Origin of Species, The

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On the species of origin: diagnosing the source of symbiotic transcripts

On the species of origin: diagnosing the source of symbiotic transcripts

For a sequence isolated from interacting symbionts, deter- mining its cellular role (or roles) is complicated by not knowing which species expressed the sequence [18]. We refer to this challenge as ‘the problem’: given a sequence x expressed in an interaction between species A and B, did x originate from A or B? Various solutions are readily con- ceived, each with merits and faults. Here, we show that a comparative lexical analysis of word counts (specifically, hexamer frequencies), previously used to detect library cont- amination in sequencing projects [19], provides a powerful computational basis to infer a transcript’s species of origin. Experimentally, one can attempt to solve the problem by hybridizing a clone (as probe) to genomic DNA (target) from both species and determining to which target the probe hybridizes. This approach can produce very reliable results. However, if a sequence is highly conserved in the two taxa, hybridization stringency conditions can influence the outcome considerably. For high-throughput EST sequence analysis, source verification by hybridization is impractical in terms of time and reagents. As an alternative to in vitro hybridization, several computational solutions are possible. Were the genome sequence of both species completely deter- mined, one could simply use sequence similarity searching [20-22]. However, most plant hosts and their microbial sym- bionts have little or no genomic sequence data available, which makes this approach very unreliable. Strong similarity to a sequence from one organism does not preclude the possi- bility that a similar sequence is present in the other species. Conclusions based upon such partial knowledge have been informative, but are potentially misleading [18,23].

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The Temperature-Sensitive and Attenuation Phenotypes Conferred by Mutations in the Influenza Virus PB2, PB1, and NP Genes Are Influenced by the Species of Origin of the PB2 Gene in Reassortant Viruses Derived from Influenza A/California/07/2009 and A/WSN/

The Temperature-Sensitive and Attenuation Phenotypes Conferred by Mutations in the Influenza Virus PB2, PB1, and NP Genes Are Influenced by the Species of Origin of the PB2 Gene in Reassortant Viruses Derived from Influenza A/California/07/2009 and A/WSN/33 Viruses

Licensed seasonal influenza LAIVs in the United States are gener- ated with a backbone from the AA ca virus. Alternative backbones have been considered for the development of LAIVs against avian and swine influenza viruses and against novel animal origin influ- enza viruses that emerge in humans. Although the genetic signa- ture responsible for the ts phenotype of the AA ca vaccine virus has been mapped to PB1 (391E, 581G, and 661T), PB2 (265S), and NP (34G) (4), inserting the ts signature into swine or avian viruses leads to only a partial ts phenotype in vitro and att phenotype in vivo (7–9). Our results demonstrate that the 265S mutation con- fers the ts phenotype if the PB2 gene is derived from the WSN virus but not if it is derived from the CA07 virus, which contains a mammalian-adapted avian-lineage PB2 gene. This suggests that the species origin of the PB2 gene segment determines the pheno- type of viruses that contain the ts signature.

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Recurrent origin of peripheral, coastal (sub)species of Mediterranean Senecio (Asteraceae)

Recurrent origin of peripheral, coastal (sub)species of Mediterranean Senecio (Asteraceae)

The origin of incipient (neo-)species on the periphery of a species ’ range or at disjunct peripheral sites is a topic of long-standing interest in evolutionary biology (e.g. Mayr 1963; Eldredge and Gould 1972; Carson and Templeton 1984; Gould and Eldredge 1993; Levin 2000, 2001; Gaston 2003; Hardie and Hutchings 2010). Indeed, small popula- tions isolated at species’ range margins (‘peripheral iso- lates’ sensu Mayr 1963) may play an important role in population genetic divergence and the formation of species because of the increased efficiency of genetic drift, reduced gene flow, and/or intensified selective pressures (Soulé 1973; Lesica and Allendorf 1995; Bridle and Vines 2006; Hardie and Hutchings 2010). Likewise, it has been argued that peripheral isolates are formed ‘on a regular basis’ in many plant species (Stebbins 1974; Grant 1981; Levin 2000, 2001). Building on earlier empirical studies (e.g. Turesson 1922; Gregor 1939; Clausen et al. 1948), it is feasible therefore that peripherally isolated populations occurring in the same range of habitats within an ancestral species contribute to the recurrent formation of phenotypi- cally similar ecotypes (varieties, subspecies, and perhaps even new species) via parallel adaptation to similar selec- tive pressures (e.g. Schluter 2004; Rundle and Nosil 2005; Abbott and Comes 2007; reviewed in Ostevik et al. 2012).

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Investigating the origin and transport of methylated arsenic species in plants

Investigating the origin and transport of methylated arsenic species in plants

reported that rice plants are also able to reduce TMAO to volatile TMA gas (Jia et al., 2012). Trivalent DMA is very unstable (Gong et al., 2001) which may explain the lack of detection of this As species in plants, although it has been found in human urine (Le et al., 2000). Rice plants may even be able to demethylate As, as MMA was detected in roots after exposure to DMA (Figure 3.3; Table S3.2). MMA has also been detected in the As hyperaccumulators, P. vittata and Pteris cretica and As-tolerant Boehmeria nivea exposed to DMA in sand culture (Huang et al., 2008), and in radish (Raphanus sativus) grown in soil amended with DMA. De-methylation of DMA (Huang et al., 2007) and MMA (Yoshinaga et al., 2011) mediated by micro-organisms has also been observed in soils, however the significance of this process to the global As biogeocycle is not yet fully understood. The lack of methylated As species in red clover with nodulation from R. leguminosarum (Figures 3.6; 3.7) is unsurprising as a BLAST search (tBlastn) failed to find any genes with homology to arsM from Rhodopseudomonas palustris (accession number: NP_948900.1; Qin et al., 2006) in the genomes of Rhizobium species. However, the possibility cannot be excluded that As methylation by other symbiotic micro-organisms may result in

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Families of transposable elements, population structure and the origin of species

Families of transposable elements, population structure and the origin of species

Active TEs may develop complex relationships with each other and with the host environment [16,54], which may lead to a competitive relationship and negative cor- relation between families derived from biologically unre- lated TEs such as LTR and non-LTR retrotransposons. On the other hand, the CASP hypothesis predicts positive correlation between the total number of diverse families and the number of subpopulations in metapopulations. This implies that any two subsets of biologically unre- lated families should also positively correlate with each other as they both correlate with the number of subpopu- lations. To test this prediction, we analyzed correlation between the overall numbers of families of long terminal repeats (LTRs) and all the remaining families derived from non-LTR retrotransposons and DNA transposons, for 111 groups of species represented in Repbase [49,50]. The species were combined into groups based on the first part of their binomial names. For example, all Dro- sophilidae (D. melanogaster, D. mojavensis, D. pseudoobs- cura, etc.) were combined into a single group. In the next step, we calculated the total number of different LTRs deposited in Repbase, and the analogous combined num- ber of all the remaining TEs for the same group of spe- cies. Each sequence deposited in Repbase represents a single family of TEs [51]. In this way we obtained 111 pairs of numbers representing the total counts of LTR families and of the remaining TE families for each group of species, excluding mammals, which were analyzed separately. We calculated linear correlation between loga- rithmic values of the corresponding family counts due to a substantial positive skew in their distribution (Figure 2: r = 0.43; P < 0.0001). In a separate analysis, a significant positive correlation was also found between analogous sets of mammalian repetitive families less than 15% divergent from their consensus sequences (r = 0.74; P < 0.0001). However, the significance was marginal for families < 5% divergent from their consensus sequences due to relative underrepresentation of young families in mammals.

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The Population Genetics of the Origin and Divergence of the Drosophila simulans Complex Species

The Population Genetics of the Origin and Divergence of the Drosophila simulans Complex Species

speciation events that overlap in their time course. In A different genetic approach to understanding specia- such cases we must consider “phylogeny” more broadly tion is to study the history of species divergence as it as concerning the genesis of phyla, however complex is revealed in the polymorphism pattern at randomly or slow that process might have been. If speciation selected genes. In recent years, comparative DNA se- events have been recent, and if they have been complex quence data (especially mitochondrial) have been fre- and not instantaneous, it may be possible to reveal the quently used to address basic questions about the relat- complexities using a population genetics approach. edness of close sister taxa and populations (Avise 1989). This report brings together the efforts of several inves- Conceptually, the idea is a direct extension of basic tigators interested in the speciation events that have led population genetic questions (i.e., questions about pop- to our current simulans complex species. To date, DPG ulation subdivision, gene flow, and natural selection) studies on the simulans complex have been done for to the species level. However, the use of DNA sequence five different nuclear loci (Hey and Kliman 1993; Kli- data also permits the use of genealogical coalescent man and Hey 1993a; Hilton et al. 1994). Here we report models, which incorporate classical population genetic on patterns of DNA sequence divergence at an addi- parameters (e.g., effective population size and migration tional nine loci. Together these data permit a broad, rate) within a gene tree framework (Hudson 1990), genome-wide assessment of speciation.

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Evolution of mammalian pregnancy and the origin of the decidual stromal cell

Evolution of mammalian pregnancy and the origin of the decidual stromal cell

in the four eyed opossum, Philander opossum, “slightly enlarged fibroblasts which may constitute a primitive decidual reaction” at the localized sites of LE penetration (Enders and Enders, 1969). In Monodelphis during pregnancy as well during the sexual cycle the stroma becomes edematic and cell poor (Wick and Kress, 2002) and the dense layer of sub-epithelial fibroblast cells essentially disappears (K. Kin and G.P. Wagner, in preparation). Endometrial fibroblasts do exist in marsupials but do not seem to play an im- portant role in the fetal-maternal interface. In contrast, ancestrally in eutherians, the conceptus first establishes contact with the LE and breaches the LE and then establishes a new contact with en- dometrial stromal cells. The novel interface between the conceptus and the mother is formed by a specialized stromal cell type, the decidual cell, discussed below. An apparent exception in a non- mammalian species is the African lizard Trachylepis ivensi where trophoblast cells penetrate the LE and undermine the LE leading to the complete erosion of LE (Blackburn and Flemming, 2012). Based on this histology a direct contact between trophoblast and the connective tissue that separates the LE from the myometrium seems possible, but the trophoblast remains separated from the maternal tissue by the basal membrane of the LE (Blackburn, personal communication). No decidua-like reaction is observed.

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Fire disturbance favours exotic species at Kaituna Wetland, Bay of Plenty

Fire disturbance favours exotic species at Kaituna Wetland, Bay of Plenty

The fire reduced the native species richness count as compared to the exotic species (Fig. 3). At 48 months: the exotic species numbers in the burnt area (14) was 140% of the comparative unburnt plots (10); the native species numbers in the burnt area (10) was 56% of the comparative unburnt plots (18). Species richness, evenness and diversity of native species origin, and total live foliage cover (sum of cover over all height classes) showed significant interactions between the fire treatment (burnt and unburnt areas) and time (Table 1). Mean species richness (± standard error) in the burnt quadrats increased by 2 ± 0.35, and 5.17 ± 0.41 for native and exotic species respectively, whereas there was little change in mean species richness within the unburnt quadrats. Evenness and diversity of exotics showed a statistically significant interaction between the fire treatment and time. Mean evenness in the burnt quadrats decreased for both native and exotic species, whereas the decrease in mean evenness within the unburnt quadrats was minimal. Mean diversity (± standard error)

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The Avian-Origin PB1 Gene Segment Facilitated Replication and Transmissibility of the H3N2/1968 Pandemic Influenza Virus

The Avian-Origin PB1 Gene Segment Facilitated Replication and Transmissibility of the H3N2/1968 Pandemic Influenza Virus

Avian PB1 facilitates replication and transmission of the re- assortant human viruses. The recombinant viruses of each pair showed similar replication kinetics in Calu-3 cells, a continuous FIG 1 Modeling of the gene reassortment event which led to the emergence of the 1968 pandemic influenza virus. (a) Genesis of the pandemic virus. An avian-origin H3 subtype virus (H3N?-Av) reassorted with a seasonal human H2N2 virus in undefined host species, producing the H3N2 reassortant virus with HA and PB1 gene segments from the avian parent (red) and the remaining 6 gene segments from the human parent (blue). This virus could have circulated in mammals for 1 to 2 years (4) before it caused the 1968 pandemic (H3N2/1968). (b) Phylogenetic tree of concatenated nucleotide sequences of 6 gene segments (PB2, PA, NP, NA, M, and NS) of human influenza viruses which circulated in 1965 to 1968. Blue branches represent seasonal human H2N2 viruses; the red branch represents pandemic H3N2 viruses isolated in 1968. Blue and red dots depict virus strains A/California/1/66 (H2N2) and A/Hong Kong/1/68 (H3N2), which were used in this study as donors of human and avian gene segments, respectively. (c) Two pairs of recombinant viruses prepared to study effects of the PB1 segment on viral replication. Viruses of each pair differed by the origin of PB1 and shared either 7 gene segments of Cal (PB1 pair) or 6 gene segments of Cal and the HA gene segment of HK (HA ⫹ PB1 pair).

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The origin and evolution of the nervous system

The origin and evolution of the nervous system

As pointed out recently, the progressive reinforcement and stabilization of developmental processes will buffer the individual from the effect of mutation, and the population as a whole may therefore carry more genetic variation (Kirschner and Gerhart, 1998). Populations with a wider polymorphism may diversify faster under selective conditions, thus improving the «evolvability» of the species, and the success of its genome. This potential for rapid diversification would of course be particularly advantageous during the extensive radiations that followed massive extinctions. The rule of conservative changes puts the emphasis on nega- tive selection - screening for the adaptation of each new element to all other elements with which it interacts, and removing any change that alters the pattern of interactions (and thereby the developmental programme). This view is complementary to the more usual view of evolution as based on positive selection - selection for the fittest. While the latter focuses on the interaction of the individual with the external world, the former focuses on the adaptation of individual gene products to the internal world. Given that all internal interactions are optimized in any given species (for, if they were not, positive selection would quickly ensure that they are), it follows that any non-conservative change will be detrimental and can only be, at best, tolerated (Garcia-Bellido, 2000).

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Commercially Important Marine Mollusks for Human Consumption in Acapulco, México

Commercially Important Marine Mollusks for Human Consumption in Acapulco, México

Acapulco, offers for international tourism a variety of mollusks that are delightful to the palate and a source of eco- nomic revenue for its residents; however there are no studies on the species consumed. Furthermore, data from the State agencies responsible for registration of these products are unclear. This work is aimed to develop an inventory of Gas- tropoda, Bivalvia and Polyplacophora marketed as food, to gain knowledge on the species native to Acapulco and the introduced ones. The places that sell shellfish were interviewed from 2008 to 2011 in order to determine the geographi- cal origin of their products being offered. We identified 42 species: 15 species of gastropods are captured locally and three are introduced. On Bivalvia, seven species are caught locally and 16 are introduced. There are Bivalvia species caught locally; however, their capture is now unaffordable. It is likely that this situation is due to overfishing and/or the transmission of diseases or parasites caused by the introduction of foreign living organisms to Acapulco. Within the list of species caught locally, there are some listed as of subject protection; all of these organisms are exploited in Acapulco without control. The wealth of marine mollusks for human consumption in Acapulco is very high. The capture does not satisfy local market demand and the amount of introduced species is very high. It is necessary to make a diagnostic analysis of mollusk fishing industry in the state of Guerrero, also implement a management program, including the sanitary measures and control of introduced species, as they arrive alive and stay alive in the waters of Acapulco. A significant number of native species that have aquaculture potential should be studied for commercial culture practice as well as to conduct studies on their biology on those species that are considered over-exploited and allow recovery of the species in its habitat.

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The discursive configuration, from the word to the image: Duality of Rufino Tamayo and the origin of art

The discursive configuration, from the word to the image: Duality of Rufino Tamayo and the origin of art

From our prospective, the work of the Mexican painter connects contemporary art with prehistoric art because its plastic expression is the bridge that unites primitive man with a modern man. García Ponce refers to the spaces where Tamayo's themes are developed and says that these are worlds of stone that he creates from painting. We consider that in his analysis, García Ponce, matches the work of Tamayo with the plastic expression of Lascaux because, using the proposal of Georges Bataille about ugliness, both expressions manifest, paradoxically, their beauty by the apparent ugliness of their contents. The grotesque acquires in both its aesthetic splendor. According to García Ponce: “all these paintings are surprising with their beauty coming out of an apparent ugliness, they give us the sensation of being entering a new world” (García Ponce, 2002, page 171). In this sense, Tamayo leads us to the birth of art and the origin of the plastic expression in which man confronts the world and is surprised by it. This is the same meaning that Georges Bataille and Maurice Blanchot give to Lascaux.

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The role of plant species and soil condition in the structural development of the rhizosphere

The role of plant species and soil condition in the structural development of the rhizosphere

Plant roots donate carbon to encourage the development of beneficial populations of microbes in the rhizosphere. For example, phosphate ‐ solubilizing microorganisms can mobilize previously inaccessi- ble pools of this important nutrient for plants (Wang, Shi, Jiang, Zhang, & Feng, 2016). Microorganisms growing on the root surface contribute to the disruption of soil structure at the root surface that can aid aeration and the pathway for nutrient and water delivery to the root surface (Helliwell et al., 2014). Our finding that the extent of this root surface phenomenon, the zone of influence, differs between species and depends on soil type and density (Figures 6 and 7) is worthy of further investiga- tion. For example, pea showed more sensitivity to the soil type when compared with wheat and tomato at higher bulk density (Figures 6c,d). In the thicker pea roots (Figure 5), the production of specialized exudates particularly rich in hydroxyproline ‐ rich cell wall glycoprotein when compared with cereals (Knee et al., 2001) may be depend on soil type. There may be the potential to improve this trait in future crop breeding programmes by manipulating root exudate composition. In addition, the considerable differences in root ‐ induced structure around and away from the root surface and the varied response to soil texture and bulk density highlight the needs for plants breeders to undertake studies under more natural conditions when screening for beneficial root traits.

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Serological survey of Australian native reptiles for exposure to ranavirus

Serological survey of Australian native reptiles for exposure to ranavirus

The measurable antibody response in sera from reptiles challenged with BIV was highly variable in this study. A proportion of Emydura macquarii krefftii turtles sero-converted after 1 intracoelomic exposure, while other individuals failed to convert after a single or repeated injections. None of the Myuchelys latis- ternum turtles, 3 species of snakes and freshwater crocodiles produced a detectable antibody response to IC exposure in this study, while sera from all 3 Tropidonophis mairii snakes exposed per os had an increase in titre over the course of the experiment. None of the experimental animals discussed here showed clinical signs or evidence of an infection dur- ing post mortem investigation (Ariel et al. 2015).

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On the origin of the tensile strength of insect swarms

On the origin of the tensile strength of insect swarms

Figure 1. Theoretical predictions for swarm density profiles match data from numerical simulations. The swarms are being pulled away from their respective swarm markers (dashed-lines) and displaced towards the origin. The swarms therefore appear in tension with a tensile strength that increases as centre-of-mass movements increase. Predictions (solid line) obtained from equation (12) are shown for a = 0.8, b = 0.1 and B 0 = 1 with B 1 = 0.1 (left), 0.3 (middle) and 0.5 (right). Simulation data (●) were obtained from

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On the origin of amniotic stem cells: of mice and men

On the origin of amniotic stem cells: of mice and men

ABSTRACT A common characteristic of mammals is the development of extraembryonic supporting tissues and organs that are required for embryonic implantation, survival and development in utero. The amnion is the innermost extraembryonic membrane that eventually surrounds the fetus of amniotes, and contains the amniotic fluid. Next to its function in in utero development, the amnion has been shown to have an important potential for clinical applications. It is mainly used as a dressing to stimulate healing in skin and ocular wounds. Moreover, cells derived from the amniotic membrane and amniotic fluid have been reported to possess stem cell features, like pluripotent differentiation ability. Little is known about the early development of this membrane in humans. The mouse is a powerful genetic model organism that can be used to address the dynamics and the developmental origin of amnion and amnion-derived stem cells. Here, we discuss some fundamental differences in amnion development in the disc-shaped primate embryo and in the cup-shaped mouse embryo. We emphasize the consequences that this may have on the derivation of amniotic "stem" cells. After revision of the different isolation procedures of amniotic (fluid) derived "stem" cells from rodents, we reveal striking differences in the sources used to derive these cells across studies. The profound differences in the development of the extraembryonic membranes and cavities between primates and rodents may result in comparing cell types of different developmental origins, eventually leading to missinterpretations.

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Biological activity is the likely origin of the intersection between the photoreceptor inner and outer segments of the rat retina as determined by optical coherence tomography

Biological activity is the likely origin of the intersection between the photoreceptor inner and outer segments of the rat retina as determined by optical coherence tomography

Background: Recent research on macular diseases has prompted investigations into the condition of the intersection between the photoreceptor inner and outer segments (IS/OS) and the relationship with retinal photoreceptor abnormalities. Although the origin of the IS/OS in optical coherence tomography (OCT) images is unclear, it may be related to either the cellular activity of the photoreceptors or the structure of the OS disks. To address this question, we compared the IS/OS status in OCT images of rat retinas before and after euthanasia.

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Revisiting old vaginal topics: conversion of the Müllerian vagina and origin of the "sinus" vagina

Revisiting old vaginal topics: conversion of the Müllerian vagina and origin of the "sinus" vagina

The caudal vaginal primordium remains solid until the onset of sexual maturity. The origin of vaginal epithelium thus becomes a major concern. As discussed, solid evidence refutes the conven- tional concept that the urogenital sinus epithelium ascends to participate in vaginal organogenesis. Thus, a question arises if the solid vaginal primordium is able to generate the epithelium by itself. The EMT can revert to generate the epithelium through the mesenchymal-epithelial transition (MET), which is crucial for ver- tebrate organogenesis. BMP4 expression is reduced in the uro- genital sinus with gestation (Kuslak and Marker, 2007), indicating that its ability of EMT induction declines. On the other hand, Wnt4 is expressed in the vaginal primordium, and can be up-regulated by the estrogen (Hou et al., 2004). One of key roles of Wnt4 in organogenesis is induction of the MET. Wnt4 positively regulates Rac1 and JNK pathways, which are involved in the MET (Osafune et al., 2006). It is shown that Wnt4 is involved in epithelial genera- tion in some mesoderm-derived organs, such as the kidney and the Müllerian duct derivatives. 1) Wnt4 is absolutely required for epithelialization in kidney development (Stark et al., 1994, Kispert et al., 1998). In Wnt4-deficient mice, the metanephric mesen- chyma never enters the MET (Stark et al., 1994). 2) Wnt4 is also essential for formation of the Müllerian duct. Wnt4-null animals lack the Müllerian duct (Vainio et al., 1999). Adult vagina expresses Wnt4 in the epithelium only (Miller et al., 1998). Therefore, vaginal epithelium can be generated through Wnt4-induced MET (Fig. 2B).

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The origin and evolution of appendages

The origin and evolution of appendages

In this paper I will not attempt to review the bulky, and precious, recent literature on the developmental genetics of the few model systems investigated thus far. I will outline, instead, a few points I regard as critical for an understanding of the origin of appendages, in both developmental and evolutionary terms. I will start with a few remarks on the diversity of metazoan body appendages. I will then discuss a few questions of ontog- eny; in particular, how appendages are developmentally re- lated to the main body axis, how the different germ layers contribute to the production of the appendages, and whether the notion of gene co-option may be relevant to an understand- ing of the origin of appendages. The latter point will lead us straight to the evolutionary aspects of our enquiry. Here, two main points will be discussed: whether we can legitimately imagine that the common ancestor of all triploblastic animals, the Urbilateria, was already provided with appendages from which those of all modern animals should have been derived, and whether we can legitimately search for a ‘default’ ancestral kind of appendage in those animals, like insects, which are endowed with several different kinds of specialized append- ages such as antennae, mandibles, and legs.

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ENDOS ” shall be considered as the existence of Human race and other plants and

ENDOS ” shall be considered as the existence of Human race and other plants and

It is hypothesized that the philosophy of mari language might be derived from the philosophy of “Thai-e” language family of “MARUTHAI” origin. Mari shall be considered as “family name” of “mari-e” population of MARUTHAI. Further Mari is a feminine name in the Breton, Japanese, Estonian, Hungarian, Finnish welsh, Swedish, and Norweigian languages such as “mari akasaka”, “mari amachi”, “marikodama” etc.

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