disagreed with certain details of our analysis. (PsycINFO Database Record (c) 2009 APA, all rights reserved).

Evolutionary Design and Simulation of a Tube Crawling Inspection Robot

NASA Technical Reports Server (NTRS)

Craft, Michael; Howsman, Tom; ONeil, Daniel; Howell, Joe T. (Technical Monitor)

2002-01-01

The Space Robotics Assembly Team Simulation (SpaceRATS) is an expansive concept that will hopefully lead to a space flight demonstration of a robotic team cooperatively assembling a system from its constitutive parts. A primary objective of the SpaceRATS project is to develop a generalized evolutionary design approach for multiple classes of robots. The portion of the overall SpaceRats program associated with the evolutionary design and simulation of an inspection robot's morphology is the subject of this paper. The vast majority of this effort has concentrated on the use and modification of Darwin2K, a robotic design and simulation software package, to analyze the design of a tube crawling robot. This robot is designed for carrying out inspection duties in relatively inaccessible locations within a liquid rocket engine similar to the SSME. A preliminary design of the tube crawler robot was completed, and the mechanical dynamics of the system were simulated. An evolutionary approach to optimizing a few parameters of the system was utilized, resulting in a more optimum design.

Classification of Medical Datasets Using SVMs with Hybrid Evolutionary Algorithms Based on Endocrine-Based Particle Swarm Optimization and Artificial Bee Colony Algorithms.

PubMed

Lin, Kuan-Cheng; Hsieh, Yi-Hsiu

2015-10-01

The classification and analysis of data is an important issue in today's research. Selecting a suitable set of features makes it possible to classify an enormous quantity of data quickly and efficiently. Feature selection is generally viewed as a problem of feature subset selection, such as combination optimization problems. Evolutionary algorithms using random search methods have proven highly effective in obtaining solutions to problems of optimization in a diversity of applications. In this study, we developed a hybrid evolutionary algorithm based on endocrine-based particle swarm optimization (EPSO) and artificial bee colony (ABC) algorithms in conjunction with a support vector machine (SVM) for the selection of optimal feature subsets for the classification of datasets. The results of experiments using specific UCI medical datasets demonstrate that the accuracy of the proposed hybrid evolutionary algorithm is superior to that of basic PSO, EPSO and ABC algorithms, with regard to classification accuracy using subsets with a reduced number of features.

An evolutionary perspective on gradual formation of superego in the primal horde

PubMed Central

Pulcu, Erdem

2014-01-01

Freud proposed that the processes which occurred in the primal horde are essential for understanding superego formation and therefore, the successful dissolution of the Oedipus complex. However, Freud theorized superego formation in the primal horde as if it is an instant, all-or-none achievement. The present paper proposes an alternative model aiming to explain gradual development of superego in the primitive man. The proposed model is built on knowledge from evolutionary and neural sciences as well as anthropology, and it particularly focuses on the evolutionary significance of the acquisition of fire by hominids in the Pleistocene period in the light of up-to-date archaeological findings. Acquisition of fire is discussed as a form of sublimation which might have helped Prehistoric man to maximize the utility of limited evolutionary biological resources, potentially contributing to the rate and extent of bodily evolution. The limitations of both Freud's original conceptualization and the present model are discussed accordingly in an interdisciplinary framework. PMID:24478740

Asymmetric Evolutionary Games

PubMed Central

McAvoy, Alex; Hauert, Christoph

2015-01-01

Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner’s Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games. PMID:26308326

A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms

PubMed Central

Werner, Gijsbert D. A.; Cornwell, William K.; Sprent, Janet I.; Kattge, Jens; Kiers, E. Toby

2014-01-01

Symbiotic associations occur in every habitat on earth, but we know very little about their evolutionary histories. Current models of trait evolution cannot adequately reconstruct the deep history of symbiotic innovation, because they assume homogenous evolutionary processes across millions of years. Here we use a recently developed, heterogeneous and quantitative phylogenetic framework to study the origin of the symbiosis between angiosperms and nitrogen-fixing (N2) bacterial symbionts housed in nodules. We compile the largest database of global nodulating plant species and reconstruct the symbiosis’ evolution. We identify a single, cryptic evolutionary innovation driving symbiotic N2-fixation evolution, followed by multiple gains and losses of the symbiosis, and the subsequent emergence of ‘stable fixers’ (clades extremely unlikely to lose the symbiosis). Originating over 100 MYA, this innovation suggests deep homology in symbiotic N2-fixation. Identifying cryptic innovations on the tree of life is key to understanding the evolution of complex traits, including symbiotic partnerships. PMID:24912610

Evolutionary Wavelet Neural Network ensembles for breast cancer and Parkinson's disease prediction.

PubMed

Khan, Maryam Mahsal; Mendes, Alexandre; Chalup, Stephan K

2018-01-01

Wavelet Neural Networks are a combination of neural networks and wavelets and have been mostly used in the area of time-series prediction and control. Recently, Evolutionary Wavelet Neural Networks have been employed to develop cancer prediction models. The present study proposes to use ensembles of Evolutionary Wavelet Neural Networks. The search for a high quality ensemble is directed by a fitness function that incorporates the accuracy of the classifiers both independently and as part of the ensemble itself. The ensemble approach is tested on three publicly available biomedical benchmark datasets, one on Breast Cancer and two on Parkinson's disease, using a 10-fold cross-validation strategy. Our experimental results show that, for the first dataset, the performance was similar to previous studies reported in literature. On the second dataset, the Evolutionary Wavelet Neural Network ensembles performed better than all previous methods. The third dataset is relatively new and this study is the first to report benchmark results.

Evolutionary Wavelet Neural Network ensembles for breast cancer and Parkinson’s disease prediction

PubMed Central

Mendes, Alexandre; Chalup, Stephan K.

2018-01-01

Wavelet Neural Networks are a combination of neural networks and wavelets and have been mostly used in the area of time-series prediction and control. Recently, Evolutionary Wavelet Neural Networks have been employed to develop cancer prediction models. The present study proposes to use ensembles of Evolutionary Wavelet Neural Networks. The search for a high quality ensemble is directed by a fitness function that incorporates the accuracy of the classifiers both independently and as part of the ensemble itself. The ensemble approach is tested on three publicly available biomedical benchmark datasets, one on Breast Cancer and two on Parkinson’s disease, using a 10-fold cross-validation strategy. Our experimental results show that, for the first dataset, the performance was similar to previous studies reported in literature. On the second dataset, the Evolutionary Wavelet Neural Network ensembles performed better than all previous methods. The third dataset is relatively new and this study is the first to report benchmark results. PMID:29420578

Evolutionary ethnobiology and cultural evolution: opportunities for research and dialog.

PubMed

Santoro, Flávia Rosa; Nascimento, André Luiz Borba; Soldati, Gustavo Taboada; Ferreira Júnior, Washington Soares; Albuquerque, Ulysses Paulino

2018-01-09

The interest in theoretical frameworks that improve our understanding of social-ecological systems is growing within the field of ethnobiology. Several evolutionary questions may underlie the relationships between people and the natural resources that are investigated in this field. A new branch of research, known as evolutionary ethnobiology (EE), focuses on these questions and has recently been formally conceptualized. The field of cultural evolution (CE) has significantly contributed to the development of this new field, and it has introduced the Darwinian concepts of variation, competition, and heredity to studies that focus on the dynamics of local knowledge. In this article, we introduce CE as an important theoretical framework for evolutionary ethnobiological research. We present the basic concepts and assumptions of CE, along with the adjustments that are necessary for its application in EE. We discuss different ethnobiological studies in the context of this new framework and the new opportunities for research that exist in this area. We also propose a dialog that includes our findings in the context of cultural evolution.

Evolutionary Software Development (Developpement Evolutionnaire de Logiciels)

DTIC Science & Technology

2008-08-01

development processes. While this may be true, frequently it is not. MIL-STD-498 was explicitly introduced to encourage iterative development; ISO /IEC... 12207 was carefully worded not to prohibit iterative development. Yet both standards were widely interpreted as requiring waterfall development, as

Evolutionary Software Development (Developpement evolutionnaire de logiciels)

DTIC Science & Technology

2008-08-01

development processes. While this may be true, frequently it is not. MIL-STD-498 was explicitly introduced to encourage iterative development; ISO /IEC... 12207 was carefully worded not to prohibit iterative development. Yet both standards were widely interpreted as requiring waterfall development, as

The evolutionary development of high specific impulse electric thruster technology

NASA Technical Reports Server (NTRS)

Sovey, James S.; Hamley, John A.; Patterson, Michael J.; Rawlin, Vincent K.; Myers, Roger M.

1992-01-01

Electric propulsion flight and technology demonstrations conducted in the USA, Europe, Japan, China, and USSR are reviewed with reference to the major flight qualified electric propulsion systems. These include resistojets, ion thrusters, ablative pulsed plasma thrusters, stationary plasma thrusters, pulsed magnetoplasmic thrusters, and arcjets. Evolutionary mission applications are presented for high specific impulse electric thruster systems. The current status of arcjet, ion, and magnetoplasmadynamic thrusters and their associated power processor technologies are summarized.

The kW power module evolution study: Executive summary

NASA Technical Reports Server (NTRS)

1979-01-01

Using the Marshall Space Flight Center 25 kW Power Module (PM) reference design as a point of departure, the study defined evolutionary growth paths to 100 kW and above. A recommended development approach and initial configurations were described. Specific hardware changes from the reference design are recommended for the initial PM configuration to ensure evolutionary growth, improved replicability, and reduced cost. Certain functional changes are also recommended to enhance system capabilities.

The Test and Evaluation of Unmanned and Autonomous Systems

DTIC Science & Technology

2008-12-01

robotic/ intelli - gent machines for the U.S. Department of Defense (DoD). Although the technology is still nascent and advancing, we are faced with the...evolutionary nature of UAS acquisition must be met with evolutionary test capabilities yet to be discovered and developed. Test capabilities must be deployed...at a faster pace than UAS deployment to satisfy the demand for warfighter improvements. The DoD is stimulating this new area of innovation with

Eco-evolutionary feedbacks, adaptive dynamics and evolutionary rescue theory

PubMed Central

Ferriere, Regis; Legendre, Stéphane

2013-01-01

Adaptive dynamics theory has been devised to account for feedbacks between ecological and evolutionary processes. Doing so opens new dimensions to and raises new challenges about evolutionary rescue. Adaptive dynamics theory predicts that successive trait substitutions driven by eco-evolutionary feedbacks can gradually erode population size or growth rate, thus potentially raising the extinction risk. Even a single trait substitution can suffice to degrade population viability drastically at once and cause ‘evolutionary suicide’. In a changing environment, a population may track a viable evolutionary attractor that leads to evolutionary suicide, a phenomenon called ‘evolutionary trapping’. Evolutionary trapping and suicide are commonly observed in adaptive dynamics models in which the smooth variation of traits causes catastrophic changes in ecological state. In the face of trapping and suicide, evolutionary rescue requires that the population overcome evolutionary threats generated by the adaptive process itself. Evolutionary repellors play an important role in determining how variation in environmental conditions correlates with the occurrence of evolutionary trapping and suicide, and what evolutionary pathways rescue may follow. In contrast with standard predictions of evolutionary rescue theory, low genetic variation may attenuate the threat of evolutionary suicide and small population sizes may facilitate escape from evolutionary traps. PMID:23209163

Evolutionary and Comparative Genomics to Drive Rational Drug Design, with Particular Focus on Neuropeptide Seven-Transmembrane Receptors.

PubMed

Furlong, Michael; Seong, Jae Young

2017-01-01

Seven transmembrane receptors (7TMRs), also known as G protein-coupled receptors, are popular targets of drug development, particularly 7TMR systems that are activated by peptide ligands. Although many pharmaceutical drugs have been discovered via conventional bulk analysis techniques the increasing availability of structural and evolutionary data are facilitating change to rational, targeted drug design. This article discusses the appeal of neuropeptide-7TMR systems as drug targets and provides an overview of concepts in the evolution of vertebrate genomes and gene families. Subsequently, methods that use evolutionary concepts and comparative analysis techniques to aid in gene discovery, gene function identification, and novel drug design are provided along with case study examples.

Evolutionary Games with Randomly Changing Payoff Matrices

NASA Astrophysics Data System (ADS)

Yakushkina, Tatiana; Saakian, David B.; Bratus, Alexander; Hu, Chin-Kun

2015-06-01

Evolutionary games are used in various fields stretching from economics to biology. In most of these games a constant payoff matrix is assumed, although some works also consider dynamic payoff matrices. In this article we assume a possibility of switching the system between two regimes with different sets of payoff matrices. Potentially such a model can qualitatively describe the development of bacterial or cancer cells with a mutator gene present. A finite population evolutionary game is studied. The model describes the simplest version of annealed disorder in the payoff matrix and is exactly solvable at the large population limit. We analyze the dynamics of the model, and derive the equations for both the maximum and the variance of the distribution using the Hamilton-Jacobi equation formalism.

Evolutionary and Comparative Genomics to Drive Rational Drug Design, with Particular Focus on Neuropeptide Seven-Transmembrane Receptors

PubMed Central

Furlong, Michael; Seong, Jae Young

2017-01-01

Seven transmembrane receptors (7TMRs), also known as G protein-coupled receptors, are popular targets of drug development, particularly 7TMR systems that are activated by peptide ligands. Although many pharmaceutical drugs have been discovered via conventional bulk analysis techniques the increasing availability of structural and evolutionary data are facilitating change to rational, targeted drug design. This article discusses the appeal of neuropeptide-7TMR systems as drug targets and provides an overview of concepts in the evolution of vertebrate genomes and gene families. Subsequently, methods that use evolutionary concepts and comparative analysis techniques to aid in gene discovery, gene function identification, and novel drug design are provided along with case study examples. PMID:28035082

Phylomemetics—Evolutionary Analysis beyond the Gene

PubMed Central

Howe, Christopher J.; Windram, Heather F.

2011-01-01

Genes are propagated by error-prone copying, and the resulting variation provides the basis for phylogenetic reconstruction of evolutionary relationships. Horizontal gene transfer may be superimposed on a tree-like evolutionary pattern, with some relationships better depicted as networks. The copying of manuscripts by scribes is very similar to the replication of genes, and phylogenetic inference programs can be used directly for reconstructing the copying history of different versions of a manuscript text. Phylogenetic methods have also been used for some time to analyse the evolution of languages and the development of physical cultural artefacts. These studies can help to answer a range of anthropological questions. We propose the adoption of the term “phylomemetics” for phylogenetic analysis of reproducing non-genetic elements. PMID:21655311

Links between Evolution, Development, Human Anatomy, Pathology, and Medicine, with A Proposition of A Re-defined Anatomical Position and Notes on Constraints and Morphological "Imperfections".

PubMed

Diogo, Rui; Molnar, Julia

2016-06-01

Surprisingly the oldest formal discipline in medicine (anatomy) has not yet felt the full impact of evolutionary developmental biology. In medical anatomy courses and textbooks, the human body is still too often described as though it is a "perfect machine." In fact, the study of human anatomy predates evolutionary theory; therefore, many of its conventions continue to be outdated, making it difficult to study, understand, and treat the human body, and to compare it with that of other, nonbipedal animals, including other primates. Moreover, such an erroneous view of our anatomy as "perfect" can be used to fuel nonevolutionary ideologies such as intelligent design. In the section An Evolutionary and Developmental Approach to Human Anatomical Position of this paper, we propose the redefinition of the "human standard anatomical position" used in textbooks to be consistent with human evolutionary and developmental history. This redefined position also simplifies, for students and practitioners of the health professions, the study and learning of embryonic muscle groups (each group including muscles derived from the same/ontogenetically closely related primordium/primordia) and joint movements and highlights the topological correspondence between the upper and lower limbs. Section Evolutionary and Developmental Constraints, "Imperfections" and Sports Pathologies continues the theme by describing examples of apparently "illogical" characteristics of the human body that only make sense when one understands the developmental and evolutionary constraints that have accumulated over millions of years. We focus, in particular, on musculoskeletal functional problems and sports pathologies to emphasize the links with pathology and medicine. These examples demonstrate how incorporating evolutionary theory into anatomy education can be helpful for medical students, teachers, researchers, and physicians, as well as for anatomists, functional morphologists, and evolutionary and developmental biologists. © 2016 Wiley Periodicals, Inc.

What to expect from an evolutionary hypothesis for a human disease: The case of type 2 diabetes.

PubMed

Watve, Milind; Diwekar-Joshi, Manawa

2016-10-01

Evolutionary medicine has a promise to bring in a conceptual revolution in medicine. However, as yet the field does not have the same theoretical rigour as that of many other fields in evolutionary studies. We discuss here with reference to type 2 diabetes mellitus (T2DM) what role an evolutionary hypothesis should play in the development of thinking in medicine. Starting with the thrifty gene hypothesis, evolutionary thinking in T2DM has undergone several transitions, modifications and refinements of the thrift family of hypotheses. In addition alternative hypotheses independent of thrift are also suggested. However, most hypotheses look at partial pictures; make selective use of supportive data ignoring inconvenient truths. Most hypotheses look at a superficial picture and avoid getting into the intricacies of underlying molecular, neuronal and physiological processes. Very few hypotheses have suggested clinical implications and none of them have been tested with randomized clinical trials. In the meanwhile the concepts in the pathophysiology of T2DM are undergoing radical changes and evolutionary hypotheses need to take them into account. We suggest an approach and a set of criteria to evaluate the relative merits of the alternative hypotheses. A number of hypotheses are likely to fail when critically evaluated against these criteria. It is possible that more than one selective process are at work in the evolution of propensity to T2DM, but the intercompatibility of the alternative selective forces and their relative contribution needs to be examined. The approach we describe could potentially lead to a sound evolutionary theory that is clinically useful and testable by randomized controlled clinical trials. Copyright © 2016 Elsevier GmbH. All rights reserved.

Emerging Concepts of Data Integration in Pathogen Phylodynamics.

PubMed

Baele, Guy; Suchard, Marc A; Rambaut, Andrew; Lemey, Philippe

2017-01-01

Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise insights in infectious diseases and to increase opportunities for statistical hypothesis testing. Here, we review how the emerging concept of data integration is stimulating new advances in Bayesian evolutionary inference methodology which formalize a marriage of statistical thinking and evolutionary biology. These approaches include connecting sequence to trait evolution, such as for host, phenotypic and geographic sampling information, but also the incorporation of covariates of evolutionary and epidemic processes in the reconstruction procedures. We highlight how a full Bayesian approach to covariate modeling and testing can generate further insights into sequence evolution, trait evolution, and population dynamics in pathogen populations. Specific examples demonstrate how such approaches can be used to test the impact of host on rabies and HIV evolutionary rates, to identify the drivers of influenza dispersal as well as the determinants of rabies cross-species transmissions, and to quantify the evolutionary dynamics of influenza antigenicity. Finally, we briefly discuss how data integration is now also permeating through the inference of transmission dynamics, leading to novel insights into tree-generative processes and detailed reconstructions of transmission trees. [Bayesian inference; birth–death models; coalescent models; continuous trait evolution; covariates; data integration; discrete trait evolution; pathogen phylodynamics.

Emerging Concepts of Data Integration in Pathogen Phylodynamics

PubMed Central

Baele, Guy; Suchard, Marc A.; Rambaut, Andrew; Lemey, Philippe

2017-01-01

Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise insights in infectious diseases and to increase opportunities for statistical hypothesis testing. Here, we review how the emerging concept of data integration is stimulating new advances in Bayesian evolutionary inference methodology which formalize a marriage of statistical thinking and evolutionary biology. These approaches include connecting sequence to trait evolution, such as for host, phenotypic and geographic sampling information, but also the incorporation of covariates of evolutionary and epidemic processes in the reconstruction procedures. We highlight how a full Bayesian approach to covariate modeling and testing can generate further insights into sequence evolution, trait evolution, and population dynamics in pathogen populations. Specific examples demonstrate how such approaches can be used to test the impact of host on rabies and HIV evolutionary rates, to identify the drivers of influenza dispersal as well as the determinants of rabies cross-species transmissions, and to quantify the evolutionary dynamics of influenza antigenicity. Finally, we briefly discuss how data integration is now also permeating through the inference of transmission dynamics, leading to novel insights into tree-generative processes and detailed reconstructions of transmission trees. [Bayesian inference; birth–death models; coalescent models; continuous trait evolution; covariates; data integration; discrete trait evolution; pathogen phylodynamics. PMID:28173504

Brain maps, great and small: lessons from comparative studies of primate visual cortical organization

PubMed Central

Rosa, Marcello G.P; Tweedale, Rowan

2005-01-01

In this paper, we review evidence from comparative studies of primate cortical organization, highlighting recent findings and hypotheses that may help us to understand the rules governing evolutionary changes of the cortical map and the process of formation of areas during development. We argue that clear unequivocal views of cortical areas and their homologies are more likely to emerge for ‘core’ fields, including the primary sensory areas, which are specified early in development by precise molecular identification steps. In primates, the middle temporal area is probably one of these primordial cortical fields. Areas that form at progressively later stages of development correspond to progressively more recent evolutionary events, their development being less firmly anchored in molecular specification. The certainty with which areal boundaries can be delimited, and likely homologies can be assigned, becomes increasingly blurred in parallel with this evolutionary/developmental sequence. For example, while current concepts for the definition of cortical areas have been vindicated in allowing a clarification of the organization of the New World monkey ‘third tier’ visual cortex (the third and dorsomedial areas, V3 and DM), our analyses suggest that more flexible mapping criteria may be needed to unravel the organization of higher-order visual association and polysensory areas. PMID:15937007

Morphological diversity of microstructures occurring in selected recent bivalve shells and their ecological implications

NASA Astrophysics Data System (ADS)

Brom, Krzysztof Roman; Szopa, Krzysztof

2016-12-01

Environmental adaptation of molluscs during evolution has led to form biomineral exoskeleton - shell. The main compound of their shells is calcium carbonate, which is represented by calcite and/or aragonite. The mineral part, together with the biopolymer matrix, forms many types of microstructures, which are differ in texture. Different types of internal shell microstructures are characteristic for some bivalve groups. Studied bivalve species (freshwater species - duck mussel (Anodonta anatina Linnaeus, 1758) and marine species - common cockle (Cerastoderma edule Linnaeus, 1758), lyrate Asiatic hard clam (Meretrix lyrata Sowerby II, 1851) and blue mussel (Mytilus edulis Linnaeus, 1758)) from different locations and environmental conditions, show that the internal shell microstructure with the shell morphology and thickness have critical impact to the ability to survive in changing environment and also to the probability of surviving predator attack. Moreover, more detailed studies on molluscan structures might be responsible for create mechanically resistant nanomaterials.

High-resolution rock-magnetic variability in shallow marine sediment: a sensitive paleoclimatic metronome

NASA Astrophysics Data System (ADS)

Arai, Kohsaku; Sakai, Hideo; Konishi, Kenji

1997-05-01

An outer shelf deposit in central Japan centered on the Olduvai normal polarity event in the reversed Matuyama chron reveals a close correlation of both the magnetic susceptibility and remanent intensity with the sedimentary cyclicities apparent in lithologies and molluscan assemblages. Two sedimentary cycles are characterized by distinctly similar, but double-peaked magnetic cyclicities. The rock-magnetic variability is primarily attributed to the relative abundance of terrigenous magnetic minerals, and the double peak of the variability is characterized by the concentration of finer-grained magnetic minerals. The concentration is suspected to be controlled by both climatic change and shifting proximity of the shoreline as a function of rise and fall of the sea level due to glacio-eustasy. Rock-magnetic study reveals the record of a 21 ka period of orbital precession cycles within the sedimentary cyclicity attributable to a 41 ka period of orbital obliquity forcing.

Recovery of primary sporocysts in vivo in the Schistosoma mansoni/Biomphalaria glabrata model using a simple fixation method suitable for extraction of genomic DNA and RNA.

PubMed

Allienne, Jean-François; Théron, André; Gourbal, Benjamin

2011-09-01

Detailed studies of host/parasite interactions are currently limited because in situ gene sequencing or monitoring of parasite gene expression is so far limited to genes presenting a high loci copy number in the Schistosome genome or a high level of expression. Indeed, how to investigate the host parasite molecular interplay when parasites are not directly accessible in vivo? Here we describe a method to circumvent this problem and to analyze DNA and RNA of Schistosoma mansoni during the interaction with its intermediate snail host Biomphalaria glabrata. We propose a technique for improved DNA and RNA extraction from the intra-molluscan stage of the parasite recovered after fixation of infected snails in Raillet-Henry solution. The extractions can be used for genetic analysis, transcription studies and microsatellite genotyping. Copyright © 2011 Elsevier Inc. All rights reserved.

Calcium carbonate mineralization mediated by in vitro cultured mantle cells from Pinctada fucata.

PubMed

Kong, Wei; Li, Shiguo; Xiang, Liang; Xie, Liping; Zhang, Rongqing

2015-08-07

Formation of the molluscan shell is believed to be an extracellular event mediated by matrix proteins. We report calcium carbonate mineralization mediated by Pinctada fucata mantle cells. Crystals only appeared when mantle cells were present in the crystallization solution. These crystals were piled up in highly ordered units and showed the typical characteristics of biomineralization products. A thin organic framework was observed after dissolving the crystals in EDTA. Some crystals had etched surfaces with a much smoother appearance than other parts. Mantle cells were observed to be attached to some of these smooth surfaces. These results suggest that mantle cells may be directly involved in the nucleation and remodeling process of calcium carbonate mineralization. Our result demonstrate the practicability of studying the mantle cell mechanism of biomineralization and contribute to the overall understanding of the shell formation process. Copyright © 2015 Elsevier Inc. All rights reserved.

Synaptic Neurotransmitter-Gated Receptors

PubMed Central

Smart, Trevor G.; Paoletti, Pierre

2012-01-01

Since the discovery of the major excitatory and inhibitory neurotransmitters and their receptors in the brain, many have deliberated over their likely structures and how these may relate to function. This was initially satisfied by the determination of the first amino acid sequences of the Cys-loop receptors that recognized acetylcholine, serotonin, GABA, and glycine, followed later by similar determinations for the glutamate receptors, comprising non-NMDA and NMDA subtypes. The last decade has seen a rapid advance resulting in the first structures of Cys-loop receptors, related bacterial and molluscan homologs, and glutamate receptors, determined down to atomic resolution. This now provides a basis for determining not just the complete structures of these important receptor classes, but also for understanding how various domains and residues interact during agonist binding, receptor activation, and channel opening, including allosteric modulation. This article reviews our current understanding of these mechanisms for the Cys-loop and glutamate receptor families. PMID:22233560

Herbicide trials in the snail habitats of the Egypt 49 project*

PubMed Central

Dawood, Ismail K.; Farooq, M.; Dazo, B. C.; Miguel, Luis C.; Unrau, G. O.

1965-01-01

The molluscan hosts of Schistosoma haematobium, Schistosoma mansoni and Fasciola spp. have been found to flourish in association with certain submersed, floating and emergent weeds in the irrigation system of the Egypt 49 project area. The efficacy of acrolein in killing Potamogeton crispus, an important submersed weed, has been previously established. The present paper deals with field trials of different herbicides, alone or combined, against the other predominant types of floating and emergent weeds—Eichhornia crassipes, Panicum repens, Typha ungustata and Scirpus inclinatus. The trials showed that some of the herbicides are effective and have economic advantages over the manual removal of weeds, besides eliminating the health hazard involved in manual removal. Laboratory tests showed that the herbicides also have ovicidal properties. Aquatic-weed control by the use of appropriate herbicides as an adjunct to molluscicides is therefore advocated. PMID:14310915

Secondary carbonate porosity as related to early teritiary depositional facies, Zelten field, Libya

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bebout, D.G.; Pendexter, C.

1975-04-01

Production from the Zelten field, Libya, is from the highly porous shelf limestones of the Zelten Member (Main Pay) of the Paleocene and lower Eocene Ruaga Limestone. Fifteen facies are recognized, mapped, and predicted. Seven of the facies comprise the larger part of the Zelten Member. These include miliolid-foraminiferal micrite, argillaceous bryozoan/echinoid micrite, argillaceous-molluscan micrite, coralgal micrite. Discocyclina-foraminiferal calcarenite, foraminiferal calcarenite and micrite, and Discocyclina-foraminiferal micrite. In the Zelten field secondary porosity is recorded as much as 40%; this porosity is related to the original depositional fabric of the sediment and, therefore, is facies controlled. Porosity is highest in themore » coralgal micrite and Discocyclina-foraminiferal calcarenite, which together form a NW.-SE. trend across the N. part of the field, and in the formaniniferal calcarenite and micrite. (10 refs.)« less

Protozoa interaction with aquatic invertebrate: interest for watercourses biomonitoring.

PubMed

Palos Ladeiro, M; Bigot, A; Aubert, D; Hohweyer, J; Favennec, L; Villena, I; Geffard, A

2013-02-01

Toxoplasma gondii, Cryptosporidium parvum, and Giardia duodenalis are human waterborne protozoa. These worldwide parasites had been detected in various watercourses as recreational, surface, drinking, river, and seawater. As of today, water protozoa detection was based on large water filtration and on sample concentration. Another tool like aquatic invertebrate parasitism could be used for sanitary and environmental biomonitoring. In fact, organisms like filter feeders could already filtrate and concentrate protozoa directly in their tissues in proportion to ambient concentration. So molluscan shellfish can be used as a bioindicator of protozoa contamination level in a site since they were sedentary. Nevertheless, only a few researches had focused on nonspecific parasitism like protozoa infection on aquatic invertebrates. Objectives of this review are twofold: Firstly, an overview of protozoa in worldwide water was presented. Secondly, current knowledge of protozoa parasitism on aquatic invertebrates was detailed and the lack of data of their biological impact was pointed out.

Connecting theory and data to understand recombination rate evolution.

PubMed

Dapper, Amy L; Payseur, Bret A

2017-12-19

Meiotic recombination is necessary for successful gametogenesis in most sexually reproducing organisms and is a fundamental genomic parameter, influencing the efficacy of selection and the fate of new mutations. The molecular and evolutionary functions of recombination should impose strong selective constraints on the range of recombination rates. Yet, variation in recombination rate is observed on a variety of genomic and evolutionary scales. In the past decade, empirical studies have described variation in recombination rate within genomes, between individuals, between sexes, between populations and between species. At the same time, theoretical work has provided an increasingly detailed picture of the evolutionary advantages to recombination. Perhaps surprisingly, the causes of natural variation in recombination rate remain poorly understood. We argue that empirical and theoretical approaches to understand the evolution of recombination have proceeded largely independently of each other. Most models that address the evolution of recombination rate were created to explain the evolutionary advantage of recombination rather than quantitative differences in rate among individuals. Conversely, most empirical studies aim to describe variation in recombination rate, rather than to test evolutionary hypotheses. In this Perspective, we argue that efforts to integrate the rich bodies of empirical and theoretical work on recombination rate are crucial to moving this field forward. We provide new directions for the development of theory and the production of data that will jointly close this gap.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'. © 2017 The Author(s).

HBC-Evo: predicting human breast cancer by exploiting amino acid sequence-based feature spaces and evolutionary ensemble system.

PubMed

Majid, Abdul; Ali, Safdar

2015-01-01

We developed genetic programming (GP)-based evolutionary ensemble system for the early diagnosis, prognosis and prediction of human breast cancer. This system has effectively exploited the diversity in feature and decision spaces. First, individual learners are trained in different feature spaces using physicochemical properties of protein amino acids. Their predictions are then stacked to develop the best solution during GP evolution process. Finally, results for HBC-Evo system are obtained with optimal threshold, which is computed using particle swarm optimization. Our novel approach has demonstrated promising results compared to state of the art approaches.

Advances in understanding tumour evolution through single-cell sequencing.

PubMed

Kuipers, Jack; Jahn, Katharina; Beerenwinkel, Niko

2017-04-01

The mutational heterogeneity observed within tumours poses additional challenges to the development of effective cancer treatments. A thorough understanding of a tumour's subclonal composition and its mutational history is essential to open up the design of treatments tailored to individual patients. Comparative studies on a large number of tumours permit the identification of mutational patterns which may refine forecasts of cancer progression, response to treatment and metastatic potential. The composition of tumours is shaped by evolutionary processes. Recent advances in next-generation sequencing offer the possibility to analyse the evolutionary history and accompanying heterogeneity of tumours at an unprecedented resolution, by sequencing single cells. New computational challenges arise when moving from bulk to single-cell sequencing data, leading to the development of novel modelling frameworks. In this review, we present the state of the art methods for understanding the phylogeny encoded in bulk or single-cell sequencing data, and highlight future directions for developing more comprehensive and informative pictures of tumour evolution. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes.

PubMed

Weaver, Steven; Shank, Stephen D; Spielman, Stephanie J; Li, Michael; Muse, Spencer V; Kosakovsky Pond, Sergei L

2018-01-02

Inference of how evolutionary forces have shaped extant genetic diversity is a cornerstone of modern comparative sequence analysis. Advances in sequence generation and increased statistical sophistication of relevant methods now allow researchers to extract ever more evolutionary signal from the data, albeit at an increased computational cost. Here, we announce the release of Datamonkey 2.0, a completely re-engineered version of the Datamonkey web-server for analyzing evolutionary signatures in sequence data. For this endeavor, we leveraged recent developments in open-source libraries that facilitate interactive, robust, and scalable web application development. Datamonkey 2.0 provides a carefully curated collection of methods for interrogating coding-sequence alignments for imprints of natural selection, packaged as a responsive (i.e. can be viewed on tablet and mobile devices), fully interactive, and API-enabled web application. To complement Datamonkey 2.0, we additionally release HyPhy Vision, an accompanying JavaScript application for visualizing analysis results. HyPhy Vision can also be used separately from Datamonkey 2.0 to visualize locally-executed HyPhy analyses. Together, Datamonkey 2.0 and HyPhy Vision showcase how scientific software development can benefit from general-purpose open-source frameworks. Datamonkey 2.0 is freely and publicly available at http://www.datamonkey. org, and the underlying codebase is available from https://github.com/veg/datamonkey-js. © The Author 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.