International Journal of Evolutionary Biology The latest articles from Hindawi © 2018 , Hindawi Limited . All rights reserved. Corrigendum to “A Survey of Eyespot Sexual Dimorphism across Nymphalid Butterflies” Thu, 27 Jul 2017 00:00:00 +0000 Christopher K. Tokita, Jeffrey C. Oliver, and Antónia Monteiro Copyright © 2017 Christopher K. Tokita et al. All rights reserved. New Insights into the Effects of Several Environmental Parameters on the Relative Fitness of a Numerically Dominant Class of Evolved Niche Specialist Thu, 22 Dec 2016 12:03:09 +0000 Adaptive radiation in bacteria has been investigated using Wrinkly Spreaders (WS), a morphotype which colonises the air-liquid (A-L) interface of static microcosms by biofilm formation with a significant fitness advantage over competitors growing lower down in the O2-limited liquid column. Here, we investigate several environmental parameters which impact the ecological opportunity that the Wrinkly Spreaders exploit in this model system. Manipulation of surface area/volume ratios suggests that the size of the WS niche was not as important as the ability to dominate the A-L interface and restrict competitor growth. The value of this niche to the Wrinkly Spreaders, as determined by competitive fitness assays, was found to increase as O2 flux to the A-L interface was reduced, confirming that competition for O2 was the main driver of WS fitness. The effect of O2 on fitness was also found to be dependent on the availability of nutrients, reflecting the need to take up both for optimal growth. Finally, the meniscus trap, a high-O2 region formed by the interaction of the A-L interface with the vial walls, was also important for fitness during the early stages of biofilm formation. These findings reveal the complexity of this seemingly simple model system and illustrate how changes in environmental physicality alter ecological opportunity and the fitness of the adaptive morphotype. Anna Kuśmierska and Andrew J. Spiers Copyright © 2016 Anna Kuśmierska and Andrew J. Spiers. All rights reserved. The Challenges and Relevance of Exploring the Genetics of North Africa’s “Barbary Lion” and the Conservation of Putative Descendants in Captivity Tue, 30 Aug 2016 09:58:48 +0000 The lions of North Africa were unique in ecological terms as well as from a human cultural perspective and were the definitive lions of Roman and Medieval Europe. Labelled “Barbary” lions, they were once numerous in North Africa but were exterminated by the mid-20th century. Despite subsequent degeneration of the Atlas Mountain ecosystem through human pressures, the feasibility of lion reintroduction has been debated since the 1970s. Research on the long-established captive lion collection traditionally kept by the sultans and kings of Morocco has enabled selective breeding coordinated across Moroccan and European zoos involving a significant number of animals. Molecular genetic research has recently provided insights into lion phylogeny which, despite previous suggestions that all lions share recent common ancestry, now indicates clear distinctions between lions in North, West, and Central Africa, the Middle East, and India versus those in Southern and Eastern Africa. A review of the evolutionary relevance of North African lions highlights the important challenges and opportunities in understanding relationships between Moroccan lions, extinct North African lions, and extant lion populations in India and West and Central Africa and the potential role for lions in ecosystem recovery in those regions. Simon A. Black Copyright © 2016 Simon A. Black. All rights reserved. The Heavy Links between Geological Events and Vascular Plants Evolution: A Brief Outline Thu, 04 Feb 2016 13:33:23 +0000 Since the rise of photosynthesis, life has influenced terrestrial atmosphere, particularly the O2 and the CO2 content (the latter being originally more than 95%), changing the chemistry of waters, atmosphere, and soils. Billions of years after, a far offspring of these first unicellular forms conquered emerging lands, not only completely changing landscape, but also modifying geological cycles of deposition and erosion, many chemical and physical characteristics of soils and fresh waters, and, more, the cycle of various elements. So, there are no doubts that vascular plants modified geology; but it is true that also geology has affected (and, more, has driven) plant evolution. New software, PyRate, has determined vascular plant origin and diversification through a Bayesian analysis of fossil record from Silurian to today, particularly observing their origination and extinction rate. A comparison between PyRate data and geological history suggests that geological events massively influenced plant evolution and that also the rise of nonflowering seed plants and the fast diffusion of flowering plants can be explained, almost partly, with the environmental condition changes induced by geological phenomena. Aldo Piombino Copyright © 2016 Aldo Piombino. All rights reserved. An Evolutionary Perspective of Nutrition and Inflammation as Mechanisms of Cardiovascular Disease Sun, 29 Nov 2015 13:41:59 +0000 When cardiovascular diseases are viewed from an evolutionary biology perspective, a heightened thrifty and an inflammatory design could be their mechanisms. Human ancestors confronted a greater infectious load and were subjected to the selection for proinflammatory genes and a strong inflammatory function. Ancestors also faced starvation periods that pressed for a thrifty genotype which caused fat accumulation. The pressure of sustaining gluconeogenesis during periods of poor nourishment selected individuals with insulin resistance. Obesity induces a proinflammatory state due to the secretion of adipokines which underlie cardiometabolic diseases. Our actual lifestyle needs no more of such proinflammatory and thrifty genotypes and these ancestral genes might increase predisposition to diseases. Risk factors for atherosclerosis and diabetes are based on inflammatory and genetic foundations that can be accounted for by excess fat. Longevity has also increased in recent times and is related to a proinflammatory response with cardiovascular consequences. If human ancestral lifestyle could be recovered by increasing exercise and adapting a calorie restriction diet, obesity would decrease and the effects on chronic low-grade inflammation would be limited. Thereby, the rates of both atherosclerosis and diabetes could be reduced. María Esther Rubio-Ruiz, Ana Elena Peredo-Escárcega, Agustina Cano-Martínez, and Verónica Guarner-Lans Copyright © 2015 María Esther Rubio-Ruiz et al. All rights reserved. Evolutionary Consequences of Male Driven Sexual Selection and Sex-Biased Fitness Modifications in Drosophila melanogaster and Members of the simulans Clade Tue, 01 Sep 2015 06:09:31 +0000 Males have evolved a variety of behavioral, morphological, and physiological traits to manipulate their mates in order to maximize their chances of success. These traits are bound to influence how females respond to male behaviors and influence the nature of sexual selection/conflict. A common consequence of aggressive male mating strategies in Drosophila melanogaster is the reduction of female lifespan. Our study shows that this is common across members of the simulans clade. Reduced life expectancy of females implies that female contribution to a population is less than that of males per generation. Fitness differences between the sexes in every generation will invariably affect overall population fitness. How natural selection responds to the female deaths and thereby the unequal fitness of the sexes has rarely been addressed. We shed light on this issue and provide evidence, which suggests that additional gains of fitness by males due to their longevity and continued mating may provide one explanation as to why the loss of female fitness may be “invisible” (effectively neutral) to natural selection. Male driven sexual selection and additional, transgenerational gains of male fitness can be an important force of evolutionary change and need to be tested with other organisms. Santosh Jagadeeshan, Wilfried Haerty, Monika Moglinicka, Abha Ahuja, Scot De Vito, and Rama S. Singh Copyright © 2015 Santosh Jagadeeshan et al. All rights reserved. The Evolutionary History of Daphniid α-Carbonic Anhydrase within Animalia Sun, 29 Mar 2015 08:05:46 +0000 Understanding the mechanisms that drive acid-base regulation in organisms is important, especially for organisms in aquatic habitats that experience rapidly fluctuating pH conditions. Previous studies have shown that carbonic anhydrases (CAs), a family of zinc metalloenzymes, are responsible for acid-base regulation in many organisms. Through the use of phylogenetic tools, this present study attempts to elucidate the evolutionary history of the α-CA superfamily, with particular interest in the emerging model aquatic organism Daphnia pulex. We provide one of the most extensive phylogenies of the evolution of α-CAs, with the inclusion of 261 amino acid sequences across taxa ranging from Cnidarians to Homo sapiens. While the phylogeny supports most of our previous understanding on the relationship of how α-CAs have evolved, we find that, contrary to expectations, amino acid conservation with bacterial α-CAs supports the supposition that extracellular α-CAs are the ancestral state of animal α-CAs. Furthermore, we show that two cytosolic and one GPI-anchored α-CA in Daphnia genus have homologs in sister taxa that are possible candidate genes to study for acid-base regulation. In addition, we provide further support for previous findings of a high rate of gene duplication within Daphnia genus, as compared with other organisms. Billy W. Culver and Philip K. Morton Copyright © 2015 Billy W. Culver and Philip K. Morton. All rights reserved. Network Analysis of Plasmidomes: The Azospirillum brasilense Sp245 Case Mon, 29 Dec 2014 09:17:58 +0000 Azospirillum brasilense is a nitrogen-fixing bacterium living in association with plant roots. The genome of the strain Sp245, isolated in Brazil from wheat roots, consists of one chromosome and six plasmids. In this work, the A. brasilense Sp245 plasmids were analyzed in order to shed some light on the evolutionary pathways they followed over time. To this purpose, a similarity network approach was applied in order to identify the evolutionary relationships among all the A. brasilense plasmids encoded proteins; in this context a computational pipeline specifically devoted to the analysis and the visualization of the network-like evolutionary relationships among different plasmids molecules was developed. This information was supplemented with a detailed (in silico) functional characterization of both the connected (i.e., sharing homology with other sequences in the dataset) and the unconnected (i.e., not sharing homology) components of the network. Furthermore, the most likely source organism for each of the genes encoded by A. brasilense plasmids was checked, allowing the identification of possible trends of gene loss/gain in this microorganism. Data obtained provided a detailed description of the evolutionary landscape of the plasmids of A. brasilense Sp245, suggesting some of the molecular mechanisms responsible for the present-day structure of these molecules. Valerio Orlandini, Giovanni Emiliani, Marco Fondi, Isabel Maida, Elena Perrin, and Renato Fani Copyright © 2014 Valerio Orlandini et al. All rights reserved. A Syntenic Region Conserved from Fish to Mammalian X Chromosome Tue, 18 Nov 2014 11:29:50 +0000 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Alberto Civetta, José M. Eirín-López, Rob Kulathinal, and Jeremy L. Marshall Copyright © 2013 Alberto Civetta et al. All rights reserved.