Evolutionary Genetic Studies Research Articles

Genetic population structure in Nacella magellanica: Evidence of rapid range expansion throughout the entire species distribution on the Atlantic coast

Nacella magellanica, the most abundant limpet in the Magellanic biogeographic Province of Argentina and Chile, is characterized by a noticeable variability in shell morphology and color patterns. Ecological as well as evolutionary features make this limpet an interesting species for evolutionary and population genetic studies. Here, arbitrary nuclear molecular markers, inter-simple sequence repeat-PCR, are used to analyze the population genetic structure in 14 localities of N. magellanica along 2900km on the Atlantic coast of the Magellanic Province. We compare the present results, based on nuclear markers, with previous findings of a phylogeographic study that used the mitochondrial COI gene. All the results presented here suggest little genetic structure within N. magellanica, with moderate to high genetic connectivity among populations. The short time elapsed since the expansion of this species plus a possible long larval lifespan and the oceanographic and environmental conditions of the Magellanic Province might explain the lack of genetic structuring and the low levels of genetic differentiation in the species throughout its distribution range along the Argentine coast.

Plasmodium falciparum and Plasmodium vivax specific lactate dehydrogenase: Genetic polymorphism study from Indian isolates

Control and eradication of malaria is hindered by the acquisition of drug resistance by Plasmodium species. This has necessitated a persistent search for novel drugs and more efficient targets. Plasmodium species specific lactate dehydrogenase is one of the potential therapeutic and diagnostic targets, because of its indispensable role in endoerythrocytic stage of the parasite. A target molecule that is highly conserved in the parasite population can be more effectively used in diagnostics and therapeutics, hence, in the present study polymorphism in PfLDH (Plasmodiumfalciparum specific LDH) and PvLDH (Plasmodiumvivax specific LDH) genes was analyzed using PCR-single strand confirmation polymorphism (PCR-SSCP) and sequencing. Forty-six P. falciparum and thirty-five P. vivax samples were screened from different states of India. Our findings have revealed presence of a single PfLDH genotype and six PvLDH genotypes among the studied samples. Interestingly, along with synonymous substitutions, nonsynonymous substitutions were reported to be present for the first time in the PvLDH genotypes. Further, through amino acid sequence alignment and homology modeling studies we observed that the catalytic residues were conserved in all PvLDH genotypes and the nonsynonymous substitutions have not altered the enzyme structure significantly. Evolutionary genetics studies have confirmed that PfLDH and PvLDH loci are under strong purifying selection. Phylogenetic analysis of the pLDH gene sequences revealed that P. falciparum compared to P. vivax, has recent origin. The study therefore supports PfLDH and PvLDH as suitable therapeutic and diagnostic targets as well as phylogenetic markers to understand the genealogy of malaria species.

The complete mitochondrial genome of Glyptothorax sinense (Siluriformes, Sisoridae)

Glyptothorax sinense (Siluriformes, Sisoridae), is a kind of small-sized freshwater fish which mainly distributes in the middle and upper reaches of the Yangtze River in China. In this study, the complete mitochondrial genome of G. sinense was first determined using a PCR-based method. The complete mtDNA sequence is 16,531 bp in length, including 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes, and a non-coding control region (D-loop). The overall-based composition was 31.61% A, 26.66% T, 15.38% G and 26.34% C, with a relatively high A + T content (58.27%). This will provide a useful tool for evolutionary and population genetic studies of G. sinense.

Optimization of Virus-induced Gene Silencing to Facilitate Evo-devo Studies in the Emerging Model SpeciesMimulus guttatus(Phrymaceae)1

Abstract Mimulus guttatus DC. (yellow monkey-flower; Phrymaceae) is an important model species for ecological and evolutionary studies, being locally adapted to a wide range of elevation, moisture and temperature gradients, soil types, and pollinator availabilities. In order to advance this species as a model for evolutionary genetic studies, we have developed virus-induced gene silencing (VIGS) using the tobacco rattle virus (TRV) to assay gene function. We demonstrate the effectiveness of Agrobacterium-mediated VIGS in two divergent populations of M. guttatus, Iron Mountain 767 (IM767) and Point Reyes (PR). Plants infected with a fragment of the carotenoid biosynthesis pathway gene PHYTOENE DESATURASE (PDS) cloned into the TRV2 vector exhibited endogenous PDS silencing and photobleached phenotypes. We further assayed for VIGS-induced floral phenotypes by silencing paralogous genes putatively affecting floral symmetry, CYCLOIDEA1 (CYC1) and CYCLOIDEA2 (CYC2). Simultaneous silencing of CYC1 and CYC2 resul...

WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans.

High-throughput experimental technologies gradually shift the paradigm of biological research from hypothesis-validation toward hypothesis-generation science. Translating diverse types of large-scale experimental data into testable hypotheses, however, remains a daunting task. We previously demonstrated that heterogeneous genomics data can be integrated into a single genome-scale gene network with high prediction power for ribonucleic acid interference (RNAi) phenotypes in Caenorhabditis elegans, a popular metazoan model in the study of developmental biology, neurobiology and genetics. Here, we present WormNet version 3 (v3), which is a new network-assisted hypothesis-generating server for C. elegans. WormNet v3 includes major updates to the base gene network, which substantially improved predictions of RNAi phenotypes. The server generates various gene network-based hypotheses using three complementary network methods: (i) a phenotype-centric approach to ‘find new members for a pathway’; (ii) a gene-centric approach to ‘infer functions from network neighbors’ and (iii) a context-centric approach to ‘find context-associated hub genes’, which is a new method to identify key genes that mediate physiology within a specific context. For example, we demonstrated that the context-centric approach can be used to identify potential molecular targets of toxic chemicals. WormNet v3 is freely accessible at http://www.inetbio.org/wormnet.

The complete mitochondrial genome of Rhinogobio typus (Teleostei, Cyprinidae, Gobioninae)

In the present study, the complete mitochondrial genome sequence of Rhinogobio typus (Teleostei, Cyprinidae, Gobioninae) was obtained using a PCR-based method. The total length of the mitochondrial genome is 16,608 bp, including 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes, and a non-coding control region (D-loop), which is similar to that observed in many other reported fishes. The overall-based composition is 31.3% A, 26.6% T, 15.9% G and 26.2% C, with high A + T content (57.9%). These results will provide a useful tool for species identification, evolutionary and population genetic studies of R. typus and its related species.

Синергетический сциентизм и социальная картина мира

The paper discusses possible ways of solving the fundamental problem of the community of scientific knowledge – the integration of natural and social sciences and humanities. Attempts to find common patterns of special scientific pictures of the world, in particular, biological and social, have led to a discussion of an interdisciplinary science as sociobiology which attempts to explain the social behavior of living beings by set of certain advantage generated in the course of evolution. Research field of sociobiology intersects with the study of evolutionary theory, zoology, genetics and other disciplines. In the field of social sciences it is close to evolutionary psychology exploring the behavior theory. Attempts to explain such behaviors as altruism, aggression are made using evolutionary mechanisms. Today we are witnessing the birth of the third, synergetic paradigm based on emerging, formation, development and change (evolution) of complex open nonlinear nonequilibrium systems. The theory of self-organization claims to interdisciplinarity and universality, including in the field of creation of the modern social picture of the world. The central problem under the consideration is the fact that synergy deals with the collective, mass processes, with complex social systems and is the most rational key to this problem solving.

Size and Shape Variability in Human Molars during Odontogenesis

Under the patterning cascade model (PCM) of cusp development inspired by developmental genetic studies, it is predicted that the location and the size of later-forming cusps are more variable than those of earlier-forming ones. Here we assessed whether differences in the variability among cusps in total and each particular crown component (enamel-dentin junction [EDJ], outer enamel surface [OES], and cement-enamel junction [CEJ]) could be explained by the PCM, using human maxillary permanent first molars (UM1) and second deciduous molars (um2). Specimens were µCT-scanned, and 3D models of EDJ and OES were reconstructed. Based on these models, landmark-based 3D geometric morphometric analyses were conducted. Size variability in both tooth types was generally consistent with the above prediction, and the differences in size variation among cusps were smaller for the crown components completed in later stages of odontogenesis. With a few exceptions, however, the prediction was unsupported regarding shape variability, and UM1 and um2 showed different patterns. Our findings suggested that the pattern of size variability would be caused by temporal factors such as the order of cusp initiation and the duration from the beginning of mineralization to the completion of crown formation, whereas shape variability may be affected by both topographic and temporal factors.

The Hox genes Ultrabithorax and abdominal-A specify three different types of abdominalappendage in the springtail Orchesella cincta (Collembola)

BackgroundIn Drosophila and many other insects, the Hox genes Ultrabithorax (Ubx) and abdominal-A (abd-A) suppress limb formation on most or all segments of the abdomen. However, a number of basal hexapod lineages retain multiple appendages on the abdomen. In the collembolans or springtails, three abdominal segments develop specialized organs that originate from paired appendage primordia which fuse at the midline: the first abdominal segment bears the collophore (ventral tube), involved in osmoregulation; the fourth segment bears the furca, the leaping organ, and the third segment bears the retinaculum, which retains the furca at rest. Ubx and abd-A are known to be expressed in the springtail abdomen, but what role they play in specifying these distinct abdominal appendages is not known. This is largely because no genetic model has been established in collembolans or any other non-insect hexapod.ResultsWe have developed a convenient method for laboratory culture of the collembolan Orchesella cincta on defined media, a method for in-situ hybridization to embryos and a procedure for gene knockdown by parental injection of double-stranded RNA (RNAi). We show that Orchesella Ubx transcripts are detectable in the first to third abdominal segments, and abd-A transcripts in the second to fourth segments. Knockdown of Oc-Ubx leads to the homeotic transformation of the collophore into a pair of walking legs (a more anterior identity) but the retinaculum into a furca (a more posterior identity). Knockdown of Oc-abd-A leads to the transformation of the retinaculum into a collophore and of the furca into legs (both anterior transformations). Simultaneous silencing of both Oc-Ubx and Oc-abd-A transformed all three of these appendages into paired legs, but did not cause appendages to develop on the second, or on the most posterior abdominal segments.ConclusionsWe conclude that, in Orchesella, Oc-Ubx alone specifies the collophore on the first and Oc-abd-A alone specifies the furca on the fourth abdominal segment. Oc-Ubx and Oc-abd-A function together, apparently combinatorially, to specify the retinaculum on the third segment. The efficiency of RNAi in Orchesella makes this an attractive model for further genetic studies of development and physiology in basal hexapods.Electronic supplementary materialThe online version of this article (doi:10.1186/2041-9139-5-2) contains supplementary material, which is available to authorized users.

New microsatellite markers for the neotropical malaria vector Anopheles nuneztovari sensu lato.

Anopheles nuneztovari sensu lato consists of cryptic species and genetic lineages, one of which is an important human malaria vector in the northern part of South America. Population structure and evolutionary genetics studies may help in the definition and delimitation of the species and lineages within this species complex, which is relevant information for organizations involved in malaria control efforts. In this study, 10 new microsatellite markers were isolated from 2 repeat-enriched genomic libraries of A. nuneztovari s.l. and were characterized in 37-48 mosquitoes of this species. All loci were highly polymorphic and encompassed 5-25 alleles per locus. The observed (HO) and expected (HE) heterozygosities ranged from 0.354 to 0.866 and from 0.613 to 0.932, respectively. Six of the 10 new loci showed significant deviations from the Hardy-Weinberg equilibrium, and no linkage disequilibrium was detected. The loci described in this study were more polymorphic than the 18 previously characterized loci and appear to be promising markers for use in investigating the fine-scale population genetic structure and the boundaries of the cryptic species and lineages within the A. nuneztovari complex.

Reptile genomes open the frontier for comparative analysis of amniote development and regeneration.

Developmental genetic studies of vertebrates have focused primarily on zebrafish, frog and mouse models, which have clear application to medicine and well-developed genomic resources. In contrast, reptiles represent the most diverse amniote group, but have only recently begun to gather the attention of genome sequencing efforts. Extant reptilian groups last shared a common ancestor ?280 million years ago and include lepidosaurs, turtles and crocodilians. This phylogenetic diversity is reflected in great morphological and behavioral diversity capturing the attention of biologists interested in mechanisms regulating developmental processes such as somitogenesis and spinal patterning, regeneration, the evolution of "snake-like" morphology, the formation of the unique turtle shell, and the convergent evolution of the four-chambered heart shared by mammals and archosaurs. The complete genome of the first non-avian reptile, the green anole lizard, was published in 2011 and has provided insights into the origin and evolution of amniotes. Since then, the genomes of multiple snakes, turtles, and crocodilians have also been completed. Here we will review the current diversity of available reptile genomes, with an emphasis on their evolutionary relationships, and will highlight how these genomes have and will continue to facilitate research in developmental and regenerative biology.

Why Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS

The ratio of divergence at nonsynonymous and synonymous sites, dN/dS, is a widely used measure in evolutionary genetic studies to investigate the extent to which selection modulates gene sequence evolution. Originally tailored to codon sequences of distantly related lineages, dN/dS represents the ratio of fixed nonsynonymous to synonymous differences. The impact of ancestral and lineage-specific polymorphisms on dN/dS, which we here show to be substantial for closely related lineages, is generally neglected in estimation techniques of dN/dS. To address this issue, we formulate a codon model that is firmly anchored in population genetic theory, derive analytical expressions for the dN/dS measure by Poisson random field approximation in a Markovian framework and validate the derivations by simulations. In good agreement, simulations and analytical derivations demonstrate that dN/dS is biased by polymorphisms at short time scales and that it can take substantial time for the expected value to settle at its time limit where only fixed differences are considered. We further show that in any attempt to estimate the dN/dS ratio from empirical data the effect of the intrinsic fluctuations of a ratio of stochastic variables, can even under neutrality yield extreme values of dN/dS at short time scales or in regions of low mutation rate. Taken together, our results have significant implications for the interpretation of dN/dS estimates, the McDonald–Kreitman test and other related statistics, in particular for closely related lineages.

Evolutionary Reconstruction and Population Genetics Analysis of Aurora Kinases

BackgroundAurora kinases belong to the highly conserved kinase family and play a vital role in cell cycle regulation. The structure and function of these kinases are inter-related and sometimes they also act as substitutes in case of knockdown of other aurora kinases.MethodIn this work we carried out the evolutionary reconstruction and population genetic studies of aurora kinase proteins. Substitution saturation test, CAI (Codon adaptation index), gene expression and RSCU (Relative synonymous codon usage) values were computed for all the three aurora kinases. Linear regression method was used to check the dependency of gene expression on their CAI values.ResultsThe results suggested that aurora-B and aurora-C has shown convergence in their evolutionary pathway. Moreover, the aurora-A I57V mutation showed high penetrance in human population and exist at very high frequency (84.4%) when compared to the native residue (15.6%). The mutation showed notable range of functional gain and seemed to be promising for the evolution of aurora-A function. Mutant allele might also become a challenging prospect for understanding the pattern of evolution followed by cell cycle kinases.ConclusionThe overall result suggested that the aurora-A is currently under the evolutionary transition and to determine the functional significance of the mutation further investigation are required.

Characterization, Polymorphism and Selection of Major Histocompatibility Complex (MHC) DAB Genes in Vulnerable Chinese Egret (Egretta eulophotes)

The major histocompatibility complex (MHC) is an excellent molecular marker for the studies of evolutionary ecology and conservation genetics because it is a family of highly polymorphic genes that play a key role in vertebrate immune response. In this study, the functional genes of MHC Class II B (DAB) were isolated for the first time in a vulnerable species, the Chinese egret ( Egretta eulophotes ). Using a full length DNA and cDNA produced by PCR and RACE methods, four potential MHC DAB loci were characterized in the genome of this egret and all four were expressed in liver and blood. At least four copies of the MHC gene complex were similar to two copies of the minimal essential MHC complex of chicken, but are less complex than the multiple copies expressed in passerine species. In MHC polymorphism, 19 alleles of exon 2 were isolated from 48 individuals using PCR. No stop codons or frameshift mutations were found in any of the coding regions. The signatures of positive selection detected in potential peptide-binding regions by Bayesian analysis, suggesting that all of these genes were functional. These data will provide the fundamental basis for further studies to elucidate the mechanisms and significance of MHC molecular adaptation in vulnerable Chinese egret and other ardeids.

Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes

BackgroundThe green anole lizard, Anolis carolinensis, is a key species for both laboratory and field-based studies of evolutionary genetics, development, neurobiology, physiology, behavior, and ecology. As the first non-avian reptilian genome sequenced, A. carolinesis is also a prime reptilian model for comparison with other vertebrate genomes. The public databases of Ensembl and NCBI have provided a first generation gene annotation of the anole genome that relies primarily on sequence conservation with related species. A second generation annotation based on tissue-specific transcriptomes would provide a valuable resource for molecular studies.ResultsHere we provide an annotation of the A. carolinensis genome based on de novo assembly of deep transcriptomes of 14 adult and embryonic tissues. This revised annotation describes 59,373 transcripts, compared to 16,533 and 18,939 currently for Ensembl and NCBI, and 22,962 predicted protein-coding genes. A key improvement in this revised annotation is coverage of untranslated region (UTR) sequences, with 79% and 59% of transcripts containing 5’ and 3’ UTRs, respectively. Gaps in genome sequence from the current A. carolinensis build (Anocar2.0) are highlighted by our identification of 16,542 unmapped transcripts, representing 6,695 orthologues, with less than 70% genomic coverage.ConclusionsIncorporation of tissue-specific transcriptome sequence into the A. carolinensis genome annotation has markedly improved its utility for comparative and functional studies. Increased UTR coverage allows for more accurate predicted protein sequence and regulatory analysis. This revised annotation also provides an atlas of gene expression specific to adult and embryonic tissues.

Sequencing of isolated sperm cells for direct haplotyping of a human genome

There is increasing evidence that the phenotypic effects of genomic sequence variants are best understood in terms of variant haplotypes rather than as isolated polymorphisms. Haplotype analysis is also critically important for uncovering population histories and for the study of evolutionary genetics. Although the sequencing of individual human genomes to reveal personal collections of sequence variants is now well established, there has been slower progress in the phasing of these variants into pairs of haplotypes along each pair of chromosomes. Here, we have developed a distinct approach to haplotyping that can yield chromosome-length haplotypes, including the vast majority of heterozygous single-nucleotide polymorphisms (SNPs) in an individual human genome. This approach exploits the haploid nature of sperm cells and employs a combination of genotyping and low-coverage sequencing on a short-read platform. In addition to generating chromosome-length haplotypes, the approach can directly identify recombination events (averaging 1.1 per chromosome) with a median resolution of <100 kb.

Flower color as a model system for studies of plant evo-devo.

Even though pigmentation traits have had substantial impacts on the field of animal evolutionary developmental biology, they have played only relatively minor roles in plant evo-devo. This is surprising given the often direct connection between flower color and fitness variation mediated through the effects of pollinators. At the same time, ecological and evolutionary genetic studies have utilized the molecular resources available for the anthocyanin pathway to generate several examples of the molecular basis of putatively adaptive transitions in flower color. Despite this opportunity to synthesize experimental approaches in ecology, evolution, and developmental biology, the investigation of many fundamental questions in evo-devo using this powerful model is only at its earliest stages. For example, a long-standing question is whether predictable genetic changes accompany the repeated evolution of a trait. Due to the conserved nature of the biochemical and regulatory control of anthocyanin biosynthesis, it has become possible to determine whether, and under what circumstances, different types of mutations responsible for flower color variation are preferentially targeted by natural selection. In addition, because plants use anthocyanin and related compounds in vegetative tissue for other important physiological functions, the identification of naturally occurring transitions from unpigmented to pigmented flowers provides the opportunity to examine the mechanisms by which regulatory networks are co-opted into new developmental domains. Here, we review what is known about the ecological and molecular basis of anthocyanic flower color transitions in natural systems, focusing on the evolutionary and developmental features involved. In doing so, we provide suggestions for future work on this trait and suggest that there is still much to be learned from the evolutionary development of flower color transitions in nature.

Substitution bias and evolutionary rate of mitochondrial protein-encoding genes in four species of Cecidomyiidae.

Five mitochondrial protein-encoding genes (COX1, COX2, CytB, ND4 and ND5) from the wheat midge, Sitodiplosis mosellana (Diptera: Cecidomyiidae), were sequenced and compared with those of 3 other Cecidoidae species, Mayetiola destructor, Rhopalomyia pomum and Asphondylia rosetta. These genes shared similar AT content (74.0-80.1%) and base substitution bias in favour of transversions (68.87-79.72%) over transitions (20.28-37.04%). Substitution saturation analyses indicated fast saturation of transitional substitutions in COX2, CytB, ND4 and ND5, especially at the 3rd codon positions. Analysis of interspecific divergence among the 4 species showed that the sequence divergence rates (evolutionary rates) were in the order of ND4 = CytB > COX2 = ND5 > COX1. Intraspecific genetic polymorphism analysis within the field populations of S. mosellana indicated that ND4 had the highest genetic polymorphism and COX1 the lowest. Genetic variation patterns suggested that COX1 could be used as a molecular marker for phylogenetic analysis across a relatively wide taxonomic range in Cecidomyiidae, while COX2 and ND5 may be useful for estimating relationships at a subgenus level or among closely related species. With its high genetic polymorphism, ND4 was the molecular market most suitable for population genetics studies. These findings will be valuable for our further understanding and studies in evolutionary biology and population genetics for S. mosellana and other Cecidomyiidae insects.

Improving the reconstructed sapiens reference sequence of mitochondrial DNA

Recently, Behar et al. [1] proposed to use a new reference sequence, the so-called reconstructed sapiens reference sequence (RSRS), instead of the traditionally utilized by the scientific community (in medical, forensic, and population and evolutionary genetic studies) the revised Cambridge Reference Sequence (rCRS) of human mitochondrial DNA (mtDNA) [2]. While the rCRS belongs to the peripheral European haplogroup H2a2a1, the RSRS represents the deepest root in the known human mtDNA phylogeny and corresponds to the bifurcation of haplogroups L0 and L1′2′3′4′5′6, after combining information from all available mitochondrial genomes from Homo neanderthalensis and 15,451 H.

Spurs in a Spur: Perianth Evolution in the Delphinieae (Ranunculaceae)

Delphinieae (Ranunculaceae) comprise ∼650 species of temperate herbs in Eurasia, North America, and Africa. Their zygomorphic flowers have been the object of numerous studies in morphology, ecology, and developmental genetics, and new phylogenetic insights make it timely to synthesize knowledge about their evolution. Key features of Delphinieae flowers are unusual nectaries consisting of paired organs of the inner perianth whorl that are completely enclosed by a single dorsal organ of the outer whorl. We investigated the floral development of five annual, unicarpellate species of Delphinium, focusing on perianth organization. The results show that the nectar-storing organ in these species results from the postgenital fusion of two primordia of the internal perianth whorl. Eleven floral traits traced on a phylogeny of Delphinieae reveal only two homoplasies in the perianth, namely, the nightcap shape of the dorsal organ of the external perianth whorl and the reduction of the internal perianth whorl to two ...