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https://www.readbyqxmd.com/read/30232363/long-term-evolution-on-complex-fitness-landscapes-when-mutation-is-weak
#1
David M McCandlish
Understanding evolution on complex fitness landscapes is difficult both because of the large dimensionality of sequence space and the stochasticity inherent to population-genetic processes. Here, I present an integrated suite of mathematical tools for understanding evolution on time-invariant fitness landscapes when mutations occur sufficiently rarely that the population is typically monomorphic and evolution can be modeled as a sequence of well-separated fixation events. The basic intuition behind this suite of tools is that surrounding any particular genotype lies a region of the fitness landscape that is easy to evolve to, while other pieces of the fitness landscape are difficult to evolve to (due to distance, being across a fitness valley, etc...
September 19, 2018: Heredity
https://www.readbyqxmd.com/read/30209292/epistasis-regulates-the-developmental-stability-of-the-mouse-craniofacial-shape
#2
Ceferino Varón-González, Nicolas Navarro
Fluctuating asymmetry is a classic concept linked to organismal development. It has traditionally been used as a measure of developmental instability, which is the inability of an organism to buffer environmental fluctuations during development. Developmental stability has a genetic component that influences the final phenotype of the organism and can lead to congenital disorders. According to alternative hypotheses, this genetic component might be either the result of additive genetic effects or a by-product of developmental gene networks...
September 12, 2018: Heredity
https://www.readbyqxmd.com/read/30209291/genomic-comparisons-reveal-biogeographic-and-anthropogenic-impacts-in-the-koala-phascolarctos-cinereus-a-dietary-specialist-species-distributed-across-heterogeneous-environments
#3
Shannon R Kjeldsen, Herman W Raadsma, Kellie A Leigh, Jennifer R Tobey, David Phalen, Andrew Krockenberger, William A Ellis, Emily Hynes, Damien P Higgins, Kyall R Zenger
The Australian koala is an iconic marsupial with highly specific dietary requirements distributed across heterogeneous environments, over a large geographic range. The distribution and genetic structure of koala populations has been heavily influenced by human actions, specifically habitat modification, hunting and translocation of koalas. There is currently limited information on population diversity and gene flow at a species-wide scale, or with consideration to the potential impacts of local adaptation. Using species-wide sampling across heterogeneous environments, and high-density genome-wide markers (SNPs and PAVs), we show that most koala populations display levels of diversity comparable to other outbred species, except for those populations impacted by population reductions...
September 12, 2018: Heredity
https://www.readbyqxmd.com/read/30202084/is-molecular-evolution-faster-in-the-tropics
#4
Matthew G Orton, Jacqueline A May, Winfield Ly, David J Lee, Sarah J Adamowicz
The evolutionary speed hypothesis (ESH) suggests that molecular evolutionary rates are higher among species inhabiting warmer environments. Previously, the ESH has been investigated using small numbers of latitudinally-separated sister lineages; in animals, these studies typically focused on subsets of Chordata and yielded mixed support for the ESH. This study analyzed public DNA barcode sequences from the cytochrome c oxidase subunit I (COI) gene for six of the largest animal phyla (Arthropoda, Chordata, Mollusca, Annelida, Echinodermata, and Cnidaria) and paired latitudinally-separated taxa together informatically...
September 10, 2018: Heredity
https://www.readbyqxmd.com/read/30190561/environmental-pleiotropy-and-demographic-history-direct-adaptation-under-antibiotic-selection
#5
Danna R Gifford, Rok Krašovec, Elizabeth Aston, Roman V Belavkin, Alastair Channon, Christopher G Knight
Evolutionary rescue following environmental change requires mutations permitting population growth in the new environment. If change is severe enough to prevent most of the population reproducing, rescue becomes reliant on mutations already present. If change is sustained, the fitness effects in both environments, and how they are associated-termed 'environmental pleiotropy'-may determine which alleles are ultimately favoured. A population's demographic history-its size over time-influences the variation present...
September 6, 2018: Heredity
https://www.readbyqxmd.com/read/30190560/power-law-fitness-landscapes-and-their-ability-to-predict-fitness
#6
Diogo Passagem-Santos, Simone Zacarias, Lilia Perfeito
Whether or not evolution by natural selection is predictable depends on the existence of general patterns shaping the way mutations interact with the genetic background. This interaction, also known as epistasis, has been observed during adaptation (macroscopic epistasis) and in individual mutations (microscopic epistasis). Interestingly, a consistent negative correlation between the fitness effect of beneficial mutations and background fitness (known as diminishing returns epistasis) has been observed across different species and conditions...
September 6, 2018: Heredity
https://www.readbyqxmd.com/read/30190559/correction-characterization-of-hybridization-within-a-secondary-contact-region-of-the-inshore-fish-bostrychus-sinensis-in-the-east-china-sea
#7
Shaoxiong Ding, Mrinal Mishra, Haohao Wu, Shuang Liang, Michael M Miyamoto
Following the publication of this article, the authors have requested that the Acknowledgements section be amended to thank Weidi Yang for his assistance with their Bostrychus sinensis photograph that was chosen for the front cover of the January 2018 issue of the journal. This error has been corrected in both the PDF and HTML versions of the paper. Also, the legends for Supplementary Figures 1 and 2 were not posted online. This error has been corrected in the HTML version of the paper.
September 6, 2018: Heredity
https://www.readbyqxmd.com/read/30185924/complex-fine-scale-spatial-genetic-structure-in-epidendrum-rhopalostele-an-epiphytic-orchid
#8
Elena Torres, María-Lorena Riofrío, José M Iriondo
Orchid seeds are presumably dispersed by wind due to their very small size and thus can potentially travel long distances. However, the few related studies indicate that seeds fall close to their mother plants. Because seed dispersal and colonization patterns can have relevant consequences for long-term species persistence, we assessed the fine-scale genetic structure of the epiphytic orchid Epidendrum rhopalostele to provide insight into these patterns. All individuals in the studied population were georeferenced and genotyped with AFLP-markers...
September 5, 2018: Heredity
https://www.readbyqxmd.com/read/30171190/disentangling-the-genetic-effects-of-refugial-isolation-and-range-expansion-in-a-trans-continentally-distributed-species
#9
B N Reid, J M Kass, S Wollney, E L Jensen, M A Russello, E M Viola, J Pantophlet, J B Iverson, M Z Peery, C J Raxworthy, E Naro-Maciel
In wide-ranging taxa with historically dynamic ranges, past allopatric isolation and range expansion can both influence the current structure of genetic diversity. Considering alternate historical scenarios involving expansion from either a single refugium or from multiple refugia can be useful in differentiating the effects of isolation and expansion. Here, we examined patterns of genetic variability in the trans-continentally distributed painted turtle (Chrysemys picta). We utilized an existing phylogeographic dataset for the mitochondrial control region and generated additional data from nine populations for the mitochondrial control region (n = 302) and for eleven nuclear microsatellite loci (n = 247)...
August 31, 2018: Heredity
https://www.readbyqxmd.com/read/30139962/a-wolbachia-infection-from-drosophila-that-causes-cytoplasmic-incompatibility-despite-low-prevalence-and-densities-in-males
#10
Kelly M Richardson, Philippa C Griffin, Siu F Lee, Perran A Ross, Nancy M Endersby-Harshman, Michele Schiffer, Ary A Hoffmann
Wolbachia bacteria are common insect endosymbionts transmitted maternally and capable of spreading through insect populations by cytoplasmic incompatibility (CI) when infected males cause embryo death after mating with uninfected females. Selection in the Wolbachia endosymbiont occurs on female hosts and is expected to favour strong maternal transmission to female offspring, even at the cost of reduced CI. With maternal leakage, nuclear genes are expected to be selected to suppress cytoplasmic incompatibility caused by males while also reducing any deleterious effects associated with the infection...
August 23, 2018: Heredity
https://www.readbyqxmd.com/read/30131516/hidden-diversity-in-the-genus-tethya-comparing-molecular-and-morphological-techniques-for-species-identification
#11
Megan R Shaffer, Simon K Davy, James J Bell
Correctly determining species' identity is critical for estimating biodiversity and effectively managing marine populations, but is difficult for species that have few morphological traits or are highly plastic. Sponges are considered a taxonomically difficult group because they lack multiple consistent diagnostic features, which coupled with their common phenotypic plasticity, makes the presence of species complexes likely, but difficult to detect. Here, we investigated the evolutionary relationship of Tethya spp...
August 21, 2018: Heredity
https://www.readbyqxmd.com/read/30127530/the-utility-of-fitness-landscapes-and-big-data-for-predicting-evolution
#12
EDITORIAL
J Arjan G M de Visser, Santiago F Elena, Inês Fragata, Sebastian Matuszewski
No abstract text is available yet for this article.
August 20, 2018: Heredity
https://www.readbyqxmd.com/read/30127529/the-fitness-landscape-of-the-codon-space-across-environments
#13
Inês Fragata, Sebastian Matuszewski, Mark A Schmitz, Thomas Bataillon, Jeffrey D Jensen, Claudia Bank
Fitness landscapes map the relationship between genotypes and fitness. However, most fitness landscape studies ignore the genetic architecture imposed by the codon table and thereby neglect the potential role of synonymous mutations. To quantify the fitness effects of synonymous mutations and their potential impact on adaptation on a fitness landscape, we use a new software based on Bayesian Monte Carlo Markov Chain methods and re-estimate selection coefficients of all possible codon mutations across 9 amino acid positions in Saccharomyces cerevisiae Hsp90 across 6 environments...
August 20, 2018: Heredity
https://www.readbyqxmd.com/read/30120367/a-singular-value-decomposition-bayesian-multiple-trait-and-multiple-environment-genomic-model
#14
Osval A Montesinos-López, Abelardo Montesinos-López, José Crossa, Kismiantini, Juan Manuel Ramírez-Alcaraz, Ravi Singh, S Mondal, P Juliana
Today, breeders perform genomic-assisted breeding to improve more than one trait. However, frequently there are several traits under study at one time, and the implementation of current genomic multiple-trait and multiple-environment models is challenging. Consequently, we propose a four-stage analysis for multiple-trait data in this paper. In the first stage, we perform singular value decomposition (SVD) on the resulting matrix of trait responses; in the second stage, we perform multiple trait analysis on transformed responses...
August 17, 2018: Heredity
https://www.readbyqxmd.com/read/30120366/a-coalescent-based-estimator-of-genetic-drift-and-acoustic-divergence-in-the-pteronotus-parnellii-species-complex
#15
Liliana M Dávalos, Winston C Lancaster, Miguel S Núñez-Novas, Yolanda M León, Bonnie Lei, Jon Flanders, Amy L Russell
Determining the processes responsible for phenotypic variation is one of the central tasks of evolutionary biology. While the importance of acoustic traits for foraging and communication in echolocating mammals suggests adaptation, the seldom-tested null hypothesis to explain trait divergence is genetic drift. Here we derive FST values from multi-locus coalescent isolation-with-migration models, and couple them with estimates of quantitative trait divergence, or PST , to test drift as the evolutionary process responsible for phenotypic divergence in island populations of the Pteronotus parnellii species complex...
August 17, 2018: Heredity
https://www.readbyqxmd.com/read/30082919/quantitative-trait-loci-on-lgs-9-and-14-affect-the-reproductive-interaction-between-two-oreochromis-species-o-niloticus-and-o-aureus
#16
Andrey Shirak, Tatyana Zak, Lior Dor, Ayana Benet-Perlberg, Joel I Weller, Micha Ron, Eyal Seroussi
Effective farming of tilapia requires all-male culture, characterized by uniformity and high growth rate. Males of O. aureus (Oa) and females of O. niloticus (On) produce all-male offspring, but there is a behavioral reproductive barrier between the two species that prevents mass production. In crosses between Oa and On broodstocks, few hybrid females are attracted to the Oa male nests (denoted responders), and if they harbor the On alleles for the sex determination (SD) sites on linkage groups (LGs) 1, 3, and 23, all-male progeny are produced...
August 6, 2018: Heredity
https://www.readbyqxmd.com/read/30082918/dissection-by-genomic-and-plumage-variation-of-a-geographically-complex-hybrid-zone-between-two-australian-non-sister-parrot-species-platycercus-adscitus-and-platycercus-eximius
#17
Ashlee Shipham, Leo Joseph, Daniel J Schmidt, Alex Drew, Ian Mason, Jane M Hughes
The study of hybrid zones advances understanding of the speciation process, and approaches incorporating genomic data are increasingly used to draw significant conclusions about the impact of hybridisation. Despite the progress made, the complex interplay of factors that can lead to substantially variable hybridisation outcomes are still not well understood, and many systems and/or groups remain comparatively poorly studied. Our study aims to broaden the literature on avian hybrid zones, investigating a potentially geographically and temporally complex putative hybrid zone between two native Australian non-sister parrot species, the pale-headed and eastern rosellas (Platycercus adscitus and Platycercus eximius, respectively)...
August 6, 2018: Heredity
https://www.readbyqxmd.com/read/30072800/approximate-bayesian-computation-analysis-of-est-associated-microsatellites-indicates-that-the-broadleaved-evergreen-tree-castanopsis-sieboldii-survived-the-last-glacial-maximum-in-multiple-refugia-in-japan
#18
K Aoki, I Tamaki, K Nakao, S Ueno, T Kamijo, H Setoguchi, N Murakami, M Kato, Y Tsumura
Climatic changes have played major roles in plants' evolutionary history. Glacial oscillations have been particularly important, but some of their effects on plants' populations are poorly understood, including the numbers and locations of refugia in Asian warm temperate zones. In the present study, we investigated the demographic history of the broadleaved evergreen tree species Castanopsis sieboldii (Fagaceae) during the last glacial period in Japan. We used approximate Bayesian computation (ABC) for model comparison and parameter estimation for the demographic modeling using 27 EST-associated microsatellites...
August 2, 2018: Heredity
https://www.readbyqxmd.com/read/30050062/strong-impact-of-thermal-environment-on-the-quantitative-genetic-basis-of-a-key-stress-tolerance-trait
#19
Michael Ørsted, Ary Anthony Hoffmann, Palle Duun Rohde, Peter Sørensen, Torsten Nygaard Kristensen
Most organisms experience variable and sometimes suboptimal environments in their lifetime. While stressful environmental conditions are normally viewed as a strong selective force, they can also impact directly on the genetic basis of traits such as through environment-dependent gene action. Here, we used the Drosophila melanogaster Genetic Reference Panel to investigate the impact of developmental temperature on variance components and evolutionary potential of cold tolerance. We reared 166 lines at five temperatures and assessed cold tolerance of adult male flies from each line and environment...
July 26, 2018: Heredity
https://www.readbyqxmd.com/read/30050061/application-of-partial-least-squares-in-exploring-the-genome-selection-signatures-between-populations
#20
Hao Sun, Zhe Zhang, Babatunde Shittu Olasege, Zhong Xu, Qingbo Zhao, Peipei Ma, Qishan Wang, Yuchun Pan
Natural and artificial selection have led to substantial variation in the phenotypic traits of different populations. Therefore, there is a need to develop methods that are based on cross-population comparisons to discover loci related to specific traits. Here, we suggested a strategy to detect the genome selection signatures between populations based on the partial least squares (PLS) theory. Using the binary population indicator as the response variable in the PLS analysis, alleles under selection between populations were identified from the first PLS component...
July 26, 2018: Heredity
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