Insects constitute 85% of the world’s animal biodiversity and deserve increased attention in regions of the world, such as Madagascar(Graoomridge 1992)(Fisher and Robertson, 2002), where species-rich habitats are under threat. Although invertebrates and plants make up the vast majority of species in forest habitats land scape level patterns of invertebrate biodiversity are little known for tropical ecosystem. Such distributional data will largely determine how effective conservation areas are at representing district assemblages of specis. Species richness, the number of species in a given area is the currency of biodiversity but for most groups, we lack knowledge of how to inventory species(Fisher 1999).

Conservation methods that prioritize areas based on diversity patterns (species richness and l0cal endemism) of birds and mammals and do not include insect diversity overlook most organism and thus do not guarantee preservation of the greatest diversity. Pearson and Cassola showed that for dridded squares 275 km on a side, across North America the Indian subcontinent, and Australia, species richness levels of tiger beetles, birds and butterflies were positively correlated. However there is evidence that vertebrate diversity is not an accurate indicator of invertebrate biodiversity. Predergast et al showed low overlap between highly diverse sites of butterflies, dragonflies, liverworts, aquatic plants and breeding birds in Britian. At 32 sites in southeastern Austrailia, Yen found no correlation between the number of species of vertebrates and beetles. Scharff conclude that sites in tropical rain forests of eastern Africa where linyphiid spiders showed the highest diversity were not necessarily the same as those documented for birfs, mammals amphibians and reptiles. Thus arthropod patterns of diversity ca not be assumed to correlated with those of vertebrates and methods are needed to quantify species richness and endemism in insect taxa. This is the reason for supporting inventory methodologies to survey leaf litter ant diversity along an elevational gradient.( Fisher, B.L. 1996, Fisher, B.L. 1997)

The first survey in 1996 involving in a combination of pitfall and leaf litter sampling showed there were 27.866 ants belong to 114 species and 28 genera and general collecting yield an additional 34 species  at 4 sites in a 250m transect.(Fisher, 1999) Species accumulation curves demonstrate the efficacy of these techniques in sampling the majority of the ants in the leaf litter. The species collected and their relative abundance are presented. Species diversity decreased with elevation. Species turnover and faunal similarity measures showed a division in ant communities between the lowest elevation site and the highest elevation sits that corresponded to the cloud forest transition. This intensive study provided a unique basis studying how species composition and diversity change with elevation and latitude.

After 2 years, the second study collected and identified 24.586 ants belong to 189 species and 25 genera in d’ Anjanaharibe-Sub and 35 species in general collecting yielded. On the Masoala Peninsula, pitfall and leaf litter collections yielded 52.307 ant comprising 167 species and 25 genera, and 30 more species for general collected. Combination, there are a total of 325 species and 34 genera were collected. For each elevation, 2 different species richness estimators, incidence-based coverage estimator and first-order jackknife, gave comparable results. Species accumulation curves approached an asymptote and demonstrated the efficacy of these inventory techniques. Species collected and their relative abundances are presented. Species richness peaked at midelevation. Species turnover and faunal similarity measures demonstrated a division in ant communities beteen lowland forest <= 875 m and montane fores >=1200m. A midelevation peak in species richness in argued to be the result of the mixing of two distinct, lower and montane forest ant assemblages.

The most recent research until now about the effects of elevational gradient is the third survey in 1999.  There were 12.285 ants belonging to 25 genera and 11 species; an additional 28 species by general collecting. For each elevation 2 species richness estimators-incidence-based coverage estimator and first order jackknife gave comparable results. Species accumulation curves showed decreased rates of species detection and demonstrated the efficacy of these inventory techniques. Species turnover, complementarily and faunal similarity measures demonstrated a division in ant communities between lowland forest at <= 800 m and montane forest at 1250m. A mid-elevation peak in richness is probably the result of the mixing of two distinct, lower and montane forest, ant assemblages.

The increasing loss of biodiversity presents a daunting challenge to taxonomists and requires the discovery and analysis of biodiversity at a greatly accelerated pace. If we are really serious about “zero biodiversity loss” in Madagascar and elsewhere, then conservation planning needs to be based more fundamentally on biodiversity data, and this requires taxonomic knowledge. The renovation of systematics, as proposed here, is an extremely ambitious program requiring innovation, and large-scale application of tools in systematic research, from collecting to dissemination of results. In addition, this initiative requires the systematic community to work together at a level never before realized, focusing attention on global revision of select taxa and ensuring the repre-sentation of results in the conservation process, thereby enhancing the perceived value of taxonomy.

Groombridge, B., ed 1992.Global Biodiversity: statues of earth’s living resources. World Conservation Monitoring Centre. Chapman and hall. London.

Fisher, B.L. 1996. Ant diversity patterns along an elevational gradient in the Réserve Naturelle Intégrale d’Andringitra, Madagascar. Fieldiana: Zoology (n.s.) 85:93–108.

Fisher, B.L. 1997. Ant Diversity Patterns and Conservation Planning in Madagascar. Ph.D. Dissertation, University of California, Davis, USA. 241 pp.

Fisher, B. L., 1999. Improving inventory efficiency: A case study of leaf-litter ant diversity in Madagascar. Ecological Applications. 9, 714-731.

Fisher, B. L., Robertson, H. G., 2002. Comparison and origin of forest and grassland ant assemblages in the high plateau of Madagascar (Hymenoptera : Formicidae). Biotropica. 34, 155-167.

Diversity is a critical environmental topic that concerned people from all walks of life are rallying around(Kennedy & Smith 1995).

Soil probably harbours most of our planet’s undiscovered biodiversity. Recent results from both, culturing and nucleic acidbased approaches indicate soil microbial diversity is even higher than previously imagined(Tiedje et al. 1999), the highly diverse bacterial communities with up to 50,000 or even up to millions of different 16S rRNA gene sequences. So far, it has remained unclear whether functional redundancy or a multitude of ecological niches and adaptive mechanisms governs the composition of soil bacterial communities(Zul et al. 2007).

Soil bacteria and fungi play pivotal roles in various biogeochemical cycles(BGC), they also play important roles in soil quality and plant productivity.

The methods for analysis composition and diversity of soil microbial has advantaged in the past years. Traditionally, taxonomic classification of bacteria has been determined based on metabolic, morphologic, and physiological traits. This approach emulates the methodological approach of botanists and zoologists; however, it requires the isolation and cultivation of individual bacterial species. Assessments of bacterial communities from a number of environments have found that the fraction of cells that may be cultured is not representative of the abundance or diversity of the microbial community present in the environment; it is often observed that direct microscopic counts exceed viable cell counts by several orders of magnitude. Trosvik et al.(1990)have suggested that typical soils may contain 10⁴ species g^-1, at least half(and perhaps as many as 95%) of which are likely to be unculturable by current techniques.Clearly, culture-based methodology is inadequate to serve the needs of microbial ecologists seeking to describe the diversity of bacterial communities in environmental samples, and as a consequence a number of culture-independent approaches have been applied to the study of microbial diversity in soil.(Kent and Triplett 2002)

Methods for acessing composition and diversity of soil microbial community

As the methods is very important for us to analysis the divertity of soil mirobialcommunity, I ‘ll introduce two main group methods (Hill et al. 2000, Kirk et al. 2004).

1. Biochemical-based techniques to study microbial diversity

1.1 Dilution plating and culturing methods.

1.2 Sole carbon source utilization patterns/community level physiological profiling for measuring microbial diversity.

1.3 Fatty acid methyl ester (FAME) analysis

2. Molecular-based techniques to study microbial diversity.

2.1 Guanine plus cytosine (G+C) content.

2.2 Nucleic acid reassociation and hybridization.

2.3 DNA microarrays.

2.4 PCR-based approaches.

2.4.1 Denaturing gradient gel electrophoresis (DGGE)/temperature gradient gel. electrophoresis (TGGE).

2.4.2 Single strand conformation polymorphism (SSCP).

2.4.3 Restriction fragment length polymorphism (RFLP)/amplified ribosomal DNA restriction analysis (ARDRA).

2.4.4 Terminal restriction fragment length polymorphism (T-RFLP) Ribosomal intergenic spacer analysis (RISA)/ automated ribosomal intergenic spacer analysis (ARISA).

2.4.5 Highly repeated sequence characterization or microsatellite regions.

Althrough the methods is advantaged, it is difficult for us to know the diversity and composition of soil microbial community clearly. Not only did us lack of knowledge about the soil microbe, but also the soil environment is strongly infecting the diversity and function of soil microbial community (Yang 2000, Zul et al. 2007). There are many factor significantly effecting the diversity of soil microbe.

1. Soil bacterial diversity was found to be dependent on soil pH.

2. Site temperature, latitude also the important factor effect on the soil microbe.

3. Organic carbon content and C:N ratio is very important for soil microorganism.

4. The structure of the soil is effecting on the water content of soil, it’s relatting to the micro-environment of soil microorganism .

5. Plant diversity, it’s especially effect on the rhizospheric microorganism.

In the end , as soil is very important for human, many scientists also thought that the soil microbial diversity is a black box. Understanding the dynamics of microbial communities is at the heart of contemporary microbial ecology, and understanding of the soil microbial community is probably the most challenging because of the exceptionally high microbial diversity in soil and the complex and variable matrix in which soil microbes are embedded. Nonetheless, it is time to open the soil black box.

Reference

Hill, G. T., N. A. Mitkowski, L. Aldrich-Wolfe, L. R. Emele, D. D. Jurkonie, A. Ficke, S. Maldonado-Ramirez, S. T. Lynch, and E. B. Nelson. 2000. Methods for assessing the composition and diversity of soil microbial communities. Applied Soil Ecology 15:25-36.

Kennedy, A. and K. Smith. 1995. Soil microbial diversity and the sustainability of agricultural soils. Plant and Soil 170:75-86.

Kent, A. D. and E. W. Triplett. 2002. Microbial communities and their interactions in soil and rhizosphere ecosystems. Annual Reviews in Microbiology 56:211-236.

Kirk, J. L., L. A. Beaudette, M. Hart, P. Moutoglis, J. N. Klironomos, H. Lee, and J. T. Trevors. 2004. Methods of studying soil microbial diversity. Journal of Microbiological Methods 58:169-188.

Tiedje, J., S. Asuming-Brempong, K. Nüsslein, T. Marsh, and S. Flynn. 1999. Opening the black box of soil microbial diversity. Applied Soil Ecology 13:109-122.

Torsvik, V., J. Goksoyr, and F. Daae. 1990. High diversity in DNA of soil bacteria. Applied and Environmental Microbiology 56:782-787.

Yang, Y. H. 2000. Effects of agricultural chemicals on DNA sequence diversity of soil microbial community: a study with RAPD marker. Microbial Ecology 39:72-79.

Zul, D., S. Denzel, A. Kotz, and J. Overmann. 2007. Effects of plant biomass, plant diversity, and water content on bacterial communities in soil lysimeters: implications for the determinants of bacterial diversity? Applied and Environmental Microbiology 73:6916-6929.

Ecologists have long debated over the mechanisms that govern biodiversity at local and regional scales (Ricklefs & Schluter 1994). There are two contrasting group of thoughts that are commonly cited to explain the nature of organization of ecological communities. Niche based theory states that communities are structured by interacting species whose presence, absence and even abundance is governed by the functional role or ecological niche (McArthur 1970, Diamond 1975). The Dispersal assembly theory on the other hand asserts that species assemblages are a result of chance, history, random dispersal and stochastic extinction (e.g. IBT of McArthur and Wilson, 1967). The classical dispersal assembly theory has been recently revived by Hubbel (2001) by taking the neutrality mechanism further, from level of species to the level of an individual. The theory has once again challenged the niche assembly theory by proposing that ecological drift is the sole process regulating species coexistence.

There are a good number of studies which provide evidence in favor of both niche and dispersal assembly and we now know beyond doubt that both mechanisms operate to shape the ecological communities. The focus of the research therefore has now shifted to understanding the relative importance of these theories.  Studying species distribution and deciphering the mechanisms that generate species turnover has proved to be useful in testing and separating niche and dispersal assembly theories. Hubbel’s neutral theory (2001) has stimulated a lot of research in this field and attracted considerable attention to this issue. As mentioned above the most common approach has been to partition the variation in beta diversity along a gradient into percentage explained by the habitat /environmental variable and by space/ distance alone. The chain of CTFS plots has proved especially useful for such studies. Spatially referenced data on species diversity and composition has helped a great deal to disentangle the contribution of each of the above mentioned processes.

A study carried out by Condit et al (2002) is one of the influential studies which generating considerable controversy. The study tested the validity of neutral theory in predicting species turnover rates with distance. The results of the study were consistent with the predictions of the neutral theory at intermediate distances (0.2 to 50 km) between plots. This shows that dispersal limitation does play an important role in structuring forest communities. However the theory does not consider habitat, environmental and historical processes which also play a role in shaping species distributions. Therefore at scales when role of environment becomes prominent, the theory fails to predict the similarity in species composition. Even when environmental variables were used together with geographic distance it could only explain a small fraction of variable in species similarity. Duivenvoorden et al (2002) reanalyzed the data and finally concluded that dispersal may have small effect on beta diversity in tropical forests. This conclusion however was based on the Panama plot data which have a very high habitat heterogeneity and rather sharp gradient in rainfall.

Contrary to these results, another very similar large scale study carried out in Africa provides evidence in favor of dispersal as primary factor affecting species clumping. They found this particularly true for habitat generalist species. However this questions the generality of the theory given the high number of rare species in the tropics. Chust et al (2006) provide another elegant study once again highlighting the relative importance of geographic distance in predicting species similarity although climatic and topographic variables also explained some variation.

Potts et al (2002) based on  105 plots in Borneo, tested the effect of habitat and geographical distance on local, landscape to community scale. They found that, there exists a resource threshold above which the habitat    effect weakens and similarity between sites is then dominated by geographical distance effects. They concluded that community composition is governed by interplay of habitat and distance effects. A study carried out by Legendre et al (2009) is one of the latest studies targeted at investigating the effect of habitat and space on species richness and composition. The study is unique in several ways. There entire results are based on a scale of single 24ha permanent plot which unlike the other permanent plots falls in the subtropical broad leaved vegetation category. The study showed that the niche and the neutral process both are  equally important in governing species diversity and composition. These two processes in-fact work together in regulating beta diversity.

The neutral theory is a significant theoretical advancement of our understanding of factors that govern species diversity. Most studies which have followed the variance partitioning approach indicate that dispersal limitation might be more important at least in explaining species similarity. However it is still too early to make strong conclusions  since scale seems to be an important issue in such studies and the role of different factors could vary with scale of the study. Also in most of these studies it is difficult to segregate the effect of distance alone from environmental heterogeneity since the two are often correlated. The drawback of the theory perhaps is that it’s a completely stochastic theory based on very simplistic and unrealistic assumptions. However this also is its greatest strength since it is able to make predictions regarding mean dispersal distance and species similarity in spite of having simple assumptions.  Overall the theory promises to serve as a useful tool for predicting species turnover.

Essay on ‘Urban aerosols harbor diverse and dynamic

bacterial populations’

This article is focus on the diversity and dynamic bacterial populations in the air. Finally, they demonstrate that temporal and meteorological influences are stronger than location in shaping the biological composition of air we breathe.

It brings me a concept that bacterial population is connected with air pollution after reading this article, nowadays, a number of problems are caused by the environmental contaminations, such as the overuse of the energy, cutting forests which cause lacking of O3 and destroy the ozonosphere that can protect human body form UV radiation. More over, as the economics increases, we will face more critical health problems. Lots of plants trees and corps are destroyed by bad air. Many fish die of poisonous water. Thousands of people get chronic disease or even worse, they die from eating poisoned fish or breathing in poisonous gas . Farmers make use of great amounts of insecticides to have bumper harvests. However, they pollute air, water and land. Plants produced natural ‘pesticides’ in which human diet contains. This is to protect themselves from insects and other predators. It has been proved that many plants can concrete some kind of chemical molecular which can protect human from cancer or improve our health. Therefore, environmental pollution should be responsible for these diseases that are disabling, or bringing death not only to human beings, but also to wild life.

The existence of bacteria in the atmosphere is important because they may spread diseases. From literature, at temperatures of −1 °C, some certain species of bacteria can affect ice nuclei which can be found  living on plant leaves and the surface layer in the ocean. Because of that the bacteria can be easily transported into the air.

Also, it has been proved that aerosols bacterial populations have influence on the dental problems. For a long time, spread of infections is considered as the mainly concerns in the dental community. Actually, it’s not only in dental community, but also in all kinds of medical problems. Indeed, infectious can be easily transmitted to patients and by the instruments and air. But bioaerosols are an important consideration for infection control and occupational health, if more bacteria suspended in the air, more chances to get infection through this agent. Also, the air is made up of different kinds of bacteria, some of them may cause allergens and some are even toxic substances Infective causative agents may include bacteria, viruses, fungi, and possibly even prisons.

From above, we can find that aerosols bacterial populations are closely related to human health. I think there are four reasons to explain why environmental contaminations are affect our health, the primary is the reason of harmful substances into environment. For example, to prevent insects, farmers make use of great amounts of insecticides, so as to have bumper harvests. However, they pollute air, water and land. Second, the gas coming from the car engines and factories also make environment polluted badly. The third reason actually is the result of a growing population in the world. Everyday, so much litter and waste are poured out from houses, and the other problem it has brings is over-consumption which can pollute the circumstances we live. The significance for controlling pollution noted that it’s high time that more effective measures should be taken. Therefore, new laws should be passed to limit the amount of pollutants from factories. Moreover, in the households; there is an obvious need to reduce litter and waste. We should do something such as planting more trees, equipping cars with pollution-control devices and learning to recycling natural resources to improve the present situation, let’s make our good efforts, and the world will be a safer place to live for us. I do believe everything will be better in the future.

References:

1. Ames BN, Gold LS, FASEB JOURNAL, 11:1041-1052

2. Mihály Pósfai^{a, ,} , Jia Li^b, James R. Anderson^c and Peter R. Buseck, Aerosol bacteria over the Southern Ocean during ACE-1.

3. J Contemp Dent Pract 2004 November;(5)4:091-100.

Chen Sichong

Success of most plants is greatly dependent on effective seed dispersal. On the other hand, evidence from plant demography research is revealing that seed dispersal might have an important role in determining patterns of tree diversity and distribution. The limited mobility of plants makes them to develop a variety of dispersal strategies, including both abiotic and biotic. Generally, scientists define five major modes of seed dispersal: gravity, wind, explosion, water and animals delivery. A fundamental goal of plant population ecology is to understand the consequences for plant fitness of seed dispersal by animals.

In Dr. Wenny and Dr. Levey’s PNAS paper, they used Ocotea endresiana (Lauraceae) as an example (Wenny D.G. and Levey D.J., 1997). This is a tree species from Latin America which is dispersed by five species of birds, including the three-wattled bellbird (Procnias tricarunculata). This certain disperser nonrandomly place seeds in sites that benefit seedling establishment. Male bellbirds perch on dead trees in order to attract mates, and often defecate seeds beneath these perches where the seeds have a high chance of survival because of high light conditions and escape from fungal pathogens. Such specific habitats are seedlings’ favorable for survival, known as directed dispersal.

The Process of seed dispersal by animals can be divided as epizoochory and endozoochory. Epizoochory, that seeds are transported on the outside of animals, is much rarer (below 5%) than endozoochory which via ingestion by animals. Lots of fruits are really tasty to animals, such as blackberries, apples and gooseberries. In this way, animals get benefit of nutrition. So, what do plants get in response? Besides the directed dispersal hypothesis mentioned above, seed dispersal is likely to have several benefits for plant species. Away from the parent plant, seed is often (but not always) tend to have a higher survival, which may result from the actions of density-dependent seed predators and pathogens. Competition either with adult plants or with peer individuals may also be lower when seeds are transported relative far away. If the seeds simply fell and grew beneath the parent plants, they would be too overcrowded and would be starved of nutrients. Further, the transport of seeds may allow plants to colonize vacant habitats and geographic regions.

This animal-plant interaction involves a co-evolution process of both disperser animals and seed dispersal plants. These plants evolve some phenotypic traits that attract their dispersers. In Dr. Wang and Dr. Chen’s Ecology paper (Wang B. and Chen J., 2008), they controlled seed traits by making artificial seeds with variance of seed size, tannin and nutrient content. Such method separates the original association of seed size and energy content per seed, ruling out the limitation of trait covariation. They found that it is mainly seed size rather than tannin and nutrient content that influence an Old World rodent’s behavior of dispersal. The rodents consumed small seeds in the original site, removed medium-sized seeds, and transported bigger seeds farther. So, by teasing apart different seed traits on the behavior of dispersal, we could insight into the co-evolutionary dynamic of plants and dispersers.

Besides some vertebrates like birds, rodents, sheep, monkeys, champanzee that can be important seed dispersers, invertebrates also have concernful roles in this process. In another paper of Dr. Chen’s research group (Zhou H., et al. 2007), they discussed the effect of ant transport on local spatial pattern and genetic structure of Globba lancangensis (Zingiberaceae). They detected a patchy structure of genetic and geographical distances within 4 m, suggesting the associated restriction of seed dispersal by ants. Meanwhile in the ant-excluded control treatment, seed dispersal of G. lancangensis could form a similar pattern. So they argued ant-mediated dispersal plays only a minor role in developing and maintaining the local spatial genetic structure of G. lancangensis, but mainly contributes to seedling clustering degree reduction, due to the limitation of ant dispersal distance. This result could stimulate our thoughts about the distance and species in seed dispersal. Generally, 100 m is a commonly used threshold for long-distance dispersal (Russo S. E., et al. 2006). This long-distance dispersal is mainly completed by vertebrates. However, considering the species of plants, the relatively meaningful distance should also be taken into account.

In the end, confirming and quantifying seed dispersal’s effect on vegetation structure is quite a challenge. In Dr. Wang and Dr. Smith’s review about seed dispersal loop (Wang B. C. and Smith T. B., 2002), they mentioned seed dispersal as a linkage between the end of plant reproductive cycle and the establishment of the offspring. Seed dispersal study and plant demography research could contribute in determining patterns of tree diversity and distribution.

Reference:

Wenny D. G. and Levey D. J. (1997) Directed seed dispersal by bellbirds in a tropical forest. PNAS. 95: 6204-6207.

Wang B. and Chen J. (2009) Seed size, more than nutrient or tannin content, affects seed caching behavior of a common genus of Old World rodents. Ecology. (maybe in press)

Zhou H., Chen J. and Chen F. (2007) Ant-mediated seed dispersal contributes to the local spatial pattern and genetic structure of Globba lancangensis (Zingiberaceae). Journal of Heredity. 32

Russo S. E., Portnoy S., and Augspurger C. K. (2006) Incorporating animal behavior into seed dispersal models: Implications for seed shadows. Ecology. 87: 3160-3174

Wang B. C. and Smith T. B. (2002) Closing the seed dispersal loop. TRENDS in Ecology & Evolution. 17: 379-385.

Mutualism is an interaction between two organisms that increases fitness of one another, either through trading resources or increase survival rate from predator. Throughout the Afec-X course we’ve learned several classical examples of mutualism, for example fig and fig wasp, ant-plant interaction, etc. In the case of Sepiolid squid and Vibrio bacteria, symbiotic relationship not only increases the fitness of both organisms, it also allows them to occupy new habitat niches (Nishiguchi 2004). Symbiosis and mutualism are not supposed to be used as synonymous because symbiosis is a larger category and mutualistic is just one of the categories. But the interaction between Sepiolid squid and Vibrio bacteria is both symbiotic and mutualistic. The Vibro bacteria live inside the squid and produce light to help the host hunting its prey. The squid, in return, provides food for the bacteria. Thus, perhaps it is O.K. to use the term ‘symbiotic’ to interpret mutualism in the rest of the paper.

Sepiolidae-Vibro symbiosis has been intensively studied for decades, and most of the hypotheses have probably been tested and examined. One of the first things we would like to know was that how did squid and bacteria form a species-specific relationship? Several common hypotheses have been proposed to explain how natural selection worked in this symbiosis relationship (Nishiguchi 2004): i)Multiple bacteria species could infest Sepiolid squid, but Vibrio bacteria gave highest fitness to the host. So evolution has selected Sepiolid squid with Vibrio bacteria. Both organisms have co-evolved and eventually became a species-specific relationship. ii) Evolution of symbiotic bacteria was due to similar environmental factors with the host, and not due to specific host. If that was the case, the bacteria from the same habitat should be closely related and could infest multiple host species. As what stated in Nishiguchi (2004), many studies have shown that same Vibrio species that infest Sepiolid squid and monocentrid fish are genetically distinct, and they cannot infest different host family. So the idea of the cospeciation of Sepiolid squid and Vibrio bacteria has been supported, in general.

Then, how do the species stabilize the mutualistic interaction? That leads to the second part of Dr. Yu’s talk, Partner Choice. Partner Choice is a concept where the host can increase the rewards for cooperative partner and reduce the reward for non-cooperative partner (Sachs et al. 2004). The concept of Partner Choice has been strongly supported by the ant-plant mutualism in Edwards et al. (2006). However, the testing of Partner Choice hypothesis in squid-bacteria relationship is extremely difficult because there is no way we can examine the changes in host’s reward for the symbiotic bacteria.

In the last part of Dr. Yu’s lecture, he used economic theory of information to explain the Sepiolidae-Vibro symbiosis. I was really hoping to read the paper that Dr. Yu cited in the PowerPoint to better understand the economic theory. Unfortunately, I failed to locate the paper from the Web of Science. So the only thing I could do is write down my own understanding of that part of the lecture, and hopefully I won’t misinterpret the brilliant idea of Dr Yu and his colleagues.

The economic theory that Dr. Yu presented involves three parts: adverse selection, signaling and moral hazard. Adverse selection occurs when buyers and sellers have asymmetry information. For example, insurance companies tend to adversely or negatively select individuals with higher risk. So, the companies increase the insurance fee. The consequence of that is that individuals with lower risk become less likely to buy insurance. This will eventually end up with the collapse of the insurance industry. To avoid that, buyers and sellers need a signaling progress to be on the same page. Buyers provide the insurance company with some basic information of their heath, and insurance company will offer plans with different prices for different individuals based on their risks. Lastly, the moral hazard concept suggests that individuals who provide incorrect information (in other word less cooperative) will be punished and their services will be discontinued.

To apply the economic theory to biology, here is a direct quote from Nishiguchi (2004), ‘These types of functional interactions between host and symbiont can only be established when an avenue for the exchange of information has evolved specifically within the symbiosis.’ As indicated, signaling is an important procedure for the host and symbiont to establish and stabilize the mutualistic relationship. However, the study of signaling procedure in the Sepiolidae-Vibrio symbiosis was very challenging, for it was unclear what signals and how the host passed on to the symbionts, or vice versa. In 1999, Edward and Margaret discovered that light organ in the Sepiolid squid has enzymes that can transform oxygen into toxic component. Light-emitting bacteria can use up all the oxygen in the light organ to produce light, thus allowing them to live symbiotically with the Sepiolid squid. Edward’s finding presented a possibility that the Sepiolid squid selectively ‘chooses’ the light-emitting bacteria (and not other types of bacteria) to increase their fitness, which perhaps can be considered as a signaling procedure. Similar to partner choice study, moral hazard concept is very difficult to examine in an empirical research. If partner choice or moral hazard did happen in the squid-bacteria relationship, we would expect to see variation in Vibro bacteria concentration in squids that live in high resource habitat and low resource habitat. Perhaps in later future when molecular data can be used to quantify the amount of Vibrio bacteria in Sepiolid squid (maybe higher amplification means more bacteria?), the partner choice or moral hazard concepts can then be examined.

To summarize my understanding on the Sepiolidae-Vibrio symbiosis, the Sepiolid squid and Vibrio has been co-evolving to form a species-specific symbiotic relationship. During the cospeciation, Sepiolid squid has evolved a mechanism to stabilize the symbiotic relationship. Economic theory can be used to understand the interaction between organisms. However, limited research may be available to support the economic theory.

References

DouglasYu’s Lecture on ‘Mutualism’. PowerPoint slides available at

http://afec-x.ecologicalevolution.org/files/ppt/Douglas_Yu-Mutualisms_talk_AFEC-X.pdf

Edwards, D. P., M. Hassall, W. J. Sutherland, and D. W. Yu. 2006. Selection for protection in ant-plant mutualism: host sanctions, host modularity, and the principal-agent game. Proceedings of the Royal Society B 273:595-602.

Edward G. R. and J.M. Margaret. 1999. Oxygen-utilizing reactions and symbiotic colonization of the squid light organ by Vibro fischeri. Trends in Microbiology 7(10): 414-420.

Nishiguchi, M.K. 2004. Cospeciation between hosts and symbionts: The Sepiolid squid-Vibrio Mutualism. Cellular Origin, Life in Extreme Habitats and Astrobiology 4: 757-774.

Wollenberg, M.S. and Ruby, E.G. 2009. Population structure of Vibrio fischeri within the light organs of Euprymna scolopes squid from two Oahu (Hawaii) populations. Applied and Environmental Microbiology 75(1): 193-202.

I am not a biological people (but ecological) going to give myself a challenge so I choose the totally new topic (for me)— phylogenetics just because it’s so cool and so first-cutting for me.

Human has been studying their environment for a long time, for the community, which might know the structure and then the function first, that means we already have ideas about what it looks like and how it works from large scale based on human’s own vision (because we don’t know how it is from other species’ vision). However, we get more powerful technique ( finds? Theory? ) today that is phylogenetics, it provides another eyes to human to look the actual dynamics of the world (I just got the idea from Matt’s lecture yesterday).  In biology, people use molecular traits or morphological data matrics to study evolution of speciation, population and community—phylogenetics. And then the tree of life was made based on phylogenic evident of species (or population, community), the all kind of trees tell us the one information that is how diversification of species (population, community) on the earth look like in the past and present, and how these living things are interacting with time.

How the diversity in tropical forest look like? And what are the mechanisms of species coexistence? We’ve been discussed a lot in our last student roundtable… and everyone of you have very good explaining, but today I am going to say something more about mine. There is another interesting new discipline called multiagent modeling who these are doing the research think the world is bottom-up, that means every tiny substantial interaction make the complexity, e.g. every man cut down the tree then it’s will be a big loss if there are 1000 people go to cut down treeS, which shows any accumulation from the individuals’ behavior and interaction can make a completely complex world. I was wondering if we go down to the small scale, molecular level, to look for what is the dynamics of large scale world, e.g. species coexistence… that would be very cool (that what is phylogenetics telling us), maybe human and any species on the earth just puppets of the molecular world, which means what we did just follow the orders of molecular of ourselves… this is totally a bottom-up world?

Then we can explain how the world should look like? Why these species coexistence why not others from phylogenetics? Sure, every scientific question is not easy to get answer and phylogenetics also is not an exception (and I am not it can answer all of questions too, because human ourselves has such short life span and limited technique as far.). And some wide men did the kind of works; they use phylogenetic methods to test how species coexistence—phylodiversity dependent seeding mortality and size structure, which we discussed” the Janzen- Connell effect” host-specific pests reduce recruitment near reproductive adults. 2006, Webb et al. use phylogenetic relationship among organisms—can move beyond ranks such as family and genus—to use phylogenetic distance among the taxa to get the conclusions that a seedling survives increases if surrounding plants are not closely related to it in a small scale.

And we know the interaction between plants and animals on pollinators and seed dispersers mould earth’s biodiversity (from large scale, that what I mention— human’s vision).2007, Rezenda et al. use phylogenetic method to simulate coexitinctions, which was finding a answer for understanding of structure and fate of species-rich communities, because these kind of interaction are partially dependent on past evolutionary history, and cannot be exclusively explained by current ecological processes. 2004, Cavender-Bares use phylogenetic idea to test competitive exclusion of oak communities in North Central Florida, and found environmental filtering in oak communities does not lead to clustering of closely related species, which means co-occuring oak species are more phylogenetic distantly related than oaks which are phylogenetic overdispersion.

As far, people have already used lots of phylogenetic method to test the relationships in the large scale world, but how about the smaller scale? How the interaction between pathogen-host (is a biological agent that causes disease or illness to its host) on plant? Most of researches of pathogens were record but only on high economically value plant, 2007Gilbert used phylogenetic distance get the result that spread rate of disease on pathogen-host depend strongly on the phylogenetic structure of the community. And current regulatory approaches strongly underestimate the local risks of global movement of plant pathogens or their hosts.

From now on, phylogenetic approaches may provide more and more powerful evidence for supporting what we know about the large scale world from the phylogenetic network, through visualizing evolutionary relationships between sequences, genes, chromosomes, genomes, species, population, community…  human’s curiosity has never stopped, so this may lead our to use totally new and powerful approaches to detect the world. Then maybe we can find out all of secrete of nature one day, e.g. how is the species coexistence in tropical forest…

Reference:

S.Joseph Wright (2002)Plant diversity in tropical forests: a review of mechanisms of species coexistence.Oecologia 130:1-14;

J.Cavender-Bares, D.D.acherly, D.A.Baum, F.A.Bazzaz (2004) Phylogenetic overdispersion in Floridian Oak Communities.The American Naturalist163: 823-843;

J. Cavender-Bares, A.Keen, B.Miles (2006)Phylogenetic structure of Floridian plant communities depends on taxonomic and spatial scale. Ecology87(7):S109-S122;

E.L.Rezende, J.E.Lavabre,P.R.Guimaraes Jr, P.Jardano, J.Bascompte(2007)Non-random coextinctions in phylogenetically structured mutualistic networks.Nature448:925-929;

C.O.Webb, G.S.Gilbert, M.J.Donoghue(2006)Phylodiversity-dependent seedling mortality, size structure, and disease in a Baonean rain forest. Ecology87(7):S123-S131;

Phylogenetics, http://en.wikipedia.org/wiki/Phylogenetics

Pathogen, http://en.wikipedia.org/wiki/Pathogen

Phylogenetic network, http://en.wikipedia.org/wiki/Phylogenetic_network

Tropical regions are rich in biological flora and fauna. Many researches have been done in the field of tropical forest ecosystem. People are presenting their views on degrading situation of tropical forest based on their findings. However, no-one has come across or predict the exact realities, infact what is going on around tropical regions. Observing the increasing trend of human populations and their excessive pressure on forestry, it was predicted that humans in rural settings contribute most to deforestation of extant tropical forests and deforestation and habitat loss are expected to lead to an extinction crisis among tropical forest species. However, “Trends such as slowing population growth and intense urbanization give reason to hope that deforestation will slow, regeneration will accelerate, and mass extinction of tropical forest species will be avoided,” (S.J. Wright). Studies suggest that deforestation rates will decrease as population growth slows, and a much larger area will continue to be forested than previous. It is the truth that Tropical forests diminished during repeated Pleistocene glacial events in Africa and more recently in selected areas that supported large prehistoric human populations. Despite many caveats, the projections for forest cover provide hope that many tropical forest species will be able to survive the current wave of deforestation and human population growth. Consequently, it can be believed that creative strategies to preserve tropical biodiversity might include policies to improve conditions in tropical urban settings to encourage urbanization and preemptive conservation efforts in countries with large areas of extant forest and large projected rates of future human population growth. In addition that land-use history interacts with natural forces to influence the severity of disturbance events and the rate and nature of recovery processes in tropical forests. Although we are far from an integrated view of forest recovery processes, some generalizations can be made. Despite evidence of rapid forest recovery following large-scale deforestation, many degraded areas of today’s tropics will require human assistance to recover forest structure, species composition, and species interactions typical of mature tropical forests.

Similarly, it is complicated to predicate the relationships between rural and urban population growth and the scenario of deforestation. Even though, the general assumption produced for the ecological value that primary secondary and degraded forest can be treated as equally. Secondary forests play a crucial role in tropical forest landscapes providing a suitable habitat for many species and the necessary haven for species currently restricted to small patches of native habitat, there the role of degraded and secondary forest are pivotal. Contradictorily, naturally regenerating forests in the tropics depends on old growth forest and which has a high biological value. However, the existing studies provide an important service in identifying secondary forests as being more favorable for conservation than many other land-use options (e.g., agriculture, plantations), although the fact that they are often undervalued has frequently resulted in over-exploitation or conversion. So, the many more scientific papers were assessed to find out the role of secondary forest for the conservation of tropical forest species which have stated the importance of regenerating lands for tropical forest species. The evidences are not clear, shows a poor and weak sampling design, no inter-study comparison, and flaws in data analysis and interpretation which always create the differences or gap between primary and secondary forest for biodiversity conservation.

In focusing on the importance recovery and species richness that species composition recovers much more slowly, where mature-forest species can still be absent from secondary forests. If this pattern is generally true, then secondary forests will not provide a reliable and effective safety net for the many tropical forest species ,and areas of the world that are undergoing rapid loss of primary habitat will permanently lose many species. The value of secondary forests for the conservation of tropical forest species highlights the importance of an objective evaluation of the current status of our knowledge. Although the analysis indicates that species richness and composition exhibit limited recovery where the conclusions were made based on fewer unreplicated studies.

In the long-term degraded and the potential forest could attain a structure and species composition similar to primary forest if we protect from further disturbances. First most species have a small range sizes relative to the mean range size, increasing their probability of extinction by chance alone (Gatson1994) and second species with small ranges also tend to be scarce within those range (Brawon 1984), so the probability of extinction is increased on two counts. Most of these areas of co-occurrence of species with small range are disproportionately threatened by human activity (Cincotta et al.2000). Species are being extinct from biogeographically distinctive hotspots due to habitat loss. The main reason is secondary forest are highly heterogeneous, heavily degraded, isolated by hostile matrix habitat and poorly connected to regenerating forests where forest fires, alien species, pathogens and hunting further eroding the biodiversity value. Changing land use pattern causing heavy soil erosion and nutrient depletion may inhabit in natural regeneration due to abandoned after intensive agriculture.

Therefore, tropical forests are currently facing different kinds of threat from multiple factors including land-use change on a massive scale, habitat loss, wildfires, and hunting. So, the urgency is needed to know the conservation value of secondary forest. Secondary forests are more favorable for all the prospective like species coexistences to agriculture point of view. However, prediction about the conservation value of tropical forest secondary forests for most species still lacking a scientific data.

References:

S.J.Wright. 2006. The future of tropical forests. Smithsonian Tropical Research Institute and H.C. Muller-Landau, University of Minnesota, in Biotropica online.

Brawon, J. H. 1984. On the relationship between abundance and disturbance of species. The American Naturalist 124:255-297.

Cincotta, P.R., J. Wisnewski, and R. Engelman. 2000. Human population in the biodiversity hotspots. Nature 404:990-992.

Gatson, K.J. 1994. Rarity. Chapman and hall, London.

Why LUC is so important to biodivesity?.

Land-use and land-cover Changes were considered the key factors for global environmental change (Turner et al. 1995), affect the global biosphere and climate（William E.R.1994）. For terrestrial ecosystems, land-use change probably will have the largest effect to the biodiversity (Osvaldo E.S et al, 2000). Also it is a major cause of the decline in biodiversity in recent decades (Soulé 1991).

At present, loss of biodiversity, including high rates of extinction and a worldwide depletion of biological diversity at genetic, species and ecosystem levels,can be linked to the destruction of natural habitats as a result of land use change at different scale, and is presently considered one of the most urgent environmental problems( Shao et al. 2005) and losing habitats is the greatest threat to biodiversity. According to the Millennium Ecosystem Assessment, over the past 50 years people have changed ecosystems faster and more extensively than in any period in human history.（http://www.nerc.ac.uk/research/issues/biodiversity/pressures.asp）

How LUC affects the biodiversity?

The types of land use are distinguished as land cover conversion, i.e., the complete replacement of one cover type by another, and land cover modification. Land use change happens at every spatio-temporal scale( Shao et al. 2005). Land use changes are affecting many aspects of the Earth system (Shao et al. 2005). In most landscapes within the region, land-use is a major determinant of composition, spatial patterns and function at the species, community and landscape levels (Pan et al. 2001) Timber harvesting and associated silvicultural practices (e.g., clearcutting, thinning, plantation forestry, and prescribed burning), and road building alter spatial and successional patterns as well as the underlying processes and dynamics of forest ecosystems. The quality of water, soil and air resources, ecosystem processes and function and the climate system itself through greenhouse gas fluxes and surface albedo effects have all undergone important changes in the past century ( Shao et al. 2005). These changes are likely to be even greater in this century.

Land use has also caused declines in biodiversity through the loss, modification, and fragmentation of habitats; degradation of soil and water; and overexploitation of native species. Nowadays,biological species live in increasingly fragmented habitat islands embeded in a matrix of human civilization( Shao et al. 2005). Habitat or forest fragmentation is the result of land converted into farmland from forests,grassland and othere natural habitats, which also is the result of land use and habitat conversion.

What about the dilemma that LUC faces?

Land use occurs in local places, with real-world social and economic benefits, while potentially causing ecological degradation across local, regional, and global scales. Society faces the challenge of developing strategies that reduce the negative environmental impacts of land use across multiple services and scales while maintaining social and economic benefits（Jonathan A. Foley, et al.2005）. Land use thus presents us with a dilemma. On one hand, many land-use practices are absolutely essential for humanity, because they provide critical natural resources and ecosystem services, such as food, fiber, shelter, and fresh­water. On the other hand, some forms of land use are degrading the ecosystems and services upon which we depend（Jonathan A. Foley, et al.2005）

Although, some scientists point out that the biodiversity will be not so seserously as predicted by the predicting the decreasing deforestation rates, as well as natural forest regeneration through secondary succession to accelerate and an increase in secondary forest area. But it is undoubtable that the world are facing more and more serious biodiversity loss.

The conclusion

Determining the effects of land use change on the Earth system especially biodiversity depends on an understanding of past land use practices, current land use patterns, and projections of future land use, as affected by human institutions, population size and distribution, economic development, technology, and other factors. ( Shao et al. 2005).

Land use has been received increasing attention in the life cycle assessment. At the same time, the ecological responses of land use change have been paid increasing attention. But the interaction between land use and biodiversity is poorly understood. And it is highly likely that we will fully understand the co nservation value of biodiversity before we have already converted most of the remaining primary forest to other land uses. So great attention still need to be paid on the underlying processes and mechanisms of biodiversity impacts of land use change.

REFERENCE

1. Euskirchen E.S., Chen J. and Bi R.C. 2001. Effects of edges on plant communities in a managed landscape in northern Wisconsin Forest Ecology and Management 148: 93–108.
2. Jonathan A. Foley, Ruth DeFries, Gregory P. Asner, Carol Barford,1 Gordon Bonan, Stephen R. Carpenter, F. Stuart Chapin, Michael T. Coe,1. Gretchen C. Daily, Holly K. Gibbs, Joseph H. Helkowski, Tracey Holloway, Erica A. Howard,  Christopher J. Kucharik, Chad Monfreda,1 Jonathan A. Patz, I. Colin Prentice,8 Navin Ramankutty, Peter K. Snyder.  2005. Global Consequences of Land Use。Science 309, 570-574;
3. Osvaldo E. Sala, F. Stuart Chapin , III, Juan J. Armesto, Eric Berlow,  Janine Bloomfield, Rodolfo Dirzo,  Elisabeth Huber-Sanwald,  Laura F. Huenneke,Robert B. Jackson,  Ann Kinzig,  Rik Leemans,  David M. Lodge, Harold A. Mooney, Martín Oesterheld,  N. LeRoy Poff, Martin T. Sykes, Brian H. Walker, Marilyn Walker, Diana H. Wall .2000. Global Biodiversity Scenarios for the Year 2100, Science 10,Vol. 287: 1770 – 1774
4. Pan D., Domon G., Marceau D. and Bouchard A. 2001. Spatial patterns of coniferous and deciduous forest patches in an Eastern North America agricultural landscape: the influence of land use and physical attributes. Landscape Ecology 16: 99–110.
5. Shao Jingan, Ni Jiupai, Wei Chaofu, Xie Deti. 2005.Land use change and its corresponding ecological responses: a review. Journal of Geographical Sciences 15, 3, 305-328
6. Soulé, M. E.  1991.  Conservation:  tactics for a constant crisis.  Science 253:744-750.
7. Turner II, B. L., Skole, D., Sanderson, S., Fischer, G., Fresco, L. and Leemans, R..1995. Land-use and land-cover change. Science/research plan. IGBP Report: 35/HDP Report 7.
8. William E. Riebsame，William B.  Meyer and B.L. Turner II. 1994，Modeling Land Use And Cover As Part Of Global Environmental Change，Climatic Change28: 45-64.

Tropical forests are the one of the largest carbon pools on earth and make a big contribution to the global carbon cycle. The scientists try to estimate the carbon stock in different carbon pools from a long time ago. They have followed different methods, techniques and approaches to assess the carbon stocks and balances in different stocks. This paper is a critical reassessment of the quality and the robustness of these models across tropical forest types and a good approach to test the allometric regression models which is crucial when estimating the above ground biomass.

They have made a big assumption when estimating the carbon stock which not mention in the paper was the carbon stock is equal to the above ground biomass. Have neglected the dead wood which comprises a minor potion of the total amount of carbon stock.

They have partitioned the forests as young and old-growth forests but have not stated the decisive factor used to split them. So the decision can be subjective when using the common sense. Further they have categorized the forest types to understand the allometric patterns based on rainfall data. As rainfall is not the only factor that affect to the tree growth this partitioning may not accurate when applying the regression analysis as example a heath forest and a rain forest can be appear in the same group based on the rainfall data but their allomatric relationships are totally different.

They have tested two models, biomass-diameter-height regression and biomass-diameter regression models and they predict four best representative models for four forest types which is useful for future estimations.

The global warming will becoming the most challenging environmental impact in upcoming centaury and the concept of carbon trading getting more popular day by day.  To implement such kind of concepts these findings may really useful.

References:

1. R. B. Myneni et al. A large carbon sink in the woody biomass of Northern forests, Proc. Natl. Acad. Sci. USA, 10.1073/pnas.261555198, 2001
2. Heather Keith, Brendan G. Mackey, and David B. Lindenmayer
   Re-evaluation of forest biomass carbon stocks and lessons from the world’s most carbon-dense forests
   PNAS 2009 106: 11635-11640.