16

In your question, your assumption that animal species are less diverse phenotypically than humans is wrong. I am sure you will appreciate @terdon's answer to this post and @rg255 answer to this post. Don't forget that we are good at detecting differences among humans (because we evolved for this purpose). We are doing much worse at telling apart animals ...


7

You may be interested in this 2005 Nature paper from the Chimpanzee Sequencing and Analysis Consortium: Initial sequence of the chimpanzee genome and comparison with the human genome. It breaks down the most common categories of genetic variation: Single-nucleotide substitutions occur at a mean rate of 1.23% between copies of the human and chimpanzee ...


6

This is to a large extent a question of how reliable the data in the database needs to be. Reliability (and spatial scale) will differ between datasets and between species groups within datasets, and it is difficult to give a general recommendation. I doubt that you will find a single database with good coverage over all taxonomic groups, even if it is in ...


6

Bearing in mind that the information is bound to be incomplete (as is the list of existing species), you could use the NCBI taxonomy database. For example, checking the page for the Drosophila genus will give you an idea of its size. For more precise numbers, you can download the taxdump.tar.gz file from NCBI's FTP server (link), extract it and run the ...


6

I'd like to add that the variations in individuals within a species are a fundamental observation upon which modern biology is standing. Darwin wrote at least 2 chapters of Origin of Species demonstrating how animals and plants have a lot of individual variations: Darwin's argument involved four steps. First, he noted the wide variation between many ...


6

Have a look at the Wikipedia page on Diversity Index Here are the indices that the wikipedia page describes "True Diversity" Index Species Richness Shannon Index Rényi entropy Simpson index Inverse Simpson index Gini–Simpson index Berger–Parker index The article also links to related concepts such as $\alpha$ Diversity $\beta$ Diversity $\gamma$ ...


5

The methods that come immediately to mind are mostly related to next-generation sequencing. You can do deep sequencing on your sample, which is just increasing the coverage as much as possible to find rare events. You can do RNA-seq to look at the transcriptome, ChIP-seq to look at chromatin modifications, and single-cell sequencing (a form of deep ...


5

This is a big question and a very active field of research. I'm not deeply into this litterature, but you should look into the the different scaling relationships (often power laws) that have been described on metabolism vs body size, species-area relationships and species richness vs biomass. Also consider that energy-use by species in a community is ...


5

I didn't believe this was a real thing, and I'm still very skeptical, but it is something that's claimed to happen! Their stems & leaves have a siliceous epidermis, so if rubbing b/n 2 horsetails occurs, a forest fire may be produced --The Bottled Ocean of Biology, by Nisarg Desai, 2017 Why don't other plants show same thing? Another plant, bamboo, ...


4

I think you may have covered the answer in your question... but here's my take; The 'mowing' occurs at a distinct time-point and is highly destructive and uniform, so the selection pressure is very high and only highly competitive species that are fast to grow and reproduce will be successful. As you point out, animals will defecate and naturally fertilize ...


4

Nice question! For the concern of plant diversity over altitudinal gradient it has been shown in several studies in the alps and in Andes that the greatest abundance and diversity is not found in high altitude neither in low altitude but in middle altitude. Some argue that the abundance and diversity depends on temperature and human impact that is what ...


4

It sounds like you are interested in beta diversity which is the change in taxa composition (i.e., alpha diversity) between plots. There are a number of approaches to calculating beta diversity and the correct choice generally depends on the question(s) you are trying to answer. The most common approaches are very well described in this paper: Anderson, ...


4

From http://education.nationalgeographic.org/encyclopedia: A keystone species is a plant or animal that plays a unique and crucial role in the way an ecosystem functions. Without keystone species, the ecosystem would be dramatically different or cease to exist altogether. [...] The sea otter is an example of a keystone species in the Pacific ...


4

The answer given by leekaiinthesky and partially in the comments on the question give a good general picture. I also think that the variation within the respective species is way less than between the species. Keep in mind that also archaic humans like Neandertals fall outside of the variation of present-day humans when you do a genome-wide (nuclear genome ...


4

I mostly concur with @Nathan's answer, and in particular with the references he provided. As Shannon & Simpson indices can be hard to interpret and can be non-intuitive, I prefer using Hill diversities as suggested by Nathan (the Jost 2006 and 2007 refs are great to read up on this). The main argument is that Hill diversities give effective number of ...


3

I'll give you an example, because this question is pretty case specific. In Delhi, my hometown, they kept areas of the forest, the 'Sanjay Van' free from construction and people and only very recently started cleaning it up. As a result, an invasive variety of the Acacia tree (known locally as keekar) more or less took over the forest and has basically ...


3

Theoretically the index for two habitats of different areas are not directly comparable. Consider the species area relationship. You see more species when you look over a larger area. So you will potentially see a different index just from considering a larger area, and not necessarily because there is something different about the habitats. Borda-de-Agua ...


3

The GBIF database that was suggested can give you locations of occurrences given a specific animal. But you asked for lists of animals given some location. An excellent tool to give a list of animals given a location in the world is the Map of Life. Click on "Species by Location" which gives a map of the world, and click anywhere to get lists of species that ...


3

You might be interested in the below works as well as the references that they cite. May, R. M. (1988). How many species are there on Earth? Science, 241(4872), 1441–1449. Millennium Ecosystem Assessment. (2005). Ecosystems and Human Well-Being: Synthesis (p. 137). Washington, D.C.: Island Press. It's worth noting that many estimates of species richness ...


3

There are photosynthetic organisms that use retinal-rhodopsin complex. However, the mechanism of photosynthesis is different in these organisms than those that employ chlorophyll dependent photosystems. In these organisms, the light causes the rhodopsin-like membrane proteins to pump proton out of the cell and create a proton gradient which in turn is used ...


3

The reptiles mostly were ploughed away and replaced with soy beans. The low reptile diversity zone matches the Mississippi Alluvial Plain which includes the Mississippi Floodplain. The Mississipi drains nearly half of the USA's geographic area, so the flood plain is massive. The Silt Plain is very flat, mostly has hills left by oxbow lakes and river ...


3

Simpson's estimator, which assumes that sample frequencies are not population frequencies, is unbiased on the probability scale. As @fileunderwater noted, it can be helpful to quantify diversity in terms of effective number of species, or Hill numbers. On this scale (the reciprocal of Simpson's concentration in this case), Simpson's estimator is no longer ...


3

From Raup (1986). Up to 4 billion species of plants and animals are estimated to have lived at some tlme m the geologic past (2), most of these in the last 600 million years (Phanerozoic time). Yet there are only a few million species living today. Thus, extinction of species has been almost as common as origination. I am not sure how exactly has ...


2

You might want to look at Koleff's paper (open access @ JAE http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2656.2003.00710.x/abstract). Given that you have quantitative data, you should look at the difference between presence/absence and quantitative measures. A Bry-Curtis measure or something to that effect would be way better than a Sorensen or ...


2

I don't know anything about the "Disney index" but the equation you use looks like it's a version of Simpson's D, a very common biodiversity index. If you're just estimating two different kinds of sites (your two management strategies) I would suggest a rarefaction method. This can be estimated in either the vegan package in R, or EstimateS http://viceroy....


2

I've studied diversity of euglossine bees along altitudinal gradients in amazonian mountains. The references I've read showed no consensus regarding altitude. For some groups, diversity were higher at low altitudes; for other groups, it was in the middle. I've found the biggest diversity in the middle altitudes (the mountains were around Equator line). One ...


2

Dead wood is indeed very important to the food chain, and to the ecology and biodiversity of a forest. Lots of biota depend on the presence of dead wood; many species of insects and fungi only live on dead wood. See for example this study of fungi in Danish Beech forests. The amount of dead wood present depends, apart from management, on the type of forest, ...


2

That's an estimator for Simpson index, $$ \sum_i p_i^2 $$ where $p_i$ is the probability that $i$-th species is sampled. This is sum of the probability that two independent samples are from the same species. There are multiple ways of estimating this quantity from observations $n_i$. When $n_i$ is small, $$\hat{p} = \frac{n_i}{N}$$ is unbiased but has high ...


2

She was probably referring to ex-situ conservation as a way to complement in-situ conservation. Indeed, if a population is endangered and fragmentation it thought to be one of the main factors causing the decline, it can sometime be hard to restore the habitat in a way that would permit the population reestablishment (in-situ conservation). Ex-situ ...


2

Biodiversity is the opposite of monoculture, and we know that one possible consequence of monoculture is disease transmission -- bananas being the modern poster child for monoculture leading to disease spread. The concept seems to have been most clearly presented in Schmidt, K.A. & Ostfeld, R.S. Biodiversity and the dilution effect in disease ...


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