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‣ Conceptual Barriers to Progress Within Evolutionary Biology

Laland, Kevin N.; Odling-Smee, John; Feldman, Marcus W.; Kendal, Jeremy
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /08/2009 Português
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In spite of its success, Neo-Darwinism is faced with major conceptual barriers to further progress, deriving directly from its metaphysical foundations. Most importantly, neo-Darwinism fails to recognize a fundamental cause of evolutionary change, “niche construction”. This failure restricts the generality of evolutionary theory, and introduces inaccuracies. It also hinders the integration of evolutionary biology with neighbouring disciplines, including ecosystem ecology, developmental biology, and the human sciences. Ecology is forced to become a divided discipline, developmental biology is stubbornly difficult to reconcile with evolutionary theory, and the majority of biologists and social scientists are still unhappy with evolutionary accounts of human behaviour. The incorporation of niche construction as both a cause and a product of evolution removes these disciplinary boundaries while greatly generalizing the explanatory power of evolutionary theory.

‣ Reflections on Behavior Analysis and Evolutionary Biology: A Selective Review of Evolution Since Darwin—The First 150 Years. Edited by M. A. Bell, D. J. Futuyama, W. F. Eanes, & J. S. Levinton

Donahoe, John W
Fonte: Society for the Experimental Analysis of Behavior, Inc Publicador: Society for the Experimental Analysis of Behavior, Inc
Tipo: Artigo de Revista Científica
Publicado em /03/2012 Português
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This review focuses on parallels between the selectionist sciences of evolutionary biology and behavior analysis. In selectionism, complex phenomena are interpreted as the cumulative products of relatively simple processes acting over time—natural selection in evolutionary biology and reinforcement in behavior analysis. Because evolutionary biology is the more mature science, an examination of the factors that led to the triumph of natural selection provides clues whereby reinforcement may achieve a similar fate in the science of behavior.

‣ Towards a postmodern synthesis of evolutionary biology

Koonin, Eugene V.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Português
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In 2009, we are celebrating the 200th anniversary of Charles Darwin and the 150th jubilee of his masterpiece, the Origin of Species. Darwin developed the first coherent and compelling narrative of biological evolution and thus founded evolutionary biology—and modern biology in general, remembering the famous dictum of Dobzhansky. It is, however, counter-productive, and ultimately, a disservice to Darwin’s legacy, to define modern evolutionary biology as neo-Darwinism. The current picture of evolution, informed, in particular, by results of comparative genomics and systems biology, is by far more complex than that presented in the Origin of Species, so that Darwinian principles, including natural selection, are incorporated into the evolving new synthesis as important but certainly not all-embracing tenets. This expansion of evolutionary biology does not denigrate Darwin in the least but rather emphasizes the fertility of his ideas.

‣ Evolution of microbes and viruses: a paradigm shift in evolutionary biology?

Koonin, Eugene V.; Wolf, Yuri I.
Fonte: Frontiers Media S.A. Publicador: Frontiers Media S.A.
Tipo: Artigo de Revista Científica
Publicado em 13/09/2012 Português
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When Charles Darwin formulated the central principles of evolutionary biology in the Origin of Species in 1859 and the architects of the Modern Synthesis integrated these principles with population genetics almost a century later, the principal if not the sole objects of evolutionary biology were multicellular eukaryotes, primarily animals and plants. Before the advent of efficient gene sequencing, all attempts to extend evolutionary studies to bacteria have been futile. Sequencing of the rRNA genes in thousands of microbes allowed the construction of the three- domain “ribosomal Tree of Life” that was widely thought to have resolved the evolutionary relationships between the cellular life forms. However, subsequent massive sequencing of numerous, complete microbial genomes revealed novel evolutionary phenomena, the most fundamental of these being: (1) pervasive horizontal gene transfer (HGT), in large part mediated by viruses and plasmids, that shapes the genomes of archaea and bacteria and call for a radical revision (if not abandonment) of the Tree of Life concept, (2) Lamarckian-type inheritance that appears to be critical for antivirus defense and other forms of adaptation in prokaryotes, and (3) evolution of evolvability...

‣ The Impact of Trans-Regulation on the Evolutionary Rates of Metazoan Proteins

Chen, Yi-Ching; Cheng, Jen-Hao; Tsai, Zing Tsung-Yeh; Tsai, Huai-Kuang; Chuang, Trees-Juen
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
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Transcription factor (TF) and microRNA (miRNA) are two crucial trans-regulatory factors that coordinately control gene expression. Understanding the impacts of these two factors on the rate of protein sequence evolution is of great importance in evolutionary biology. While many biological factors associated with evolutionary rate variations have been studied, evolutionary analysis of simultaneously accounting for TF and miRNA regulations across metazoans is still uninvestigated. Here, we provide a series of statistical analyses to assess the influences of TF and miRNA regulations on evolutionary rates across metazoans (human, mouse and fruit fly). Our results reveal that the negative correlations between trans-regulation and evolutionary rates hold well across metazoans, but the strength of TF regulation as a rate indicator becomes weak when the other confounding factors that may affect evolutionary rates are controlled. We show that miRNA regulation tends to be a more essential indicator of evolutionary rates than TF regulation, and the combination of TF and miRNA regulations has a significant dependent effect on protein evolutionary rates. We also show that trans-regulation (especially miRNA regulation) is much more important in human/mouse than in fruit fly in determining protein evolutionary rates...

‣ Making Evolutionary Biology a Basic Science for Medicine

Nesse, Randolph M.; Bergstrom, Carl T.; Ellison, Peter T.; Flier, Jeffrey S.; Gluckman, Peter; Govindaraju, Diddahally R.; Niethammer, Dietrich; Omenn, Gil S.; Perlman, Robert L.; Schwartz, Mark; Thomas, Mark G.; Stearns, Stephen C.; Valle, David
Fonte: Harvard University Publicador: Harvard University
Tipo: Artigo de Revista Científica
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New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to utilize them fully. This article summarizes suggestions from several groups who have considered how evolutionary biology can be useful in medicine, what physicians should learn about it, and when and how they should learn it. Our general conclusion is that evolutionary biology is a crucial basic science for medicine. In addition to established evolutionary methods and topics, such as population genetics and pathogen evolution, the article also highlights questions about why natural selection leaves bodies vulnerable to disease. Knowledge about volution provides physicians with an integrative framework that links otherwise disparate bits of knowledge. It replaces the revalent view of bodies as machines with a biological view of bodies shaped by evolutionary processes. Like other basic sciences, evolutionary biology needs to be taught both before and during medical school. Most introductory biology courses are insufficient to establish competency in evolutionary biology. Premedical students need evolution courses, possibly ones that emphasize medically relevant aspects. In medical school...

‣ Within and between Whorls: Comparative Transcriptional Profiling of Aquilegia and Arabidopsis

Voelckel, Claudia; Borevitz, Justin O.; Hodges, Scott A.; Baxter, Ivan; Kramer, Elena M.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Português
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Background: The genus Aquilegia is an emerging model system in plant evolutionary biology predominantly because of its wide variation in floral traits and associated floral ecology. The anatomy of the Aquilegia flower is also very distinct. There are two whorls of petaloid organs, the outer whorl of sepals and the second whorl of petals that form nectar spurs, as well as a recently evolved fifth whorl of staminodia inserted between stamens and carpels. Methodology/Principal Findings: We designed an oligonucleotide microarray based on EST sequences from a mixed tissue, normalized cDNA library of an A. formosa x A. pubescens F2 population representing 17,246 unigenes. We then used this array to analyze floral gene expression in late pre-anthesis stage floral organs from a natural A. formosa population. In particular, we tested for gene expression patterns specific to each floral whorl and to combinations of whorls that correspond to traditional and modified ABC model groupings. Similar analyses were performed on gene expression data of Arabidopsis thaliana whorls previously obtained using the Ath1 gene chips (data available through The Arabidopsis Information Resource). Conclusions/Significance: Our comparative gene expression analyses suggest that 1) petaloid sepals and petals of A. formosa share gene expression patterns more than either have organ-specific patterns...

‣ A Sex-Ratio Meiotic Drive System in Drosophila Simulans. I: An Autosomal Suppressor

Tao, Yun; Masly, John P; Araripe, Luciana Ordunha; Ke, Yeyan; Hartl, Daniel L.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Português
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Sex ratio distortion (sex-ratio for short) has been reported in numerous species such as Drosophila, where distortion can readily be detected in experimental crosses, but the molecular mechanisms remain elusive. Here we characterize an autosomal sex-ratio suppressor from D. simulans that we designate as not much yang (nmy, polytene chromosome position 87F3). Nmy suppresses an X-linked sex-ratio distorter, contains a pair of near-perfect inverted repeats of 345 bp, and evidently originated through retrotransposition from the distorter itself. The suppression is likely mediated by sequence homology between the suppressor and distorter. The strength of sex-ratio is greatly enhanced by lower temperature. This temperature sensitivity was used to assign the sex-ratio etiology to the maturation process of the Y-bearing sperm, a hypothesis corroborated by both light microscope observations and ultrastructural studies. It has long been suggested that an X-linked sex-ratio distorter can evolve by exploiting loopholes in the meiotic machinery for its own transmission advantage, which may be offset by other changes in the genome that control the selfish distorter. Data obtained in this study help to understand this evolutionary mechanism in molecular detail and provide insight regarding its evolutionary impact on genomic architecture and speciation.; Organismic and Evolutionary Biology

‣ Similar Genetic Mechanisms Underlie the Parallel Evolution of Floral Phenotypes

Zhang, Wenheng; Kramer, Elena M.; Davis, Charles Cavender
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Português
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The repeated origin of similar phenotypes is invaluable for studying the underlying genetics of adaptive traits; molecular evidence, however, is lacking for most examples of such similarity. The floral morphology of neotropical Malpighiaceae is distinctive and highly conserved, especially with regard to symmetry, and is thought to result from specialization on oil-bee pollinators. We recently demonstrated that CYCLOIDEA2–like genes (CYC2A and CYC2B) are associated with the development of the stereotypical floral zygomorphy that is critical to this plant–pollinator mutualism. Here, we build on this developmental framework to characterize floral symmetry in three clades of Malpighiaceae that have independently lost their oil bee association and experienced parallel shifts in their floral morphology, especially in regard to symmetry. We show that in each case these species exhibit a loss of CYC2B function, and a strikingly similar shift in the expression of CYC2A that is coincident with their shift in floral symmetry. These results indicate that similar floral phenotypes in this large angiosperm clade have evolved via parallel genetic changes from an otherwise highly conserved developmental program.; Organismic and Evolutionary Biology

‣ An Anatomical Description of a Miniaturized Acorn Worm (Hemichordata, Enteropneusta) with Asexual Reproduction by Paratomy

Worsaae, Katrine; Sterrer, Wolfgang; Kaul-Strehlow, Sabrina; Hay-Schmidt, Anders; Giribet, Gonzalo
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Português
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The interstitial environment of marine sandy bottoms is a nutrient-rich, sheltered habitat whilst at the same time also often a turbulent, space-limited, and ecologically challenging environment dominated by meiofauna. The interstitial fauna is one of the most diverse on earth and accommodates miniaturized representatives from many macrofaunal groups as well as several exclusively meiofaunal phyla. The colonization process of this environment, with the restrictions imposed by limited space and low Reynolds numbers, has selected for great morphological and behavioral changes as well as new life history strategies. Here we describe a new enteropneust species inhabiting the interstices among sand grains in shallow tropical waters of the West Atlantic. With a maximum body length of 0.6 mm, it is the first microscopic adult enteropneust known, a group otherwise ranging from 2 cm to 250 cm in adult size. Asexual reproduction by paratomy has been observed in this new species, a reproductive mode not previously reported among enteropneusts. Morphologically, Meioglossus psammophilus gen. et sp. nov. shows closest resemblance to an early juvenile stage of the acorn worm family Harrimaniidae, a result congruent with its phylogenetic placement based on molecular data. Its position...

‣ FREQ-Seq: A Rapid, Cost-Effective, Sequencing-Based Method to Determine Allele Frequencies Directly from Mixed Populations

Chubiz, Lon M; Lee, Ming-Chun; Delaney, Nigel Francis; Marx, Christopher J
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Português
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Understanding evolutionary dynamics within microbial populations requires the ability to accurately follow allele frequencies through time. Here we present a rapid, cost-effective method (FREQ-Seq) that leverages Illumina next-generation sequencing for localized, quantitative allele frequency detection. Analogous to RNA-Seq, FREQ-Seq relies upon counts from the >105 reads generated per locus per time-point to determine allele frequencies. Loci of interest are directly amplified from a mixed population via two rounds of PCR using inexpensive, user-designed oligonucleotides and a bar-coded bridging primer system that can be regenerated in-house. The resulting bar-coded PCR products contain the adapters needed for Illumina sequencing, eliminating further library preparation. We demonstrate the utility of FREQ-Seq by determining the order and dynamics of beneficial alleles that arose as a microbial population, founded with an engineered strain of Methylobacterium, evolved to grow on methanol. Quantifying allele frequencies with minimal bias down to 1% abundance allowed effective analysis of SNPs, small in-dels and insertions of transposable elements. Our data reveal large-scale clonal interference during the early stages of adaptation and illustrate the utility of FREQ-Seq as a cost-effective tool for tracking allele frequencies in populations.; Organismic and Evolutionary Biology

‣ Cooperation and the Fate of Microbial Societies

Allen, Benjamin Isaac; Nowak, Martin A.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Português
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Microorganisms have been cooperating with each other for billions of years: by sharing resources, communicating with each other, and joining together to form biofilms and other large structures. These cooperative behaviors benefit the colony as a whole; however, they may be costly to the individuals performing them. This raises the question of how such cooperation can arise from natural selection. Mathematical modeling is one important avenue for exploring this question. Evolutionary experiments are another, providing us with an opportunity to see evolutionary dynamics in action and allowing us to test predictions arising from mathematical models. A new study in this issue of PLOS Biology investigates the evolution of a cooperative resource-sharing behavior in yeast. Examining the competition between cooperating and “cheating” strains of yeast, the authors find that, depending on the initial mix of strains, this yeast society either evolves toward a stable coexistence or collapses for lack of cooperation. Using a simple mathematical model, they show how these dynamics arise from eco-evolutionary feedback, where changes in the frequencies of strains are coupled with changes in population size. This study and others illustrate the combined power of modeling and experiment to elucidate the origins of cooperation and other fundamental questions in evolutionary biology.; Mathematics; Organismic and Evolutionary Biology

‣ The Time Scale of Evolutionary Innovation

Chatterjee, Krishnendu; Pavlogiannis, Andreas; Adlam, Ben; Nowak, Martin A.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Português
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A fundamental question in biology is the following: what is the time scale that is needed for evolutionary innovations? There are many results that characterize single steps in terms of the fixation time of new mutants arising in populations of certain size and structure. But here we ask a different question, which is concerned with the much longer time scale of evolutionary trajectories: how long does it take for a population exploring a fitness landscape to find target sequences that encode new biological functions? Our key variable is the length, of the genetic sequence that undergoes adaptation. In computer science there is a crucial distinction between problems that require algorithms which take polynomial or exponential time. The latter are considered to be intractable. Here we develop a theoretical approach that allows us to estimate the time of evolution as function of We show that adaptation on many fitness landscapes takes time that is exponential in even if there are broad selection gradients and many targets uniformly distributed in sequence space. These negative results lead us to search for specific mechanisms that allow evolution to work on polynomial time scales. We study a regeneration process and show that it enables evolution to work in polynomial time.

‣ Discord between morphological and phylogenetic species boundaries: incomplete lineage sorting and recombination results in fuzzy species boundaries in an asexual fungal pathogen

Stewart, Jane E.; Timmer, Lavern W.; Lawrence, Christopher; Pryor, Barry M.; Peever, Tobin L.
Fonte: BioMed Central (BMC Evolutionary Biology); BioMed Central (BMC Evolutionary Biology) Publicador: BioMed Central (BMC Evolutionary Biology); BioMed Central (BMC Evolutionary Biology)
Tipo: mixed material
Publicado em //2014 Português
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Stewart et al. BMC Evolutionary Biology 2014, 14:38 http://www.biomedcentral.com/1471-2148/14/38; Pages 1-14; doi:10.1186/1471-2148-14-38 Cite this article as: Stewart et al.: Discord between morphological and phylogenetic species boundaries: incomplete lineage sorting and recombination results in fuzzy species boundaries in an asexual fungal pathogen. BMC Evolutionary Biology 2014 14:38

‣ Molecular evidence for convergent evolution and allopolyploid speciation within the Physcomitrium- Physcomitrella species complex

Beike, Anna K.; Stackelberg, Mark Von; Schallenberg-Rudinger, Mareike; Hanke, Sebastain T.; Follo, Marie
Fonte: Bio-Med Central (BMC Evolutionary Biology); Bio-Med Central (BMC Evolutionary Biology) Publicador: Bio-Med Central (BMC Evolutionary Biology); Bio-Med Central (BMC Evolutionary Biology)
Tipo: mixed material
Publicado em //2014 Português
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Beike et al. BMC Evolutionary Biology 2014, 14:158 http://www.biomedcentral.com/1471-2148/14/158; Pages 1-19; doi:10.1186/1471-2148-14-158 Cite this article as: Beike et al.: Molecular evidence for convergent evolution and allopolyploid speciation within the Physcomitrium- Physcomitrella species complex. BMC Evolutionary Biology 2014 14:158.

‣ Evolutionary cell biology: two origins, one objective

Lynch, Michael; Field, Mark C; Goodson, Holly V; Malik, Harmit S; Pereira-Leal, José B; Roos, David S; Turkewitz, Aaron P; Sazer, Shelley
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
Publicado em 02/12/2014 Português
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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...

‣ The evolution of antibiotic susceptibility and resistance during the formation of Escherichia coli biofilms in the absence of antibiotics

Tyerman, Jabus G.; Ponciano, Jose M.; Joyce, Paul; Forney, Larry J.; Harmon, Luke J.
Fonte: BioMed Central (BMC Evolutionary Biology; BioMed Central (BMC Evolutionary Biology Publicador: BioMed Central (BMC Evolutionary Biology; BioMed Central (BMC Evolutionary Biology
Tipo: mixed material
Publicado em //2013 Português
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Publication of this article was funded in part by the University of Florida Open-Access publishing Fund. In addition, requestors receiving funding through the UFOAP project are expected to submit a post-review, final draft of the article to UF's institutional repository, IR@UF, (www.uflib.ufl.edu/UFir) at the time of funding. The institutional Repository at the University of Florida community, with research, news, outreach, and educational materials.; Tyerman et al. BMC Evolutionary Biology 2013, 13:22 http://www.biomedcentral.com/1471-2148/13/22; Pages 1-7; doi:10.1186/1471-2148-13-22 Cite this article as: Tyerman et al.: The evolution of antibiotic susceptibility and resistance during the formation of Escherichia coli biofilms in the absence of antibiotics. BMC Evolutionary Biology 2013 13:22.

‣ An Application of Evolutionary Game Theory to Social Dilemmas: The Traveler's Dilemma and the Minimum Effort Coordination Game

Iyer, Swami; Reyes, Joshua; Killingback, Timothy
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Português
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The Traveler's Dilemma game and the Minimum Effort Coordination game are two social dilemmas that have attracted considerable attention due to the fact that the predictions of classical game theory are at odds with the results found when the games are studied experimentally. Moreover, a direct application of deterministic evolutionary game theory, as embodied in the replicator dynamics, to these games does not explain the observed behavior. In this work, we formulate natural variants of these two games as smoothed continuous-strategy games. We study the evolutionary dynamics of these continuous-strategy games, both analytically and through agent-based simulations, and show that the behavior predicted theoretically is in accord with that observed experimentally. Thus, these variants of the Traveler's Dilemma and the Minimum Effort Coordination games provide a simple resolution of the paradoxical behavior associated with the original games.

‣ Evolutionary biology in biodiversity science, conservation, and policy: A call to action

Hendry, Andrew P.; Lohmann, Lucia G.; Conti, Elena; Cracraft, Joel; Crandall, Keith A.; Faith, Daniel P; Hauser, Christoph; Joly, Carlos A.; Kogure, Kazuhiro; Larigauderie, Anne; Magallon, Susana; Moritz, Craig
Fonte: Society for the Study of Evolution Publicador: Society for the Study of Evolution
Tipo: Artigo de Revista Científica
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Evolutionary biologists have long endeavored to document how many species exist on Earth, to understand the processes by which biodiversity waxes and wanes, to document and interpret spatial patterns of biodiversity, and to infer evolutionary relationships. Despite the great potential of this knowledge to improve biodiversity science, conservation, and policy, evolutionary biologists have generally devoted limited attention to these broader implications. Likewise, many workers in biodiversity science have underappreciated the fundamental relevance of evolutionary biology. The aim of this article is to summarize and illustrate some ways in which evolutionary biology is directly relevant. We do so in the context of four broad areas: (1) discovering and documenting biodiversity, (2) understanding the causes of diversification, (3) evaluating evolutionary responses to human disturbances, and (4) implications for ecological communities, ecosystems, and humans. We also introduce bioGENESIS, a new project within DIVERSITAS launched to explore the potential practical contributions of evolutionary biology. In addition to fostering the integration of evolutionary thinking into biodiversity science, bioGENESIS provides practical recommendations to policy makers for incorporating evolutionary perspectives into biodiversity agendas and conservation. We solicit your involvement in developing innovative ways of using evolutionary biology to better comprehend and stem the loss of biodiversity.

‣ Darwin's legacy in South African evolutionary biology

Johnson,S.D.
Fonte: South African Journal of Science Publicador: South African Journal of Science
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/12/2009 Português
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In the two decades after publication of the Origin of Species, Charles Darwin facilitated the publication of numerous scientific papers by settler naturalists in South Africa. This helped to establish the strong tradition of natural history which has characterised evolutionary research in South African museums, herbaria and universities. Significant developments in the early 20th century included the hominid fossil discoveries of Raymond Dart, Robert Broom, and others, but there was otherwise very little South African involvement in the evolutionary synthesis of the 1930s and 1940s. Evolutionary biology developed into a distinct discipline in South Africa during the 1970s and 1980s when it was dominated by mammalian palaeontology and a vigorous debate around species concepts. In the post-apartheid era, the main focus of evolutionary biology has been the construction of phylogenies for African plants and animals using molecular data, and the use of these phylogenies to answer questions about taxonomic classification and trait evolution. South African biologists have also recently contributed important evidence for some of Darwin's ideas about plant-animal coevolution, sexual selection, and the role of natural selection in speciation. A bibliographic analysis shows that South African authors produce 2-3% of the world's publications in the field of evolutionary biology...