This parody of evo devo makes it sound a lot like ID

_{News
December 19, 2017

Cell biology, Evolution, Evolutionary biology

1}_{Categories
Cell biology
Evolution
Evolutionary biology}

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“This is how we go from single cells to people.” Hmmm.

See also: From Biology Direct: Darwinism, now thoroughly detached from its historical roots as a falsifiable theory, “must be abandoned”

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Systematists and geneticists study biological diversity, but they use different approaches that rarely intersect. A very common pattern that is of interest for both researchers is the rapid evolution of genitalia, a trait of significant taxonomic utility in several sexually reproducing animal clades. The idea that both male and female genitalia are species-specific and play a role in reproductive isolation has long been controversial but has recently gained a renewed interest by speciation and developmental geneticists. Here, I highlight six unresolved questions in genitalia coevolution and I argue that systematists, with their well training in comparative morphology, usage of large and geographically diverse collections, and ability to apply molecular genetics techniques, can make important contributions. Such an extension of systematics into the speciation and developmental genetics realms is a promising opportunity to expand “integrative taxonomy” comparisons between DNA and morphology into more explanatory relationships between the two sources of taxonomic data. Yassin, Amir. (2016). Unresolved questions in genitalia coevolution: bridging taxonomy, speciation, and developmental genetics. Organisms Diversity & Evolution. 16. . 10.1007/s13127-016-0286-2.Dionisio_{January 21, 2018
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Recently a new species of bombyliid fly, Marleyimyia xylocopae, was described by Marshall & Evenhuis (2015) based on two photographs taken during fieldwork in the Republic of South Africa. This species has no preserved holotype. The paper generated some buzz, especially among dipterists, because in most cases photographs taken in the field provide insufficient information for properly diagnosing and documenting species of Diptera. Amorim, Dalton & Santos, Charles & Krell, Frank-Thorsten & Dubois, Alain & Nihei, Silvio & Oliveira, Otto & Pont, Adrian & SONG, HOJUN & Verdade, Vanessa & Fachin, Diego & Klassa, Bruna & Lamas, Carlos & Oliveira, Sarah & De Carvalho, Claudio & Mello-Patiu, Cátia & Hajdu, Eduardo & S. COURI, MÁRCIA & Silva, Vera & Capellari, Renato & Grimaldi, David. (2016). Timeless standards for species delimitation. Zootaxa. 4137. 121. 10.11646/zootaxa.4137.1.9. https://www.researchgate.net/profile/Antonio_Marques8/publication/305039414_Timeless_standards_for_species_delimitation/links/577fa7bf08ae9485a439a574/Timeless-standards-for-species-delimitation.pdfDionisio_{January 21, 2018
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Evolutionary developmental biology (evo-devo) suggests a distinction between modular and systemic variation. In the case of modular change, the conservation of the overall structure helps recognizing affinities, while a single, fast evolving module is likely to produce a bonanza for the taxonomist, while systemic changes produce strongly deviating morphologies that cause problems in tracing homologies. Similarly, changes affecting the whole life cycle are more challenging than those limited to one stage. Developmental modularity is a precondition for heterochrony. Analyzing a matrix of morphological data for paedomorphic taxa requires special care. It is, however, possible to extract phylogenetic signal from heterochronic patterns. The taxonomist should pay attention to the intricacies of the genotype-->. phenotype map. When using genetic data to infer phylogeny, a comparison of gene sequences is just a first step. To bridge the gap between genes and morphology we should consider the spatial and temporal patterns of gene expression, and their regulation. Minor genetic change can have major phenotypic effects, sometimes suggesting saltational evolution. Evo-devo is also relevant in respect to speciation: changes in developmental schedules are often implicated in the divergence between sympatric morphs, and a developmental modulation of 'temporal phenotypes' appears to be responsible for many cases of speciation. Minelli, Alessandro. (2015). Biological Systematics in the Evo-Devo era. European Journal of Taxonomy. 0. . 10.5852/ejt.2015.125. https://www.researchgate.net/profile/Alessandro_Minelli/publication/279250861_Biological_Systematics_in_the_Evo-Devo_era/links/55ddd06e08ae45e825d39045/Biological-Systematics-in-the-Evo-Devo-era.pdfDionisio_{January 21, 2018
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The chordates are usually characterized as bilaterians showing deuterostomy, i.e. the mouth developing as a new opening between the archenteron and the ectoderm, serial gill pores/slits, and the complex of chorda and neural tube. Both numerous molecular studies and studies of morphology and embryology demonstrate that the neural tube must be considered homologous to the ventral nerve cord(s) of the protostomes, but the origin of the 'new' mouth of the deuterostomes has remained enigmatic. However, deuterostomy is known to occur in several protostomian groups, such as the chaetognaths and representatives of annelids, molluscs, arthropods and priapulans. This raises the question whether the deuterostomian mouth is in fact homologous with that of the protostomes, viz. the anterior opening of the ancestral blastopore divided through lateral blastopore fusion, i.e. amphistomy. A few studies of gene expression show identical expression patterns around mouth and anus in protostomes and deuterostomes. Closer studies of the embryology of ascidians and vertebrates show that the mouth/stomodaeum differentiates from the anterior edge of the neural plate. Together this indicates that the chordate mouth has moved to the anterior edge of the blastopore, so that the anterior loop of the ancestral circumblastoporal nerve cord, which is narrow in the protostomes, has become indistinguishable. In the vertebrates, the mouth has moved further around the anterior pole to the 'ventral' side. The conclusion must be that the chordate mouth (and that of the deuterostomes in general) is homologous to the protostomian mouth and that the latest common ancestor of protostomes and deuterostomes developed through amphistomy, as suggested by the trochaea theory. Nielsen, Claus. (2015). Evolution of deuterostomy - and origin of the chordates. Biological reviews of the Cambridge Philosophical Society. 92. . 10.1111/brv.12229.Dionisio_{January 21, 2018
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Hox proteins are one of the best studied sets of transcription factors in developmental biology. They are major determinants for establishing morphological differences along the anterior-posterior axis of animals and are generally regarded as highly conserved in function. This view is based on experiments comparing a few (anterior) Hox proteins, however, the extent to which central or abdominal Hox proteins share sequence features or functions remains largely unexplored. To shed light on the origin and functional divergence of the central Hox proteins, we combine a powerful bioinformatics tool (CLANS) with a large-scale phylogeny of species. CLANS is used to differentiate between the various types of central Hox protein sequences, while the phylogeny provides an evolutionary context to the analysis. The combination of both enables us to infer the relative timepoint at which a given central Hox protein type arose. We identify seven distinct central Hox protein sequence types, only one of which is common to all protostome and deuterostome clades (Antp/Hox7). Together, these results lead us to suggest reevaluating the usefulness of the increasingly depicted synteny-based classification scheme that assumes a one-to-one orthology between protostome and deuterostome central Hox proteins. Instead, we propose that the use of sequence-based classification schemes able to resolve the central and posterior Hox proteins provides a more promising and biologically meaningful alternative to resolving these groups. This analysis, which provides a unique overview of the Hox protein sequence types present across protostomes and deuterostomes as well as a relative dating for the emergence of the central Hox protein types, provides a crucial clue to illuminate how and when the distinct developmental blueprints for organisms evolved within the evolutionarily immensely successful bilaterian lineage. Hueber, Stefanie & Rauch, Jens & Djordjevic, Michael & Gunter, Helen & Weiller, Georg & Frickey, Tancred. (2013). Analysis of central Hox protein types across bilaterian clades: On the diversification of central Hox proteins from an Antennapedia/Hox7-like protein. Developmental biology. 383. . 10.1016/j.ydbio.2013.09.009.Dionisio_{January 21, 2018
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Hox genes encode a family of transcriptional regulators that elicit distinct developmental programmes along the head-to-tail axis of animals. The specific regional functions of individual Hox genes largely reflect their restricted expression patterns, the disruption of which can lead to developmental defects and disease. Here, we examine the spectrum of molecular mechanisms controlling Hox gene expression in model vertebrates and invertebrates and find that a diverse range of mechanisms, including nuclear dynamics, RNA processing, microRNA and translational regulation, all concur to control Hox gene outputs. We propose that this complex multi-tiered regulation might contribute to the robustness of Hox expression during development. The regulation of Hox gene expression during animal development Moisés Mallo, Claudio R. Alonso Development 2013 140: 3951-3963; doi: 10.1242/dev.068346 http://dev.biologists.org/content/140/19/3951.full.pdfDionisio_{January 21, 2018
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This Special Issue of Journal of Developmental Biology (JDB) covers an indeed very “special” (at least to me) family of highly evolutionarily conserved genes, the Hox genes. Despite over three decades having passed since the discovery of the homeobox, the excellent level and the wide range of topics of the articles and reviews published in this Special Issue testify the long-standing and ongoing interest in the functions of this unique gene family. The studies gathered in this issue of JDB cover subjects ranging from the use of Hox genes as a paradigm for the development of computational methods of protein family classification, to the role of Hox genes in the development and evolution of appendices, and the mechanisms underlying the expression of specific Hox proteins Zappavigna, Vincenzo. (2017). Special Issue on HOX Genes in Development. Journal of Developmental Biology. 5. 5. 10.3390/jdb5020005. http://www.mdpi.com/2221-3759/5/2/5/pdfDionisio_{January 21, 2018
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Phylogenetic methods are key to providing models for how a given protein family evolved. However, these methods run into difficulties when sequence divergence is either too low or too high. Here, we provide a case study of Hox and ParaHox proteins so that additional insights can be gained using a new computational approach to help solve old classification problems. For two (Gsx and Cdx) out of three ParaHox proteins the assignments differ between the currently most established view and four alternative scenarios. We use a non-phylogenetic, pairwise-sequence-similarity-based method to assess which of the previous predictions, if any, are best supported by the sequence-similarity relationships between Hox and ParaHox proteins. The overall sequence-similarities show Gsx to be most similar to Hox2–3, and Cdx to be most similar to Hox4–8. The results indicate that a purely pairwise-sequence-similarity-based approach can provide additional information not only when phylogenetic inference methods have insufficient information to provide reliable classifications (as was shown previously for central Hox proteins), but also when the sequence variation is so high that the resulting phylogenetic reconstructions are likely plagued by long-branch-attraction artifacts. Hueber, Stefanie & Frickey, Tancred. (2016). Solving Classification Problems for Large Sets of Protein Sequences with the Example of Hox and ParaHox Proteins. Journal of Developmental Biology. 4. 8. 10.3390/jdb4010008. http://www.mdpi.com/2221-3759/4/1/8/pdfDionisio_{January 21, 2018
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Here, we provide an update of our review on homeobox genes that we wrote together with Walter Gehring in 1994. Since then, comprehensive surveys of homeobox genes have become possible due to genome sequencing projects. Using the 103 Drosophila homeobox genes as example, we present an updated classification. In animals, there are 16 major classes, ANTP, PRD, PRD-LIKE, POU, HNF, CUT (with four subclasses: ONECUT, CUX, SATB, and CMP), LIM, ZF, CERS, PROS, SIX/SO, plus the TALE superclass with the classes IRO, MKX, TGIF, PBC, and MEIS. In plants, there are 11 major classes, i.e., HD-ZIP (with four subclasses: I to IV), WOX, NDX, PHD, PLINC, LD, DDT, SAWADEE, PINTOX, and the two TALE classes KNOX and BEL. Most of these classes encode additional domains apart from the homeodomain. Numerous insights have been obtained in the last two decades into how homeodomain proteins bind to DNA and increase their specificity by interacting with other proteins to regulate cell- and tissue-specific gene expression. Not only protein-DNA base pair contacts are important for proper target selection; recent experiments also reveal that the shape of the DNA plays a role in specificity. Using selected examples, we highlight different mechanisms of homeodomain protein-DNA interaction. The PRD class of homeobox genes was of special interest to Walter Gehring in the last two decades. The PRD class comprises six families in Bilateria, and tinkers with four different motifs, i.e., the PAIRED domain, the Groucho-interacting motif EH1 (aka Octapeptide or TN), the homeodomain, and the OAR motif. Homologs of the co-repressor protein Groucho are also present in plants (TOPLESS), where they have been shown to interact with small amphipathic motives (EAR), and in yeast (TUP1), where we find an EH1-like motif in MAT?2. Electronic supplementary material The online version of this article (doi:10.1007/s00412-015-0543-8) contains supplementary material, which is available to authorized users. R Bürglin, Thomas & Affolter, Markus. (2015). Homeodomain proteins: an update. Chromosoma. 125. . 10.1007/s00412-015-0543-8. http://link.springer.com/content/pdf/10.1007%2Fs00412-015-0543-8.pdfDionisio_{January 21, 2018
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We report the complete sequence analysis of the entire complement of eight typical homeobox (Hox) genes (Lab, Pb, Dfd, Scr, Antp, Ubx, Abd-A, and Abd-B) and two other genes (Hox3 and Ftz) in a 324.6-kb region in the water flea Daphnia magna. In the water flea D. magna Hox genes, we found one long interspersed nuclear element (LINE)/R2-NeSL between Ubx and Abd-A, but it was not present in Daphnia pulex Hox genes. In basal expression of Hox genes on different developmental stages, biothorax complex genes (Ubx, Abd-A, and Abd-B) and some of antennapedia complex genes (Lab, Scr, Antp) were moderately expressed but Hox3 gene was barely expressed, while three homeobox genes (Antp, Ubx, Abd-A) were highly expressed in 6-7 days after releasing from brood chamber and/or adult stage. The structural array and transcribed orientation of Dm-Hox genes were identical to the sister species D. pulex (~340 kb), indicating that the Hox gene structure in daphnids is highly conserved. However, the structural array and transcribed orientation of Dm- and Dp-Hox3, -deformed (Dfd), -fushi tarazu (Ftz) genes varied from orthologous genes in pancrustacean species. Kim, Duck-Hyun & Lee, Bo-Young & Kim, Hui-Su & Jeong, Chang-Bum & Hwang, Dae-sik & Kim, Il-Chan & Lee, Jae-Seong. (2018). Identification and characterization of homeobox (Hox) genes and conservation of the single Hox cluster (324.6 kb) in the water flea Daphnia magna. Journal of Experimental Zoology Part B Molecular and Developmental Evolution. 0. 0. https://www.researchgate.net/profile/Jae-Seong_Lee/publication/320798695_Identification_and_characterization_of_homeobox_Hox_genes_and_conservation_of_the_single_Hox_cluster_3246_kb_in_the_water_flea_Daphnia_magna/links/5a62bd95aca272a15819a8c2/Identification-and-characterization-of-homeobox-Hox-genes-and-conservation-of-the-single-Hox-cluster-3246-kb-in-the-water-flea-Daphnia-magna.pdfDionisio_{January 21, 2018
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The discovery of the broad conservation of embryonic regulatory genes across animal phyla, launched by the cloning of homeotic genes in the 1980s, was a founding event in the field of evolutionary developmental biology (evo-devo). While it had long been known that fundamental cellular processes, commonly referred to as housekeeping functions, are shared by animals and plants across the planet-processes such as the storage of information in genomic DNA, transcription, translation and the machinery for these processes, universal codon usage, and metabolic enzymes-Hox genes were different: mutations in these genes caused "bizarre" homeotic transformations of insect body parts that were certainly interesting but were expected to be idiosyncratic. The isolation of the genes responsible for these bizarre phenotypes turned out to be highly conserved Hox genes that play roles in embryonic patterning throughout Metazoa. How Hox genes have changed to promote the development of diverse body plans remains a central issue of the field of evo-devo today. For this Memorial article series, I review events around the discovery of the broad evolutionary conservation of Hox genes and the impact of this discovery on the field of developmental biology. I highlight studies carried out in Walter Gehring's lab and by former lab members that have continued to push the field forward, raising new questions and forging new approaches to understand the evolution of developmental mechanisms. Pick, Leslie. (2015). Hox genes, evo-devo, and the case of the ftz gene. Chromosoma. 125. . 10.1007/s00412-015-0553-6. https://www.researchgate.net/profile/Leslie_Pick/publication/284562965_Hox_genes_evo-devo_and_the_case_of_the_ftz_gene/links/5811fa0108ae8b130d0bceac/Hox-genes-evo-devo-and-the-case-of-the-ftz-gene.pdf There yet? :)Dionisio_{January 21, 2018
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The role of allometry in producing the variation in autopodial morphology observed among the lizards is not well understood. Allometry of metapodial and digit lengths in the manus and pes of the primitively padless gekkotan (Eublepharis macularius) is explored using maximum-likelihood repeated-measures ANCOVAs with body length as the covariate. Estimated variance–covariance matrices differed significantly within and between autopodia, and integration was stronger among the metapodials than the digits. The first metapodial and the first digit of each autopodium exhibit the strongest covariances with each of the remaining components in each variance–covariance matrix, suggesting that the lengths of the first rays are important for allometric integration of both manus and pes. Metapodials scale isometrically and digits negatively allometrically; both display allometric heterogeneity among themselves in both autopodia. Both autopodia exhibit changes in proportion over the ontogenetic size range, attributable to variation in scaling among the components of the rays. Allometric coefficients do not vary among pedal digits, despite differences in phalanx number, although phalanx number is associated with differences in slope in the manual digits. This is suggestive of heterogeneity in allometry among the manual phalanges, which thus may be associated with variation in phalanx length within gekkotan digits. Powell, G & J. Osgood, Geoffrey & P. Russell, Anthony. (2017). Ontogenetic allometry of the digital rays of the leopard gecko (Gekkota: Eublepharidae; Eublepharis macularius). Acta Zoologica. . 10.1111/azo.12215.Dionisio_{January 21, 2018
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Chameleon species have recently been adopted as models for evo-devo and macroevolutionary processes. However, most anatomical and developmental studies of chameleons focus on the skeleton , and information about their soft tissues is scarce. Here, we provide a detailed morphological description based on contrast enhanced micro-CT scans and dissections of the adult phenotype of all the forelimb and hindlimb muscles of the Veiled Chameleon (Chamaeleo calyptratus) and compare these muscles with those of other chameleons and lizards. We found the appendicular muscle anatomy of chameleons to be surprisingly conservative considering the remarkable structural and functional modifications of the limb skeleton, particularly the distal limb regions. For instance, the zygodactyl autopodia of chameleons are unique among tetrapods, and the carpals and tarsals are highly modified in shape and number. However, most of the muscles usually present in the manus and pes of other lizards are present in the same configuration in chameleons. The most obvious muscular features related to the peculiar opposable autopodia of chameleons are: (1) presence of broad, V-shaped plantar and palmar aponeuroses, and absence of intermetacarpales and intermeta-tarsales, between the digits separated by the cleft in each autopod; (2) oblique orientation of the superficial short flexors originating from these aponeuroses, which may allow these muscles to act as powerful adductors of the " super-digits " ; and (3) well-developed abductor digiti minimi muscles and abductor pollicis/hallucis brevis muscles, which may act as powerful abductors of the " super-digits. Molnar, Julia & Diaz, Raul & Skorka, Tautis & , Grant & Diogo, Rui. (2017). Comparative musculoskeletal anatomy of chameleon limbs, with implications for the evolution of arboreal locomotion in lizards and for teratology. Journal of morphology. 278. . 10.1002/jmor.20708.Dionisio_{January 21, 2018
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gooshy @157, Is your comment related to the comment @5? https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-645907 I haven't had the opportunity to listen to the named Canadian singer, but have heard dolphins.Dionisio_{January 21, 2018
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Since the rise of evo-devo (evolutionary developmental biology) in the 1980s, few authors have attempted to combine the increasing knowledge obtained from the study of model organisms and human medicine with data from comparative anatomy and evolutionary biology in order to investigate the links between development, pathology, and macroevolution. Fortunately, this situation is slowly changing, with a renewed interest in evolutionary developmental pathology (evo-devo-path) in the past decades, as evidenced by the idea to publish this special, and very timely, issue on “Developmental Evolution in Biomedical Research.” As all of us have recently been involved, independently, in works related in some way or another with evolution and developmental anomalies, we decided to join our different perspectives and backgrounds in the present contribution for this special issue. Specifically, we provide a brief historical account on the study of the links between evolution, development, and pathologies, followed by a review of the recent work done by each of us, and then by a general discussion on the broader developmental and macroevolutionary implications of our studies and works recently done by other authors. Our primary aims are to highlight the strength of studying developmental anomalies within an evolutionary framework to understand morphological diversity and disease by connecting the recent work done by us and others with the research done and broader ideas proposed by authors such as Étienne Geoffroy Saint-Hilaire, Waddington, Goldschmidt, Gould, and Per Alberch, among many others to pave the way for further and much needed work regarding abnormal development and macroevolution. Diogo, Rui & Guinard, Geoffrey & Diaz, Raul. (2016). Dinosaurs, Chameleons, Humans, and Evo?Devo Path: Linking Étienne Geoffroy's Teratology, Waddington's Homeorhesis, Alberch's Logic of “Monsters,” and Goldschmidt Hopeful “Monsters”. Journal of Experimental Zoology Part B Molecular and Developmental Evolution. 328. . 10.1002/jez.b.22709.Dionisio_{January 21, 2018
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Sorry if somebody told this already, but in re canadian pop stars: What's the difference between Justin Bieber and a dolphin? One makes really annoying high-pitched squeaks. The other is a large marine mammal.gooshy_{January 21, 2018
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It's worth reminding all about these two insightful comments by gpuccio @122 & @123: https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-649412Dionisio_{January 21, 2018
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This paper describes and summarizes approaches for visualization and statistical analysis using data from Ralstonia solanacearum infection experiments based on methods and concepts that are broadly applicable. Members of the R. solanacearum species complex cause bacterial wilt disease. Bacterial wilt is a lethal plant disease and has been studied for over 100 years. During this time various methods to quantify disease and different ways to analyze the generated data have been employed. Here, I aim to provide a general background on three distinct and commonly used measures of disease: the area under the disease progression curve, longitudinal recordings of disease severity and host survival. I will discuss how one can proceed with visualization, statistical analysis, and interpretation using different datasets while revisiting the general concepts of statistical analysis. Datasets and R code to perform all analyses discussed here are included in the supplement. Schandry, Niklas. (2017). A Practical Guide to Visualization and Statistical Analysis of R. solanacearum Infection Data Using R. Frontiers in Plant Science. 8. . 10.3389/fpls.2017.00623. https://www.researchgate.net/profile/Niklas_Schandry/publication/316459410_A_Practical_Guide_to_Visualization_and_Statistical_Analysis_of_R_solanacearum_Infection_Data_Using_R/links/59082b43a6fdccd580dd0ce1/A-Practical-Guide-to-Visualization-and-Statistical-Analysis-of-R-solanacearum-Infection-Data-Using-R.pdfDionisio_{January 21, 2018
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Various classes of plant pathogenesis-related proteins have been identified in the past several decades. PR-Q, a member of the PR3 family encoding chitinases, has played an important role in regulating plant resistance and preventing pathogen infection. In this paper, we functionally characterized NtPR-Q in tobacco plants and found that the overexpression of NtPR-Q in tobacco Yunyan87 resulted in higher resistance to Ralstonia solanacearum inoculation. Surprisingly, overexpression of NtPR-Q led to the activation of many defense-related genes, such as salicylic acid (SA)-responsive genes NtPR1a/c, NtPR2 and NtCHN50, JA-responsive gene NtPR1b and ET production-associated genes NtACC Oxidase and NtEFE26. Consistent with the role of NtPR-Q in multiple stress responses, NtPR-Q transcripts were induced by the exogenous hormones SA, ethylene and methyl jasmonate, which could enhance the resistance of tobacco to R. solanacearum. Collectively, our results suggested that NtPR-Q overexpression led to the up-regulation of defense-related genes and enhanced plant resistance to R. solanacearum infection. Tang, Yuanman & Liu, Qiuping & Liu, Ying & Zhang, Linli & Ding, Wei. (2017). Overexpression of NtPR-Q Up-Regulates Multiple Defense-Related Genes in Nicotiana tabacum and Enhances Plant Resistance to Ralstonia solanacearum. Frontiers in Plant Science. 08. 1963. 10.3389/fpls.2017.01963. https://www.researchgate.net/publication/321100396_Overexpression_of_NtPR-Q_Up-Regulates_Multiple_Defense-Related_Genes_in_Nicotiana_tabacum_and_Enhances_Plant_Resistance_to_Ralstonia_solanacearum/fulltext/5a0d8e6d0f7e9b9e33ab51dd/321100396_Overexpression_of_NtPR-Q_Up-Regulates_Multiple_Defense-Related_Genes_in_Nicotiana_tabacum_and_Enhances_Plant_Resistance_to_Ralstonia_solanacearum.pdfDionisio_{January 21, 2018
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F-box proteins are substrate adaptors used by the SKP1-CUL1-F-box protein (SCF) complex, a type of E3 ubiquitin ligase complex in the ubiquitin proteasome system (UPS). SCF-mediated ubiquitylation regulates proteolysis of hundreds of cellular proteins involved in key signaling and disease systems. However, our knowledge of the evolution of the F-box gene family in Euarchontoglires is limited. In the present study, 559 F-box genes and nine related pseudogenes were identified in eight genomes. Lineage-specific gene gain and loss events occurred during the evolution of Euarchontoglires, resulting in varying F-box gene numbers ranging from 66 to 81 among the eight species. Both tandem duplication and retrotransposition were found to have contributed to the increase of F-box gene number, whereas mutation in the F-box domain was the main mechanism responsible for reduction in the number of F-box genes, resulting in a balance of expansion and contraction in the F-box gene family. Thus, the Euarchontoglire F-box gene family evolved under a birth-and-death model. Signatures of positive selection were detected in substrate-recognizing domains of multiple F-box proteins, and adaptive changes played a role in evolution of the Euarchontoglire F-box gene family. In addition, single nucleotide polymorphism (SNP) distributions were found to be highly non-random among different regions of F-box genes in 1092 human individuals, with domain regions having a significantly lower number of non-synonymous SNPs. Wang, Ailan & Fu, Mingchuan & Jiang, Xiaoqian & Y.H., Mao & Li, Xiangchen & Tao, Shiheng. (2014). Evolution of the F-Box Gene Family in Euarchontoglires: Gene Number Variation and Selection Patterns. PloS one. 9. e94899. 10.1371/journal.pone.0094899. https://www.researchgate.net/profile/Mingchuan_Fu/publication/261608607_Evolution_of_the_F-Box_Gene_Family_in_Euarchontoglires_Gene_Number_Variation_and_Selection_Patterns/links/5506a0430cf231de077824c8/Evolution-of-the-F-Box-Gene-Family-in-Euarchontoglires-Gene-Number-Variation-and-Selection-Patterns.pdfDionisio_{January 21, 2018
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I don't recall seeing DiEb's response to gpuccio's nice invitation to present his math-based ideas. gpuccio's nice invitation was posted @103 here: https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-649277 Did I miss the response? Was it posted in another website? Can someone point to the response for me? Thanks.Dionisio_{January 21, 2018
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Added website names in the list. Please, note that no web info service is 100% reliable. Also note that the numbers keep fluctuating. However, the different reports confirm that UD is comfortably within 1% of the currently active websites. KF's OP title was very cautious, but still provoked some objectors to bark up the wrong trees. That's unavoidable in a free forum like this. https://www.alexa.com/siteinfo/uncommondescent.com MIT.edu___________481 Nature.com________860 Harvard.edu_________873 Biblegateway.com_______1,001 mtgsalvation.com______10,201 Desiringgod.org_______10,908 Answersingenesis.org_____28,882 Ligonier.org__________40,278 Truthforlife.org______42,349 Gty.org_______45,516 Samaritanspurse.org_____51,000 freethoughtblogs.com_____76,655 Icr.org_______77,874 sermonsearch.com______81,317 Religionnews.com_____96,212 Royalsociety.org_____102,052 keepbelieving.com______144,829 sermonnotebook.org_____146,899 Rzim.org_______148,154 Evolutionnews.org_____168,380 gospelinlife.com______231,645 Kodugamelab.com______311,217 Reasons.org___________346,070 fpcjackson.org_______358,074 asa3.org_____________428,374 Jamesmacdonald.com_____460,457 discovery.org__________542,905 Uncommondescent.com_____644,999 Pandasthumb.org__________906,313 intelligentdesign.org_____932,239 ideacenter.org___________1,655,821 arn.org__________________1,956,610 theskepticalzone.com______5,147,609 biologicinstitute.org_____6,450,899 Evoinfo.org_______________10,309,075 * Active websites (10%): 132M to 173M UD 0.4% – 0.5% PT. 0.5% – 0.7% TSZ 3% – 4% All websites UD 0.04% – 0.05% (*) mentioned @25Dionisio_{January 21, 2018
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The Red Queen Hypothesis proposes that perpetual co-evolution among organisms can result from purely biotic drivers. After more than four decades, there is no satisfactory understanding as to which mechanisms trigger Red Queen dynamics or their implications for ecosystem features such as biodiversity. One reason for such a knowledge gap is that typical models are complicated theories where limit cycles represent an idealized Red Queen, and therefore cannot be used to devise experimental setups. Here, we bridge this gap by introducing a simple model for microbial systems able to show Red Queen dynamics. We explore diverse biotic sources that can drive the emergence of the Red Queen and that have the potential to be found in nature or to be replicated in the laboratory. Our model enables an analytical understanding of how Red Queen dynamics emerge in our setup, and the translation of model terms and phenomenology into general underlying mechanisms. We observe, for example, that in our system the Red Queen offers opportunities for the increase of biodiversity by facilitating challenging conditions for intraspecific dominance, whereas stasis tends to homogenize the system. Our results can be used to design and engineer experimental microbial systems showing Red Queen dynamics. Bonachela, Juan & Wortel, Meike & Chr. Stenseth, Nils. (2017). Eco-evolutionary Red Queen dynamics regulate biodiversity in a metabolite-driven microbial system. Scientific Reports. 7. . 10.1038/s41598-017-17774-4. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5732168/pdf/Dionisio_{January 20, 2018
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In antagonistic symbioses, such as host-parasite interactions, one population's success is the other's loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the "Red Queen effect"), but disfavored in certain mutualistic symbioses (the "Red King effect"). However, it remains unclear which biological parameters drive these effects. Here, we analyze the effects of the various determinants of evolutionary rate: generation time, mutation rate, population size, and the intensity of natural selection. Our main results hold for the case where mutation is infrequent. Slower evolution causes a long-term advantage in an important class of mutualistic interactions. Surprisingly, less intense selection is the strongest driver of this Red King effect, whereas relative mutation rates and generation times have little effect. In antagonistic interactions, faster evolution by any means is beneficial. Our results provide insight into the demographic evolution of symbionts. Veller, Carl & K Hayward, Laura & Hilbe, Christian & Nowak, Martin. (2017). The Red Queen and King in finite populations. Proceedings of the National Academy of Sciences of the United States of America. 114. . 10.1073/pnas.1702020114.Dionisio_{January 20, 2018
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Host plants possibly represent the strongest selection pressure for the evolution of reproductive traits in phytophagous insects. In a first part of this chapter, we review how plant quality affects both female and male life history traits and their respective reproductive success, and how the production and transfer to females of male sperm and associated nongametic substances (spermatophores as nuptial gifts) also depend on the host plant choice. At first glance, it seems that reproductive traits in phytophagous insects should be selected to maximize the success of this short-term interaction between host plant and phytophagous insects. This, however, ignores the fact that variation in reproductive success is detrimental to long-term fitness, which may explain that reproductive traits depart from their short-term expectation in unpredictable environments. Bet-hedging strategies – as exemplified by spatial or temporal dispersal (e.g., prolonged diapause) – can therefore evolve in such environments, as described in the second part of this chapter. The knowledge reviewed in this chapter is also integrated in the broader applied perspective of insect pest population management. Moreau, Jérôme & Desouhant, Emmanuel & Louâpre, Philippe & Goubault, Marlène & Rajon, Etienne & Jarrige, Alicia & Menu, F & Thiery, Denis. (2017). How Host Plant and Fluctuating Environments Affect Insect Reproductive Strategies?. Advances in Botanical Research. 259-288. 10.1016/bs.abr.2016.09.008. https://www.researchgate.net/profile/Marlene_Goubault/publication/309280375_How_Host_Plant_and_Fluctuating_Environments_Affect_Insect_Reproductive_Strategies/links/59db7221a6fdcc0ffd1aa093/How-Host-Plant-and-Fluctuating-Environments-Affect-Insect-Reproductive-Strategies.pdfDionisio_{January 20, 2018
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evo devo despacito? Many life-history traits are important determinants of the generation time. For instance, semelparous species whose adults reproduce only once have shorter generation times than iteroparous species that reproduce on several occasions, assuming equal development duration. A shorter generation time ensures a higher growth rate in stable environments where resources are in excess and is therefore a positively selected feature in this situation. In a stable and limiting environment, all combinations of traits that produce the same number of viable offspring are selectively equivalent. Here we study the neutral evolution of life-history strategies with different generation times and show that the slowest strategy represents the most likely evolutionary outcome when mutation is considered. Indeed, strategies with longer generation times generate fewer mutants per time unit, which makes them less likely to be replaced within a given time period. This turnover bias favors the evolution of strategies with long generation times. Its real impact, however, depends on both the population size and the nature of selection on life-history strategies. The latter is primarily impacted by the relationships between life-history traits whose estimation will be crucial to understanding the evolution of life-history strategies. Verin, Mélissa & Bourg, Salomé & Menu, Frédéric & Rajon, Etienne. (2017). The Biased Evolution of Generation Time. The American Naturalist. 190. E000-E000. 10.1086/692324.Dionisio_{January 20, 2018
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Project Mutation, Randomness and Evolution (book) Arlin Stoltzfus Goal: The randomness doctrine appears to refer to a property of mutation, but when examined more closely, it emerges as one facet of a broad and deep commitment to the unequal marriage of variation and selection proposed by Darwin, in which selection is a governing principle, while variation is relegated to the provision of raw material--- clay to be shaped by the potter---, supplying substance only, not initiative, direction, or creativity. This book uses a dissection of the randomness doctrine to re-think the role of variation in evolution, providing (1) a fresh and useful explanation of how mutation works, and why it is not "random" in any precise sense, (2) how there are different domains of population genetics, only some of which correspond to the neo-Darwinian verbal theories of causation used by nearly all evolutionary biologists, (3) how a commitment to the Darwinian view of roles continues to shape evolutionary thinking, and (4) new analyses showing how mutation operates importantly as a source of initiative and direction, violating the role assigned to it in neo-Darwinism. https://www.researchgate.net/project/Mutation-Randomness-and-Evolution-bookDionisio_{January 20, 2018
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In 2011, the serial of the European Group on Biological Invasions Neobiota was relaunched as an international, open access journal by Pensoft Publishers. In the editorial of the first issue, a large group of co-editors claimed for openness in covering a broad range of issues in invasion science, including the intersections with applied and social sciences, and referring to different groups of taxa and geographical regions. What happened since then? We here shortly reflect how the new NeoBiota journal has developed in the first years of its infancy – based on some data on the published papers, the addressed topics and the geographical background of our contributing authors. Kühn, Ingolf & Pyšek, Petr & Kowarik, Ingo. (2017). Seven years of NeoBiota – the times, were they a changin’?. NeoBiota. 36. 57-69. 10.3897/neobiota.36.21926. https://neobiota.pensoft.net/article/21926/download/pdf/Dionisio_{January 20, 2018
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We identified emerging scientific, technological, and sociopolitical issues likely to affect how biological invasions are studied and managed over the next two decades. Issues were ranked according to their probability of emergence, pervasiveness, potential impact, and novelty. Top-ranked issues include the application of genomic modification tools to control invasions, effects of Arctic globalization on invasion risk in the Northern Hemisphere, commercial use of microbes to facilitate crop production, the emergence of invasive microbial pathogens, and the fate of intercontinental trade agreements. These diverse issues suggest an expanding interdisciplinary role for invasion science in biosecurity and ecosystem management, burgeoning applications of biotechnology in alien species detection and control, and new frontiers in the microbial ecology of invasions. Ricciardi, Anthony & Blackburn, Tim & Carlton, James & Dick, Jaimie & E. Hulme, Philip & Iacarella, Josephine & M. Jeschke, Jonathan & Liebhold, Andrew & L. Lockwood, Julie & MacIsaac, Hugh & Pyšek, Petr & Richardson, David & Ruiz, Gregory & Simberloff, Daniel & Sutherland, William & Wardle, David & Aldridge, David. (2017). Invasion Science: A Horizon Scan of Emerging Challenges and Opportunities. Trends in Ecology & Evolution. 32. . 10.1016/j.tree.2017.03.007. https://www.researchgate.net/profile/Josephine_Iacarella/publication/315948056_Invasion_Science_A_Horizon_Scan_of_Emerging_Challenges_and_Opportunities/links/58ee541faca2724f0a28a0bf/Invasion-Science-A-Horizon-Scan-of-Emerging-Challenges-and-Opportunities.pdfDionisio_{January 20, 2018
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Bottlenecks in population size can reduce fitness and evolutionary potential, yet introduced species often become invasive. This poses a dilemma referred to as the genetic paradox of invasion. Three characteristics must hold true for an introduced population to be considered paradoxical in this sense. First, it must pass through a bottleneck that reduces genetic variation. Second, despite the bottleneck, the introduced population must not succumb to the many problems associated with low genetic variation. Third, it must adapt to the novel environment. Some introduced populations are not paradoxical as they do not combine these conditions. In some cases, an apparent paradox is spurious, as seen in introduced populations with low diversity in neutral markers that maintain high genetic variation in ecologically relevant traits. Even when the genetic paradox is genuine, unique aspects of a species’ biology can allow a population to thrive. We propose research directions into remaining paradoxical aspects of invasion genetics. Estoup, Arnaud. (2016). IS THERE A GENETIC PARADOX OF BIOLOGICAL INVASION?. Annual Review of Ecology and Systematics. . 10.1146/annurev-ecolsys-121415–032116.Dionisio_{January 20, 2018
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