Focus group: Competition and Diversity

Question 1

Define adaptive radiation theory

Answer 1

Predicts that niches are partitioned early in the clade history in the presence of ecological opportunity

Question 2

What is correlated evolution?

Answer 2

Tries to answer if changes in one trait are correlated with changes in another
Use statistical analysis to see if the differences observed are down to chance or not
Regression or correlation analysis is the most common form of comparative analysis

Question 3

What did Buckey & Jetz discover about the correlation between Anolis lizard density on islands and presence of competitors/predators? What did they control for? What potential trigger of ecological release did this provide evidence for?

Answer 3

Lizard density found to be higher on islands with fewer competitors and predators.
They controlled resource availability (variation in energy use and primary productivity) on these different islands and still found this
This shows density compensation as a result of ecological release.

Question 4

What would happen to intraspecies interactions as population density increases?

Answer 4

Intraspecies interactions could become more frequent and stronger
Increased intraspecific competition would favour niche expansion, and increased phenotypic diversity of the population

Question 5

What did Svanback & Bolnick do to those sticklebacks? What did they find out about ecological release?

Answer 5

Svanback & Bolnick, 2007
They manipulated the population density of three-spine sticklebacks.
Used a paired experimental design
Control measures were taken outside of the enclosures
They found that:
Prey density declined at high biomass
Thus increased population density reduced prey availability
Individuals added alternative prey types to their diets
Diet variation among individuals INCREASED relative to low-density control enclosures
Niche breadth increased across the whole population
EVIDENCE FOR ECOLOGICAL RELEASE

Question 6

Divergence in Pseudomonas fluoresces - a study into niche availability
Three morphs:
S—– spreader
W—— spready
F—– spreader

All 3 mediums grow in a h————– medium in distinct areas, suggesting distinct niches associated with each morph

They compared h————– to h———— environments, finding the range of morphs to increase initially dramatically in the h————– environment compared to the h———–.
NO morphological divergence found for the h——— microcosms showing that niche availability WAS favouring divergence

Answer 6

Pseudomonas fluoresces, Rainey & Travisano, 1998’
Three morphs:
Smooth spreader
Wrinkly spready
Fuzzy spreader

All 3 mediums grow in a heterogenous medium in distinct areas, suggesting distinct niches associated with each morph

They compared heterogeneous to homogeneous environments, finding the range of morphs to increase initially dramatically in the heterogeneous environment compared to the homogeneous.
NO morphological divergence found for the homogeneous microcosms showing that niche availability WAS favouring divergence

Is it stable?
As long as heterogeneous conditions are maintained
Declines if returned to a homogeneous environment

Question 7

Lab study on Pseudomonas found that niche availability c——- divergence in Pseudomonas m——— as the number of evolved m——– DECLINED as occupied niches INCREASED.
These results show that lack of ecological o——— CAN constrain d——– and that niche o——– CAN limit a—— r———

Answer 7

Brockhurst et al., 2007
Constraints, Microcosms, morphotypes
Opportunity, divergence, occupation, adaptive radiation

Question 8

Define the Ecological Limits Hypothesis

Answer 8

Species richness at a biogeographic scale exists in a state of dynamic equilibrium
This equilibrium results from diversity dependence of speciation and / or extinction rates, much like population density dependent factors
That diversity dependence of evolutionary rates results from constraints of natural resource availability

Question 9

In the ELH:
———-rate declines as species richness increases
———- increases as species richness increases

Answer 9

Speciation,
Extinction

Question 10

Give the 3 assumptions of the ELH hypothesis

Answer 10

Species richness at a biogeographic scale exists in a state of dynamic equilibrium
This equilibrium results from diversity dependence of speciation and / or extinction rates, much like population density-dependent factors
That diversity dependence of evolutionary rates results from constraints of natural resource availability

Question 11

Asymptotic diversity dependence:
There is a limit on the total of potential ——
Asymptotic described how the graph for this p——- as it gets closer and closer to the hypothetical m———— value for species diversity
- This constrains ——– diversity and ——— diversity/disparity too

Answer 11

niches,
plateaus,
maximum,
species, phenotypic

Question 12

How does darwinian diversity dependence differ from asymptotic diversity dependence?

Answer 12

So, in Darwinian, Interspecific competition influences the dynamics of evolution above the species level (trait evolution, speciation and extinction)
So, unlike in asymptotic dependence, this doesn’t EXPLICITLY model an upper limit for diversity, but this can still emerge anyways

Question 13

Which one is the process and which one is the pattern of diversity dependence?
1. Macroevolutionary diversity trajectory that shows evidence of diversity regulation similar to logistic growth in population ecology
2. : Effect of interspecific competition on macroevolutionary rates of speciation and / or extinction

Answer 13

1. Is the pattern and 2 is the process

Question 14

Give some assumptions of diversity-dependent diversification (3)

Answer 14

1. Assumes each lineage has the same rates of speciation and extinction
2. Assumes that there is a theoretical maximum number of species a clade can support
3. Assumes that that speciation and extinction rates are linear functions of the number of extant species
   SEE LECTURE 9 for equations

Question 15

E——- and s——- dynamics in a model adaptive r——- of island lizards (A—-) -
What did they do?
What did this show about ecological opportunity?

Answer 15

Equilibrium & Speciation dynamics in a model adaptive radiation of island Lizards (Anolis) - Rabosky & Glor, 2010
- They modelled different equilibrium & speciation dynamics, and saw which model seemed to fit best.
- This was the one which assumed diversification rates were the same initial between islands, with island-specific linear changes in rate then occuring through time
- Model IMPERFECT but quite good
- Rate of decline correlated with island area, which is a proxy for ecological opportunity

Question 16

What is a phenomenological model?

Answer 16

Describes a statistical pattern, instead of describing a mechanism for thiat pattrn. This is problematic for diversity dependence as same patterns can emerge from distinct evolutionary processes. The Brownian Model is an example of a phenomenological model

Question 17

What is the adaptive landscape? What does it show us?

Answer 17

It shows us a theoretical environment in which species can evolve. There are multiple phenotypes leading to a fitness peak.
As time elapses, peaks are filled up.
This could model how some phylogenies appear to have an early burst of diversification before niches are filled up

Question 18

Define limiting similarity and give an example

Answer 18

The principle that two species which are too ecologically similar to one another cannot co exist due to competitive exclusion. Examples:
- Macarthur’s American warblers, 1967 - warblers show an initial early burst of diversification and then appear to plateau - diversity dependent selection
- Georgy Gause’s yeast
- Hutchinson’s ratios, 1959 - different size amongst sympatric species often consisten across the taxa (a 1.3 ratio)

Question 19

What were Jared Diamonds community assembly ‘rules’?

Answer 19

Relative to all the possibilites of species combinations, only a limited number co occur - Species exist in a “checkerboard” and there are “forbidden” species combinations dictated by principles around limiting similarity

Question 20

Explain the difference between a hypothetical habitat filtered, and competition structured community.

Answer 20

In habitat filtering, similar species would be attracted to similar habitats, ie. similar size class of fish
In competition structuring, fish communities would be divided up by size due to competitive exclusion principles.
Therefore,habitat filtering may have more similar distributions of species across the tree of life, and competition structured ones may have more dispersed ones.

Question 21

Define phylogenetic community structure. Why can it be helpful?

Answer 21

The phylogenetic community structure provides insights into how closely related species are distributed within a community and whether there are patterns of clustering or dispersion based on their evolutionary history. Relates to phylogenetic niche conservatism wherin closely related species may be expected to be more similar in traits to one another.
This can be helpful, as the ecological niche is multidimensional, and it can be difficult to measure all axes of niche variation

Question 22

Phylogenetic o——–: The sum of branch lengths connecting species in a community is high (they are spread out) indicating potentially high competition

Answer 22

Overdispersal

Question 23

Phylogenetic c———-: Sum of branch lengths connecting species in a community is low indicating perhaps habitat filtering

Answer 23

clustering

Question 24

Compare randomisation and simulation null models used in understanding phylogenetic community structure

Answer 24

So randomisation would compare observed with expected patterns of species presence in a community based on chance alone. Simulation would generate emergent patterns based on plausible processes like colonization, extinction and speciation.
Both sum the resultant branch lengths of the species generated

Question 25

A study looked at at 142 communities across 3 m—— clades and found a COMMON tendency for phylogenetic o——– across overall communities suggesting c———- is at play. Used the r——— null model

Answer 25

Cooper et al. 2008
Mammal,
Overdispersal
Competition
Randomisation

Question 26

What are the limitations of randomization based models in testing for phylogenetic overdispersal?

Answer 26

They do NOT test for any ecological or evolutionary processes such as extinction and colonization for example

Question 27

Using a dynamic null model to test for phylogenetic overdispersal, what do we find?

Answer 27

Low extinction can result in communities which would appear overdispersed under the random model. Thus extinction, not competition could result in overdispersal relative to the random null.
Look at lecture 10 for the actual method if u want

Question 28

A study using the random AND null model on communities of mammals and birds in Peru national park found that phylogenetic community structure is consistent with the combined effects of al——– speciation, ex——– and c———– NOT competition

Answer 28

Phylogenetic community structure is consistent with the combined effects of allopatric speciation, extinction and colonisation

Question 29

Define ecological communities

Answer 29

Collections of potentially interacting organisms

Question 30

Evolutionary allometry definition

Answer 30

how the proportions of different body parts or functions change as the size of an organism evolves amongst species.

Question 31

Define Adaptive Radiation and the predictions of Adaptive Radiation Theory

Answer 31

Adaptive radiation: Ecological and phenotypic divergence in the presence of ecological opportunity
Adaptive radiation theory: Predicts that niches will be partitioned early on in a clade history in the presence of ecological opportunity

Question 32

Give the 3 main axis of evolutionary radiations (an evolutionary, or adaptive, radiation basically describes the ways in which species can evolve in the event of opportunity)

Answer 32

• Phenotypic disparity
• Ecological niche diversity
• Species diversity

You can have many different species which are morphologically similar. Thus why they form different axis.

Question 33

Yoder et al. 2010 - a review
You do not need to remember the citation, but explain this statement:
We propose that ecological opportunity could promote adaptive radiation by generating specific changes to the selective regimes acting on natural populations, both by relaxing effective stabilizing selection and by creating conditions that ultimately generate diversifying selection
What does Yodis look at for this, and what did they find?

Answer 33

• Ecological release could apply different selective pressures to a population of a species, by relaxing stabilizing selection which can result in widened phenotypic diversity, and creating conditions that promote diversification of species.

Surprise surprise, they look at studies on Anolis lizards and find some evidence for processes linking ecological release to adaptive radiations. They suggest that more study is required to discern the type of natural selection acting on natural populations and to better describe the relationship between ecological opportunity and speciation rates.

Question 34

Anolis lizards, again
Mahler et al. 2010
Evolutionary rate modelled as function of the number of lineages and time
Accounts for sympatry (animals in same areas) as niches filled depended on species present on the islands, not just total number of lineages in tree
Compare lineage (diversity-dependent), time-dependent, and constant rate (time and diversity-independent) models
Which model/s fitted the best for the trait of body size? Does this support diversity-dependent diversification or not?

Answer 34

The lineage model fitted the best to the trait of body size, supporting diversity-dependent diversification, with rate of diversification declining as lineage expands and fills

HOWEVER
the time-dependent model also fitted, making the results NON-conclusive with respect to density-dependent trait evolution

Question 35

Give the main types of ecological opportunity which can lead to ecological release (3)
These again come from the Yoder et al. 2010 paper

Answer 35

1. Key innovations, meaning novel adaptations
2. New habitats
3. Antagonist extinction - extinction of a competitor or a predator

Question 36

Give some consequences of ecological release, again from that Yoder et al. 2010 review paper (3)

Answer 36

1. Density compensation
2. Increased trait variation - Phenotypic diversification- as shown in Spiny-finned teleost fish
3. Broader habitat and resource use - Ecological niche breadth change - as shown in sticklebacks and drosophila

Question 37

The Hugh and Eastwood 2006 study looks at high-altitude plant diversity in the Andes after the relatively recent uplift of the Andeas.
What does it look at?
What does it find? Does it support ecological release or not?

Answer 37

Looks at DNA sequence data and phylogenetic analysis in Lupins
With the age the clade is estimated to be, gives evidence for a remarkable explosive diversification rate
Lack of key innovations suggest this WAS because of ecological release with the emergence of island-like habitats after the Andes arose.
Compared to all those studies on cichlid fish, suggesting the recent rapid diversification of the cichlids is NOT unique
Data in other Andean flora genera also shows this pattern of rapid species diversification, adding to our knowledge of this process

Question 38

Controversial example:
Friedman 2010:
Explosive morphological diversification of spiny-finned teleost fish after the end- cretaceous extinction
What is the evidence for ecological release?
What makes it controversial?

Answer 38

• Looks at morphological diversity of the Teleost group (which make up a large proportion of modern vertebrtes) by looking at database of over 600 extinct species.
• Finds evidence for a post-extinction burst in diversification of one spiny-finned subclade in particular, and is suggested they filled the morphospace left by another species following mass extinction.
• HOWEVER some aspects of morphological diversification suggest that factors beyond ecological release also contributed to the extensive anatomical radiation of Acanthomorpha. ie. also doubts about accuracy of molecular clock models

Question 39

Give Simpson’s key innovation hypothesis:

Answer 39

“Acquisition, by any process, of such prospective adaptation may and frequently does lead to occupation of a new zone without involving physical movement of the group or ecological change around it

Question 40

Give the Herman et al. 2021 definition of ecological release

Answer 40

Niche expansions and shifts when a constraining interspecific interaction is reduced or removed

Question 41

Explain the Bolnick 2001 study to yourself which found evidence for niche expansion promoted by high intraspecific completion in Drosophila.
What was the experiment?
What did it test?
What did this suggest about the adaptive landscape?

Answer 41

Ecologists have proposed that when interspecific competition is reduced, competition within a species becomes a force for rapid diversification
Niche expansion can be associated with an increase in phenotypic variance (known as character release), with the evolution of polymorphisms, or with divergence into many species using distinct resources (adaptive radiation)
The competition in this experiment was in the form of Intraspecific competition - ie. frequency-dependent competition.
Introduced cadmium-intolerant Drosophila melanogaster populations to environments containing both cadmium-free and cadmium-laced resources.
Populations experiencing high competition adapted to cadmium more rapidly than low-competition populations
Provides evidence that competition in a population can drive niche expansion and associated phenotypic diversification onto new resources for which competition is less severe
The results reported here and retrospective studies in natural populations suggest that competition can favour adaptation to fitness valleys. Frequency-dependent effects argue for a more fluid vision of an “adaptive landscape”, in which fitness peaks can be depressed by competition, to be level with or below what once were fitness valleys constraining phenotypic evolution. This is because fitness peaks change if a once advantageous trait becomes too common or selected against. A fluid adaptive landscape appears far more likely to produce population diversification and adaptive radiation.

Question 42

Try and explain the difference between asymptotic DD and Darwinian DD

Answer 42

So in Darwinian DD, Interspecific competition influences the dynamics of evolution above the species level by potentially increasing the rate of trait evolution, speciation and extinction.
It does not explicitly model upper limits to diversity but asymptotic patterns can still emerge
Asymptotic DD DOES have a hypothetical maxmium constrained by niche availability

Question 43

Kmax =

Answer 43

Theoretical maximum number of species

Question 44

S0 =

Answer 44

rate of speciation in the absence of DD

Question 45

n =

Answer 45

Number of species

Question 46

S(n) =

Answer 46

Speciation rate given the number of species

Question 47

What is this equation for?
S(n)= S0 -(n/Kmax) * S0

Answer 47

It is for diversity dependent speciation. It shows how a theoretical maximum number of species constrains speciation, and I believe it would form an asymptotic graph

Question 48

w=

Answer 48

Linear effect of diversity on extinction

Question 49

E(n)

Answer 49

Extinction rate given the number of species

Question 50

Explain this graph:
En= E0 * wn

Answer 50

Extinction rate equals the number of species multiplied by the linear effect of diversity on extinction times the number of species.
This is just the equation for a straight line. It is a linear relationship.

Question 51

K eq =

Answer 51

Species equilibrium in an environment. Species richness in the environment, in other words.

Question 52

K eq = (S0-E0)Kmax / wKmax + S0
Explain this graph to yourself

Answer 52

So, equilibrium of species in the environment is a balance of speciation and extinction rates. It is constrained by the linear effect of diversity on extinction (w) and a theoretical maximum number of species known as Kmax.

Question 53

In a study of – vertebrate clades using phylogenetic c———– data on body s— and s—- phenotypic slowdowns found to be —- across the tree of life. B——, or SSP models fitted more. Thus, little evidence is found for early burst in d———– models. The dominant pattern was one of c———- shaping evolution continually through time rather than rapid evolution followed by stasis.

Answer 53

Harmon et al. 2010.
SSPs are single stationary peaks, similar to pattern seen in stabilizing selection
49, comparative, size, shape, rare, Brownian, diversification, constraints

Question 54

Give some critical analysis as to why that study on the 49 vertebrate clades (Harmon et al. 2010) did NOT find any evidence of phenotypic slowdowns

Answer 54

Reasons:
Only models time-dependent bursts, not lineage-dependent - ie. the lineage ‘filling up’
Assumes slowdowns must originate at root of tree
Noisy data - intraspecific species variation and measurement error masking slowdowns. Such as too small sample size, etc
Rates of evolution can be decoupled from morphological disparity

Question 55

Define character displacement. Is it a deterministic or a stochastic process?

Answer 55

Arises when individuals most dissimilar from the average resource-use or reproductive phenotypes of another species are more successful at acquiring resources or reproduction than other members of their population
Thus species shift resource use to reduce niche overlap
It is a deterministic process as it is dependent on the phenotypic distributions of other species

Question 56

How does the Puttick et al. 2018 study contradict findings for an early-burst in diversification, using the jawed fish? What fish feature do they look at?

Answer 56

Morphological disparity in jaw shape is found to be higher in extant species
Makes a case AGAINST early burst-diversification models
Less than half of potential morphological spaces are occupies
Unoccupied spaces or gaps within the morphospace are crucial for understanding how lower jaw morphospace occupation is affected through time by historical, functional, temporal, ecological and environmental factors.

Question 57

When character displacement is modelled, it is made out of a d————– and a s———- component. Thus, competition is added in addition to Brownian evolution alone.

Answer 57

deterministic, stochastic

Question 58

What signals for competition / character displacement can we see in phylogenies (3)?

Answer 58

1. A flattened distribution of trait values as different phenotypes are favoured. It is not normal and may form a ‘batman’ distribution curve as tail distributions increase.
2. An increased accumulation of variance as species diverge from one another
3. A stronger phylogenetic signal as the strength of competition increases

Question 59

What can competition affect apart from character displacement? (3)

Answer 59

• Speciation probability - more species less speciation as less niches? Or more as more competition?
• Extinction probability - more species more extinction?
• Trait evolution

Question 60

What is an incipient species?

Answer 60

In modelling, these are species which have not yet fully diverged into a new species. They can either complete speciation, or collapse back into one species

Question 61

Chira et al. 2020: Evidence for competition as a cause for beak evolution

In many previous studies, it has been assumed that tempo and mode of evolution (rate and way) have used models which assume non-lineage dependent evolution
Thus, role of species interactions in macroevolution remains limited
This studies looks for signatures of competition in the phylogenies of related bird species and the evolution of ecomorphological traits

What do they find out? How strong is the signature for competition?

What model do they use?

Answer 61

Finds that:
Where it occurs, the signature of competition generally coincides with positive species diversity-dependence, driven by the accumulation of lineages with similar ecologies, and we find scarce evidence for trait-dependent or negative diversity-dependent phenotypic evolution. Overall, our results suggest that the footprint of interspecific competition is often eroded in long-term patterns of phenotypic diversification, and that other selection pressures may predominantly shape ecomorphological diversity among extant species at macroevolutionary scales.
The MODEL: The Matching Competition model. This models character displacement by modelling lineages moving away from a single mean trait value
Our results indicate that differentiation in one axis of phenotypic divergence is generally sufficient to minimize competition for shared resources.
Basically, in some examples models assuming strong effect of species interactions on phenotypic evolution are most suitable. However, overall, patterns for geomorphological divergence best captured when assuming they evolve independently from one another. In deep-time, the signature of competition between close relatives appears eroded due to other selective pressures
Still, with some prolific examples of competition driving phenotypic evolution in bird traits, study makes case for competition to be included in trait evolutionary models to improve model fit.

Question 62

Etienne and Rosindell 2012 created the protracted speciation model, to explain the pull of the present.
What model did they build off?
How did this help explain the pull of the present? What evolutionary processes can this help model for?

Answer 62

Birth-death model of speciation predicts constant speciation and extinction rates, thus species numbers increasing or accelerating as they approach the present.
This does not work to explain the observed phylogenetic slowdown towards the present
Their proposed model addresses this.
It incorporates the protracted speciation model into the birth-death model of diversification. This proves a good fit to 4 bird phylogenies which it is tested upon.
In the protracted speciation model, speciation is NOT instantaneous, and instead there is a stochastic period describing the time taken for speciation to be completed
Speciation initiation rate is independent of other species, and speciation completion is dependent on accumulating ‘enough’ differences. Speciation completion rate increases with accumulation of phenotypic differences. This fits with the principles of limiting similarity and competitive exclusion. Thus, they can create a model accounting for the time take for speciation to be completed in the phylogenies.
Extinction is accounted for too, which is how the model produces the phenomena known as the ‘pull of the present’ - these species have simply not had time to become extinct, forming this pattern of apparent accelerated diversification.

Question 63

Why can new models, such as the protracted speciation model, be useful? Give around 3 reasons.

Answer 63

1. Process-based, we can make predictions of observable outcomes - ie. the underlying principles of limiting similarity and competitive exclusion
2. Emergent patterns can be measured in real data, although this is hard
3. This can provide new insights into the origins and dynamics generating the diversity of life on Earth

Question 64

What four main things can competition effect?

Answer 64

1. Diversification rates through time
2. Number of species.
3. Rate of trait evolution
4. Trait values and distribution

Question 65

What model accounts for this principle: Competition-driven trait divergence facilitates speciation completion and reduces extinction

Answer 65

The protracted speciation model - more differences = higher likelihood of speciation completion

Question 66

How do modelled outcomes of competition show the effect of competition on these processes?
1. Speciation completion
2. Overall Diversficiation
3. Trait evolution

Answer 66

1. Elevated rate, as increases trait value distributions thus accumulation of differences . This is for an INTERMEDIATE level of competition though, as if it was too high processes such as competitive exclusion could take precedence.
2. Increases initially but may plateau due again to a reduction in ecological opportunity. Thus, competition surpresses net diversification rates (s-e)
3. INCREASES if no impact of increased trait diversity on competition

Question 67

Who said this, and about what bird subspecies?
“It is only by adaptations to different sorts of food, or modes of food getting, that more than one species can occupy the same locality. Two species of approximately the same food habits are not likely to remain long evenly balanced in numbers in the same region.”

Answer 67

Grinnell in 1904, about the Chestnut-backed Chickadee.
This is an early description of limiting similarity

Question 68

Explain Gause’s 1934 yeast experiment

Answer 68

Testing principles of co-existence on two species of yeast
Shows how growth in volume for both species is suppressed in mixed populations, and one species (P.caudatum) begins to be outcompeted for resources by the other.
One species ends up entirely displaced by another, in line with mathematical theory.
They are not sure of the exact mechanism for this.

Question 69

Mcarthur and Levins pioneer a description of the principles of limiting similarity, following observations such as that of feeding behaviour in Northamerican Tree Warblers.
What do they describe about niche availability?
How do the Warblers support this?

Answer 69

Theoretical paper describing how there is a limit on how many species an environment can contain, constrained by principles of limiting similarity, and niche availability
Niche breadth said to increase with environmental instability - in other words, species become more generalist in these conditions
Mcarthurs warblers in 1958 helped support this, by showing niche partitioning in action, with warblers feeding in different parts of conifer trees to reduce competition

Question 70

What two birds can provide evidence for Jared Diamons community assembly rules? How?

Answer 70

The Bismarck black myzomela and the black sunbird. Both are nectarivorous. The Bismarck black myzomela occurs on roughly half of the islands in the Bismarck Archipelago, but none which contain the black sunbird too.
They have ‘more exclusive distributions than expected by chance’

Question 71

What does the random model do?

Answer 71

So it just randomly picks species from across the phylogeny to generate a community. This is repeated 1000s of times to generate a phylogenetic distribution of expected values. The branch levels are summed to see the null level of dispersal

Question 72

“A common tendency for phylogenetic overdispersion in mammalian assemblages”
What model do they use?
What mammalian clades do they look at?
Do they find significant overdispersion in individual communities?
Does this support competition-structured communities?

Answer 72

They look at phylogenetic structure of 142 assemblages across 3 mammalian clades - new world monkeys, north american ground squirrels and australian possums.
They use randomisation to generate null model of community assemblages. They look at mean phylogenetic distance, and mean nearest neighbour distance.
Overall, significant overdispersion was rare in single communities, but there is a tendency for phylogenetic overdispersal across the assemblages, meaning that animals are more distantly related from one another than chance alone would dictate.
This is the first demonstration of widespread overdispersion in mammal assemblages and implies an important role for either competition between close relatives where traits are conserved, habitat filtering where distant relatives share convergent traits, or both. This is as traits allowing species to exist in a habitat could have evolved convergently. We cannot see which reason this may be from a phylogeny alone. You would need trait data on traits mediating competition and resource use to be able to do this

Question 73

Define how you obtain mean phylogenetic distance, and how you obtain mean nearest neighbour distance, as they did in that overdispersal study in mammalian clades

Answer 73

Mean phylogenetic distance - for each species calculate branch length to all other species in the community, take the mean across all species in the community

Mean nearest neighbour distance - for each species calculate branch length to its closest relative in the community, take the mean across all species in the community

Question 74

“A dynamic null model for phylogenetic community structure”
What is the dynamic null model? Which model do the use?

Answer 74

They use the ‘DAMOCLES’ model to do this - Dynamic Assembly Model of Colonisation, Local Extinction and Speciation
The dynamic null model developed here considers underlying processes of community structure, such as allopatry, colonization and local extinction

Question 75

“A dynamic null model for phylogenetic community structure”
What did they apply the dynamic null model to?
What did they find?

Answer 75

Applies model to bird and mammal communities to South America, showing that processes often attributed to negative biotic interactions could be a result of the
processes of allopatry, colonization and local extinction.
Used mean nearest neighbour distance, and mean phylogenetic distance again in their models
They find phylogenetic overdispersal for the mammals and birds of Manu national park, but this is consistent with what would be found in environments with low extinction and colonization rates.
The dynamic null model suggests that the phylogenetic community structure is consistent with the combined effects of allopatric speciation, extinction, and colonisation
Conclusion: Phylogenetic history MUST be accounted for when making conclusions about phylogenetic overdispersal

Question 76

“A dynamic null model for phylogenetic community structure”
What questions can dynamic null models help to establish?

Answer 76

Dynamic assembly models can also address other questions such as: ‘what are the typical rates of colonisation and local extinction underlying community assembly?’, ‘how do these rates depend on environmental conditions, traits or geographic area?’, ‘do rates of colonisation slow-down through time as niches are filled?’.

Question 77

Define the matching competition model

Answer 77

Computationally simple, this model is used to investigate the presence of competition by modelling how species diverge from the mean trait value across the studied clades

Question 78

explain the Clarke competition model - what does it test for? what has it successfully been applied to?

Answer 78

Models for comparative data have previously lacked inclusion of the processes of competition
This model, called the Clarke Model, fills that gap by modelling for interspecific competition in sympatric species, modeled as a tendency of sympatric species to evolve toward difference from one another, producing trait overdispersion and high phylogenetic signal
Model found to have power in detecting competition compared with Brownian and OU model in sufficiently large species trees
Model is applied successfully to detect for competition affecting the evolution of bill length in Darwin’s finches using trait variation

Question 79

New paper 1: Phylogenetic clustering and overdispersal in bacterial communities
Is more evidence found for clustering or overdispersal? Why may this be?
What is the citation?

Answer 79

Horner-Devine and Brendan, 2006
Uses random / null model to look at if bacterial communities are phylogenetically structured
Phylogenies found to be clustered, potentially reflecting habitat filtering in this community
Clustering could ALSO be a result of different dispersal/colonization capacities however
Phylogenetic SCALE i.e. taxa level is shown to influence the observation of phylogenetic clustering / overdispersion

Question 80

what is a traits-based, pairwise species co-occurrence approach ?

Answer 80

Traits-Based Approach: This involves considering the characteristics or traits of species as a primary focus. Traits can include various biological features such as body size, reproductive strategy, feeding behavior, or other ecological characteristics. A traits-based approach aims to understand how these traits influence the interactions and coexistence of species within a community.

Pairwise Species Co-occurrence: Co-occurrence refers to the presence of two or more species in the same geographic area or habitat. In a pairwise species co-occurrence analysis, researchers examine the relationships between pairs of species. They investigate whether certain pairs of species tend to occur together more or less frequently than expected by chance.

Combining these concepts, a traits-based, pairwise species co-occurrence approach involves analyzing how specific traits of two species influence their likelihood of co-occurring in the same environment. This method seeks to uncover patterns in the ecological associations between species pairs based on their traits.

Question 81

Giam & Olden 2016- environment and predation structure fish communities
- What did they study?
- What method did they use?
- What was found to primarily structure communities?

Answer 81

Paper on evidence for Jared Diamonds community assembly rules:
Looks at non-random community structures across fish communities in temperate stream environments from multiple watersheds across a broad environmental gradient
Aims to establish 1) are fish communities structured non-randomly, and (2) what is the relative importance of environmental filtering, predator–prey interactions and interspecific competition in driving species associations?
Compares fish communities to null models. Looks at the traits of body-size, feeding strategy and phylogeny using a traits-based, pairwise species co-occurence approach. Compared actual co-occurences to a randomly generated metacommunity
Majority had non-random community assemblies
Competition strength didnt appear to increase segregation (non-randomness)
Species pairs engaging in predator-prey interactions more segregated than those which were not
communities are structured in an increasingly non-random way the more diverse their different environmental requirements, inferring the important role of the environment in structuring species communities - environment a better predictor of species segregation than competition, thus more important → Supports HABITAT-FILTERING not competition
Previous research has found contrary patterns - is possible that competition was present in these communities, but at an even smaller spatial scale

Question 82

Explain the difference between intrinsic and extrinsic models of diversification

Answer 82

Intrinsic - acquisition of a key innovation
Extrinsic - Extinction of an antagonist / a new ecological niche

Question 83

PERSONAL RESEARCH: How exceptional are the classic adaptive radiations of passerine birds - Miles et al. 2023

What does the study study?
What is found about disparity in island bird species?
How exceptional were adaptive bird variations found to be? What other processes were involved?
Why should these results be seen as slightly cautionary?

Answer 83

Looks at trait data in 8 morphological traits (diversity in size and shape) and morphological disparity across island passerine bird radiations, and compared this to mainland passerine bird radiations. The distribution of disparity did NOT differ significantly from a normal distribution. Disparity on island species WAS slightly significantly higher (in line with potential positive role of ecological opportunity on islands) , but key innovations, and ecological opportunity, do NOT overall seem to explain morphological diversity. Effects of species number, age, and tropical vs. temperate also ambiguous.
SOME truly extreme in phenotypic disparity: i.e. birds of paradise and honey-creepers, but OVERALL pattern amongst all clades is normal
SO: Variation could just be the result of stochastic environmental processes in line with Brownian modelling and not things such as key innovations
Investigation regarded as preliminary: larger morphological datasets and more refined statistical approaches, would be welcome next steps

Question 84

Are floral nectar spurs a key innovation?
Explain this paper. What evidence shows that they CAN be a key innovation

Answer 84

Difficult to definitively discern if a key innovation was the cause for an observed explosion in species diversity
Change in the morphology of nectar spurs could strongly influencd reproductive success and reproductive isolation in plants.
This paper looks for evidence that nectar spurs DID lead to acceleration in species diversity and finds strong support: A correlation between acquisition of nectar spurs and an increase in species diversity in a wide array of plant groups

Question 85

Ecological character displacement

Answer 85

Character displacement in traits associated with resource use i.e. drosophila and Mcarthur’s Warblers (I think)

Question 86

Explain that tadpole paper to yourself and how it provides evidence for niche breadth expansion in the presence of ecological opportunities.
Looks at different morphs of tadpoles. There are omnivorous and carnivorous forms. Experimental manipulations showed that competition and ecological opportunities increased morph types. A wider abundance and diversity of resource use resulted in more morphs, as did a higher level of intramorph competition. The alternative diet types (niche breadth expansion) resulted in increased polymorphisms.