Science topics: EcologyEcology and Evolution
Ecology and Evolution - Science topic
Evolution of new species is significantly controlled and directed by the environment the species dwells in, its niche requirements, its adaptability to the most subtle changes in its niche as well as the whole ecosystem in which its niche lies. A discussion in this forum are: behavioral ecology, marshland ecology, bio-fuels and evolution of animal societies. The focus of discussion can be broadly divided into two different direction apart the basic ecology aspects of evolution i.e. molecular evolution as well the mathematical aspect, both understanding and modelling of evolutionary ecology.
Questions related to Ecology and Evolution
Phylogeny analysis seems beyond my capacity right now, however, there are so much information in my dataset of seed traits along with climate, phenology, any suggestion will be appricitated.
I am searching for good recordings of distress calls emitted by American crocodiles, in particular by hatchlings. The longer the better. If not, also distress call recordings of other crocodilian species are fine.
In 2016 I have published a series of recommendations for improving water quality in recirculating systems. This was published by my contractor (a public research center) in their website as an open access file (no ISSN, DOI...). https://www.juntadeandalucia.es/agriculturaypesca/ifapa/servifapa/registro-servifapa/bf663551-17f0-4c55-bbde-fe777f15da77
Eventually, this was cited in Sempere et al. (2018). Should this be counted as an "oficial" citation?
Thanks for your opinions,
Sempere-Valverde, J., Sedano, F., Megina, C., García-Gómez, J. C., & Espinosa, F. (2019). Feeding behaviour of Patella caerulea L. and P. rustica L. under spring and neap simulated tides. An innovative approach for quick quantification of grazing activity. Ethology Ecology & Evolution, 31(3), 283-292.
I have a question, when I used the picante function to analyze the phylogenetic community structure and phylogenetic signals in R, it appeared an error:"'phylo' is not rooted and fully dichotomous", I don't understand what's the problem, the attached file is my phylogenetic information, please check it, I am sorry to trouble you all, but I really want to solve this problem, thanks a lot.
The solution for immediate stabilization of DNA, RNA, and protein in tissues.
I would like to know if anyone knows about other software other than Genemapper/Genamarker to visualise peaks, or whether there is any online platform available? Thanks in advance.
Please help me in the identification of this well preserved fossil plant found in Tufa . Thank you in advance !
I am using linear mixed effect models in my experiment (using r package). I would like to show a measurement of the fitting quality of the model. I see that there are lot of methods but two of the most frequently are:
1) Xu, R. (2003). Measuring explained variation in linear mixed effects models. Statistics in medicine, 22(22), 3527-3541.
2) Nakagawa, S., & Schielzeth, H. (2013). A general and simple method for obtaining R2 from generalized linear mixed‐effects models. Methods in Ecology and Evolution, 4(2), 133-142.
I have tried to use those aproach to my data obtaining different results. Please look:
Approach 1. Method from Nakagawa et al.(2012) basing on this post: https://ecologyforacrowdedplanet.wordpress.com/2013/08/27/r-squared-in-mixed-models-the-easy-way/
[1,] 0.02128424 0.5280393
Approach 2. Method from Xu(2013) basing on this post:https://stats.stackexchange.com/questions/95054/how-to-get-an-overall-p-value-and-effect-size-for-a-categorical-factor-in-a-mi
As you can see R^2 marginal from the Nakagawa formula is very similar to the R^2 obtained with the formula of Ronghui Xu but in other post I have read that it is better to use the R^2 marginal from the Nagawaka formula. Could someone give me some idea of the differences between R^2 marginal and R^2 conditional? Which one I should comment in my paper if I would like to talk about how the model fits? In my case the R^2 conditional is moreless high (0.52) but the R^2 marginal is very low (0.02)
Thanks very much,
The second law is generally considered as a dissipative law, whereas, many evolution processes show that order could arise spontaneously, in my opinion, the second law itself contains the mechanism of evolution.
In the fundamental equation of the second law,
here diS is the total entropy production, and diSj is the partial differential of diS in process j.
The equation does not require each of diSj≥0, it only requires that the total entropy production is positive definite, but the partial differentials of which can be less than zero. In the case diSj=k<0, order may arise spontaneously in process k.
I am interested in the phylogeny of vertebrates, i.e. the phylogenetic relationship among fishes, amphibians, reptiles, mammals and birds. I find a cool article published in 2003 (see below), and want to know the recent advances in this field.
Could you provide any more recent information on the phylogeny of vertebrates?
AxelMeyer, RafaelZardoya. Recent advances in the (molecular) phylogeny of vertebrates. Annual Review of Ecology, Evolution, and Systematics. 2003, 34: 311-338.
Based on my research, this method is used to assess the adequacy of sampling, but I don't know what the difference is between them.
Can anyone help me regarding this subject?
Which individual based and sample based method is better for determining the adequacy of sampling?
My study was carried out in two regions with different climates and in each region, we are sampling in two different management regimes.
Which scale (management, climate regime or total data) must be used in analysis to assess the adequacy of sampling?
What we'll do when after 40 years we use all global proved oil reserves? The global economy consumes approximately 1.26 trillion U.S. gallons of oil. One trillion U.S. gallons is about one cubic mile of oil (1 CMO). The world consumes ca. 3 CMO equivalent energy annually from all sources. Global proved oil reserves are estimated roughly at 43 cubic miles, or 43 CMO. After 40 years we will used all of them. What we 'll do later?
World's urban tales had been told many years ago that polar bears are wandering through Polish country. It was never true in historical times, however Alfred Jahn has written in his "Ice and glaciations" (PWN 1971): "In Poland, snow begins to fall mostly in December, and in January and February already covers the earth with a thin layer. This happens when the air temperature drops below 0deg, when the water freezes and the earth is covered with a hard, soggy clod. The change takes place in March. Just a few days of thaw ..." This winter we have here up to 9degC and a thin layer of snow was with breaks for... four weeks no more. In late December I've found the willow flowers at the walk. Daisies bloomed on the lawns. It's a rule now. However, it is not question in plant biology. We start to enjoy with a mediterrenian climate, now. And the mediterrenians? Now it is hard to stay there in the summer time. We also are the most calm country in the Europe with longest white-and-yellow sandy sunny beaches at the seaside. Will Poland be the best place to live for next few centuries?
This winter season the first thin layer of snow occurred here on 5th January 2020.
I am preparing MS which partly deals with relationship between trophic level and niche breath. I search literature for relevant examples but apparently miss papers that dealt with these topics; except some general speculations and quite few case studies. If you remember some papers dealing with following hypothesizes (1, 2) please give me some hints.
1. Species of higher trophic levels are characterized by more generalized trophic habits
2. Habitat generalists are food generalists
Obviously, one can argue that there are good reasons for strong, weak or no relationship for 1,2. I search for papers showing patters and dismissing them. They could be both empirical and theoretical ones.
I appreciate any help you can provide.
According to Quieros et al. 2013, Carcinus maenas falls within the bioturbation class of 'Regenerators'.
'Regenerators' are excavators that dig and continuously maintain burrows in the sediment, such as the fiddler crab Uca spp (see Kristensen et al. 2012). However, I doubt C. maenas is a typical regenerator as it does not maintain a burrow system.
My question to you is, how would you classify this species in terms of bioturbation? In my opinion it could be classified as a surficial biodiffusor as it finds most of its food in the top few cm of the sediment (even though it may occasionally dig deeper for food). I have to mention that the study site is a Dutch intertidal sandflat where we mostly find small specimens.
It would be very helpfull if you can let me know on how you think about it!
Queirós, A. M., Birchenough, S. N. R., Bremner, J., Godbold, J. a, Parker, R. E., Romero-Ramirez, A., … Widdicombe, S. (2013). A bioturbation classification of European marine infaunal invertebrates. Ecology and Evolution, 3(11), 3958–85. https://doi.org/10.1002/ece3.769
Kristensen, E., Penha-Lopes, G., Delefosse, M., Valdemarsen, T., Quintana, C. O., & Banta, G. T. (2012). What is bioturbation? the need for a precise definition for fauna in aquatic sciences. Marine Ecology Progress Series, 446, 285–302. https://doi.org/10.3354/meps09506
Could you give me some principles / concepts on ecology of spread of diseases? For example, deforestation causes spread of disease because their niche was destroyed. What concept would best explains this?
I'm doing a population genetic study on microsnail and I've found very high intraspecific genetic divergence between isolated population at very small scale. I'm curious to compare my results with similar studies on population structure of small organisms with very poor dispersal ability. Do you have any paper in mind?
It could be fresh water organisms in close-by ponds, or two population of invertebrates on the opposite sides of a river.
I know that "small scale" is relative to size and dispersal ability, but I'm curious to see what is the absolute shorter distance at which we can observe conspicuous allopatric divergence between populations in eukaryotes.
I have the data for both morphological and reproductive traits for 22 species and the phylogenetic tree built by maximum likelihood with branch length. I need to estimate the evolution rate between these two trait categories to show whether reproductive traits evolve faster than morphological traits. Which parameter I should calculate it for comparison? dose any body have R codes for doing this kind of comparison?
Any hints or recommendations?
and the best way to identify variables which used in analysis?
Ecological data : physiochemical factors ( DO,pH,....etc...) ,Time (Months, seasons...) , Stations
Statistic : CCA, PCA , DCA....
This specimen of Carabus intricatus (Linnaeus, 1761) raised and lowered the abdomen alternating and spread the cerci (?). There was no other specimen present. It was in the natural environment, in 2016-05-21 in the evening, Germany, Bavaria. I noticed this about a quarter of an hour.
I think to use statistical tools of niche modeling like Environmental Niche Factor Analysis or PCA-Env to analyse niche of species not studied in certain part of distribution range, but is this relevant enough to be published? if yes what kind of article?
The salinity of the dead sea is too great to support life. The freshwater rivers that run into the dead sea are therefore ecologically isolated. How is it that river crabs occur in these locations. Could it's eggs have been transferred by the wind, or was there a time when the dead sea was at a higher level, and was therefore less saline?
Neutral theory suggests that most of the genetic variation in the population is the result of mutation and genetic drift. But what are the implications for interpreting pattterns of genetic variation?
In addition, as a new species emerges, what happens to the population of the previous species? Do they evolve into new species as well or competition with the emergent species causes their extinction? And if the emerging species did interbreed with the existing species, could that affect the speciation process?
Which category would you put Chionanthus africanus in (between pioneer or climax species, in other words, could it be an early succession or late succession species?
Does the Ampullariid snail Lanistes show indeterminate growth. I find there is very limited biological and ecological information available on this genus
I am looking for African passerine nests, specially in American collections.
Weaverbird nests in particular. Thanks!
It is widely accepted that the major factor affecting the evolutionary optimization of animal life histories is energy balance, therefore studies focus on the energy costs and benefits of adaptations, the efficiency of energy acquisition and investment, and limits to energy budgets. However, at the very least in heterotrophs, equally important seems to be the problem of maintaining stoichiometric balance.
There are two approaches in eco-evo studies that consider the matter balance as complementary to the energy balance: ecological stoichiometry and nutritional geometry. However, in my opinion, such studies are limited and after 30 years after Tilman's and Reiners' works (below), still "energocentric" point of view dominates in ecology and evolution, that carelessly underrates the need to balance the diet also in terms of the matter (including the Law of Conservation of Mass).
This is only my point of view, possibly the wrong one. I would like to ask all of you: what is your opinion?
My question was introduced as briefly as possible, don't hesitate to dig deeper and extend it!
Below I present four important studies related to the topic, just to start with.
For discussion: To what extent the ecological change could generate a substantial adaptive evolution on a short time scales (20 to 30 years or within few decades)?
with kind regards,
Has anyone ever tried to rear bee larvae using pollen diluted with alpha-cellulose? It has been used previously to manipulate the quality of pollen for collection by foraging bees, but I wondered if it would harm larvae to consume this diluted pollen, since alpha-cellulose is typically described as 'indigestable'?
Many thanks in advance!
For what I understand, to be considered invasive species, a species has to displace one or more native species. However, I have seen some publications about invasive species, where the mentioned invasive species have not displaced any native one. Am I missing something here?
We discussed in class how the Galapagos finches have developed different beak sizes due to environmental conditions (sympatry, allopatry, available food resources), and gave rise to Geospiza fuliginosa, G. fortis, and G. magnirostris (small-, medium-, and large-beaked in order). However, how can one classify which species one belongs to if the determining factor is a polygenic trait such as beak size?
We have also defined "species" as a group of similar organisms who can interbreed and produce fertile offspring. Does this mean that small finches cannot mate with medium finches and produce fertile offspring? If yes, why is this so? Aside from changes in beak size due to adaptation, what genetic changes have occurred such that they cannot be considered to be of the same species?
Communication involves multiple individuals (at least a sender and a receiver). On the other hand natural selection will act based on the fitness value of communication for each individual involved in the communication process. In such case, when should selection affect on the receiver, and when will it act on the sender? (edited)
This photo is taken in the region of Azilal, Morocco, where the author lives. It has almost all the branches of plants in a photo.
plant evolution is not a fact?
I am building a sheet with morphological data to run evolutionary tests with New World Astragalus.
Mutualism and Protocooperation are ecological interactions in which there is advantage for both partners. The first can be mandatory at least for one species, the second no.
Among vascular plants, facilitation (or comensalism) is well-known.
However, is there true possibility of Mutualism and Protocooperation between two vascular plant species?
I'm looking for case studies of biological observations in floodplains that could follow the Intermediate Disturbance Hypothesis. The study noted below seems to be one of the only ones, but I'm guessing there should be similar observations looking at biota.
How many classes were there in the world at the beginning of Cambrian explosion?
I know how many phyla were there at the beginning of the Cambrian explosion. But for the classes, I have no ideal. Could someone tell me about that and origin of data?
Huxley's modification of Wallace's line separates Palawan from eastern Philippines. Kano's line demarcates Taiwan and Ryukyus from northern Philippines. The connection between these Kano's and Huxley's has not been resolved.
For more than half of the time since the earth has been in existence, there was no oxygen. Many bacteria survived without oxygen. However that isn't my concern. I'm concerned with how this was determined. Can someone help me out?
When we do studies in ecology, what is our ultimate goal beyond the immediate goals of answering questions the paper? What are we as a discipline attempting to work towards? Note: I am asking what the discipline is moving towards, not motivations or goals of individual researchers such as tenure, renown, etc.
Please also include your status (graduate student, undergrad, professor, industry, etc) and the decade in which you received your highest degree.
Full disclosure: This question is part of an informal survey I am completing and your answer may be incorporated into future work exploring this question.
Is there a measure more appropriate than others?
I am looking for bibliographical references on the first record of a member of the Order Carnivora in South America (also including marine forms such as proto-pinnipeds, pinnipeds, otters, etc).
All your help is welcome.
Thanks in advance
Please send me the link on distribution map of Brown trout (Salmo trutta) and other related species, native for the Europe and Asia.
Example of a case study : When the "Grey wolf" was reintroduced into the Greater Yellowstone Ecosystem in 1995, there was only one beaver colony in the park, said Doug Smith, a wildlife biologist in charge of the Yellowstone Wolf Project. Today, the park is home to nine beaver colonies, with the promise of more to come, as the reintroduction of wolves continues to astonish biologists with a ripple of direct and indirect consequences throughout the ecosystem. Cases of how the re-introduction of wolves , changed the river patterns significantly, is also a remarkable study!
I observed an interesting phenomenon in the Rain Forest of Western Ghat, India. The male fly usually waits, for a long time, sometimes for hours, inside the flower and it defends its little territory against other males, actively. When a female fly comes in, it starts its elaborate dancing. I read a bit about Hawaiian Drosophila's mating behavior, where they defend leaf surface (if I am not wrong). But I never came across any literature where insects are using flower as a site for male display and competition (lek). It poses interesting questions like "how long the male should wait inside a flower?" (If it waits too long in the "wrong" flower, then it will be in "trouble" and if it is too impatient then also, I guess. So there should be an optimum). Does anybody have any suggestion, information, thought or reference to share?
Is it possible that we might have miscalculated species richness in Lepidoptera and indeed other orders if some species exhibit polyphenisms in wing colouration and patterning?
I do realize this works on the assumption that wing colouration and wing patterning are all thats required to positively ID lepidopterans however running DNA tests on all of the butterflies you catch would surely be too expensive.
Do we instead have to rely on anatomical features for positive ID in butterflies that exhibit the type of polyphenism I am talking about?
I'm having 3 species that I have to estimate the relative fitness with only binary survival data. I was thinking about using a fitness function taken from a GAM by applying a smoothing factor on the PC1 and PC2 of 3 traits.
Do I have to compute the GAM with all species in the model?
Do I have to compute the model with species in covariate?
Do I have to compute the model and add species as a covariate?
Will all species have the same scale?
Is the fitness function estimated from the GAM relative fitness for a particular trait?
If the reproductive fitness of a parasite remained 50-60% of its total life span, then what would be possible reasons for its remaining developments? It this an example of evolutionary selection?
I am planning a research project on the interactions between 'hedgehog galls' and bur oak (Quercus macrocarpa) in southeastern Québec (Canada).
I am searching for good song recordings of African Reed Warblers. The longer the better. Or maybe somebody works near the habitat of these birds and it's not a big deal to record several minutes for me :)
There are some recordings on xeno-canto.org, but they are way too short for the analysis :(
Hi. I'm looking to add some photographs to a publication I am doing on the Rodrigues fruit bat (Pteropus rodricensis) for the journal Mammalian Species. I need a photo of a live animal, plus a photo/illlustration of the skull-mandible (see attached file for an example). The specifications for the skull plates are fairly strict (but see image):
SKULL PLATE. Illustrations of the skull (dorsal, ventral, and lateral views) and lateral view of the mandible must be included. These either can be good quality images or line drawings. Do not include a scale bar. In the figure legend, indicate age and sex of specimen, the collection locality, full name of museum where specimen is on deposit, catalog number of specimen, and greatest length of skull or a similar measure. A statement including the origin of the photographs or name of illustrator (if other than the authors) and permission for use must be included. All views must be exactly to the same scale.
Can anyone help? Thanks.
I want to use Moran I index for spatial autocorrelation. My input files are two matrices; (1) distance matrice of individuals based from a UPGMA tree and (2) Geographic distances between individuals
So I have two questions
(1) since I have two matrices, do I place them in one input file or separate input files?
(2) Whenever I load it up in SPAGEDI, it always produce an error message on how I formatted the input file. I followed the user manual for inputting matrices in SPAGEDI however it still gives me an error message.
I hope you can help me on this endeavor. Thanks!!
Habitat templet theory predicts that species inhabiting similar environments converge on their traits.
Competition however has an opposite effect, and communities structured by competition are expected to present trait overdispersion.
Resource limitations are likely to increase competition.
Resource availability is expected to comply with the number of species and the possible strategies. At least this would be true if comparing equally favorable habitats and with similar evolutionary times and regimes of disturbance.
I’d expect that species niche partitioning takes place on abundant resources prior than on rare ones.
I failed to find any work relating habitat templet and resource availability over evolutionary times and their effects on niche partitioning.
Could you please suggest me some references on the topic?
Thanks in advance
Some Orient genotypes of Brassica rapa have so called A-type seed coat. Large cells of outer layer with walls made of polymer are swelling in water. The seed coat is formed by mother plant but A-type is controlled by genes in embryo.
Primate fecal samples stored in formalin (for later analyses of parasites) and kept at room temperature (in tropical areas).
I'm studying moth's community structure in several habitats of the Balearic Islands (Western Mediterranean), and it is a shame not to get major information and benefits of research for most of our captures. We are creating a moth's collection which is completely available for scientific purposes (not for collecting).
If anyone is interested please send me a private e-mail.
Under the CFI/ERF Australian Govt. programs, its not very clear what will be the tentative (baseline) price of C for abatement of CO2 emissions or for sequestration of C in the near future. Any idea would be helpful.
We are studying dispersal in Spanish moss using genetic markers and we need a ("safe") way to retrieve samples from up in the canopy. Obviously, we can get the low-lying stuff (via ladder and extension trimmer), but we are struggling to get samples that are higher than ~10 m. I've heard of some people using ropes, but only on TV, and I am not sure how to get trained to do this sort of thing, and whether it is safe for some of the trees. Any ideas or citations are welcome.
It would be good to know whether protocols of measuring telomere length in vertebrates are also suitable for measuring telomeres in vertebrates.
Is DNA sequence information sufficient by itself to solve this problem?
I have struggled to do this with Powerpoint, but am sure that there must be simpler, better, more efficient software programmes for this purpose. Any suggestions? How have others done this? This is a good examples: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3146880/pdf/1471-2148-11-172.pdf
Sadly, a number of journals seem to have done away with the option of publishing short commentaries or insights, unless they are a direct response to a paper published recently in a journal. Our lab has been generating some interesting ideas about the current ebola epidemic and ways forward in understanding the natural history of ebola viruses and are looking for a venue with which to share them with the scientific community.
So far we have found the following potential options but any additional suggestions would be greatly appreciated:
Emerging infectious diseases - Commentaries, but need to be invited,
EcoHealth - Forum
Trends in Ecology & Evolution - Letter
Samples or issues from Afghan Pika for a genetic analysis
I want to do some interspecies comparative research. And I'd like to run PGLS in R. But I've got a tree with out branch lengths. The common ways to run PGLS need a tree which includes branch lengths. Then how shall I do it with a tree without branch lengths? How shall I set the branch lengths to make it adequately statistic? what's the detailed codes?
I would like a key to distinguish all the taxa, or at least those closely related to F. hexapetala. Phylogeography and phylogenetic studies would be interesting too.
It is usually assumed that the demographic transition (major intrinsic changes in fertility / mortality and life expectancy) is a purely human population phenomenon. There are several explanatory theories that suggest the next causes: (1) social development [Condorcet, 1794], (2) economical/technological changes [Galor,O. 2011], (3) evolutionary change [Clark, G. 2007].
However, these factors (in some degrees) operate within non-human populations. Moreover, some of the eco-evolutionary models indicate that the demographic transition may be a common consequence of co-selection adaptation of individual to each others within group) in hierarchically structured populations.
There are several (not all) cases in which demographic transition can be suspected:
- Regular extinction/ reemerging of local populations without apparent external reasons.
- Pronounced long-term demographic changes, which cannot be explained by environment variations or inbreeding depression.
- Sudden appearance of unusually old or unusually big individuals in populations.
- Sadden epidemic outbreaks of previously limited infections.
- Visible absence of equilibrium size (carrying capacity); variations of population size weakly correlated with environment factors.
- Fusion/split of local populations.
So, is a demographic transition in the non-human populations? I would be very grateful if you share your thoughts or maybe data that will help answer this question.
Anuran tadpoles respond to chemical cues of predation reducing foraging and swimming activity. In many cases this behavior is produced by a predation event releasing different kind of cues, in particular alarm cues, coming from tadpole itself, seem to play a key role in elicit antipredatory responses, even if they often need to be associated to kairomone (from predator) to have the whole response.