Genetic diversity, host-specificity and unusual phylogeography of a cryptic, host-associated species complex of gall-inducing scale insects

ABSTRACTIt has long been hypothesized that polyomaviruses (PyV; familyPolyomaviridae) codiverged with their animal hosts. In contrast, recent analyses suggested that codivergence may only marginally influence the evolution of PyV. We reassess this question by focusing on a single lineage of PyV infecting hominine hosts, the Merkel cell polyomavirus (MCPyV) lineage. By characterizing the genetic diversity of these viruses in seven African great ape taxa, we show that they exhibit very strong host specificity. Reconciliation analyses identify more codivergence than noncodivergence events. In addition, we find that a number of host and PyV divergence events are synchronous. Collectively, our results support codivergence as the dominant process at play during the evolution of the MCPyV lineage. More generally, our results add to the growing body of evidence suggesting an ancient and stable association of PyV and their animal hosts.IMPORTANCEThe processes involved in viral evolution and the interaction of viruses with their hosts are of great scientific interest and public health relevance. It has long been thought that the genetic diversity of double-stranded DNA viruses was generated over long periods of time, similar to typical host evolutionary timescales. This was also hypothesized for polyomaviruses (familyPolyomaviridae), a group comprising several human pathogens, but this remains a point of controversy. Here, we investigate this question by focusing on a single lineage of polyomaviruses that infect both humans and their closest relatives, the African great apes. We show that these viruses exhibit considerable host specificity and that their evolution largely mirrors that of their hosts, suggesting that codivergence with their hosts played a major role in their diversification. Our results provide statistical evidence in favor of an association of polyomaviruses and their hosts over millions of years.

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Genetic diversity in the trypanorhynch cestode Tentacularia coryphaenae Bosc, 1797: evidence for a cosmopolitan distribution and low host specificity in the teleost intermediate host

Parasitology Research ◽

10.1007/s00436-006-0435-1 ◽

2007 ◽

Vol 101 (1) ◽

pp. 153-159 ◽

Cited By ~ 25

Author(s):

Harry W. Palm ◽

A. Waeschenbach ◽

D. T. J. Littlewood

Keyword(s):

Genetic Diversity ◽

Intermediate Host ◽

Host Specificity ◽

Cosmopolitan Distribution ◽

Trypanorhynch Cestode

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Resolving the Tetrastigma loheri s. l. Species Complex (Vitaceae) in the Philippines: No Evidence for Recognizing More than One Species

Systematic Botany ◽

10.1600/036364421x16312067913327 ◽

2021 ◽

Author(s):

Jasper John A. Obico ◽

Julie F. Barcelona ◽

Vincent Bonhomme ◽

Marie Hale ◽

Pieter B. Pelser

Keyword(s):

Genetic Diversity ◽

Species Complex ◽

Species Recognition ◽

Principal Component ◽

The Philippines ◽

Geometric Morphometric ◽

Putative Species ◽

Principal Coordinates ◽

Multiple Species ◽

Vegetative Characters

Tetrastigma loheri (Vitaceae) is a vine species native to Borneo and the Philippines. Because it is a commonly encountered forest species in the Philippines, T. loheri is potentially suitable for studying patterns of genetic diversity and connectivity among fragmented forestecosystems in various parts of this country. However, previous research suggests that T. loheri is part of a species complex in the Philippines (i.e. the T. loheri s. l. complex) that potentially also contains Philippine plants identified as T. diepenhorstii, T. philippinense, T. stenophyllum, andT. trifoliolatum. This uncertainty about its taxonomic delimitation can make it challenging to draw conclusions that are relevant to conservation from genetic studies using this species. Here, we tested the hypothesis that T. loheri s. l. is composed of more than one species in the Philippines.For this, we used generalized mixed Yule coalescent (GMYC) and Poisson tree process (PTP) species delimitation models to identify clades within DNA sequence phylogenies of T. loheri s. l. that might constitute species within this complex. Although these methods identified several putative species, these are statistically poorly supported and subsequent random forest analyses using a geometric morphometric leafshape dataset and several other vegetative characters did not result in the identification of characters that can be used to discriminate these putative species morphologically. Furthermore, the results of principal component and principal coordinates analyses of these data suggest the absence of morphological discontinuities within the species complex. Under a unified species concept that uses phylogenetic and morphological distinction as operational criteria for species recognition, we therefore conclude that the currently available data do not support recognizing multiple species in the T. loheri s. l. complex. This implies that T. loheri is best considered as a single, morphologically variable specieswhen used for studying patterns of genetic diversity and connectivity in the Philippines.

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Genetic Diversity in the Paramecium aurelia Species Complex

Molecular Biology and Evolution ◽

10.1093/molbev/msn266 ◽

2008 ◽

Vol 26 (2) ◽

pp. 421-431 ◽

Cited By ~ 56

Author(s):

F. Catania ◽

F. Wurmser ◽

A. A. Potekhin ◽

E. Przybos ◽

M. Lynch

Keyword(s):

Genetic Diversity ◽

Species Complex

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Multiple markers, niche modelling, and bioregions analyses to evaluate the genetic diversity of a plant species complex

BMC Evolutionary Biology ◽

10.1186/s12862-017-1084-y ◽

2017 ◽

Vol 17 (1) ◽

Cited By ~ 10

Author(s):

Ana Lúcia A. Segatto ◽

Maikel Reck-Kortmann ◽

Caroline Turchetto ◽

Loreta B. Freitas

Keyword(s):

Genetic Diversity ◽

Plant Species ◽

Species Complex ◽

Niche Modelling ◽

Multiple Markers

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Host specificity in the Giardia duodenalis species complex

Infection Genetics and Evolution ◽

10.1016/j.meegid.2017.12.001 ◽

2018 ◽

Vol 66 ◽

pp. 335-345 ◽

Cited By ~ 51

Author(s):

Simone M. Cacciò ◽

Marco Lalle ◽

Staffan G. Svärd

Keyword(s):

Host Specificity ◽

Species Complex ◽

Giardia Duodenalis

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Genetic Diversity of the Ralstonia solanacearum Species Complex in the Southwest Indian Ocean Islands

Frontiers in Plant Science ◽

10.3389/fpls.2017.02139 ◽

2017 ◽

Vol 8 ◽

Cited By ~ 7

Author(s):

Noura Yahiaoui ◽

Jean-Jacques Chéron ◽

Santatra Ravelomanantsoa ◽

Azali A. Hamza ◽

Bobb Petrousse ◽

...

Keyword(s):

Genetic Diversity ◽

Indian Ocean ◽

Ralstonia Solanacearum ◽

Species Complex ◽

Southwest Indian Ocean ◽

Ocean Islands

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Comparison of Colletotrichum orbiculare and Several Allied Colletotrichum spp. for mtDNA RFLPs, Intron RFLP and Sequence Variation, Vegetative Compatibility, and Host Specificity

Phytopathology ◽

10.1094/phyto-97-10-1305 ◽

2007 ◽

Vol 97 (10) ◽

pp. 1305-1314 ◽

Cited By ~ 20

Author(s):

B. Liu ◽

L. A. Wasilwa ◽

T. E. Morelock ◽

N. R. O'Neill ◽

J. C. Correll

Keyword(s):

Host Specificity ◽

Restriction Fragment ◽

Fragment Length ◽

Species Complex ◽

Sequence Variation ◽

Distinct Species ◽

Vegetative Compatibility ◽

Haplotype A ◽

Restriction Fragment Length ◽

Mtdna Haplotype

Based on spore morphology, appressorium development, sequence similarities of the rDNA, and similarities in amplified restriction fragment length polymorphism (AFLP), it has been proposed that Colletotrichum orbiculare, C. trifolii, C. lindemuthianum, and C. malvarum represent a single phylogenetic species, C. orbiculare. In the current study, the phylogenetic relationship among isolates in the C. orbiculare species complex was reassessed. In all, 72 isolates of C. orbiculare from cultivated cucurbit or weed hosts, C. trifolii from alfalfa, C. lindemuthianum from green bean, and C. malvarum from prickly sida (Sida spinosa) were examined for mitochondrial DNA (mtDNA) restriction fragment length polymorphisms (RFLPs), RFLPs and sequence variation of a 900-bp intron of the glutamine synthetase gene and a 200-bp intron of the glyceraldehyde-3-phosphate dehydrogenase gene, and vegetative compatibility. In addition, host specificity was examined in foliar inoculations on cucurbit, bean, and alfalfa hosts. Inoculations also were conducted on cucumber fruit. Genetically distinct isolates, based on vegetative compatibility, within the species complex (C. orbiculare, C. trifolii, and C. malvarum) had an identical mtDNA haplotype (haplotype A) when examined with each of three different restriction enzymes. Isolates of C. lindemuthianum had a very similar mtDNA haplotype to haplotype A, with a single polymorphism detected with the enzyme HaeIII. The four species represent a phylogenetically closely related group based on a statistical analysis of the 900- and 200-bp intron sequences. However, distinct RFLPs in the 900-bp intron were consistently associated with each species and could be used to qualitatively and quantitatively distinguish each species. Furthermore, each of the species showed distinct host specificity, with isolates of C. orbiculare (from cucurbits), C. lindemuthianum, and C. trifolii being pathogenic only on cucurbits, green bean, and alfalfa, respectively. Consequently, distinct and fixed nucleotide, or genotypic (intron sequences and RFLPs) and phenotypic (host specificity) characteristics can be used to distinguish C. orbiculare, C. lindemuthianum, and C. trifolii from one another; therefore, they should be recognized as distinct species. This species delineation is consistent with the most current species concepts in fungi. More isolates and further characterization is needed to determine whether C. orbiculare from cocklebur and C. malvarum represent distinct species. RFLPs of the 900-bp intron may represent a relatively inexpensive, reliable, and useful diagnostic tool for general species differentiation in the genus Colletotrichum.

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