scholarly journals An exploration of the complex biogeographical history of the Neotropical banner-wing damselflies (Odonata: Polythoridae)

2020 ◽  
Author(s):  
Melissa Sanchez Herrera ◽  
Christopher Beatty ◽  
Renato Nunes ◽  
Camilo Salazar ◽  
Jessica L Ware
Keyword(s):  
Amazon Basin ◽  
Middle Eocene ◽  
Climatic Variability ◽  
Recent Common Ancestor ◽  
Mountain Building ◽  
Northern Andes ◽  
Short Branch ◽  
Intrinsic Factors ◽  
Most Recent Common Ancestor ◽  
Spatial Diversification

Abstract Background: The New World Tropics has experienced a dynamic landscape across evolutionary history and harbors a high diversity of flora and fauna. While there are some studies addressing diversification in Neotropical vertebrates and plants, there is still a lack of knowledge in arthropods. Here we examine temporal and spatial diversification patterns in the damselfly family Polythoridae; which comprises seven genera with a total of 58 species distributed across much of Central and South America.Results: Our time-calibrated phylogeny for 48 species suggests that this family radiated during the early Eocene (~56 Ma), diversifying during the middle Eocene. As with other neotropical groups, the Most Recent Common Ancestor (MRCA) of most of the Polythoridae genera has a primary origin in the Northern Andes though the MRCA of at least one genus may have appeared in the Amazon Basin. Diversification rates have been uniform in all genera except one—Polythore—where a significant increase in the late Pliocene (~3 mya) correlates with mountain uplift. While our molecular clock suggests correlations with some major geographical events, our biogeographical modeling (with BioGeoBEARS and RASP) found little influence of the formation of the Pebas and Acre systems or Andean mountain building, possibly due to the short branch lengths in our time-dated phylogeny, or perhaps to climatic variability during the period in question. Conclusion: The biogeographical models implemented here were unable to explain the effect of South American major geological events (i.e Pebas and Acre systems, Andes uplift) on the diversification of this damselfly family; while diversification in the tree shows some correlation with mountain building events, it is possible that other abiotic and biotic changes during our study period have influenced diversification as well. The high diversification rate observed in Polythore could be explained by the late uplift of the Northern Andes. However, it is possible that other intrinsic factors like sexual and natural selection acting on color patterns could be involved in the diversification of this genus.

scholarly journals An exploration of the complex biogeographical history of the Neotropical banner-wing damselflies (Odonata: Polythoridae)

2020 ◽  
Author(s):  
Melissa Sanchez Herrera ◽  
Christopher Beatty ◽  
Renato Nunes ◽  
Camilo Salazar ◽  
Jessica L Ware
Keyword(s):  
Amazon Basin ◽  
Middle Eocene ◽  
Recent Common Ancestor ◽  
Northern Andes ◽  
Intrinsic Factors ◽  
Most Recent Common Ancestor ◽  
Early Diversification ◽  
Dynamic Landscape ◽  
History Of ◽  
Spatial Diversification

Abstract Background: The New World Tropics has experienced a dynamic landscape across evolutionary history and harbors a high diversity of flora and fauna. While there are some studies addressing diversification in Neotropical vertebrates and plants, there is still a lack of knowledge in arthropods. Here we examine temporal and spatial diversification patterns in the damselfly family Polythoridae, which comprises seven genera with a total of 58 species distributed across much of Central and South America. Results Our time-calibrated phylogeny for 48 species suggests that this family radiated during the early Eocene (~56 Ma), diversifying during the middle Eocene. As with other neotropical groups, the Most Recent Common Ancestor (MRCA) of most of the Polythoridae genera has a primary origin in the Northern Andes though the MRCA of at least one genus may have appeared in the Amazon Basin. Our molecular clock suggests correlations with some major geographical events, and our biogeographical modeling (with BioGeoBEARS and RASP) found a significant influence of the formation of the Pebas and Acre systems on the early diversification of these damselflies, though evidence for the influence of the rise of the different Andean ranges was mixed. Diversification rates have been uniform in all genera except one—Polythore—where a significant increase in the late Pliocene (~3 mya) may have been influenced by recent Andean uplift. Conclusion The biogeographical models implemented here suggest that the Pebas and Acre Systems were significant geological events associated with the diversification of this damselfly family; while diversification in the tree shows some correlation with mountain building events, it is possible that other abiotic and biotic changes during our study period have influenced diversification as well. The high diversification rate observed in Polythore could be explained by the late uplift of the Northern Andes. However, it is possible that other intrinsic factors like sexual and natural selection acting on color patterns could be involved in the diversification of this genus.

scholarly journals An exploration of the complex biogeographical history of the Neotropical banner-wing damselflies (Odonata: Polythoridae)

2020 ◽  
Author(s):  
Melissa Sanchez Herrera ◽  
Christopher Beatty ◽  
Renato Nunes ◽  
Camilo Salazar ◽  
Jessica L Ware
Keyword(s):  
Amazon Basin ◽  
Late Eocene ◽  
Recent Common Ancestor ◽  
Northern Andes ◽  
Intrinsic Factors ◽  
Most Recent Common Ancestor ◽  
Early Diversification ◽  
Dynamic Landscape ◽  
History Of ◽  
Spatial Diversification

Abstract Background: The New World Tropics has experienced a dynamic landscape across evolutionary history and harbors a high diversity of flora and fauna. While there are some studies addressing diversification in Neotropical vertebrates and plants, there is still a lack of knowledge in arthropods. Here we examine temporal and spatial diversification patterns in the damselfly family Polythoridae, which comprises seven genera with a total of 58 species distributed across much of Central and South America. Results Our time-calibrated phylogeny for 48 species suggests that this family radiated during the late Eocene (~33 Ma), diversifying during the Miocene. As with other neotropical groups, the Most Recent Common Ancestor (MRCA) of most of the Polythoridae genera has a primary origin in the Northern Andes though the MRCA of at least one genus may have appeared in the Amazon Basin. Our molecular clock suggests correlations with some major geographical events, and our biogeographical modeling (with BioGeoBEARS and RASP) found a significant influence of the formation of the Pebas and Acre systems on the early diversification of these damselflies, though evidence for the influence of the rise of the different Andean ranges was mixed. Diversification rates have been uniform in all genera except one— Polythore —where a significant increase in the late Pliocene (~3 mya) may have been influenced by recent Andean uplift. Conclusion The biogeographical models implemented here suggest that the Pebas and Acre Systems were significant geological events associated with the diversification of this damselfly family; while diversification in the tree shows some correlation with mountain building events, it is possible that other abiotic and biotic changes during our study period have influenced diversification as well. The high diversification rate observed in Polythore could be explained by the late uplift of the Northern Andes. However, it is possible that other intrinsic factors like sexual and natural selection acting on color patterns could be involved in the diversification of this genus.

scholarly journals Calling the Banners: exploring the complex biogeographical history of the Neotropical banner-wing damselflies (Odonata: Polythoridae)

2019 ◽  
Author(s):  
Melissa Sanchez Herrera ◽  
Christopher D Beatty ◽  
Renato Nunes ◽  
Camilo Salazar ◽  
Jessica L Ware
Keyword(s):  
Amazon Basin ◽  
Habitat Diversity ◽  
Molecular Dating ◽  
Mountain Building ◽  
Short Branch ◽  
Branch Lengths ◽  
History Of ◽  
Primary Origin ◽  
Biogeographical Analysis ◽  
Dated Phylogeny

Abstract Background Sorting out the biogeographical history of species in the New World Tropics is challenging. We here examine the roles of evolution and biogeography in driving the distribution and diversification of the damselflies of the family Polythoridae. This family comprises seven genera with a total of 57 species, distributed across much of Central and South America. Results Through phylogenetic analysis, relaxed-clock molecular dating and biogeographical analysis we find these genera originated ~56 Ma and started diversifying ~45 Ma. As with other neotropical groups, the Polythoridae have a primary origin in the Northern Andes; at least one genus first appears in the Amazon Basin. Diversification rates have been uniform in all genera except one—Polythore—where a significant increase in the late Pliocene (~3 mya) correlates with mountain building. While our molecular clock suggests correlations with some major geographical events, our biogeographical modeling (with BioGeoBEARS and RASP) found little influence of the formation of the Pebas and Acre systems or Andean mountain building, possibly due to the short branch lengths in our time-dated phylogeny. Conclusion We conclude that this family of damselflies, despite its relatively young age, has developed into genera with diverse distributions and some surprisingly high diversity, despite relatively low habitat diversity. Polythore is a recent radiation where biogeographical events may not be the main drivers of diversification. Other factors like sexual and natural selection acting on color patterns could be involved in generate the extreme diversity in this genus.

scholarly journals Whole genome sequencing reveals the emergence of aPseudomonas aeruginosashared strain sub-lineage among patients treated within a single cystic fibrosis centre

2018 ◽  
Author(s):  
Bryan A. Wee ◽  
Anna S. Tai ◽  
Laura J. Sherrard ◽  
Nouri L. Ben Zakour ◽  
Kirt R. Hanks ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Short Branch ◽  
Synonymous Mutations ◽  
Most Recent Common Ancestor

AbstractBackgroundChronic lung infections byPseudomonas aeruginosaare a significant cause of morbidity and mortality in people with cystic fibrosis (CF). SharedP. aeruginosastrains, that can be transmitted between patients, are of concern and in Australia the AUST-02 shared strain is predominant in individuals attending CF centres in Queensland and Western Australia. M3L7 is a multidrug resistant sub-type of AUST-02 that was recently identified in a Queensland CF centre and was shown to be associated with poorer clinical outcomes. The main aim of this study was to resolve the relationship of the emergent M3L7 sub-type within the AUST-02 group of strains using whole genome sequencing.ResultsA whole-genome core phylogeny of 63 isolates indicated that M3L7 is a monophyletic sub-lineage within the context of the broader AUST-02 group. Relatively short branch lengths connected all of the M3L7 isolates. A phylogeny based on nucleotide polymorphisms present across the genome showed that the chronological estimation of the most recent common ancestor was around 2001 (± 3 years). SNP differences between sequential M3L7 isolates collected 3-4 years apart from five patients suggested both continuous infection of the same strain and cross-infection of some M3L7 variants between patients. The majority of polymorphisms that were characteristic of M3L7 (i.e. acquired after divergence from all other AUST-02 isolates sequenced) were found to produce non-synonymous mutations in virulence and antibiotic resistance genes.ConclusionsM3L7 has recently diverged from a common ancestor indicating descent from a single carrier at a CF treatment centre in Australia. Both adaptation to the lung and transmission of M3L7 between adults attending this centre may have contributed to its rapid dissemination. The study emphasises the importance of clinical management in controlling the emergence of shared strains in CF.

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.

scholarly journals Testing the spatial and temporal framework of speciation in an ancient lake species flock: the leech genus <i>Dina</i> (Hirudinea: Erpobdellidae) in Lake Ohrid

2010 ◽  
Vol 7 (11) ◽  
pp. 3387-3402 ◽  
Author(s):  
S. Trajanovski ◽  
C. Albrecht ◽  
K. Schreiber ◽  
R. Schultheiß ◽  
T. Stadler ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Abiotic Factors ◽  
Time Frame ◽  
Recent Common Ancestor ◽  
Species Flock ◽  
Ancient Lake ◽  
Lake Ohrid ◽  
Most Recent Common Ancestor ◽  
Extant Species

Abstract. Ancient Lake Ohrid on the Balkan Peninsula is considered to be the oldest ancient lake in Europe with a suggested Plio-/Pleistocene age. Its exact geological age, however, remains unknown. Therefore, molecular clock data of Lake Ohrid biota may serve as an independent constraint of available geological data, and may thus help to refine age estimates. Such evolutionary data may also help unravel potential biotic and abiotic factors that promote speciation events. Here, mitochondrial sequencing data of one of the largest groups of endemic taxa in the Ohrid watershed, the leech genus Dina, is used to test whether it represents an ancient lake species flock, to study the role of potential horizontal and vertical barriers in the watershed for evolutionary events, to estimate the onset of diversification in this group based on molecular clock analyses, and to compare this data with data from other endemic species for providing an approximate time frame for the origin of Lake Ohrid. Based on the criteria speciosity, monophyly and endemicity, it can be concluded that Dina spp. from the Ohrid watershed, indeed, represents an ancient lake species flock. Lineage sorting of its species, however, does not seem to be complete and/or hybridization may occur. Analyses of population structures of Dina spp. in the Ohrid watershed indicate a horizontal zonation of haplotypes from spring and lake populations, corroborating the role of lake-side springs, particularly the southern feeder springs, for evolutionary processes in endemic Ohrid taxa. Vertical differentiation of lake taxa, however, appears to be limited, though differences between populations from the littoral and the profundal are apparent. Molecular clock analyses indicate that the most recent common ancestor of extant species of this flock is approximately 1.99 ± 0.83 million years (Ma) old, whereas the split of the Ohrid Dina flock from a potential sister taxon outside the lake is estimated at 8.30 ± 3.60 Ma. Comparisons with other groups of endemic Ohrid species indicated that in all cases, diversification within the watershed started ≤2 Ma ago. Thus, this estimate may provide information on a minimum age for the origin of Lake Ohrid. Maximum ages are less consistent and generally less reliable. But cautiously, a maximum age of 3 Ma is suggested. Interestingly, this time frame of approximately 2–3 Ma ago for the origin of Lake Ohrid, generated based on genetic data, well fits the time frame most often used in the literature by geologists.

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