Genetic Diversity and Geographic Distribution of Genetically Distinct Rabies Viruses in the Philippines

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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Assessment of genetic diversity of Benguet pine from seed production areas in the Philippines using microsatellite markers

SciVee ◽

10.4016/29129.01 ◽

2011 ◽

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Seed Production ◽

The Philippines ◽

Production Areas

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Genetic diversity of species A rotaviruses detected in clinical and environmental samples, including porcine-like rotaviruses from hospitalized children in the Philippines

Infection Genetics and Evolution ◽

10.1016/j.meegid.2020.104465 ◽

2020 ◽

Vol 85 ◽

pp. 104465

Author(s):

Toshifumi Imagawa ◽

Mayuko Saito ◽

Dai Yamamoto ◽

Mariko Saito-Obata ◽

Yoshifumi Masago ◽

...

Keyword(s):

Genetic Diversity ◽

Environmental Samples ◽

The Philippines ◽

Hospitalized Children

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An Ecological Study of Lactococci Isolated from Raw Milk in the Camembert Cheese Registered Designation of Origin Area

Applied and Environmental Microbiology ◽

10.1128/aem.64.12.4729-4735.1998 ◽

1998 ◽

Vol 64 (12) ◽

pp. 4729-4735 ◽

Cited By ~ 90

Author(s):

D. Corroler ◽

I. Mangin ◽

N. Desmasures ◽

M. Gueguen

Keyword(s):

Genetic Diversity ◽

Geographic Distribution ◽

Ecological Study ◽

Raw Milk ◽

Randomly Amplified Polymorphic Dna ◽

Histidine Biosynthesis ◽

Subspecies Level ◽

Camembert Cheese ◽

Reference Strains ◽

Origin Area

ABSTRACT The genetic diversity of lactococci isolated from raw milk in the Camembert cheese Registered Designation of Origin area was studied. Two seasonal samples (winter and summer) of raw milk were obtained from six farms in two areas (Bessin and Bocage Falaisien) of Normandy. All of the strains analyzed had a Lactococcus lactis subsp.lactis phenotype, whereas the randomly amplified polymorphic DNA (RAPD) technique genotypically identified the strains as members of L. lactis subsp. lactis orL. lactis subsp. cremoris. The genotypes were confirmed by performing standard PCR with primers corresponding to a region of the histidine biosynthesis operon. The geographic distribution of each subspecies of L. lactis was determined; 80% of the Bocage Falaisien strains were members ofL. lactis subsp. lactis, and 30.5% of the Bessin strains were members of L. lactis subsp.lactis. A dendrogram was produced from a computer analysis of the RAPD profiles in order to evaluate the diversity of the lactococci below the subspecies level. The coefficient of similarity for 117 of the 139 strains identified as members of L. lactis subsp.cremoris was as high as 66%. The L. lactis subsp. lactis strains were more heterogeneous and formed 10 separate clusters (the level of similarity among the clusters was 18%). Reference strains of L. lactissubsp. lactis fell into 2 of these 10 clusters, demonstrating that lactococcal isolates are clearly different. As determined by the RAPD profiles, some L. lactis subsp.lactis strains were specific to the farms from which they originated and were recovered throughout the year (in both summer and winter). Therefore, the typicality of L. lactissubsp. lactis strains was linked to the farm of origin rather than the area. These findings emphasize the significance of designation of origin and the specificity of “Camembert de Normandie” cheese.

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You Will Never Walk Alone: Codispersal of JC Polyomavirus with Human Populations

Molecular Biology and Evolution ◽

10.1093/molbev/msz227 ◽

2019 ◽

Vol 37 (2) ◽

pp. 442-454 ◽

Cited By ~ 1

Author(s):

Diego Forni ◽

Rachele Cagliani ◽

Mario Clerici ◽

Uberto Pozzoli ◽

Manuela Sironi

Keyword(s):

Geographic Distribution ◽

Human Population ◽

Strong Support ◽

Time Frame ◽

Genetic Distances ◽

The Philippines ◽

Molecular Dating ◽

Human Populations ◽

Jc Polyomavirus ◽

Reconciliation Analysis

Abstract JC polyomavirus (JCPyV) is one of the most prevalent human viruses. Findings based on the geographic distribution of viral subtypes suggested that JCPyV codiverged with human populations. This view was however challenged by data reporting a much more recent origin and expansion of JCPyV. We collected information on ∼1,100 worldwide strains and we show that their geographic distribution roughly corresponds to major human migratory routes. Bayesian phylogeographic analysis inferred a Subsaharan origin for JCPyV, although with low posterior probability. High confidence inference at internal nodes provided strong support for a long-standing association between the virus and human populations. In line with these data, pairwise FST values for JCPyV and human mtDNA sampled from the same areas showed a positive and significant correlation. Likewise, very strong relationships were found when node ages in the JCPyV phylogeny were correlated with human population genetic distances (nuclear-marker based FST). Reconciliation analysis detected a significant cophylogenetic signal for the human population and JCPyV trees. Notably, JCPyV also traced some relatively recent migration events such as the expansion of people from the Philippines/Taiwan area into Remote Oceania, the gene flow between North-Eastern Siberian and Ainus, and the Koryak contribution to Circum-Arctic Americans. Finally, different molecular dating approaches dated the origin of JCPyV in a time frame that precedes human out-of-Africa migration. Thus, JCPyV infected early human populations and accompanied our species during worldwide dispersal. JCPyV typing can provide reliable geographic information and the virus most likely adapted to the genetic background of human populations.

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Genetic diversity, species phylogeny and historical biogeography of the Aquarius paludum group (Heteroptera: Gerridae)

Insect Systematics & Evolution ◽

10.1163/187631203788964791 ◽

2003 ◽

Vol 34 (3) ◽

pp. 313-327 ◽

Cited By ~ 18

Author(s):

Herbert Zettel ◽

Jakob Damgaard

Keyword(s):

Genetic Diversity ◽

Sequence Data ◽

Mitochondrial Gene ◽

Taxonomic Status ◽

Species Group ◽

Genetic Distances ◽

The Philippines ◽

Disjunct Distribution ◽

Gene Encoding ◽

Vicariance Event

AbstractWe investigated genetic diversity and phylogeny of all water strider species assigned to the Aquarius paludum species group on basis of 425 bp DNA sequence data from the mitochondrial gene encoding cytochrome oxidase subunit I (COI). Parsimony analyses and genetic distances confirmed the taxonomic status of the two recently described species Aquarius lili Polhemus & Polhemus, 1994 from Timor and A. philippinensis Zettel & Ruiz, 2003 from the Philippines as being separate from the widespread Oriental A. adelaidis (Dohrn, 1860). Molecular clock estimates suggest that the disjunct zoogeographical pattern among the three species is due to a Pliocene/Pleistocene long-range dispersal, rather than a Mesozoic vicariance event as previously suggested. However, when we superimposed the disjunct distribution of Southern Hemisphere representatives of the paludum-group onto their phylogenetic relationship, the pattern indicated vicariance events following the break-up of Gondwana.

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