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

The purpose of this study was to investigate the L. monocytogenes occurrence and genetic diversity in three Belgian pork cutting plants. We specifically aim to identify harborage sites and niche locations where this pathogen might occur. A total of 868 samples were taken from a large diversity of food and non-food contact surfaces after cleaning and disinfection (C&D) and during processing. A total of 13% (110/868) of environmental samples tested positive for L. monocytogenes. When looking in more detail, zone 3 non-food contact surfaces were contaminated more often (26%; 72/278) at typical harborage sites, such as floors, drains, and cleaning materials. Food contact surfaces (zone 1) were less frequently contaminated (6%; 25/436), also after C&D. PFGE analysis exhibited low genetic heterogeneity, revealing 11 assigned clonal complexes (CC), four of which (CC8, CC9, CC31, and CC121) were predominant and widespread. Our data suggest (i) the occasional introduction and repeated contamination and/or (ii) the establishment of some persistent meat-adapted clones in all cutting plants. Further, we highlight the importance of well-designed extensive sampling programs combined with genetic characterization to help these facilities take corrective actions to prevent transfer of this pathogen from the environment to the meat.

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Prevalence and genetic diversity of gastroenteritis viruses in hospitalized children < 5 years of age in Maharashtra state, Western India, 2017‐2019

Journal of Medical Virology ◽

10.1002/jmv.27085 ◽

2021 ◽

Author(s):

Varanasi Gopalkrishna ◽

Madhuri S. Joshi ◽

Nutan A. Chavan ◽

Manohar S. Shinde ◽

Atul M. Walimbe ◽

...

Keyword(s):

Genetic Diversity ◽

Western India ◽

Hospitalized Children

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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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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, 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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