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Genetic assignment methods
for reconstruction of postmortem corpse relocation
In common blow5lies' population structure, patterns of local relatedness occur as carrion 5lies trapped together at a bait are predominantely comprised of related individuals. This in not only true for adults in general, but also for gravid females, which were likely to oviposit on the same corpse. Therefore, this pattern of local relatedness might also be found in the larvae on a body. In consequence, the test of a population's genetic structure may help to con5irm or negate an inferred postmortem relocation of a corpse – due to larvae which fell off a body at the original scene as it is moved. à blow%lies: Lucilia sericata (& Phormia regina -­‐ former studies) à Idea: "stray" larvae at ∆ location à evidence: corpse was moved à methods: specimen collections, DNA extractions, AFLP genotyping (249 polymorphic loci), à population genetic analysis (i.a. AMOVA, ΦST) & assignment tests (i.a. MLD) Melanie Egli Picard & Wells, Forensic Science International (2010) AMOVA
analysis of molecular variance
Relative Relatedness
Coefficient (R)
0  Φ statistic (analogous to F-­‐statistic) •  determination: partitioning of genetic variation 0  majority of variation was within the samples 0  Among samples: 22%, P = 0.001 •  are genetically distinct from each other STRUCTURE
module-based clustering method
0  detects the underlying genetic population among a set of individuals genotyped at multiple markers 0  computes the proportion of the genome of an individual originating from each Melanie Egli 0  pairwise comparisons among all individuals •  determination: degree of overall relatedness within each sample 0  SPAGeDi: based on allele frequency (entire dataset) •  relative estimates à R>0: 2 individuals share more alleles than expected by chance 0  Ø (across entire dataset): mean relatedness coef5icient = 0.294 (cf. range above)
STRUCTURE
Concerns: What about...?
modul-based clustering method
0  Simulation: 2-­‐12 possible subpopulations (K) •  K = 3 (most likely number), made up of: •  a) Ohio(US), West Virginia (US), New Brunswick (Ca), 0  ... geographic-­‐based structures? ü  not detected 0  ... using maggot gut contents? x  = corpse DNA: digested < 24h in live larva Ontario (Ca) & New Mexico (US) ü  assignment à advantage •  b) Alabama (US) •  c) Rhode Island (US), New York (US), Washington (US) 0  ... potentially large populations of larvae in a corpse? & California (US) x  pot. weakness: larvae numbers vary a lot: 0  Bar plot beneath illustrates the estimated L. sericata a few tens – hundreds of thousands structure when K = 3 à sampling task = complicated 0  Each vertical line represents each individual's membership fraction to a particular color-­‐coded subpopulation. Melanie Egli Inbreeding after a founder effect
Definition:
when a new habitat is colonized only by a few individuals from a source
population and therefore only a part of a source population`s gene pool
will contribute to the new developing population  founder effect
the mating of related individuals i.e. because of a lack of non-related
individuals due to no migration, isolation  inbreeding
Example:
History and fate of a small isolated population of Weddell seals
at White Island, Antactica
20.11.2014 Nora Hungerbühler
Gelatt et al. (2010). Conserv. Genet., 11, pp. 721-735
Melina-Lea Wyss
20.11.2014
Inbreeding depression
Definition:
Inbreeding depression is the reduction in fitness (survival and fertility)
of offspring resulting from matings between related individuals.
Example:
Inbreeding depression in red deer calves (Cervus elaphus)
(Walling et al. BMC Evolutionary Biology 2011)
Birth- date / birth- weight / first-year-survival
Both parents + at least one grandparent:
22% inbred individuals
Both parents + all four grandparents:
42% inbred individuals
Melina-Lea Wyss
20.11.2014
Inbreeding depression
Definition:
Inbreeding depression is the reduction in fitness (fertility and survival) of
offspring resulting from matings between related individuals.
Decreased first year survival with increasing inbreeding coefficient (F)
Survival probability F0.25 = 0.15 vs. F0 = 0.62
Bottlenecks drive temporal and spatial genetic changes in alpine caddisfly metapopulations
Shama et al. 2011
Heterozygosity excess (D)
for one allele:
for all:
boldsystems.org
H = heterozygot frequency
k = number of alleles
Pudovkin et al. 1996
No heterozygosity excess
found after bottleneck!
 sensitivity of detection
method
 population recovery
(expansion and
immigration)
Evolutionary Genetics 2014
Dominik Vogt
Bottlenecks drive temporal and spatial genetic changes in alpine caddisfly metapopulations
Shama et al. 2011
M ratio:
Bottlenecks detected in all populations.
No migration across valleys.
k = number of alleles
r = range of allele sizes
Garza and Williamson 2001
Genetic divergence of valleys.
Allelic diversity is more
sensitive to bottlenecks
than heterozygosity.
At least in the short run.
Evolutionary Genetics 2014
Dominik Vogt
MHCs lose more genetic
Diversity than neutral
Markers
Genetic drift is stronger
than selection
MHC could be important
in conservation biology
Cultural inheritance
Definition: The part of the phenotypic variation that is
inherited socially or learned from others
Example: Cultural inheritance drives site fidelity and migratory connectivity in a
long-distance migrant (2010, Harrison et al.)
Kolja Smailus
Evolutionary Genetics 2014
Application of high complexity modelling in
population dynamics
Population Genetics Models of Local Ancestry (Gravel, 2012)
Pool & Nielsen(2009): Simulation and analysis of migration patterns (based on Wright-Fischer)
Gravel (2012): Inclusion of recombination in migrants by „markovian chain“ models.
Simon Schwarz 20.11.2014
Gaëlle Pauquet
Evolutionary Genetics 2014: Population Genetics
Effective Population Size (Ne)
The effective population size (Ne) is the size of an ‘ideal population’. ‘Ideal’ refers to the
hypothetical population, which meets the Hardy-Weinberg assumptions such as equal sex
ratio, no selection, random mating and constant population size, that would experience the
effects of inbreeding or genetic drift to the same degree as the population of interest (->Ne =
Nc).
Natural populations mostly do not behave ideal. Thus, the Ne will usually be smaller than the
number of individuals in the population (census population size, Nc). The concept of Ne helps
to quantify how a population will be affected through inbreeding and genetic drift, which can
have severe impacts on small populations.
Example: Short-Term Genetic Changes: Evaluating Effective Population Size
Estimates in a Comprehensively Described Brown Trout (Salmo trutta) Population
-  Comparison of several different methods to estimate Ne in a semi-isolated resident brown
trout (Salmo trutta)
-  Data from 5 annual (multi-cohort) and 8 consecutive single cohort samples
-  Two approaches to estimate Ne: genetic and demographic
Serbezov et al. (2012): Genetics, Vol.191, 579-592
Gaëlle Pauquet
Evolutionary Genetics: Population Genetics
Table 4 Estimated per-generation and seasonal effective sizes of brown trout in Bellbekken by different methods and data
All individuals
Method
Estimates of per-generation Ne
Data: consecutive annual (autumn) samples
Moments, Fk (Pollak 1983)
Moments, Fs (Jorde and Ryman 2007)
ML, closed (Wang and Whitlock 2003)
ML, open (Wang and Whitlock 2003)
Coalescent (Beaumont 2003)
Data: single annual (autumn) samples
LD (Waples and Do 2008)
Data: consecutive cohort samples
Moments, Fk (Pollak 1983)
Moments, Fs (Jorde and Ryman 2007)
ML, closed (Wang and Whitlock 2003)
ML, open (Wang and Whitlock 2003)
Coalescent (Beaumont 2003)
Data: demographic (Serbezov et al. 2010)
Lifetime Vk (Hill 1979)
Estimates of effective number of breeders Nb
Data: single cohort samples
LD (Waples and Do 2008)
Sibship (Wang and Whitlock 2003)
Data: demographic (Serbezov et al. 2010)
Seasonal Vk
a
Correctiona
Excluding immigrants
Nx
95% C.I.
Nx
95% C.I.
1/G
1/G
1/G
1/G
1/G
121
81
127
106
87
89–176
58–143
106–154
89–130
66–111
106
69
NA
NA
91
77–153
47–128
None
100
58–142
93
53–132
C/G
C/G
C/G
C/G
C/G
105
81
326
221
141
93–117
68–101
305–351
206–237
128–144
103
78
NA
NA
143
90–115
65–98
135–144
None
104
44–215
96
45–205
69–117
(modified)
None
None
53
56
22–84
15–97
52
NA
17–87
None
40
32–49
31
27–35
Consecutive annual samples yield an estimate of drift per year. The tabulated estimates of per-generation effective size (Ne) were calculated by multiplying the annual
estimate by 1/G (Hill 1979, Equation 4), where G = 5.73 is the average generation length. For consecutive cohorts the estimate refers to temporal allele frequency shifts
among cohorts, and Ne estimates have been corrected by multiplying by the factor C/G or 1.87 (Equation 2). Estimates of per-season effective number of breeders (Nb: LD,
sibship, and demographic methods only) were not adjusted. C.I. is the 95% confidence interval for the point estimates, either as given directly by the respective software or
as calculated from standard errors for the relevant statistic (F or 1/2Ne), assuming normal distributed statistics, and was corrected with 1/G or C/G as for the corresponding
Serbezov et al. (2012): Genetics, Vol.191, 579-592
point estimate.
Outbreeding Depression
Definition: Outbreeding depression is a reduction in reproductive fitness
in the first or later generations following attempted crossing of
populations of a species that previously had a continuos distribution
Decision tree for determining
the probability of outbreeding
depressions (OD) between two
populations.
Frankham et al., 2010
(Predicting the Probability of
Outbreeding Depression)
Nils Niepagen
20.11.2014