Oral microbiomes from hunter‐gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet

Maladaptation to modern diets has been implicated in several chronic disorders. Given the higher prevalence of disease such as dental caries and chronic gum diseases in industrialized societies, we sought to investigate the impact of different subsistence strategies on oral health and physiology, as documented by the oral microbiome. To control for confounding variables such as environment and host genetics, we sampled saliva from three pairs of populations of hunter‐gatherers and traditional farmers living in close proximity in the Philippines. Deep shotgun sequencing of salivary DNA generated high‐coverage microbiomes along with human genomes. Comparing these microbiomes with publicly available data from individuals living on a Western diet revealed that abundance ratios of core species were significantly correlated with subsistence strategy, with hunter‐gatherers and Westerners occupying either end of a gradient of Neisseria against Haemophilus, and traditional farmers falling in between. Species found preferentially in hunter‐gatherers included microbes often considered as oral pathogens, despite their hosts' apparent good oral health. Discriminant analysis of gene functions revealed vitamin B5 autotrophy and urease‐mediated pH regulation as candidate adaptations of the microbiome to the hunter‐gatherer and Western diets, respectively. These results suggest that major transitions in diet selected for different communities of commensals and likely played a role in the emergence of modern oral pathogens.     

Local Mangrove Planting in the Philippines: Are Fisherfolk and Fishpond Owners Effective Restorationists?

Local fisherfolk and fishpond owners have been practicing “restoration” of mangrove forests in some parts of the Philippines for decades, well before governments and non‐government organizations began to promote the activity as a conservation tool. This paper examines ecological characteristics of these mangrove plantations and compares them to natural mangroves in the same areas. Mangrove planters were interviewed and plantation and natural mangrove forests were surveyed to measure forest structure, composition and regeneration. Compared with natural forests, mangrove plantations were characterized by high densities of small stems, shorter and narrower canopies, and fewer species. For both economic and ecological reasons, the vast majority of people dispersed and planted only Rhizophora mucronata/stylosa and, furthermore, they often thinned other species out of planted areas. There was remarkably little subsequent recruitment of other, nonplanted mangrove species into plantations up to 50 and 60 years of age. This pattern held across a diversity of sites, including plantations that had not been selectively cut or weeded. Important ecological and economic benefits result from local mangrove planting, but catalyzing diverse forest regeneration—at least in the short to medium term—is not one of them. The lesson: if you want to restore diverse mangrove forests, you have to plant diverse mangrove forests.     

"Kissing a Baby Is Not at All Good for Him": Infant Mortality, Medicine, and Colonial Modernity in the U.S.-Occupied Philippines

Feminist scholars have begun to consider the ways indigenous practices of child rearing were and are challenged in (post)colonial discourse and practice, and how these practices have become a terrain on which definitions of nation, state, and economy are contested. In this article, I adopt a historical anthropological approach to consider how Filipino child-rearing strategies were described and stigmatized in educational, public health, and public welfare discourses in the U.S.-occupied Philippines in the early 20th century. I demonstrate how public health practices and discourses that were generated as part of a "benevolent" campaign against high rates of infant mortality were strategically used as a weapon against Filipino arguments for independence. I also consider how discourses constructing Filipino caregivers as overly indulgent were linked to metropolitan concerns about production of the "new industrial man" and were used to develop a racialized critique of the cultural practices of Filipinos.     

Genetic differentiation and distribution of Pyropia acanthophora (Bangiales,Rhodophyta) in the Philippines

Pyropia acanthophora is a foliose Bangiales with widely known endemic populations in Indo-Pacific region. This alga has expanded its range recently as a consequence of introduction. In an attempt to explore the genetic diversity of Py. acanthophora within the Philippines and the impact of the introduction of the species from elsewhere, an examination of molecular differentiation and distribution was undertaken using the mitochondrial COI-5P and plastid rbcL gene sequences. The results revealed that the populations of Py. acanthophora in the Philippines exhibited high haplotypic and genetic diversities, and were found to be distinct from those previously reported as conspecific populations found in Taiwan, India, Japan, Hawaii, and from those introduced populations from Brazil. The network analyses as inferred from rbcL and from the combined COI-5P and rbcL genes showed evidence that the Philippine populations of Py. acanthophora exhibited a chaotic patchiness pattern characterized by a population with highly site-exclusive haplotypes, wide genetic variability and lack of local geographic patterns. The distribution of Py. acanthophora within the Philippines was also found to be greater than what was previously known, ranging from the extreme northwest to extreme northeast mainland Luzon coasts, including Camiguin Is., Cagayan. Understanding the genetic diversity and distribution of Py. acanthophora in the Philippines provides valuable information in relation to the conservation and effective resource management of native populations of Py. acanthophora in the tropical Asian region.     

Coastal Resource Management and Social Differences in Philippine Fishing Communities

Class, ethnic, and gender differences among fisherfolk powerfully influence how the benefits and costs of coastal resource management programs are perceived and experienced in Philippine fishing communities. These and other social differences also limit the efficacy of community participation in these programs and hence the role that local communities can be expected to play in fisheries co-management regimes. Greater attention to institutional changes is needed if the management potential of such regimes is to be realized.     

The roles of geological history and colonization abilities in genetic differentiation between mammalian populations in the Philippine archipelago

Aim To test hypotheses that: (1) late Pleistocene low sea‐level shorelines (rather than current shorelines) define patterns of genetic variation among mammals on oceanic Philippine islands; (2) species‐specific ecological attributes, especially forest fidelity and vagility, determine the extent to which common genetic patterns are exhibited among a set of species; (3) populations show reduced within‐population variation on small, isolated oceanic islands; (4) populations tend to be most highly differentiated on small, isolated islands; and (5) to assess the extent to which patterns of genetic differentiation among multiple species are determined by interactions of ecological traits and geological/geographic conditions. Location The Philippine Islands, a large group of oceanic islands in Southeast (SE) Asia with unusually high levels of endemism among mammals. Methods Starch‐gel electrophoresis of protein allozymes of six species of small fruit bats (Chiroptera, Pteropodidae) and one rodent (Rodentia, Muridae). Results Genetic distances between populations within all species are not correlated with distances between present‐day shorelines, but are positively correlated with distances between shorelines during the last Pleistocene period of low sea level; relatively little intraspecific variation was found within these ‘Pleistocene islands’. Island area and isolation of oceanic populations have only slight effects on standing genetic variation within populations, but populations on some isolated islands have heightened levels of genetic differentiation, and reduced levels of gene flow, relative to other islands. Species associated with disturbed habitat (all of which fly readily across open habitats) show more genetic variation within populations than species associated with primary rain forest (all of which avoid flying out from beneath forest canopy). Species associated with disturbed habitats, which tend to be widely distributed in SE Asia, also show higher rates of gene flow and less differentiation between populations than species associated with rain forest, which tend to be Philippine endemic species. One rain forest bat has levels of gene flow and heterozygosity similar to the forest‐living rodent in our study. Main conclusions The maximum limits of Philippine islands that were reached during Pleistocene periods of low sea level define areas of relative genetic homogeneity, whereas even narrow sea channels between adjacent but permanently isolated oceanic islands are associated with most genetic variation within the species. Moreover, the distance between ‘Pleistocene islands’ is correlated with the extent of genetic distances within species. The structure of genetic variation is strongly influenced by the ecology of the species, predominantly as a result of their varying levels of vagility and ability to tolerate open (non‐forested) habitat. Readily available information on ecology (habitat association and vagility) and geological circumstances (presence or absence of Pleistocene land‐bridges between islands, and distance between oceanic islands during periods of low sea level) are combined to produce a simple predictive model of likely patterns of genetic differentiation (and hence speciation) among these mammals, and probably among other organisms, in oceanic archipelagos.     

Population impacts of collecting sea anemones and anemonefish for the marine aquarium trade in the Philippines

Tropical marine ornamentals comprise an increasingly important fishery worldwide. Although the potential for overexploitation of marine ornamentals is great, few studies have addressed the population-level impacts of ornamental exploitation and few ornamental fisheries are managed. Analysis of catch records obtained from collectors over a four-month period in the vicinity of Cebu, Philippines, showed that anemonefish and anemones comprised close to 60% of the total catch. Underwater visual census surveys revealed that both anemone and anemonefish densities were significantly lower in exploited areas than in protected areas. The low density of anemones on exploited reefs accounted for over 80% of the reduced density of anemonefish at those sites. There were similar numbers of anemonefish per unit area of anemone in protected and exploited sites; however, biomass of anemonefish per unit area of anemone was lower in exploited areas. Reduction of anemone removals is recommended to support the sustainable harvest of anemonefish from this region.     

Floral biology of Philippine morphospecies of the grape relative Leea (Leeaceae)

I observed the floral biology of three Leea morphospecies in a Philippine natural forest habitat. The red-flowered morphospecies Leea guineensis limits selfing through synchronized dichogamy, with male and female flowers temporally separated in the same inflorescence, whereas the two morphospecies of the white-flowered Leea indica might be prone to geitonogamous selfing. Light and soil pH are correlated with phenology. In addition to bees and flies, Leea is visited by wasps, butterflies, beetles, bugs and spiders.     

Type specimens in the Vidal Herbarium at the Real Jardín Botánico,Madrid

Ninety eight type specimens collected by Sebastián Vidal in the Philippines, and kept at the Real Jardín Botánico Herbarium, Madrid (MA), are compiled. Most of these specimens are types of Vidal's names. Only a few are names of other authors (Hoogland, Merrill, and Rolfe). A list of specimens, as well as the indicatio locotypica and number in MA, is presented. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 292–299.     

Adjusting count period strategies to improve the accuracy of forest bird abundance estimates from point transect distance sampling surveys

Although point transect distance sampling methods have become widely used in surveys of forest birds, there has been no attempt to tailor field methods to maximize the accuracy of abundance estimates by minimizing the effects of violations of the method's critical assumptions, which are: (1) birds at distance 0 m are detected with certainty, (2) birds are detected at their initial location and (3) distances to objects are measured accurately. We investigate the effects on abundance estimates for Philippine forest birds of varying the count period from 2 to 10 min, and of including and excluding a pre‐count settling down period. Encounter rates were highly sensitive to count period length but density estimates from 10‐min count periods were, on average, only 13% higher than those from 2‐min periods, and in several cases were actually lower than those from periods of 6–8 min. This was because birds tended to be recorded at greater distances from the recorder as the count period went on, thus ‘stretching out’ detection functions while having little effect on detection rates close to the recorder. For some bird groups, including canopy frugivores and upperstorey gleaning insectivores, density estimates were more than twice as high without than with a settling down period. We suggest that movement away from the recorder is more common than attraction to the recorder, and that unless pilot studies show otherwise, similar studies should not use a settling down period for surveying many species. Count periods that maximized probability of bird detection close to the central point while minimizing the unwanted effects of bird movement during the count period were: 4 min for omnivores, 6 min for nectarivores and upperstorey gleaning insectivores, 8 min for understorey insectivores and canopy frugivores, and a full 10 min for sallying insectivores, ground‐dwellers, carnivores and coucals/koels. We use the results to suggest ‘group‐specific’ count period regimes that could help maximize the accuracy of density estimates from similar studies of tropical forest birds.