Citations with the tag: DIVERGENCE (Biology)

Results 151 - 200

  • Mesozoic fossils (>145 Mya) suggest the antiquity of the subgenera of Daphnia and their coevolution with chaoborid predators.
    Kotov, Alexey A.; Taylor, Derek J. // BMC Evolutionary Biology; 2011, Vol. 11 Issue 1, p129 

    Background: The timescale of the origins of Daphnia O. F. Mueller (Crustacea: Cladocera) remains controversial. The origin of the two main subgenera has been associated with the breakup of the supercontinent Pangaea. This vicariance hypothesis is supported by reciprocal monophyly, present day...

  • Palaeoclimatic events, dispersal and migratory losses along the Afro-European axis as drivers of biogeographic distribution in Sylvia warblers.
    Voelker, Gary; Light, Jessica E. // BMC Evolutionary Biology; 2011, Vol. 11 Issue 1, p163 

    Background: The Old World warbler genus Sylvia has been used extensively as a model system in a variety of ecological, genetic, and morphological studies. The genus is comprised of about 25 species, and 70% of these species have distributions at or near the Mediterranean Sea. This distribution...

  • Phylogeography and demographic history of Lacerta lepida in the Iberian Peninsula: multiple refugia, range expansions and secondary contact zones.
    Miraldo, Andreia; Hewitt, Godfrey M.; Paulo, Octavio S.; Emerson, Brent C. // BMC Evolutionary Biology; 2011, Vol. 11 Issue 1, p170 

    Background: The Iberian Peninsula is recognized as an important refugial area for species survival and diversification during the climatic cycles of the Quaternary. Recent phylogeographic studies have revealed Iberia as a complex of multiple refugia. However, most of these studies have focused...

  • From Antarctica or Asia? New colonization scenario for Australian-New Guinean narrow mouth toads suggested from the findings on a mysterious genus Gastrophrynoides.
    Kurabayashi, Atsushi; Matsui, Masafumi; Belabut, Daicus M.; Hoi-Sen Yong; Ahmad, Norhayati; Sudin, Ahmad; Kuramoto, Mitsuru; Hamidy, Amir; Sumida, Masayuki // BMC Evolutionary Biology; 2011, Vol. 11 Issue 1, p175 

    Background: Microhylidae is a geographically widespread family of anurans. Although several extensive molecular analyses have attempted to elucidate their subfamilial relationships, and correlate these with Mesozoic and Cenozoic continental drifts, consensus has not been reached. Further,...

  • Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation.
    Nakatani, Masanori; Miya, Masaki; Mabuchi, Kohji; Saitoh, Kenji; Nishida, Mutsumi // BMC Evolutionary Biology; 2011, Vol. 11 Issue 1, p177 

    Background: Freshwater harbors approximately 12,000 fish species accounting for 43% of the diversity of all modern fish. A single ancestral lineage evolved into about two-thirds of this enormous biodiversity (≈ 7900 spp.) and is currently distributed throughout the world's continents...

  • Genetic mechanisms involved in the evolution of the cephalopod camera eye revealed by transcriptomic and developmental studies.
    Yoshida, Masa-aki; Ogura, Atsushi // BMC Evolutionary Biology; 2011, Vol. 11 Issue 1, p180 

    Background: Coleoid cephalopods (squids and octopuses) have evolved a camera eye, the structure of which is very similar to that found in vertebrates and which is considered a classic example of convergent evolution. Other molluscs, however, possess mirror, pin-hole, or compound eyes, all of...

  • Variations on a theme: diversification of cuticular hydrocarbons in a clade of cactophilic Drosophila.
    Yoshida, Masa-aki; Ogura, Atsushi // BMC Evolutionary Biology; 2011, Vol. 11 Issue 1, p179 

    The article reports on the quantitative differences analysis in chemical composition of epicuticular hydrocarbons (CHCs) in seven species of the drosophila buzzatii cluster. It states the analysis was done to assess the concordance of CHC differentiation with species divergence. Multivariate...

  • Predictors for reproductive isolation in a ring species complex following genetic and ecological divergence.
    Yoshida, Masa-aki; Ogura, Atsushi // BMC Evolutionary Biology; 2011, Vol. 11 Issue 1, p194 

    The article reports on quantitative analysis of genetic interactions at several stages of divergence within the ring species complex ensatina eschscholtzi to assess the contribution of genetic and ecological divergence for the development of reproductive isolation (RI). The results show, in...

  • Population connectivity: dam migration mitigations and contemporary site fidelity in arctic char.
    Yoshida, Masa-aki; Ogura, Atsushi // BMC Evolutionary Biology; 2011, Vol. 11 Issue 1, p207 

    The article reports on a study which examines genetic population connectivity of highly migrating lake-dwelling Arctic char, within two subalpine lakes separated by a dam with a subterranean tunnel and spill gates. Char populations, with similar genetic structuring and diversity observed across...

  • CpG site degeneration triggered by the loss of functional constraint created a highly polymorphic macaque drug-metabolizing gene, CYP1A2.
    Yoshida, Masa-aki; Ogura, Atsushi // BMC Evolutionary Biology; 2011, Vol. 11 Issue 1, p283 

    The article presents information on a study on the pattern of divergence and polymorphisms of major drug-metabolizing genes in humans including macaque CYP1A1 and CYP1A2 genes. The study found that the CYP1A1/2 gene copy number and orientation is highly conserved in mammalian genomes. The study...

  • Molecular identification of five Indian sciaenids (pisces: perciformes, sciaenidae) using RAPD markers.
    Lakra, Wazir; Goswami, M.; Mohindra, V.; Lal, K.; Punia, P. // Hydrobiologia; May2007, Vol. 583 Issue 1, p359 

    The randomly amplified polymorphic DNA (RAPD) markers were used to detect interspecific genetic variability and genetic relatedness among five Indian sciaenids namely Otolithes cuvieri, Johnieops sina, Johnieops macrorhynus, Johnieops vogleri and Protonibea diacanthus for the first time. Eight...

  • Integrative analyses of speciation and divergence in Psammodromus hispanicus (Squamata: Lacertidae).
    Lakra, Wazir; Goswami, M.; Mohindra, V.; Lal, K.; Punia, P. // BMC Evolutionary Biology; 2011, Vol. 11 Issue 1, p347 

    The article focuses on the genetic, phenotype and ecological divergence within a lineage. It states that this divergence is caused because of ongoing evolutionary processes. It mentions that this study uses phylogenetic, phenotypic, geographic, and environmental data for investigating the...

  • Relationships Among Ecologically Important Dimensions of Plant Trait Variation in Seven Neotropical Forests.
    Ian J. Wright; David D. Ackerly; Frans Bongers; Kyle E. Harms; Guillermo Ibarra-Manriquez; Miguel Martinez-Ramos; Susan J. Mazer; Helene C. Muller-Landau; Horacio Paz; Nigel C. A. Pitman; Lourens Poorter; Miles R. Silman; Corine F. Vriesendorp; Cam O. Webb; Mark Westoby; S. Joseph Wright // Annals of Botany; May2007, Vol. 99 Issue 5, p1003 

    Background and AimsWhen ecologically important plant traits are correlated they may be said to constitute an ecological ‘strategy’ dimension. Through identifying these dimensions and understanding their inter-relationships we gain insight into why particular trait...

  • Positive selection drives a correlation between non-synonymous/synonymous divergence and functional divergence.
    Ian J. Wright; David D. Ackerly; Frans Bongers; Kyle E. Harms; Guillermo Ibarra-Manriquez; Miguel Martinez-Ramos; Susan J. Mazer; Helene C. Muller-Landau; Horacio Paz; Nigel C. A. Pitman; Lourens Poorter; Miles R. Silman; Corine F. Vriesendorp; Cam O. Webb; Mark Westoby; S. Joseph Wright // Bioinformatics; Jun2008, Vol. 24 Issue 12, p1421 

    Motivation: Functional divergence among proteins is often assumed to be strongly influenced by natural selection, as inferred from the ratio of non-synonymous nucleotide divergence (dN) to synonymous nucleotide divergence (dS). That is, the more a mutation changes protein function, the more...

  • Positive selection drives a correlation between non-synonymous/synonymous divergence and functional divergence.
    Ian J. Wright; David D. Ackerly; Frans Bongers; Kyle E. Harms; Guillermo Ibarra-Manriquez; Miguel Martinez-Ramos; Susan J. Mazer; Helene C. Muller-Landau; Horacio Paz; Nigel C. A. Pitman; Lourens Poorter; Miles R. Silman; Corine F. Vriesendorp; Cam O. Webb; Mark Westoby; S. Joseph Wright // Bioinformatics; Jun2008, Vol. 24 Issue 12, p1421 

    Motivation: Functional divergence among proteins is often assumed to be strongly influenced by natural selection, as inferred from the ratio of non-synonymous nucleotide divergence (dN) to synonymous nucleotide divergence (dS). That is, the more a mutation changes protein function, the more...

  • Mature habitats associated with genetic divergence despite strong dispersal ability in an arthropod.
    Ishida, Seiji; Taylor, Derek J. // BMC Evolutionary Biology; 2007, Vol. 7, p52 

    Background: Populations may be bound by contemporary gene flow, selective sweeps, and extinction-recolonization processes. Indeed, existing molecular estimates indicate that species with low levels of gene flow are rare. However, strong priority effects and local selective regimes may hinder...

  • Evolutionary divergence of chloroplast FAD synthetase proteins.
    Yruela, Inmaculada; Arilla-Luna, Sonia; Medina, Milagros; Contreras-Moreira, Bruno // BMC Evolutionary Biology; 2010, Vol. 10, p311 

    Background: Flavin adenine dinucleotide synthetases (FADSs) - a group of bifunctional enzymes that carry out the dual functions of riboflavin phosphorylation to produce flavin mononucleotide (FMN) and its subsequent adenylation to generate FAD in most prokaryotes - were studied in plants in...

  • Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists.
    Burki, Fabien; Kudryavtsev, Alexander; Matz, Mikhail V.; Aglyamova, Galina V.; Bulman, Simon; Fiers, Mark; Keeling, Patrick J.; Pawlowski, Jan // BMC Evolutionary Biology; 2010, Vol. 10, p377 

    Background: Recent phylogenomic analyses have revolutionized our view of eukaryote evolution by revealing unexpected relationships between and within the eukaryotic supergroups. However, for several groups of uncultivable protists, only the ribosomal RNA genes and a handful of proteins are...

  • A systematic evaluation of hybridization-based mouse exome capture system.
    Gao, Qingsong; Wei Sun; Xintian You; Froehler, Sebastian; Wei Chen // BMC Genomics; 2013, Vol. 14 Issue 1, p1 

    Background: Exome sequencing is increasingly used to search for phenotypically-relevant sequence variants in the mouse genome. All of the current hybridization-based mouse exome capture systems are designed based on the genome reference sequences of the C57BL/6 J strain. Given that the...

  • Ancient lineage, young troglobites: recent colonization of caves by Nesticella spiders.
    Yuanyuan Zhang; Shuqiang Li // BMC Evolutionary Biology; 2013, Vol. 13 Issue 1, p1 

    Background: The evolution and origin of cave organisms is a recurring issue in evolutionary studies, but analyses are often hindered by the inaccessibility of caves, morphological convergence, and complex colonization processes. Here we investigated the evolutionary history of Nesticella cave...

  • A new approach for the analysis of bacterial microarray-based Comparative Genomic Hybridization: insights from an empirical study.
    Taboada, Eduardo N; Acedillo, Rey R; Luebbert, Christian C; Findlay, Wendy A; Nash, John HE // BMC Genomics; 2005, Vol. 6, p78 

    Background: Microarray-based Comparative Genomic Hybridization (M-CGH) has been used to characterize the extensive intraspecies genetic diversity found in bacteria at the whole-genome level. Although conventional microarray analytical procedures have proved adequate in handling M-CGH data, data...

  • Cross-Neutralization Potential of Native Human Papillomavirus N-Terminal L2 Epitopes.
    Conway, Michael J.; Cruz, Linda; Alam, Samina; Christensen, Neil David; Meyers, Craig // PLoS ONE; 2011, Vol. 6 Issue 2, p1 

    Background: Human papillomavirus (HPV) capsids are composed of 72 pentamers of the major capsid protein L1, and an unknown number of L2 minor capsid proteins. An N-terminal ''external loop'' of L2 contains cross-neutralizing epitopes, and native HPV16 virions extracted from 20-day-old...

  • Zoogeography of Intertidal Communities in the West Indian Ocean as Determined by Ocean Circulation Systems: Patterns from the Tetraclita Barnacles.
    Ling Ming Tsang; Yair Achituv; Ka Hou Chu; Benny Kwok Kan Chan; Senjie Lin // PLoS ONE; Sep2012, Vol. 7 Issue 9, Special section p1 

    The Indian Ocean is the least known ocean in the world with the biogeography of marine species in the West Indian Ocean (WIO) understudied. The hydrography of WIO is characterized by four distinct oceanographic systems and there were few glacial refugia formations in the WIO during the...

  • molecular clock (1967) Biology.
    Ling Ming Tsang; Yair Achituv; Ka Hou Chu; Benny Kwok Kan Chan; Senjie Lin // Dictionary of Theories; 2002, p349 

    Information on the theory of molecular clock is presented. The theory states that the rate of accumulation of genetic difference between two species is approximately proportional to the evolutionary time that has passed since the species diverged. The studies suggest that the divergence occurred...

  • Functional Divergence among Silkworm Antimicrobial Peptide Paralogs by the Activities of Recombinant Proteins and the Induced Expression Profiles.
    Yang, Wanying; Cheng, Tingcai; Ye, Mingqiang; Deng, Xiaojuan; Yi, Huiyu; Huang, Yadong; Tan, Xiang; Han, Dong; Wang, Bo; Xiang, Zhonghuai; Cao, Yang; Xia, Qingyou // PLoS ONE; 2011, Vol. 6 Issue 3, p1 

    Antimicrobial peptides are small-molecule proteins that are usually encoded by multiple-gene families. They play crucial roles in the innate immune response, but reports on the functional divergence of antimicrobial peptide gene families are rare. In this study, 14 paralogs of antimicrobial...

  • A Passerine Bird's Evolution Corroborates the Geologic History of the Island of New Guinea.
    Deiner, Kristy; Lemmon, Alan R.; Mack, Andrew L.; Fleischer, Robert C.; Dumbacher, John P. // PLoS ONE; 2011, Vol. 6 Issue 5, p1 

    New Guinea is a biologically diverse island, with a unique geologic history and topography that has likely played a role in the evolution of species. Few island-wide studies, however, have examined the phylogeographic history of lowland species. The objective of this study was to examine...

  • Comparing the Usefulness of Distance, Monophyly and Character-Based DNA Barcoding Methods in Species Identification: A Case Study of Neogastropoda.
    Shanmei Zou; Qi Li; Lingfeng Kong; Hong Yu; Xiaodong Zheng // PLoS ONE; 2011, Vol. 6 Issue 10, p1 

    Background: DNA barcoding has recently been proposed as a promising tool for the rapid species identification in a wide range of animal taxa. Two broad methods (distance and monophyly-based methods) have been used. One method is based on degree of DNA sequence variation within and between...

  • Phylogenetic Status and Timescale for the Diversification of Steno and Sotalia Dolphins.
    Cunha, Haydeé A.; Moraes, Lucas C.; Medeiros, Bruna V.; Lailson-Brito Jr., José; Silva, Vera M. F. da; Solé-Cava, Antonio M.; Schrago, Carlos G. // PLoS ONE; 2011, Vol. 6 Issue 12, p1 

    Molecular data have provided many insights into cetacean evolution but some unsettled issues still remain. We estimated the topology and timing of cetacean evolutionary relationships using Bayesian and maximum likelihood analyses of complete mitochondrial genomes. In order to clarify the...

  • An Integrative Method for Delimiting Cohesion Species: Finding the Population-Species Interface in a Group of Californian Trapdoor Spiders with Extreme Genetic Divergence and Geographic Structuring.
    Bond, Jason E.; Stockman, Amy K. // Systematic Biology; Aug2008, Vol. 57 Issue 4, p628 

    Here we present an objective, repeatable approach to delineating species when populations are divergent and highly structured geographically using the Californian trapdoor spider species complex Aptostichus atomarius Simon as a model system. This system is particularly difficult because under...

  • Repeated Lake-Stream Divergence in Stickleback Life History within a Central European Lake Basin.
    Moser, Dario; Roesti, Marius; Berner, Daniel // PLoS ONE; Dec2012, Vol. 7 Issue 12, p1 

    Life history divergence between populations inhabiting ecologically distinct habitats might be a potent source of reproductive isolation, but has received little attention in the context of speciation. We here test for life history divergence between threespine stickleback inhabiting Lake...

  • The personal experience of parenting a child with Juvenile Huntington's Disease: perceptions across Europe.
    Eatough, Virginia; Santini, Helen; Eiser, Christine; Goller, Marie-Louise; Krysa, Wioletta; de Nicola, 'Annunziata'; Paduanello, Matteo; Petrollini, Martina; Rakowicz, Maria; Squitieri, Ferdinando; Tibben, Aad; Lee Weille, Katie; Landwehrmeyer, Bernhard; Quarrell, Oliver; Smith, Jonathan A // European Journal of Human Genetics; Oct2013, Vol. 21 Issue 10, p1042 

    The study reported here presents a detailed description of what it is like to parent a child with juvenile Huntington's disease in families across four European countries. Its primary aim was to develop and extend findings from a previous UK study. The study recruited parents from four European...

  • A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria.
    Sojo, Víctor; Pomiankowski, Andrew; Lane, Nick // PLoS Biology; Aug2014, Vol. 12 Issue 8, p1 

    The deepest split in the tree of life is between archaea and bacteria. We show this split can be explained by the late evolution of impermeable membranes, for energetic reasons.

  • Laser Transmission Holograms Maximum Permissible Exposure.
    Dawson, Paula; Wilksch, P. A. // AIP Conference Proceedings; 5/31/2010, Vol. 1226 Issue 1, p147 

    The laser illumination of holograms for public display is governed by international standard IEC 60825-3, to which the Australian Standard AS/NZS 2211.3 conforms. These standards do not accommodate vital mitigating factors of hologram replay that impinge on the level of laser power i.e. angle of...

  • Systematics of the North American menhadens: molecular evolutionary reconstructions in the genus Brevoortia (Clupeiformes: Clupeidae).
    Anderson, Joel D. // Fishery Bulletin; Jul2007, Vol. 105 Issue 3, p368 

    Evolutionary associations among the four North American species of menhadens (Brevoortia spp.) have not been thoroughly investigated. In the present study, classifications separating the four species into small-scaled and large-scaled groups were evaluated by using DNA data, and genetic...

  • Evolution of Dystaenia takesimana (Apiaceae), endemic to Ullung Island, Korea.
    Pfosser, M.; Jakubowsky, G.; Schl�ter, P.; Fer, T.; Kato, H.; Stuessy, T.; Sun, B.-Y. // Plant Systematics & Evolution; Nov2005, Vol. 256 Issue 1-4, p159 

    Dystaenia (Apiaceae) consists of two species, one distributed in Japan ( D. ibukiensis), and the other endemic to Ullung Island, Korea ( D. takesimana). In comparison with representative outgroup taxa in Ligusticum, Seseli, Angelica, and Osmorhiza, Dystaenia is shown to be monophyletic based on...

  • Normapolles plants: a prominent component of the Cretaceous rosid diversification.
    Friis, E.; Pedersen, K.; Sch�nenberger, J. // Plant Systematics & Evolution; Sep2006, Vol. 260 Issue 2-4, p107 

    The Normapolles complex, characterised by its oblate and triaperturate pollen, constitutes an important and diverse element of many Late Cretaceous and Early Cainozoic floras of the Northern Hemisphere. Based on the dispersed pollen record alone it has been difficult to assess systematic...

  • Genetic structure of peripheral, island-like populations: a case study of Saponaria bellidifolia Sm. (Caryophyllaceae) from the Southeastern Carpathians.
    Cserg�, Anna-M�ria; Sch�nswetter, Peter; Mara, Gy�ngyv�r; De�k, Tam�s; Boscaiu, Nicolae; H�hn, M�ria // Plant Systematics & Evolution; Mar2009, Vol. 278 Issue 1/2, p33 

    Geographically peripheral populations often experience a reduction of genetic diversity and divergence from the core populations. Habitat geometry and quality can induce a local genetic diversity pattern, which overlies the regional variability issued from the range-wide phylogeography. We...

  • Genetic Structure in Contemporary South Tyrolean Isolated Populations Revealed by Analysis of Y-Chromosome, mtDNA, and Alu Polymorphisms.
    Pichler, Irene; Mueller, Jakob C.; Stefanov, Stefan A.; de Grandi, Alessandro; Volpato, Claudia Beu; Pinggera, Gerd K.; Mayr, Agnes; Ogriseg, Martin; Ploner, Franz; Meitinger, Thomas; Pramstaller, Peter P. // Human Biology; Aug2006, Vol. 78 Issue 4, p441 

    Most of the inhabitants of South Tyrol in the eastern Italian Alps can be considered isolated populations because of their physical separation by mountain barriers and their sociocultural heritage. We analyzed the genetic structure of South Tyrolean populations using three types of genetic...

  • Prevalence of monochloroacetate degrading genotypes among soil isolates of Pseudomonas sp.
    Kocabiyik, Semra; Caba, Ebru // Biodegradation; 1998, Vol. 8 Issue 6, p371 

    This study reports the isolation of Pseudomonas sp. strains with monochloroacetate (MCA) degradation function, from uncontaminated soil, and the use of Southern blot hybridization technique to detect MCA degrading catabolic genes and their divergence. Based on their capacity to remove Cl- from...

  • An outline of the theory of the genetic divergence of dry-land and bog populations of Pinus sylvestris L.
    Sannikov, S.; Petrova, I. // Russian Journal of Ecology; Sep2010, Vol. 41 Issue 5, p393 

    The thesis of the genetic divergence of Pinus sylvestris L. populations that have spread to bogs from the original dry-land populations has been deduced from the concept of the cyclicity of helio- and geophysical processes, derivative postulates on climatic cycles, formation of Holocene high...

  • Late ontogeny growth acceleration and size form transformations in Transbaikalian Arctic charr, Salvelinus alpinus complex: evidence from fin ray cross section growth layers.
    Alekseyev, Sergey; Mina, Mikhail; Smirina, Ella; Sokolov, Aleksey // Environmental Biology of Fishes; Dec2009, Vol. 86 Issue 4, p487 

    In some polymorphic populations of Arctic charr in Transbaikalia, an individual can transform from a smaller to larger size form during their lifetime as a result of accelerated growth that follows a period of slow growth and reproduction as a small size form. Alternating periods of slow and...

  • Ecological diversity and speciation in land snails of the genus Mandarina from the Bonin Islands.
    Chiba, Satoshi // Population Ecology; Dec2002, Vol. 44 Issue 3, p0179 

    Endemic land snails of the genus Mandarina of the oceanic Bonin Islands offer an example of habitat and character divergence among closely related species. The molecular phylogenies of Mandarina show that a divergence of arboreal, semiarboreal, and ground-dwelling species has occurred repeatedly...

  • The origins of postmating reproductive isolation: testing hypotheses in the grasshopper Chorthippus parallelus.
    Tregenza, Tom; Pritchard, Victoria L.; Butlin, Roger K. // Population Ecology; Dec2002, Vol. 44 Issue 3, p0137 

    Although there are several well-established hypotheses for the origins of postmating isolation during allopatric divergence, there have been very few attempts to determine their relative importance in nature. We have developed an approach based on knowledge of the differing evolutionary...

  • Antitropicality of Pacific Fishes: Molecular Insights.
    Burridge, Christopher P. // Environmental Biology of Fishes; Oct2002, Vol. 65 Issue 2, p151 

    Twenty-one molecular genetic studies of thirteen antitropical Pacific fishes are herein reviewed. High dispersal potentials and Plio-Pleistocene transequatorial divergence are suggested for approximately half of the taxa studied, consistent with movement across the tropics during glacial...

  • Estimating Divergence Times in Large Phylogenetic Trees.
    Britton, Tom; Anderson, Cajsa Lisa; Jacquet, David; Lundqvist, Samuel; Bremer, K�re // Systematic Biology; Oct2007, Vol. 56 Issue 5, p741 

    A new method, PATHd8, for estimating ultrametric trees from trees with edge (branch) lengths proportional to the number of substitutions is proposed. The method allows for an arbitrary number of reference nodes for time calibration, each defined either as absolute age, minimum age, or maximum...

  • Accounting for Solvent Accessibility and Secondary Structure in Protein Phylogenetics Is Clearly Beneficial.
    SI QUANG LE; GASCUEL, OLIVIER // Systematic Biology; May2010, Vol. 59 Issue 3, p277 

    Amino acid substitution models are essential to most methods to infer phylogenies from protein data. These models represent the ways in which proteins evolve and substitutions accumulate along the course of time. It is widely accepted that the substitution processes vary depending on the...

  • Accommodating Heterogenous Rates of Evolution in Molecular Divergence Dating Methods: An Example Using Intercontinental Dispersal of Plestiodon (Eumeces) Lizards.
    BRANDLEY, MATTHEW C.; YUEZHAO WANG; XIANGUANG GUO; NIETO MONTES DE OCA, ADR�A N.; FER�A-ORT�Z, MANUEL; HIKIDA, TSUTOMU; OTA, HIDETOSHI // Systematic Biology; Jan2011, Vol. 60 Issue 1, p3 

    Identifying and dating historical biological events is a fundamental goal of evolutionary biology, and recent analytical advances permit the modeling of factors known to affect both the accuracy and the precision of molecular date estimates. As the use of multilocus data sets becomes...

  • Fitness Landscapes in Individual-Based Simulation Models of Adaptive Radiation.
    Paperin, Greg; Green, David; Dorin, Alan // AIP Conference Proceedings; 11/2/2007, Vol. 952 Issue 1, p268 

    We provide a brief overview of the use of FLs in evolutionary biology and introduce an FL model suitable for individual-based models of species evolution. Our model combines different features of several analytic FL models used in evolutionary biology. Our new model overcomes several...

  • Maximum tree: a consistent estimator of the species tree.
    Liang Liu; Yu, Lili; Pearl, Dennis K. // Journal of Mathematical Biology; Jan2010, Vol. 60 Issue 1, p95 

    We propose a model based approach to use multiple gene trees to estimate the species tree. The coalescent process requires that gene divergences occur earlier than species divergences when there is any polymorphism in the ancestral species. Under this scenario, speciation times are restricted to...

  • An irregular complex valued solution to a scalar uniformly elliptic equation.
    Frehse, Jens // Calculus of Variations & Partial Differential Equations; Nov2008, Vol. 33 Issue 3, p263 

    We present an irregular weak solution $${u : \mathbb {R}^n \to \mathbb {C}}$$ of a uniformly elliptic scalar equation in divergence form with measurable coefficients. The solution has a square integrable gradient. Such examples have been known for dimension n = 5 only.

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