Ecology and Evolution - Science topic

Differences in distress: Variance and production of American Crocodile ( Crocodylus acutus ) distress calls in Belize

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Yes, i think too

*The unrooted tree should be transformed into rooted tree. Try this code, phy=multi2di(phy1), where phy1 is the unrooted tree.

Thanks Wenjie Wan

Unfortunately it's proprietary.

I do agree with mr. Rileys suggestions. Or try to collaborate with a gp that hsa the ABI tools

Jean-Jacques Châteauneuf Thnak you very much for your comment. Best regards.

You may want to look at the function "get_variance()" from the "insight"-package (see https://easystats.github.io/insight/ resp. https://easystats.github.io/insight/reference/get_variance.html).

This function extracts all variance-components of mixed models and supports different packages (like lme4, glmmTMB, GLMMadaptive, lme, rstanarm, afex, ...). The code is based on the latest proposals from Nakagawa et al 2017 and Johnson 2014.

There is currently a package that will be based on this functions to compute R2 and ICC (intraclass correlation coefficient) for mixed models, but you can easily compute the values by yourself for now, which will also help you understand what the R2 values mean:

m <- lmer(Reaction ~ Days + (1 + Days | Subject), data = sleepstudy)

vars <- insight::get_variance(m)

rsq.marginal <- vars$var.fixef / (vars$var.fixef + vars$var.ranef + vars$var.resid)

rsq.conditional <- (vars$var.fixef + vars$var.ranef) / (vars$var.fixef + vars$var.ranef + vars$var.resid)

So, the marginal R2 is the fixed effects variance, divided by the total variance (i.e. fixed + random + residual). This value indicates how much of the "model variance" is explained by the fixed effects part only.

The conditional R2 is the fixed+random effects variance divided by the total variance, and indicates how much of the "model variance" is explained by your "complete" model.

If you would like to know how much of the proportion of variance can be explained by the random effects only, then you have the ICC. This is simply:

icc_adjusted <- vars$var.random / (vars$var.random + vars$var.residual)

"r2()" and "icc()" are currently implemented in the "sjstats"-package, but will be re-implemented in another package ("performance"), which will be released within this month...

Yesterday I occasionally deleted my long answer to this question. Briefly.

The second law of thermodynamics is valid only for isolated systems. The Earth is not the isolated system. The origin of life does not violate the second law. Chemical reactions commonly proceed with a decrease of entropy. A reaction might proceed spontaneously if the change in free Gibb's energy is negative. If the reaction is thermodynamically favorable, this does mean that the reaction will proceed. The reaction rates rae controlled not only by thermodynamics but also by kinetics. All living organisms (as well as all organized systems) are thermodynaically unstable but stable kinetically.

Tang Suye My friendly advise. Learn chemical thermodynamics instead of writing such out of ordinary text:

"Consider a chemical reaction, -ΔG/T≥0 (ΔG≤0), the changes in the system involve the two items, one is the change in the internal energy, another one is the change in the molecular structure, the first item relates to calorimetric entropy,"

New facts or new interpretations are presented every year. (Some of the new advances, however, soon proved to be erroneous.) As a starting point safe, I suggest a good textbook – e.g., Vertebrate life (Pearson, 2013, 9 ed.), by F H Pough et al.

Species accumulation curves (or collector’s curves) are used to estimate the number of species (i.e. species richness) in a particular area. A species accumulation curve records the total number of species observed, during the process of data collection, as additional individuals are added to the pool of all previously observed or collected individuals or samples. Accumulation curves may be either individual-based or sample-based.

A species rarefaction curve answers the question "how many species would a smaller sample include? Say you had two samples, 'A' with 100 individuals total and those 100 individuals distributed among 9 species and sample 'B' with 25 individuals distributed among 4 species. Rarefaction answers the question "How many species would I expect in sample A if I had caught only 25 individuals in all instead of 100?" The species diversity of two samples, containing 100 and 25 individuals respectively, can be compared directly by rarefying the larger sample down to 25 individuals.

Dear Dr. Barbara Motyka , it is an interesting issue.

Before we run out of oil, we would have moved to alternate fuels. Not because oil scarcity, but because of climate change. In the world of companies like Tesla, such a shift might not take long.

Germany has mostly moved in solar and China is fast following. India is also making some of the biggest solar plants that has dramatically brought the cost down to near the levels of coal. India's big move into solar is already paying off. In another 6 years, India alone plans to add 100 GW to the solar capacity. India Aims To Achieve Colossal Renewable Energy Targets 2 Years In Advance

Thus, on the one end we are already making great strides on producing energy without fossil fuels. The next part comes in storage and distribution. As you know, solar power doesn't come at night. People are already working on creating multiple energy sources mix to reduce this problem as well as researching a lot on batteries. Within another 10 years, Tesla powerwall and its competitors could be in all our homes. This is not hard to envision - a lot of people in India already have battery  inverters at home that store and release electricity given the unreliable supply.

Until we get there on battery storage, we might have a temporary point of time where we might be firing a lot of coal plants merely to balance load. That should be ok.

The third part comes in energy usage. Companies like Tesla are already making electric cars a reality. In parallel, there is the electrification and almost all trains would run on electricity in a decade [replacing Diesel]. A lot of metro train projects are underway in the developing world where again they replace diesel powered buses with electric powered trains, whose energy source would eventually be solar. 

While the drastic drop in oil prices have somewhat slowed the progress in clean energy, definite progress is occurring there. We are not far from a time where almost everything would run on solar, that will then be stored and used efficiently.

Based on the comments below, let address a few things.

Fact 1: We are rapidly moving into clean energy. This is the fastest shift in our energy usage since the dawn of time. Here is how Germany draws electricity through a day. Fossil [coal, natural gas, diesel] is now less than 50%. At various points of the day, solar supplies nearly half the power.  You can follow this blog - CleanTechnica [no association to me] for latest news on this.

France uses nearly nothing of fossil fuels for electricity.

While I'm a proponent of nuclear power, I don't think nuclear replaces the need for solar/wind for the following reasons.

That part is much more complicated.

It would really be an interesting world. In short, stop worrying about the stuff running out underneath us. Worry about the stuff we are filling above us.

In Greenland the Inuit home rule government has a policy to install hydropower in every town tapping the energy from the meltwater. So far they have build six. Each city supplied has ceased to use their diesel generator power plant.

The second photo is of the Sisimut plant close to my universities Sisimut campus.

Hi Marcin,

An animal can be both a habitat generalist and a feeding specialist. I work with an endangered carrion beetle that is said to be a habitat generalist and a breeding/feeding specialist. Nicorphorus americanus (American burying beetle) buries small dead animals as a breeding and feeding resource to raise its young. (Yes, it's an insect that uses parental care) There are other Nicrophorus species around the world that are great study subjects due to their interesting life histories. The beetle is considered a habitat generalist because it isn't tied to the habitat per se, but rather is tied to what dead animals are found in that habitat. Here is a link to the beetle webpage that has all kinds of info about the little critter.

Hi Pieter

The bioturbative effects of the shore crab Carcinus maenas are limited, since many live in hard-substratum environments. But indeed, in sandy areas it shows either locomotion (small footprint but many legs!) or temporary burrowing activity. Burrowing may be either for finding food with chaelae or for hiding. In sandy areas, the shore crab may temporary hide in the sediment completely by digging in backwards. It does not dig deep as it keeps contact with the sediment surface.

This being said, following Kristensen et al. (2012), I would consider the shore crab an 'epifaunal biodiffusor'. C. maenas is not well adapted for living in and moving through the sediment like the examples mentioned for 'surficial biodiffusors' (e.g. burrowing sea urchins). Also following Kristensen et al. (2012) it cannot be considered a 'regenerator' as does not maintain burrows continuously.

Hello John Vincent!

I agree with Katrina, that among the factors that affect the spread of a disease is the population size, like in the case of parasites. In the simple equation for the number of infected hosts in parasitism (Rp), Rp = NBL (where N is the population, B is the transmission rate of disease, and L is the virulence of the disease), it is inferred that the greater populations have higher susceptibility to the disease since there are more hosts to infect.

On the genetic level, a more genetically diverse population has a higher chance of surviving an epidemic. Genetic diversity could act as a buffer in the spread of a disease. Aside from this, climate could also play a part in an epidemic as pathogens are known to thrive in warmer conditions. Hence, an increasing temperature will also increase disease in several hosts such as plants and humans.

Should you wish to find a more thorough discussion on these, you can find them here: https://www.nceas.ucsb.edu/science/disease#

Hello Giacomo;

     Species of ants in which the new queens disperse by walking are good candidates for differentiating populations in the fashion that you are thinking about. Here is a reference for an example that might be of interest.

      Jowers, MJ, et. al. 2014. Recent speciation and secondary contace in endemic ants. Molecular Ecol. doi: 10.1111/mec.12749.

Regards, Jim des Lauriers

Nicely summarised David - thanks.

The updated link is:

Thank you Dr. Provete for your suggestion.

All my data are continuous trait like wing length, wing width for morphological & testis size for reproductive traits. As you mentioned parameter (sigma) you mean by Variance? Please can I have your email address, I prefer to be in contact with you through email, and this is my email:

aram.afrasiaw@gmail.com   

If you have a variety of variables (time, pH,... n var.). I would recommend using the NMDS multivariate statistical technique. Because you have multiple scales in your variables. However, the statistical technique that you need to use depends on the nature of your data and the question you want to answer.

Best regards

Cristian Martínez

Dear Rudi and Rinaldo,

these appendages are unique to female beetles and very prominent in ground beetles. If a pheromone was released, you could not have noticed. However, up to now no sex pheromone is known for ground beetles although it supposedly should exist.

In the past I have also seen female ground beetles with extracted genitalia as seen in your photos after an interrupted copula or if the specimens underwent pressure. So there may actually be different explanations ...

Best,

Fabian

Mokrane, What is your definition of niche? What is your challenge according to the niche concepts?

Firstly you should specify the niche concepts and niche dimensions in your study. For example, ¿Are you interested in the fundamental niche or the realized niche? This is a much-debated issue in the bibliography. Here, I suggest you several references. Good luck!

References: 

Barve, N., Barve, V., Jiménez-Valverde, A., Lira-Noriega, A., Maher, S. P., Peterson, A. T., … Villalobos, F. (2011). The crucial role of the accessible area in ecological niche modeling and species distribution modeling. Ecological Modelling, 222(11), 1810–1819.

McInerny, G. J., & Etienne, R. S. (2012). Stitch the niche - a practical philosophy and visual schematic for the niche concept. Journal of Biogeography, 39(12), 2103–2111.

Peterson, A. T., Soberón, J., Pearson, R. G., Anderson, R. P., Martínez-Meyer, E., Nakamura, M., & Bastos Araujo, M. (2011). Ecological niches and geographic distributions (Vol. 49). Princeton, NJ: Princeton University Press.

Pulliam, H. R. (2000). On the relationship between niche and distribution. Ecology Letters, 3(4), 349–361. 

Soberón, J., & Townsend Peterson, A. (2005). Interpretation of Models of Fundamental Ecological Niches and Species’ Distributional Areas. Biodiversity Informatics, 2, 1–10.

Soberón, J. (2007). Grinnellian and Eltonian niches and geographic distributions of species. Ecology Letters, 10(12), 1115–1123. 

No one seems to have noticed that Potamon potamios is a semi-terrestrial crab. Its areal is whole of Eastern Mediterranean and it requires neither continuous water paths, nor birds for its dispersal.

Dear Ellynn,

The recent and very interesting paper by Fujisawa et al. (2014) would be helpful in this regard:

"Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles"  

Best wishes,

Temim

Hi all,

New developments this week:

DNA hints at earlier human exodus from Africa

http://www.bbc.co.uk/news/science-environment-37408014 

All non-Africans alive today likely descend from people within a single migration out of Africa

https://www.sciencedaily.com/releases/2016/09/160921131354.htm 

Genetic ‘trace’ in Papuan genomes suggests two expansions out of Africa

https://www.sciencedaily.com/releases/2016/09/160921131119.htm 

The first genomic history of Australia’s peopling

https://www.sciencedaily.com/releases/2016/09/160921131116.htm 

Hello again,

I would like to ask Agevi Humphrey if you have a reference for the successional status of Chionanthus africanus as a late successional sp. would you please share it with me. Thank you

Hey Ranjeev,  Good question - and I bet that nobody really knows!  The problem arises that because of the often severe Ca limits to growth, the snails are probably constrained most of their short lives - so it might appear as indeterminate in a Ca-rich habitat, or determinate in a less Ca-rich environment.  Sorry that I cannot provide an easy answer - but that is the nature of the beast!  Good luck! 

Having done similar searches myself, I can give you the advice that helped me the most:  Simply write to the curators directly and individually.  This will only be 15-20 emails and you will get to know - professionally - the curatorial staff and manner of each museum and/or collection manager.  In addition, nests are often not fully online yet, so you might get the best results by reaching out to each ornithology department and the people rather than trying the searches online.  Good luck!

Hi,

The question is how to integrate the stoichiometric concepts into the field data recalculations calculation ? Now field hydrobiologist can use coefficients of tempreture dependend functional indices like respiration or production, and amadements on oxygen concentrtation. But how to calculate disbalance or lack???

Andrey

Short-lived species can go through hundreds or thousands of generations in that time period, which is ample time for substantial genetic change IF there is pre-existing genetic variation that can be selected for and against. If there isn't, evolutionary change would have to rely on mutation, and would be several orders of magnitude slower. Long-lived trees may go through no generations in 20-30 years, so cannot evolve, but even a single generation can lead to substantial genetic change if there is a high mortality, strong selection and variation for it to act on. Epigenetic variation can also be heritable, at least in plants, and may be an important source of adaptive capacity in long-lived species (or may not - the evidence is currently unclear!).

It will survive but it will be relatively small. You need a preliminary study designed especially for your research question, to check exact ratio of pollen:cellulose that you want to use. And remember that pollen itself may show variability in nutritional quality.

Best!

Hi.

About invasive plants may be good to read this important reference, which link is:

http://onlinelibrary.wiley.com/doi/10.1046/j.1472-4642.2000.00083.x/abstract 

Sometimes there is confusion with the concepts "invasive", "naturalized", etc.

Best regards. 

So you are asking how to tell when speciation is "complete"? This is actually a very difficult question, and one for which we don't really have a generalizable answer yet. The definition for "species" is not quite as simple as the one you gave. What you refer to is the "biological species concept", which defines species as discrete units which are reproductively isolated from other such units... And there is much debate surrounding the application of various species concepts (see attached commentary by John Avise).

One problem with answering the question you have posed, is that speciation itself is a continuous process, where the parameters used to define its "progress" vary along a gradient.. For example various types of reproductive isolation (extrinsic vs. intrinsic, premating vs postmating, etc) can exist to varying degrees between populations, or "subspecies", or recognized species, or even members of different genera. We can see examples of hybridization (thus "incomplete reproductive isolation") throughout nature- does this mean that these are not "true species"?

So, along this continuum, diverging populations accumulate mutations, and accumulate reproductive isolation, either as a result of allopatry+time (geographic separation), or via divergent selection (and the cumulative effect of many other processes). Things are more complicated when we consider that the net effects of these processes are heterogeneous throughout the genome- thus the "amount" of divergence will vary depending on which locus we assay... Attempting to delineate classifications (such as "species" or "sub-species") along this continuum requires that we either treat it as discrete, or determine some arbitrary threshold at which we consider speciation to have progressed (for example, we might say "2% sequence divergence at X locus constitutes species-level divergence).. I'm not sure how far you have made it in your class, but probably you can think of many ways that this sort of attempt to quantify speciation progress might not be generalizable. I've attached another paper by Sara Via which might be interesting to read.

TL;DR- You really can't quantitatively determine when speciation is "complete", because the term "species" (and other various classifications of biodiversity) are human constructs which attempt to apply discrete delineations on a continuous process.

Just my take though

It is not necessary that sender and receiver both benefit from a new communication process. Many signals arise by 'exploiting' the sensory system of the receiver. For example, guppy males attract more attention by females when their color matches that of the most preferred food of the females. This way, males can evolve a certain color that later plays an important role in sexual selection. The color trait (it depends on your definition from which point onward you call it a 'signal') may spread even if mating with colored males would be disadvantageous for females. A recent review article on this 'sensory exploitation hypothesis' is Ter Hofstede et al. (2015) in Current Biology.

Abderrazak:

Brilliant photos, but why do you think that all the plant groups do not support Evolution? Whether Animal or Plant , primitive and evolved forms can co-exist at a given point of time but in geological past several groups of Life forms simply became extinct. You need to study some basic books dealing with the theory of Evolution.

Best

Syed

Guilherme:

This link would provide some insight you are looking for.

Best

Syed

There was a previous thread on ResearchGate on this topic:

https://www.researchgate.net/post/Can_anybody_provide_an_example_of_mutualistic_plant-plant_interaction).

The answers were not particularly illuminating, but perhaps you could open a conversation with Guido Lingua.

Dear Mauricio

Budke, J. C., Jarenkow, J. A., & de Oliveira-Filho, A. T. (2010). Intermediary disturbance increases tree diversity in riverine forest of southern Brazil. Biodiversity and Conservation, 19(8), 2371-2387.

Montero, J. C., Piedade, M. T. F., & Wittmann, F. (2014). Floristic variation across 600 km of inundation forests (Igapó) along the Negro River, Central Amazonia. Hydrobiologia, 729(1), 229-246.

Rosales, J., Blanco-Belmonte, L., & Bradley, C. (2008). Hydrogeomorphological and ecological interactions in tropical floodplains: The significance of confluence zones in the Orinoco Basin, Venezuela. Hydroecology and Ecohydrology: Past, Present and Future, 295-316.

This way of posing the question is wrong. There were no classes then because classes do not exist in the real world. Classes are just concepts used by taxonomists to communicate about the organisms and taxa, not "objects" or "individuals".

Kano' s line? What and where

?

In addition to the useful comments above, I guess you can link it back to extremophiles phylogenetics. That will give substantial support to how basic "organism" strive in that environment, and thus, validate that theory of earth without oxygen is logical.

 I have been reading the various answers with great interest, trying to form an opinion. Now that I have started writing, I hope my “opinion” does not turn into a rant, and my apologies if you see it as such.

 I agree, that the inclusion of human activity is a must in ecological studies these days. The study of social-ecological systems was (re)born from this need.

 Where are we going with ecological research? I would like to pose a number of questions to answer that...

How much of our ecological research is put into actual practice to improve conservation, environmental management etc.? Research grant applications may require a statement of how important the research is in practice, but how many of us actually publish our findings in a “farmer's weekly”? Farmers in Africa and Australia (and probably all over the world) are the primary owners / managers of the land. How well do we inform them? Universities don't give much credit to such “popular” publication. You need to publish in journals with the highest possible ISI rating – generally read by other academics and post-graduates who can afford the subscription (undergraduates just copy and paste the contents but don't read it). The openAccess policies that are being implemented now may help with the dissemination of information. All we need to do then is to get the farmers to read such journal articles in the hope that they understand our jargon… Until then, many of us are doing research because it's fun – in my case this is probably even more true, as I am not working in my field at the moment. I do research in my spare time.

 How many long-term ecological studies do we see? With much of our research done by post-graduates we are looking generally at 2yrs for an M.Sc. and 3yr for a PhD – maybe double that for part-time students. Students and/or universities are penalised for taking much longer than that. What are six years (-1 year for project proposal, analysis and write-up) for a forestry ecological study? Or in an arid system where the rainfall regimes dictate outcomes? Working with a series of post-docs? How many agencies are prepared to fund 50yr studies in ecology? Will you start a project (like the foresters of old) that you will never see the end of? Space-for-time approaches can only be taken so far… Do we have the leisure / time to do long-term studies? Ecological problems generally need a fast management response … make that “...fast, appropriate management response”.

Basically I see our research as part of a system that follows the instant everything approach – instant messages, fast food, instant pudding - but sadly a “just add water” approach will not work in ecological studies (no pun intended for arid systems ecologists). Universities are required to “perform” but we can't agree on how to measure performance in the first place. As a result, we have taken money as an easy indicator (grants received, student fees and government support per student etc) so we are now focussing on counting beans rather than on … whatever it is that we are supposed to focus on.

That might be topic of another RG question?

 So in answer to the original question… at the moment we seem to be building up an enormous knowledge base that needs to be tapped a lot more.

Regards to you all,

PS - Dr. in forest management 2005, 14 years of teaching and research.

Thank you Hamdy, Marcelo has already uploaded those papers.

As far as I remember, the first record of terrestrial carnivorans in South America should be some Procyonidae, possibly as early as 6 Ma, and Mustelidae during the Miocene.

See those references and herein.

Cheers!

Antoine

Hi Oleksandr,

you might want to check out AquaMaps:

There you can search for distribution maps for several fish species.

Hope that helps you getting started,

Michael

Just a word of caution on terminology:

Reintroductions and Introductions are two very different issues: the former indicates the release of a taxon to an area where it was present in earlier - historical - times and later got extinct, whereas the latter indicates the release of an alien (allochthonous) taxon to a new area. The release of wolves to Yellowstone has been a reintroduction, but the release of South American coypus and North American grey squirrels to Europe or that of red foxes to Australia have been introductions. The former are positive operations - if properly conducted - and tend to restore pristine zoocoenoses, whereas the latter are quite negative operations as they tend to upset ecosystems.

In both cases you should expect consequences on the ecosystems, usually favourable in the first case, nearly always negative in the second case. The effects of weather and climate integrate with these consequences (or rather the other way round!).

The D. elegans is a digital photo by my field assistant Takao in Iriomotejima.

I've collected the specimens and identified them.  I'm an entomolgist with emphasis on drosophilidae.

Reliabilities of estimates of species richness for a given fauna are directly related to the completeness of taxonomic understanding of the group being counted.  For butterflies, many polymorphic taxa were recognized as such by the early 20th Century (see, for example, GAK Marshall's discussion of Heliconius in Trans. Ent. Soc. 1908).  There may be overestimates due to polymorphisms and/or synonymic taxonomic descriptions, or there may be underestimates because there are a lot of undescribed taxa.

Hi Marc-Olivier, selection acts on traits of individual species, so you need a model for each species separately. If your response variable and phenotypic traits are the same, you may probably get results in the same scale. After you fit the models, you can compute selection gradients and check for significance using the R package gsg. Also check for the work of Morrissey & Sakrejda (2013) "Unification of regression-based methods for the analysis of natural selection". Hope this helps

Our article published in peer-reviewed Journal "Communicative & Integrative Biology". A few major points discussed in the paper:

(1) Brain is not the source of consciousness.

(2) Consciousness is ubiquitous in all living organisms, starting from bacteria to human beings.

(3) The individual cells in the multicellular organisms are also individually cognitive entities.

(4) Proposals like “artificial life”, “artificial intelligence”, “sentient machines” and so on are only fairytales because no designer can produce an artifact with the properties like internal teleology (Naturzweck) and formative force (bildende Kraft).

(5) The material origin of life and objective evolution are only misconceptions that biologists must overcome.

Try contact Dr. Spungis in Riga or Dr. Mamaev in Moscow - these are leading taxonomists for gall midges and may suggest something useful 

In Yellowhammer Dialects project, I am exploiting many sources of recordings:) Surprisingly, some yellowhammer song are also on Flicker, however I bet this is not the case of African warblers.

One is on AvoCet (http://avocet.zoology.msu.edu/recordings?scientific_name_search=Acrocephalus+baeticatus&name_search=&Search=Search+Recordings)

The best would be to contact British library - they have about 47 songs: http://cadensa.bl.uk/uhtbin/cgisirsi/?ps=jvO7LMNQhB/WORKS-FILE/325200049/123 I will send you a contact to a responsible person through email, Nika:-)

Hi John!

Unfortunately my photos of Pteropus rodricensis are really of poor quality (and I do not have any of the skull). I suggest to ctc 

Mauritian Wildlife Foundation

Grannum Road

Vacoas

Mauritius

Phone Number (230) 697-6097

Fax (230) 697-6512

Email executive@mauritian-wildlife.org

Website Address http://www.mauritian-wildlife.org

or

Mauritian Wildlife Foundation

Forestry Quarters

Solitude

Rodrigues

Phone Number (230) 831-4558

Fax (230) 831-4559

Email mwfrod@mauritian-wildlife.org

Website Address http://www.mauritian-wildlife.org

or

Mauritius Natural History Museum

under Mauritius Museums Council

All the best.

Marco

Hi,

If you have already matrices of spatial and genetic distances, SPAGeDi is not really useful to analyse them. You could make a Mantel test or compute average genetic distances for a set of spatial distance intervals using for example scripts in R. SPAGeDi would be useful if you have raw genetic data of individuals (with spatial coordinates) from which you'd like to compute genetic distances.

all the best,

Olivier

Sorry. of course, I would say "Synusien 2. Grades".

To compensate my mistake a little, I found in intgernet a publication about a particular synusie structure in plants. Unfortunately, it is in Russian but with English summary

It has been studied recently in arabidopsis plant - seed coat mucilage secretory cell devel

opment. 

1. Windsor JB, Symonds VV, Mendenhall J, Lloyd AM.

2000.Arabidopsis seed coat development: morphological differenti

ation of the outer integument. Plant Journal22: 483493.

2. Western TL. 2012.The sticky tale of seed coat mucilages: produc

tion, genetics, and role in seed germination and dispersal.Seed

Science Research22: 1 25.

3. Yang X, Baskin J, Baskin C, Huang Z. 2012b. More than just a coat

ing: ecological importance, taxonomic occurrence and phylogenetic

relationships of seed coat mucilage.Perspectives in Plant Ecology,

Evolution and Systematics14: 434 442.

4. Western TL, Skinner DJ, Haughn GW. 2000. Differentiation of

mucilage secretory cells of the Arabidopsis seed coat.Plant

Physiology122: 345 356.

5. Western TL, Burn J, Tan WL,et al. 2001. Isolation and characteriza

tion of mutants defective in seed coat mucilage secretory cell devel

opment in Arabidopsis.Plant Physiology127: 9981011.

6. North HM, Berger A, SaezAguayo S, Ralet MC. Understanding

polysaccharide production and properties using seed coat mutants:

future perspectives for the exploitation of natural variants. Ann Bot.

2014 Oct;114(6):125163. doi: 10.1093/aob/mcu011.

7. Western TL, Young DS, Dean GH, Tan WL, Samuels AL, Haughn

GW. 2004. MUCILAGEMODIFIED4 encodes a putative pectin

biosynthetic enzyme developmentally regulated by APETALA2,

TRANSPARENT TESTA GLABRA1, and GLABRA2 in the Arabidopsis

seed coat. Plant Physiology 134: 296306.

8. Zou HF, Zhang YQ, Wei W, Chen HW, Song QX, Liu YF, Zhao MY,

Wang F, Zhang BC, Lin Q, Zhang WK, Ma B, Zhou YH, Zhang JS,

Chen SY. The transcription factor AtDOF4.2 regulates shoot branch

ing and seed coat formation in Arabidopsis. Biochem J. 2013 Jan

15;449(2):37388. doi: 10.1042/BJ20110060.

9. Esfandiari E, Jin Z, Abdeen A, Griffiths JS, Western TL, Haughn GW.

Identification and analysis of an outerseedcoatspecific promoter

from Arabidopsis thaliana. Plant Mol Biol. 2013 Jan;81(12):93104.

doi:10.1007/s1110301299840.

Hi David - if it was stored in EtOH or another OH for long periods of time at RT or frozen, you have already started the extraction process. As long as that time of 'extraction' is the same, none of the fluid is lost, and the subsequent extraction method is the same, you might be OK. (though, in other words, I do not think that samples stored in EtOH at RT are an ideal way to store fecal samples for subsequent extraction of hormone metabolites).

For formalin, I am not sure because it isn't clear to me if the metabolites will start to be extracted from the feces. There is also the issue of microbial activity in the feces, which is a problem if at RT but perhaps not if the samples stored in formalin are thoroughly mixed up in formalin. Coming to think of it, we have meerkat feces that were split in half and stored either as a) immediately frozen or b) stored in formalin at RT (for parasite work). It could be possible to assay fecal Cort metabolites to assess differences.

If freezing is impossible in the field, there are other methods to preserve the metabolites without a freezer rather than storing in EtOH or formalin at RT. See Jacinta Beehner's work in geladas and other primate species. She directly extracts the metabolites in the field and stores them on cartridges at RT and found that to be as good as directly freezing.

Benton is right. The ERF auction is intended to be 'blind' - that is, no-one will know the results. The government has stated that its chief criterion for awarding acceptable bids is PRICE - that is, the lower the prices for winning bids, the larger the number of tonnes of abatement it can buy for its budget. It may well be that, within the additionality rules, bidders with projects which can afford to invest for very low carbon prices (sub $10/tonne, I suspect) will be the successful ones. There have been no auctions as yet.  Regard, Bill (Sydney)

I’ve spent enough time climbing trees to know that if you want samples, there’s usually a quicker way than climbing the tree (though few are as much fun). I’d agree that the shotgun method is probably the fastest and easiest. As I don’t have access to a shotgun or a marksman, I’d resort to my bigshot catapult & a throw bag/line:

It takes a little practice to get the aim right (I recommend practicing with overripe fruit rather than stones) but you can get a line over the branch you’re interested in very easily, even at 50m high. The trick is to know that you need the string to be 3x longer than the height of the branch. Once you get the line in approximately the right place, attach a square of carpet to the string and pull that over the branch to rub off the tillandsia & other epiphytes. Alternatively, you could tie in one of those wire saws (eg. http://www.amazon.co.uk/BCB-CM020A-Commando-Lightweight-Wrist/dp/B002C3PPEE) and sample the entire branch.

Read a review "Are Drosophila telomeres an exception or the rule? by

Edward J Louis

Genome Biology 2002; and can be found online at: http://genomebiology.com/2002/3/10/reviews/0007

A Reading List on the “Ancient Passerine” Proposal:

1. Schizocerate (“split horn”) finding of a doubled spinal cord dorsal horn in many modern bird families, but not in passerines, paleognaths, rails cranes and pigeons, which all share the leiocerate (normal spinal cord with one dorsal horn) condition found in all other amniotes.

Woodbury, Jeffery. C. 1998 Two spinal cords in birds: novel insights into early avian evolution. 
Proc. R. Soc. Lond. B 265: 1721-1729, doi: 10.1098/rspb.0494

2. Molecular studies showing that passerines are found at the root of the avian tree, with paleognaths. All the “cherry-picked” studies below agree on this, except iii, where passerines are still basal, but are usurped from the earliest branch by the Galloanserines, an artificial assemblage of two otherwise unrelated groups of birds (galliforms and anseriforms) that appear to be ancient only by virtue of shared, extraordinarily high, mutation rate.

i. MINDELL, D. P., M. D. SORENSON, D. E. DIMCHEFF, M. HASEGAWA, J. C. AST, AND T. YURI. 1999. Interor- dinal relationships of birds and other reptiles based on whole mitochondrial genomes. Syst. Biol. 48:138– 152. The basal position of passerines in this study was not generally accepted at first; “long branch attraction” was thought to be responsible for the heterodox phylogeny of passerines.

ii. JOHNSON KP (2001) Taxon Sampling and the Phylogenetic Position of Passeriformes: Evidence from 916 Avian Cytochrome b Sequences. Syst. Biol. 50(1):128–136 This study has a very large data set compared with i. and convincingly despatches the idea that “long branch attraction” accounts for the basal position of passerines.

iii. Kerryn E. Slack a,b, Frédéric Delsuc a,1, Patricia A. Mclenachan a, Ulfur Arnason b, David Penny (2007) Molecular Phylogenetics and Evolution 42: 1–13 Resolving the root of the avian mitogenomic tree by breaking up long branches. These authors are expert at correcting for biases in DNA that can influence phylogenetic reconstruction such as base composition and taxon sampling, but they have not been completely successful at correcting for large, circular, variations in mutation rate. For this reason, the basal position of passerines is confirmed, even lying outside the paleognaths, but the Galloanserines, with a very large rate anomaly, intrude (see 2 above).

iv. Slack KE, Jankea A, Penny D., Arnason U. (2003) Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features. Gene 302 (2003) 43–52 In this study, Galloanserines are more appropriately placed than iii, but are still outside the paleognaths, outside of which are the passerines, in keeping with the present thesis. A nice feature of this study is the use of non-avian amniotes as outgroups. Passerines prove to be the closest sister group to the non-avian amniotes in their cladogram.

Royal paulownia (Paulownia tomentosa) is an introduced ornamental that has become well established in this country. It is also known as princess-tree, empress-tree, or paulownia. Aside from its continuing ornamental use, the species has value for its small saw logs that are in demand for specialty products. Its capacity to "pioneer" disturbed exposed sites has made royal paulownia a favorite for stripmine spoilbank reclamation

Royal paulownia is a native of eastern Asia. It has been widely planted in North America from Montreal to Florida and west to Missouri and Texas. It has also been planted in some Pacific States. The tree is moderately cold hardy and has naturalized principally in the East and South. In China, the natural range is south of the 0° C (32° F) January isotherm in areas which receive an annual rainfall of at least 1020 mm (40 in) Naturally seeded or planted royal paulownia survives and grows best on moist, well-drained soils of steep slopes or open valleys, but it will germinate and grow on almost any moist, bare soil. A highly adaptable "escapee" such as royal paulownia is found in many site, soil, and forest type conditions, including soils commonly found in the order Alfisols.

Bonner, F. T., and James D. Burton. 1974. Paulownia tomentosa (Thunb.) Sieb. & Zuec. Royal paulownia. In Seeds of woody plants in the United States. p. 572-573. C. S. Schopmeyer, tech. coord. U.S. Department of Agriculture, Agriculture Handbook 450. Washington, DC.

Carpenter, S. B. 1981. Personal correspondence. University of Kentucky, Lexington.

Carpenter, S. B., and Donald H. Graves. (n. d.) Paulownia-a valuable new timber resource. University of Kentucky Cooperative Extension Service, FOR-11. Lexington, KY. 7 p.

Hepting, George A. 1971. Diseases of forest and shade trees of the United States. U.S. Department of Agriculture, Agriculture Handbook 386. Washington, DC. 658 p.

Hu, Shiu-Ying. 1961. The economic botany of the paulownias. Economic Botany 15:11-27.

Immel, M. J., E. M. Tackety, and S. B. Carpenter. 1980. Paulownia seedlings respond to increased daylength. Tree Planters'Notes 31(l):3-5.

Tang, R. C., S. B. Carpenter, R. F. Wittwer, and D. H. Graves. 1980. Paulownia-a crop tree for wood products and reclamation of surface-mined land. Southern Journal of Applied Forestry 4(l):19-24.

I've found an interesting software, developed by Jessica W. Leigh: popART (http://popart.otago.ac.nz/index.shtml).

May be this blog will help : http://blog.f1000research.com/

Good morning,

I write from Argentina, I am a dendrochronologist working on semiarid environments. I do not have the samples that you are asking for but do not hesitate to contact me for any other question that you have.

Best wishes.

I agree with Jan that setting branch lengths equal to 1 is a good starting point if you don't have a robust phylogeny. If you have some idea of the relationships between your species then you can make your own informed tree with branch lengths set at one, but it is nearly always going to be advantageous to build a tree using molecular / morphological data if you can. GenBank has many sequences available that you may be able to use, and there are various R packages that allow you to trim down trees so that you can exclude unwanted species from published phylogenies. Hope that helps a bit

Good luck

Gbolade AA, Olayemi JO, Elujoba AA, Sofowora A, Adesina SK. 1992 Factors affecting the levels of steroidal sapogenins in Nigerian Agave and Furcraea species Fitoterapia 63. 45-48. (EBBD, 190204324).

Bogler DJ, Simpson BB. 1995 A chloroplast DNA study of the Agavaceae. Syst. Bot. 20. 191-205. 40 taxa. Agav:Dracaena, Sansevieria, Beaucarnea, Calibanus, Dasylirion, Nolina, Beschorneria, Agave, Manfreda, Polianthes, Prochnyanthes, Furcraea, Yucca, Hesperaloe. Hypox:Hypoxis. Lili:Asparagus, Aspidistra, Convallaria, Liriope, Maianthemum, Cordyline, Hemerocallis, Hosta. Xanthor:Xanthorrhoea. (PMBD, 186000297).

Ojeda Revah L, Ludlow Wiechers B. 1995 Palinologia de Agavaceae, una contribucion biosistematica. Bol. Soc. bot. Mex. 56. 25-43. LM, SEM. 15 gen., 36 spp. Agave (3 spp.), Beaucarnea (3), Beschorneria, Cordyline (2), Dasylirion (2), Dracaena (2), Furcraea (4), Hesperaloe (2), Hosta, Manfreda (5), Nolina (2), Phormium, Polianthes (2), Sansevieria (2), Yucca (5). (PMBD, 186000774).

Alvarez de Zayas A. 1996 El genero Furcraea (Agavaceae) en Cuba. (The genus Furcraea (Agavaceae) in Cuba.) An. Inst. Biol. Univ. Nac. Auton. Mex., Bot. 67. (2): 329-346 (1996) - illus. Icones, Maps, Anatomy and morphology, Keys. Furcraea antillana sp. nov. Geog=4 (KR, 199700692).

Souza Chies TT, Bittar G, Nadot S, Carter L, Besin E, Lejeune B. 1997 Phylogenetic analysis of Iridaceae with parsimony and distance methods using the plastid gene rps4. Pl. Syst. Evol. 204. 109-123. Alophia, Aristea, Babiana, Belamcanda, Bobartia, Crocosmia, Crocus, Cypella, Dietes, Freesia, Gladiolus, Iris, Isophysis, Lapeirousi a, Libertia, Micranthus, Moraea, Neomarica, Nivenia, Patersonia, Pillansia, Romulea, Sisyrinchium, Sparaxis, Tigridia, Trimezia, Wat sonia, Agav:Agave, Asparagus, Furcraea, Haemanthus, Hymenocallis, Narcissus, Nerine, Yucca. (PMBD, 186001815).

Khan HA. 1997 Morphotaxonomical studies of Furcraea (Agavaceae) of India. J. Pl. Anat. Morphol. 7. (2): 140-147 (1997) - illus. Icones, Keys. Geog=6 (KR, 199904195).

Garcia Mendoza A. 1999 Una especie nueva de Furcraea (Agavaceae) de Chiapas, Mexico. Novon 9. (1): 42-45 (1999) - illus. Icones, Anatomy and morphology. Furcraea niquivilensis sp. nov. Geog=4 (KR, 199900858).

Kauff F, Rudall PJ, Conran JG. 2000 Systematic root anatomy of Asparagales and other monocotyledons. Pl. Syst. Evol. 223. 139-154. LM. . Agap:Agapanthus; Agav:Agave, Furcraea, Hosta, Yucca; All:Allium, Tulbaghia; Amaryll:Amaryllis, Clivia, Hessea, Hippeastrum, Nerine; Antheric:Anthericum, Chlorophytum; Aphyll:Aphyllanthes; Asp:Asparagus; Behn:Behnia; Convall:Aspidistra, Beaucarnea, Convallaria, Dasylirion, Dracaena, Eriospermum, Nolina, Peliosanthes, Polygonatum, Reineckea, Sansevieria, Danae, Ruscus, Semele; Herreria, Hyac.:Albuca, Eucomis, Ledebouria, Muscari, Ornithogalum... (PMBD, 186100541).

Garcia Mendoza A. 2000 Revision taxonomica de las especies arborescentes de Furcraea (Agavaceae) en Mexico y Guatemala. Bol. Soc. Bot. Mex. no.66. 113-129 (2000) - illus. Icones, Maps, Chromosome numbers, Anatomy and morphology, Keys. Furcraea martinezii sp. nov. Geog=4 (KR, 200200674).

Nadaf AB, Shukla SR, Krishnan S. 2001 Some new observations in Furcraea foetida L. J. Econ. Taxon. Bot. 25. (2): 275-278 (2001) - illus. Icones, Anatomy and morphology. Geog=6 (KR, 200203359).

I'm not convinced that a "simple, logical, biologically-based explanation" for DT is possible.  The social/political/economic behavior of humans is too complicated to be completely explained by biology.  The key feature in the DT is initial decline in death rate and then decline in birth rate.  Decline in DR occurs with better health care, hygiene and sanitation systems, improved nutrition and reliable food supply. Decline in BR occurs with greater willingness of females (and males) to use contraceptives. Use of contraceptives and family planning becomes more prevalent as women become better educated and take control of their own reproductive futures.  At a fundamental level, DT is the composite outcome of choices that humans make. Certainly, there may be some innate biology in action when a person makes a social and economic choice.  But this innate biology certainly does not explain DT.  It is tempting to want a biologically-based explanation for DT because if it is based in biology it might be seen as more scientific and valid.  However, it already is scientific and valid.  I agree that "the theory with greater scientific value will have a greater impact" .... but with regard to DT, "impact" on what?  We need DT to have an impact on politicians and policy-makers (particularly in the USA) in the form of awareness and realization that it is a good thing for a country and humanity in general. A speculative and unnecessary biological explanation will not help.

In terms of actual chemical characterization, none have been described (to my knowledge). However, Fraker et al 2009 (Horm Behav) showed a nice neuroendocrine response from a skin-released compound in larval amphibians. Fish have been well described (e.g., ostariophysan alarm pheromone). The Fraker paper has a nice summary of what is known as well. I doubt my answer helps, but I would also love to know if you have any updates on this question.