9 votes
Accepted

How close genetically is the most human-like chimpanzee to the most chimp-like human?

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 ...
leekaiinthesky's user avatar
6 votes
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How to compare diversity between different ecosystems?

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 ...
Remi.b's user avatar
  • 68.1k
6 votes

How close genetically is the most human-like chimpanzee to the most chimp-like human?

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 ...
AlexDeLarge's user avatar
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6 votes
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What is the weight percentage of all people as compared to all Natural life?

This has been studied in this paper, and they came up with: Total biomass = 550 gigatons of carbon Human biomass = 0.06 gigatons of carbon So this would make humans about 0.01% of all biomass. If ...
Dave's user avatar
  • 296
5 votes

What is the best way to calculate the biological diversity of samples from bacterial/viral OTU tables?

I mostly concur with @Nathan's answer, and in particular with the references he provided. As Shannon & Simpson indices can ...
Lymond's user avatar
  • 51
5 votes

Measuring tumor heterogeneity

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 ...
MattDMo's user avatar
  • 15.3k
5 votes

How do I explain "effective number of types" to a lay audience?

For a lay audience, I don't think you need to explain too much of the math, just the general concept, and an example will work best. Let's think about trees. You have 5 types of trees in a forest. If ...
Bryan Krause's user avatar
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4 votes
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Based on this diagram, how do you deduce the keystone species?

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 ...
Alice Dias's user avatar
4 votes

Can I compare Shannon-Wiener diversity indices between plots of different sizes (area)?

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 ...
Shawn's user avatar
  • 435
4 votes
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Forest Fires and Horsetails

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 ...
iayork's user avatar
  • 14.2k
4 votes
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Are there any photosynthetic catalysts in use other than chlorophyll?

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 ...
WYSIWYG's user avatar
  • 35.6k
4 votes

Beta-diversity for data with zeros

I would recommend using a Bray-Curtis dissimilarity matrix since it accounts for abundances and can handle the so called double zero problem. I'm on my commute now and so must return to this for a ...
theforestecologist's user avatar
4 votes
Accepted

What does genetic diversity in one species have to do with survival rate when an epidemic spreads?

Genetic diversity could be understood as a variation in alleles (gene variants) and their frequencies in a population. Due to these allelic variations, we would expect an inherent variability in ...
theforestecologist's user avatar
3 votes

What are the negative consequences of a narrowed biodiversity to the planet?

From an ecological sense, cycles of living beings are intertwined. Breaking cycles affects life being able to live, reproduce, and die in a manageable way. Insects, animals, and plants help feed each ...
Alex Reynolds's user avatar
3 votes

How many different species have existed on Earth?

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). ...
WYSIWYG's user avatar
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3 votes
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Which plant's part is this?

This is a bit hard to say exactly, since there is a number of possibilities. We can be pretty sure that these sample is from a Cypress, belonging to the family of Cupressaceae, but which subfamily or ...
Chris's user avatar
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3 votes
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Measure of diversity, accounting for known species

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 ...
Michael Roswell's user avatar
3 votes

Why is there an apparent reduction of reptile species near the Mississippi River?

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 ...
bandybabboon's user avatar
  • 10.4k
3 votes

Database of Geographic Range of Species

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 ...
Shawn's user avatar
  • 435
3 votes

Does leaving land alone actually help nature conservation?

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 ...
Malhar Khushu's user avatar
2 votes
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Conservation Ex Situ

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 ...
Nico Coallier's user avatar
2 votes
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How important is dead wood to the ecology of a forest and how much dead wood should remain?

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 ...
RHA's user avatar
  • 3,685
2 votes

What is the best way to calculate the biological diversity of samples from bacterial/viral OTU tables?

The vegan package is suitable for your needs, but you may find you need to use others or code your own functions. Due to sequencing biases, you shouldn't trust ...
Nathan's user avatar
  • 166
2 votes

Bird diversity and the avian flu

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 ...
iayork's user avatar
  • 14.2k
2 votes

How close genetically is the most human-like chimpanzee to the most chimp-like human?

I found at least one example of genes where the same genes and the same alleles exist in both humans and other primates but the frequencies of the different alleles are different in different primate ...
Agerhell's user avatar
  • 590
2 votes

Using proportion or a diversity index when dealing with just two strains

Extended upon the suggested statistic The proportion $p$ is definitely not a good measure of diversity. A proportion of 0 or 1 both indicates no species diversity as only one species exist. If one ...
Remi.b's user avatar
  • 68.1k
2 votes
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What is the minimum sample size to get reliable results in haplotype and nucleotide estimations?

I'm still a little unclear on what the analysis looks like, but I'm going to assume for the sake of this answer that it's a single locus sequenced across multiple populations, with some number of ...
Maximilian Press's user avatar
2 votes
Accepted

Shannon diversity index: Pi relates to all found species, or number of species by site?

I am trying to dig into Shannon's species diversity index to compare the species diversity between different sites Shannon's diversity index is a measure of alpha diversity, or diversity within a ...
MikeyC's user avatar
  • 4,724
2 votes

Can a species include only one subspecies?

Think about it like this: How can a you subdivide 1 individual and still get a whole? The answer is, you can't. For there to be subspecies you need to have defining characteristics that can be used ...
bob1's user avatar
  • 12.1k
1 vote

Time taken for species to become endemic

From wikipedia > endemism: Endemism is the ecological state of a species being unique to a defined geographic location, such as an island, nation, country or other defined zone, or habitat type. ...
Remi.b's user avatar
  • 68.1k

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