scholarly journals Evolutionary Spread and Recombination of Porcine Endogenous Retroviruses in the Suiformes

2005 ◽  
Vol 79 (1) ◽  
pp. 649-654 ◽  
Author(s):  
Marcus Niebert ◽  
Ralf R. Tönjes
Keyword(s):  
Long Terminal Repeat ◽  
Related Species ◽  
Sus Scrofa ◽  
Endogenous Retroviruses ◽  
Phylogenetic Distance ◽  
African Origin ◽  
Closely Related Species ◽  
Separate Event ◽  
Porcine Endogenous Retroviruses ◽  
The Common

ABSTRACT Different Suiformes with increasing phylogenetic distance to the common pig (Sus scrofa) were assayed for the presence of porcine endogenous retroviruses (PERV) in general (pol gene), while the distribution of long terminal repeat (LTR) types (with or without repeats in U3) and env genes (classes A, B, and C) were determined in detail. PERV was not detectable in the most distantly related species, while classes PERV-A and PERV-B are present in Suiformes originating in the Pliocene epoch, and class PERV-C was detectable only in S. scrofa and in closely related species originating in the Holocene epoch. This distribution pattern of PERV classes is in line with our previous study on the age of PERV (45) and suggests an African origin of about 7.5 million years ago (MYA) and a gradual spread of PERV through the Suiformes. It seems likely that PERV-C originated more recently (1.5 to 3.5 MYA) by recombination with a homologue of unknown descent, while the origin of the repeatless LTR was a separate event approximately 3.5 MYA.

scholarly journals Comparative transcriptomics of the venoms of continental and insular radiations of West African cones

2020 ◽  
Vol 287 (1929) ◽  
pp. 20200794
Author(s):  
Samuel Abalde ◽  
Manuel J. Tenorio ◽  
Carlos M. L. Afonso ◽  
Rafael Zardoya
Keyword(s):  
Related Species ◽  
Common Ancestor ◽  
West African ◽  
Generic Level ◽  
Closely Related Species ◽  
Functional Convergence ◽  
Venom Glands ◽  
Phylogenetic Framework ◽  
The Common ◽  
Secreted Peptides

The transcriptomes of the venom glands of 13 closely related species of vermivorous cones endemic to West Africa from genera Africonus and Varioconus were sequenced and venom repertoires compared within a phylogenetic framework using one Kalloconus species as outgroup. The total number of conotoxin precursors per species varied between 108 and 221. Individuals of the same species shared about one-fourth of the total conotoxin precursors. The number of common sequences was drastically reduced in the pairwise comparisons between closely related species, and the phylogenetical signal was totally eroded at the inter-generic level (no sequence was identified as shared derived), due to the intrinsic high variability of these secreted peptides. A common set of four conotoxin precursor superfamilies (T, O1, O2 and M) was expanded in all studied cone species, and thus, they are considered the basic venom toolkit for hunting and defense in the West African vermivorous cone snails. Maximum-likelihood ancestral character reconstructions inferred shared conotoxin precursors preferentially at internal nodes close to the tips of the phylogeny (between individuals and between closely related species) as well as in the common ancestor of Varioconus . Besides the common toolkit, the two genera showed significantly distinct catalogues of conotoxin precursors in terms of type of superfamilies present and the abundance of members per superfamily, but had similar relative expression levels indicating functional convergence. Differential expression comparisons between vermivorous and piscivorous cones highlighted the importance of the A and S superfamilies for fish hunting and defense.

scholarly journals Parallel evolution of metazoan mitochondrial proteins

2016 ◽  
Author(s):  
Galya V. Klink ◽  
Georgii A. Bazykin
Keyword(s):  
Amino Acid ◽  
Related Species ◽  
Parallel Evolution ◽  
Phylogenetic Reconstruction ◽  
Acid Sites ◽  
Mitochondrial Proteins ◽  
Phylogenetic Distance ◽  
Closely Related Species ◽  
Epistatic Interactions ◽  
The Mean

AbstractAmino acid propensities at amino acid sites change with time due to epistatic interactions or changing environment, affecting the probabilities of fixation of different amino acids. Such changes should lead to an increased rate of homoplasies (reversals, parallelisms, and convergences) at closely related species. Here, we reconstruct the phylogeny of twelve mitochondrial proteins from several thousand metazoan species, and measure the phylogenetic distances between branches at which either the same allele originated repeatedly due to homoplasies, or different alleles originated due to divergent substitutions. The mean phylogenetic distance between parallel substitutions is ∼20% lower than the mean phylogenetic distance between divergent substitutions, indicating that a variant fixed in a species is more likely to be deleterious in a more phylogenetically remote species, compared to a more closely related species. These findings are robust to artefacts of phylogenetic reconstruction or of pooling of sites from different conservation classes or functional groups, and imply that single-position fitness landscapes change at rates similar to rates of amino acid changes.

scholarly journals Relative Age of Proviral Porcine Endogenous Retrovirus Sequences in Sus scrofa Based on the Molecular Clock Hypothesis

2003 ◽  
Vol 77 (22) ◽  
pp. 12363-12368 ◽  
Author(s):  
Ralf R. Tönjes ◽  
Marcus Niebert
Keyword(s):  
Sus Scrofa ◽  
Endogenous Retrovirus ◽  
Endogenous Retroviruses ◽  
Relative Age ◽  
Repeat Structure ◽  
Porcine Endogenous Retrovirus ◽  
Porcine Endogenous Retroviruses ◽  
Different Types ◽  
Pecari Tajacu ◽  
Recent Origin

ABSTRACT Porcine endogenous retroviruses (PERV) are discussed as putative infectious agents in xenotransplantation. PERV classes A, B, and C harbor different envelope proteins. Two different types of long terminal repeat (LTR) structures exist, of which both are present only in PERV-A. One type of LTR contains a distinct repeat structure in U3, while the other is repeatless, conferring a lower level of transcriptional activity. Since the different LTR structures are distributed unequally among the proviruses and, apparently, PERV is the only virus harboring two different LTR structures, we were interested in determining which LTR is the ancestor. Replication-competent viruses can still be found today, suggesting an evolutionary recent origin. Our studies revealed that the age of PERV is at most 7.6 × 106 years, whereas the repeatless LTR type evolved approximately 3.4 × 106 years ago, being the phylogenetically younger structure. The age determined for PERV correlates with the time of separation between pigs (Suidae, Sus scrofa) and their closest relatives, American-born peccaries (Tayassuidae, Pecari tajacu), 7.4 × 106 years ago.

scholarly journals Temporal niche partitioning of Swiss black scavenger flies in relation to season and substrate age (Diptera, Sepsidae)

2019 ◽  
Vol 3 ◽  
pp. 1-10 ◽  
Author(s):  
Patrick T. Rohner ◽  
Jean-Paul Haenni ◽  
Athene Giesen ◽  
Juan Pablo Busso ◽  
Martin A. Schäfer ◽  
...  
Keyword(s):  
Related Species ◽  
Species Coexistence ◽  
Species Turnover ◽  
Niche Partitioning ◽  
Temporal Distribution ◽  
Niche Differentiation ◽  
Ecological Niches ◽  
Phylogenetic Distance ◽  
Closely Related Species ◽  
Temporal Niche

Understanding why and how multiple species manage to coexist represents a primary goal of ecological and evolutionary research. This is of particular relevance for communities that depend on resource rich ephemeral habitats that are prone to high intra- and interspecific competition. Black scavenger flies (Diptera: Sepsidae) are common and abundant acalyptrate flies associated with livestock dung decomposition in human-influenced agricultural grasslands worldwide. Several widespread sepsid species with apparently very similar ecological niches coexist in Europe, but despite their ecological role and their use in evolutionary ecological research, our understanding of their ecological niches and spatio-temporal distribution is still rudimentary. To gain a better understanding of their ecology, we here investigate niche partitioning at two temporal scales. First, we monitored the seasonal occurrence, often related to thermal preference, over multiple years and sites in Switzerland that differ in altitude. Secondly, we also investigate fine-scale temporal succession on dairy cow pastures. In accordance with their altitudinal and latitudinal distribution in Europe, some species were common over the entire season with a peak in summer, hence classified as warm-loving, whereas others were primarily present in spring or autumn. Phenological differences thus likely contribute to species coexistence throughout the season. However, the community also showed pronounced species turnover related to cow pat age. Some species colonize particularly fresh dung and are gradually replaced by others. Furthermore, the correlation between co-occurrence and phylogenetic distance of species revealed significant under-dispersion, indicating that more closely related species are frequently recovered at the same location. As a whole, our data suggests temporal niche differentiation of closely related species that likely facilitates the rather high species diversity on Swiss cattle pastures. The underlying mechanisms allowing close relatives to co-occur however require further scrutiny.

Notes on Indian Neolitsea (Lauraceae)—two new varietal combinations under N. cassia and N. foliosa and typification of five names

Phytotaxa ◽  
2019 ◽  
Vol 419 (2) ◽  
pp. 209-214
Author(s):  
TAPAS CHAKRABARTY
Keyword(s):  
Related Species ◽  
Closely Related Species ◽  
The Common ◽  
Terminal Buds ◽  
Distinct Variety

During the course of revision of the genus Neolitsea (Bentham 1880: 161) Merrill (1906: 56) for India and adjoining countries it was found that N. foliosa (Nees 1831: 64) Gamble (1925a: 1240) and N. cassia (Linnaeus 1753: 369) Kostermans (1952: 85) are two closely related species, the former differing from the latter “by having much broader, coriaceous leaves with a pronounced areolation, the completely glabrous terminal buds and branches, and the glabrous outer bud scales of the flower umbels.” (Kostermans 1995: 169). Further, both these species have two types of fruits, mostly globose to subglobose but occasionally oblong, oblong-ellipsoid to ovoid-oblong. The present study revealed that these two forms of fruits merit recognition as distinct varieties in each species, having no intergradations. The variety of N. cassia, characterized by such oblong fruits has been described previously as Litsea zeylanica (Nees & T. Nees 1823: 58, pl. 5) var. rigescens Meissner (1864: 226), which therefore is transferred to N. cassia here with designation of a lectotype. In N. foliosa, an isolectotype (G00694474: image!) bears oblong to oblong-ellipsoid fruits but the common form with globose to subglobose fruits has been described previously as Litsea scrobiculata (Meissner 1864: 223), treated in Indian Floras (e.g. Gamble 1925a, Saldanha & Ramesh 1984, Vajravelu 1990, Mohanan & Henry 1994) as Neolitsea scrobiculata (Meisn.) Gamble (1925a: 1240), eventually reduced to a synonym of N. foliosa by Kostermans (1995: 168–169). Hence Litsea scrobiculata is reinstated here and treated as a distinct variety of N. foliosa with designation of a lecotype. Furthermore, lectotypes are also designated for the names Tetradenia foliosa Nees (1831: 64), basionym of Neolitsea foliosa, N. fischeri Gamble (1925b: 132) and Tetradenia umbrosa Nees (1831: 64), basionym of Neolitsea umbrosa (Nees) Gamble (1914: 79).

Studies on the Life History of Brachylaimus oesophagei Shaldybin, 1953 (Digenea: Brachylaimidae)

1969 ◽  
Vol 43 (1-2) ◽  
pp. 79-98 ◽  
Author(s):  
J. W. Lewis
Keyword(s):  
Life History ◽  
Digestive Gland ◽  
Related Species ◽  
Life Histories ◽  
Common Shrew ◽  
Sorex Araneus ◽  
Morphological Features ◽  
Closely Related Species ◽  
History Of ◽  
The Common

1. Brachylaimus oesophagei Shaldybin, 1953 from the common shrew, Sorex araneus castaneus Jenyns is described and compared with that of Shaldybin (1953) and a closely related species B. fulvus Dujardin, 1843.2. Despite unsuccessful attempts in hatching the egg of B. oesophagei, some morphological features of the miracidium are described and compared with previous studies on brachylaimid miracidia. Neither flame cells nor epidermal plates have been observed in miracidia of this family and present observations confirm this.3. A description is given of the cercaria and metacercaria of B. oesophagei from the kidney of the hollowed snail Zonitoides excavatus (Bean) at Aberystwyth, but no sporocysts or cercariae were found in the digestive gland.4. Previous work on brachylaimid life histories is discussed, together with a resumé of the life history of B. oesophagei.

scholarly journals Antagonism correlates with metabolic similarity in diverse bacteria

2017 ◽  
Vol 114 (40) ◽  
pp. 10684-10688 ◽  
Author(s):  
Jakob Russel ◽  
Henriette L. Røder ◽  
Jonas S. Madsen ◽  
Mette Burmølle ◽  
Søren J. Sørensen
Keyword(s):  
Related Species ◽  
Metabolic Networks ◽  
Resource Competition ◽  
Bacterial Species ◽  
Carbon Sources ◽  
Similar Species ◽  
Phylogenetic Distance ◽  
Closely Related Species ◽  
Origin Of Species ◽  
Natural Carbon

In the Origin of Species, Charles R. Darwin [Darwin C (1859) On the Origin of Species] proposed that the struggle for existence must be most intense among closely related species by means of their functional similarity. It has been hypothesized that this similarity, which results in resource competition, is the driver of the evolution of antagonism among bacteria. Consequently, antagonism should mostly be prevalent among phylogenetically and metabolically similar species. We tested the hypothesis by screening for antagonism among all possible pairwise interactions between 67 bacterial species from 8 different environments: 2,211 pairs of species and 4,422 interactions. We found a clear association between antagonism and phylogenetic distance, antagonism being most likely among closely related species. We determined two metabolic distances between our strains: one by scoring their growth on various natural carbon sources and the other by creating metabolic networks of predicted genomes. For both metabolic distances, we found that the probability of antagonism increased the more metabolically similar the strains were. Moreover, our results were not compounded by whether the antagonism was between sympatric or allopatric strains. Intriguingly, for each interaction the antagonizing strain was more likely to have a wider metabolic niche than the antagonized strain: that is, larger metabolic networks and growth on more carbon sources. This indicates an association between an antagonistic and a generalist strategy.

Postovipositional maternal care in the burrower bug, Adomerus rotundus (Hemiptera: Cydnidae)

2014 ◽  
Vol 146 (2) ◽  
pp. 211-218 ◽  
Author(s):  
Kouichi Inadomi ◽  
Maiko Wakiyama ◽  
Mantaro Hironaka ◽  
Hiromi Mukai ◽  
Lisa Filippi ◽  
...  
Keyword(s):  
Related Species ◽  
Maternal Care ◽  
Egg Production ◽  
Common Ancestor ◽  
Japanese Species ◽  
Closely Related Species ◽  
Egg Hatch ◽  
Additional Information ◽  
The Third ◽  
The Common

AbstractComplex subsociality involving guarding, progressive provisioning, and trophic egg production behaviours in herbivorous Hemiptera is known in only a few genera in the Cydnidae subfamily Sehirinae and in Parastrachiidae. Because progressive provisioning and trophic egg production are apparently specific to these closely related species, phylogenetically it seems likely that the behaviours emerged once in the common ancestor of this clade. However, the scarcity of information on species in the clade precludes any reliable exploration of this hypothesis. To ameliorate this situation, it is necessary to accumulate additional information for as many related species as possible. To this end, we first targeted Japanese representatives of the genus Adomerus Mulsant and Rey (Hemiptera: Cydnidae), three species of which are distributed in Japan. Complex subsocial behaviours in two of these species, Adomerus triguttulus (Motschulsky) and Adomerus variegatus (Signoret), have been well characterised and analysed. The third Japanese species, Adomerus rotundus (Hsiao), was identified to display complex maternal care, but, with the exception of egg hatch synchronisation, parental behaviours have not been characterised. In this study, we examined the parental behaviours of A. rotundus. Additional investigations on subsocial behaviours, in addition to morphological and molecular analyses, should gradually clarify whether the complex subsociality represents a homologous or convergent adaptation.

scholarly journals Description of Poecilia (Acanthophacelus) wingei n. sp. from the Paría Peninsula, Venezuela, including notes on Acanthophacelus Eigenmann, 1907 and other subgenera of Poecilia Bloch and Schneider, 1801 (Teleostei, Cyprinodontiformes, Poeciliidae)

2005 ◽  
Vol 74 (1-2) ◽  
pp. 97-115 ◽  
Author(s):  
Fred. N. Poeser ◽  
Michael Kempkes ◽  
Isaäc J. H. Isbrücker
Keyword(s):  
New Species ◽  
Related Species ◽  
Poecilia Reticulata ◽  
Character Displacement ◽  
Molecular Data ◽  
Shared Environment ◽  
Closely Related Species ◽  
The Andes ◽  
The Common

The taxonomy of the common guppy, Poecilia reticulata Peters, 1859, is reviewed and the closely related Campoma guppy, P. wingei n. sp., is described. Formerly, the common guppy was not judged to be closely related to any other species of Poecilia, but the new species is the second species to be allocated in the subgenus Acanthophacelus Eigenmann, 1907. The recognition of P. wingei results from observed character displacement, i.e., on the interaction between two closely related species in a shared environment. In addition to differences in coloration, behaviour also indicates specific differences. The area in which P. wingei occurs, the Campoma region at the base of the Paría Peninsula in Venezuela, hints to an origin of the subgenus Acanthophacelus prior to the uplift of the Cordilleras, i.e., the eastern orogenesis of the Andes. Moreover, an explanation is offered for aberrant molecular data in Trinidadian guppies.

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