The importance of cross-validation, accuracy, and precision for measuring plumage color: A comment on Vaquero-Alba et al. (2016)

Vaquero-Alba and colleagues published a study in The Auk: Ornithological Advances comparing objective color measurements of plumage taken in the field directly on a bird’s body to those taken in the lab on collected feathers arranged to emulate the appearance of a bird’s natural plumage. Although the field measures of plumage color were less repeatable than lab measures, the authors concluded that measurements taken in the field were more representative of a bird’s ‘‘true color.’’ Accordingly, they recommend that researchers should bring spectrophotometers into the field to measure color on live birds. We question the assumption that their field measurements represent true color and highlight concerns regarding their experimental design and methodology. Because they did not measure color of live birds in the lab or the color of plucked feathers in the field, they cannot directly test whether the assessment of color in the field on a live bird is superior. Also, rather than assume field measures are the most accurate or precise way to assess plumage color, we suggest cross-validation with other methodologies, such as digital photography, pigment biochemistry, or measures of a known color standard in both environments. Importantly, researchers should be aware of the limitations and advantages of various methods for measuring plumage color so they can use the method most appropriate for their study. Vaquero-Alba y sus colaboradores publicaron un estudio en The Auk comparando medidas objetivas del color del plumaje tomadas en el campo directamente en el cuerpo del ave con medidas tomadas en el laboratorio en plumas recolectadas y organizadas para emular la apariencia natural del plumaje. Aunque las medidas de campo del color del plumaje fueron menos repetibles que las de laboratorio, los autores concluyeron que las medidas tomadas en el campo fueron ma´s representativas del ‘‘color verdadero’’ de un ave. En consecuencia, recomendaron que los investigadores deben llevar espectrofot ´ ometros a los sitios de campo para medir el color en aves vivas. Cuestionamos la suposici ´on de que sus mediciones de campo representan el ‘‘color verdadero’’ y resaltamos nuestras preocupaciones con respecto a su dise ˜no experimental y metodolog´ıa. Debido a que ellos no midieron el color de las aves vivas en el laboratorio ni el color de las plumas sueltas en el campo, no pueden evaluar directamente si la evaluaci ´on del color en el campo en un ave viva es superior. Tambi´en, en vez de asumir que las medidas de campo son la forma ma´s exacta o precisa de determinar el color del plumaje, sugerimos que se haga una validaci ´on cruzada con otras metodolog´ıas como la fotograf´ıa digital, la bioqu´ımica de los pigmentos o las medidas de un esta´ndar de un color conocido en ambos ambientes. Es importante que los investigadores tengan en cuenta las limitaciones y avances en varios m´etodos para medir el color del plumaje para que puedan usar el m´etodo ma´s apropiado para su estudio

Local Parasite Lineage Sharing In Temperate Grassland Birds Provides Clues About Potential Origins Of Galapagos Avian Plasmodium

Oceanic archipelagos are vulnerable to natural introduction of parasites via migratory birds. Our aim was to characterize the geographic origins of two Plasmodium parasite lineages detected in the Galapagos Islands and in North American breeding bobolinks (Dolichonyx oryzivorus) that regularly stop in Galapagos during migration to their South American overwintering sites. We used samples from a grassland breeding bird assemblage in Nebraska, United States, and parasite DNA sequences from the Galapagos Islands, Ecuador, to compare to global data in a DNA sequence registry. Homologous DNA sequences from parasites detected in bobolinks and more sedentary birds (e.g., brown-headed cowbirds Molothrus ater, and other co-occurring bird species resident on the North American breeding grounds) were compared to those recovered in previous studies from global sites. One parasite lineage that matched between Galapagos birds and the migratory bobolink, Plasmodium lineage B, was the most common lineage detected in the global MalAvi database, matching 49 sequences from unique host/site combinations, 41 of which were of South American origin. We did not detect lineage B in brown-headed cowbirds. The other Galapagos-bobolink match, Plasmodium lineage C, was identical to two other sequences from birds sampled in California. We detected a close variant of lineage C in brown-headed cowbirds. Taken together, this pattern suggests that bobolinks became infected with lineage B on the South American end of their migratory range, and with lineage C on the North American breeding grounds. Overall, we detected more parasite lineages in bobolinks than in cowbirds. Galapagos Plasmodium had similar host breadth compared to the non-Galapagos haemosporidian lineages detected in bobolinks, brown-headed cowbirds, and other grassland species. This study highlights the utility of global haemosporidian data in the context of migratory bird–parasite connectivity. It is possible that migratory bobolinks bring parasites to the Galapagos and that these parasites originate from different biogeographic regions representing both their breeding and overwintering sites

The importance of cross-validation, accuracy, and precision for measuring plumage color: A comment on Vaquero-Alba et al. (2016)

Vaquero-Alba and colleagues published a study in The Auk: Ornithological Advances comparing objective color measurements of plumage taken in the field directly on a bird’s body to those taken in the lab on collected feathers arranged to emulate the appearance of a bird’s natural plumage. Although the field measures of plumage color were less repeatable than lab measures, the authors concluded that measurements taken in the field were more representative of a bird’s ‘‘true color.’’ Accordingly, they recommend that researchers should bring spectrophotometers into the field to measure color on live birds. We question the assumption that their field measurements represent true color and highlight concerns regarding their experimental design and methodology. Because they did not measure color of live birds in the lab or the color of plucked feathers in the field, they cannot directly test whether the assessment of color in the field on a live bird is superior. Also, rather than assume field measures are the most accurate or precise way to assess plumage color, we suggest cross-validation with other methodologies, such as digital photography, pigment biochemistry, or measures of a known color standard in both environments. Importantly, researchers should be aware of the limitations and advantages of various methods for measuring plumage color so they can use the method most appropriate for their study. Vaquero-Alba y sus colaboradores publicaron un estudio en The Auk comparando medidas objetivas del color del plumaje tomadas en el campo directamente en el cuerpo del ave con medidas tomadas en el laboratorio en plumas recolectadas y organizadas para emular la apariencia natural del plumaje. Aunque las medidas de campo del color del plumaje fueron menos repetibles que las de laboratorio, los autores concluyeron que las medidas tomadas en el campo fueron ma´s representativas del ‘‘color verdadero’’ de un ave. En consecuencia, recomendaron que los investigadores deben llevar espectrofot ´ ometros a los sitios de campo para medir el color en aves vivas. Cuestionamos la suposici ´on de que sus mediciones de campo representan el ‘‘color verdadero’’ y resaltamos nuestras preocupaciones con respecto a su dise ˜no experimental y metodolog´ıa. Debido a que ellos no midieron el color de las aves vivas en el laboratorio ni el color de las plumas sueltas en el campo, no pueden evaluar directamente si la evaluaci ´on del color en el campo en un ave viva es superior. Tambi´en, en vez de asumir que las medidas de campo son la forma ma´s exacta o precisa de determinar el color del plumaje, sugerimos que se haga una validaci ´on cruzada con otras metodolog´ıas como la fotograf´ıa digital, la bioqu´ımica de los pigmentos o las medidas de un esta´ndar de un color conocido en ambos ambientes. Es importante que los investigadores tengan en cuenta las limitaciones y avances en varios m´etodos para medir el color del plumaje para que puedan usar el m´etodo ma´s apropiado para su estudio

The Long Island Breast Cancer Study Project: description of a multi-institutional collaboration to identify environmental risk factors for breast cancer

The Long Island Breast Cancer Study Project is a federally mandated, population-based case-control study to determine whether breast cancer risk among women in the counties of Nassau and Suffolk, NY, is associated with selected environmental exposures, assessed by blood samples, self-reports, and environmental home samples. This report describes the collaborative project’s background, rationale, methods, participation rates, and distributions of known risk factors for breast cancer by case-control status, by blood donation, and by availability of environmental home samples. Interview response rates among eligible cases and controls were 82.1% (n=1,508) and 62.8% (n=1,556), respectively. Among case and control respondents who completed the interviewer-administered questionnaire, 98.2 and 97.6% self-completed the food frequency questionnaire; 73.0 and 73.3% donated a blood sample; and 93.0 and 83.3% donated a urine sample. Among a random sample of case and control respondents who are long-term residents, samples of dust (83.6 and 83.0%); soil (93.5 and 89.7%); and water (94.3 and 93.9%) were collected. Established risk factors for breast cancer that were found to increase risk among Long Island women include lower parity, late age at first birth, little or no breast feeding, and family history of breast cancer. Factors that were found to be associated with a decreased likelihood that a respondent would donate blood include increasing age and past smoking; factors associated with an increased probability include white or other race, alcohol use, ever breastfed, ever use of hormone replacement therapy, ever use of oral contraceptives, and ever had a mammogram. Long-term residents (defined as 15+ years in the interview home) with environmental home samples did not differ from other long-term residents, although there were a number of differences in risk factor distributions between long-term residents and other participants, as anticipated

Efficacy Results of a Trial of a Herpes Simplex Vaccine

Two previous studies of a herpes simplex virus type 2 (HSV-2) subunit vaccine containing glycoprotein D in HSV-discordant couples revealed 73% and 74% efficacy against genital disease in women who were negative for both HSV type 1 (HSV-1) and HSV-2 antibodies. Efficacy was not observed in men or HSV-1 seropositive women

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity