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Diversification rate

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https://www.readbyqxmd.com/read/29142334/approaches-to-macroevolution-2-sorting-of-variation-some-overarching-issues-and-general-conclusions
#1
David Jablonski
Approaches to macroevolution require integration of its two fundamental components, within a hierarchical framework. Following a companion paper on the origin of variation, I here discuss sorting within an evolutionary hierarchy. Species sorting-sometimes termed species selection in the broad sense, meaning differential origination and extinction owing to intrinsic biological properties-can be split into strict-sense species selection, in which rate differentials are governed by emergent, species-level traits such as geographic range size, and effect macroevolution, in which rates are governed by organism-level traits such as body size; both processes can create hitchhiking effects, indirectly causing the proliferation or decline of other traits...
2017: Evolutionary Biology
https://www.readbyqxmd.com/read/29134623/repeated-evolution-and-reversibility-of-self-fertilization-in-the-volvocine-green-algae
#2
Erik R Hanschen, Matthew D Herron, John J Wiens, Hisayoshi Nozaki, Richard E Michod
Outcrossing and self-fertilization are fundamental strategies of sexual reproduction, each with different evolutionary costs and benefits. Self-fertilization is thought to be an evolutionary "dead-end" strategy, beneficial in the short term but costly in the long term, resulting in self-fertilizing species that occupy only the tips of phylogenetic trees. Here, we use volvocine green algae to investigate the evolution of self-fertilization. We use ancestral-state reconstructions to show that self-fertilization has repeatedly evolved from outcrossing ancestors and that multiple reversals from selfing to outcrossing have occurred...
November 14, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29132312/genomic-analysis-of-endemic-clones-of-toxigenic-and-non-toxigenic-corynebacterium-diphtheriae-in-belarus-during-and-after-the-major-epidemic-in-1990s
#3
Steffen Grosse-Kock, Valentina Kolodkina, Edward C Schwalbe, Jochen Blom, Andreas Burkovski, Paul A Hoskisson, Sylvain Brisse, Darren Smith, Iain C Sutcliffe, Leonid Titov, Vartul Sangal
BACKGROUND: Diphtheria remains a major public health concern with multiple recent outbreaks around the world. Moreover, invasive non-toxigenic strains have emerged globally causing severe infections. A diphtheria epidemic in the former Soviet Union in the 1990s resulted in ~5000 deaths. In this study, we analysed the genome sequences of a collection of 93 C. diphtheriae strains collected during and after this outbreak (1996 - 2014) in a former Soviet State, Belarus to understand the evolutionary dynamics and virulence capacities of these strains...
November 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29129356/multilocus-sequence-analysis-of-homologous-recombination-and-diversity-in-arthrobacter-sensu-lato-named-species-and-glacier-inhabiting-strains
#4
Qing Liu, Yu-Hua Xin, Yu-Guang Zhou, Wen-Xin Chen
Members of the bacterial genus Arthrobacter sensu lato are Gram-positive actinomycetes distributed worldwide and found in numerous environments including soil, water, glacier ice, and sewage. Homologous recombination is an important driving force in bacterial evolution, but its impact on Arthrobacter sensu lato evolution is poorly understood. We evaluated homologous recombination among 41 Arthrobacter sensu lato named species, using multilocus sequence analysis (MLSA). A high level of recombination was found, associated with strong diversification and a reticulate evolutionary pattern of Arthrobacter sensu lato...
November 3, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29126122/mode-and-rate-of-evolution-of-haemosporidian-mitochondrial-genomes-timing-the-radiation-of-avian-parasites
#5
M Andreína Pacheco, Nubia E Matta, Gediminas Valkiunas, Patricia G Parker, Beatriz Mello, Craig E Stanley, Miguel Lentino, M Alexandra Garcia-Amado, Michael Cranfield, Sergei L Kosakovsky Pond, Ananias A Escalante
Haemosporidians are a diverse group of vector-borne parasitic protozoa that includes the agents of human malaria; however, most of the described species are found in birds and reptiles. Although our understanding of these parasites' diversity has expanded by analyses of their mitochondrial genes, there is limited information on these genes' evolutionary rates. Here, 114 mitochondrial genomes (mtDNA) were studied from species belonging to four genera: Leucocytozoon, Haemoproteus, Hepatocystis, and Plasmodium...
November 6, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29118135/mass-extinction-in-tetraodontiform-fishes-linked-to-the-palaeocene-eocene-thermal-maximum
#6
Dahiana Arcila, James C Tyler
Integrative evolutionary analyses based upon fossil and extant species provide a powerful approach for understanding past diversification events and for assessing the tempo of evolution across the Tree of Life. Herein, we demonstrate the importance of integrating fossil and extant species for inferring patterns of lineage diversification that would otherwise be masked in analyses that examine only one source of evidence. We infer the phylogeny and macroevolutionary history of the Tetraodontiformes (triggerfishes, pufferfishes and allies), a group with one of the most extensive fossil records among fishes...
November 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29107221/factors-promoting-polyploid-persistence-and-diversification-and-limiting-diploid-speciation-during-the-k-pg-interlude
#7
REVIEW
Donald A Levin, Douglas E Soltis
The large wave of polyploidization following the Cretaceous-Paleogene (K-Pg) mass extinction has been explained by enhanced polyploid persistence arising from adaptive properties of the polyploids themselves, as well as an increase in unreduced gamete production and diploid hybridization. We propose that the demise of diploids afforded opportunities for polyploid establishment and expansion into novel habitats. Augmented polyploid gene pools from diploid and polyploid relatives, in association with their multiple and independent origins (of both autopolyploids and allopolyploids), facilitated their subsequent diversification...
October 27, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/29097664/high-frequency-recombination-between-members-of-an-ltr-retrotransposon-family-during-transposition-bursts
#8
Diego H Sanchez, Hervé Gaubert, Hajk-Georg Drost, Nicolae Radu Zabet, Jerzy Paszkowski
Retrotransposons containing long terminal repeats (LTRs) form a substantial fraction of eukaryotic genomes. The timing of past transposition can be estimated by quantifying the accumulation of mutations in initially identical LTRs. This way, retrotransposons are divided into young, potentially mobile elements, and old that moved thousands or even millions of years ago. Both types are found within a single retrotransposon family and it is assumed that the old members will remain immobile and degenerate further...
November 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/29096324/modern-methods-for-laboratory-diversification-of-biomolecules
#9
REVIEW
Sinisa Bratulic, Ahmed H Badran
Genetic variation fuels Darwinian evolution, yet spontaneous mutation rates are maintained at low levels to ensure cellular viability. Low mutation rates preclude the exhaustive exploration of sequence space for protein evolution and genome engineering applications, prompting scientists to develop methods for efficient and targeted diversification of nucleic acid sequences. Directed evolution of biomolecules relies upon the generation of unbiased genetic diversity to discover variants with desirable properties, whereas genome-engineering applications require selective modifications on a genomic scale with minimal off-targets...
October 30, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/29082336/genome-variation-across-cancers-scales-with-tissue-stiffness-an-invasion-mutation-mechanism-and-implications-for-immune-cell-infiltration
#10
Charlotte R Pfeifer, Cory M Alvey, Jerome Irianto, Dennis E Discher
Many different types of soft and solid tumors have now been sequenced, and meta-analyses suggest that genomic variation across tumors scales with the stiffness of the tumors' tissues of origin. The opinion expressed here is based on a review of current genomics data, and it considers multiple 'mechanogenomics' mechanisms to potentially explain this scaling of mutation rate with tissue stiffness. Since stiff solid tissues have higher density of fibrous collagen matrix, which should decrease tissue porosity, cancer cell proliferation could be affected and so could invasion into stiff tissues as the nucleus is squeezed sufficiently to enhance DNA damage...
April 2017: Current opinion in systems biology
https://www.readbyqxmd.com/read/29080214/transcription-factor-yy1-can-control-aid-mediated-mutagenesis-in-mice
#11
Kristina Zaprazna, Arindam Basu, Nikola Tom, Vibha Jha, Suchita Hodawadekar, Lenka Radova, Jitka Malcikova, Boris Tichy, Sarka Pospisilova, Michael L Atchison
Activation-induced cytidine deminase (AID) is crucial for controlling the immunoglobulin (Ig) diversification processes of somatic hypermutation (SHM) and class switch recombination (CSR). AID initiates these processes by deamination of cytosine, ultimately resulting in mutations or double strand DNA breaks needed for SHM and CSR. Levels of AID control mutation rates, and off-target non-Ig gene mutations can contribute to lymphomagenesis. Therefore, factors that control AID levels in the nucleus can regulate SHM and CSR, and may contribute to disease...
October 28, 2017: European Journal of Immunology
https://www.readbyqxmd.com/read/29073071/phylogenetic-diversity-anomaly-in-angiosperms-between-eastern-asia-and-eastern-north-america
#12
Hong Qian, Yi Jin, Robert E Ricklefs
Although eastern Asia (EAS) and eastern North America (ENA) have similar climates, plant species richness in EAS greatly exceeds that in ENA. The degree to which this diversity difference reflects the ages of the floras or their rates of evolutionary diversification has not been quantified. Measures of species diversity that do not incorporate the ages of lineages disregard the evolutionary distinctiveness of species. In contrast, phylogenetic diversity integrates both the number of species and their history of evolutionary diversification...
October 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29069434/estimating-age-dependent-extinction-contrasting-evidence-from-fossils-and-phylogenies
#13
Oskar Hagen, Tobias Andermann, Tiago B Quental, Alexandre Antonelli, Daniele Silvestro
The estimation of diversification rates is one of the most vividly debated topics in modern systematics, with considerable controversy surrounding the power of phylogenetic and fossil-based approaches in estimating extinction. Van Valen's seminal work from 1973 proposed the "Law of constant extinction" which states that the probability of extinction of taxa is not dependent on their age. This assumption of age-independent extinction has prevailed for decades with its assessment based on survivorship curves, which, however, do not directly account for the incompleteness of the fossil record, and have rarely been applied at the species level...
October 23, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29069354/the-diversification-of-zika-virus-are-there-two-distinct-lineages
#14
Zhen Gong, Xiaoyu Xu, Guan-Zhu Han
Zika virus (ZIKV) has caused explosive epidemics in the Pacific and the Americas, posing a serious threat to public health. Conventional opinion advocates that ZIKV evolved into two distinct lineages, namely, African and Asian. Descendants of this latter lineage dispersed globally causing major epidemics. However, based on shared amino acid replacements and phylogenetic analyses, it was recently contentiously proposed that the Asian lineage was a direct descendant of the African lineage. To address this contentious issue, we reconstructed a phylogenetic tree of ZIKV using the method based on shared amino acid replacements and found that ZIKV evolved into two distinct lineages...
November 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29062117/phenotypic-innovation-and-adaptive-constraints-in-the-evolutionary-radiation-of-palaeozoic-crinoids
#15
David F Wright
To better understand the patterns and processes shaping large-scale phenotypic diversification, I integrate palaeobiological and phylogenetic perspectives to investigate a ~200-million-year radiation using a global sample of Palaeozoic crinoid echinoderms. Results indicate the early history of crinoid diversification is characterized by early burst dynamics with decelerating morphologic rates. However, in contrast with expectation for a single "early burst" model, morphospace continued to expand following a slowdown in rates...
October 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29061890/phylogenetic-tests-for-evolutionary-innovation-the-problematic-link-between-key-innovations-and-exceptional-diversification
#16
REVIEW
Daniel L Rabosky
Evolutionary innovation contributes to the spectacular diversity of species and phenotypes across the tree of life. 'Key innovations' are widely operationalized within evolutionary biology as traits that facilitate increased diversification rates, such that lineages bearing the traits ultimately contain more species than closely related lineages lacking the focal trait. In this article, I briefly review the inference, analysis and interpretation of evolutionary innovation on phylogenetic trees. I argue that differential rates of lineage diversification should not be used as the basis for key innovation tests, despite the statistical tractability of such approaches...
December 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29056939/developmental-changes-in-time-and-space-promote-evolutionary-diversification-of-flowers-a-case-study-in-dipsacoideae
#17
Somayeh Naghiloo, Regine Claßen-Bockhoff
Diversification in flower shape and function is triggered by the high plasticity of flower meristems. Minute changes in space and time can profoundly affect the formation of adult structures. Dipsacoideae provides an excellent model system to investigate the evolutionary aspects of temporal and spatial changes in flower development due to its small size, the resolved phylogenetic framework, and significant diversity of perianth form and merosity. In the present study, we investigated the sequence of floral organ initiation and quantified the interactions between flower meristem expansion and petal primordium size in eight species representing two major clades of Dipsacoideae...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29055133/estimating-diversification-rates-for-higher-taxa-bamm-can-give-problematic-estimate-of-rates-and-rate-shifts
#18
Andreas L S Meyer, John J Wiens
Estimates of diversification rates are invaluable for many macroevolutionary studies. Recently, an approach called BAMM (Bayesian Analysis of Macro-evolutionary Mixtures) has become widely used for estimating diversification rates and rate shifts. At the same time, several papers have concluded that estimates of net diversification rates from the method-of-moments (MS) estimators are inaccurate. Yet, no studies have compared the ability of these two methods to accurately estimate clade diversification rates...
October 21, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29054168/early-evolutionary-diversification-of-mandible-morphology-in-the-new-world-monkeys-primate-platyrrhini
#19
Guido Rocatti, Leandro Aristide, Alfred L Rosenberger, S Ivan Perez
New World monkeys (order Primates) are an example of a major mammalian evolutionary radiation in the Americas, with a contentious fossil record. There is evidence of an early platyrrhine occupation of this continent by the Eocene-Oligocene transition, evolving in isolation from the Old World primates from then on, and developing extensive morphological and size variation. Previous studies postulated that the platyrrhine clade arose as a local version of the Simpsonian ecospace model, with an early phase involving a rapid increase in morphological and ecological diversity driven by selection and ecological opportunity, followed by a diversification rate that slowed due to niche-filling...
December 2017: Journal of Human Evolution
https://www.readbyqxmd.com/read/29047258/identification-and-expression-analyses-of-equine-endogenous-retroviruses-in-horses
#20
Jeong-An Gim, Heui-Soo Kim
Endogenous retroviruses (ERVs) have been integrated into vertebrate genomes and have momentously affected host organisms. Horses (Equus caballus) have been domesticated and selected for elite racing ability over centuries. ERVs played an important role in the evolutionary diversification of the horse genome. In the present study, we identified six equine ERV families (EqERVs-E1, I1, M2, P1, S1, and Y4), their full-length viral open reading frames (ORFs), and elucidated their phylogenetic relationships. The divergence time of EqERV families assuming an evolutionary rate of 0...
October 2017: Molecules and Cells
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