International Journal of Evolutionary Biology http://www.hindawi.com The latest articles from Hindawi Publishing Corporation © 2014 , Hindawi Publishing Corporation . All rights reserved. A Syntenic Region Conserved from Fish to Mammalian X Chromosome Tue, 18 Nov 2014 11:29:50 +0000 http://www.hindawi.com/journals/ijeb/2014/873935/ Sex chromosomes bearing the sex-determining gene initiate development along the male or female pathway, no matter which sex is determined by XY male or ZW female heterogamety. Sex chromosomes originate from ancient autosomes but evolved rapidly after the acquisition of sex-determining factors which are highly divergent between species. In the heterogametic male system (XY system), the X chromosome is relatively evolutionary silent and maintains most of its ancestral genes, in contrast to its Y counterpart that has evolved rapidly and degenerated. Sex in a teleost fish, the Nile tilapia (Oreochromis niloticus), is determined genetically via an XY system, in which an unpaired region is present in the largest chromosome pair. We defined the differences in DNA contents present in this chromosome with a two-color comparative genomic hybridization (CGH) and the random amplified polymorphic DNA (RAPD) approach in XY males. We further identified a syntenic segment within this region that is well conserved in several teleosts. Through comparative genome analysis, this syntenic segment was also shown to be present in mammalian X chromosomes, suggesting a common ancestral origin of vertebrate sex chromosomes. Guijun Guan, Meisheng Yi, Tohru Kobayashi, Yunhan Hong, and Yoshitaka Nagahama Copyright © 2014 Guijun Guan et al. All rights reserved. Plasticity-Mediated Persistence in New and Changing Environments Wed, 15 Oct 2014 10:06:57 +0000 http://www.hindawi.com/journals/ijeb/2014/416497/ Baldwin’s synthesis of the Organicist position, first published in 1896 and elaborated in 1902, sought to rescue environmentally induced phenotypes from disrepute by showing their Darwinian significance. Of particular interest to Baldwin was plasticity’s mediating role during environmental change or colonization—plastic individuals were more likely to successfully survive and reproduce in new environments than were nonplastic individuals. Once a population of plastic individuals had become established, plasticity could further mediate the future course of evolution. The evidence for plasticity-mediated persistence (PMP) is reviewed here with a particular focus on evolutionary rescue experiments, studies on invasive success, and the role of learning in survival. Many PMP studies are methodologically limited, showing that preexistent plasticity has utility in new environments (soft PMP) rather than directly demonstrating that plasticity is responsible for persistence (hard PMP). An ideal PMP study would be able to demonstrate that (1) plasticity preexisted environmental change, (2) plasticity was fortuitously beneficial in the new environment, (3) plasticity was responsible for individual persistence in the new environment, and (4) plasticity was responsible for population persistence in succeeding generations. Although PMP is not ubiquitous, Baldwin’s hypotheses have been largely vindicated in theoretical and empirical studies, but much work remains. Matthew R. J. Morris Copyright © 2014 Matthew R. J. Morris. All rights reserved. Is the Frequency Content of the Calls in North American Treefrogs Limited by Their Larynges? Tue, 23 Sep 2014 11:05:16 +0000 http://www.hindawi.com/journals/ijeb/2014/198069/ A high diversity of mating calls is found among frogs. The calls of most species, however, are simple, in comparison to those of mammals and birds. In order to determine if the mechanics of the larynx could explain the simplicity of treefrog calls, the larynges of euthanized males were activated with airflow. Laryngeal airflow, sound frequency, and sound intensity showed a positive direct relationship with the driving air pressure. While the natural calls of the studied species exhibit minimal frequency modulation, their larynges produced about an octave of frequency modulation in response to varying pulmonary pressure. Natural advertisement calls are produced near the higher extreme of frequency obtained in the laboratory and at a slightly higher intensity (6 dB). Natural calls also exhibit fewer harmonics than artificial ones, because the larynges were activated with the mouth of the animal open. The results revealed that treefrog larynges allow them to produce calls spanning a much greater range of frequencies than observed in nature; therefore, the simplicity of the calls is not due to a limited frequency range of laryngeal output. Low frequencies are produced at low intensities, however, and this could explain why treefrogs concentrate their calling at the high frequencies. Marcos Gridi-Papp Copyright © 2014 Marcos Gridi-Papp. All rights reserved. Individual Genetic Contributions to Genital Shape Variation between Drosophila simulans and D. mauritiana Mon, 08 Sep 2014 08:52:05 +0000 http://www.hindawi.com/journals/ijeb/2014/808247/ External genitalia are one of the most rapidly evolving morphological features in insects. In the Drosophila melanogaster species subgroup, males possess a nonfertilizing external genital structure, called the posterior lobe, which is highly divergent among even closely related species. A previous study on this subgroup mapped two genomic regions that affect lobe size and four that affect lobe shape differences between D. mauritiana and D. sechellia; none of the regions affected both size and shape. Here, we investigate whether three of these significant regions also affect lobe size and shape differences between the overlapping species pair D. mauritiana and D. simulans. We found that the same three regions of D. mauritiana, previously shown to affect lobe morphology in a D. sechellia genetic background, also affect lobe morphology in a D. simulans genetic background, with one of the regions affecting both size and shape. Two of the regions also affected morphology when introgressed in the reciprocal direction. The overlap of regions affecting genital morphology within related species pairs indicates either that there is a common underlying genetic basis for variation in genital morphology within this species group or that there are multiple adjacent loci with the potential to influence genital morphology. Hélène LeVasseur-Viens and Amanda J. Moehring Copyright © 2014 Hélène LeVasseur-Viens and Amanda J. Moehring. All rights reserved. Genetics of Sub-Saharan African Human Population: Implications for HIV/AIDS, Tuberculosis, and Malaria Mon, 18 Aug 2014 12:58:33 +0000 http://www.hindawi.com/journals/ijeb/2014/108291/ Sub-Saharan Africa has continued leading in prevalence and incidence of major infectious disease killers such as HIV/AIDS, tuberculosis, and malaria. Epidemiological triad of infectious diseases includes susceptible host, pathogen, and environment. It is imperative that all aspects of vertices of the infectious disease triad are analysed to better understand why this is so. Studies done to address this intriguing reality though have mainly addressed pathogen and environmental components of the triad. Africa is the most genetically diverse region of the world as well as being the origin of modern humans. Malaria is relatively an ancient infection in this region as compared to TB and HIV/AIDS; from the evolutionary perspective, we would draw lessons that this ancestrally unique population now under three important infectious diseases both ancient and exotic will be skewed into increased genetic diversity; moreover, other evolutionary forces are also still at play. Host genetic diversity resulting from many years of malaria infection has been well documented in this population; we are yet to account for genetic diversity from the trio of these infections. Effect of host genetics on treatment outcome has been documented. Host genetics of sub-Saharan African population and its implication to infectious diseases are an important aspect that this review seeks to address. Gerald Mboowa Copyright © 2014 Gerald Mboowa. All rights reserved. Conservation and Variability of Synaptonemal Complex Proteins in Phylogenesis of Eukaryotes Wed, 23 Jul 2014 11:38:04 +0000 http://www.hindawi.com/journals/ijeb/2014/856230/ The problems of the origin and evolution of meiosis include the enigmatic variability of the synaptonemal complexes (SCs) which, being morphology similar, consist of different proteins in different eukaryotic phyla. Using bioinformatics methods, we monitored all available eukaryotic proteomes to find proteins similar to known SC proteins of model organisms. We found proteins similar to SC lateral element (LE) proteins and possessing the HORMA domain in the majority of the eukaryotic taxa and assume them the most ancient among all SC proteins. Vertebrate LE proteins SYCP2, SYCP3, and SC65 proved to have related proteins in many invertebrate taxa. Proteins of SC central space are most evolutionarily variable. It means that different protein-protein interactions can exist to connect LEs. Proteins similar to the known SC proteins were not found in Euglenophyta, Chrysophyta, Charophyta, Xanthophyta, Dinoflagellata, and primitive Coelomata. We conclude that different proteins whose common feature is the presence of domains with a certain conformation are involved in the formation of the SC in different eukaryotic phyla. This permits a targeted search for orthologs of the SC proteins using phylogenetic trees. Here we consider example of phylogenetic trees for protozoans, fungi, algae, mosses, and flowering plants. Tatiana M. Grishaeva and Yuri F. Bogdanov Copyright © 2014 Tatiana M. Grishaeva and Yuri F. Bogdanov. All rights reserved. Mycobacterium tuberculosis H37Rv: In Silico Drug Targets Identification by Metabolic Pathways Analysis Tue, 25 Feb 2014 13:33:26 +0000 http://www.hindawi.com/journals/ijeb/2014/284170/ Mycobacterium tuberculosis (Mtb) is a pathogenic bacteria species in the genus Mycobacterium and the causative agent of most cases of tuberculosis. Tuberculosis (TB) is the leading cause of death in the world from a bacterial infectious disease. This antibiotic resistance strain lead to development of the new antibiotics or drug molecules which can kill or suppress the growth of Mycobacterium tuberculosis. We have performed an in silico comparative analysis of metabolic pathways of the host Homo sapiens and the pathogen Mycobacterium tuberculosis (H37Rv). Novel efforts in developing drugs that target the intracellular metabolism of M. tuberculosis often focus on metabolic pathways that are specific to M. tuberculosis. We have identified five unique pathways for Mycobacterium tuberculosis having a number of 60 enzymes, which are nonhomologous to Homo sapiens protein sequences, and among them there were 55 enzymes, which are nonhomologous to Homo sapiens protein sequences. These enzymes were also found to be essential for survival of the Mycobacterium tuberculosis according to the DEG database. Further, the functional analysis using Uniprot showed involvement of all the unique enzymes in the different cellular components. Asad Amir, Khyati Rana, Arvind Arya, Neelesh Kapoor, Hirdesh Kumar, and Mohd Asif Siddiqui Copyright © 2014 Asad Amir et al. All rights reserved. Evolution of the B-Block Binding Subunit of TFIIIC That Binds to the Internal Promoter for RNA Polymerase III Wed, 12 Feb 2014 08:29:14 +0000 http://www.hindawi.com/journals/ijeb/2014/609865/ Eukaryotic RNA polymerase III transcribes tRNA genes, and this requires the transcription factor TFIIIC. Promoters are within genes, with which the B-block binding subunit of TFIIIC associates to initiate transcription. The binding subunits are more than 1000 amino acids in length in various eukaryotic species. There are four regions with conserved sequence similarities in the subunits. The helix-turn-helix motif is included in one of these regions and has been characterized as the B-block_TFIIIC family in the Pfam database. In the NCBI and EMBL translated protein databases, there are archaeal proteins (approximately 100 amino acids in length) referred to as B-block binding subunits. Most of them contain a B-block_TFIIIC motif. DELTA-BLAST searches using these archaeal proteins as queries showed significant multiple blast hits for many eukaryotic B-block binding subunits on the same proteins. This result suggests that eukaryotic B-block binding subunits were constituted by repeating a small unit of B-block_TFIIIC over a long evolutionary period. Bacterial proteins have also been annotated as B-block binding subunits in the databases. Here, some of them were confirmed to have significant similarities to B-block_TFIIIC. These results may imply that part of the RNAP III transcription machinery existed in the common ancestry of prokaryotes and eukaryotes. Sachiko Matsutani Copyright © 2014 Sachiko Matsutani. All rights reserved. DNA Methylation, Epigenetics, and Evolution in Vertebrates: Facts and Challenges Thu, 16 Jan 2014 13:24:32 +0000 http://www.hindawi.com/journals/ijeb/2014/475981/ DNA methylation is a key epigenetic modification in the vertebrate genomes known to be involved in biological processes such as regulation of gene expression, DNA structure and control of transposable elements. Despite increasing knowledge about DNA methylation, we still lack a complete understanding of its specific functions and correlation with environment and gene expression in diverse organisms. To understand how global DNA methylation levels changed under environmental influence during vertebrate evolution, we analyzed its distribution pattern along the whole genome in mammals, reptiles and fishes showing that it is correlated with temperature, independently on phylogenetic inheritance. Other studies in mammals and plants have evidenced that environmental stimuli can promote epigenetic changes that, in turn, might generate localized changes in DNA sequence resulting in phenotypic effects. All these observations suggest that environment can affect the epigenome of vertebrates by generating hugely different methylation patterns that could, possibly, reflect in phenotypic differences. We are at the first steps towards the understanding of mechanisms that underlie the role of environment in molding the entire genome over evolutionary times. The next challenge will be to map similarities and differences of DNA methylation in vertebrates and to associate them with environmental adaptation and evolution. Annalisa Varriale Copyright © 2014 Annalisa Varriale. All rights reserved. A Mechanistic Explanation Linking Adaptive Mutation, Niche Change, and Fitness Advantage for the Wrinkly Spreader Thu, 16 Jan 2014 11:20:23 +0000 http://www.hindawi.com/journals/ijeb/2014/675432/ Experimental evolution studies have investigated adaptive radiation in static liquid microcosms using the environmental bacterium Pseudomonas fluorescens SBW25. In evolving populations a novel adaptive mutant known as the Wrinkly Spreader arises within days having significant fitness advantage over the ancestral strain. A molecular investigation of the Wrinkly Spreader has provided a mechanistic explanation linking mutation with fitness improvement through the production of a cellulose-based biofilm at the air-liquid interface. Colonisation of this niche provides greater access to oxygen, allowing faster growth than that possible for non-biofilm—forming competitors located in the lower anoxic region of the microcosm. Cellulose is probably normally used for attachment to plant and soil aggregate surfaces and to provide protection in dehydrating conditions. However, the evolutionary innovation of the Wrinkly Spreader in static microcosms is the use of cellulose as the matrix of a robust biofilm, and is achieved through mutations that deregulate multiple diguanylate cyclases leading to the over-production of cyclic-di-GMP and the stimulation of cellulose expression. The mechanistic explanation of the Wrinkly Spreader success is an exemplar of the modern evolutionary synthesis, linking molecular biology with evolutionary ecology, and provides an insight into the phenomenal ability of bacteria to adapt to novel environments. Andrew J. Spiers Copyright © 2014 Andrew J. Spiers. All rights reserved. Diversification in Monkeyflowers: An Investigation of the Effects of Elevation and Floral Color in the Genus Mimulus Sun, 05 Jan 2014 08:40:15 +0000 http://www.hindawi.com/journals/ijeb/2014/382453/ The vast diversity of floral colours in many flowering plant families, paired with the observation of preferences among pollinators, suggests that floral colour may be involved in the process of speciation in flowering plants. While transitions in floral colour have been examined in numerous genera, we have very little information on the consequences of floral colour transitions to the evolutionary success of a clade. Overlaid upon these patterns is the possibility that certain floral colours are more prevalent in certain environments, with the causes of differential diversification being more directly determined by geographical distribution. Here we examine transition rates to anthocyanin + carotenoid rich (red/orange/fuschia) flowers and examine whether red/orange flowers are associated with differences in speciation and/or extinction rates in Mimulus. Because it has been suggested that reddish flowers are more prevalent at high elevation, we also examine the macroevolutionary evidence for this association and determine if there is evidence for differential diversification at high elevations. We find that, while red/orange clades have equivalent speciation rates, the trait state of reddish flowers reverts more rapidly to the nonreddish trait state. Moreover, there is evidence for high speciation rates at high elevation and no evidence for transition rates in floral colour to differ depending on elevation. Ezgi Ogutcen, Brooklyn Hamper, and Jana C. Vamosi Copyright © 2014 Ezgi Ogutcen et al. All rights reserved. Indian Craniometric Variability and Affinities Tue, 24 Dec 2013 09:02:14 +0000 http://www.hindawi.com/journals/ijeb/2013/836738/ Recently published craniometric and genetic studies indicate a predominantly indigenous ancestry of Indian populations. We address this issue with a fuller coverage of Indian craniometrics than any done before. We analyse metrical variability within Indian series, Indians’ sexual dimorphism, differences between northern and southern Indians, index-based differences of Indian males from other series, and Indians’ multivariate affinities. The relationship between a variable’s magnitude and its variability is log-linear. This relationship is strengthened by excluding cranial fractions and series with a sample size less than 30. Male crania are typically larger than female crania, but there are also shape differences. Northern Indians differ from southern Indians in various features including narrower orbits and less pronounced medial protrusion of the orbits. Indians resemble Veddas in having small crania and similar cranial shape. Indians’ wider geographic affinities lie with “Caucasoid” populations to the northwest, particularly affecting northern Indians. The latter finding is confirmed from shape-based Mahalanobis-D distances calculated for the best sampled male and female series. Demonstration of a distinctive South Asian craniometric profile and the intermediate status of northern Indians between southern Indians and populations northwest of India confirm the predominantly indigenous ancestry of northern and especially southern Indians. Pathmanathan Raghavan, David Bulbeck, Gayathiri Pathmanathan, and Suresh Kanta Rathee Copyright © 2013 Pathmanathan Raghavan et al. All rights reserved. Modeling Extinction Risk of Endemic Birds of Mainland China Wed, 18 Dec 2013 09:44:17 +0000 http://www.hindawi.com/journals/ijeb/2013/639635/ The extinction risk of endemic birds of mainland China was modeled over evolutionary time. Results showed that extinction risk of endemic birds in mainland China always tended to be similar within subclades over the evolutionary time of species divergence, and the overall evolution of extinction risk of species presented a conservatism pattern, as evidenced by the disparity-through-time plot. A constant-rate evolutionary model was the best one to quantify the evolution of extinction risk of endemic birds of mainland China. Thus, there was no rate shifting pattern for the evolution of extinction risk of Chinese endemic birds over time. In a summary, extinction risk of endemic birds of mainland China is systematically quantified under the evolutionary framework in the present work. Youhua Chen Copyright © 2013 Youhua Chen. All rights reserved. Conservation/Mutation in the Splice Sites of Cytokine Receptor Genes of Mouse and Human Tue, 17 Dec 2013 11:58:44 +0000 http://www.hindawi.com/journals/ijeb/2013/818954/ Conservation/mutation in the intronic initial and terminal hexanucleotides was studied in 26 orthologous cytokine receptor genes of Mouse and Human. Introns began and ended with the canonical dinucleotides GT and AG, respectively. Identical configurations were found in 57% of the 5′ hexanucleotides and 28% of the 3′ hexanucleotides. The actual conservation percentages of the individual variable nucleotides at each position in the hexanucleotides were determined, and the theoretical rates of conservation of groups of three nucleotides were calculated under the hypothesis of a mutual evolutionary independence of the neighboring nucleotides (random association). Analysis of the actual conservation of groups of variable nucleotides showed that, at 5′, GTGAGx was significantly more expressed and GTAAGx was significantly less expressed, as compared to the random association. At 3′, TTTxAG and xTGCAG were overexpressed as compared to a random association. Study of Mouse and Human transcript variants involving the splice sites showed that most variants were not inherited from the common ancestor but emerged during the process of speciation. In some variants the silencing of a terminal hexanucleotide determined skipping of the downstream exon; in other variants the constitutive splicing hexanucleotide was replaced by another potential, in-frame, splicing hexanucleotide, leading to alterations of exon lengths. Rosa Calvello, Antonia Cianciulli, and Maria Antonietta Panaro Copyright © 2013 Rosa Calvello et al. All rights reserved. No Experimental Evidence for Sneaking in a West African Cichlid Fish with Extremely Long Sperm Tue, 10 Dec 2013 09:26:21 +0000 http://www.hindawi.com/journals/ijeb/2013/714304/ Alternative reproductive tactics are widespread in fishes, increasing the potential for sperm competition. Sperm competition has enormous impact on both variation in sperm numbers and sperm size. In cichlids, the sperm competition risk is very divergent and longer sperm are usually interpreted as adaptation to sperm competition. Here we examined whether sneaking tactics exist in Pelvicachromis taeniatus, a socially monogamous cichlid with biparental brood care from West Africa. The small testis indicates low gonadal investment which is typical for genetically monogamous species. In contrast, sperm length with up to 85 μm is extraordinarily long. We examined the reproductive behaviour of ten groups with a male-biased sex ratio under semi-natural conditions via continuous video recording. We recorded spawning site preferences and correlates of reproductive success and conducted paternity tests using microsatellites. Safe breeding sites that could be successfully defended were preferred. All offspring could be assigned to their parents and no multiple paternities were detected. Body size of spawning pairs predicted their spawning probability and offspring hatching rate suggesting benefits from mating with large individuals. Our study suggests low risk of sperm competition under the given conditions in P. taeniatus and thus first evidence for genetic monogamy in a substrate breeding cichlid. Kathrin Langen, Timo Thünken, and Theo C. M. Bakker Copyright © 2013 Kathrin Langen et al. All rights reserved. A Survey of Eyespot Sexual Dimorphism across Nymphalid Butterflies Thu, 05 Dec 2013 11:28:38 +0000 http://www.hindawi.com/journals/ijeb/2013/926702/ Differences between sexes of the same species are widespread and are variable in nature. While it is often assumed that males are more ornamented than females, in the nymphalid butterfly genus Bicyclus, females have, on average, more eyespot wing color patterns than males. Here we extend these studies by surveying eyespot pattern sexual dimorphism across the Nymphalidae family of butterflies. Eyespot presence or absence was scored from a total of 38 wing compartments for two males and two females of each of 450 nymphalid species belonging to 399 different genera. Differences in eyespot number between sexes of each species were tallied for each wing surface (e.g., dorsal and ventral) of forewings and hindwings. In roughly 44% of the species with eyespots, females had more eyespots than males, in 34%, males had more eyespots than females, and, in the remaining 22% of the species, there was monomorphism in eyespot number. Dorsal and forewing surfaces were less patterned, but proportionally more dimorphic, than ventral and hindwing surfaces, respectively. In addition, wing compartments that frequently displayed eyespots were among the least sexually dimorphic. This survey suggests that dimorphism arises predominantly in “hidden” or “private” surfaces of a butterfly’s wing, as previously demonstrated for the genus Bicyclus. Christopher K. Tokita, Jeffrey C. Oliver, and Antónia Monteiro Copyright © 2013 Christopher K. Tokita et al. All rights reserved. Analysis of a Larger SNP Dataset from the HapMap Project Confirmed That the Modern Human A Allele of the ABO Blood Group Genes Is a Descendant of a Recombinant between B and O Alleles Tue, 29 Oct 2013 07:53:41 +0000 http://www.hindawi.com/journals/ijeb/2013/406209/ The human ABO blood group gene consists of three main alleles (A, B, and O) that encode a glycosyltransferase. The A and B alleles differ by two critical amino acids in exon 7, and the major O allele has a single nucleotide deletion (Δ261) in exon 6. Previous evolutionary studies have revealed that the A allele is the most ancient, B allele diverged from the A allele with two critical amino acid substitutions in exon 7, and the major O allele diverged from the A allele with Δ261 in exon 6. However, a recent phylogenetic network analysis study showed that the A allele of humans emerged through a recombination between the B and O alleles. In the previous study, a restricted dataset from only two populations was used. In this study, therefore, we used a large single nucleotide polymorphism (SNP) dataset from the HapMap Project. The results indicated that the A101-A201-O09 haplogroup was a recombinant lineage between the B and O haplotypes, containing the intact exon 6 from the B allele and the two critical A type sites in exon 7 from the major O allele. Its recombination point was assumed to be located just behind Δ261 in exon 6. Masaya Itou, Mitsuharu Sato, and Takashi Kitano Copyright © 2013 Masaya Itou et al. All rights reserved. Undersampling Taxa Will Underestimate Molecular Divergence Dates: An Example from the South American Lizard Clade Liolaemini Wed, 09 Oct 2013 16:10:06 +0000 http://www.hindawi.com/journals/ijeb/2013/628467/ Methods for estimating divergence times from molecular data have improved dramatically over the past decade, yet there are few studies examining alternative taxon sampling effects on node age estimates. Here, I investigate the effect of undersampling species diversity on node ages of the South American lizard clade Liolaemini using several alternative subsampling strategies for both time calibrations and taxa numbers. Penalized likelihood (PL) and Bayesian molecular dating analyses were conducted on a densely sampled (202 taxa) mtDNA-based phylogenetic hypothesis of Iguanidae, including 92 Liolaemini species. Using all calibrations and penalized likelihood, clades with very low taxon sampling had node age estimates younger than clades with more complete taxon sampling. The effect of Bayesian and PL methods differed when either one or two calibrations only were used with dense taxon sampling. Bayesian node ages were always older when fewer calibrations were used, whereas PL node ages were always younger. This work reinforces two important points: (1) whenever possible, authors should strongly consider adding as many taxa as possible, including numerous outgroups, prior to node age estimation to avoid considerable node age underestimation and (2) using more, critically assessed, and accurate fossil calibrations should yield improved divergence time estimates. James A. Schulte II Copyright © 2013 James A. Schulte II. All rights reserved. RNA-Mediated Gene Duplication and Retroposons: Retrogenes, LINEs, SINEs, and Sequence Specificity Thu, 01 Aug 2013 08:13:32 +0000 http://www.hindawi.com/journals/ijeb/2013/424726/ A substantial number of “retrogenes” that are derived from the mRNA of various intron-containing genes have been reported. A class of mammalian retroposons, long interspersed element-1 (LINE1, L1), has been shown to be involved in the reverse transcription of retrogenes (or processed pseudogenes) and non-autonomous short interspersed elements (SINEs). The -end sequences of various SINEs originated from a corresponding LINE. As the -untranslated regions of several LINEs are essential for retroposition, these LINEs presumably require “stringent” recognition of the -end sequence of the RNA template. However, the -ends of mammalian L1s do not exhibit any similarity to SINEs, except for the presence of -poly(A) repeats. Since the -poly(A) repeats of L1 and Alu SINE are critical for their retroposition, L1 probably recognizes the poly(A) repeats, thereby mobilizing not only Alu SINE but also cytosolic mRNA. Many flowering plants only harbor L1-clade LINEs and a significant number of SINEs with poly(A) repeats, but no homology to the LINEs. Moreover, processed pseudogenes have also been found in flowering plants. I propose that the ancestral L1-clade LINE in the common ancestor of green plants may have recognized a specific RNA template, with stringent recognition then becoming relaxed during the course of plant evolution. Kazuhiko Ohshima Copyright © 2013 Kazuhiko Ohshima. All rights reserved. Evolution of Three Parent Genes and Their Retrogene Copies in Drosophila Species Wed, 05 Jun 2013 13:34:11 +0000 http://www.hindawi.com/journals/ijeb/2013/693085/ Retrogenes form a class of gene duplicate lacking the regulatory sequences found outside of the mRNA-coding regions of the parent gene. It is not clear how a retrogene’s lack of parental regulatory sequences affects the evolution of the gene pair. To explore the evolution of parent genes and retrogenes, we investigated three such gene pairs in the family Drosophilidae; in Drosophila melanogaster, these gene pairs are CG8331 and CG4960, CG17734 and CG11825, and Sep2 and Sep5. We investigated the embryonic expression patterns of these gene pairs across multiple Drosophila species. Expression patterns of the parent genes and their single copy orthologs are relatively conserved across species, whether or not a species has a retrogene copy, although there is some variation in CG8331 and CG17734. In contrast, expression patterns of the retrogene orthologs have diversified. We used the genome sequences of 20 Drosophila species to investigate coding sequence evolution. The coding sequences of the three gene pairs appear to be evolving predominantly under negative selection; however, the parent genes and retrogenes show some distinct differences in amino acid sequence. Therefore, in general, retrogene expression patterns and coding sequences are distinct compared to their parents and, in some cases, retrogene expression patterns diversify. Ryan S. O'Neill and Denise V. Clark Copyright © 2013 Ryan S. O'Neill and Denise V. Clark. All rights reserved. Erratum to “New Insights into Ligand-Receptor Pairing and Coevolution of Relaxin Family Peptides and Their Receptors in Teleosts” Wed, 24 Apr 2013 08:16:17 +0000 http://www.hindawi.com/journals/ijeb/2013/807326/ Sara Good, Sergey Yegorov, Joran Martijn, Jens Franck, and Jan Bogerd Copyright © 2013 Sara Good et al. All rights reserved. The Evolution of Sex-Related Traits and Genes 2012 Thu, 21 Mar 2013 17:15:37 +0000 http://www.hindawi.com/journals/ijeb/2013/590769/ Alberto Civetta, José M. Eirín-López, Rob Kulathinal, and Jeremy L. Marshall Copyright © 2013 Alberto Civetta et al. All rights reserved. Drosophila melanogaster Selection for Survival after Infection with Bacillus cereus Spores: Evolutionary Genetic and Phenotypic Investigations of Respiration and Movement Thu, 21 Mar 2013 10:46:10 +0000 http://www.hindawi.com/journals/ijeb/2013/576452/ Laboratory populations of D. melanogaster have been subjected to selection for survival after live spores of B. cereus were introduced as a pathogenic agent. The present study was designed to investigate correlated traits: respiration as a metabolic trait and movement as a behavioral trait. An underlying hypothesis was that the evolution of increased survival after B. cereus infection exerts a metabolic cost associated with elevated immunity and this would be detected by increased respiration rates. There was support for this hypothesis in the male response to selection, but not for selected-line females. Two phenotypic effects were also observed in the study. Females especially showed a marked increase in respiration after mating compared to the other assay stages regardless of whether respiration was measured per fly or adjusted by lean mass or dry weight. Given that mating stimulates egg production, it is feasible that elevated metabolism was needed to provision oocytes with yolk. Females also moved less than males, perhaps due to behaviors related to oviposition whereas elevated male activity might be due to behaviors associated with seeking females and courtship. Relatively low movement of females indicated that their elevated respiration after mating was not due to a change in locomotion. Junjie Ma, Andrew K. Benson, Stephen D. Kachman, Deidra J. Jacobsen, and Lawrence G. Harshman Copyright © 2013 Junjie Ma et al. All rights reserved. Pathogen-Driven Selection in the Human Genome Mon, 04 Mar 2013 12:52:15 +0000 http://www.hindawi.com/journals/ijeb/2013/204240/ Infectious diseases and epidemics have always accompanied and characterized human history, representing one of the main causes of death. Even today, despite progress in sanitation and medical research, infections are estimated to account for about 15% of deaths. The hypothesis whereby infectious diseases have been acting as a powerful selective pressure was formulated long ago, but it was not until the availability of large-scale genetic data and the development of novel methods to study molecular evolution that we could assess how pervasively infectious agents have shaped human genetic diversity. Indeed, recent evidences indicated that among the diverse environmental factors that acted as selective pressures during the evolution of our species, pathogen load had the strongest influence. Beside the textbook example of the major histocompatibility complex, selection signatures left by pathogen-exerted pressure can be identified at several human loci, including genes not directly involved in immune response. In the future, high-throughput technologies and the availability of genetic data from different populations are likely to provide novel insights into the evolutionary relationships between the human host and its pathogens. Hopefully, this will help identify the genetic determinants modulating the susceptibility to infectious diseases and will translate into new treatment strategies. Rachele Cagliani and Manuela Sironi Copyright © 2013 Rachele Cagliani and Manuela Sironi. All rights reserved. Sex-Biased Networks and Nodes of Sexually Antagonistic Conflict in Drosophila Tue, 22 Jan 2013 16:14:02 +0000 http://www.hindawi.com/journals/ijeb/2013/545392/ Sexual antagonism, or conflict, can occur when males and females harbor opposing reproductive strategies. The large fraction of sex-biased genes in genomes present considerable opportunities for conflict to occur, suggesting that sexual antagonism may potentially be a general phenomenon at the molecular level. Here, we employ a novel strategy to identify potential nodes of sexual conflict in Drosophila melanogaster by coupling male, female, and sex-unbiased networks derived from genome-wide expression data with available genetic and protein interaction data. We find that sex-biased networks comprise a large fraction (~1/3) of the total interaction network with the male network possessing nearly twice the number of nodes (genes) relative to the female network. However, there are far less edges or interaction partners among male relative to female subnetworks as seen in their power law distributions. We further identified 598 sex-unbiased genes that can act as indirect nodes of interlocus sexual conflict as well as 271 direct nodal pairs of potential conflict between male- and female-biased genes. The pervasiveness of such potentially conflicting nodes may explain the rapid evolution of sex-biased as well as non-sex-biased genes via this molecular mechanism of sexual selection even among taxa such as Drosophila that are nominally sexually dimorphic. Matthew E. B. Hansen and Rob J. Kulathinal Copyright © 2013 Matthew E. B. Hansen and Rob J. Kulathinal. All rights reserved. Infectious Disease, Endangerment, and Extinction Wed, 16 Jan 2013 09:50:15 +0000 http://www.hindawi.com/journals/ijeb/2013/571939/ Infectious disease, especially virulent infectious disease, is commonly regarded as a cause of fluctuation or decline in biological populations. However, it is not generally considered as a primary factor in causing the actual endangerment or extinction of species. We review here the known historical examples in which disease has, or has been assumed to have had, a major deleterious impact on animal species, including extinction, and highlight some recent cases in which disease is the chief suspect in causing the outright endangerment of particular species. We conclude that the role of disease in historical extinctions at the population or species level may have been underestimated. Recent methodological breakthroughs may lead to a better understanding of the past and present roles of infectious disease in influencing population fitness and other parameters. Ross D. E. MacPhee and Alex D. Greenwood Copyright © 2013 Ross D. E. MacPhee and Alex D. Greenwood. All rights reserved. Divergence in Defence against Herbivores between Males and Females of Dioecious Plant Species Sun, 23 Dec 2012 11:01:40 +0000 http://www.hindawi.com/journals/ijeb/2012/897157/ Defensive traits may evolve differently between sexes in dioecious plant species. Our current understanding of this process hinges on a partial view of the evolution of resistance traits that may result in male-biased herbivory in dioecious populations. Here, we present a critical summary of the current state of the knowledge of herbivory in dioecious species and propose alternative evolutionary scenarios that have been neglected. These scenarios consider the potential evolutionary and functional determinants of sexual dimorphism in patterns of resource allocation to reproduction, growth, and defence. We review the evidence upon which two previous reviews of sex-biased herbivory have concluded that male-biased herbivory is a rule for dioecious species, and we caution readers about a series of shortcomings of many of these studies. Lastly, we propose a minimal standard protocol that should be followed in any studies that intend to elucidate the (co)evolution of interactions between dioecious plants and their herbivores. Germán Avila-Sakar and Cora Anne Romanow Copyright © 2012 Germán Avila-Sakar and Cora Anne Romanow. All rights reserved. Noncompetitive Gametic Isolation between Sibling Species of Cricket: A Hypothesized Link between Within-Population Incompatibility and Reproductive Isolation between Species Thu, 29 Nov 2012 19:18:48 +0000 http://www.hindawi.com/journals/ijeb/2012/593438/ Postmating, prezygotic phenotypes are a common mechanism of reproductive isolation. Here, we describe the dynamics of a noncompetitive gametic isolation phenotype (namely, the ability of a male to induce a female to lay eggs) in a group of recently diverged crickets that are primarily isolated from each other by this phenotype. We not only show that heterospecific males are less able to induce females to lay eggs but that there are male by female incompatibilities in this phenotype that occur within populations. We also identify a protein in the female reproductive tract that correlates with the number of eggs that she was induced to lay. Functional genetic tests using RNAi confirm that the function of this protein is linked to egg-laying induction. Moreover, the dysfunction of this protein appears to underlie both within-population incompatibilities and between-species divergence—thus suggesting a common genetic pathway underlies both. However, this is only correlative evidence and further research is needed to assess whether or not the same mutations in the same genes underlie variation at both levels. Jeremy L. Marshall and Nicholas DiRienzo Copyright © 2012 Jeremy L. Marshall and Nicholas DiRienzo. All rights reserved. Horizontal Transfer and the Evolution of Host-Pathogen Interactions Mon, 26 Nov 2012 15:34:54 +0000 http://www.hindawi.com/journals/ijeb/2012/679045/ Horizontal gene transfer has been long known in viruses and prokaryotes, but its importance in eukaryotes has been only acknowledged recently. Close contact between organisms, as it occurs between pathogens and their hosts, facilitates the occurrence of DNA transfer events. Once inserted in a foreign genome, DNA sequences have sometimes been coopted by pathogens to improve their survival or infectivity, or by hosts to protect themselves against the harm of pathogens. Hence, horizontal transfer constitutes a source of novel sequences that can be adopted to change the host-pathogen interactions. Therefore, horizontal transfer can have an important impact on the coevolution of pathogens and their hosts. Elena de la Casa-Esperón Copyright © 2012 Elena de la Casa-Esperón. All rights reserved. What Can Phages Tell Us about Host-Pathogen Coevolution? Sun, 18 Nov 2012 18:07:47 +0000 http://www.hindawi.com/journals/ijeb/2012/396165/ The outcomes of host-parasite interactions depend on the coevolutionary forces acting upon them, but because every host-parasite relation is enmeshed in a web of biotic and abiotic interactions across a heterogeneous landscape, host-parasite coevolution has proven difficult to study. Simple laboratory phage-bacteria microcosms can ameliorate this difficulty by allowing controlled, well-replicated experiments with a limited number of interactors. Genetic, population, and life history data obtained from these studies permit a closer examination of the fundamental correlates of host-parasite coevolution. In this paper, I describe the results of phage-bacteria coevolutionary studies and their implications for the study of host-parasite coevolution. Recent experimental studies have confirmed phage-host coevolutionary dynamics in the laboratory and have shown that coevolution can increase parasite virulence, specialization, adaptation, and diversity. Genetically, coevolution frequently proceeds in a manner best described by the Gene for Gene model, typified by arms race dynamics, but certain contexts can result in Red Queen dynamics according to the Matching Alleles model. Although some features appear to apply only to phage-bacteria systems, other results are broadly generalizable and apply to all instances of antagonistic coevolution. With laboratory host-parasite coevolutionary studies, we can better understand the perplexing array of interactions that characterize organismal diversity in the wild. John J. Dennehy Copyright © 2012 John J. Dennehy. All rights reserved.