Modeling colonization rates over time: Generating null models and testing model adequacy in phylogenetic analyses of species assemblages*

Abstract Vertebrate retrotransposons have been used extensively for phylogenetic analyses and studies of molecular evolution. Information can be obtained from specific inserts either by comparing sequence differences that have accumulated over time in orthologous copies of that insert or by determining the presence or absence of that specific element at a particular site. The presence of specific copies has been deemed to be an essentially homoplasy-free phylogenetic character because the probability of multiple independent insertions into any one site has been believed to be nil. Mys elements are a type of LTR-containing retrotransposon present in Sigmodontine rodents. In this study we have shown that one particular insert, mys-9, is an extremely old insert present in multiple species of the genus Peromyscus. We have found that different copies of this insert show a surprising range of sizes, due primarily to a continuing series of SINE (short interspersed element) insertions into this locus. We have identified two hot spots for SINE insertion within mys-9 and at each hot spot have found that two independent SINE insertions have occurred at identical sites. These results have major repercussions for phylogenetic analyses based on SINE insertions, indicating the need for caution when one concludes that the existence of a SINE at a specific locus in multiple individuals is indicative of common ancestry. Although independent insertions at the same locus may be rare, SINE insertions are not homoplasy-free phylogenetic markers.

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Phenotypic Analysis Reveals that the 2010 Haiti Cholera Epidemic Is Linked to a Hypervirulent Strain

Infection and Immunity ◽

10.1128/iai.00189-16 ◽

2016 ◽

Vol 84 (9) ◽

pp. 2473-2481 ◽

Cited By ~ 28

Author(s):

Karla J. F. Satchell ◽

Christopher J. Jones ◽

Jennifer Wong ◽

Jessica Queen ◽

Shivani Agarwal ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Event Analysis ◽

Phenotypic Analysis ◽

Genetic Event ◽

Content Type ◽

Virulence Potential ◽

Selection For ◽

El Tor ◽

Early Isolate ◽

Over Time

Vibrio choleraeO1 El Tor strains have been responsible for pandemic cholera since 1961. These strains have evolved over time, spreading globally in three separate waves. Wave 3 is caused by altered El Tor (AET) variant strains, which include the strain with the signaturectxB7allele that was introduced in 2010 into Haiti, where it caused a devastating epidemic. In this study, we used phenotypic analysis to compare an early isolate from the Haiti epidemic to wave 1 El Tor isolates commonly used for research. It is demonstrated that the Haiti isolate has increased production of cholera toxin (CT) and hemolysin, increased motility, and a reduced ability to form biofilms. This strain also outcompetes common wave 1 El Tor isolates for colonization of infant mice, indicating that it has increased virulence. Monitoring of CT production and motility in additional wave 3 isolates revealed that this phenotypic variation likely evolved over time rather than in a single genetic event. Analysis of available whole-genome sequences and phylogenetic analyses suggested that increased virulence arose from positive selection for mutations found in known and putative regulatory genes, includinghnsandvieA, diguanylate cyclase genes, and genes belonging to thelysRandgntRregulatory families. Overall, the studies presented here revealed thatV. choleraevirulence potential can evolve and that the currently prevalent wave 3 AET strains are both phenotypically distinct from and more virulent than many El Tor isolates.

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Adenoviral Infections in Singapore: Should New Antiviral Therapies and Vaccines Be Adopted?

The Journal of Infectious Diseases ◽

10.1093/infdis/jiz489 ◽

2019 ◽

Author(s):

Kristen K Coleman ◽

Chui Ching Wong ◽

Jayanthi Jayakumar ◽

Tham T Nguyen ◽

Abigail W L Wong ◽

...

Keyword(s):

Odds Ratio ◽

Pediatric Patients ◽

Phylogenetic Analyses ◽

Severe Disease ◽

Human Adenovirus ◽

Clinical Samples ◽

Antiviral Therapies ◽

Increased Risk ◽

Patients At Risk ◽

Over Time

Abstract Background A number of serious human adenovirus (HAdV) outbreaks have been recently reported: HAdV-B7 (Israel, Singapore, and USA), HAdV-B7d (USA and China), HAdV-D8, -D54, and -C2 (Japan), HAdV-B14p1 (USA, Europe, and China), and HAdV-B55 (China, Singapore, and France). Methods To understand the epidemiology of HAdV infections in Singapore, we studied 533 HAdV-positive clinical samples collected from 396 pediatric and 137 adult patients in Singapore from 2012 to 2018. Genome sequencing and phylogenetic analyses were performed to identify HAdV genotypes, clonal clusters, and recombinant or novel HAdVs. Results The most prevalent genotypes identified were HAdV-B3 (35.6%), HAdV-B7 (15.4%), and HAdV-E4 (15.2%). We detected 4 new HAdV-C strains and detected incursions with HAdV-B7 (odds ratio [OR], 14.6; 95% confidence interval [CI], 4.1–52.0) and HAdV-E4 (OR, 13.6; 95% CI, 3.9–46.7) among pediatric patients over time. In addition, immunocompromised patients (adjusted OR [aOR], 11.4; 95% CI, 3.8–34.8) and patients infected with HAdV-C2 (aOR, 8.5; 95% CI, 1.5–48.0), HAdV-B7 (aOR, 3.7; 95% CI, 1.2–10.9), or HAdV-E4 (aOR, 3.2; 95% CI, 1.1–8.9) were at increased risk for severe disease. Conclusions Singapore would benefit from more frequent studies of clinical HAdV genotypes to identify patients at risk for severe disease and help guide the use of new antiviral therapies, such as brincidofovir, and potential administration of HAdV 4 and 7 vaccine.

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Evolution of gene-rich germline restricted chromosomes in black-winged fungus gnats through introgression (Diptera: Sciaridae)

10.1101/2021.02.08.430288 ◽

2021 ◽

Author(s):

Christina N. Hodson ◽

Kamil S. Jaron ◽

Susan Gerbi ◽

Laura Ross

Keyword(s):

Sequence Similarity ◽

Phylogenetic Analyses ◽

Genomic Analysis ◽

Sequence Coverage ◽

Large Gene ◽

Hybridization Event ◽

Fungus Gnats ◽

Fungus Gnat ◽

Over Time ◽

Ancient Hybridization

AbstractGermline restricted DNA has evolved in diverse animal taxa, and is found in several vertebrate clades, nematodes, and flies. In these lineages, either portions of chromosomes or entire chromosomes are eliminated from somatic cells early in development, restricting portions of the genome to the germline. Little is known about why germline restricted DNA has evolved, especially in flies, in which three diverse families, Chironomidae, Cecidomyiidae, and Sciaridae exhibit germline restricted chromosomes (GRCs). We conducted a genomic analysis of germline restricted chromosomes in the fungus gnat Bradysia (Sciara) coprophila (Diptera: Sciaridae), which carries two large germline restricted “L” chromosomes. We sequenced and assembled the genome of B. coprophila, and used differences in sequence coverage and k-mer frequency between somatic and germ tissues to identify GRC sequence and compare it to the other chromosomes in the genome. We found that the GRCs in B. coprophila are large, gene-rich, and have many genes with paralogs on other chromosomes in the genome. We also found that the GRC genes are extraordinarily divergent from their paralogs, and have sequence similarity to another Dipteran family (Cecidomyiidae) in phylogenetic analyses, suggesting that these chromosomes have arisen in Sciaridae through introgression from a related lineage. These results suggest that the GRCs may have evolved through an ancient hybridization event, raising questions about how this may have occurred, how these chromosomes became restricted to the germline after introgression, and why they were retained over time.

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Multilocus Sequence Typing Supports the Hypothesis that Cow- and Human-Associated Salmonella Isolates Represent Distinct and Overlapping Populations

Applied and Environmental Microbiology ◽

10.1128/aem.01174-06 ◽

2006 ◽

Vol 72 (12) ◽

pp. 7575-7585 ◽

Cited By ~ 43

Author(s):

S. D. Alcaine ◽

Y. Soyer ◽

L. D. Warnick ◽

W.-L. Su ◽

S. Sukhnanand ◽

...

Keyword(s):

New York ◽

Multilocus Sequence Typing ◽

Phylogenetic Analyses ◽

New York State ◽

York State ◽

Mlst Scheme ◽

Combined Use ◽

Rapid Diversification ◽

Sequence Types ◽

Over Time

ABSTRACT A collection of 179 human and 156 bovine clinical Salmonella isolates obtained from across New York state over the course of 1 year was characterized using serotyping and a multilocus sequence typing (MLST) scheme based on the sequencing of three genes (fimA, manB, and mdh). The 335 isolates were differentiated into 52 serotypes and 72 sequence types (STs). Analyses of bovine isolates collected on different farms over time indicated that specific subtypes can persist over time on a given farm; in particular, a number of farms showed evidence for the persistence of a specific Salmonella enterica serotype Newport sequence type. Serotypes and STs were not randomly distributed among human and bovine isolates, and selected serotypes and STs were associated exclusively with either human or bovine sources. A number of common STs were geographically widespread. For example, ST6, which includes isolates representing serotype Typhimurium as well as the emerging serotype 4,5,12:i:-, was found among human and bovine isolates in a number of counties in New York state. Phylogenetic analyses supported the possibility that serotype 4,5,12:i:- is closely related to Salmonella serotype Typhimurium. Salmonella serotype Newport was found to represent two distinct evolutionary lineages that differ in their frequencies among human and bovine isolates. A number of Salmonella isolates carried two copies of manB (33 isolates) or showed small deletion events in fimA (nine isolates); these duplication and deletion events may provide mechanisms for the rapid diversification of Salmonella surface molecules. We conclude that the combined use of an economical three-gene MLST scheme and serotyping can provide considerable new insights into the evolution and transmission of Salmonella.

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Rapoport effect in South American Carnivora (Mammalia): null models under geometric and phylogenetic constraints

Brazilian Journal of Biology ◽

10.1590/s1519-69842002000300006 ◽

2002 ◽

Vol 62 (3) ◽

pp. 437-444 ◽

Cited By ~ 7

Author(s):

J. A. F. DINIZ-FILHO ◽

N. M. TÔRRES

Keyword(s):

Phylogenetic Analyses ◽

Null Model ◽

Geographic Range ◽

Climatic Conditions ◽

Null Models ◽

Geometric Constraints ◽

South American ◽

Phylogenetic Structure ◽

Geographic Range Size ◽

Northern Regions

Rapoport effect predicts that species geographic range sizes will increase toward higher latitudes, probably reflecting adaptations to extreme climatic conditions that increase species tolerance. Recently, studies about spatial patterns in species richness and geographic range size may be associated with the geometry of species' ranges. In this context, null models can be used to search for the causal mechanisms associated with these patterns. In this paper, we analyzed Rapoport effect using a null model to evaluate how phylogenetic structure and geometric constraints simultaneously affect latitudinal extents of 40 species of South American terrestrial Carnivora. The latitudinal extents of Carnivora tended to decrease toward Southern latitudes, in the opposite direction expected under a simple Rapoport effect, but in accordance to geometric expectations of position of midpoints in the continent. Using 5000 simulations, it was possible to show that the null regression coefficients of latitudinal extents against midpoints are positively biased, reflecting the geometric constraints in the latitudinal extents. The results were equivalent in phylogenetic and non-phylogenetic analyses. The observed regression coefficient was significantly smaller (line is less inclined) than expected by chance alone, demonstrating that the geometric constraints in the latitudinal extents exist even after controlling for phylogenetic structure in data using eigenvector regressions. This suggests that the "spirit" of Rapoport effect (sensu Lyons & Willig, 1997) could be maintained, i.e., that latitudinal extents in Southern region of the continent are relatively larger than those in Northern regions, even after controlling for phylogenetic effects.

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Testing model adequacy for some Markov regression models for time series

Biometrika ◽

10.1093/biomet/78.1.83 ◽

1991 ◽

Vol 78 (1) ◽

pp. 83-89 ◽

Cited By ~ 14

Author(s):

W. K. LI

Keyword(s):

Time Series ◽

Regression Models ◽

Testing Model ◽

Model Adequacy

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Intrahost speciations and host switches shaped the evolution of herpesviruses

10.1101/418111 ◽

2018 ◽

Cited By ~ 1

Author(s):

Anderson F. Brito ◽

John W. Pinney

Keyword(s):

Early Cretaceous ◽

Late Cretaceous ◽

Evolutionary History ◽

Phylogenetic Analyses ◽

Continental Drift ◽

Divergence Times ◽

Crucial Information ◽

Host Evolution ◽

Over Time

ABSTRACTCospeciation has been suggested to be the main force driving the evolution of herpesviruses, with viral species co-diverging with their hosts along more than 400 million years of evolutionary history. Recent studies, however, have been challenging this assumption, showing that other co-phylogenetic events, such as intrahost speciations and host switches play a central role on their evolution. Most of these studies, however, were performed with undated phylogenies, which may underestimate or overestimate the frequency of certain events. In this study we performed co-phylogenetic analyses using time-calibrated trees of herpesviruses and their hosts. This approach allowed us to (i) infer co-phylogenetic events over time, and (ii) integrate crucial information about continental drift and host biogeography to better understand virus-host evolution. We observed that cospeciations were in fact relatively rare events, taking place mostly after the Late Cretaceous (~100 Millions of years ago). Host switches were particularly common among alphaherpesviruses, where at least 10 transfers were detected. Among beta- and gammaherpesviruses, transfers were less frequent, with intrahost speciations followed by losses playing more prominent roles, especially from the Early Jurassic to the Early Cretaceous, when those viral lineages underwent several intrahost speciations. Our study reinforces the understanding that cospeciations are uncommon events in herpesvirus evolution. More than topological incongruences, mismatches in divergence times were the main disagreements between host and viral phylogenies. In most cases, host switches could not explain such disparities, highlighting the important role of losses and intrahost speciations in the evolution of herpesviruses.

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