Review: Turner W, Spector S, Gardiner N, Fladeland M, Sterling E, Steininger M (2003) Remote sensing for biodiversity science and conservation. TRENDS in Ecology and Evolution, 18(6):306-314.

Feature Paper: DOWNLOAD Turner W, Spector S, Gardiner N, Fladeland M, Sterling E, Steininger M (2003) Remote sensing for biodiversity science and conservation. TRENDS in Ecology and Evolution, 18(6):306-314.

Author Abstract: Remote-sensing systems typically produce imagery that averages information over tens or even hundreds of square meters – far too coarse to detect most organisms – so the remote sensing of biodiversity would appear to be a fool’s errand. However, advances in the spatial and spectral resolutions of sensors now available to ecologists are making the direct remote sensing of certain aspects of biodiversity increasingly feasible; for example, distinguishing species assemblages or even identifying species of individual trees. In cases where direct detection of individual organisms or assemblages is still beyond our grasp, indirect approaches offer valuable information about diversity patterns. Such approaches derive meaningful environmental parameters from biophysical characteristics that are revealed by remote sensing.

Note to Readers: Follow links above for author email, full article text, or the publishing scientific journal. Author notes in my review are in quotes.

Review: This is the second paper of our 12-week course in biogeography, and the first paper of week 2. We'll review this paper first, followed on Saturday by the second paper. Both of the papers for this week deal with approaches meant to discover, map, and quantify patterns of diversity of various organisms in space.

Remote sensing (the topic of this paper) uses images or data gathered from above an ecosystem or organism as opposed to direct observation and measurement in situ (or in the field). Typically, remote sensing involves either balloons, airplanes, or satellites to capture images of environments and then classify those environments in a variety of ways, which this paper outlines.

The authors define remote sensing, for the terms of their paper, as "the detection of electromagnetic energy from aircraft or satellites" and outline the basics of such systems in an excellent figure (below).

The authors point out that there are three environmental "parameters" often detected through remote-sensing technologies: "primary productivity, climate and habitat structure (including topography)." Other variables listed by the authors that are presently detectable (with varying errors) through remote sensing include: species composition (plants and animals), land cover, chlorophyll (primary productivity), ocean color and circulation, rainfall, soil moisture, phenology, topography, and vertical canopy cover.

The authors list multiple satellites presently used for remote sensing of the environment, with links to each satellite's website. Almost anyone can purchase images produced by such satellites or direct flyovers using specific instruments or parameters for specific regions of the globe.

And while the authors focus on environmental applications, scientists also use remote sensing equipment to detect human encroachment on the environment or to track devastation following natural disasters.

The authors discuss how increases in satellite resolution, coupled with increases in the ability to detect specific spectra along electromagnetic wavelengths and how spectral discrimination of certain plant and animal species has allowed "species-specific land-cover classification from the use of airborne and spaceborne" instruments.

Perhaps the greatest asset of remote sensing is the ability to map and classify large tracks of land, coastal, or aquatic regions and follow changes in their composition over time.

The authors go through the various parameters discussed above and deal with the specific satellites, airplanes, helicopters, etc. and instruments that have been useful thus far in collecting data of various types as outlined above. For anyone thinking about a project involving remote sensing of a specific type of data, I recommend referencing the article section on the remote-sensing instrument you intend to use, as the authors do a good job of outlining the resolutions, accuracies, type of data available from each instrument, and several examples of how each instrument is used presently.

Despite the advantages of remote-sensing (especially for remote areas that are difficult for scientists to access, or as compliments to small-scale surveys that can be expanded regionally using remote sensing coupled with ground trotting) there are still "major challenges involved in working with remote-sensing data." The authors outline the following:

• "Costs for imagery and other data products are often high"
• "Handling even small quantities of satellite imagery requires special software and hardware tools."
• "The technical expertise required to handle imagery and other data products [involve] training and hours spent working with the imagery [as] a prerequisite for understanding what one is looking at."
• "Many of the remote-sensing data types are still largely or exclusively in the research phase of development and might currently be beyond the capabilities of most researchers."
• It is "tremendously important to get accurate information to validate what the remote-sensing data products appear to be telling the user. Such 'ground-truth' information might come from researchers in the field, ground-based sensors, or even higher resolution remote-sensing sources (e.g. aerial photography). [Therefore] remote-sensing products should not be taken at face value."
• "Atmospheric phenomena, mechanical problems with the sensor and numerous other effects might be distorting one's view."
• "Ecological models have a vital role in the process of converting remote-sensing data products into actual knowledge of species distributions and richness."

Despite the challenges, the authors note that remote sensing applications show great promise and more researchers are using such products every year. Yet, "to make progress, ecologists, evolutionary biologists and conservation biologists must bring their data sets on species distributions, levels of species richness, areas of endemism, and so on, to the table and combine them with the global, regional and local data sets of, for example, primary productivity and climate, which have been generated by remote-sensing researchers."

Next we'll cover a paper dealing with the latitudinal species gradient, one of the largest and typically most uniform features in biogeography. Be sure and download the paper and read before the summary.

Review: Crisci, JV (2001) Historical biogeography and patterns of diversity. Journal of Biogeography, 28(2):157-168.

Feature Paper: Crisci, JV (2001) Historical biogeography and patterns of diversity. Journal of Biogeography, 28(2):157-168.


Author Abstract: Historical biogeography is going through an extraordinary revolution concerning its foundations, basic concepts, methods, and relationships to other disciplines of comparative biology. There are external and internal forces that are shaping the present of historical biogeography. The external forces are: global tectonics as the dominant paradigm in geosciences, cladistics as the basic language of comparative biology and the biologist's perception of biogeography. The internal forces are: the proliferation of competing articulations, recourse to philosophy and the debate over fundamentals. The importance of the geographical dimension of life's diversity to any understanding of the history of life on earth is emphasized. Three different kinds of processes that modify the geographical spatial arrangement of the organisms are identified: extinction, dispersal and vicariance. Reconstructing past biogeographic events can be done from three different perspectives: (1) the distribution of individual groups (taxon biogeography) (2) areas of endemism (area biogeography), and (3) biotas (spatial homology). There are at least nine basic historical biogeographic approaches: centre of origin and dispersal, panbiogeography, phylogenetic biogeography, cladistic biogeography, phylogeography, parsimony analysis of endemicity, event-based methods, ancestral areas, and experimental biogeography. These nine approaches contain at least 30 techniques (23 of them have been proposed in the last 14 years). The whole practice and philosophy of biogeography depend upon the development of a coherent and comprehensive conceptual framework for handling the distribution of organisms and events in space.


Note to Readers: Follow links above for author email, full article text, or the publishing scientific journal. Author notes in my review are in quotes.


Review: Since this will be the first paper in a 12-week course on biogeography, I thought I'd take a moment to mention why this paper was chosen for week 1. Crisci (the author) provides a great summary of various kinds of historical biogeography, summarized in his table (below).





But before we get into interpreting Crisci's table (above, which should be referenced throughout this review whenever needed) I thought we'd take a moment to review biogeography in general, even though we've discussed it through multiple Science Corner posts in the past. Biogeography is a branch of science bridging "biology" and "geography" and concerns itself with trying to describe patterns of biodiversity and abundance of organisms of all kinds around the world… in essence, trying to describe how and why organisms occur in the populations they do in space and time. Different biogeographers study different groups of organisms as well as concentrate on whether they merely want to describe patterns of diversity or try to determine reasons why such patterns exist, as well as concerning themselves with various spatial scales. However, biogeographers, regardless of their organisms or focus, often have overlap in their findings, with one of the largest and most uniform (though not universal) observations being that there are distinct latitudinal gradients in species diversity, with tropical regions (at the most basic definition, regions between the Tropics of Cancer and Capricorn, or between 23.5º N or S of the equator) often being the centers of highest species diversity across a wide range of organisms (but not all).


Now that we know "what" biogeography is, we can start to focus, with this 12-week course aimed at discussing multiple ideologies of biogeography as a review before getting into applications of biogeography in "the real world." This first paper is an overview of historical biogeography, which is a branch of biogeography concerned with describing the historical reasons (often at geological timeframes) why organisms occur in their present patterns of diversity today (or within the recent, recorded past). As the author notes, there is a great debate over what factors are the most important in determining present patterns of biodiversity.


But why is this important? Managers use principles of historical biogeography to try to set up effective conservation zones (e.g., National Parks, Marine Protected Areas, etc.) that are able to provide protected areas where "seed populations" can reproduce and settle areas outside of such protected zones, thereby allowing sustainable harvest of environmental resources.


In essence, historical biogeography is a form of "comparative biology concerned with evolutionary processes over millions of years on a large, often global scale." Crisci notes his objectives for his paper being "to discuss the overall situation in which historical biogeography occurs, to outline the contemporary methodologies and to discuss several of the critical issues that need to be tackled."


In attempting to define the present state of historical biogeography, the author draws a comparison to Charles Dickens' opening paragraph of "A tale of two cities" in so much as there is a lot of debate, a lot of discovery, a lot of bias, etc. (i.e., "the best of times, the worst of times"). In essence, historical biogeography is still a young field that has only made its greatest progress since the 1970s.


Crisci outlines "three external forces" as influencing the discipline of historical biogeography: "global tectonics as the dominant paradigm in geosciences, cladistics as the basic language of comparative biology and the biologist's perception of biogeography."


While many today might take for granted the existence of plate tectonics, debate existed into the 1960s on whether the continents on Earth were static or whether they had broken up and separated, as is known today. As Crisci states, "the biogeographical consequences of plate movements and interactions are enormous. The rearrangement of continental landmasses and island areas and the opening and closing of sea and ocean basins initiated by these movements and interactions have profoundly affected the distribution and history of organisms." It was during this era that Charles Darwin's theory of atoll formation (through gradual subsidence of volcanic islands combined with continuous growth upward of fringing reef systems) was also proved, though there is still debate about the universality of his basic principles for atolls around the world.


Crisci then goes on to not how "cladograms" became "a powerful language to communicate a system of relationships to other biologists" through defining the biological and historical "phylogenetic relationships between taxa and their geographical distribution" and noting how they are tied together. Currently, the integration of genetic cladograms with area cladograms (relationships about how different individuals, species / taxa, or localities are similar or dissimilar to each other) is serving an important role in "forcing biogeographers towards a more precise formulation of methodological practices and theoretical ideas and the exact quantification of their implications."


The final external force on historical biogeography outlined by the author is the perception of biogeography by biologists. Crisci notes that many biologists don't understand or like biogeography, either through its complexity or through the diversity of approaches and debates within the field of biogeography. This perspective is exemplified by Nelson (1978):


"Biogeography is a strange discipline. In general, there are no institutes of biogeography; there are no departments of it. There are no professional biogeographers -- no professors of it, no curators of it. It seems to have few traditions. It seems to have few authoritative spokesmen."


Of course, while a number of points are still valid (biogeographers tend either to be biologists or geographers who study organisms in space and time and therefore, necessitate an understanding of biogeographical principles), the science of biogeography has really matured over the last 30-odd years since Nelson's statements.


Crisci then describes the "internal forces shaping the present of historical biogeography" as "the proliferation of competing articulations (e.g. ecology vs. history, panbiogeography vs. cladistic biogeography, event-based methods vs. pattern-based methods); and recourse to philosophy and the debate over fundamentals (e.g. conceptions of space: absolute space vs. relative space)."


Crisci notes that "of the 30 techniques of historical biogeography currently in use, 23 (76%) have been proposed in the last 14 years." The mere presence of such internal debate within just one branch of the growing field of biogeography clearly shows an increase in interest on the subject and in quantifying distribution patterns of organisms around the world.


Crisci then goes on to describe current understanding of a main pillar of biogeography: the spatial arrangement of organisms geographically and throughout time.


There are "three different space-time processes that can modify the geographical spatial arrangement of organisms:
    1)    extinction (the death of all individuals in a local population, a species, or a higher taxon,
    2)    dispersal ([when an organism's] common ancestor originally occurred in one of the areas [studied] and later dispersed into other ones, where descendants survive to present day),
    3)    vicariance ([where an organism's] ancestor was originally widespread in greater areas, which became fragmented, and its descendants have survived in the fragments until now)."


Dispersalism as a doctrine came about through religious interpretations of the Bible's creation story where organisms dispersed from a "garden of Eden" throughout the world, backed up by an erroneous belief that the Earth was stable and that continents never moved. It wasn't until "two botanists, Stanley Cain and Léon Croizat, were among the first scientists to challenge vocally the dispersal explanation as the main process in biogeography and promote vicariance as an equally important process." Today, while debate still exists, some biogeographers push towards recognizing both dispersal and vicariance "as important processes by which organisms achieve their geographical distributions by applying a biogeographic model involving alternating cycles of dispersal and vicariance."


Cricsi then defines the three kinds of vicariance events known to exist:
    1)    "vicariance followed by speciation,
    2)    vicariance events that lack allopatric speciation, and
    3)    vicariance events followed by speciation after a previous speciation event indecent of the vicariance of the area."


Crisci then describes the "nine basic historical biogeographic approaches" summarized in his excellent table copied at the beginning of this review.


    1)    Centre of origin and dispersal: "Originated in the Darwin-Wallace tradition" and believing that "species originate in one centre of origin, from which some individuals subsequently disperse by chance, and then change through natural selection" into different species.


    2)    Panbiogeography: "Originally proposed by Croizat, [it] basically plots distributions of organisms on maps and connects the disjunct distribution areas or collection localities together with lines called tracks. The area where two or more generalized tracks intersect is called [a] node, [meaning] that different ancestral biotic and geological fragments interrelate in space / time."


    3)    Phylogenetic biogeography: "The first approach [proposed by Brundin] to consider a phylogenetic hypothesis for a given group of organisms as the basis for inferring its biogeographic history [and] defined as the study of the history of monophyletic groups in time and space, applying two basic rules: (a) Progression rule (primitive members of a taxon found closer to its centre of origin [compared to variant forms on the periphery], (b) Devitation rule (in any speciation event, an unequal cleavage of the original population is produced [with peripheral populations being variant compared to conservative sister species]."


    4)    Cladistic biogeography: "Developed by Rosen, and Nelson & Platnick, [and[ assumes that the correspondence between phylogenetic relationships and area relationships is biogeographically informative. Analysis comprises two steps: the construction of area cladograms from different taxon cladograms and the derivation of general area cladogram(s)."


    5)    Phylogeography: "Proposed by Avise et al. (1987) and is the study of the principles and processes governing the geographical distribution of genealogical lineages at [the] intraspecific level using mitochondrial DNA in animals and chloroplast DNA in plants. In this approach the individuals are genotyped and assigned to maternal lineages and the resulting phylogeny is related to patterns of geographical distribution."


    6)    Parsimony analysis of endemicity: This approach uses "biota similarity" to classify "localities, quadrates or areas according to their shared taxa by means of the most parsimonious solution."


    7)    Event-based methods: "Postulates explicit models of the processes that have an effect on the geographical distribution of living organisms. The different types of processes (dispersal, extinction, and vicariance) are identified and assigned values of benefit-cost under an explicit model of functioning of nature."


    8)    Ancestral areas: "A cladistic procedure based on a dispersalist approach. The procedure (Bremer 1992) allows one to identify the ancestral area of a group from the topological information of its cladogram given the information of their presence on deep and numerous branches in that cladogram."


    9)    Experimental biogeography: "This approach exploits computers to model faunal build-up repeatedly against a fixed vicariate background over ecological and evolutionary time scales, [enabling] a biogeographer to know both vicariate history and actual phylogeny."
Again, look at Crisci's Table 1 (figure above) for a summary of the approaches compared to each other and look at his paper for greater details about each of the main approaches of historical biogeography, including citations for the main authors or proponents of each theory or approach.


Crisci points out, however, that despite the great growth in techniques aimed at understanding the distribution of organisms throughout the geological history of the Earth in an attempt to accurately describe why we see the current patterns that we do, and that "we have started to babble in the language with which the traces of the past are telling us the history of life on Earth," it is also likely that "this history is so complex that probably we will never see it totally revealed."


Does this mean that the pursuit of imperfect knowledge is a futile waste of time? While I suppose that answer is a deeply internal and personal one for every person in the world (since any of our actions or pursuits in life are likely to be forgotten relatively shortly after we die), I'll conclude with two quotes aimed at helping you determine the answer for yourself.


Karl Popper (1959): "Science never pursues the illusory aim of making its answers final, or even probable. Its advance is, rather, toward the infinite yet attainable aim of ever discovering new, deeper, and more general problems, and of subjecting its ever tentative answers to ever renewed and ever more rigorous tests."


Marcus Aurelius (167-168): "Do not act as if you were going to live ten thousand years. Death hangs over you. While you live, while it is in your power, be good. He who has a vehement desire for posthumous fame does not consider that all those who remember him will themselves also die very soon; then again also they who have succeeded them, until the whole remembrance shall have been extinguished as it is transmitted through people who foolishly admire and perish. But suppose that those who will remember are even immortal, and that the remembrance will be immortal, what then is this to you? And I say not what is it to the dead, but what is it to the living? What is praise except indeed so far as it has a certain utility? For you now reject unseasonably the gift of nature, clinging to something else…."

Review: Porter JW (1974). Community structure of coral reefs on opposite sides of the Isthmus of Panama. Science, 186(4163):543-545.

Feature Paper: Porter JW (1974). Community structure of coral reefs on opposite sides of the Isthmus of Panama. Science, 186(4163):543-545.

Author Abstract: Competition for space among reef corals includes interspecific destruction by extracoelenteric digestion, rapid growth, and overtopping. No Caribbean species excels in all strategies, and on western Caribbean coral reefs there is a positive correlation between coral abundance and diversity. On eastern Pacific coral reefs, however, Pocillopora damicornis excludes other corals, and on these reefs there is an inverse relation between coral abundance and diversity, except in areas where disturbances, such as Acanthaster predation, offset space monopolization.


Note to Readers: Follow links above for author email, full article text, or the publishing scientific journal. Author notes in my review are in quotes.


Review: Before continuing with a scientific journal article review this week, I'll mention just one more point: I've completed the first brief underwater surveys for an island north of Mindanao, Philippines, but I haven't worked up the data yet, so as soon as I can finish that, I'll post the results here on Science Corner.


Okay, on with the review. The paper I've chosen this week is a classic paper and it has ramifications for another classic paper by Connell where he compared the diversity of tropical rainforests and coral reefs and found that their diversities were a result of "intermediate disturbance" on a consistent basis. However, as this week's paper shows, such a result is only likely among Pacific reefs and not among Caribbean reefs. Thus, the common theme in a lot of science is that one should be careful of extrapolating findings from one area of the world to another. Unfortunately, since the highest diversity of corals and reef fishes lies in the coral triangle (central Philippines to central Indonesia and east to the Solomon Islands and northern Papua New Guinea), a lot more coral reef research effort today tends to be given to those reefs compared to the rest of the world. Granted, there are few countries today that don't have relatively well-surveyed reefs, but my main point is that one must be careful with extrapolating their research findings.


In this week's paper, the author found that in the Caribbean surrounding Panama, "there is a positive correlation between coral abundance and diversity" while the opposite, inverse relationship is found in the eastern Pacific Panamanian coast. The author found that Caribbean scleractinian (hard, reef-building) corals are not as competitive as Pacific corals. This means that as coral numbers (abundance) increases, so too does coral diversity (# species) because there are no individual corals that are particularly aggressive to the point where they can outcompete their neighbors and create monospecific stands. In the Pacific, on the other hand, there are corals that are very competitive such that as abundance (coral numbers) increase, the chances that a few very competitive corals make up a larger proportion of the faunal community increases. As a result, coral diversity does not increase with increasing abundance.


The only exceptions to the inverse relationship in the Pacific (that the author found) were during cases of disturbance, such as after hurricanes or when Acanthaster planci (crown of thorns seastars) predated large areas of corals, paving the way for recolonization by other coral recruits.


In Pacific Panama, the coral Pocillopora damicornis was the strongest competitor on their reefs, though elsewhere in the Pacific (such as in the coral triangle), Acropora spp. tend to be the dominant competitors.


The author also found that "although the relative abundances of the coral species change markedly [in Pacific Panama following crown of thorns seastar predation events], for the most part, the order of abundance does not." Hierarchies of dominance followed levels of competitiveness among various coral species.


These results contrast with those of the Caribbean, where "except for several acroporids, which calcify relatively rapidly, no consistent relation exists between a coral's calcification rate and its prevalence on a Jamaican reef."


The reasons why such a dynamic occurs were succinctly summarized by the author: "In the eastern Pacific, rapid growth and high digestive dominance are present in the same species. In the Caribbean, the opposite is true: The species that calcify and grow most rapidly are the least capable of eating other species, while the species that grow most slowly are highest on the digestive dominance scale." As a result, in the Caribbean, high-diversity areas have lots of slow-growing corals that are able to protect their immediate surrounds from competitors through specialized "sweeper tentacles" that digest closely growing neighbors. In the Pacific, fast-growing and competitive corals outcompete slower-growing taxa to the point where areas of high-diversity tend to be lacking in highly competitive species.


Hopefully by revisiting this classic paper, some good principles can be applied to now-extensive global coral assemblage data to determine how extensive the results of this limited study apply.

Review: Laurance WF (2006). Have we overstated the tropical biodiversity crisis? Trends in Ecology and Evolution, 22(2):65-70. doi:10.1016/j.tree.2006.09.014

Feature Paper: Laurance WF (2006). Have we overstated the tropical biodiversity crisis? Trends in Ecology and Evolution, 22(2):65-70. doi:10.1016/j.tree.2006.09.014

Author Abstract: Tropical forests are the most biologically diverse and ecologically complex of terrestrial ecosystems, and are disappearing at alarming rates. It has long been suggested that rapid forest loss and degradation in the tropics, if unabated, could ultimately precipitate a wave of species extinctions, perhaps comparable to mass extinction events in the geological history of the Earth. However, a vigorous debate has erupted following a study by Wright and Muller-Landau that challenges the notion of large-scale tropical extinctions, at least over the next century. Here, I summarize this controversy and describe how the debate is stimulating a serious examination of the causes and biological consequences of future tropical deforestation.

Note to Readers: Follow links above for author email, full article text, or the publishing scientific journal. Author notes in my review are in quotes.

Review: This week we address a topic best elucidated by the author's topic sentence: "Are we on the verge of a massive die-off of tropical species?" While the author uses the examples of tropical forests through various means, the ramifications of the article are significant for coral reefs, another threatened habitat restricted mostly to tropical regions. And as mentioned multiple times in this weekly column, the 1998 El Niño-Southern Oscillation Event killed a full 16+ % of corals worldwide (but up to 100% in some locations, most noticeably in the Maldives and other central Indian Ocean islands). This meant that 1 out of 8 shallow-water, reef-building (hermatypic) corals worldwide died over the course of a few weeks, including some corals determined to be between 600 and 1,000 years old. But before we continue on the thread of marine conservation, we'll get back to the points presented by the author for tropical forests.

The key hypothesis tested in this paper is whether the idea of ecosystem collapse following "rapid forest loss and degradation" is possible for the tropics in the form of mass extinctions.

The author argues that there are scientists both whom believe that mass extinctions are imminent at current rates of degradation and those whom believe that such claims are exaggerated. Certainly, predicting future events (in this case, extinctions) from current trends, especially when data for such trends is less than uniform or under-reported (in the case of illegal logging) is always difficult.

The author's stated purpose in this paper, from the last sentence of the abstract, is to "summarize this controversy and describe how the debate is stimulating a serious examination of the causes and biological consequences of future tropical deforestation."

The first circumstantial evidence presented to claim rapid extinction is occuring is that we know: "most tropical forests are extraordinarily rich in species, remarkably complex ecologically and disappearing at truly alarming rates." Therefore, since scientists cannot ever know the complete biodiversity of the world, it is suspected that many species, even before they are recorded scientifically, go extinct through anthropogenic means. And IF tropical forests are diverse (known through extensive but not exhaustive surveys), and IF such forests are being cut down quicker than they can be surveyed, then it follows logically that a lot of biodiversity is being lost in the process. 

The author then looks at whether such biodiversity lost is consistent with extinctions or with culling (as in "sustainable harvest" of resources) and whether current exploitation rates justify claims of future ecosystem collapse.

The key dissenting position is summarized by the ecologist Dr. S. Joseph Wright, who concluded through extensive research that future "deforestation will slow, regeneration
will accelerate, and mass extinction of tropical forest species will be avoided."

In evaluating the two sides, the author discusses the key assumptions of the Wright and Muller-Landau position of a predicted avoidance of mass extinctions.

Those authors state that most deforestation of an unsustainable kind comes from rural populations (so-called "slash and burn" agriculture, whereby all trees and plants are cut down and then the open area is burned to encourage the regrowth of grasses, which are among the first resettlers after a fire, and which are used to feed cattle and other animals for human consumption). Urban populations are not as linked to deforestation as poor, rural populations. 

One could also say the same about over-fishing, where traditional fishermen tend to sustainably harvest catch for generations while rural immigrants to urban coastal areas tend to take up fishing as a quick way to earn income and therefore don't care about sustainable harvesting techniques.

Wright and Muller-Landau claim that because the trend in population growth favors increasing population density in urban areas over rural areas, that as a result of the "expected minor growth in rural populations, net forest cover [from today] will not change dramatically, especially in Asia and the Americas." The authors claim that as a result, extinction rates in tropical forest should not increase more than 15 - 35% of current levels over the next 20+ years, and while this amount is a significant chunk of biodiversity, the authors claim that it does not justify claims of predicted ecosystem collapse and mass extinctions.

Of particular note though is that nothing is mentioned of keystone species (individual, usually enigmatic or large species), with whose extinction multitude other species also die out because their fates are intertwined. Thus, in the Caribbean, a die-off of several species of sea urchins, coupled with mass coral bleaching and overfishing of herbivorous fish caused phase-shifts of reefs from coral dominated to algal dominated through a cascading "domino" effect. Whether the "more important" species will die off in the predicted 15 - 35% noted above is not known. Still, an eighth to a third of species loss is better than the reverse, where only an eighth to a third of species survive!

Wright and Muller-Landau further predict that with increasing urbanization, many rural slash-and-burn agricultural lands will be abandoned, leaving time to buffer against extinctions and help encourage forest regeneration.

Wright and Muller-Landau also point out that between 2 million to 12,000 years ago, "especially [in] Equatorial Africa, forests repeatedly contracted into small refugia during cooling and drying phases of the Pleistocene." Coupled with the long history of human hunting in the "Amazon, Congo Basin and New Guinea," the authors feel that "such areas would have already lost [before today] many of their extinction-prone species, rendering them less vulnerable to future species losses from deforestation." However, such peoples rarely had a history of extensive agriculture and were instead traditionally hunters and gatherers. Therefore, those forests are unlikely to have experienced the scale of slash-and-burn agriculture they experience today.

However, Wright and Muller-Landau do concede that extinction rates are "likely to be higher in biodiversity hotspots, such as Madagascar, the Philippines and the Brazilian Atlantic forests." Laurance points out that "The 25 biodiversity hotspots identified by Myers et al.
include the entire known ranges of nearly half (44%) of all known vascular plants and over a third (35%) of all vertebrates, and the 16 hotspots that sustain tropical forest have already lost, on average, 90% of their forest cover. Because many local endemics in these hotspots are outside of protected areas, species extinctions are likely to be substantially higher than those projected by Wright and Muller-Landau for the major continental regions."

Laurance points out other uncertainties with the Wright and Muller-Landau paper:

1. Local endemics can be found even within areas where the majority of species have large geographical ranges.

2. Old-growth forests house more species than just net forest cover of similar amounts.

3. Uncertain population trends have variable global projections, from "7 to 15 billion people" by 2100.

4. Growing industrialization and globalization is not uniform (Equatorial Africa is remaining largely rural despite population growth and time) and industrial farming companies and cattle ranches are becoming the norm, leading to larger tracts of deforestation in a given area (rather than patchiness from small-scale farming) than historically.

5. The link between rural populations and forests may not be as clear as Wright and Muller-Landau conclude.

6. The magnitude of extinctions is greatly contested and debated.

7. The precautionary principle "maintains that one should err on the side of caution in conservation matters," which Wright and Muller-Landau don't appear to do.

Nevertheless, despite continuing ongoing debate and obvious work for Wright and Muller-Landau to continue, it would be nice if the future weren't so grim as many predict. 

As a result, I believe that it IS better to proceed with caution and to conserve as much as possible because we never know what the future may hold and it would be a shame if a lot would be gone before it's even discovered!

Review: Connell JH, Hughes TP, Wallace CC (1997). A 30-year study of coral abundance, recruitment, and disturbance at several scales in space and time. Ecological Monographs, 67(4):461-488.

Feature Paper: Connell JH, Hughes TP, Wallace CC (1997). A 30-year study of coral abundance, recruitment, and disturbance at several scales in space and time. Ecological Monographs, 67(4):461-488.

Author Abstract: Observations over a 30-yr period revealed a considerable degree of natural variation in the abundance of corals on Heron Island, Great Barrier Reef, Queensland, Australia. Cover ranged from 0.1% to 0.80%, with a similar large range in colony density, at several temporal and spatial scales. Much of this variation was due to the type, intensity, and spatial scale of disturbances that occurred. Coral assemblages usually recovered from acute disturbances, both on Heron Island and on other Indo-Pacific reefs. In contrast, corals did not recover from chronic disturbances of either natural or human origins, or from gradual declines. Recovery was slower after acute disturbances that altered the physical environment than after disturbances that simply killed or damaged corals. The space and time scales of declines and recoveries in abundance were much smaller on the wave-exposed side of the reef than on the side protected from storms. Recruitment rates were reduced by preemption of space by corals or macroalgae, and by storms that altered the substratum. Thus, the dynamics of abundance in this coral community can be largely understood through the variation in types and scales of disturbances that occurred, and the processes that took place where disturbances were rare.

Note to Readers: Follow links above for author email, full article text, or the publishing scientific journal. Author notes in my review are in quotes.

Review: Considering that today's Saturday Science Corner Post falls on Christmas Day (in the Western Hemisphere), many people are preparing for a New Year and considering the passage of time. With another year, many feel the need to make various resolutions. Therefore, I thought it appropriate that today we'd discuss a paper covering 30 years of data… plenty to reflect upon!

This paper is even more relevant today than before because in 1998 a global El Niño-Southern Oscillation event killed roughly 18% of corals worldwide (through temperature-induced coral bleaching, which we've discussed in several past Science Corner posts). Because this paper was published in 1997 (based on coral reef surveys between 1962 and 1992), it means that the study provides a baseline for coral health pre-1998 El Niño-induced bleaching. Granted, the study described by the authors was specific to Heron Island on the central Great Barrier Reef, meaning that results may not apply to other reef types in other areas of the world.

However, during the 30-year study period, 17 cyclones (hurricanes / typhoons) struck the reefs meaning that responses of corals and benthos to disturbances were recorded (which may have ramifications for understanding coral recovery following El Niños, which are becoming much more frequent). 

The authors' study methods including replicating quadrats and transects over several reefs at Heron Island, including photographs of quadrats (photoquadrats) for individual census areas for 16 censuses.

All coral colonies and other benthos (zoanthids, algae, etc.) were recorded and individual colonies were tracked as they recruited or died within quadrats. Growth and percentage cover of benthos was recorded, as were percentages of non-living substrates (rock, sand, etc.). Belt transects and line-intercept transects, as well as larger quadrats, supplemented permanent quadrats, some of which were resampled periodically throughout the study period.

The authors also tried to "investigate the reasons that some cyclones were more destructive than others to corals" by using "changes in abundance of corals during those 11 intervals between censuses when cyclones passed within 200 km of Heron Island." 

Recruitment rates of corals was calculated using "sequential sets of photographs of the permanent quadrats, or from maps made at successive censuses of the permanently marked belt transects" at one site.

Individual questions the authors addressed in their paper were:

1. "Are abundance estimates from the permanent quadrats representative of the local habitat?"

2. "Spatial and temporal autocorrelation in abundance among samples."

3. "Long-term patterns of change in abundance of corals."

4. "Acute disturbances that affected only the corals."

5. "Recovery after acute or chronic disturbances that affected only the corals."

6. "Acute disturbances that directly affected both the physical environment and the corals."

7. "Recovery after acute disturbances that affected both the physical environment and the corals."

8. "Effects of gradual changes in the physical environment and the corals, with little or no disturbance."

9. "Differences in effects among the different cyclones."

10. "Patterns of recruitment of corals."

11. "Scales of variation in abundance and recruitment of corals."

12. "Scales of variation in recruitment."

Several important conclusions of the authors were:

1. "Studies at all scales of time and space are necessary to understand the mechanisms that determine the dynamics of coral reefs."

2. "Studies over short time spans complement longer term ones. The questions posed should determine the scales of observation needed to answer them."

3. "The great variations in abundance and recruitment of corals at different scales at Heron reef, and at other reefs as well, underline the need for observational and experimental studies at as many scales as possible, if we are to understand the mechanisms underlying these variations."

Review: Barber PH, Palumbi SR, Erdmann MV, Moosa MK (2000). Biogeography: A marine Wallace's line? Nature, 406:692-693.

Feature Paper: Barber PH, Palumbi SR, Erdmann MV, Moosa MK (2000). Biogeography: A marine Wallace's line? Nature, 406:692-693. 


Author Abstract: As most coral reef organisms with a pelagic larval phase are presumed to be readily dispersed between distant populations, sea-surface current patterns should be crucial for predicting ecological and genetic connections among threatened reef populations. Here we investigate this idea by examining variations in the genetic structuring of populations of the mantis shrimp Haptosquilla pulchellataken from 11 reef systems in Indonesia, in which a series of 36 protected areas are presumed to be connected by strong ocean currents. Our results reveal instead that there is a strong regional genetic differentiation that mirrors the separation of ocean basins during the Pleistocene low-sea-level stands, indicating that ecological connections are rare across distances as short as 300–400 km and that biogeographic history also influences contemporary connectivity between reef ecosystems.


Note to Readers: Follow links above for author email, full article text, or the publishing scientific journal. Author notes in my review are in quotes.


Review: The paper we'll review this week addresses a concept known on on land in Australasia called Wallace's line, which among other things, is the biogeographical boundary that separates marsupial and mammalian faunas (with the exception of some bat species) in Australia and parts of Melanesia with Indonesia and the rest of Asia (see figure below from Wikipedia that shows Wallace's line terrestrially, which is demarcated by deep ocean "passes" between islands from Indonesia to Australia).

 

Wallace's line is named after the esteemed 19th century naturalist (and contemporary of Charles Darwin), Alfred Russel Wallace. The "line" varies in distance between land masses but at its shortest (between Bali and Lombok islands in Indonesia) it is only 35 km wide, yet many plants and animals (including birds) fairly consistently show abrupt distribution changes according to the "line." The figure above also shows a few other "lines" that were noted, depending on geomorphology or specific other organism groups, but the main observation is that at some point in the vicinity of central-east Indonesia, the plants and animals of Asia are no longer found, while the plants and animals of Australia and New Guinea (and a few other Indonesian islands) replace them.


The purpose of this week's paper is to show that even though many marine organisms are "presumed to be readily dispersed between distant populations," in fact many boundaries exist (often based on sea-surface and sub-surface oceanic current patterns) that keep populations from dispersing over seemingly invisible boundaries. The entire basis of the field of biogeography is to try and determine why such demarcations and boundaries exist. Sometimes the answer is simple, with deserts or mountains or vast oceans creating natural barriers to dispersal. But sometimes organisms are found in one location but not a nearby and seemingly suitable location, with the reasons less clear.


As the authors point out, "genetic connections among threatened reef populations" must be understood to effectively manage marine protected areas. The authors looked at mantis shrimp population genetics from 11 Indonesian reef systems (encompassing 36 marine protected areas, or MPAs) straddling Wallace's line. They found "a strong regional genetic differentiation that mirrors the separation of ocean basins during the Pleistocene low-sea-level stands, indicating that ecological connections are rare across distances as short as 300-400 km and that biogeographic history also influences contemporary connectivity between reef ecosystems."


What is interesting about the authors' results is that oceanographic drifters (instruments released into the ocean at a given spot and recovered later, allowing a map of known drift) released in the study area "traversed 1,500 km through the Celebes Sea and Makassar Strait in four weeks, indicating that planktonic larvae may travel great distances, yielding high connectivity between distant populations."


In other words, if the mantis shrimp larvae (in this example) could cross Wallace's line, why didn't they? The authors found "a broad genetic break perpendicular to Wallace's line" between marine populations (of a single mantis shrimp species) as close as 300 km despite a predicted larval dispersal distance of 600 km based on benthic reef crustacean larval periods.


The "answer" to the authors' "why" turns out to be "the greater isolation of ocean basins during Pleistocene low-sea-level stands" that preserves separate genetic populations to this day, despite "6,000 - 10,000 years of modern oceanographic conditions" that should have presumably "erased these historical boundaries." 


Because of the clear "break" in genetic connectivity of mantis shrimp populations in the study area over such a short geographic distance corresponding roughly to the historic area of Wallacea (the area between Wallace's line and the Australian continental shelf that consisted of islands during the Pleistocene low-sea-level stand), the authors "suggest the presence of a marine equivalent of Wallace's line."


The ramifications of the authors' finding are that biogeographers must consider historic oceanographic and biogeographic patterns and not just generalized ocean currents.
One might ask whether the authors' results were biased by their case organism, but they found "genetically homogenous populations" in various parts of Indonesia across distances from 10 - 400 km. The authors also found genetic connectivity at low levels (through the occurrence of rare haplotypes) between distant marine populations, even across Wallace's line. However, even terrestrial fauna and flora shows exceptions to Wallace's line and the important point is that most genetic connectivity is effectively stopped by the boundary the authors' examined.


It is also important to point out that the authors looked at a single species that did in fact distribute across the whole of the study area in central Indonesia. Yet, despite being a single species, the authors found divergence in the genetic code of examined specimens. That divergence is the basis for eventual speciation. Therefore, it is important also for biogeographers to consider genetic breaks that can reveal both cryptic species (distinct species that look morphologically the same through conservation of phenotypes but are distinct genetically and do not share genetic connections today) as well as distinct populations of the same species. This is important to know because when scientists and managers create MPAs they want to ensure that healthy populations within MPA boundaries can distribute to regions outside of MPAs.


The authors found that "the association of stomatopod populations with old ocean basins suggests that reef populations throughout Indonesia cannot simply be assumed to be interconnected units; marine reserves need to be designed that also take biogeography and historical oceanography into account." 


The study also shows that animal distribution patterns do not always conform to political boundaries. As a result, greater cooperation is needed to perform surveys between countries as well as to ensure that uniform data are collected within a given country's borders. Even in Indonesia, a country in the center of the coral triangle and a region of peak coral reef diversity for many organisms, significant variation can exist between islands less than 300 km apart.

Review: Kennedy D, Norman C (2005). What don't we know? Science, Special Supplement, 309: 75-102. DOI:10.1126/science.309.5731.75

Feature Paper: Kennedy D, Norman C (2005). What don't we know? Science, Special Supplement, 309: 75-102. DOI:10.1126/science.309.5731.75

Author Abstract: At Science, we tend to get excited about new discoveries that lift the veil a little on how things work, from cells to the universe. That puts our focus firmly on what has been added to our stock of knowledge. For this anniversary issue, we decided to shift our frame of reference, to look instead at what we don’t know: the scientific puzzles that are driving basic scientific research.

 
We began by asking Science’s Senior Editorial Board, our Board of Reviewing Editors, and our own editors and writers to suggest questions that point to critical knowledge gaps. The ground rules: Scientists should have a good shot at answering the questions over the next 25 years, or they should at least know how to go about answering them. We intended simply to choose 25 of these suggestions and turn them into a survey of the big questions facing science. But when a group of editors and writers sat down to select those big questions, we quickly realized that 25 simply wouldn’t convey the grand sweep of cutting-edge research that lies behind the responses we received. So we have ended up with 125 questions, a fitting number for Science’s 125th anniversary.
 
First, a note on what this special issue is not: It is not a survey of the big societal challenges that science can help solve, nor is it a forecast of what science might achieve. Think of it instead as a survey of our scientific ignorance, a broad swath of questions that scientists themselves are asking. As Tom Siegfried puts it in his introductory essay, they are “opportunities to be exploited.”


We selected 25 of the 125 questions to highlight based on several criteria: how fundamental they are, how broad-ranging, and whether their solutions will impact other scientific disciplines. Some have few immediate practical implications—the composition of the universe, for example. Others we chose because the answers will have enormous feasible, or how much the carbon dioxide we are pumping into the atmosphere will warm our planet, for example. Some, such as the nature of dark energy, have come to prominence only recently; others, such as the mechanism behind limb regeneration in amphibians, have intrigued scientists for more than a century. We listed the 25 highlighted questions in no special order, but we did group the 100 additional questions roughly by discipline.
 
Our sister online publications are also devoting special issues to Science’s 125th anniversary. The Science of Aging Knowledge Environment, SAGE KE (www.sageke.org), is surveying several big questions confronting researchers on aging. The Signal Transduction Knowledge Environment, STKE (www.stke.org), has selected classic Science articles that have had a high impact in the field of cell signaling and is highlighting them in an editorial guide. And Science’s Next Wave (www.nextwave.org) is looking at the careers of scientists grappling with some of the questions Science has identified.

 
We are acutely aware that even 125 un- knowns encompass only a partial answer to the question that heads this special section: What Don’t We Know? So we invite you to participate in a special forum on Science’s Web site (www.sciencemag.org/sciext/eletters/125th), in which you can comment on our 125 questions or nominate topics we missed—and we apol- ogize if they are the very questions you are working on.From the nature of the cosmos to the nature of societies, the following 100 questions span the sciences. Some are pieces of questions discussed above; others are big questions in their own right. Some will drive scientific inquiry for the next century; others may soon be answered. Many will undoubtedly spawn new questions.

Note to Readers: Follow links above for author email, full article text, or the publishing scientific journal. Author notes in my review are in quotes.

Review: The paper we'll review this week is a special supplement published by the eminent scientific journal "Science," which tries to outline 125 of the most important questions still remaining in science across a variety of fields. Since only the top questions have a dedicated single-page review written up for them (while remaining questions are only given a few sentences), I think the best way to approach a review this week is to merely list all of the questions mentioned and provide a copy of the special supplement so those interested can read further.

I would point out that the below list is not reflective of my personal views, but those of the Science journal staff, which seem predisposed to physics. Also remember that below is a list of scientific questions so questions such as "Does God exist?" will not be addressed since they can't be addressed scientific.

1. What is the universe made of?
2. Is ours the only universe?
3. What drove cosmic inflation?
4. What is the biological basis of consciousness?
5. When and how did the first stars and galaxies form?
6. Where do ultra-high-energy cosmic rays come from?
7. What powers quasars?
8. What is the nature of black holes?
9. Why do humans have so few genes?
10. Why is there more matter than antimatter?
11. Does the proton decay?
12. What is the nature of gravity?
13. Why is time different from other dimensions?
14. To what extent are genetic variation and personal health linked?
15. Are there smaller building blocks than quarks?
16. Are neutrinos their own antiparticles?
17. Is there a unified theory explaining all correlated electron systems?
18. What is the most powerful laser researchers can build?
19. Can the laws of physics be unified?
20. Can researchers make a perfect optical lens?
21. Is it possible to create magnetic semiconductors that work at room temperature?
22. What is the pairing mechanism behind high-temperature superconductivity?
23. Can we develop a general theory of the dynamics of turbulent flows and the motion of granular materials?
24. How much can human life span be extended?
25. Are there stable high-atomic-number elements?
26. Is superfluidity possible in a solid? If so, how?
27. What is the structure of water?
28. What is the nature of the glassy state?
29. Are there limits to rational chemical synthesis?
30. What controls organ regeneration?
31. What is the ultimate efficiency of photovoltaic cells?
32. Will fusion always be the energy source of the future?
33. What drives the solar magnetic cycle?
34. How do planets form?
35. How can a skin cell become a nerve cell?
36. What causes ice ages?
37. What causes reversals in Earth's magnetic field?
38. Are there earthquake precursors that can lead to useful predictions?
39. Is there -- or was there -- life elsewhere in the solar system?
40. How does a single somatic cell become a whole plant?
41. What is the origin of homochirality in nature?
42. Can we predict how proteins will fold?
43. How many proteins are there in humans?
44. How do proteins find their partners?
45. How does Earth's interior work?
46. How many forms of cell death are there?
47. What keeps intracellular traffic running smoothly?
48. What enables cellular components to copy themselves independent of DNA?
49. What roles to different forms of RNA play in genome function?
50. Are we alone in the universe?
51. What role do telomeres and centromeres play in genome function?
52. Why are some genomes really big and others quite compact?
53. What is all that "junk" doing in our genomes?
54. How much will new technologies lower the cost of sequencing?
55. How and where did life on Earth arise?
56. How do organs and whole organisms know when to stop growing?
57. How can genome changes other than mutations be inherited?
58. How is asymmetry determined in the embryo?
59. How do limbs, fins, and faces develop and evolve?
60. What determines species diversity?
61. What triggers puberty?
62. Are stem cells at the heart of all cancers?
63. Is cancer susceptible to immune control?
64. Can cancers be controlled rather than cured?
65. What genetic changes made us uniquely human?
66. Is inflammation a major factor in all chronic diseases?
67. How do prion diseases work?
68. How much do vertebrates depend on the innate immune system to fight infection?
69. Does immunologic memory require chronic exposure to antigens?
70. How are memories stored and retrieved?
71. Why doesn't a pregnant woman reject her fetus?
72. What synchronizes an organism's circadian clocks?
73. How do migrating organisms find their way?
74. Why do we sleep?
75. How did cooperative behavior evolve?
76. Why do we dream?
77. Why are there critical periods for language learning?
78. Do pheromones influence human behavior?
79. How do general anesthetics work?
80. How will big pictures emerge from a sea of biological data?
81. What causes schizophrenia?
82. What causes autism?
83. To what extent can we stave off Alzheimer's?
84. What is the biological basis of addiction?
85. How far can we push chemical self-assembly?
86. Is morality hard-wired into the brain?
87. What are the limits of learning by machines?
88. How much of personality is genetic?
89. What is the biological root of sexual orientation?
90. What are the limits of conventional computing?
91. Will there ever be a tree of life that systematists can agree on?
92. How many species are there on Earth?
93. What is a species?
94. Why does lateral transfer occur in so many species and how?
95. Who was LUCA (the last universal common ancestor)?
96. Can we selectively shut off immune responses?
97. How did flowers evolve?
98. How do plants make cell walls?
99. How is plant growth controlled?
100. Why aren't all plants immune to all diseases?
101. What is the basis of variation in stress tolerance in plants?
102. Do deeper principles underlie quantum uncertainty and nonlocality?
103. What caused mass extinctions?
104. Can we prevent extinction?
105. Why were some dinosaurs so large?
106. How will ecosystems respond to global warming?
107. Is an effective HIV vaccine feasible?
108. How many kinds of humans coexisted in the recent past, and how did they relate?
109. What gave rise to modern human behavior?
110. What are the roots of human culture?
111. What are the evolutionary roots of language and music?
112. How hot will the Greenhouse World be?
113. What are human races, and how did they develop?
114. Why do some countries grow and others stagnate?
115. What impact do large government deficits have on a country's interest rates and economic growth rate?
116. Are political and economic freedom closely tied?
117. Why has poverty increased and life expectancy declined in sub-Saharan Africa?
118. What can replace cheap oil -- and when?
119. Is there a simple test for determining whether an elliptic curve has an infinite number of rational solutions?
120. Can a Hodge cycle be written as a sum of algebraic cycles?
121. Will Malthus continue to be wrong?
122. Will mathematicians unleash the power of the Navier-Stokes equations?
123. Does Poincaré's test identify spheres in four-dimensional space?
124. Do mathematically interesting zero-value solutions of the Riemann zeta function all have the form of a + bi?
125. Does the Standard Model of particle physics rest on solid mathematical foundations?