species and speciation

evolution
chapter 14

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speciation and species

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 speciation and species
• taxonomy: classifying organisms into taxa
• systematics: studying diversity and
relationships (and their classification)
• use species concepts

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 species concepts
• evolutionary species concept
• species: a lineage with “distinct evolutionary
fate”
• a group of individuals that share a history and
a future
• how to delineate species in practice?

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 species concepts
• phenetic species concept
• biological species concept
• ecological species concept
• phylogenetic species concept

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 phenetic species concept
• group individuals/populations based on
phenotypic trait similarity

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 phenetic species concept
• numerical taxonomy: summarizing large
number of traits in 2-3 dimensions
– principle components analysis
– other summary and clustering methods
• still widely used for fossils & microorganisms

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 phenetic species concept
• 3 principle
components
summarizing
variation in
12 traits

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 phenetic species concept -
Irhoud example
• 300 kyo skulls from Irhoud, Morocco
• Homo sapiens or not?

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http://www.nature.com/nature/journal/v546/n7657/full/nature22336.html
phenetic species concept -
Irhoud example
facial shape cranial shape

RMH (blue): recent modern humans, Ir (red): Irhoud

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http://www.nature.com/nature/journal/v546/n7657/full/nature22336.html
 phenetic species concept -
Irhoud example
• 300 kyo skulls from Irhoud, Morocco
• for some traits, inside Homo sapiens diversity
• for other traits, outside Homo sapiens
diversity
• à could be an ancestor or very closely related
group
• but is it Homo sapiens?

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 phenetic species concept: problems
• grouping only based on phenotypic data
(without genetic data) has complications
• treat all traits equally, or assign weights?
• convergent evolution?
• how to decide on objective criteria to
delineate groups?
– populations vs. subspecies vs. species

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 biological species concept
• gene flow, or not

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 biological species concept
• Ernst Mayr: “groups of actually or potentially
interbreeding populations, reproductively
isolated from others”
• à uses an objective criterion
– also, not individual but population-based
• reproductive isolation à independent fates of
populations
• potential problems/limitations?

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 biological species concept

• most mules are sterile, but c.1% female mules

can mate w donkey or horse and have
offspring à species or not?
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 biological species concept

• high genetic differentiation (e.g. measured by

Fst) indicates lack of gene flow in the past –
but how to decide if Fst is "high"?
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https://theg-cat.com/tag/speciation-continuum/
 biological species concept: problems
• only works for extant organisms
• detecting interbreeding potential is difficult
– lack of past gene flow != gene flow impossible
• only for sexual organisms
• subjective treatment of:
– incipient (ongoing) speciation cases
– partial hybridization cases

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 ecological species concept
• populations adapted to filling unique niches
• individuals of same species compete more
with each other than with other species
• different niches à independent fates of
populations
• applies to asexuals

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ecological species concept

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ecological species concept

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 ecological species concept: problems
• how to define distinct niches?

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 phylogenetic species concept
• use both genetic and phenotypic data
• smallest monophyletic group distinguished by
shared derived characters

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phylogenetic species concept

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 phylogenetic species concept for
microbes
• draw phylogenetic tree
• identify tips of branches
• if a group’s 16S rRNA gene >3% different to a
known species à consider a new species

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 phylogenetic species concept:
problems
• what do shared derived traits mean
ecologically or physiologically?
• no reference to independent fates of
populations
– only multiple major distinct characters may
indicate reproductive isolation
• can cause over-estimation of species numbers

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 species concepts
• all concepts can be useful
• all concepts are consistent when species
boundaries apparent (when groups have
separated long ago & diverged a lot)
– e.g. humans and chimps
• but may be inconsistent in cases of recent
divergence, hybridization, etc
– e.g. humans and Neanderthals, chimps and
bonobos
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 incipient species
• local adaptation but partial isolation à
usually isolation will soon evolve

• full isolation but limited local adaptation à

local adaptation will eventually evolve

• so in the long term, incipient species many

times evolve into full species
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 political aspect of taxonomy
• being liberal in species number estimation
(e.g. overestimating endemic species)
• à usually helps conservation efforts

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political aspect of taxonomy

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political aspect of taxonomy

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speciation models

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 allopatric speciation

continuous range river divides 2 populations river dries

shared gene pool no gene flow different genotypes biological barriers

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 allopatric speciation
• geographic isolation of ≥2 populations
• genetic drift + new mutations + local
adaptation + selfish elements
• à differentiation
• à reproductive isolation, even if brought
together
• (we do not assume a hybrid zone)

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 allopatric speciation
• drift alone could suffice: neutral sequence
divergence between geographically isolated
populations à meiosis fails à hybrid sterility

• meiotic drive elements (selfish elements that

fix in 1 pop) can further speed up the process

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 allopatric speciation
• vicariance (dumbbell) vs
peripheral isolate models

• speciation expected to be
faster in peripheral isolate
model (with founder effect)
than in vicariance = dumbbell
model ß by faster drift

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allopatric speciation: vicariance model

• only 1% of matings between

trans-isthmus shrimp
species pairs produce viable
clutches of offspring

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allopatric speciation: isolate model

black spruce and red spruce

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allopatric speciation: isolate model

• red spruce alleles a

subset of black
spruce alleles
• red spruce
geographic range
smaller than black
spruce range
• à red spruce a
peripheral isolate
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parapatric speciation

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 parapatric speciation
• mechanism involves no geographic barrier
• spatial cline of some environmental
parameter à selection & local adaptation
• selection leads to genetic and phenotypic
divergence between the extremes
• gene flow continues
• intermediate zone becomes a hybrid zone
• hybrids may be selected against
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parapatric speciation

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 parapatric speciation
• most times, hybrids are mismatched (less fit)
in either environment
– under intermediate dominance: hybrid phenotype
may less fit than either parents
– under one phenotype is dominant: F2 will contain
mismatched individuals
• à causes selection against hybridization
– i.e. alleles that promote assortative mating will be
positively selected
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 parapatric speciation
• if selection against hybridization
• à reproductive isolation mechanisms evolve
• à gene flow reduces à 2 species emerge

• but hybrids may also have higher fitness in

hybrid zone à 3 species may emerge

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parapatric speciation

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 parapatric speciation

• local adaptation + hybrid zone, but low

amount of gene flow (e.g. flowering time diff)
• à eventually may give rise to 2 species
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 parapatric speciation

• hybrids with highest fitness in hybrid zone

• à may eventually give rise to 3 species
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ring species

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 ring species
• gene flow along a circular cline / space
• reproductive isolation where the ring ends
meet
• can be driven by both allopatric & parapatric
mechanisms (mutation & drift, local
adaptation)

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ring species

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ring species

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 ring species
• greenish warblers – spread from south of
Tibet
• arms of the ring overlap in Siberia
• in Siberia they behave like separate species:
genetically distinct, different songs, different
feather patterns

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 sympatric speciation
• speciation without boundaries
• e.g. two cichlids in Lake Apoyo
• small shallow lake without boundaries
• genetic data: sister species (not independent
origin)
• how?

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sympatric speciation

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 sympatric speciation
• no boundaries, but either:
1. ecological divergence in heterogeneous
environment à local adaptation (resource
specialization) à assortative mating and/or
selection against hybrids
2. abrupt reproductive isolation by polyploidy

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ecological divergence-driven
sympatric speciation

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 ecological divergence-driven
sympatric speciation
• apples introduced recently to N America
• local flies living in hawthorn trees colonise
apple trees
• adaptation to apple fruits and apple fruiting
times à reproductive divergence w hawthorn
à limited gene flow

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 ecological divergence-driven
sympatric speciation
• one generation selection of hawthorn flies on
apple conditions: 154 loci allele frequencies
shift to apple-like values
• à is adaptation polygenic or Mendelian?

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 ecological divergence-driven
sympatric speciation

• disruptive selection + assortative mating, or

• disruptive selection + spatial segregation à
speciation

• disruptive selection can be caused by resource

competition in heterogenous environments

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resource competition in
sympatric speciation

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polyploidy-driven sympatric speciation
• allopolyploidy (hybridization) or
autopolyploidy à sterile offspring

• à but if polyploids can asexually propagate

by vegetative growth, parthenogenesis, etc à
new species emerge
• abrupt (as opposed to gradual in ecologically-
driven sympatric speciation)

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polyploidy-driven sympatric speciation

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polyploidy-driven sympatric speciation
• some Darevskia lizards (e.g. of Erzurum)
• only parthenogenetic females
• hybrids between two parental sexual sp

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http://www.bayramgocmen.com/album/picture.php?/19/category/41
 reproductive isolation
• prezygotic isolating mechanisms
• postzygotic isolating mechanisms
• before or after conception
• which one more costly?

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reproductive isolation

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 reproductive isolation
• what is causing this diversification?

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reproductive isolation

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secondary contact & reinforcement
• secondary contact: incipient species (usually
allopatric) meeting again - what to expect?

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secondary contact & reinforcement
• secondary contact: incipient species (usually
allopatric) meeting again - what to expect?
a. since their split, full isolation already evolved
à 2 full species
b. free gene flow à merge into one
c. intermediate scenario à hybridization occurs,
but hybrids are unhealthy/sterile à
secondary reinforcement

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secondary contact & reinforcement
• when hybrids unhealthy/sterile:
• natural selection acts to reinforce (prezygotic)
isolation
– e.g. alleles that prevent population A individuals from
mating with population B individuals have high fitness
• à selection for assortative mating alleles that
prevent mating
• à selection for incompatible reproductive
characters = reproductive character displacement
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reproductive character displacement

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 reproductive character displacement

• reinforcement: among the drivers of rapid

reproductive character evolution
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 secondary reinforcement
• if horse-donkey hybridization occurred in
nature, what would we expect to happen?

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 genetic mechanisms of isolation
• isolation usually develops over time, but can
also be fast or extremely slow

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 genetic mechanisms of isolation
• single mutations (rare)
• chromosome number changes & polyploidy
• chromosomal rearrangement
• Dobzhansky–Muller incompatibility
• Haldane's rule & sex chromosomes

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 genetic mechanisms of isolation –
single mutations
• isolation
through single
mutation:
• observed, but
rare

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 genetic mechanisms of isolation -
polyploidy
• common in plants, rare in animals
• polyploids are usually large & robust, but sterile
• allopolyploidy:
– first step: cross-fertilization à sterile allopolyploids:
can reproduce by cloning
– second step: chromosome doubling à fertile
polyploid
• autopolyploidy: also leads to sterility (due to
meiotic imbalance), reproduce by cloning
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genetic mechanisms of isolation -
polyploidy

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genetic mechanisms of isolation -
chromosomal rearrangements

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 genetic mechanisms of isolation -
chromosomal rearrangements
• complicate meiosis and/or lead to unbalanced
gametes
• à reduce fertility and/or reduce
recombination

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 genetic mechanisms of isolation -
Dobzhansky-Muller incompatibilities

• analogous to the chromosomal rearrangement model 80

 genetic mechanisms of isolation -
Dobzhansky-Muller incompatibilities

• assume 2 (or more) epistatic loci

• after pops separate, novel alleles fix in one
• after pops join: the novel allele combinations
do not function together

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 genetic mechanisms of isolation -
Dobzhansky-Muller incompatibilities
• Drosophila simulans & D.
melanogaster: split 5
mya
• fixed different alleles in
Hmr & Lhr genes
• Hmr & Lhr: transposable
element repressing
heterochromatin
regulator genes in fruit
fly
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 Haldane's rule
• Haldane’s rule: “in hybrids the heterogametic
sex is either absent or sterile”

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 Haldane's rule
• XY males in mammals and fruit flies, ZW
females in birds and butterflies (lepidoptera)
• possible causes : hemizygosity of the
heterogametic sex (and expression of
recessive alleles deleterious in the other
genome), among others

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 speciation in the lab

• mate choice evolved in fruit flies in 37 gen

• on CMY media vs starch media
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 speciation in the lab
• hologenome effect?
• starch diet à more Lactobacillus w amylase
à cuticle hydrocarbons à mate choice?
• antibiotics remove mate choice

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 speciation in the lab
• Dobzhansky-Muller incompatibility in yeast
experimental evolution

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