scholarly journals Phylogenetic revision of the psammophilic Trogloderus LeConte (Coleoptera: Tenebrionidae), with biogeographic implications for the Intermountain Region

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8039 ◽  
Author(s):  
M. Andrew Johnston
Keyword(s):  
New Species ◽  
Great Basin ◽  
Colorado Plateau ◽  
Recent Common Ancestor ◽  
Owens Valley ◽  
Most Recent Common Ancestor ◽  
Western Colorado ◽  
Intermountain Region ◽  
Mohave Desert ◽  
Phylogenetic Revision

The genus Trogloderus LeConte, 1879, which is restricted to dunes and sandy habitats in the western United States, is revised using morphological and molecular information. Six new species are described from desert regions: Trogloderus arcanus New Species (Lahontan Trough); Trogloderus kandai New Species (Owens Valley); Trogloderus major New Species (Mohave Desert); Trogloderus skillmani New Species (eastern Great Basin and Mohave Desert); Trogloderus verpus New Species (eastern Colorado Plateau); and Trogloderus warneri New Species (western Colorado Plateau). A molecular phylogeny is presented for the genus and used to infer its historical biogeography. The most recent common ancestor of Trogloderus is dated to 5.2 mya and is inferred to have inhabited the Colorado Plateau. Current species most likely arose during the mid-Pleistocene where the geographic features of the Lahontan Trough, Bouse Embayment and Kaibab Plateau were significant factors driving speciation.

THE MIMALLONIS GROUP OF THE GENUS EUXOA HBN. (LEPIDOPTERA: NOCTUIDAE) WITH DESCRIPTIONS OF THREE NEW SPECIES

1975 ◽  
Vol 107 (2) ◽  
pp. 155-165 ◽  
Author(s):  
J. D. Lafontaine
Keyword(s):  
New Species ◽  
Great Basin ◽  
Colorado Plateau ◽  
Northern California ◽  
Key To Species ◽  
Diagnostic Characters ◽  
Three New Species ◽  
Lepidoptera Noctuidae

AbstractDiagnostic characters of Euxoa mimallonis (Grt.) and E. biformata Sm. are discussed. Three species are described as new: condita from Forestville, Que., shasta from northern California, and intermontana from the Great Basin and Colorado Plateau. Adults and genitalia of the species are illustrated and a key to species is included.

Two new species of Schistonchus (Nematoda: Aphelenchoididae) associated with Ficus hispida in China

Nematology ◽  
2007 ◽  
Vol 9 (2) ◽  
pp. 169-187 ◽  
Author(s):  
Weimin Ye ◽  
Yongsan Zeng ◽  
Robin Giblin-Davis
Keyword(s):  
New Species ◽  
Excretory Pore ◽  
Large Subunit ◽  
Recent Common Ancestor ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Male Tail ◽  
Most Recent Common Ancestor ◽  
Ficus Hispida ◽  
Tail Tip

AbstractTwo new nematode species of the genus Schistonchus were recovered from syconia from a single Ficus hispida caprifig tree in Guangzhou, China. They are described herein as Schistonchus guangzhouensis n. sp. and S. centerae n. sp. Schistonchus guangzhouensis n. sp. is characterised by possessing the longest postuterine sac (PUS) of all currently described females in the genus (84-148 μm or >3.5 vulval body diam. (VBD) long), excretory pore situated near the level of the metacorpus, two pairs of subventral papillae on the male tail, and unique recurved and mitten-shaped spicules. Schistonchus centerae n. sp. is characterised by a unique fusiform tail tip and short PUS (8-20 μm or <1.0 VBD long) in reproductive females, excretory pore located near the head, spicules with an indistinct rostrum, male tail with three pairs of papillae, and broadly truncate tail tip. Both new species were easily differentiated from each other and other members of the genus for which sequences of the D2/D3 expansion segments of the large subunit rRNA gene (LSU) and partial small subunit rRNA gene (SSU) were available. Phylogenetic analysis also supported a monophyletic Schistonchus within a well-supported clade of Aphelenchoididae (sensu Hunt, 1993) and shared a most recent common ancestor with Aphelenchoides and Laimaphelenchus.

scholarly journals The Phylogeographic Relationships and the Evolution History of Carassius Auratus Complex With a Newborn Homodiploid Crucian Carp-like Fish (2nNCRC)

2021 ◽  
Author(s):  
Qianhong Gu ◽  
Shi Wang ◽  
Hui Yuan ◽  
Hui Zhong ◽  
Junliu Yang ◽  
...  
Keyword(s):  
New Species ◽  
Carassius Auratus ◽  
Demographic History ◽  
Molecular Dating ◽  
Early Pleistocene ◽  
Hybrid Origin ◽  
Recent Common Ancestor ◽  
Distant Hybridization ◽  
Most Recent Common Ancestor ◽  
Close Relationship

Abstract Background: One of the important aspects of studying evolution is to understand how new species are formed and their uniqueness maintained. Hybridization can lead to the formation of new species with the reorganization of adaptive system and significant changes in phenotype. It is wondrous that eight stable strains of 2nNCRC derived from the interspecies hybridization have been established in our laboratory. To examine the phylogeographical pattern of the wildly distributed genus Carassius in the Eurasia, and investigate the possible hybrid origin of Carassius auratus lineage, in light of past climatic events, the mitochondrial genome (mtDNA) were used to reconstruct the phylogenetic relationship between the C. auratus complex and the 2nNCRC, and to assess how demographic history, dispersal and barriers to gene flow have led to the current distribution of mtDNA lineages for C. auratus complex. Results: As expected, the 2nNCRC had a very close relationship with the C. auratus complex, which was distinctly separated with other three species of Carassius. The C. auratus lineage possibly originated from China during the Late Pliocene, far postdated the diversification of C. carassius in Europe and C. cuvieri in Japan. The admixture of mtDNA haplotype lineages of C. auratus detected across the whole Eurasia has experienced a rapid diversification since Early PleistoceneConclusion: Combined the molecular dating analyses, species distribution modeling and ancestral area reconstruction, the speciation of C. auratus seemed not to be the processing of lineage diversification from the most recent common ancestor of C. carassius or C. cuvieri. The formation of 2nNCRC in our laboratory could be a good candidate explaining for the hybrid origin species for C. auratus lineage, as well as the paleoclimate oscillation and geological event during Pliocene and Pleistocene in China supplying an opportunity for the distant hybridization. The most wildly distributed C. auratus lineage could be attributed to the dispersal during the glacial period and the recent human-facilitated dispersal.

scholarly journals Molecular phylogeny of Hiptage (Malpighiaceae) reveals a new species from Southwest China

PhytoKeys ◽  
2019 ◽  
Vol 135 ◽  
pp. 91-104 ◽  
Author(s):  
Ke Tan ◽  
Hai-Lei Zheng ◽  
Shu-Peng Dong ◽  
Ming-Xun Ren
Keyword(s):  
New Species ◽  
Molecular Phylogeny ◽  
Internal Transcribed Spacer ◽  
Southwest China ◽  
Common Ancestor ◽  
Its Region ◽  
Recent Common Ancestor ◽  
Most Recent Common Ancestor ◽  
First Time ◽  
A New Species

Hiptage is an Asia-endemic genus of Malpighiaceae currently placed in the tetrapteroid clade, representing one of the seven inter-continent dispersions from New to Old World. A molecular phylogeny based on sequences of the internal transcribed spacer (ITS) region was recovered for the first time for the genus. Our results showed that the most recent common ancestor of Hiptage probably originated in the South Indo-China Peninsula and diversified in this region. Based on phylogenetic evidence and relevant morphological traits, we propose a new species; Hiptage incurvatum is characterised by mericarps with arcuate anterior lateral wings, two large glands on the dorsal sepals, and small glands on the remaining sepals. The new species is from Mt. Cangshan, Dali City (25°35'N, 100°02'E) in North Yunnan, Southwest China and is notable for its occurrence at high altitude, 1400 m (the highest distribution currently known for the genus). The implications of this unusual species for the dispersal and evolution of the genus are discussed.

scholarly journals Allelic Genealogies in Sporophytic Self-Incompatibility Systems in Plants

Genetics ◽  
1998 ◽  
Vol 150 (3) ◽  
pp. 1187-1198 ◽  
Author(s):  
Mikkel H Schierup ◽  
Xavier Vekemans ◽  
Freddy B Christiansen
Keyword(s):  
Dominance Hierarchy ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Self Incompatibility ◽  
Most Recent Common Ancestor ◽  
Dominance Interactions ◽  
Turnover Process ◽  
Neutral Gene ◽  
Interspecific Comparisons ◽  
Coalescence Times

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.

scholarly journals Molecular epidemiological characteristics of echovirus 6 in mainland China: extensive circulation of genotype F from 2007 to 2018

2021 ◽  
Author(s):  
Wenjun Cheng ◽  
Tianjiao Ji ◽  
Shuaifeng Zhou ◽  
Yong Shi ◽  
Lili Jiang ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Mainland China ◽  
Recent Common Ancestor ◽  
Genetic Characteristics ◽  
Most Recent Common Ancestor ◽  
Significant Difference ◽  
Echovirus 6 ◽  
Epidemiological Characteristics ◽  
Highest Posterior Density ◽  
Genotype F

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.

scholarly journals Molecular epidemiology of coxsackievirus A16 circulating in children in Beijing, China from 2010 to 2019

2021 ◽  
Author(s):  
Ya-Fang Hu ◽  
Li-Ping Jia ◽  
Fang-Yuan Yu ◽  
Li-Ying Liu ◽  
Qin-Wei Song ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Evolutionary Rate ◽  
Foot And Mouth Disease ◽  
Recent Common Ancestor ◽  
Rt Pcr ◽  
Coxsackievirus A16 ◽  
Most Recent Common Ancestor ◽  
Etiological Agents ◽  
High Level ◽  
And Control

Abstract Background Coxsackievirus A16 (CVA16) is one of the major etiological agents of hand, foot and mouth disease (HFMD). This study aimed to investigate the molecular epidemiology and evolutionary characteristics of CVA16. Methods Throat swabs were collected from children with HFMD and suspected HFMD during 2010–2019. Enteroviruses (EVs) were detected and typed by real-time reverse transcription-polymerase chain reaction (RT-PCR) and RT-PCR. The genotype, evolutionary rate, the most recent common ancestor, population dynamics and selection pressure of CVA16 were analyzed based on viral protein gene (VP1) by bioinformatics software. Results A total of 4709 throat swabs were screened. EVs were detected in 3180 samples and 814 were CVA16 positive. More than 81% of CVA16-positive children were under 5 years old. The prevalence of CVA16 showed obvious periodic fluctuations with a high level during 2010–2012 followed by an apparent decline during 2013–2017. However, the activities of CVA16 increased gradually during 2018–2019. All the Beijing CVA16 strains belonged to sub-genotype B1, and B1b was the dominant strain. One B1c strain was detected in Beijing for the first time in 2016. The estimated mean evolutionary rate of VP1 gene was 4.49 × 10–3 substitution/site/year. Methionine gradually fixed at site-23 of VP1 since 2012. Two sites were detected under episodic positive selection, one of which (site-223) located in neutralizing linear epitope PEP71. Conclusions The dominant strains of CVA16 belonged to clade B1b and evolved in a fast evolutionary rate during 2010–2019 in Beijing. To provide more favorable data for HFMD prevention and control, it is necessary to keep attention on molecular epidemiological and evolutionary characteristics of CVA16.

scholarly journals The Ancestry of a Sample of Sequences Subject to Recombination

Genetics ◽  
1999 ◽  
Vol 151 (3) ◽  
pp. 1217-1228 ◽  
Author(s):  
Carsten Wiuf ◽  
Jotun Hein
Keyword(s):  
Genetic Distance ◽  
Population Size ◽  
Upper Bound ◽  
Recombination Rate ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Sequence Length ◽  
Most Recent Common Ancestor ◽  
The Mean ◽  
Mean Time

Abstract In this article we discuss the ancestry of sequences sampled from the coalescent with recombination with constant population size 2N. We have studied a number of variables based on simulations of sample histories, and some analytical results are derived. Consider the leftmost nucleotide in the sequences. We show that the number of nucleotides sharing a most recent common ancestor (MRCA) with the leftmost nucleotide is ≈log(1 + 4N Lr)/4Nr when two sequences are compared, where L denotes sequence length in nucleotides, and r the recombination rate between any two neighboring nucleotides per generation. For larger samples, the number of nucleotides sharing MRCA with the leftmost nucleotide decreases and becomes almost independent of 4N Lr. Further, we show that a segment of the sequences sharing a MRCA consists in mean of 3/8Nr nucleotides, when two sequences are compared, and that this decreases toward 1/4Nr nucleotides when the whole population is sampled. A measure of the correlation between the genealogies of two nucleotides on two sequences is introduced. We show analytically that even when the nucleotides are separated by a large genetic distance, but share MRCA, the genealogies will show only little correlation. This is surprising, because the time until the two nucleotides shared MRCA is reciprocal to the genetic distance. Using simulations, the mean time until all positions in the sample have found a MRCA increases logarithmically with increasing sequence length and is considerably lower than a theoretically predicted upper bound. On the basis of simulations, it turns out that important properties of the coalescent with recombinations of the whole population are reflected in the properties of a sample of low size.

scholarly journals Genome Sequence Analysis of First Ross River Virus Isolate from Papua New Guinea Indicates Long-Term, Local Evolution

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 482
Author(s):  
Alice Michie ◽  
John S. Mackenzie ◽  
David W. Smith ◽  
Allison Imrie
Keyword(s):  
Papua New Guinea ◽  
Large Scale ◽  
Solomon Islands ◽  
Febrile Illness ◽  
New Guinea ◽  
Recent Common Ancestor ◽  
Ross River Virus ◽  
Most Recent Common Ancestor ◽  
Mean Time

Ross River virus (RRV) is the most medically significant mosquito-borne virus of Australia, in terms of human morbidity. RRV cases, characterised by febrile illness and potentially persistent arthralgia, have been reported from all Australian states and territories. RRV was the cause of a large-scale epidemic of multiple Pacific Island countries and territories (PICTs) from 1979 to 1980, involving at least 50,000 cases. Historical evidence of RRV seropositivity beyond Australia, in populations of Papua New Guinea (PNG), Indonesia and the Solomon Islands, has been documented. We describe the genomic characterisation and timescale analysis of the first isolate of RRV to be sampled from PNG to date. Our analysis indicates that RRV has evolved locally within PNG, independent of Australian lineages, over an approximate 40 year period. The mean time to most recent common ancestor (tMRCA) of the unique PNG clade coincides with the initiation of the PICTs epidemic in mid-1979. This may indicate that an ancestral variant of the PNG clade was seeded into the region during the epidemic, a period of high RRV transmission. Further epidemiological and molecular-based surveillance is required in PNG to better understand the molecular epidemiology of RRV in the general Australasian region.

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