scholarly journals Evidence from molecules and morphology expands Podonomopsis Brundin (Diptera : Chironomidae : Podonominae) to include ‘genus Chile'

2015 ◽  
Vol 29 (6) ◽  
pp. 610 ◽  
Author(s):  
Peter S. Cranston ◽  
Matt Krosch

The informal taxon ‘genus Chile’ of Brundin, based solely on pupal exuviae of a podonomine Chironomidae, has remained inadequately known for half a century. New collections reveal life associations, and provide molecular data to hypothesise a precise phylogenetic placement in the austral Podonominae. A densely sampled molecular phylogeny based on two nuclear and one mitochondrial DNA markers shows ‘genus Chile’ to be the sister group to Podonomopsis Brundin, 1966. Within Podonomopsis a clade of South American species is sister to all Australian species. We discuss how to rank such a sister group taxon and treat ‘genus Chile’ as a new subgenus Araucanopsis, subg. nov. with the new species, Podonomopsis (Araucanopsis) avelasse, sp. nov. from Chile and Argentina as genotype of the monotypic subgenus. We describe P. (A.) avelasse in all stages and provide an expanded diagnosis and description of Podonomopsis to include Araucanopsis. A dated biogeographic hypothesis (chronogram) infers the most recent common ancestor (tmcra) of expanded Podonomopsis at 95 million years ago (Mya) (68–122 Mya 95% highest posterior density), ‘core’ Podonomopsis at 83 Mya (58–108) and Australian Podonomopsis at 65 Mya (44–87). All dates are before the South America–Australia geological separation through Antarctica, supporting previous conclusions that the taxon distribution is ‘Gondwanan’ in origin. Podonomopsis, even as expanded here, remains unknown from New Zealand or elsewhere on extant Zealandia. http://zoobank.org/urn:lsid:zoobank.org:act:B242009B-0CEF-41CA-8C78-17B9D3B57025

Author(s):  
Wenjun Cheng ◽  
Tianjiao Ji ◽  
Shuaifeng Zhou ◽  
Yong Shi ◽  
Lili Jiang ◽  
...  

AbstractEchovirus 6 (E6) is associated with various clinical diseases and is frequently detected in environmental sewage. Despite its high prevalence in humans and the environment, little is known about its molecular phylogeography in mainland China. In this study, 114 of 21,539 (0.53%) clinical specimens from hand, foot, and mouth disease (HFMD) cases collected between 2007 and 2018 were positive for E6. The complete VP1 sequences of 87 representative E6 strains, including 24 strains from this study, were used to investigate the evolutionary genetic characteristics and geographical spread of E6 strains. Phylogenetic analysis based on VP1 nucleotide sequence divergence showed that, globally, E6 strains can be grouped into six genotypes, designated A to F. Chinese E6 strains collected between 1988 and 2018 were found to belong to genotypes C, E, and F, with genotype F being predominant from 2007 to 2018. There was no significant difference in the geographical distribution of each genotype. The evolutionary rate of E6 was estimated to be 3.631 × 10-3 substitutions site-1 year-1 (95% highest posterior density [HPD]: 3.2406 × 10-3-4.031 × 10-3 substitutions site-1 year-1) by Bayesian MCMC analysis. The most recent common ancestor of the E6 genotypes was traced back to 1863, whereas their common ancestor in China was traced back to around 1962. A small genetic shift was detected in the Chinese E6 population size in 2009 according to Bayesian skyline analysis, which indicated that there might have been an epidemic around that year.


2016 ◽  
Vol 61 (3) ◽  
Author(s):  
Andreas F. Wendel ◽  
Martin Kaase ◽  
Ingo B. Autenrieth ◽  
Silke Peter ◽  
Philipp Oberhettinger ◽  
...  

ABSTRACT The metallo-beta-lactamase GIM-1 has been found in various bacterial host species nearly exclusively in western Germany. However, not much is known about the epidemiology of GIM-1-positive Serratia marcescens. Here we report on a surprisingly protracted regional dissemination. In-hospital transmission was investigated by using conventional epidemiological tools to identify spatiotemporal links. Strain typing was performed using pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS). Bayesian phylogeny was used to infer the time axis of the observed occurrence. Thirteen S. marcescens strains from 10 patients from 6 different German hospitals were investigated. Suspected in-hospital transmissions were confirmed by molecular typing at a higher resolution by WGS than by PFGE. A detailed sequence analysis demonstrated the spread of one predominant strain variant but also provided evidence for transfer of the bla GIM-1 gene cassette between different strains. A Bayesian phylogenetic analysis showed that the most recent common ancestor of the identified clonal cluster could be dated back to April 1993 (95% highest posterior density interval, January 1973 to March 2003) and that this strain might have already harbored the bla GIM-1 at that time and, therewith, years before the first detection of this resistance gene in clinical specimens. This study shows a long-standing clonal and plasmid-mediated expansion of GIM-1-producing S. marcescens that might have gone unnoticed in the absence of a standardized and effective molecular screening for carbapenemases. The systematic and early detection of resistance is thus highly advisable, especially for the prevention of potentially long-term dissemination that may progress beyond control.


PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3844 ◽  
Author(s):  
Cara Van Der Wal ◽  
Shane T. Ahyong ◽  
Simon Y.W. Ho ◽  
Nathan Lo

The crustacean order Stomatopoda comprises seven superfamilies of mantis shrimps, found in coastal waters of the tropics and subtropics. These marine carnivores bear notable raptorial appendages for smashing or spearing prey. We investigated the evolutionary relationships among stomatopods using phylogenetic analyses of three mitochondrial and two nuclear markers. Our analyses recovered the superfamily Gonodactyloidea as polyphyletic, withHemisquillaas the sister group to all other extant stomatopods. A relaxed molecular clock, calibrated by seven fossil-based age constraints, was used to date the origin and major diversification events of stomatopods. Our estimates suggest that crown-group stomatopods (Unipeltata) diverged from their closest crustacean relatives about 340 Ma (95% CRI [401–313 Ma]). We found that the specialized smashing appendage arose after the spearing appendage ∼126 Ma (95% CRI [174–87 Ma]). Ancestral state reconstructions revealed that the most recent common ancestor of extant stomatopods had eyes with six midband rows of hexagonal ommatidia. Hexagonal ommatidia are interpreted as plesiomorphic in stomatopods, and this is consistent with the malacostracan ground-plan. Our study provides insight into the evolutionary timescale and systematics of Stomatopoda, although further work is required to resolve with confidence the phylogenetic relationships among its superfamilies.


Author(s):  
María B Pisano ◽  
Andrés C A Culasso ◽  
Nancy Altabert ◽  
Maribel G Martínez Wassaf ◽  
Silvia V Nates ◽  
...  

Abstract Background Few studies about the evolutionary history of the hepatitis E virus (HEV) have been conducted. The aim of our work was to investigate and make inferences about the origin and routes of dispersion of HEV-3 in Argentina. Methods Phylogenetic, coalescent and phylogeographic analyses were performed using a 322-bp ORF2 genomic fragment of all HEV-3 sequences with known date and place of isolation published at GenBank until May 2018 (n=926), including 16 Argentinian sequences (isolated from pigs, water and humans). Results Phylogenetic analysis revealed two clades within HEV-3: abchij and efg. All Argentinian samples were grouped intermingled within clade 3abchij. The coalescent analysis showed that the most recent common ancestor for the clade 3abchij would have existed around the year 1967 (95% highest posterior density (HPD): 1963–1970). The estimated substitution rate was 1.01×10−2 (95%HPD: 9.3×10ˉ3–1.09×10ˉ2) substitutions/site/y, comparable with the rate previously described. The phylogeographic approach revealed a correspondence between phylogeny and place of origin for Argentinian samples, suggesting many HEV introductions in the country, probably from Europe and Japan. Conclusions This is the first evolutionary inference of HEV-3 that includes Argentinian strains, showing the circulation of many HEV-3 subtypes, obtained from different sources and places, with recent diversification processes. Accession numbers [KX812460], [KX812461], [KX812462], [KX812465], [KX812466], [KX812467], [KX812468], [KX812469].


2003 ◽  
Vol 17 (4) ◽  
pp. 605 ◽  
Author(s):  
Philip S. Ward ◽  
Seán G. Brady

We investigated phylogenetic relationships among the 'primitive' Australian ant genera Myrmecia and Nothomyrmecia (stat. rev.) and the Baltic amber fossil genus Prionomyrmex, using a combination of morphological and molecular data. Outgroups for the analysis included representatives from a variety of potential sister-groups, including five extant subfamilies of ants and one extinct group (Sphecomyrminae). Parsimony analysis of the morphological data provides strong support (~95% bootstrap proportions) for the monophyly of (1) genus Myrmecia, (2) genus Prionomyrmex, and (3) a clade containing those two genera plus Nothomyrmecia. A group comprising Nothomyrmecia and Prionomyrmex is also upheld (85% bootstrap support). Molecular sequence data (~2200 base pairs from the 18S and 28S ribosomal RNA genes) corroborate these findings for extant taxa, with Myrmecia and Nothomyrmecia appearing as sister-groups with ~100% bootstrap support under parsimony, neighbour-joining and maximum-likelihood analyses. Neither the molecular nor the morphological data set allows us to identify unambiguously the sister-group of (Myrmecia + (Nothomyrmecia + Prionomyrmex)). Rather, Myrmecia and relatives are part of an unresolved polytomy that encompasses most of the ant subfamilies. Taken as a whole, our results support the contention that many of the major lineages of ants – including a clade that later came to contain Myrmecia, Nothomyrmecia and Prionomyrmex – arose at around the same time during a bout of diversification in the middle or late Cretaceous. On the basis of Bayesian dating analysis, the estimated age of the most recent common ancestor of Myrmecia and Nothomyrmecia is 74 million years (95% confidence limits, 53–101�million years), a result consistent with the origin of the myrmeciine stem lineage in the Cretaceous. The ant subfamily Myrmeciinae is redefined to contain two tribes, Myrmeciini (genus Myrmecia) and Prionomyrmecini (Nothomyrmecia and Prionomyrmex). Phylogenetic analysis of the enigmatic Argentine fossils Ameghinoia and Polanskiella demonstrates that they are also members of the Myrmeciinae, probably more closely related to Prionomyrmecini than to Myrmeciini. Thus, the myrmeciine ants appear to be a formerly widespread group that retained many ancestral formicid characteristics and that became extinct everywhere except in the Australian region.


Author(s):  
Francisco Díez-Fuertes ◽  
María Iglesias-Caballero ◽  
Sara Monzón ◽  
Pilar Jiménez ◽  
Sarai Varona ◽  
...  

AbstractObjectivesSARS-CoV-2 whole-genome analysis has identified three large clades spreading worldwide, designated G, V and S. This study aims to analyze the diffusion of SARS-CoV-2 in Spain/Europe.MethodsMaximum likelihood phylogenetic and Bayesian phylodynamic analyses have been performed to estimate the most probable temporal and geographic origin of different phylogenetic clusters and the diffusion pathways of SARS-CoV-2.ResultsPhylogenetic analyses of the first 28 SARS-CoV-2 whole genome sequences obtained from patients in Spain revealed that most of them are distributed in G and S clades (13 sequences in each) with the remaining two sequences branching in the V clade. Eleven of the Spanish viruses of the S clade and six of the G clade grouped in two different monophyletic clusters (S-Spain and G-Spain, respectively), with the S-Spain cluster also comprising 8 sequences from 6 other countries from Europe and the Americas. The most recent common ancestor (MRCA) of the SARS-CoV-2 pandemic was estimated in the city of Wuhan, China, around November 24, 2019, with a 95% highest posterior density (HPD) interval from October 30-December 17, 2019. The origin of S-Spain and G-Spain clusters were estimated in Spain around February 14 and 18, 2020, respectively, with a possible ancestry of S-Spain in Shanghai.ConclusionsMultiple SARS-CoV-2 introductions have been detected in Spain and at least two resulted in the emergence of locally transmitted clusters, with further dissemination of one of them to at least 6 other countries. These results highlight the extraordinary potential of SARS-CoV-2 for rapid and widespread geographic dissemination.


Viruses ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 632
Author(s):  
Sarah E. Lauterbach ◽  
Dillon S. McBride ◽  
Brendan T. Shirkey ◽  
Jacqueline M. Nolting ◽  
Andrew S. Bowman

Active influenza A virus (IAV) surveillance in wild waterfowl in the United States has revolved around convenience-based sampling methods, resulting in gaps in surveillance during the spring season. We conducted active IAV surveillance in mallards continuously from July 2017 to July 2019 in the coastal marshes of Lake Erie near Port Clinton, Ohio. We aimed to understand ecological and evolutionary dynamics of IAV across multiple seasons, including the under-sampled spring season. We collected 2096 cloacal swabs and estimated a 6.1% (95% confidence interval (CI): 0.050–0.071) prevalence during the study period. Prevalence was lowest during spring (1.0%, 95% CI: 0.004–0.015). Time-stamped phylogenetic analyses revealed local persistence of genetic lineages of multiple gene segments. The PA segment consists of a lineage detected in multiple seasons with a time to most recent common ancestor of 2.48 years (95% highest posterior density: 2.16–2.74). Analysis of the H3 and H6 segments showed close relation between IAVs detected in spring and the following autumn migration. Though the mechanisms behind viral persistence in a single location are not well understood, we provide evidence that viruses can persist across several seasons. Current surveillance methods should be evaluated to ensure they are capturing the breadth of genetic diversity of IAV in waterfowl and prepare for IAV outbreaks in both animals and humans.


1992 ◽  
Vol 6 ◽  
pp. 297-297
Author(s):  
Heyo Van Iten

Phylogenetic relationships among the cnidarian classes Anthozoa, Hydrozoa and Scyphozoa, and between Cnidaria and other metazoan phyla, continue to be subject to widely divergent interpretations. Also controversial are the affinities of numerous fossil groups, including Byronia Bischoff, Sphenothallus Hall and conulariids, that have been interpreted as extinct cnidarians. Currently favored interpretations of evolution within Cnidaria are generally consistent with one of two alternative hypotheses of phylogenetic relationships: scyphozoans and anthozoans are members of a monophylclic group that excludes hydrozoans; or scyphozoans and hydrozoans are members of a monophyletic group that excludes anthozoans. Putative anthozoan-scyphozoan synapomorphies include (1) gastric septa present; (2) cnidae present in both ectoderm and gastroderm; (3) sex cells gastrodermal; and (4) mesoglea contains amoeboid cells. Putative hydrozoan-scyphozoan synapomorphies include (1) medusa present; (2) tetraradial symmetry; (3) rhopaloid nematocysts; and (4) similarities in sperm structure.Evaluation of alternative hypotheses of relationships within Cnidaria is complicated by uncertainty surrounding relationships between this and other metazoan phyla. While some investigators have interpreted Cnidaria and Ctenophora as members of a monophyletic group that excludes other phyla, others have argued that ctenophorans are more closely related to platyhelminths than they are to cnidarians. Putative cnidarian-ctenophoran synapomorphies include (1) production of cells modified for prey capture; and (2) presence of a medusa. Putative ctenophoran-platyhelminth synapomorphies include (1) presence of gonoducts; (2) ciliated cells with several to many cilia; (3) determinate cleavage; and (4) muscle cells developed from mesoderm. Comparisons of these and other phyla indicate that the strongest hypotheses of synapomorphy are those between cnidarians and ctenophorans. Ctenophorans do not have a mesoderm, and they lack complex reproductive structures that can be homologized with platyhelminth gonoducts. Similarities between ctenophorans and platyhelminths in ciliation and cleavage type are either non-homologous or shared primitive. The most recent common ancestor of ctenophorans and cnidarians was probably a medusa-like animal with circular and meridional muscle fibers and a non-septate digestive cavity having four radial canals. This cavity probably lacked cells specialized for prey capture, but glutinant prey-capture structures may have been present on tentacles. Sperm produced by this common ancestor were most similar to sperm of extant ctenophorans, hydrozoans and scyphozoans. Anatomical features unique to ctenophorans or cnidarians, regarded by some investigators as evidence against a close relationship between these two groups, are autapomorphies. These interpretations imply that putative hydrozoan-scyphozoan synapomorphies are actually shared primitive, and that the presence of gastric septa and cnidae-bearing gastric filaments in scyphozoans and anthozoans is shared derived. This would mean that the most parsimonious hypothesis of phylogenetic relationships within Cnidaria is that anthozoans and scyphozoans are members of a monophyletic group that excludes hydrozoans.Debate over relationships among these extant taxa has heightened interest in the affinities of prominent groups of problematic fossil cnidarians. Byronia Bischoff, Sphenothallus Hall and conulariids, all characterized by an apatitic, multilamellar theca, show detailed anatomical similarities to hydrozoans and/or scyphozoans. Putative synapomorphies linking Byronia and coronatid scyphozoans include the presence of multiple whorls of thorn-like nodes projecting into the thecal cavity, with each whorl consisting of eight nodes arranged in two sets of four nodes each. Sphenothallus, characterized by a pair of tentacles and, in some species, multiple branching, is most similar to hydrozoan and scyphozoan polyps, many of which are colonial or exhibit a single pair of tentacles early in their development. Similarities in hard- and soft-part anatomy between scyphozoans and conulariids suggest that conulariids, like scyphozoans, possessed four gastric septa and produced medusae through polydisc strobilation. Although conulariids have been interpreted as ancestral to extant cnidarians, they are more likely either a sister group to Scyphozoa or members of this class.


2003 ◽  
Vol 17 (3) ◽  
pp. 361 ◽  
Author(s):  
Philip S. Ward ◽  
Seán G. Brady

We investigated phylogenetic relationships among the 'primitive' Australian ant genera Myrmecia and Nothomyrmecia (stat. rev.) and the Baltic amber fossil genus Prionomyrmex, using a combination of morphological and molecular data. Outgroups for the analysis included representatives from a variety of potential sister-groups, including five extant subfamilies of ants and one extinct group (Sphecomyrminae). Parsimony analysis of the morphological data provides strong support (~95% bootstrap proportions) for the monophyly of (1) genus Myrmecia, (2) genus Prionomyrmex, and (3) a clade containing those two genera plus Nothomyrmecia. A group comprising Nothomyrmecia and Prionomyrmex is also upheld (85% bootstrap support). Molecular sequence data (~2200 base pairs from the 18S and 28S ribosomal RNA genes) corroborate these findings for extant taxa, with Myrmecia and Nothomyrmecia appearing as sister-groups with ~100% bootstrap support under parsimony, neighbour-joining and maximum-likelihood analyses. Neither the molecular nor the morphological data set allows us to identify unambiguously the sister-group of (Myrmecia + (Nothomyrmecia + Prionomyrmex)). Rather, Myrmecia and relatives are part of an unresolved polytomy that encompasses most of the ant subfamilies. Taken as a whole, our results support the contention that many of the major lineages of ants – including a clade that later came to contain Myrmecia, Nothomyrmecia and Prionomyrmex – arose at around the same time during a bout of diversification in the middle or late Cretaceous. On the basis of Bayesian dating analysis, the estimated age of the most recent common ancestor of Myrmecia and Nothomyrmecia is 74 million years (95% confidence limits, 53–101million years), a result consistent with the origin of the myrmeciine stem lineage in the Cretaceous. The ant subfamily Myrmeciinae is redefined to contain two tribes, Myrmeciini (genus Myrmecia) and Prionomyrmecini (Nothomyrmecia and Prionomyrmex). Phylogenetic analysis of the enigmatic Argentine fossils Ameghinoia and Polanskiella demonstrates that they are also members of the Myrmeciinae, probably more closely related to Prionomyrmecini than to Myrmeciini. Thus, the myrmeciine ants appear to be a formerly widespread group that retained many ancestral formicid characteristics and that became extinct everywhere except in the Australian region.


Genetics ◽  
1998 ◽  
Vol 150 (3) ◽  
pp. 1187-1198 ◽  
Author(s):  
Mikkel H Schierup ◽  
Xavier Vekemans ◽  
Freddy B Christiansen

Abstract Expectations for the time scale and structure of allelic genealogies in finite populations are formed under three models of sporophytic self-incompatibility. The models differ in the dominance interactions among the alleles that determine the self-incompatibility phenotype: In the SSIcod model, alleles act codominantly in both pollen and style, in the SSIdom model, alleles form a dominance hierarchy, and in SSIdomcod, alleles are codominant in the style and show a dominance hierarchy in the pollen. Coalescence times of alleles rarely differ more than threefold from those under gametophytic self-incompatibility, and transspecific polymorphism is therefore expected to be equally common. The previously reported directional turnover process of alleles in the SSIdomcod model results in coalescence times lower and substitution rates higher than those in the other models. The SSIdom model assumes strong asymmetries in allelic action, and the most recessive extant allele is likely to be the most recent common ancestor. Despite these asymmetries, the expected shape of the allele genealogies does not deviate markedly from the shape of a neutral gene genealogy. The application of the results to sequence surveys of alleles, including interspecific comparisons, is discussed.


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