A large data set containing coincident in situ chlorophyll and remote sensing reflectance measurements was used to evaluate the accuracy, precision, and suitability of a wide variety of ocean color chlorophyll algorithms for use by SeaWiFS (Sea-viewing Wide Field-of-view Sensor). The radiance-chlorophyll data were assembled from various sources during the SeaWiFS Bio-optical Algorithm Mini-Workshop (SeaBAM) and is composed of 919 stations encompassing chlorophyll concentrations between 0.019 and 32.79 μg L−1. Most of the observations are from Case I nonpolar waters, and ∼20 observations are from more turbid coastal waters. A variety of statistical and graphical criteria were used to evaluate the performances of 2 semianalytic and 15 empirical chlorophyll/pigment algorithms subjected to the SeaBAM data. The empirical algorithms generally performed better than the semianalytic. Cubic polynomial formulations were generally superior to other kinds of equations. Empirical algorithms with increasing complexity (number of coefficients and wavebands), were calibrated to the SeaBAM data, and evaluated to illustrate the relative merits of different formulations. The ocean chlorophyll 2 algorithm (OC2), a modified cubic polynomial (MCP) function which uses Rrs490/Rrs555, well simulates the sigmoidal pattern evident between log-transformed radiance ratios and chlorophyll, and has been chosen as the at-launch SeaWiFS operational chlorophyll a algorithm. Improved performance was obtained using the ocean chlorophyll 4 algorithm (OC4), a four-band (443, 490, 510, 555 nm), maximum band ratio formulation. This maximum band ratio (MBR) is a new approach in empirical ocean color algorithms and has the potential advantage of maintaining the highest possible satellite sensor signal: noise ratio over a 3-orders-of-magnitude range in chlorophyll concentration.

/pdf/ocean-color-chlorophyll-algorithms-for-seawifs-68regm2asj.pdf

Ocean Color Chlorophyll Algorithms for SEAWIFS

Safeguarding human health in the Anthropocene epoch: report of The Rockefeller Foundation–Lancet Commission on planetary health

Habitat loss has pervasive and disruptive impacts on biodiversity in habitat remnants. The magnitude of the ecological impacts of habitat loss can be exacerbated by the spatial arrangement -- or fragmentation -- of remaining habitat. Fragmentation per se is a landscape-level phenomenon in which species that survive in habitat remnants are confronted with a modified environment of reduced area, increased isolation and novel ecological boundaries. The implications of this for individual organisms are many and varied, because species with differing life history strategies are differentially affected by habitat fragmentation. Here, we review the extensive literature on species responses to habitat fragmentation, and detail the numerous ways in which confounding factors have either masked the detection, or prevented the manifestation, of predicted fragmentation effects. Large numbers of empirical studies continue to document changes in species richness with decreasing habitat area, with positive, negative and no relationships regularly reported. The debate surrounding such widely contrasting results is beginning to be resolved by findings that the expected positive species-area relationship can be masked by matrix-derived spatial subsidies of resources to fragment-dwelling species and by the invasion of matrix-dwelling species into habitat edges. Significant advances have been made recently in our understanding of how species interactions are altered at habitat edges as a result of these changes. Interestingly, changes in biotic and abiotic parameters at edges also make ecological processes more variable than in habitat interiors. Individuals are more likely to encounter habitat edges in fragments with convoluted shapes, leading to increased turnover and variability in population size than in fragments that are compact in shape. Habitat isolation in both space and time disrupts species distribution patterns, with consequent effects on metapopulation dynamics and the genetic structure of fragment-dwelling populations. Again, the matrix habitat is a strong determinant of fragmentation effects within remnants because of its role in regulating dispersal and dispersal-related mortality, the provision of spatial subsidies and the potential mediation of edge-related microclimatic gradients. We show that confounding factors can mask many fragmentation effects. For instance, there are multiple ways in which species traits like trophic level, dispersal ability and degree of habitat specialisation influence species-level responses. The temporal scale of investigation may have a strong influence on the results of a study, with short-term crowding effects eventually giving way to long-term extinction debts. Moreover, many fragmentation effects like changes in genetic, morphological or behavioural traits of species require time to appear. By contrast, synergistic interactions of fragmentation with climate change, human-altered disturbance regimes, species interactions and other drivers of population decline may magnify the impacts of fragmentation. To conclude, we emphasise that anthropogenic fragmentation is a recent phenomenon in evolutionary time and suggest that the final, long-term impacts of habitat fragmentation may not yet have shown themselves.

Confounding factors in the detection of species responses to habitat fragmentation

Human coronaviruses (HCoVs) have long been considered inconsequential pathogens, causing the “common cold” in otherwise healthy people. However, in the 21st century, 2 highly pathogenic HCoVs—severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV)—emerged from animal reservoirs to cause global epidemics with alarming morbidity and mortality. In December 2019, yet another pathogenic HCoV, 2019 novel coronavirus (2019-nCoV), was recognized in Wuhan, China, and has caused serious illness and death. The ultimate scope and effect of this outbreak is unclear at present as the situation is rapidly evolving. Coronaviruses are large, enveloped, positivestrand RNA viruses that can be divided into 4 genera: alpha, beta, delta, and gamma, of which alpha and beta CoVs are known to infect humans.1 Four HCoVs (HCoV 229E, NL63, OC43, and HKU1) are endemic globally and account for 10% to 30% of upper respiratory tract infections in adults. Coronaviruses are ecologically diverse with the greatest variety seen in bats, suggesting that they are the reservoirs for many of these viruses.2 Peridomestic mammals may serve as intermediate hosts, facilitating recombination and mutation events with expansion of genetic diversity.

/pdf/coronavirus-infections-more-than-just-the-common-cold-31pt8u66xv.pdf

Coronavirus Infections-More Than Just the Common Cold.

Climate change and livestock: Impacts, adaptation, and mitigation

https://apha.confex.com/apha/responses/129am/165.pdf

Effects of environmental change on emerging parasitic diseases.

To examine the impact of tropical rain-forest destruction on malaria, we conducted a year-long study of the rates at which the primary malaria vector in the Amazon, Anopheles darlingi, fed on humans in areas with varying degrees of ecological alteration in the Peruvian Amazon. Mosquitoes were collected by human biting catches along the Iquitos-Nauta road at sites selected for type of vegetation and controlled for human presence. Deforested sites had an A. darlingi biting rate that was more than 278 times higher than the rate determined for areas that were predominantly forested. Our results indicate that A. darlingi displays significantly increased human-biting activity in areas that have undergone deforestation and development associated with road development.

The effect of deforestation on the human-biting rate of Anopheles darlingi, the primary vector of Falciparum malaria in the Peruvian Amazon.

This study examined the larval breeding habitat of a major South American malaria vector, Anopheles darlingi, in areas with varying degrees of ecologic alteration in the Peruvian Amazon. Water bodies were repeatedly sampled across 112 km of transects along the Iquitos-Nauta road in ecologically varied areas. Field data and satellite imagery were used to determine the landscape composition surrounding each site. Seventeen species of Anopheles larvae were collected. Anopheles darlingi larvae were present in 87 of 844 sites (10.3%). Sites with A. darlingi larvae had an average of 24.1% forest cover, compared with 41.0% for sites without A. darlingi (P < 0.0001). Multivariate analysis identified seasonality, algae, water body size, presence of human populations, and the amount of forest and secondary growth as significant determinants of A. darlingi presence. We conclude that deforestation and associated ecologic alterations are conducive to A. darlingi larval presence, and thereby increase malaria risk.

https://faculty.washington.edu/timbillo/Readings%20and%20documents/interoceanic%20Highway/Peru_from_Darby/Peru_transoceanic/Vittor2009.pdf

Linking deforestation to malaria in the Amazon: characterization of the breeding habitat of the principal malaria vector, Anopheles darlingi.

Considerable interest in the relationship between biodiversity and disease has recently captured the attention of the research community, with important public policy implications. In particular, malaria in the Amazon region is often cited as an example of how forest conservation can improve public health outcomes. However, despite a growing body of literature and an increased understanding of the relationship between malaria and land use / land cover change (LULC) in Amazonia, contradictions have emerged. While some studies report that deforestation increases malaria risk, others claim the opposite. Assessing malaria risk requires examination of dynamic processes among three main components: (i) the environment (i.e. LULC and landscape transformations), (ii) vector biology (e.g. mosquito species distributions, vector activity and life cycle, plasmodium infection rates), and (iii) human populations (e.g. forest-related activity, host susceptibility, movement patterns). In this paper, we conduct a systematic literature review on malaria risk and deforestation in the Amazon focusing on these three components. We explore key features that are likely to generate these contrasting results using the reviewed articles and our own data from Brazil and Peru, and conclude with suggestions for productive avenues in future research. This article is part of the themed issue ‘Conservation, biodiversity and infectious disease: scientific evidence and policy implications9.

https://royalsocietypublishing.org/doi/pdf/10.1098/rstb.2016.0125

Does deforestation promote or inhibit malaria transmission in the Amazon? A systematic literature review and critical appraisal of current evidence.

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Effects of environmental change on emerging parasitic diseases.

The effect of deforestation on the human-biting rate of Anopheles darlingi, the primary vector of Falciparum malaria in the Peruvian Amazon.

Linking deforestation to malaria in the Amazon: characterization of the breeding habitat of the principal malaria vector, Anopheles darlingi.

Does deforestation promote or inhibit malaria transmission in the Amazon? A systematic literature review and critical appraisal of current evidence.