Being a clover isn’t always so lucky

Happy St. Patrick’s Day! I thought that covering an article about Trifolium (clover) seemed very appropriate. In a recent paper, Matthias Schleuning and colleagues examine the population dynamics of Trifolium montanum, a species in decline in central Germany. They examined the relative threats of habitat fragmentation and degradation on T. montanum’s population dynamics. They found that both degradation and fragmentation were having serious negative impacts. Degraded habitats in this system mean the shift away from nutrient-poor conditions and include the invasion of taller species that are better light competitors. T. montanum is a poor light competitor and maintains larger populations in mown or grazed habitats that keep taller invaders out. This species also faces the double whammy of fragmented habitats resulting in isolated populations. These isolates have lower reproductive output likely due to greater inbreeding and less genetic transfer, via pollinators, among different populations.

I always think of Trifolium species as being particularly common and widely distributed, but there are some that are threatened and potentially tell us about the threats faced by imperiled plant populations. In fact, while a number of North American Trifolium species have successfully invaded North America, but T. montanum is not, according to the USDA Plants Database. These results reveal that these negative effects affect plants at different stages of their life cycle (growth to maturity vs. recuitment) and that log-term persistence of these populations requires management activities that ameliorate both of these effects.

SCHLEUNING, M., NIGGEMANN, M., BECKER, U., & MATTHIES, D. (2009). Negative effects of habitat degradation and fragmentation on the declining grassland plant Trifolium montanum Basic and Applied Ecology, 10 (1), 61-69 DOI: 10.1016/j.baae.2007.12.002

A roadmap to generalized linear mixed models

In a recent paper in TREE, Ben Bolker (from the University of Florida) and colleagues describe the use of generalized linear mixed models for ecology and evolution. GLMMs are used more and more in evolution and ecology given how powerful they are, basically because they allow the use of random and fix effects and can analyze non-normal data better than other models. The authors made a really good job at explaining what to use when. Despite the fact that you need more than basic knowledge of stats to fully understand this guide, I think that people should take a look at it before starting to plan their projects, since it outlines really well all the possible alternatives (and challenges) that one can have when analyzing data. This article also describes what is available in each software package; this is really useful since is not obvious with program in SAS or R you need to use when dealing with some specific GLMMs.

Bolker, B., Brooks, M., Clark, C., Geange, S., Poulsen, J., Stevens, M., & White, J. (2009). Generalized linear mixed models: a practical guide for ecology and evolution Trends in Ecology & Evolution, 24 (3), 127-135 DOI: 10.1016/j.tree.2008.10.008

Salamaders and climate change -impending extinctions?

By the now the evidence of a global frog decline, perhaps even an extinction crisis, has been well documented. But what about salamanders? They are normally less abundant and less-studied compared to frogs, but is there evidence of the same general pattern of declining population sizes? According to Sean Rovito and colleagues, the answer is unfortunately yes. They repeated a plethodontid (lungless) salamander survey done in the 1970’s in Central America and found that many species have declined. In fact they failed to find a couple of previously very abundant species. They also found that species declines were phylogenetically non-random and so these declines may result in the loss of whole clades of species, meaning that the evolutionary history of these salamanders is at risk.

The authors attempted to determine the cause of these declines and found that neither habitat loss or the chytridiomycosis fungal disease implicated in other declines explained these salamander declines. The authors hypothesize that these declines are a direct result of climate change –namely changing temperature and humidity. If so, we may be witnessing some of the first extinctions that are directly caused by climate change.

S. M. Rovito, G. Parra-Olea, C. R. Vasquez-Almazan, T. J. Papenfuss, D. B. Wake (2009). Dramatic declines in neotropical salamander populations are an important part of the global amphibian crisis Proceedings of the National Academy of Sciences, 106 (9), 3231-3236 DOI: 10.1073/pnas.0813051106

Post script:
We had a comment questioning the use of climate change as an explanation and here is my response.

Science works by finding parsimonious explanations, until through experimentation or observation another, better explanation emerges. The previous explanations of habitat loss or fungal infections were not supported. These habitats, known as cloud forests, are very humid. The lungless salamanders have no lungs and instead breath through their skin, which must be kept moist. These forest are becoming drier, hence the probable connection. Here's a quote from the paper:

"Pounds et al. (25) used modeling to show that largescale warming led to a greater decrease in relative humidity at Monteverde compared to that caused by deforestation. Species of cloud forest salamanders that can still be found rely at least
in part on bromeliads. Bromeliads depend on cloud water deposition and are predicted to be articularly vulnerable to climate change (26, 27)."

Doesn't sound like "magic" to me, rather a robust hypothesized mechanism worthy of more testing. Given that species are going extinct, it is important to suggest likely mechanisms, providing an impetus for more research.

For those that think that scientists use climate change as boogey man to scare up more research funding (i.e., Crichton), please read the science. You'll discover honest, hardworking folks that are trying to understand this changing world and whose research can only benefit you , me and the salamanders.

Phytoplankton motility and morphology might influence red tides

Thin layers, intense congregations of phytoplankton that can extend horizontally for kilometers, can be either a boon or a bust to marine food webs. On the one hand, these layers can stimulate the food web from the bottom up by providing elevated concentrations of marine snow (e.g., protozoa and organic detritus), bacteria, and plankton. On the other hand, because many of the phytoplankton species found in thin layers can be toxic, these layers can disrupt grazing, cause zooplankton and fish die-offs, and seed algal blooms at the ocean’s surface that can generate red tides. Understanding the processes driving the formation of thin layers is crucial for predicting their occurrence and ecological impact.

Although thin layer formation was previously thought to be solely influenced by abiotic forces, a recent paper in Science by William M. Durham and colleagues suggests that plankton’s swimming and shape play a role. Many phytoplankton species swim upward against gravity. When the water is calm, they swim up in a straight path. But add ocean currents to the equation, and the plankton start to encounter vertical shear where layers of faster- and slower- moving water meet. These shear forces can cause the plankton to tumble and spin instead of swimming straight up. The tumbling plankton become trapped in these regions of high shear, accumulating in a thin layer. The strength of the shear forces interacts with the morphology of the plankton to determine which species get trapped. For instance, bottom heavy species require higher shear to knock them off their straight path. Durham et al.’s findings suggest that vertical shear and cell morphology could be important predictors of red tides.

W. M. Durham, J. O. Kessler, R. Stocker (2009). Disruption of Vertical Motility by Shear Triggers Formation of Thin Phytoplankton Layers Science, 323 (5917), 1067-1070 DOI: 10.1126/science.1167334

Peace and conservation biology

A recent study published in Conservation Biology found that conservation hotspots are also hotspots for wars. Most of the wars (90%!) from 1950 to 2000 have been on countries that have these key areas for conservation, and 80% of these conflicts took place directly within the conservation hotspots. The authors mention many problems, such as the destruction of vegetation (i.e. the application of Agent Orange to detect enemies), poaching by soldiers, or that the cost of war could come at the expense of other government projects, such as conservation programs. But, there is not all bad news regarding biodiversity conservation (of course is Always bad news for humans), since these wars have created spaces with very low human impact (such as buffer areas with no human activity), or reduces economic activity that can make wartime a recovery period for some exploited species, and other unique situations. They conclude that since most of our biodiversity is in unstable regions, plans to conserve biodiversity should be also active in these regions, which are not the most appealing to work in, but may the most important. Also, that we need to integrate conservation biology into military and humanitarian programs that operate in these conflict zones.

These news are really sad, and I hope that we can live in peace for the benefits of all the species living in here (including, of course, Homo sapiens).

THOR HANSON, THOMAS M. BROOKS, GUSTAVO A. B. DA FONSECA, MICHAEL HOFFMANN, JOHN F. LAMOREUX, GARY MACHLIS, CRISTINA G. MITTERMEIER, RUSSELL A. MITTERMEIER, JOHN D. PILGRIM (2009). Warfare in Biodiversity Hotspots Conservation Biology DOI: 10.1111/j.1523-1739.2009.01166.x

The incredible spreadable weeds

Research into the spread of non-native species usually assumes a long time lag between introduction and rapid spread, and many studies cite 50 years as the lag time. The reason for believing this is that it is thought that there needs to be sufficient time for adaptations to fine tune the fit between the exotic and its new environment, or that densities are so low to start with, finding mates and buffering populations from stochasticity (i.e., Allee effects) takes time. However, Curtis Daehler at the University of Hawaii, collected information on purposeful plant introductions into Hawaii in the 1920s. 23 of those planted have become serious invaders and the herbacious species showed a lag time of 5 years and 14 years for woody species. Knowing that lag times can be much shorter then we previously thought means that monitoring and management activities need to much more aggressive. It seems we can no longer assume a period of relative safety after a new species in introduced, new records of non-natives needs to be followed active assessment and perhaps intervention.

Curtis C. Daehler (2009). Short Lag Times for Invasive Tropical Plants: Evidence from Experimental Plantings in Hawai'i PLoS ONE, 4 (2) DOI: 10.1371/Journal.pone.0004462