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October 28, 2014
Parsimony analysis of unaligned sequence data: maximization of homology and minimization of homoplasy, not minimization of operationally defined total cost or minimization of equally weighted transformations
Wheeler (2012) stated that minimization of ad hoc hypotheses as emphasized by Farris (1983) always leads to a preference for trivial optimizations when analysing unaligned sequence data, leaving no basis for tree choice. That is not correct. Farris's framework can be expressed as maximization of homology, a formulation that has been used to overcome the problems with inapplicables (it leads to the notion of subcharacters as a quantity to be co-minimized in parsimony analysis) and that is known not to lead to a preference for trivial optimizations when analysing unaligned sequence data. Maximization of homology, in turn, can be formulated as a minimization of ad hoc hypotheses of homoplasy in the sense of Farris, as shown here. These issues are not just theoretical but have empirical relevance. It is therefore also discussed how maximization of homology can be approximated under various weighting schemes in heuristic tree alignment programs, such as POY, that do not take into account subcharacters. Empirical analyses that use the so-called 3221 cost set (gap opening cost three, transversion and transition costs two, and gap extension cost one), the cost set that is known to be an optimal approximation under equally weighted homology in POY, are briefly reviewed. From a theoretical point of view, maximization of homology provides the general framework to understand such cost sets in terms that are biologically relevant and meaningful. Whether or not embedded in a sensitivity analysis, this is not the case for minimization of a cost that is defined in operational terms only. Neither is it the case for minimization of equally weighted transformations, a known problem that is not addressed by Kluge and Grant's (2006) proposal to invoke the anti-superfluity principle as a rationale for this minimization.
Although these positions are for ecologists, we think this cluster hire would be of interest to the readers of evoldir. Cluster Hire in Geographic Ecology: three positions at the rank of Assistant, Associate, or Full Professor http://GE.ou.edu The Department of Biology at the University of Oklahoma invites applications for three tenured/tenure-track faculty positions at any rank, beginning in fall 2015. We are searching for creative, collaborative thinkers who use integrative approaches to address fundamental ecological questions at regional to global scales. Our ultimate goal is to enhance our expertise in geographical and aquatic ecology toward predicting ecological and evolutionary responses to global change. The search is open to theoretical, lab, and field biologists working on any taxa. In this cluster hire, we seek: * A Geographical Ecologist who studies phenomena at multiple spatial scales toward understanding large-scale patterns and processes. Innovators in biogeography, macroecology, bioinformatics, and global ecology are especially encouraged to apply. * An Aquatic Ecologist who studies freshwater ecosystems toward predicting the role of changing water supplies on ecosystem services. Innovators in biogeochemistry, ecological networks, ecological genomics, river-reservoir systems and land-water interactions are especially encouraged to apply. * A Physiological Ecologist who studies the origin and maintenance of ecological traits and their ultimate role in the dynamics of population and ecosystem responses to a changing environment. Innovators studying traits involved in metabolic, stoichiometric, thermal and water-related variation and adaptation are especially encouraged to apply. We are especially interested in candidates who use or combine some of the following three approaches in their work. The first is development and/or testing of models and theory that connect phenomena at scales from local to global. The second is an integrative use of data-from gene frequencies to biogeochemistry, species distributions to climate past and future, functional traits to landscapes-to advance theory and identify novel patterns and processes. The third is a desire to apply this research to ameliorating outstanding ecological problems, including climate change, biodiversity loss, dwindling water supplies, and the degradation of ecosystem services. The University of Oklahoma is committed to building an international center of excellence exploring the geographical ecology of our evolving biosphere. Successful candidates will join colleagues across campus, including cluster hires in the EPSCoR initiative Adapting socio-ecological systems to increased climate variability. Our shared goal is to build theoretical and empirical bridges across the sciences, to predict the interplay between biotic and climatic changes, and to better steward our natural resources and services. Join us. How to Apply Successful candidates will have a Ph.D. degree and a record of outstanding achievement as evidenced by publications. Preferred candidates will have a promising (assistant) or externally funded (associate/full) research program and the ability to lead interdisciplinary, multi-investigator projects across a range of geographic scales. Each individual will be expected to provide excellent training for graduate students and postdocs, and contribute to undergraduate and graduate teaching (one course per semester) in the department. Applicants should submit a cover letter, complete curriculum vitae, research and teaching statements, and selected reprints/preprints as PDF files to Chair, Geographical Ecology Search Committee, at email@example.com. Applicants should also arrange to have three signed letters of reference sent to firstname.lastname@example.org or Department of Biology, 730 Van Vleet Oval, University of Oklahoma, Norman, OK 73019, USA. Applicants at the rank of Associate Professor or Professor may submit names and contact information for three references in lieu of letters. Visit us at http://bit.ly/1sVS5Ut. Screening of candidates will begin 3 December 2014 and will continue until the positions are filled. The University of Oklahoma is an Affirmative Action/Equal Opportunity employer and encourages diversity in the workplace. Protected veterans and individuals with disabilities are encouraged to apply. Rosemary Knapp Professor and Director of Graduate Studies Department of Biology 730 Van Vleet Oval University of Oklahoma Norman, OK 73019 “Knapp, Rosemary” via Gmail
October 26, 2014
Background: Wild relatives in the genus Arabidopsis are recognized as useful model systems to study traits and evolutionary processes in outcrossing species, which are often difficult or even impossible to investigate in the selfing and annual Arabidopsis thaliana. However, Arabidopsis as a genus is littered with sub-species and ecotypes which make realizing the potential of these non-model Arabidopsis lineages problematic. There are relatively few evolutionary studies which comprehensively characterize the gene pools across all of the Arabidopsis supra-groups and hypothesized evolutionary lineages and none include sampling at a world-wide scale. Here we explore the gene pools of these various taxa using various molecular markers and cytological analyses. Results: Based on ITS, microsatellite, chloroplast and nuclear DNA content data we demonstrate the presence of three major evolutionary groups broadly characterized as A. lyrata group, A. halleri group and A. arenosa group. All are composed of further species and sub-species forming larger aggregates. Depending on the resolution of the marker, a few closely related taxa such as A. pedemontana, A. cebennensis and A. croatica are also clearly distinct evolutionary lineages. ITS sequences and a population-based screen based on microsatellites were highly concordant. The major gene pools identified by ITS sequences were also significantly differentiated by their homoploid nuclear DNA content estimated by flow cytometry. The chloroplast genome provided less resolution than the nuclear data, and it remains unclear whether the extensive haplotype sharing apparent between taxa results from gene flow or incomplete lineage sorting in this relatively young group of species with Pleistocene origins. Conclusions: Our study provides a comprehensive overview of the genetic variation within and among the various taxa of the genus Arabidopsis. The resolved gene pools and evolutionary lineages will set the framework for future comparative studies on genetic diversity. Extensive population-based phylogeographic studies will also be required, however, in particular for A. arenosa and their affiliated taxa and cytotypes.
Source: BMC Evolutionary Biology
Charles Darwin and Alfred Russel Wallace are usually credited with independently developing the idea that natural selection could be the important process by which new species arise, although history has apportioned most of the fame to Darwin alone.
In the first edition of his most famous book Darwin (1859) cited no sources, and credited no-one except Thomas Malthus as a source of ideas. He was criticized for this, and from the third edition onwards he provided a historical essay mentioning a few more names.
The basic issue is that the idea of natural election had been "in the air" for more than half a century, but only with respect to within-species variation. It was Darwin and Wallace who took the leap to consider between-species variation, on the basis that there is no historical boundary defining species — all individuals trace their ancestry back through a whole series of ancestors, including those who existed before the origin of their current species. That is, phylogenies trace back to the origin of life not just to the origin of each species.
So, who were the people who published, however briefly, a comment noting the idea of within-species natural selection? Joachim Dagg, of the Natural History Apostils blog, has recently been writing a series of posts discussing many of those publications that contain a clear description of selection. Here I have provided a convenient overview, in time order, with links to Joachim's blog for those of you who want more information.
Link 1 - Link 2
William Charles Wells
Link 1 - Link 2
Link 1 - Link 2 - Link 3
Link 1 - Link 2 - Link 3
John C. Loudon
Link 1 - Link 2
* Full title: The Magazine of Natural History and Journal of Zoology, Botany, Mineralogy, Geology, and Meteorology
Dear list members, Registration is open for the course “INTRODUCTION TO NETWORK TOOLS IN BIOSCIENCES - 2nd Edition”. Course Webpage: http://bit.ly/19yfo98 INSTRUCTORS: Dr. Diego Rasskin-Gutman (Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Spain) and Dr. Borja Esteve-Altava (Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Spain). DATES: April, 20-24, 2014. 34 teaching hours. PLACE: Facilities of the Centre de Restauraci i Interpretaci de Els Hostalets de Pierola, Els hostalets de Pierola, Barcelona (Spain). PROGRAM: - Complex Biological Systems: Modelling Relations: Historical and conceptual introduction. Basic concepts and representations. - Hands on Computers: Introduction to R: Presentation of the R environment and language. Basic operations in R (useful for network modelling). Packages installation. - Hands on Computers: Introduction to igraph and Network Modelling: Presentation of the package igraph. Modelling deterministic networks. Manipulating network attributes. Modelling networks from loaded data. - Complex Biological Systems: Applied Network Theory: Nodes, links and types of networks. Basic network parameters. Network architecture and null network models. - Work Example: Analysing parameters and architecture in tetrapod skull networks. - Hands on Computers: Analysing Networks: Quantifying basic network parameters. Identifying network architecture. - Work Example: Null network models of skull development to study evolution. - Hands on Computers: Modelling Network Null Models: Regular and random models. Small-world and scale-free models. Geometric models. - Complex Biological Systems: Network Properties: Robustness and the concept of secondary extinction. Modularity. - Work Example: Modularity in skull networks. - Hands on Computers: Identifying Modules: Optimization methods. Heuristic methods. Quantifying the strength of modularity. - Participants Project Preparation. Bringing your own data is not required for this part, but you are welcome to do so if you have it. Organized by: Transmitting Science, the Institut Catal de Paleontologia Miquel Crusafont and the Council of Hostalets de Pierola. Please feel free to distribute this information between your colleagues if you consider it appropriate. With best regards Soledad De Esteban Trivigno, PhD. Course Director Transmitting Science email@example.com via Gmail
October 25, 2014
The University of Washington has post-doctoral position open in their “Genetic Approaches to Aging” Training Grant (see below). The position is available immediately. Applicants must be US citizens or Green Card holders. The successful applicant will have the choice of numerous labs (information on links below) with diverse training options, including training in the Evolutionary Genetics of Aging (e.g., http://bit.ly/13eK9N6). The T32 Genetic Approaches to Aging Training Grant has one Post-doctoral slot open for a 9-month appointment The goal of our program is to train new independent investigators who will utilize contemporary molecular and genetic techniques to investigate the underlying mechanisms of aging. Applications are scored by consideration of the qualifications of the applicant and the mentoring environment, as well as how the research specifically relates to the biology of aging. Funding is at NIH stipend levels. Deadlines Applications are considered on a rolling basis, we encourage applicants to make their submissions as soon as possible. Applications for the slot will be accepted until the position is filled. For more Information: For more information on the Genetic Approaches to Aging Training Program visit http://bit.ly/1zurT7B For Application instructions visit http://bit.ly/1uXLbdE grant/application For questions regarding the application process, please contact Rachel Wilsey at firstname.lastname@example.org or 206-616-4135 Daniel Promislow Department of Pathology and Department of Biology University of Washington 1959 NE Pacific Street Box 357705, Room K-078 Seattle, WA 98195 ph: 206 616-6994 e: email@example.com Daniel Promislow via Gmail
The role of gene duplication in generating new genes and novel functions is well recognized and is exemplified by the digestion-related protein lysozyme. In ruminants, duplicated chicken-type lysozymes facilitate the degradation of symbiotic bacteria in the foregut. Chicken-type lysozyme has also been reported to show chitinase-like activity, yet no study has examined the molecular evolution of lysozymes in species that specialize on eating insects. Insectivorous bats number over 900 species, and lysozyme expression in the mouths of some of these species is associated with the ingestion of insect cuticle, suggesting a chitinase role. Here, we show that chicken-type lysozyme has undergone multiple duplication events in a major family of insect-eating bats (Vespertilionidae) and that new duplicates have undergone molecular adaptation. Examination of duplicates from two insectivorous bats—Pipistrellus abramus and Scotophilus kuhlii—indicated that the new copy was highly expressed in the tongue, whereas the other one was less tissue-specific. Functional assays applied to pipistrelle lysozymes confirmed that, of the two copies, the tongue duplicate was more efficient at breaking down glycol chitin, a chitin derivative. These results suggest that the evolution of lysozymes in vespertilionid bats has likely been driven in part by natural selection for insectivory.
Parallel Evolution of Tetrodotoxin Resistance in Three Voltage-Gated Sodium Channel Genes in the Garter Snake Thamnophis sirtalis
Members of a gene family expressed in a single species often experience common selection pressures. Consequently, the molecular basis of complex adaptations may be expected to involve parallel evolutionary changes in multiple paralogs. Here, we use bacterial artificial chromosome library scans to investigate the evolution of the voltage-gated sodium channel (Nav) family in the garter snake Thamnophis sirtalis, a predator of highly toxic Taricha newts. Newts possess tetrodotoxin (TTX), which blocks Nav’s, arresting action potentials in nerves and muscle. Some Thamnophis populations have evolved resistance to extremely high levels of TTX. Previous work has identified amino acid sites in the skeletal muscle sodium channel Nav1.4 that confer resistance to TTX and vary across populations. We identify parallel evolution of TTX resistance in two additional Nav paralogs, Nav1.6 and 1.7, which are known to be expressed in the peripheral nervous system and should thus be exposed to ingested TTX. Each paralog contains at least one TTX-resistant substitution identical to a substitution previously identified in Nav1.4. These sites are fixed across populations, suggesting that the resistant peripheral nerves antedate resistant muscle. In contrast, three sodium channels expressed solely in the central nervous system (Nav1.1–1.3) showed no evidence of TTX resistance, consistent with protection from toxins by the blood–brain barrier. We also report the exon–intron structure of six Nav paralogs, the first such analysis for snake genes. Our results demonstrate that the molecular basis of adaptation may be both repeatable across members of a gene family and predictable based on functional considerations.
Hominoid Composite Non-LTR Retrotransposons--Variety, Assembly, Evolution, and Structural Determinants of Mobilization
SVA (SINE-R-VNTR-Alu) elements constitute the youngest family of composite non-LTR retrotransposons in hominoid primates. The sequence of their assembly, however, remains unclear. Recently, a second family of VNTR-containing composites, LAVA (L1-Alu-VNTR-Alu), has been identified in gibbons. We now report the existence of two additional VNTR composite families, PVA (PTGR2-VNTR-Alu) and FVA (FRAM-VNTR-Alu), in the genome of Nomascus leucogenys. Like LAVA, they share the 5'-Alu-like region and VNTR with SVA, but differ at their 3'-ends. The 3'-end of PVA comprises part of the PTGR2 gene, whereas FVA is characterized by the presence of a partial FRAM element in its 3'-domain. Splicing could be identified as the mechanism of acquisition of the variant 3'-ends in all four families of VNTR composites. SVAs have been shown to be mobilized by the L1 protein machinery in trans. A critical role in this process has been ascribed to their 5'-hexameric repeat/ Alu-like region. The Alu-like region displays specific features in each of the VNTR composite families/subfamilies with characteristic deletions found in the evolutionary younger subfamilies. Using reciprocal exchanges between SVA_E and PVA/FVA elements, we demonstrate that the structure, not the presence of the (CCCTCT)n/ Alu-like region determines mobilization capacity. Combination of LAVA and SVA_E domains does not yield any active elements—suggesting the use of different combinations of host factors for the two major groups of VNTR composites. Finally, we demonstrate that the LAVA 3'-L1ME5 fragment attenuates mobilization capacity.
Evolution of a Genome-Encoded Bias in Amino Acid Biosynthetic Pathways Is a Potential Indicator of Amino Acid Dynamics in the Environment
Overcoming the stress of starvation is one of an organism’s most challenging phenotypic responses. Those organisms that frequently survive the challenge, by virtue of their fitness, will have evolved genomes that are shaped by their specific environments. Understanding this genotype–environment–phenotype relationship at a deep level will require quantitative predictive models of the complex molecular systems that link these aspects of an organism’s existence. Here, we treat one of the most fundamental molecular systems, protein synthesis, and the amino acid biosynthetic pathways involved in the stringent response to starvation. These systems face an inherent logical dilemma: Building an amino acid biosynthetic pathway to synthesize its product—the cognate amino acid of the pathway—may require that very amino acid when it is no longer available. To study this potential "catch-22," we have created a generic model of amino acid biosynthesis in response to sudden starvation. Our mathematical analysis and computational results indicate that there are two distinctly different outcomes: Partial recovery to a new steady state, or full system failure. Moreover, the cell’s fate is dictated by the cognate bias, the number of cognate amino acids in the corresponding biosynthetic pathway relative to the average number of that amino acid in the proteome. We test these implications by analyzing the proteomes of over 1,800 sequenced microbes, which reveals statistically significant evidence of low cognate bias, a genetic trait that would avoid the biosynthetic quandary. Furthermore, these results suggest that the pattern of cognate bias, which is readily derived by genome sequencing, may provide evolutionary clues to an organism’s natural environment.
The time required to transcribe genes with long primary transcripts may limit their ability to be expressed in cells with short mitotic cycles, a phenomenon termed intron delay. As such short cycles are a hallmark of the earliest stages of insect development, we tested the impact of intron delay on the Drosophila developmental transcriptome. We find that long zygotically expressed genes show substantial delay in expression relative to their shorter counterparts, which is not observed for maternally deposited transcripts. Patterns of RNA-seq coverage along transcripts show that this delay is consistent with their inability to completely transcribe long transcripts, but not with transcriptional initiation-based regulatory control. We further show that highly expressed zygotic genes maintain compact transcribed regions across the Drosophila phylogeny, allowing conservation of embryonic expression patterns. We propose that the physical constraints of intron delay affect patterns of expression and the evolution of gene structure of a substantial portion of the Drosophila transcriptome.
Gene loss, gain, and transfer play an important role in shaping the genomes of all organisms; however, the interplay of these processes in isolated populations, such as in obligate intracellular bacteria, is less understood. Despite a general trend towards genome reduction in these microbes, our phylogenomic analysis of the phylum Chlamydiae revealed that within the family Parachlamydiaceae, gene family expansions have had pronounced effects on gene content. We discovered that the largest gene families within the phylum are the result of rapid gene birth-and-death evolution. These large gene families are comprised of members harboring eukaryotic-like ubiquitination-related domains, such as F-box and BTB-box domains, marking the largest reservoir of these proteins found among bacteria. A heterologous type III secretion system assay suggests that these proteins function as effectors manipulating the host cell. The large disparity in copy number of members in these families between closely related organisms suggests that nonadaptive processes might contribute to the evolution of these gene families. Gene birth-and-death evolution in concert with genomic drift might represent a previously undescribed mechanism by which isolated bacterial populations diversify.
The 20 protein-coding amino acids are found in proteomes with different relative abundances. The most abundant amino acid, leucine, is nearly an order of magnitude more prevalent than the least abundant amino acid, cysteine. Amino acid metabolic costs differ similarly, constraining their incorporation into proteins. On the other hand, a diverse set of protein sequences is necessary to build functional proteomes. Here, we present a simple model for a cost-diversity trade-off postulating that natural proteomes minimize amino acid metabolic flux while maximizing sequence entropy. The model explains the relative abundances of amino acids across a diverse set of proteomes. We found that the data are remarkably well explained when the cost function accounts for amino acid chemical decay. More than 100 organisms reach comparable solutions to the trade-off by different combinations of proteome cost and sequence diversity. Quantifying the interplay between proteome size and entropy shows that proteomes can get optimally large and diverse.
Multihost Experimental Evolution of the Pathogen Ralstonia solanacearum Unveils Genes Involved in Adaptation to Plants
Ralstonia solanacearum, the causal agent of a lethal bacterial wilt plant disease, infects an unusually wide range of hosts. These hosts can further be split into plants where R. solanacearum is known to cause disease (original hosts) and those where this bacterium can grow asymptomatically (distant hosts). Moreover, this pathogen is able to adapt to many plants as supported by field observations reporting emergence of strains with enlarged pathogenic properties. To investigate the genetic bases of host adaptation, we conducted evolution experiments by serial passages of a single clone of the pathogen on three original and two distant hosts over 300 bacterial generations and then analyzed the whole-genome of nine evolved clones. Phenotypic analysis of the evolved clones showed that the pathogen can increase its fitness on both original and distant hosts although the magnitude of fitness increase was greater on distant hosts. Only few genomic modifications were detected in evolved clones compared with the ancestor but parallel evolutionary changes in two genes were observed in independent evolved populations. Independent mutations in the regulatory gene efpR were selected for in three populations evolved on beans, a distant host. Reverse genetic approaches confirmed that these mutations were associated with fitness gain on bean plants. This work provides a first step toward understanding the within-host evolutionary dynamics of R. solanacearum during infection and identifying bacterial genes subjected to in planta selection. The discovery of EfpR as a determinant conditioning host adaptation of the pathogen illustrates how experimental evolution coupled with whole-genome sequencing is a potent tool to identify novel molecular players involved in central life-history traits.
Genome-Wide SNP Analysis Reveals Population Structure and Demographic History of the Ryukyu Islanders in the Southern Part of the Japanese Archipelago
The Ryukyu Islands are located to the southwest of the Japanese archipelago. Archaeological evidence has revealed the existence of prehistoric cultural differentiation between the northern Ryukyu islands of Amami and Okinawa, and the southern Ryukyu islands of Miyako and Yaeyama. To examine a genetic subdivision in the Ryukyu Islands, we conducted genome-wide single nucleotide polymorphism typing of inhabitants from the Okinawa Islands, the Miyako Islands, and the Yaeyama Islands. Principal component and cluster analyses revealed genetic differentiation among the island groups, especially between Okinawa and Miyako. No genetic affinity was observed between aboriginal Taiwanese and any of the Ryukyu populations. The genetic differentiation observed between the inhabitants of the Okinawa Islands and the Miyako Islands is likely to have arisen due to genetic drift rather than admixture with people from neighboring regions. Based on the observed genetic differences, the divergence time between the inhabitants of Okinawa and Miyako islands was dated to the Holocene. These findings suggest that the Pleistocene inhabitants, whose bones have been found on the southern Ryukyu Islands, did not make a major genetic contribution, if any, to the present-day inhabitants of the southern Ryukyu Islands.
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology
Molecular Biology and Evolution