Natural Systems and Humans

How do the current rates of extinction vary from the background rates?

1000x higher

When was the Late Heavy Bombardment?

3.9 billion years ago

Which types of animals is the fossil record bias to?

Abundant, cosmopolitan, large, hard body parts

What % of species have been preserved in the fossil record?

1%

What is alpha diversity?

Diversity within one community

How many species did Erwin get from 19 trees?

1,100

How many species does the catalogue of life recognize?

1,578,063

What is Simpson's Diversity Index?

- The probability that two individuals are the same species - Can adjust for replacement which is the version shown here - More diverse closer to 0, so usually presented as... - 1/D — effective number of highly abundant species

What did Dodson's study (1990) reveal about dino's?

- There were between 900 and 1200 genera - 285 had been found fossilized at the time (50% only from a single fossil, rare to find full skeleton too) - 336 had been described

Who was stork and what did he do?

- 1998 - Tried to combine different researchers recordings which is hard as there is no centralized scheme - Predicted 1.8million named species

Discuss the study of the plant genus Passiflora in South America by Thomas (1990)

- 360 species of Passiflora which are host to a specific caterpillars - Specialized, only lay eggs on 1 plant species - Surveyed 12 site, 7.2 plant species and 9.7 butterflies - Would imply 485 species of butterfly - In reality there is 66 - Turns out the same butterfly species are present at multiple sites but in anyone place they specialize on a single plant species.

What were Erwins assumptions?

- 40% of arthropods are beetles - There are twice as many species in the canopy as in the forest understorey - There are 50,000 species of tropical tree

What did Novotny do (2002)?

- 51 plant species - 50,734 insect herbivores over 935 species - Feeding trials to work out actual diets - Only a few monophages - Majority are generalists - Estimated global richness of 4-6 million arthropods

What did Dyer et al., suggest in 2010?

- Calculating interaction diversity - Plots in Ecuador and Louisiana - Counted number of pairings found between plants, lepidopteran caterpillars collected from them and parasitoids which emerged form the caterpillars in the laboratory - Richness didn't seem to vary between countries but Ecuador had twice as many interactions. Ad's - Number recorded increases slower than species - more tractable target - Many interactions are rare, can use similar estimation indices to describe them - Helps deal with large number of species collected as tourists

How can we use molecular evidence to compensate for the missing fossils?

- Creating phylogenies to link extant species and combine these with molecular clocks

What is Shannons Entropy?

- Diversity Index - p i refers to the proportion of the sample made up of species i - Uncertainty of ID of a randomly-sampled individual - Assumes all species represented in samples - eH' — effective number of common species (Scale linearly unlike H alone)

What are the benefits and drawbacks of parametric sampling?

- Easy to interpret - Work for all sampling types - Many models can fit a particular curve and give widely varied estimates - Unless the graph is nearing asymtote, estimates can be inaccurate - We have to compensate for unevenness in comunities

What is a Preston plot?

- Frank Preston devised - 1948 - Represent SADS - X = Abundance (Usually in octave abundance classes - Y = Frequency - Spotted that for large samples, noticed that on the x-axis, the number of species that fall into each class often follow a normal distribution

What did Clarke and Warwick suggest? (1998)

- Method to calculate taxonomic distinctiveness giving an average for a sample

What are the important caveats with extrapolation?

- More accurate estimate from those who are nearing complete coverage - Since 1984, PCR has made the amount of species discoveries inconsistent. Should only extrapolate from before then. - Deciding if a curve is reaching the asymtote can be difficult and trying to apply a straight line could overestimate species diversity

Who was John Ray and what did he do?

- Naturalist - 1627-1705 - One of the first to attempt to catalogue species - Wildly underestimated the number of British insects to be 2,000 and those on the globe to total 20,000

Who was Carl Linnaeus and what did he do?

- Naturalist - 1707-1778 - Attempted to catalogue all known forms of life - Found that the influx of new species being discovered was too much to keep up with - 1758, published Systema Naturae, set standards for nomenclatures but only included around 9,000 species - Most were from temperate climes - Tropics remained a mystery)

What is a Whittaket plot?

- Represenst SADS - Sometimes also known as rank/abundance or dominance/diversity curves - Their essential feature is that species are ranked in terms of abundance along the x -axis, and then either their absolute or relative abundance (i.e. the proportion of the total sample made up of each species) is plotted on the y -axis

What did Lawson et al., (1998) do?

- Sample a 100x100m of rainforest in Cameroon - Collected 2,000 species over well known taxa - Project took 5 scientist years to identify - Estimated that to carry out a survey of all the species in one hectare would take 10-20% of the worlds 7000 taxonomists. Plus, there are areas much more diverse than this!

Discuss that some species are rare by artifact and not actually rare?

- The method of sampl22i2n2 may not have been designed for them, for example quadrat sampling and mammals

How long could it take to recover from the impacts of humans?

10-40my

How long was the oldest marine genus on the planet for?

160my - 5% of the history of life

When were dinosaurs alive?

230mya to 65.5mya

How do fish show uneven diversity?

28,000 species of bony fish (Osteichthyes) almost all fall within the ray finned fish (Actinopterygii). Perch like fish have 10,000 species and 1,650 of these are cichlids.

What was Erwins estimate?

30 million arthropods in tropical rain forests and 100 million species globally.

How long might it take to classify all of the species on Earth (Considering the current number of taxonomists.

360 years

Mass extinctions make up what % of extinctions in the last 400 years?

4%

When did continental crusts and liquid water form?

4.4 billion years ago

When did Earth form?

4.6 billion years ago

How long do most species persist for?

5-10my

What is the extrapolated figure for the predicted number of animals species?

6-7 million

What % of primate species are we predicted to have found? (Tavare et al., 2002)

7%

What is the estimate when basing an estimate on the accumulation of the total number of animal phyla, classes, orders etc... over time?

8.7 million

How do insects show uneven diversity?

A majority of species come from a small number of groups. For instance, most animals are arthropods, of which most are insects, and within insects the dominant group is the Coleoptera (beetles).

Who else in history stumbled upon the coverage equation? When did he suggest to stop looking for new combinations (species)

Alan Turing trying to break the enigma code - stop when there are no more singletons

What is scaling?

An entirely different technique is to use simple scaling rules in nature to extrapolate for species that have yet to be sampled. For every 10-fold decrease in body length, there are 100 times more species Smaller species have been less studied Assuming the relationship holds down to 0.2cm = 10 million species

What were the causes of the mas extinctions?

Asteroids, volcanic activity, decan traps

What % of named species does bacteria make up? How many might there be in total?

Bacteria comprise 5% of named species, though some have suggested that there might be as many as 10^7 -10^9 species of bacteria.

Are predicted divergence times typically before or after the first recorded fossil of that clade? Use the example of primates (Tavare et al., 2002)

Before Primates are predicted to have diverged 90mya whilst the first fossils appear around 55mya

If you were to plat a graph for the the number of individuals in a species over geological time, how would it look?

Bell curve, no evidence of exponential at the beginning or a plateau as they become the incumbent in a particular niche. Or a crash following displacement.

Discuss the Astraptes fulgerator...

Butterfly, though to be one species, range of caterpillar morphs, each specialized to a particular food plant, actually 10 species present. Could make global species richness rise

What alterations did Odegaard (2000), make to Erwins sample-based method

Came up with a figure of effective specialisation around 3- 5% (much reduced from the original 20%). This resulted in an estimate of 5 million arthropod species (between 2.5 and 10 million)

Do rain forest canopies or the floor have more species?

Canopies - tis where the leaves, flowers and fruits are

What did Terry Erwin do? Give one issue with his method

Canopy Fogging, An entirely different technique is to use simple scaling rules in nature to extrapolate for species that have yet to be sampled. Fogging captures tourist species, interactions aren't revealed such as specialist behaviors

What are the caveats of coverage?

Caveat 1: random sample Caveat 2: large N

What are diversity indices?

Combine both species richness and their abundances into a single metric

What does contiguous mean?

Connected

What is revision of names?

Considering if names given are synonyms, can take 10-100 years. Of species named up to 1880, fewer than 60% are considered valid. 20-33% of all taxonomic names could turn out to be incorrect.

When was the last time there was a significant spike in diversification?

Cretaceous

How many fungi are there? Is this a good estimate?

Current estimates vary from 0.8 to 5.1 million (or higher), though many of these are based on dubious scaling relationships akin to that used by Erwin and are likely to be revised downwards (Tedersoo et al., 2014).

Do we have more named plant or animal species?

Currently animals make up over 70% of named species, and plants form almost a quarter, despite there being only an estimated 350,000 plant species in total

What is gamma diversity?

Diversity of the entire landscape

What are non-parametric estimators?

Don't assume any particular form for the distribution of abundance

When and why does Sepkoski think that 95% of the planets marine species dissapeared?

End of the Permian 250mya - traps in Siberia

Why is the fact that primates are expected to have diverged earlier than has been found not surprising?

Fist individuals would have been rare and restricted in distribution. Unlikely that the conditions for fossilization were right.

Which plant type came along by the creataceous?

Flowing plants - angiosperms. Athough gymnosperm lycospid forests still dominated

We don't know much about the tropics, can we use what we know about the temperate biomes? What is the resultant estimate?

For every temperate species, it is predicted that there are roughly 2 tropical species. 2/3insects described are temperate. Leads to an estimate of 3-5 million insects worldwide.

What are some facts that researchers used to demonstrate that Erwins prediction was an underestimation?

For example, it would seem that in fact 23% of tropical rain forest arthropods are beetles and that the ratio of canopy to understorey species richness is substantially less than 2:1. Both of these amendments act to increase estimated species richness

What diversified after pteridophytes?

Gymnosperms - seed producing plants (Carboniferous arrival)

What is beta diversity?

How communities vary from eachother

What is sobs?

How many species were found in the sample

What are the 2 major flaws in the reasoning that lead to Erwins Estimate?

Increased herbivore specialization figures from large tree ranges and small insect ranges. Leads to a higher species richness If herbivores have broad ranges but specialize locally - lower sr

What are the proposed causes for uneven diversity?

It's an artefact : When given a selection of objects and instructed to place them into groups, humans employ arbitrary criteria that end up with a few large sets and lots of small ones. This is an inadequate explanation as we know that genuine evolutionary trends have created these patterns, so there must be a biological process at work. Random processes : If you create an evolutionary tree with random speciation events, it's highly unlikely that you will produce one that is symmetrical (Fig. 3.7). With random extinction there's even less chance of a phylogeny being balanced. Even assuming such a model, real groups are still more clustered than random expectation. Group traits : Perhaps the evolution of new traits allows particular groups to diversify? An innovation such as an organ or body form might permit species to evolve into novel niche space. What is the cause general Nevertheless, determining why such processes start is a matter of guesswork and usually ends up as a 'just-so' story that is eminently plausible with hindsight but untestable and makes it no easier to predict where the next source of diversity will come from. It has, for instance, been suggested that the evolution of the elytra (wing cases) was the defining innovation that allowed beetles to diversify, but how could you possibly test such a proposition? One way is to examine an innovation that has evolved independently on numerous occasions. Extrafloral nectaries are a feature of over 100 families of plants which have mutualistic relationships with arthropods that defend them in return for sugar. Weber and Agrawal (2014) found that families with extrafloral nectaries had diversification rates twice those without.

What are stromatolites?

Mats of blue-green algae that grew in mounds up from the sea floor

What is a molecular clock?

Method used by researchers that uses mutation rates in DNA to estimate the length of time that two species have been evolving independently

Are species that are here today survivors or something else?

Most species go extinct, they are descendants and replacements - not survivors

What groups have barely begun to be described due to taxonomic bias?

Nematodes and mites

What is a species accumulation curve?

Number of species caught per unit effort (which can be anything from number of individuals to length of transect)

What were the wider effects of rapid speciation in the Cambrian?

One possibility is that increased oxygen concentrations permitted the evolution of carnivores, bringing new selection pressures and more complex food webs (Sperling et al., 2013), though it is likely that a number of abiotic and biotic factors were involved in kick-starting the process (Smith and Harper, 2013).

When did the trilobites become extinct? What replaced them?

Permian, Brachiopoda, thengastrapoda and Bivalva

What were the first plants o spread on land?

Pteridophytes - ferns and horsetails

Species richness and evenness

Richness Total number of species Evenness The probability that two randomly selected individuals will be the same species

Is scaling of any use for microscopic organisms?

Rule seems to break down below 1cm

What is a sampling based method?

Scaling up from a smaller more manageable sample

What did Hill do in 1973?

Showed how S, eH' amd 1/D are all related and put them together in the Hill Plot S = Number of Species D0 eH' = Effective number of common species D1 1/D = Effective number of abundant species D2 The steepness of the relationship between values of q D is a good indication of the evenness of the community.

Which two from spiders, birds, mammals and amphibians are continuing to have species found. Which two have current know species to be rarely stable?

a) Spiders and Amphibians b) Mammals and Birds

Schao = ....

Sobs + ((f1(^2))/(2(f2)))

Whats is SADs?

Species Abundance Distributions

What else makes identification harder?

Species sitting in museums with no-one trained to classify them Homonyms - Different species given the same name Synonyms -Different names given to the same species

Do we have a better mechanism for counting the number of stars or the number of species?

Stars

In time, when are the highest rates of origination?

Straight after extinction events

What happened 520 mya?

The Cambrian explosion - hard parts. 20my later, all major animal phyla are present

Why do we randomise the order of samples?

To obtain smooth lines - log-linear relationships

When were the 5 Major Mass Extinctions? Which is the largest?

The end of the Ordovician, Devonian, Permian, Triassic, Cretaceous

What is our primary source of information about past forms of life?

The fossil Record

What is coverage? And what is 1-C

The mathematical equation for the % of species that have been found. 1 − C is the conditional (i.e. depending on your data) probability of finding a new species if one more observation (individual) were taken

What is f1 and f2

The number of singletons and the number of doubles

What can the Whitaker and Preston plots be used for ?

These are a good place to start when presented with a new dataset as they illustrate species richness, dominance, evenness and structure of samples in a clear fashion. They can also be used to make comparisons, for example, examining human impacts, the effects of ecological disturbance or changes through time.

What does Anne Chows Method estimate?

This estimates the minimum species richness of an ecological community based solely on the number of species found either only once or twice

You can create upper and lower bounds with Chao, give an example of an organization that wants each bound published as the true figure to fight their corner? Discuss the Hong Kong Bird Race

Timber company, conservation NGO (more species - stronger case - Hong Kong Bird Race, top bird watchers only found 136 of 194 species, just because they couldn't be found doesn't mean that they weren't there)

What else can cause bias?

Time of day, season,

95% of fossils are marine species whilst 85% today are terrestrial (mostly insects). What's the problem? (Vermeij and Grosberg, 2010)

Unexpected results from extrapolation

When is Schao not solvable? What do we do about this?

When f2 = 0 - created a bias-corrected form

What is the veil line on a Preston plot?

Where the left hand side of the plot is not visable