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Molecular Biology and Evolution

Eduardo de A Gutierrez, Gianni M Castiglione, James M Morrow, Ryan K Schott, Livia O Loureiro, Burton K Lim, Belinda S W Chang
Bats are excellent models for studying the molecular basis of sensory adaptation. In Chiroptera, a sensory trade-off has been proposed between the visual and auditory systems, though the extent of this association has yet to be fully examined. To investigate whether variation in visual performance is associated with echolocation, we experimentally assayed the dim-light visual pigment rhodopsin from bat species with differing echolocation abilities. While spectral tuning properties were similar among bats, we found that the rate of decay of their light-activated state was significantly slower in a non-echolocating bat relative to species that use distinct echolocation strategies, consistent with a sensory trade-off hypothesis...
July 16, 2018: Molecular Biology and Evolution
Carine Rey, Laurent Guéguen, Marie Sémon, Bastien Boussau
In the history of life, some phenotypes have been acquired several times independently, through convergent evolution. Recently, lots of genome-scale studies have been devoted to identify nucleotides or amino acids that changed in a convergent manner when the convergent phenotypes evolved. These efforts have had mixed results, probably because of differences in the detection methods, and because of conceptual differences about the definition of a convergent substitution. Some methods contend that substitutions are convergent only if they occur on all branches where the phenotype changed towards the exact same state at a given nucleotide or amino acid position...
July 7, 2018: Molecular Biology and Evolution
Zhaohui Yang, Hong Shi, Pengcheng Ma, Shilei Zhao, Qinghong Kong, Tianhao Bian, Chao Gong, Qi Zhao, Yuan Liu, Xuebin Qi, Xiaoming Zhang, Yinglun Han, Jiewei Liu, Qingwei Li, Hua Chen, Bing Su
Human skin color diversity is considered an adaptation to environmental conditions such as UV radiation. Investigations into the genetic bases of such adaptation have identified a group of pigmentation genes contributing to skin color diversity in African and non-African populations. Here we present a population analysis of the pigmentation gene KITLG with previously reported signal of Darwinian positive selection in both European and East Asian populations. We demonstrated that there had been recurrent selective events in the upstream and the downstream regions of KITLG in Eurasian populations...
June 29, 2018: Molecular Biology and Evolution
Assaf Rotem, Adrian W R Serohijos, Connie B Chang, Joshua T Wolfe, Audrey E Fischer, Thomas S Mehoke, Huidan Zhang, Ye Tao, W Lloyd Ung, Jeong-Mo Choi, João V Rodrigues, O Kolawole Abimbola, Stephan A Koehler, Susan Wu, Peter M Thielen, Naiwen Cui, Plamen A Demirev, Nicholas S Giacobbi, Timothy R Julian, Kellogg Schwab, Jeffrey S Lin, Thomas J Smith, James M Pipas, Christiane E Wobus, Andrew B Feldman, David A Weitz, Eugene I Shakhnovich
Viral evolutionary pathways are determined by the fitness landscape, which maps viral genotype to fitness. However, a quantitative description of the landscape and the evolutionary forces on it remain elusive. Here, we apply a biophysical fitness model based on capsid folding stability and antibody binding affinity to predict the evolutionary pathway of norovirus escaping a neutralizing antibody. The model is validated by experimental evolution in bulk culture and in a drop-based microfluidics that propagates millions of independent small viral sub-populations...
June 28, 2018: Molecular Biology and Evolution
Laura M Jones, Sebastian Eves-van den Akker, Patricija van-Oosten Hawle, Howard J Atkinson, Peter E Urwin
Managing the emergence and spread of crop pests and pathogens is essential for global food security. Understanding how organisms have adapted to their native climate is key to predicting the impact of climate change. The potato cyst nematodes Globodera pallida and G. rostochiensis are economically important plant pathogens that cause yield losses of up to 50% in potato. The two species have different thermal optima that may relate to differences in the altitude of their regions of origin in the Andes. Here, we demonstrate that juveniles of G...
June 28, 2018: Molecular Biology and Evolution
Hongan Long, Samuel F Miller, Emily Williams, Michael Lynch
The mutation rate of an organism is influenced by the interaction of evolutionary forces such as natural selection and genetic drift. However, the mutation spectrum (i.e. the distribution of different types of mutations) can be heavily influenced by DNA repair. Using mutation-accumulation lines of the extremophile bacterium Deinococcus radiodurans ΔmutS1 and the model soil bacterium Pseudomonas fluorescens wild-type and MMR- (Methyl-dependent Mismatch Repair-deficient) strains, we report the mutational features of these two important bacteria...
June 25, 2018: Molecular Biology and Evolution
Beatriz Mello
The main outcome of molecular dating, the timetree, provides crucial information for understanding the evolutionary history of lineages and is a requirement of several evolutionary analyses. Although essential, the estimation of divergence times from molecular data is frequently regarded as a complicated task. However, establishing biological timescales can be performed in a straightforward manner, even with large, genome-wide datasets. This protocol presents all the necessary steps to estimate a timetree in the program MEGA X...
June 21, 2018: Molecular Biology and Evolution
Chao Chen, Huihua Wang, Zhiguang Liu, Xiao Chen, Jiao Tang, Fanming Meng, Wei Shi
The mechanisms by which organisms adapt to variable environments are a fundamental question in evolutionary biology and are important to protect important species in response to a changing climate. An interesting candidate to study this question is the honey bee Apis cerana, a keystone pollinator with a wide distribution throughout a large variety of climates, that exhibits rapid dispersal. Here, we re-sequenced the genome of 180 A. cerana individuals from eighteen populations throughout China. Using a population genomics approach, we observed considerable genetic variation in A...
June 20, 2018: Molecular Biology and Evolution
Thomas Dias-Alves, Julien Mairal, Michael G B Blum
Admixture between populations provides opportunity to study biological adaptation and phenotypic variation. Admixture studies rely on local ancestry inference for admixed individuals, which consists of computing at each locus the number of copies that originate from ancestral source populations. Existing software packages for local ancestry inference are tuned to provide accurate results on human data and recent admixture events. Here, we introduce Loter, an open-source software package that does not require any biological parameter besides haplotype data in order to make local ancestry inference available for a wide range of species...
June 20, 2018: Molecular Biology and Evolution
Ana Catalán, Aide Macias-Muñoz, Adriana D Briscoe
Differences in behavior and life history traits between females and males are the basis of divergent selective pressures between sexes. It has been suggested that a way for the two sexes to deal with different life history requirements is through sex-biased gene expression. In this study, we performed a comparative sex-biased gene expression analysis of the combined eye and brain transcriptome from five Heliconius species, H. charithonia, H. sara, H. erato, H. melpomene and H. doris, representing five of the main clades from the Heliconius phylogeny...
June 19, 2018: Molecular Biology and Evolution
Quentin Helleu, Mia T Levine
The heterochromatic genome compartment mediates strictly conserved cellular processes such as chromosome segregation, telomere integrity, and genome stability. Paradoxically, heterochromatic DNA sequence is wildly unconserved. Recent reports that many hybrid incompatibility genes encode heterochromatin proteins, together with the observation that inter-species hybrids suffer aberrant heterochromatin-dependent processes, suggest that heterochromatic DNA packaging requires species-specific innovations. Testing this model of co-evolution between fast-evolving heterochromatic DNA and its packaging proteins begins with defining the latter...
June 19, 2018: Molecular Biology and Evolution
Stephanie J Spielman, Sergei L Kosakovsky Pond
The relative evolutionary rates at individual sites in proteins are informative measures of conservation or adaptation. Often used as evolutionarily-aware conservation scores, relative rates reveal key functional or strongly-selected residues. Estimating rates in a phylogenetic context requires specifying a protein substitution model, which is typically a phenomenological model trained on a large empirical dataset. A strong emphasis has traditionally been placed on selecting the "best-fit" model, with the implicit understanding that suboptimal or otherwise ill-fitting models might bias inferences...
June 19, 2018: Molecular Biology and Evolution
P K Piekarski, J M Carpenter, A R Lemmon, E Moriarty Lemmon, B J Sharanowski
The hypothesis that eusociality originated once in Vespidae has shaped interpretation of social evolution for decades and has driven the supposition that preimaginal morphophysiological differences between castes were absent at the outset of eusociality. Many researchers also consider casteless nest-sharing an antecedent to eusociality. Together, these ideas endorse a stepwise progression of social evolution in wasps (solitary → casteless nest-sharing → eusociality with rudimentary behavioral castes → eusociality with preimaginal caste-biasing → morphologically differentiated castes)...
June 19, 2018: Molecular Biology and Evolution
Zhen Gong, Guan-Zhu Han
The origin of hepadnaviruses (Hepadnaviridae), a group of reverse-transcribing DNA viruses that infect vertebrates, remains mysterious. All the known retrotransposons are only distantly related to hepadnaviruses. Here we report the discovery of two novel lineages of retroelements, which we designate hepadnavirus-like retroelement (HEART1 and HEART2), within the insect genomes through screening 1,095 eukaryotic genomes. Both phylogenetic and similarity analyses suggest that the HEART retroelements represent the closest non-viral relatives of hepadnaviruses so far...
June 19, 2018: Molecular Biology and Evolution
Rafael I Ponce-Toledo, David Moreira, Purificación López-García, Philippe Deschamps
Endosymbiosis has been common all along eukaryotic evolution, providing opportunities for genomic and organellar innovation. Plastids are a prominent example. After the primary endosymbiosis of the cyanobacterial plastid ancestor, photosynthesis spread in many eukaryotic lineages via secondary endosymbioses involving red or green algal endosymbionts and diverse heterotrophic hosts. However, the number of secondary endosymbioses and how they occurred remain poorly understood. In particular, contrasting patterns of endosymbiotic gene transfer (EGT) have been detected and subjected to various interpretations...
June 19, 2018: Molecular Biology and Evolution
Daniel J Leite, Luís Baudouin-Gonzalez, Sawa Iwasaki-Yokozawa, Jesus Lozano-Fernandez, Natascha Turetzek, Yasuko Akiyama-Oda, Nikola-Michael Prpic, Davide Pisani, Hiroki Oda, Prashant P Sharma, Alistair P McGregor
Homeobox genes are key toolkit genes that regulate the development of metazoans and changes in their regulation and copy number have contributed to the evolution of phenotypic diversity. We recently identified a whole genome duplication (WGD) event that occurred in an ancestor of spiders and scorpions (Arachnopulmonata), and that many homeobox genes, including two Hox clusters, appear to have been retained in arachnopulmonates. To better understand the consequences of this ancient WGD and the evolution of arachnid homeobox genes, we have characterised and compared the homeobox repertoires in a range of arachnids...
June 19, 2018: Molecular Biology and Evolution
Yosuke Hoshino, Eric A Gaucher
Isoprenoids and their derivatives represent the largest group of organic compounds in nature and are distributed universally in the three domains of life. Isoprenoids are biosynthesized from isoprenyl diphosphate units, generated by two distinctive biosynthetic pathways: mevalonate pathway and methylerthritol 4-phosphate pathway. Archaea and eukaryotes exclusively have the former pathway, while most bacteria have the latter. Some bacteria, however, are known to possess the mevalonate pathway genes. Understanding the evolutionary history of these two isoprenoid biosynthesis pathways in each domain of life is critical since isoprenoids are so interweaved in the architecture of life that they would have had indispensable roles in the early evolution of life...
June 14, 2018: Molecular Biology and Evolution
Jean Cury, Pedro H Oliveira, Fernando de la Cruz, Eduardo P C Rocha
Self-transmissible mobile genetic elements drive horizontal gene transfer between prokaryotes. Some of these elements integrate in the chromosome, whereas others replicate autonomously as plasmids. Recent works showed the existence of few differences, and occasional interconversion, between the two types of elements. Here, we enquired on why evolutionary processes have maintained the two types of mobile genetic elements by comparing integrative and conjugative elements (ICE) with extrachromosomal ones (conjugative plasmids) of the highly abundant MPFT conjugative type...
June 14, 2018: Molecular Biology and Evolution
Takahide Tohmonda, Akiko Kamiya, Akira Ishiguro, Takashi Iwaki, Takahiko J Fujimi, Minoru Hatayama, Jun Aruga
Zic family genes encode C2H2-type zinc finger proteins that act as critical toolkit proteins in the metazoan body plan establishment. In this study, we searched evolutionarily conserved domains among 121 Zic protein sequences from 22 animal phyla and 40 classes, and addressed their evolutionary significance. The collected sequences included those from poriferans and orthonectids. We discovered seven new conserved domains (CDs), CD0-CD6, (in order from the N- to C-terminus) using the most conserved Zic protein sequences from Deuterostomia (Hemichordata, Cephalochordata), Lophotrochozoa (Cephalopoda and Brachiopoda), and Ecdysozoa (Chelicerata, Priapulida)...
June 14, 2018: Molecular Biology and Evolution
Dennis Kostka, Alisha K Holloway, Katherine S Pollard
Some of the fastest evolving regions of the human genome are conserved non-coding elements with many human-specific DNA substitutions. These Human Accelerated Regions (HARs) are enriched nearby regulatory genes, and several HARs function as developmental enhancers. To investigate if this evolutionary signature is unique to humans, we quantified evidence of accelerated substitutions in conserved genomic elements across multiple lineages and applied this approach simultaneously to the genomes of five apes: human, chimpanzee, gorilla, orangutan, and gibbon...
June 12, 2018: Molecular Biology and Evolution
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