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evolutionary genetics

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https://www.readbyqxmd.com/read/28346136/environment-determines-evolutionary-trajectory-in-a-constrained-phenotypic-space
#1
David T Fraebel, Harry Mickalide, Diane Schnitkey, Jason Merritt, Thomas E Kuhlman, Seppe Kuehn
Constraints on phenotypic variation limit the capacity of organisms to adapt to the multiple selection pressures encountered in natural environments. To better understand evolutionary dynamics in this context, we select Escherichia coli for faster migration through a porous environment, a process which depends on both motility and growth. We find that a trade-off between swimming speed and growth rate constrains the evolution of faster migration. Evolving faster migration in rich medium results in slow growth and fast swimming, while evolution in minimal medium results in fast growth and slow swimming...
March 27, 2017: ELife
https://www.readbyqxmd.com/read/28345193/retention-of-gene-diversity-during-the-spread-of-a-non-native-plant-species
#2
Katrien Vandepitte, Kenny Helsen, Kasper Van Acker, Joachim Mergeay, Olivier Honnay
Spatial expansion, which is a crucial stage in the process to successful biological invasion, is anticipated to profoundly affect the magnitude and spatial distribution of genetic diversity in novel colonized areas. Here we show that, contrasting common expectations, Pyrenean rocket (Sisymbrium austriacum), retained SNP diversity as this introduced plant species descended in the Meuse river basin. Allele frequencies did not mirror between-population distances along the predominant expansion axis. Reconstruction of invasion history based on the genotypes of historical herbarium specimens indicated no influence of additional introductions or multiple points of entry on this non-gradual pattern...
March 27, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28344905/evolution-of-the-patellar-sesamoid-bone-in-mammals
#3
Mark E Samuels, Sophie Regnault, John R Hutchinson
The patella is a sesamoid bone located in the major extensor tendon of the knee joint, in the hindlimb of many tetrapods. Although numerous aspects of knee morphology are ancient and conserved among most tetrapods, the evolutionary occurrence of an ossified patella is highly variable. Among extant (crown clade) groups it is found in most birds, most lizards, the monotreme mammals and almost all placental mammals, but it is absent in most marsupial mammals as well as many reptiles. Here, we integrate data from the literature and first-hand studies of fossil and recent skeletal remains to reconstruct the evolution of the mammalian patella...
2017: PeerJ
https://www.readbyqxmd.com/read/28344106/molecular-phylogenetic-relationships-reveal-contrasting-evolutionary-patterns-in-gorgoniidae-octocorallia-in-the-eastern-pacific
#4
M M Soler-Hurtado, P J López-González, A Machordom
The description and delimitation of species in an evolutionary framework is essential for understanding patterns of biodiversity and distribution, and in the assessment of conservation strategies for natural resources. This study seeks to clarify the evolutionary history and genetic variation within and between closely related octocoral species that are fundamental to benthic marine ecosystems for harbouring a high diversity of associated fauna. For our study system, we focused on members of the Gorgoniidae family in the Eastern Pacific, particularly of the Ecuadorian littoral, a less studied marine ecosystem...
March 24, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28343090/developmental-systems-of-plasticity-and-trans-generational-epigenetic-inheritance-in-nematodes
#5
REVIEW
Vahan Serobyan, Ralf J Sommer
Several decades of research provided detailed insight into how genes control development and evolution, whereas recent studies have expanded this purely genetic perspective by presenting strong evidence for environmental and epigenetic influences. We summarize examples of phenotypic plasticity and trans-generational epigenetic inheritance in the nematode model organisms Pristionchus pacificus and Caenorhabditis elegans, which indicate that the response of developmental systems to environmental influences is hardwired into the organismś genome...
March 23, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28342852/effects-of-sub-culturing-on-genetic-and-physiological-parameters-in-different-beauveria-bassiana-isolates
#6
Naser Eivazian Kary, Zhila Alizadeh
Beauveria bassiana is a fungus which is widely used as a biological insecticide to control a number of economically important insect pests. Knowledge of the genetic diversity of the isolates, understanding the underlying nature of these evolutionary phenomena and finding appropriate and simple screening tools play an important role in developing effective biocontrol agents. Here, we monitored changes of electrophoretic karyotype of small molecules of extrachromosomal DNAs, presumably mitochondrial DNA or plasmids in several individual isolates of B...
March 22, 2017: Journal of Invertebrate Pathology
https://www.readbyqxmd.com/read/28341421/mutations-evolution-and-the-central-role-of-a-self-defined-fitness-function-in-the-initiation-and-progression-of-cancer
#7
Robert A Gatenby, Joel Brown
The origin and progression of cancer is widely viewed as "somatic evolution" driven by the accumulation of random genetic changes. This theoretical model, however, neglects fundamental conditions for evolution by natural selection, which include competition for survival and a local environmental context. Recent observations that the mutational burden in different cancers can vary by 2 orders of magnitude and that multiple mutations, some of which are "oncogenic," are observed in normal tissue suggests these neglected Darwinian dynamics may play a critical role in modifying the evolutionary consequences of molecular events...
March 21, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28340563/genome-evolutionary-dynamics-followed-by-diversifying-selection-explains-the-complexity-of-the-sesamum-indicum-genome
#8
Jingyin Yu, Linhai Wang, Hui Guo, Boshou Liao, Graham King, Xiurong Zhang
BACKGROUND: Whole genome duplication (WGD) and tandem duplication (TD) provide two critical sources of raw genetic material for genome complexity and evolutionary novelty. Little is known about the complexity of the Sesamum indicum genome after it diverged from a common ancestor with the paleodiploid Vitis vinifera and further experienced WGD and TD events. RESULTS: Here, we analyzed the functional divergence of different classes of inter- and intra-genome gene pairs from ancestral events to uncover multiple-layers of evolutionary dynamics acting during the process of forming the modern S...
March 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28340089/how-embryophytic-is-the-biosynthesis-of-phenylpropanoids-and-their-derivatives-in-streptophyte-algae
#9
Jan de Vries, Sophie de Vries, Claudio H Slamovits, Laura E Rose, John M Archibald
The origin of land plants from algae is a long-standing question in evolutionary biology. It is becoming increasingly clear that many characters that were once assumed to be "embryophyte-specific" can in fact be found in their closest algal relatives, the streptophyte algae. One such case is the phenylpropanoid pathway. While biochemical data indicate that streptophyte algae harbor lignin-like components, the phenylpropanoid core pathway, which serves as the backbone of lignin biosynthesis, has been proposed to have arisen at the base of the land plants...
March 13, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28338924/a-nonsynonymous-snp-catalog-of-mycobacterium-tuberculosis-virulence-genes-and-its-use-for-detecting-new-potentially-virulent-sublineages
#10
N E Mikheecheva, M V Zaychikova, A V Melerzanov, V N Danilenko
Mycobacterium tuberculosis is divided into several distinct lineages, and various genetic markers such as IS-elements, VNTR, and SNPs are used for lineage identification. We propose an M. tuberculosis classification approach based on functional polymorphisms in virulence genes. An M. tuberculosis virulence genes catalog has been established, including 319 genes from various protein groups, such as proteases, cell wall proteins, fatty acid and lipid metabolism proteins, sigma factors, toxin-antitoxin systems...
March 11, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338786/recombination-mediated-host-adaptation-by-avian-staphylococcus-aureus
#11
Susan Murray, Ben Pascoe, Guillaume Méric, Leonardos Mageiros, Koji Yahara, Matthew D Hitchings, Yasmin Friedmann, Thomas S Wilkinson, Fraser J Gormley, Dietrich Mack, James E Bray, Sarah Lamble, Rory Bowden, Keith A Jolley, Martin C J Maiden, Sarah Wendlandt, Stefan Schwarz, Jukka Corander, J Ross Fitzgerald, Samuel K Sheppard
Staphylococcus aureus are globally disseminated among farmed chickens causing skeletal muscle infections, dermatitis and septicaemia. The emergence of poultry-associated lineages has involved zoonotic transmission from humans to chickens but questions remain about the specific adaptations that promote proliferation of chicken pathogens. We characterised genetic variation in a population of genome-sequenced S. aureus isolates of poultry and human origin. Genealogical analysis identified a dominant poultry-associated sequence cluster within the CC5 clonal complex...
February 28, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338720/from-teeth-to-baleen-and-raptorial-to-bulk-filter-feeding-in-mysticete-cetaceans-the-role-of-paleontological-genetic-and-geochemical-data-in-feeding-evolution-and-ecology
#12
Annalisa Berta, Agnese Lanzetti, Eric G Ekdale, Thomas A Deméré
The origin of baleen and filter feeding in mysticete cetaceans occurred sometime between approximately 34 and 24 million years ago and represents a major macroevolutionary shift in cetacean morphology (teeth to baleen) and ecology (raptorial to filter feeding). We explore this dramatic change in feeding strategy by employing a diversity of tools and approaches: morphology, molecules, development, and stable isotopes from the geological record. Adaptations for raptorial feeding in extinct toothed mysticetes provide the phylogenetic context for evaluating morphological apomorphies preserved in the skeletons of stem and crown edentulous mysticetes...
December 16, 2016: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/28337179/characterization-of-a-novel-nicotine-degradation-gene-cluster-ndp-in-sphingomonas-melonis-ty-and-its-evolutionary-analysis
#13
Haixia Wang, Xiao-Yang Zhi, Jiguo Qiu, Longxiang Shi, Zhenmei Lu
Sphingomonas melonis TY utilizes nicotine as a sole source of carbon, nitrogen, and energy through a variant of the pyridine and pyrrolidine pathways (VPP). A 31-kb novel nicotine-degrading gene cluster, ndp, in strain TY exhibited a different genetic organization with the vpp cluster in strains Ochrobactrum rhizosphaerae SJY1 and Agrobacterium tumefaciens S33. Genes in vpp were separated by a 20-kb interval sequence, while genes in ndp were localized together. Half of the homolog genes were in different locus in ndp and vpp...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28335728/allelic-incompatibility-can-explain-female-biased-sex-ratios-in-dioecious-plants
#14
Pascal Pucholt, Henrik R Hallingbäck, Sofia Berlin
BACKGROUND: Biased sex ratios are common among dioecious plant species despite the theoretical prediction of selective advantage of even sex ratios. Albeit the high prevalence of deviations from even sex ratios, the genetic causes to sex biases are rarely known outside of a few model species. Here we present a mechanism underlying the female biased sex ratio in the dioecious willow species Salix viminalis. RESULTS: We compared the segregation pattern of genome-wide single nucleotide polymorphism markers in two contrasting bi-parental pedigree populations, the S3 with even sex ratio and the S5 with a female biased sex ratio...
March 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28335721/transcriptomic-insights-into-the-genetic-basis-of-mammalian-limb-diversity
#15
Jennifer A Maier, Marcelo Rivas-Astroza, Jenny Deng, Anna Dowling, Paige Oboikovitz, Xiaoyi Cao, Richard R Behringer, Chris J Cretekos, John J Rasweiler, Sheng Zhong, Karen E Sears
BACKGROUND: From bat wings to whale flippers, limb diversification has been crucial to the evolutionary success of mammals. We performed the first transcriptome-wide study of limb development in multiple species to explore the hypothesis that mammalian limb diversification has proceeded through the differential expression of conserved shared genes, rather than by major changes to limb patterning. Specifically, we investigated the manner in which the expression of shared genes has evolved within and among mammalian species...
March 23, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28335712/exploring-the-evolutionary-origin-of-floral-organs-of-erycina-pusilla-an-emerging-orchid-model-system
#16
Anita Dirks-Mulder, Roland Butôt, Peter van Schaik, Jan Willem P M Wijnands, Roel van den Berg, Louie Krol, Sadhana Doebar, Kelly van Kooperen, Hugo de Boer, Elena M Kramer, Erik F Smets, Rutger A Vos, Alexander Vrijdaghs, Barbara Gravendeel
BACKGROUND: Thousands of flowering plant species attract pollinators without offering rewards, but the evolution of this deceit is poorly understood. Rewardless flowers of the orchid Erycina pusilla have an enlarged median sepal and incised median petal ('lip') to attract oil-collecting bees. These bees also forage on similar looking but rewarding Malpighiaceae flowers that have five unequally sized petals and gland-carrying sepals. The lip of E. pusilla has a 'callus' that, together with winged 'stelidia', mimics these glands...
March 23, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28335420/efforts-and-challenges-in-engineering-the-genetic-code
#17
REVIEW
Xiao Lin, Allen Chi Shing Yu, Ting Fung Chan
This year marks the 48th anniversary of Francis Crick's seminal work on the origin of the genetic code, in which he first proposed the "frozen accident" hypothesis to describe evolutionary selection against changes to the genetic code that cause devastating global proteome modification. However, numerous efforts have demonstrated the viability of both natural and artificial genetic code variations. Recent advances in genetic engineering allow the creation of synthetic organisms that incorporate noncanonical, or even unnatural, amino acids into the proteome...
March 14, 2017: Life
https://www.readbyqxmd.com/read/28334822/posigene-automated-and-easy-to-use-pipeline-for-genome-wide-detection-of-positively-selected-genes
#18
Arne Sahm, Martin Bens, Matthias Platzer, Karol Szafranski
Many comparative genomics studies aim to find the genetic basis of species-specific phenotypic traits. A prevailing strategy is to search genome-wide for genes that evolved under positive selection based on the non-synonymous to synonymous substitution ratio. However, incongruent results largely due to high false positive rates indicate the need for standardization of quality criteria and software tools. Main challenges are the ortholog and isoform assignment, the high sensitivity of the statistical models to alignment errors and the imperative to parallelize large parts of the software...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334284/genomic-diversity-guides-conservation-strategies-among-rare-terrestrial-orchid-species-when-taxonomy-remains-uncertain
#19
Collin W Ahrens, Megan A Supple, Nicola C Aitken, David J Cantrill, Justin O Borevitz, Elizabeth A James
Background and Aims: Species are often used as the unit for conservation, but may not be suitable for species complexes where taxa are difficult to distinguish. Under such circumstances, it may be more appropriate to consider species groups or populations as evolutionarily significant units (ESUs). A population genomic approach was employed to investigate the diversity within and among closely related species to create a more robust, lineage-specific conservation strategy for a nationally endangered terrestrial orchid and its relatives from south-eastern Australia...
March 15, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28334162/biparental-transmission-of-verminephrobacter-symbionts-in-the-earthworm-aporrectodea-tuberculata-lumbricidae
#20
Laura-Carlota Paz, Andreas Schramm, Marie Braad Lund
Most lumbricid earthworms harbor species-specific Verminephrobacter symbionts in their excretory organs (nephridia). These symbionts are vertically transmitted via the cocoon, where they colonize the embryos. Despite cospeciation for >100 million years with their hosts, Verminephrobacter lack genome reduction and AT bias typical of evolutionary old, vertically transmitted symbionts, caused by recurring bottlenecks. We hypothesized that biparental symbiont transmission into the cocoon enabled genetic mixing and relieved the bottleneck, and tested biparental transmission experimentally for V...
February 23, 2017: FEMS Microbiology Ecology
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