BuzzFeed: 22 Messages from creationists to evolutionists with answers based on Science at Bill Nye - Ken Ham debate

Originally posted on BuzzFeed by Matt Stopera here
22 Messages From Creationists To People Who Believe In Evolution
Asked 22 self-identifying creationists at the Bill Nye/Ken Ham debate to write a message/question/note to the other side. Here’s what they wrote.
posted on February 5, 2014 at 12:12am EST

Answers below questions from Jaye Rodger in the comment section of BuzzFeed, which I thought were well thought-out enough to repost here.

A couple personal points I'd like to make: 1) Grammar is important in being taken seriously, so please learn the proper use of "their" versus "there" versus "they're" (as well as others like "loose" versus "lose" and "monkeys" versus "apes" versus "hominids"); 2) A lot of the questions point to a lack in science education.

Enjoy.

Global warming, atoll formation, and the fate of the Maldives

The Maldives have been in the news a bit lately, sometimes for good reasons (like democratically electing the current president and moving out of a dictatorship of nearly 30 years; or for their amazing coral reefs) and sometimes for bad reasons (like a Maldivian who professed he was an atheist and was then arrested but let go after he recanted; or the western couple who had a marriage ceremony at Vilu Reef Resort and the Maldivians recited slander and curses at the couple in their local language, which was discovered after the happy couple posted their video on YouTube and it was translated by a concerned Maldivian).

Having lived in the Maldives for two years, I've been asked on multiple occasions how long the Maldives have before sinking into the ocean. I was also in the environmental documentary "The Island President" that came out in limited release in late 2011 with fuller distribution in November 2012, which discussed this issue: the fate of the Maldives in the face of global warming and climate change.

In reality, the fate of the Maldives, like those of the coral reefs that created them, is likely to follow a course whereby they are still around a hundred years from now but where they probably will look a lot different than they do today.

I thought that I would clear up a misconception: the Maldives are not sinking. Rather, it is feared that as the lowest-lying nation in the world, they will be the first to succumb to rising sea levels, which is predicted to rise by about 1 meter (3.34 feet) over the next 100 years. As a country with an average height above sea level of just over 4 feet and a highest elevation almost certainly below 20 feet (no country wide survey has taken place and satellite imagery cannot penetrate dense tree cover), the Maldives certainly has a lot to lose from rising sea levels (illustrated in the figure above from Der Spiegel, the German newspaper).

However, in my experience in the Maldives and my understanding of global climate change, I believe the Maldives will still be around in 100 years at current rates of sea level rise, but that perhaps as much as 30+ % will be submerged. Of course, if all the ice on Greenland melted, the global sea level will rise 10 meters, which will spell the doom for the Maldives and a number of other low-lying nations or regions (e.g., Bangladesh, Texas and the Gulf coast of the United States, and many Pacific Island nations).

Having lived there, I think there are 3 main threats to the survival of the Maldives: 1) die-off of corals, mostly through mass coral bleaching events, especially following the 1998 El Niño-Southern Oscillation event that killed over 70% of corals throughout the Maldives; 2) increasing beach erosion from changing weather patterns, exasperated by still-recovering reefs that no longer block sand from leaving the islands; and 3) sea level rise.

One potentially bright spot for the Maldives was noted by Dr. Paul Kench of the University of Auckland in New Zealand, whom has been conducting detailed seasonal geomorphology mapping of Maldivian islands. He discovered at least one island with evidence that 2,500 years ago, the sea level surrounding the Maldives was 50 cm higher than today's sea level. His work has shown that the Maldives can still exist with higher sea levels but also point out that their survival depends on the dynamic ability of coral sand islands to move with changing weather patterns. He found that round islands can shift around on the edge of a reef much easier than elliptical-shaped islands, which tend to be more static. Therefore, the round islands of the Maldives will likely just move around and adjust to changing weather patterns and sea levels, while the longer islands may erode away. This dynamic ability of the Maldives was noted by past explorers (and mentioned in one of Charles Darwin's works on coral reefs and atoll formation) as well as sea-farers from Zanzibar, who traded between Oman and India, calling the Maldives the land of shifting islands.

Unfortunately, there are two main obstacles standing in the way of the natural ability of the Maldives to respond to climate change.

First, the Maldives, at least for the last 1,000 years and confirmed by the oral traditions of Maldivians, have had a stable climate dominated by two shifting monsoons. The winds and rains blow in from one direction for half of the year and the other direction the other half of the year (with a buffer between the seasons). These monsoons are because of the Himalaya Mountains, whereby during winter they pump cold air down their slopes and into India and further down into the Maldives, whereas the other half of the year winds blowing off Africa and the Arabian Peninsula dominate the climate. The problem is that at least for the last 20 years, the traditional Maldivian calendar has become less accurate at predicting the shifting seasons as a result of changing weather patterns. Now, the monsoons aren't behaving exactly like they are "supposed" to (or historically have). Traditionally dry seasons are now wet and vice versa. Not only does this affect tourism but it also affects weather patterns and I have personally witnessed an out-of-season storm come through and carry away 1 meter of beachfront in a single afternoon on a small (but typical) Maldivian coral island. Because a lot of coral is still dead from the 1998 El Niño and subsequent bleaching events, most of the sand I witnessed being carried away crossed over the reef into deeper waters. Therefore, that sand was "lost" as far as island formation was concerned. This is why I personally believe that beach erosion is the greatest threat facing the Maldives today.

Secondly, people now inhabit the Maldives, along with lots of resorts. About 300 islands are now occupied out of a total 1,190 or so. With population growth good and resorts with million-dollar villas counting on specific beach configurations, people don't want to have to deal with the natural ability of islands to survive changing wave patterns through shifting around. When a beachfront villa is destroyed because all the sand surrounding it is undercut, a number of resorts (and local islands as well) have adopted sea walls around the  islands. However, most of the sea walls are built on top of the very reefs that tourists come to see (and even if tourists didn't come to see them, healthy reefs are vital to the survival of the Maldives as far as island formation goes). And while the sea walls do protect the beach and its sand, they prevent water flow (their main function), thereby killing most of the coral inside their barriers. As a result, the lagoons get static water and lower oxygen levels, leading to cyanobacteria (blue-green algae) and other nasty shifts in the ecosystem. 

However, sea walls may be one of the easiest ways to save the Maldives, though the reefs tend to die as a result of trying to save the islands in their current shape configuration to suit human needs. Unfortunately, this practice does not seem like it will change too quickly as the alternative would be to perform multi-year surveys of beachlines before building any structures. And with leases typically only 25 years long and costing millions of dollars, companies want to build right away and recoup their investment costs.

There are a few resorts with good environmental track records, but I don't want to be partisan so I just encourage interested parties to do their research. Trust me, the list is short compared to the 100-150 resorts already in (or being planned for) the Maldives. But just like I also believe that corals will survive into the 22nd century, I'm not so sure that large reefs will survive at the current rate of climate change and exploitation. Already 25% of reefs worldwide are destroyed beyond repair in our lifetimes and another 25% are severely impaired. Following the 1998 El Niño alone, nearly 13% of corals died worldwide (that's 1 out of 8 corals on the planet) as a result of temperature-induced bleaching. Most of the Caribbean is already effectively dead from a healthy ecosystem perspective and something like only 3% of Caribbean reefs are still as diverse as they were 30 years ago. Couple coral loss with overfishing and mass killing of sharks (40-200 million sharks are killed each year) and large herbivores (like sea turtles) and the fate of reefs are grim. But nature always finds a way. It just may be that the "way" that nature adjusts is in a manner completely foreign to what we as people consider beautiful. 

I believe that every environmental problem in the world can be solved by removing people. Of course, this is impractical. However, I also know that all environmental degradation can be stopped and support even higher population densities than today using technology already developed. The problem is that there's no mass will to do so. As a result, I suppose we'll all just have to witness the change while doing our small parts to stem the inevitable tide of biodiversity loss. It just may be one "movie" that we don't really want to watch.

Conservation interviews I did

An interview I did about banning shark fishing / finning and stopping the harvest of sea turtle eggs for human consumption (http://www.cdnn.info/news/eco/e090302a.html)


Finally got a copy uploaded (permanent link I hope) of a video I helped make about conservation in the Maldives by Banyan Tree resorts. It took a while to get a copy up because I had to wait for non-copyrighted music to be produced for the video. Now that it has been, I can freely distribute. Enjoy! Robert http://dl.dropbox.com/u/17064170/BANYAN%20TREE%20MARINE%20LAB-small%20-%20Computer.m4v

Return to the Marianas Trench

Cool that James Cameron has gone back to the Mariana's Trench, almost 7 miles below the sea surface. Wonder if one of these rich adventurers (e.g., Cameron, Richard Branson) will one day accomplish: deepest point on Earth's surface accessible (Mariana Trench), highest point (Mount Everest), and go to outer space (100km up). Would become the greatest adventurer in Earth's history.

Editorial: Last Post

This is the last post (for the foreseeable future) for the "Science Corner" Coral Reef Review. This blog will remain up as an archive to articles reviewed already. I chose to conclude these reviews because I think they've served their purpose: getting a couple semesters worth of reviews of [mostly] coral reef literature in a manner accessible to educated laypersons but technical enough for graduate students. I hope that everyone who's stumbled across this blog has enjoyed their time here. Thank you for reading.

For those looking to further their coral reef biogeography expertise, I recommend the following papers in addition to the ones reviewed over the last few months.

DOWNLOAD * Fredericq, Phillips, Gavio (2000) Observations on the macroalgae communities inhabiting in the northwestern deep-water hard bank Gulf of Mexico. Gulf of Mexico Science, 2:88-96.

DOWNLOAD * Hommersand (1986) The biogeography of the South African marine red algae: a model. Botanica Marina, 29:257-270.

DOWNLOAD * Santelices, Bolton, Meneses (3007) Marine algal communities. In: Witman, Roy (Eds.) Marine Macroecology. Chicago University Press, Chicago IL USA.

DOWNLOAD * Kerswell (2006) Global biodiversity patterns of benthic marine algae. Ecology, 87(10):2479-2488.

DOWNLOAD * Pielou (1977) The latitudinal spans of seaweed species and their patterns of overlap. Journal of Biogeography, 4(4):299-311.

DOWNLOAD * La Ferla, Taplin, Ockwell, Lovett (2002) Continental scale patterns of biodiversity: can higher taxa accurately predict African plant distributions? Botanical Journal of the Linnean Society,138:225-235.

DOWNLOAD * Santos, Cavalcanti, da Silva, Tabarelli (2006) Biogeographical relationships among tropical forests in north-eastern Brazil. Journal of Biogeography, 34(3):1-10.

DOWNLOAD * Grehan (1993) Conservation biogeography and the biodiversity crisis: a global problem in space / time. Biodiversity Letters, 1(5):134-140.

DOWNLOAD * Grehan (1992) Biogeography and conservation in the real world. Global Ecology and Biogeography Letters, 2(3):96-97.

DOWNLOAD * Price (2002) Simultaneous 'hotspots' and 'coldspots' of marine biodiversity and implications for global conservation. Marine Ecology Progress Series, 241:23-27.

Review: Price, Vincent, Venkatachalam, Bolton, Basson (2006) Concordance between different measures of biodiversity in Indian Ocean macroalgae. Marine Ecology Progress Series, 319:85-91.

Feature Paper: DOWNLOAD * Price, Vincent, Venkatachalam, Bolton, Basson (2006) Concordance between different measures of biodiversity in Indian Ocean macroalgae. Marine Ecology Progress Series, 319:85-91.

Author Abstract: We examine relationships between species richness (S), rarity (R) and average taxonomic distinctness (Δ+) from analysis of a comprehensive dataset for benthic marine algae (including Cyanophyta). This comprises 2894 species from 66 sites across the Indian Ocean. Ranked values for the sites, determined according to the 3 metrics, show significant positive correlation (p ≤ 0.01); Mauritius, India and Aldabra emerge as biodiversity ‘hotspots’, while Indonesia (Nias Island), Maldives (Male Atoll) and the Gulf of Aden are ‘coldspots’. Concordance between metrics was unexpected, given their disparity in robustness to sampling rigour and particularly since Δ+ is conceptually unrelated to S and R. Lack of significant latitudinal correlations was also evident except for Δ+, which increased towards temperate waters in the southern hemisphere. This contrasts with the variable patterns observed with longitude, for which significant correlations (negative, i.e. towards the west) were prevalent only for S (algae overall and separate categories except Phaeophyta), evident for R (Cyanophyta only) and absent for Δ+. Hence, use of one floral category as a surrogate for biodiversity in another is not guaranteed. Aquatic biodiversity patterns are complex, in accordance with recent findings derived mainly from faunal datasets. Relationships between different metrics can depend on both the group(s) selected and the environmental or geographical factor(s) examined. Our study is based on analysis of extensive but low resolution (presence/absence) data (Silva et al. 1996) collected from sites of variable size that were not sampled evenly. We address these constraints, but acknowledge the possibility that some patterns may prove to be artefacts, pending analysis of data from recent and ongoing studies. However, we do not expect this to significantly affect our overall conclusions.
 

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: Today's paper is the last of this week's survey of marine algae. Like the previous two papers, it looks at taxonomic diversity other than mere species richness, which is most common. This paper looked at 66 sampling locations throughout the Indian Ocean and examined 2894 species of marine algae among five major taxonomic groups. 

The authors examined species richness, rarity (as a function of range size and not abundance), and average taxonomic distinctness. The authors chose rarity because "unlike endemism it is relatively unaffected by spatial scale." The authors ranked values in each metric and determined "hotspots and coldspots of marine algal biodiversity," revealing "Mauritius, India and Aldabra as the sites of highest diversity [with] Indonesia (Nias Island), Maldives (Male Atoll) and the Gulf of Aden as the sites of lowest diversity." Look to the full paper for the complete list of rankings though some obvious disparities (from sampling effort) are apparent, with for example Kuwait and Iraq having widely varying values even though their coastlines are relatively the same and they are geographically adjacent.

The authors also examined latitudinal and longitudinal diversity patterns, noting that "significant negative correlation with longitude was evident for algae as a whole as well as for Cyanophyta, Rhodophyta and Chlorophyta [corresponding] with generally higher values of species richness in regions within 30 to 80ºE, and with lower values further east within 80 to 120ºE. Only Cyanophyta showed significant correlation (negative) with longitude [for rarity]. Average taxonomic distinctness showed significant correlation (negative) with latitude only for Phaeophyta, equating to an increase towards temperate waters in the southern hemisphere while for longitude no significant association was evident."

One problem the authors found was that for algal data, uniform geographical data are seldom available, with many sites at political levels and they had to log-transform site coastline lengths because of large variation. As a result, species richness was "highly sensitive to uneven sampling areas and effort, even though our computations of species richness attempted to standardize for area disparities."

The authors found that all three metrics "showed strong concurrence in terms of ranking sites as biodiversity hotspots and coldspots." Unlike corals and reef fishes, which we examined last week, there was a "virtual absence of significant latitudinal correlation for all 3 metrics, in contrast to the variable patterns observed with longitude, suggesting that relationships between different biodiversity measures in marine floras may not be straightforward."

One significant conclusion (echoed by the previous two papers) is that algae should probably not be grouped together as a whole, as the authors note that "algae and seaweed are ecological and not taxonomic terms," with the wide differences in seaweeds discussed previously this week. The authors did find stronger longitudinal correlations than latitudinal ones though, with the western Indian Ocean perhaps more diverse than the eastern Indian Ocean (the opposite is generally true for fishes and corals, with the exception of a minor peak in diversity in the Red Sea for those groups). 

Hopefully these three papers enlighten a bit more about algae and consider them as a unique and interesting grouping of diverse and unrelated organisms that doesn't always behave like corals and fishes, while sharing the same ecological place in space and time.

Review: Preskitt, Vroom, Smith (2004) A Rapid Ecological Assessment (REA) quantitative survey method for benthic algae using photoquadrats with scuba. Pacific Science, 58(2):201-209.

Feature Paper: DOWNLOAD * Preskitt, Vroom, Smith (2004) A Rapid Ecological Assessment (REA) quantitative survey method for benthic algae using photoquadrats with scuba. Pacific Science, 58(2):201-209.

Author Abstract: The challenge of assessing seldom-visited, benthic substrates has created the need for a method to describe benthic communities quickly and efficiently. Macroscale rapid ecological assessments (REAs) of algal assemblages provide managers of coral reefs and other benthic ecosystems with the fundamental descriptive data necessary for continued yearly monitoring studies. The high cost of monitoring marine communities, especially remote sites, coupled with the time limitations imposed by scuba, require that statistically valid data be collected as quickly as possible. A photoquadrat method using a digital camera, computer software for photographic analysis, and minimal data collection in the field was compared with the conventional method of point-intersect (grid) quadrats in estimating percentage cover in subtidal benthic communities. In timed studies, photoquadrats yielded twice the number of quadrats (and an almost infinite number of data points) as conventional methods, provided permanent historical records of each site, and minimized observer bias by having only one observer identifying algae in the field. However, photoquadrats required more post-collection computer analyses of digital photographs than conventional methods. In the manual method, observer bias in algal identification can occur depending on the degree of experience of individual divers. On the other hand, photoquadrats rely on one observer in the field and one observer in the laboratory, standardizing algal identification. Overall, photoquadrats do not yield the finer resolution in diversity that was found using point-intersect quadrats but do provide a more precise estimate of percentage cover of the abundant species, as well as establishing a permanent visual record in the time allowed by work with other teams.
 

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 algae are often considered capable of overgrowing corals and precipitating phase shifts on coral reefs that are under nutrient or other environmental stress, it is important to know how to survey them in the field. This week's paper compares various methods used to collect algal field data with the aim at discovering a rapid, scientifically valid method. Yet while algae are the focus of this week's paper, the authors describe photoquadrat techniques that are applicable towards many benthic organisms, including corals. 

Photoquadrats are uniform-sized rectangles or squares (often made of PVC) that are placed over the substrate with a camera attached to them through a frame meant to keep the camera at a set height and angle above the bottom.

The authors designed the protocol as part of remote US-territorial Pacific island surveys conducted regularly by the National Oceanic and Atmospheric Administration (NOAA). The surveys had to "describe community structure and prepare a comprehensive species list for each site [surveyed]." 

The authors compared "conventional methods using point grid, point-intersect methods, or visual estimation" with "photographic and video quadrates." Yet while there were benefits of conventional methods (typically more taxa identified and canopy effects able to be assessed), the negatives (higher training required, more field time required) were enough to veto their use for algal data, which were considered of lower value than coral or fish data. As a result of these constraints, the authors developed a rapid field method that would still allow high-quality data to be collected.

In summary, the method involved laying a transect using fiberglass tape measures, and then placing photoquadrats at pre-determined random places along each transect, taking a high-resolution photograph and then having a second diver identifying "algae within the photoquadrat, recording the relative abundance of the five most abundant algae on a scale of 1 to 5 (with 1 being most abundant), and collecting representative samples of the algal species in the quadrates from outside the framer for later identification in the laboratory."

In the field, researchers were able to collect nearly three times as many photoquadrats as conventional measurements and statistical analyses showed that photoquadrat data were more consistent (in terms of data quality and quantity) than conventional methods. As the authors point out, "photoquadrats are not new; they have been compared with a myriad of point-intersect, visual estimation, and grid quadrate methods and have often been found wanting in scale and in diversity measurements." Their purpose was not to reinvent the wheel, so to speak, but rather to "refine the standard photoquadrat method by adding a two-observer team, note taking, collection of samples, and quadrate mapping to address known concerns with cryptic species."

The authors also found that photoquadrats helped produce more flexible statistical data. "Grid quadrates are static: the number of random points are fixed, usually with too few points due to time limitations, and sometimes the observer must quickly identify algae underwater in less than ideal conditions. In comparison, the photoquadrat method is more flexible in laboratory analysis."

Finally, while photoquadrats may not be appropriate where finer-resolution of taxonomic data and canopy effects are desired, they are appropriate for "quantitatively describing an ecosystem at a macro-community level. The photoquadrat method provides adequate quantitative data, analysis flexibility, and permanent specimens that enable the investigators to determine the patterns in distribution and abundance [of taxa] in remote, inaccessible regions. A standardized rapid ecological assessment protocol not only provides the quantitative data needed to establish baselines for these communities but also ensures that comparable data are collected during the ongoing monitoring needed for management decisions."

Next we'll look at algae in the Indian Ocean and how they differ to the better-surveyed Pacific and Caribbean.

Review: Bates, Saunders, Chopin (2005) An assessment of two taxonomic distinctness indices for detecting seaweed assemblage responses to environmental stress. Botanica Marina, 48:231-243.

Feature Paper: DOWNLOAD * Bates, Saunders, Chopin (2005) An assessment of two taxonomic distinctness indices for detecting seaweed assemblage responses to environmental stress. Botanica Marina, 48:231-243.

 

Author Abstract: We tested the efficacy of two biodiversity indices, average taxonomic distinctness and variation in average taxonomic distinctness, for indicating environmental stress in seaweed assemblages from the Bay of Fundy, New Brunswick, Canada. These indices, which measure the average number of taxonomic levels between species in a sample, offer a potential panacea for biomonitoring because their calculation requires only a species list and a regional taxonomic hierarchy, they offer a statistical framework for testing whether assemblages deviate from an expected taxonomic breadth, and previous studies involving animal assemblages have demonstrated an independence from sampling effort. However, our results were not consistent with previously published studies or with our perception of site conditions. Specifically, putatively impacted sites scored above-average taxonomic distinctness values, while sites otherwise regarded as healthy were indicated as environmentally degraded. We also demonstrate that average taxonomic distinctness values can be negatively correlated with species richness, Shannon diversity and with functional diversity. Further, increasing the breadth of the regional species list to which specific sites were compared resulted in a more conservative test of impact. We recommend that a qualitative understanding of how specific biotic assemblages respond to stress is a necessary prerequisite to use the taxonomic distinctness indices for environmental stress assessments.

 

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 turn our attention to algae, an oft-maligned group of organisms in the marine environment. For those regular readers of Science Corner I have discussed algae at multiple times in the past, both from the perspective of phase shifts (whereby algae opportunistically overgrow corals and other sessile reef organisms when environmental conditions favor their growth, usually through higher nutrient inputs or physical disturbances) as well as through being a group that doesn't have the typical biodiversity patterns that corals and reef fishes do. 

This week's first paper continues the examination of taxonomic similarity that we've covered in past weeks, but applies analyses towards determining whether algae are responding to environmental stress, and therefore whether a phase shift in a reef environment may be occurring.

For those who missed the previous discussions on taxonomic diversity indices, the authors provide a good summary: "Taxonomic distinctness (TD) indices are biodiversity measures that provide a summary of the relatedness between organisms within samples from biological assemblages."

How the authors addressed assessing environmental stress was a two-part process. 

1. First, they developed an index that "incorporates the identity of species within a sample by calculating the average path length between all pairs of species, measured through a cladogram of phylogenetic relationships or a Linnaean classification."

2. Second, the authors "inferred" environmental stress "by testing for departure from an expected range of average taxonomic distinctness values calculated by resampling from a broader ‘‘master list’’ of species that could potentially inhabit the sampling region."

The authors note that their "approach is predicated on the observation that, in several types of marine invertebrate assemblages, disturbance can shift structure from a relatively diverse array of taxa to a suite of closely related species that are not representative of the potential taxonomic structure for an unimpacted site."

In other words, certain organisms are opportunistic and able to rapidly increase in numbers to the point where they overgrow other organisms and shift community compositions. When such a composition is found where a site is known to have high diversity, it could be an indicator that the system is out of balance, particularly if one knows that the environmental surveys leading to such conclusions were an accurate representation of the environmental site at the time of survey.

The authors also examined "variation in taxonomic distinctness," which relates to "the evenness of the taxonomic or phylogenetic relationships between taxa."

The authors then combined analyses of average taxonomic distinctness with variation in taxonomic distinctness to generate a "bivariate scatter plot" and then determine deviation from 95% probability contours within the scatter plots generated for each pairwise analysis.

The authors then applied their approach to surveys of algal assemblages in New Brunswick Canada because "extensive and multiple human impacts have been reported in this area." 

When the authors examined algae as an entire group rather than individual taxonomic clades, they didn't find any sites that appeared to be impacted, which went counter to their hypothesis. They then performed individual analyses on each algal clade separately: Rhodophyta, or red algae; Chlorophyta, or green algae; and Phaeophyceae, or brown algae. 

What many people don't realize is that each algal group evolved separately and independently and that each group is more distinct from each other than frogs are from fish. The brown algae are more related to bacteria, while the green algae are closer to true plants (i.e., land plants, sea grass), and red algae are actually two groups of ancient distinct organisms. All algal groups have different and distinct life histories and reproductive cycles. 

When examining individual algal groups, the authors found that the red algae exhibited deviation from 95% confidence intervals for multiple sites examined. 

While one must be careful of which taxa are grouped, since the authors note that their "results indicate that taxonomic distinctness indices may not perform equally well for all types of bioindicator groups," nevertheless the authors conclude that "average taxonomic distinctness and variation in average taxonomic distinctness offer potentially powerful tools for assessing environmental stress in situations where historical data do not exist, or exist only as species lists collected with unknown sampling effort."

Next we'll look at a good method for conducting algal surveys (which can be expanded to other benthic groups like corals, sponges, bryozoans, etc.) so that uniform sampling effort does occur.

Review: Mora, Chittaro, Sale, Kritzer, Ludsin (2003) Patterns and processes in reef fish diversity. Nature, 421:933-936.

Feature Paper: DOWNLOAD * Mora, Chittaro, Sale, Kritzer, Ludsin (2003) Patterns and processes in reef fish diversity. Nature, 421:933-936.

Author Abstract: A central aim of ecology is to explain the heterogeneous distribution of biodiversity on earth. As expectations of diversity loss grow, this understanding is also critical for effective management and conservation. Although explanations for biodiversity patterns are still a matter for intense debate, they have often been considered to be scale-dependent. At large geographical scales, biogeographers have suggested that variation in species richness results from factors such as area, temperature, environmental stability, and geological processes, among many others. From the species pools generated by these large-scale processes, community ecologists have suggested that local-scale assembly of communities is achieved through processes such as competition, predation, recruitment, disturbances and immigration. Here we analyse hypotheses on speciation and dispersal for reef fish from the Indian and Pacific oceans and show how dispersal from a major centre of origination can simultaneously account for both large-scale gradients in species richness and the structure of local communities.

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: Today we look at a good paper from the eminent journal Nature about the near-global (Indian and Pacific Oceans only) biogeography of reef fishes. The authors examined latitudinal and longitudinal diversity gradients, which for reef fishes and corals are known to peak in diversity within the "coral triangle" area centered between the Philippines and eastern Indonesia through Papua New Guinea to the Solomon Islands, summarized in the figure below.

The authors go on to determine which of "three major, yet different, hypotheses invoking speciation and dispersal [that] have been suggested to explain these large-scale patterns" seems the most plausible given their analyses. The three hypotheses are:

1. "The Centre-of-Origin hypothesis suggests that the IPR [Indo-Pacific Region] is a major centre of speciation from which species disperse to marginal locations."
2. "The Centre-of-Overlap hypothesis proposes that the high diversity in the IPR is due to the overlapping of faunas from several biogeographic provinces."
3. "the Centre-of-Accumulation hypothesis states that speciation occurs in several areas peripheral to the IPR and that species extend their ranges to the IPR by prevailing currents. A variant to the Centre-of-Accumulation hypothesis holds that after extending into the IPR, many species have suffered range reductions through the loss of populations marginal to the IPR."
4. To test the last two hypotheses, the authors note that those hypotheses "state that only the tails of species’ ranges extend into the IPR. Consequently, most species should have their range midpoints marginal to the IPR, resulting in bimodal or multi-modal distributions."
5. The authors' examination of their data revealed "plots of species mid-ranges (both longitudinal and latitudinal) show nonrandom unimodal distributions with peaks coinciding with the geographical position of the IPR (Fig. 1c, d). These distributions rule out these two hypotheses and provide support for the Centre-of-Origin hypothesis. They also support, to some extent, the variant of the Centre-of-Accumulation hypothesis because range reductions through loss of peripheral populations would shift mid-ranges towards the IPR, and, if extensive, this could result in a unimodal distribution of midranges in the vicinity of the IPR."
6. The next task of the authors was to determine whether the Centre-of-Origin hypothesis was more reasonable than the variation of the Centre-of-Accumulation hypothesis, or vice-versa. To answer this question, the authors note that while the former hypothesis predicts "speciation within the IPR" the latter hypothesis predicts "speciation in locations marginal to the IPR."
7. Rather than examining the fossil records to determine zones of speciation, the authors look at patterns of endemism. The authors "assume that centers of endemism contain a preponderance of recently derived species that are yet to expand their ranges (neo-endemics) and thus provide insights into areas where species are most likely to originate."
8. The authors mapped endemism of reef fish in the figure below.

The authors note that the IPR has the highest concentration of endemism in the Indian and Pacific oceans. Therefore, the authors conclude that "this result supports the IPR as a major centre of speciation and confirms the expectation of the Centre-of-Origin hypothesis."

Another cause for high levels of endemism might be that the IPR has "among the highest number of islands per unit of geographical area makes it a place where allopatric speciation might be frequent, especially when considering patterns of recent geological sea level change."

The authors tested various other predictions about the Centre-of-Origin hypothesis specifically and while I'll leave it to readers to look up the original paper, I'll summarize by saying that the authors found additional support for the Centre-of-Origin hypothesis.

The authors' take-home message is that "no location contributes as much to the overall alpha diversity of the Indian and Pacific oceans as does the IPR." However, I should note that certain organisms (such as algae) do not share the same diversity patterns as reef fish and corals, but considering how integral both corals and fishes are to coral reefs, obviously conservation priority should be placed on areas of high diversity (e.g., the Indo-West Pacific "coral triangle") and areas of particular uniqueness (e.g., the noted high-endemism regions in Figure 2 above). 

Next we'll examine the diversity patterns of algae since it is important to review organisms that don't share common diversity patterns since they too are integral to determining any underlying processes that may affect the distribution of algae as well as corals and fishes.

Review: Dethier, McDonald, Strathmann (2003) Colonization and connectivity of habitat patches for coastal marine species distant from source populations. Conservation Biology, 17(4):1024-1035.

Feature Paper: DOWNLOAD * Dethier, McDonald, Strathmann (2003) Colonization and connectivity of habitat patches for coastal marine species distant from source populations. Conservation Biology, 17(4):1024-1035.

Author Abstract: The exchange of propagules or mobile adults between isolated habitat patches is of critical importance for some types of preserves, especially for species that cannot propagate locally. In the marine realm, the role of planktonic dispersal in maintaining viable local populations can be tested by examining life-history traits of species that colonize (or do not colonize) isolated habitat patches. We compared the abundances of benthic species on an exposed rocky jetty surrounded by dissimilar habitats on the coast of Washington (U.S.A.) with those of species at distant bedrock sites within potential source areas. Despite its isolation, the jetty lacked only a small proportion of the potential algal species; these absences could result from the 40- to 100-km distances to larger source areas or from subtle habitat differences at the jetty. Coralline algae are expected to be poor dispersers, both because propagules are short-lived and because adults are unlikely to float. These algae were absent on the study jetty, although they occur on other isolated jetties on this coast. Short-term transplant experiments indicated that corallines can survive locally once they colonize. Few animals were absent; one was a chiton that settles and feeds on coralline algae. Animals with obligate dispersal of offspring were abundant on the jetty despite their inability to propagate locally and despite dilution of larvae dispersing in the plankton from distant sources. Conversely, some animal species with no planktonic phase were also present; thus, organisms with a wide range of life-history traits can persist at this distant and small patch of suitable habitat. Isolation along this shoreline did not eliminate either poor dispersers or obligate dispersers.

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: Today we'll look at an important topic in conservation biology… the connectivity of organisms within an aquatic region. The authors point out that connectivity is more well-known for organisms with short dispersal capacities compared to organisms with long dispersal ranges. 

As the authors point out, "the extreme variation in dispersal of marine plants and animals presents a problem for the design of systems of marine preserves. How well can any single combination of size and spacing of protected areas serve all the target species?"

The whole purpose of the paper is summarized by the authors below: 

"For terrestrial organisms, conservation practices have been informed by island biogeography, metapopulation models, and landscape analyses (Hanski & Gilpin 1997). In the marine realm, however, application of terrestrial models is problematic because most benthic organisms live in two landscapes at different stages in their life histories, one the sea bed and the other the overlying water; the water moves constantly and variably (Sammarco & Heron 1994; McEdward 1995). This connectivity via water ( and planktonic propagules ) constitutes a proposed advantage of marine reserves—their potential for extensive dispersal out into surrounding sites (e.g., Allison et al. 1998; Gerber et al. 2002)—but the connectivity over long distances is subject to debate (e.g., Roberts 1997; Cowen et al. 2000)."

To address their question of how to address connectivity of patchy or isolated marine ecosystems, the authors look at a number of case studies of isolated islands with depauperate faunas and floras and then expand their findings further.

The authors then conducted marine littoral (seashore and nearshore submerged and intertidal habitats) zones around an area of coast in the northwest Pacific coast of the Americas. The authors counted organisms within quadrates. To address whether certain groups of organisms were missing because of habitat or distribution (i.e., dispersal barriers) the authors did transplantation experiments.

The authors paid particular attention to obligate dispersers. A few final observations of the authors were:

"Algae, most or all of which are poor dispersers, were more depauperate even though a rare colonization event should have resulted in good local self-recruitment."

"Overall, our results are encouraging for the design of broadly effective systems of marine reserves. Our results indicate that such varied marine organisms can persist at an isolated site by quite different means. For species with a long pelagic larval period, connectivity and persistence can result from larvae that are dispersed far from the parental area if source populations are large. For species with little or no transport of propagules, persistence can result from much rarer transport between reserves because of a higher capacity for local recruitment."

"Moreover, the absence of some expected species, particularly algae, on isolated jetties suggests that spacing reserves at 50 km could reduce connectivity too much for their arrival or persistence, although distance from sources is not yet demonstrated to be the direct cause of these absences."

Review: Tulloss (1997) Assessment of Similarity Indices for undesirable properties and a new Tripartite Similarity Index based on cost functions, pp.122-143, In: Palm, Chapela (Eds.) Mycology in Sustainable Development: Expanding concepts, vanishing borders. Parkway Publishers, Boone NC USA.

Feature Paper: DOWNLOAD * Tulloss (1997) Assessment of Similarity Indices for undesirable properties and a new Tripartite Similarity Index based on cost functions, pp.122-143, In: Palm, Chapela (Eds.) Mycology in Sustainable Development: Expanding concepts, vanishing borders. Parkway Publishers, Boone NC USA.

Author Abstract: Comparison of lists is a common element of many studies including ethnomycological, ecological, and mycological investigations. The items on the lists might be species in a habitat, uses of a given organism by indigenous people, character states present in an individual fungus, or lists of unusual spellings in segments of the Dead Sea Scrolls. Often, it is desirable to express the similarity of two related lists by some formula (a similarity index). Such an index might be used in summarizing data otherwise presented or as input to further numerical processing, such as the creation of a dendrogram (Pankhurst, 1991:54). In examining several works using formulae to provide a single number expressing the similarity of the contents of two lists, a number of difficulties with the formulae were noted. For example, for some indices the same value was generated for two or more quite different situations, e.g., one in which a pair of lists were nearly identical, and another in which one list was much larger than the other. This problem came up during review of material for the present book, thus motivating the present chapter. The purpose of this chapter is to motivate, describe, and offer an implementation for, a working similarity index that avoids the difficulties noted for the others.

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: Today we'll finish up our review of taxonomic similarity indices with the "Tripartite Similarity Index." This analysis was developed by using mathematical formulas from outside of the biological sciences and applying them towards biology, which is an increasingly common theme as scientists across multiple disciplines are starting to communicate.

The author of today's paper developed a new similarity index because he was dissatisfied with other similarity indices for a number of reasons (summarized in his abstract above). Through his comparison, he reviewed 20 "existing and commonly used similarity indices" and determined that "no problem-free index was found in the list." However, through the review of "manufacturing engineering" cost function metrics, the author was able to create an index that solved the problems of all reviewed indices.

I won't go through all 20 similarity indices reviewed (see the original paper for that), but I highly recommend reviewing the original paper for a thorough explanation of all the pros and cons of each similarity index and considerations that all researchers should have before comparing lists for similarity.

However, for ease, I'll list the 10 indices the author spent a longer time reviewing and debunking, but leave it to the reader to look to the full paper for explanations of all the limitations involved in each index:

1. Simpson Coefficient
2. Second Kulczynski Coefficient
3. Ochiai / Otsuka Coefficient
4. Dice Coefficient
5. Jaccard Coefficient
6. Sokal and Sneath Coefficient
7. First Kulczynski Coefficient
8. Mountford Coefficient
9. Braun-Blanquet Coefficient
10. Fager and McGowan Coefficient

In developing a new similarity index, the author found 8 requirements missing (usually in part, as nearly all similarity indices qualified some of the requirements) from the indices reviewed:

1. "A similarity index shall be sensitive to the relative size of the two lists to be compared; and great difference in size shall be interpreted to reduce the value of the similarity index."
2. "A similarity index shall be sensitive to the size of the sublist shared by a pair of lists; and an increase in difference in size between the smaller of the two lists and the sublist of common entries shall be interpreted to reduce the value of the similarity index."
3. "A similarity index shall be sensitive to the percentage of entries in the larger list that are in common between the lists and to the percentage of entries in the smaller list that are in common between the two lists and shall increase as these two percentages increase."
4. "A similarity index shall yield values having fixed upper and lower bounds."
5. "A similarity index shall have the property that when two lists are identical, the similarity index for the two lists shall be equal to the upper bound of the index."
6. "A similarity index shall have the property that when two lists have no entries in common, the similarity index for the lists shall be equal to the lower bound of the index."
7. "Distribution of values of a similarity index between zero and one shall be such that (a) if the size of two input lists is fixed, then the output shall vary roughly directly as the number of entries shared between the lists; and (b) if the smaller list is a subset of the larger list, then the value of the similarity index shall vary roughly inversely as the size of the larger list."
8. "A similarity index program shall check its input data to verify that the following relationships hold: a + b > 0 and a + c > 0."

Through satisfying all 8 requirements listed above, the author came up with the following formula composed of 3 individual components (hence the name Tripartite Similarity Index): 

T = √(U x S x R) where the following subformulae apply:

The author cautions however that while the Tripartite Similarity Index does satisfy all requirements other authors have described for similarity indices, the T-values produced are a bit abstract and can't be thought of as simple percentages of similarity. Instead, the author notes that "Our primary hope is that our intuitions about a loosely defined property of points in the three dimensional space (similarity) is reflected in the position of a corresponding point on a line."

So now that you have a new formula for comparing lists of data, have fun computing some T-values and compare how the plots appear related to other more commonly taught indices, such as the Simpson, Jaccard, and Braun-Blanquet similarity indices.

Next we'll have two papers dealing with various patterns of species diversity, with links to papers below.