RATES OF DIVERSIFICATION
BACKGROUND
Rapid rate of diversification often follows the adaptive radiation
Adaptive radiation
New niches
Mutation
+ (sexual) selection
New species
Examples of adaptive radiation:
Galapagos Island finches
Tertiary radiation of birds and mammals
Cichlid fishes in the African great lakes
Galapagos finches
Archaeopteryx
Nimbochromis venustus
RATE OF DIVERSIFICATION
How does the rate of diversification vary through space and time?
How does the rate of diversification vary across taxonomic groups and region?
What methods do they use to assess the rate of diversification?
What could be the future challenges of the methods used in species rate of
diversification?
Ecological opportunity
Ecological opportunity is a primary factor regulating the tempo of diversification
(Schluter 2000; Gavrilets & Vose 2005)
Greater ecological opportunity increases the likelihood of lineage divergence
Ecological opportunity
(clade acquires species)
saturation of niche space
Rate of diversification
Example:
The role of geography and ecological opportunity in the diversification of day geckos
(Phelsuma)
(Harmon et al. 2008)
Phelsuma madagascariensis
Hypothesis that Harmon et al. (2008) tested:
Ecological opportunity: rate of speciation and morphological evolution will be
elevated following colonization of islands unoccupied by competitor species
(Baldwin & Sanderson 1998)
Speciation rate is positively correlated with island area
(Losos & Schluter 2000)
(fig from Losos & Schluter 2000)
Method:
Maximum Likelihood approach
●
Calculate diversification rate under a number of extinction scenarios (Magallón &
Sanderson 2001)
Diversification rate (ϒ-μ) = speciation rate (ϒ) - extinction rate (μ)
Extinction scenario (ε) = turnover = μ/ϒ
Test for slowing through time in diversification rate (Pybus & Harvey 2000)
●
Rate of species accumulation have slowed through time on Madagascar.
Rates of morphological evolution are higher on both the Mascarene and Seychelles
archipelagos compared to rate on Madagascar
Ecological opportunity is an important factor in diversification of day gecko species
(Harmon et al. 2008)
Issues with their model (Harmon et al. 2008)
Maximum Likelihood under the null hypothesis of a constant pure-birth process ~
speciation and extinction rates are constant through time.
(Stadler 2011)
New ML approach
The birth–death-shift process, where the speciation and extinction rates can change
through time.
Estimating the maximum-likelihood speciation and extinction rates together with the
shift times
Case of the mammalians
~ 33 mya
(Stadler 2011)
(Uyeda et al. 2011)
Divergence in body size between related
species versus the divergence time
Crazy amount of data:
Rate of evolutionary change
Divergence time
Fossil data change through time
Methods:
Multiple-burst model (“Blunderbuss” model)
=Models involving Brownian motion
Random variation of the values of the traits
around the mean
Want evolutionary change?? Wait a million years !!!
(Uyeda et al. 2011)
RATE OF DIVERSIFICATION
How does the rate of diversification vary through space and time?
How does the rate of diversification vary across taxonomic groups and region?
What methods do they use to assess the rate of diversification?
What could be the future challenges of the methods used in species rate of
diversification?
Ecological opportunity is a primary factor regulating the tempo of diversification
(Schluter 2000)
Shift to a new habitat would increase the rate of diversification
Involves geography, location, areas, range : Important role of space
Paleogeography and paleoclimate
(Hou et al. 2011)
Habitat shift from saline to fresh water
Gammarus lacustris
Gammarus balcanus
Hypothesis:
Shift to a new habitat frees species from the competition with closely related species
and would increase the rate of diversification followed by adaptive radiations
Methods:
Phylogenetic inference: to estimate the divergence times of its major lineages
to determine when the shift from saline to freshwater occurred.
Biogeographic analysis (Likelihood and Parsimony methods) to explore where
Gammarus first colonized freshwater habitats
Diversification analysis to assess the temporal diversification mode associated with
the habitat shift
(Hou et al. 2011)
Results:
Phylogenetic inference identifies an
Eocene habitat shift from saline
to freshwater
Biogeographic analysis indicates
two major range shifts
(Hou et al. 2011)
Results:
Diversification modes associated with habitat shift
Habitat shift
from saline to freshwater
+
Available bodies of
freshwater
Rapid radiation
of freshwater species
Increase of land mass
Habitat shift
from saline to freshwater
+
Available bodies of
freshwater
Rapid radiation
of freshwater species
Increase of land mass
RATE OF DIVERSIFICATION
How does the rate of diversification vary through space and time?
Geography and space
Biological history
Climate
RATE OF DIVERSIFICATION
How does the rate of diversification vary through space and time?
Geography and space
Biological history
Climate
Extrinsic causes due to new
environmental circumstances
RATE OF DIVERSIFICATION
How does the rate of diversification vary through space and time?
Geography and space
Biological history
Climate
Extrinsic causes due to new
environmental circumstances
Radiations may occur due to intrinsic characters of organisms
➔ the key innovation
How does the rate of diversification vary through space and time?
Rapid radiation due to a key innovation
Aquilegia (Ranunculaceae) (Hodges 1997)
Methods: Phylogenetic analyses
- test for monophyly – a basic assumption of adaptive radiation
- identification of sister taxa – by definition of equal age
- evolution of proposed key innovation – floral spurs
Rapid radiation due to a key innovation in Columbines (Ranunculaceae: Aquilegia)
(Hodges 1997)
Rapid radiation of Aquilegia: via key innovation or via invasion of new habitat?
Role of space
Aquilegia and its close relatives Isopyrum do not occupy a substantially
different geographic range.
It does not appear that Aquilegia has dispersed into a new habitat that its
close relatives were unable to invade.
Spur as key innovation
Underlying assumption of most species concepts: the necessity for reproductive
isolation
Characters that can promote reproductive isolation may increase speciation rate and
thus diversification
Taxa with spurs can become specialized on different pollinator types which increases
reproductive isolation and possibly speciation
(Hodges 1997)
How to know if there has actually been a change in diversification rate
between sister taxa?
Assessing weather branching rate increases with origin of traits
Change in diversification should be associated with the branch where the key
innovation evolved
Comparison of the diversification rate of the sister group lacking the key
innovation and the lineages that possess the proposed key innovation
(Sanderson & Donoghue 1994)
Methods:
Method based on ML approach
Null model as test for changes in diversification rate
Null model (Yule pure birth) assumes a (unknown) constant lineage birth rate for each
branch on the tree (1)
Calculate the likelihood of observing N species in a clade after an interval time d (2)
Markov property of (1) permit multiplication of (2) taking into account different rate
parameters in different branches
Different ML models with various number of rate parameters
(Sanderson & Donoghue 1994)
P values > 0.95
model rejected
rejected
rejected
rejected
accepted
Rapid rate of diversification often follows the adaptive radiation
Adaptive radiation
New niches
Mutation
Selection
New species
Rapid rate of diversification often follows the adaptive radiation
Adaptive radiation
New niches
Mutation
Selection
New species
(Gavrilets & Vose 2005)
Genetically based habitat choice models of large-scale evolutionary diversification
Simultaneous
Preference for
new niche
New ecological niche
environmental factors
Each individual has different neutral loci
subject to mutation
Genetically controlled
Probability of extinction is assigned per
generation
(turn over of ecological niches)
(Gavrilets & Vose 2005)
➔Larger areas allow for more intensive diversification (area effect)
new locally advantageous genes may become better protected by distance from the
diluting effect of locally deleterious genes, which otherwise can easily prevent
adaptation to a new niche.
Anolis lividus
Anolis gorgonae
Anolis nitens
(Gavrilets & Vose 2005)
➔Increasing the number of loci underlying the traits decreases diversification
a larger number of loci implies weaker selection per each individual locus and a
stronger overall effect of recombination in destroying co-adapted gene complexes.
Anolis lividus
Anolis gorgonae
Anolis nitens
(Gavrilets & Vose 2005)
The level of divergence in neutral microsatellite loci between populations from different
species is comparable to that between populations of the same species.
Lycaeides idas Lycaeides melissa
blue butterfly species
➔The number of species peaks early in the radiation
speciation events occur soon after colonization of a new environment so the genetic
constraints are less strict than later on.
Tetragnatha sp.
(Gavrilets & Vose 2005)
Summary and conclusion:
Adaptive radiation is defined as the evolution of ecological and phenotypic diversity within
a rapidly multiplying lineage.
When it occurs, adaptive radiation typically follows the colonization of a new environment
or the establishment of a “key innovation” which opens new ecological niches and/or new
paths for evolution.
The increasing availability of molecular phylogenies and associated divergence times has
spurred the development of new methods to estimate rates of speciation and extinction
from phylogenetic data of extant species and to detect changes in diversification rates
through time and across lineages.
QUESTIONS:
Phylogeny is indispensable in understanding the diversification rate, how
about its reliability?
What would be the effect of the interplay between adaptive radiation and
extinction on the tempo and timing of lineage diversification?
Recent radiation or
signature of extinction??
(Antonelli & Sanmartin 2011)