Lecture 12b: Conservation genetics 2 Flashcards
Lecture outline
*Conserving diversity among populations
–Defining the units of biodiversity conservation
–Quantifying diversity among populations:
*Wright’s F-statistics
–Isolation of populations
Defining the units of biodiversity conservation
Population: group of organisms of 1 sp. occupying a defined area & isolated to some degree from other similar groups.
Species tend to be divided into populations by natural or manmade boundaries (often physical, but sometimes reflect differences in behaviour or microhabitat).
Aim to preserve the pattern of variation among populations within a sp. as these patterns reflect natural differences in local adaptation, & make up the total variation for the sp.
^ i.e: to ensure evolutionary heritage is recognised & protected.
Isolated populations may lose diversity (small Ne), becoming at risk through reduced fitness or inbreeding depression
How do we define units for effective conservation? The development of
Evolutionary significant units (ESU)
How do we define units for effective conservation?
Darwin proposed a continuum from populations to species, but we routinely classify ‘sub-species’ though the criteria for this classification is not always consistent.
Originally considered in 1986 by Ryder: Concordant evidence (such as morphology plus genetics).
American Association of Zoological Parks and Aquariums in Philadelphia; delegates discussed the thorny issue of subspecies, and more generally variation within named species, in support of species survival programs.
Objective of new term was to characterize the range of diversity found among conspecific populations, based on various suitable metrics including natural history, morphometrics, distribution range and genetics.
1991: Waples: Substantial reproductive isolation and representing an important component in the evolutionary history of the species. Emphasizes importance of both isolation and adaptation. Equivalence with Discrete Population Segment (DPS) – metric used by the EPA.
Waples concept of how to identify species that require protection:
Substantial reproductive isolation from other con-specific population units
+
Represents an important component in the
evolutionary legacy of the species
->
Assign discrete population segment
(=ESU) under the ESA
1994: Moritz: Binary approach to ESU based on reciprocal monophyly at mtDNA markers, and significant differentiation at nuclear markers. Also proposed ‘Management Unit (MU)’ based only on significant differentiation
2000: Crandall et al.: Ecological and genetic exchangeability together with isolation for a sufficient period of time. Defined categories based on genetic or ecological, recent or historical isolation. Nuclear DNA important.
Why did we use to use mitochondrial DNA?
but now use whole genome data?
Evolves quickly – less DNA repair than in nucleus
Only matrilineal and haploid, so Ne ¼ that for nuclear DNA
Forms reciprocal monophyly more readily than nuclear DNA
BUT only reflects movement of females, and single gene tree
^Reason for using mitochondrial DNA = to ¼ nuclear DNA
^ But better to compare all 4 components
Simplified timeline of ESU
1986: Ryder: Concordant evidence (such as morphology plus genetics).
1991: Waples: Substantial reproductive isolation and representing an important component in the evolutionary
history of the species. Emphasizes importance of both isolation and adaptation. Equivalence with Discrete
Population Segment (DPS) — metric used by the EPA.
1994: Moritz: Binary approach based on reciprocal monophyly at mtDNA markers, and significant differentiation
at nuclear markers. The later paper contrasts his interpretation with that of Crandall et al. [11] and emphasizes
the need to incorporate the idiosyncratic features and needs of individuals species.
2000: Crandall et al.: Ecological and genetic exchangeability together with isolation for a sufficient period of time. Defined categories based on genetic or ecological, recent or historical isolation. Nuclear DNA important.
Where to now with the evolutionarily significant unit?
Hoelzel (2023) Where to now with the evolutionarily significant unit? TREE
CU = Conservation Unit
ESCU = Evolutionarily Sustaining
How to judge need for conservation using a decision tree from Hoelzel et al.
(see in notes)
Step 1:
Consider origins
invasive - Not a CU or ESCU
native to step 2
Step 2:
Population demography
Large - Not a CU or ESCU
reduced to step 3
Step 3:
Differentiation by drift
Isolation - CU/ESCU
panmixia to step 4
Step 4:
Differentiation by selection
adaptation - CU/ESCU
panmixia - Not a CU or ESCU
Quantifying diversity among populations
Population subdivision → decreased population size → loss of genetic variation (decreased heterozygosity) within local populations
Therefore, population subdivision → decreased heterozygosity relative to the expected heterozygosity under random mating if the whole population was a single breeding unit (panmictic)
Can be measured as a function of pairwise comparisons between individuals within and between populations.
Wright’s F-Statistic
not the F stats evaluating differences in variances.
here F stands for fixation index,
fixation is increased homozygosity resulting from inbreeding
3 fixation indices to evaluate population subdivision:
FIS (interindividual),
FST (subpopulations),
FIT (total population).
FIS (Individuals within Subpopulations)
FIS (Individuals within Subpopulations)
— deviation of genotypic frequencies from panmictic frequencies in terms of heterozygous deficiency or excess
= inbreeding coefficient (f)
* probability that two alleles in an individual are identical by descent (autozygous).
FIS = 1 - (HOBS / HEXP)
OBS = average observed heterozygosity
EXP = average expected heterozygosity based on random mating
— FIS ranges between -1 and +1.
— negative values indicate heterozygote excess (outbreeding)
— positive values indicate heterozygote deficiency (inbreeding)
FST (Subpopulations within the Total population)
If all comparisons between all individuals in the sample are taken together, this gives overall average and variance estimates for genetic variation at the locus being investigated.
When we are concerned about population structure, we would like to know the proportion of the genetic variance that is explained by variation among as opposed to variation within populations.
This measure is called FST
FST (Subpopulations within the Total population)
— measures effect of population subdivision i.e: the reduction in heterozygosity in a subpopulation due to genetic drift.
— Quantifies the proportion of the total genetic variance explained by differences between populations:
FST = (ht - hs)/ht
ht = total population expected heterozygosity
hs subpopulation (average) heterozygosity .
FST is also called co-ancestry coefficient or ‘Fixation index’
FST ranges from 0 to 1
- e.g: if FsT=0.15
This suggests 15% of genetic variance can be explained by differences among populations.
If FST=0 then panmixis (no subdivision, random mating occurring, no
genetic divergence among populations)
FST up to 0.05 means low genetic differentiation
FST >0.25 = very great genetic differentiation
FST= 1 means complete isolation
(extreme subdivision)
FST is typically calculated based on data from multiple genes.
FIT (Individual within the Total population).
FIT (Individual within the Total population).
— the overall inbreeding coefficient (F) of an
individual relative to the total population
— can indicate social kin-group structure
FST
Commonly used index for examining overall
genetic divergence among putative populations.
Relationship between FST and Nm
Relationship between FST and Nm
Wright’s Island model:
suggests a relationship between FST & gene flow: Fst = 1/(1 +4Nm)
N=Ne
m = migration rate
this assumes equal population sizes & migration rates
BUT: dependent on model assumptions
–underestimates Nm when population size or migration rates are uneven, & inaccurate when FST is very small or large (see Whitlock & McCauley 1999).
chance of coalescence = 1/2Ne
in every generation
Sewall Wright noted that the probability that 2 gene copies come from the same gene copy in the previous generation is 1/2Ne, so every generation there’s a 1/2Ne chance of coalescence.
Furthermore, the expected time of coalescence (μ) of two tips is 2Ne.
Coalescent (the chance that two individuals have the same ancestor)
John Kingman generalised Wright’s idea to include k gene copies:
The probability that k copies is reduced to k-1 = k(k-1)/4Ne
*looks at time backwards
*calculates back to when gene copies had a common ancestor.
*permits the assessment of directional gene flow (see fig.)
*see Beerli & Felsenstein (2001) PNAS 98:4563-4568
see figures of descent in notes
Geographic isolation = Reciprocal monophyly
Isolation of populations
Vicariance events:
*division of populations through natural imposition of a bio-geographical barrier e.g. glacial incursion, emerging mountain range, lava flow, etc.
Habitat fragmentation:
*disruption of extensive habitats into isolated & small patches e.g. clear cutting in forests, development of new roads, etc.
Important Implication:
newly isolated populations are smaller.
in isolation populations can differentiate = allopatry
–most common mechanism for differentiation among populations & speciation.
–Populations differentiate by Genetic Drift when gene flow is reduced
BUT: even low levels of migration may lead to panmixia, depending on the relationship among populations
Isolation of populations example: white-spotted charr:
- differentiation after habitat fragmentation (Yamamoto et al. 2004)
–dams been built since 1963
–most recent in 1991
FST values show that dams generated genetic differentiation, even among nearby populations.
Effect was strongest among smaller populations
But: populations can also differentiate when:
But: populations can also differentiate when:
- they are next to each other (parapatry),
-within the same geographic range (sympatry)
-although less common than allopatry.
when conspecific populations within same or proximate ranges adapt to different habitat or resource requirements,
or when these differences isolate the populations with respect to mate choice = assortative mating.
or, physical barriers to gene flow can be established in sympatry,
e.g: parasites adapt to different hosts & evolve distinct life histories.
Ecotypes - example Orcas
Different ecotypes – Orca ecotypes are differentiated by their diet either marine mammals or fish
See Hoelzel et al 2007
In Washington:
Residents eat fish
Transients eat marine mammals
Within the fish eating type geographic place determines isolation
^so there’s distinction between ecotypes
&
distinction related to geographic isolation
Summary
Populations can be defined by: ESU (evolutionarily sig. Units),
CU (conservation units)
or ESCU (Evolutionarily sustaining CUs)
Differences among populations can be quantified by:
- Wrights 1920’3 inbreeding coefficient
- used to estimate gene flow
Wrights inbreeding coefficient:
FST - quantifies the proportion of genetic variance explained by differences between compared to differences withinpopulations.
FST = (ht - hs)/ht
Estimating gene flow: 1/(1 + 4Nm), but coalescent method more accurate (and reveals direction of gene flow)
Differentiation
*occurs in allopatry, parapatry and sympatry
Isolation
*can be due to factors such as vicariance and habitat fragmentation or niche specialisation within or among populations
