Degree Thesis in Biology, 15 hp Bachelor’s level Spring Semester 2019
Identifying Genetic Causes of Hybrid
Necrosis in Arabidopsis lyrata
3
Identifying Genetic Causes of Hybrid
Necrosis in Arabidopsis lyrata
Abstract
Deleterious gene interactions due to accumulation of individual genetic variations
between different lineages are a cause of population diversification by creating
reproductive barriers that ultimately lead to differentiation of species. One type of
deleterious interactions is called “hybrid necrosis”, in which epistatic interactions
between some plant immunity genes (usually very variable) cause autoimmunities that
produce a necrotic and dwarf phenotype. Hybrid necrosis has been widely studied in
several plant species, such as Arabidopsis thaliana and many gene interactions were
found for that plant. This study tests the applicability of these results on a close relative,
A. lyrata, by crossing individuals from different populations and genotyping F
2progeny with polymorphic markers close to homologous sequences to those involved in
hybrid necrosis in A. thaliana. Results suggest the possibility of a homologous gene to
DM8 or DM9 in chromosome 7 to be involved in formation of hybrid necrosis.
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Table of Contents
Introduction………...5
Material and Methods……….6
5
Introduction
When two different lineages in the same species outcross, the resulting offspring may
have phenotypes that differ from their parents. Those phenotypes may have beneficial
effects in the offspring fitness (a phenomenon known as hybrid vigour), or deleterious
(Swiadek et al, 2017). Deleterious effects are considered to be caused by an accumulation
of individual changes in divergent lineages which results are innocuous or even beneficial
on their genomic context, but whose negative effects arise when combined in hybrids
(Chae et al, 2014). It may create reproductive barriers that cause population
diversification and, according to the Bateson-Dobzhanski-Muller model, ultimately leads
to differentiation of species (Orr, 1996). By studying the mechanisms that underlay
hybrid incompatibilities, the understanding of speciation and other evolutionary
dynamics may be improved (Swiadek et al, 2017).
Hybrid necrosis is one form these deleterious gene interactions take in many between
species hybrids, both wild and cultivated, such as tomato, tobacco, bean or Arabidopsis
thaliana. It may happen both in intraspecific or interspecific hybrids and usually results
in tissue necrosis (commonly leaves), wilting, dwarfism, reduced fecundity and
sometimes lethality (Bombilies, 2009). It is considered to be caused by a spontaneous
activation of plant defenses by epistatic interactions of the newly combined alleles in
hybrids (Swiadek et al, 2017), typically between two or more unlinked loci which encode
components of the immune system. Despite this, hybrids usually show increased
pathogen resistance relative to both parental strains. (Bombilies, 2009). Hybrid necrosis
is also environmentally affected. Plant immune responses are often suppressed above
certain temperatures, which also alleviates the symptoms severity (Muralidharan et al,
2014), and A. thaliana do not show a significant reduction in fitness when plants are
grown in field conditions, possibly due to the advantageous effects of the enhanced
immunity (Swiadek et al, 2017).
Due to the “arms race” between hosts and pathogens, immune system genes are very
polymorphic in many organisms, and plants are not an exception. NLRs
(nucleotide-binding domain and leucine-rich repeat proteins) are important and particularly variable
components of the plant immune system, which act as immune receptors. The
accumulation of different sequences can improve the resistance of the plant, but also
cause autoimmunities that reduce plant growth or health. (Chae et al, 2014). However,
other types of genes have been identified causing hybrid necrosis, such as ACD6
(ACCELERATED CELL DEATH 6) in Arabidopsis thaliana, which encodes a
transmembrane ankyrin repeat protein that modulates the activity of pattern recognition
receptors (Swiadek et al, 2017). Chae et al, (2014) tested this in an experiment involving
6409 crosses, finding several genes that caused necrosis when specific alleles in the same
locus interact or when alleles from two different loci do. They also found different
degrees of necrosis severity according to the genes involved.
Hybrid necrosis has been studied by several authors in Arabidopsis thaliana (Bombilies
et al, 2007; Chae et al, 2014, Swiadek et al, 2017…), but it is a phenomenon that affects
many plant species, including a close relative, Arabidopsis lyrata (unpublished results).
A. lyrata is a species present in subarctic and subalpine regions in North America,
Europe and Asia. It is usually self-incompatible (with exceptions in some populations
from North America), so its genetic diversity in individuals and populations is high
(Mable et al, 2007). However, due to close relatedness of A. thaliana and A. lyrata,
hybrid necrosis in A. lyrata is expected be controlled by genes homologous to those in A.
thaliana. The aim of this study is verifying that assumption and, by doing so, testing the
6
generation of A. lyrata hybrids with normal and necrotic phenotypes will be isolated.
Then, it will be used to score genetic markers close to A. thaliana necrosis loci and see
whether some alleles are associated with the trait. Ultimately this would lead to a better
comprehension of speciation mechanisms: whether the same genes cause the same
hybrid incompatibility phenotypes.
Materials and Methods
Plant Material
Parental generation was collected in Mayodan, USA (36°25' N, 79°58' W, 225m), A.
lyrata ssp. Lyrata; and along road leading from Pernitz to Pottenstein, Austria
(47.9181166N, 15.9741833E, 626m), A. lyrata ssp. petraea. The original crosses were
made between pairs of individuals for which the Mayodan seeds were collected from
nature and PP seeds were from crosses made in laboratory from seeds originally collected
from nature. The parental plants were named: Ma029b-3, Ma004b-1, PPBxF1 and
PPGxB2.
The between population crosses to produce F1-seeds were done between these pairs (the
maternal parent is always first and the pollen parent after):
PPBxF1 x Ma029b-3 (whole F1 family necrotic)
Ma004b-1 x PPGxB2 (necrotic and healthy F1 segregate about 1:1, but small sample size;
a healthy individual was chosen for crosses)
F2 generation, with parental controls, was germinated on petri dishes with moist filter
paper. After germination, 90 seedlings (86 F2 and 4 P controls) were individually planted
in 6x6 cm pots and grown in a greenhouse (Umeå University, Sweden) in long day
conditions. F2 grew from April to June, (more than 18 light hours per day) at a
temperature from 15 to 20 ºC and 60% humidity. The plants received mainly natural
light, but there were also solar lamps that switched on in cloudy days, from 03:00 to
21:00. A commercial soil mixture (Hasselfors K-jord) was used with vermiculite, in
approximately a 3:1 ratio. The soil mixture was composed of peat, sand and clay, and it
was fertilized (total nitrogen content 1600 mg/l) and calcified. The pH was between 5.5
and 6.5.
Necrotic individuals were identified de visu, since the difference was evident at sight.
Lab procedure
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(https://www.arabidopsis.org), and then similar sequences were located in A. lyrata in
Phytozome web portal (https://phytozome.jgi.doe.gov). By doing so, and comparing
with previous literature on microsatellite markers in A. lyrata (see table 2 and 3), the
closest markers to the candidate gene regions were selected as shown in table 1.
There were many short sequences homologous to DM6 fragments in chromosome 1, so
three markers were chosen to score the entire chromosome. The markers MSAT2.22 and
ELF3 (chromosome 4) were also used, despite not being relatively close to any gene
considered likely to have influence in the necrotic phenotype, because they were already
present in the lab. However, it was not possible to use MSAT4.35 (Loudet et al. 2002)
due to PCR optimization complications and time restrictions. A genetic map with
possible homologous sequences and chosen markers can be seen in figure 1.
Name Arabidopsis.org
code A. chromosome thaliana A. likely lyrata chromosome
A. lyrata likely
position (bp) Chosen marker
DM2/RPP1 AT3G44480 3 5 11213750-11270500/ 5824000-5828500 AthGAPAb DM9/ACD6 AT4G14400 4 7 14083250-14118000 MSAT4.35 6 23097500- 23135000 nga106 DM6/RPP7 AT1G58602 1 2 3612375-4173750 T15M6 1 widespread F20D22, AthZFPG, nga280 DM4/RPP8 AT5G43470 5 8 11975000-11986250 01_G06 DM1/SSI4 SSI4 5 4 12208250-12212750 01_N07 7 21300000-21342500 ICE9 DM8/RPP4 AT4G16860 4 7 11732500-11738750 None available DM7/RPW8 RPW8.1 3 5 15135000/15145000 None available Table 1: Genes related with hybrid necrosis in A. thaliana, their location, location of possible
homologous sequences and chosen marker to test it.
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For each marker, the optimized PCR procedure was slightly different. Some of them were
replicated individually, using a hot start DNA polymerase from Solis BioDyne provider
(HOT FIREPol
®). Each sample was replicated in a 10 μL reaction, containing 1 μL of DNA
(5-10 ng), 1 μL of 10X buffer and 0.8 μL dNTP from the same provider, a variable amount
of MgCL2, 0.2 μL of each primer (0,4 μL in total), 0,1 μL of polymerase and the remaining
volume of PCR grade water. The PCRs were run in 35 cycles of 20 s at 95ºC, 30 s at a
varying annealing temperature according to the primer, and 10 s at 72 ºC, with a starting
period of 15 min at 95ºC, and an ending of 45 min at 72ºC.
For other reactions, it was possible to make the PCR with more than one marker at the
same time. In that case, each 10 μL reaction contained 5 μL of Multiplex PCR Master Mix
(HOT FIREPol®) from Solis BioDyne, 1 μL of the primer mix, 1 μL of DNA (a variable
concentration for each sample) and 3 μL of water. The PCRs were run in 30 cycles of 30
s at 95ºC, 90 s at a varying temperature and 60 s at 75ºC, with a starting period of 15 min
at 95ºC and an ending period of 45 min at 75ºC. The PCR products were run on agarose
gels (2%) to check the correct product size and specific amplification of single locus, and
find the optimal annealing temperature and MgCl2 concentration.
Then, two different mixes were prepared to be analysed through a capillary
electrophoresis adding different amounts of PCR product (the optimum dilution was
determined by comparing the intensities of all PCR products) to 20 μL of water in each
sample. The capillary electrophoresis was made in a commercial lab of StarSEQ. See
table X and Y for more details about procedure, concentration and size of each specific
marker.
Data analysis
The obtained results were interpreted with the help of the Geneious Prime programme
to get the exact sizes of microsatellite fragments. The size standard (Gene Scan 500 LIZ,
Thermo Fischer Scientific) aligned automatically with manual checking, but the size
ranges of the loci and the bins for each allele were set mainly manually.
Marker nga106 AthZFPG MSAT2.22 F20D22 ELF3
Fluorescent Label FAM YY FAM FAM FAM
Size 100-130 140-165 200-225 170-180 290-330
PCR Procedure Individual Individual Individual Multiplex
PCR Concentration
of each primer 0.5 uM 0.5 uM 0.5 uM 0.2 uM 0.2uM
MgCl2 added to the PCR 1 μL 1 μL 0.6 μL X PCR annealing temperature 50 ºC 50 ºC 52 ºC 53ºC Amount added to the capillary electrophoresis mix 2 μL 2 μL 2 μL of a 1:4 dilution 4 μL Reference (primers)
Bell & Ecker 1994
Clauss et al. 2002
Loudet et al. 2002 Clauss et al. 2002
9
The F1 samples were run first, separately, with capillary electrophoresis to get the sizes
of the F1 alleles. Then, given the F1 alleles, the expected genotype in F2 was calculated
for every locus, and then were compared with the observed genotype in the healthy
individuals with a chi-square test, in order to test single-locus effects. Then, using the
observed F2 genotype, the expected allele distribution for every couple of locus was
calculated, and compared with the observed with a chi-square test too. Expected
interaction results can be seen in table 4. Finally,
the chi-square test was used to compare the
expected and observed number of every couple of
alleles individually (considering only two groups
for every test, the individuals who had both alleles
present and those who hadn’t). Comparison with
the necrotic individuals was used as a confirmation
for the statistic results obtained from the healthy
individuals.
Results
Lab results
From 86 F2 planted seedlings, 47 showed a healthy phenotype and 31 showed a necrotic
phenotype and an evident delay in growing, or an almost complete lack of growth (Figure
2). Only four of the necrotic plants grew to an appropriate size to allow a DNA extraction,
so it was not possible to use them to any statistical analysis. Three plants showed a
strange leaf shape phenotype that didn’t fit with any of their relatives, so they were
excluded from the statistical analysis considering a confusion with the seeds. Finally,
Marker ICE9 AthGAPAb nga280 T15M6 01_N07 01_G06
Fluorescent
Label FAM FAM FAM FAM FAM YY
Size 115-125 120-135 70-80 200-210 220-240 280-320
Procedure Individual Individual Multiplex
PCR Concentration of each primer 0.2 uM 0.2 uM 0.2 uM 0.2 uM 0.2 uM 0.2 uM MgCl2 added to the PCR 0.4 μL 0.6 μL X PCR temperature 50 ºC 54 ºC 50ºC Amount added
to the mix 2 μL 2 μL of a 1:4 dilution 3 μL
Reference Clauss et
al. 2002 Clauss et al. 2002 Clauss et al. 2002 Leppälä Savolainen &
2011
Woodhead
et al. 2007 Woodhead et al. 2007
Table 3: Information about the markers used in the second mix
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another five of them showed an aberrant
phenotype (Figure 3), and despite being
attributed to a damage during being planted, they
were excluded from the analysis as well. Results
from microsatellite size analysis can be seen in
table 5 (attachments).
Statistical analysis
Individual locus chi-square tests showed a
significant difference between the expected and
observed genotype distribution in two loci:
AthZFPG (0.005) and ICE9 (0.025).
Genotype distribution between two loci showed a
significant difference in 3 loci couples: 01_N07
and ELF3 (0,001); 01_N07 and MSAT2.22 (0.05);
and F2D22 and AthZFPG (0.001).
Results from specific allele comparison confirmed
those from genotype distribution between loci
pairs, showing a significant difference between the
same loci couples: Between 01_N07 and ELF3
there was a significant difference between the
alleles 230
and
310
(0.05, more
than
expected);
230 and 318 (0.05, less than expected); 235 and
306 (0.025, more); and 235 and 321 (0.025, less).
There was also a significant difference between
223 allele from 01_N07 and 236 from MSAT2.22
(0.05, less); and between 115 allele from F2D22
and 145 from AthZFPG (0.025, more). The alleles
were named according to their size. Results from
all statistical analysis can be seen in tables 6-116
(attachments).
Comparing segregation distorted markers and
genotypes of necrotic plants, the most
overrepresented AthZFPG genotype class in
healthy individuals (145-151) is also present in
three out of four necrotic individuals. The last
individual shows the most underrepresented
genotype class in healthy individuals, (145-153).
The ICE 9 genotype of the two necrotic individuals
that were successfully genotyped for that marker,
their combination (117-117) coincide with the
underrepresented class in healthy individuals.
Figure 2: Comparison between a healthy individual (up) and a necrotic one (down). Note the purplish color of the leaves in the necrotic one.
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Discussion
The significant result of the ICE9 loci suggest the presence of a linked gene involved in
the hybrid necrosis phenomenon. ICE9 was the chosen marker to DM1, but in A. thaliana
DM1 causes necrosis in interaction with DM2 (Chae et al, 2014), and there isn’t any
evidence of interaction between ICE9 and any other gene. However, there are two other
genes in relative proximity to it: DM9 and DM8. Despite being a bit further away from
ICE9, crossover events are relatively rare (Fernandes et al, 2018), so it could be a marker
for those genes as well. Both genes show an interaction between different alleles at the
same locus in A. thaliana, without any interaction with other genes (Chae et al, 2014).
The result from ICE9 is thus more likely to be caused by one of those genes (or both) than
from DM1. However, it is noticeable that DM8 and DM9 necrotic phenotypes in A.
thaliana (Chae et al, 2014) are less severe than found in A. lyrata.
When comparing healthy to necrotic individuals, the most common ICE9 genotype in
healthy individuals is absent in necrotic ones. However, their genotype (117-117) is also
present in many healthy individuals. This suggests that hybrid necrosis is not due to a
single allele combination, but the additive effects of the interactions between many loci.
Another possible explanation is that ICE 9 only show two segregating alleles, and it can’t
be distinguished which 117 allele the F2 individuals inherit from the F1 117-117 parent.
But the DM8 or DM9 alleles may be different.
AthZFPG showed even a more significant difference, but this difference is harder to
interpret and has to be done carefully. AthZFPG is a marker chosen to representDM6,
but on chromosome 1 there are many short homologous sequences to various parts of
DM6 in A. thaliana, located in different positions across the chromosome. Moreover, in
A. thaliana DM6 showed an interaction with DM7 (Chae et al, 2014). This interaction
could not be tested in this study because an appropriate marker was not available.
However there are no evidence of interaction with the closest available marker,
AthGAPAb. The lack of interactions could have several different possible explanations.
It could be caused by a fragment of DM6 near AthZFPG that interacts with DM7, but the
interaction between both loci can’t be recognized with the available markers. It is also
possible that different alleles at the same locus near AthZFPG interact, and that locus
may be related or not with DM6.
However, the most common AthZFPG genotype in healthy individuals (145-151) is also
present in three out of four necrotic individuals, so there may be a completely different
explanation. There is a phenomenon called “transmission ratio distortion”, in which
heterozygous alleles are not transmitted to the progeny in the expected mendelian
proportion of 50%-50%. It can be due to a different chromosomal structure, dysfunction
of gametes carrying specific alleles, or other reasons (Lyttle, 1996) and has been
identified in several species, andA. thaliana (Seymur et al, 2018) and A. lyrata (Lepällä
et al, 2013) are two examples. Moreover, it is supposed to take part in speciation
processes acting as reproductive barrier. Transmission ratio distortion has been reported
in A. lyrata to happen more often in crosses between genetically distant populations, and
especially chromosome 1 appear to be involved in many distortions. (Lepällä et al, 2013),
suggesting that the unequal genotype distribution was caused by a transmission ratio
distortion rather than an immune incompatibility.
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inheritance. If there is a low recombination rate, it supports that the results from ICE9
are caused by DM8 and DM9 incompatibilities rather than DM1, despite being further
away from the marker.
Conclusion
The results from this experiment suggest the hybrid necrosis in A. lyrata to be caused by
the same mechanisms and homologous genes as in A. thaliana, proving the applicability
of the results from the latter species to the former. Despite that the sample size is not
large enough to disentangle the effect of every gene, it proves an effect of at least one
gene in chromosome 7 causing hybrid necrosis, homologous to a gene with a similar
effect in A. thaliana. It also provides some suggestion about where more locus effects can
be found, and will hopefully contribute to the comprehension of the hybrid necrosis
phenomenon and the speciation processes in which it is involved.
Acknowledgments
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Attachments
Nam e ng a28 0 ng a1 0 6 IC E9 AthG AP Ab AthZF P G F 2D22 T 15M6 MS AT 2. 22 0 1_ N0 7 0 1_ G 0 6 EL F 3 Ma 75 75 104 106 123 123 14 5 14 5 17 5 17 5 205 205 221 221 23 2 23 2 29 6 29 6 31 8 31 8 M a P P 74 75 104 106 117 117 123 13 2 14 5 15 1 17 1 17 5 19 8 205 221 221 23 0 23 2 29 6 29 6 31 0 31 8 PP 74 74 106 106 13 2 13 2 15 1 15 1 17 1 17 3 19 8 19 8 221 221 23 0 23 0 29 6 29 6 31 0 31 0 P P M a 74 75 106 106 117 120 123 13 2 15 1 15 3 17 1 17 5 19 8 205 221 223 23 2 23 5 29 6 302 306 321 7 74 75 104 106 117 120 123 13 2 14 5 15 1 17 1 17 5 19 8 19 8 221 221 23 2 23 2 29 6 302 31 8 321 8 74 75 106 106 117 120 123 13 2 15 1 15 1 17 1 17 1 205 205 221 221 23 2 23 5 29 6 29 6 306 31 8 10 74 75 104 106 117 117 123 13 2 14 5 15 1 17 1 17 5 19 8 205 221 221 23 0 23 5 29 6 29 6 31 8 321 11 74 75 104 106 117 120 123 13 2 14 5 15 3 17 1 17 5 19 8 205 221 223 23 0 23 5 29 6 302 306 31 0 14 75 75 106 106 13 2 13 2 14 5 15 1 17 1 17 5 19 8 205 221 223 23 0 23 2 29 6 29 6 31 8 321 16 74 74 104 106 117 120 123 13 2 14 5 15 1 17 1 17 5 19 8 205 221 221 23 0 23 5 29 6 29 6 306 31 0 18 74 75 106 106 117 120 123 13 2 14 5 15 1 17 5 17 5 205 205 221 221 23 0 23 2 29 6 302 31 0 321 20 74 75 106 106 117 120 123 13 2 15 1 15 3 17 1 17 1 19 8 205 221 221 23 0 23 5 29 6 29 6 31 0 321 22 74 74 104 106 117 120 123 13 2 14 5 15 3 17 5 17 5 19 8 205 221 223 23 2 23 2 29 6 29 6 31 8 321 23 74 75 104 106 117 120 123 13 2 14 5 15 1 17 1 17 5 19 8 205 221 223 23 0 23 2 29 6 29 6 31 0 321 26 74 75 106 106 117 120 123 13 2 14 5 15 1 17 1 17 5 19 8 205 221 221 23 2 23 5 29 6 302 306 31 8 27 74 74 104 106 117 120 13 2 13 2 14 5 15 1 17 1 17 5 19 8 19 8 221 221 23 2 23 2 29 6 302 31 8 321 28 74 75 106 106 117 117 123 13 2 15 1 15 1 17 5 17 5 19 8 205 221 223 31 0 321 32 74 75 104 106 117 120 13 2 13 2 14 5 15 1 17 5 17 5 221 223 33 74 75 106 106 117 117 123 123 14 5 15 3 17 5 17 5 19 8 205 221 221 23 2 23 5 29 6 302 306 31 8 34 74 75 104 106 117 117 123 123 14 5 15 1 17 1 17 5 19 8 205 221 223 23 0 23 5 29 6 29 6 306 31 0 35 74 74 104 106 117 120 13 2 13 2 15 1 15 1 17 1 17 5 205 205 221 223 23 2 23 2 29 6 29 6 31 8 321 36 74 75 104 106 117 117 123 123 15 1 15 1 17 1 17 1 205 205 221 223 23 0 23 2 29 6 302 31 8 321 37 74 74 104 106 117 120 123 13 2 14 5 15 3 17 1 17 5 19 8 19 8 221 223 23 2 23 2 29 6 302 306 31 8 39 74 74 104 106 117 117 123 123 15 1 15 1 17 5 17 5 205 205 221 221 23 0 23 2 29 6 29 6 31 8 321 40 106 106 15 1 15 3 17 1 17 1 221 223 42 74 75 104 106 117 117 123 13 2 14 5 15 1 17 1 17 5 19 8 205 221 221 23 0 23 5 29 6 29 6 306 31 0 43 74 75 106 106 117 120 123 13 2 15 1 15 1 17 1 17 1 205 205 221 223 23 0 23 2 29 6 302 31 0 32117
Name Alleles Exp. ratio Nº ind.
Obs. Nº ind. Exp. Obs. ratio χ²
nga280 74/74 0,25 13 11,25 0,289 4,644 74/75 0,5 27 22,5 0,6 75/75 0,25 5 11,25 0,111 nga106 104/106 0,5 23 23 0,5 0 106/106 0,5 23 23 0,5 ICE9 117/117 0,5 13 21 0,31 6,095 (<0.025) 117/120 0,5 29 21 0,69 AthGAPAb 123/123 0,25 5 11,25 0,111 4,644 123/132 0,5 27 22,5 0,6 132/132 0,25 13 11,25 0,289 AthZFPG 145/151 0,25 21 11,5 0,457 13,478 (<0.005) 145/153 0,25 5 11,5 0,109 151/151 0,25 13 11,5 0,283 151/153 0,25 7 11,5 0,152 F2D22 171/171 0,25 13 11,25 0,289 1,311 171/175 0,5 24 22,5 0,533 175/175 0,25 8 11,25 0,178 T15M6 198/198 0,25 5 11 0,114 5,591 198/205 0,5 23 22 0,523 205/205 0,25 16 11 0,364 MSAT2.22 221/221 0,5 23 23 0,5 0 221/223 0,5 23 23 0,5 01_N07 230/232 0,25 13 10,25 0,317 1,439 230/235 0,25 11 10,25 0,268 232/232 0,25 8 10,25 0,195 232/235 0,25 9 10,25 0,22 01_G06 296/296 0,5 19 19 0,5 0 296/302 0,5 19 19 0,5 ELF3 306/310 0,25 11 10,5 0,262 2 306/318 0,25 9 10,5 0,214 310/321 0,25 8 10,5 0,19 318/321 0,25 14 10,5 0,333
nga280 nga106 EXP (rel) EXP (abs) OBS X
74/74 104/106 0,144 6,5 8 1,226 106/106 0,144 6,5 5 74/75 104/106 0,3 13,5 12 106/106 0,3 13,5 15 75/75 104/106 0,056 2,5 3 106/106 0,056 2,5 2
nga280 ICE9 EXP (rel) EXP (abs) OBS X
74/74 117/117 0,089 3,756 3 1,260 117/120 0,199 8,378 10 74/75 117/117 0,186 7,8 9 117/120 0,414 17,4 17 75/75 117/117 0,034 1,444 1 117/120 0,077 3,222 2
Table 6: results from individual locus chi-square tests
18
nga280 AthGAPAb EXP (rel) EXP (abs) OBS χ²
74/74 123/123 0,032 1,444 1 1,182 123/132 0,173 7,8 8 132/132 0,083 3,756 4 74/75 123/123 0,067 3 3 123/132 0,36 16,2 17 132/132 0,173 7,8 7 75/75 123/123 0,012 0,556 1 123/132 0,067 3 2 132/132 0,032 1,444 2
nga280 AthZFPG EXP (rel) EXP (abs) OBS χ²
74/74 145/151 0,132 5,935 6 2,765 145/153 0,031 1,413 2 151/151 0,082 3,674 4 151/153 0,044 1,978 1 74/75 145/151 0,274 12,33 12 145/153 0,065 2,935 2 151/151 0,17 7,630 8 151/153 0,091 4,109 5 75/75 145/151 0,051 2,283 3 145/153 0,012 0,543 1 151/151 0,031 1,413 1 151/153 0,017 0,761 0
nga280 F2D22 EXP (rel) EXP (abs) OBS χ²
74/74 171/171 0,083 3,672 3 0,693 171/175 0,154 6,779 8 175/175 0,051 2,260 2 74/75 171/171 0,173 7,627 8 171/175 0,320 14,080 13 175/175 0,107 4,693 5 75/75 171/171 0,032 1,412 1 171/175 0,059 2,607 3 175/175 0,020 0,869 1
19
nga280 T15M6 EXP (rel) EXP (abs) OBS χ²
74/74 198/198 0,033 1,444 2 2,486 198/205 0,151 6,644 5 205/205 0,105 4,622 6 74/75 198/198 0,068 3,000 2 198/205 0,314 13,800 16 205/205 0,218 9,600 8 75/75 198/198 0,013 0,556 1 198/205 0,058 2,556 2 205/205 0,040 1,778 2
nga280 MSAT2.22 EXP (rel) EXP (abs) OBS χ²
74/74 221/221 0,144 6,5 7 0,314 221/223 0,144 6,5 6 74/75 221/221 0,3 13,5 14 221/223 0,3 13,5 13 75/75 221/221 0,056 2,5 2 221/223 0,056 2,5 3
nga280 01_N07 EXP (rel) EXP (abs) OBS χ²
74/74 230/232 0,092 3,756 2 12,598 230/235 0,078 3,178 3 232/232 0,056 2,311 6 232/235 0,063 2,6 2 74/75 230/232 0,190 7,8 8 230/235 0,161 6,6 7 232/232 0,117 4,8 2 232/235 0,132 5,4 7 75/75 230/232 0,035 1,444 3 230/235 0,030 1,222 1 232/232 0,022 0,889 0 232/235 0,024 1 0
nga280 01_G06 EXP (rel) EXP (abs) OBS χ²
74/74 296/296 0,144 5,489 8 2,513 296/302 0,144 5,489 5 74/75 296/296 0,3 11,4 9 296/302 0,3 11,4 13 75/75 296/296 0,056 2,111 2 296/302 0,056 2,111 1
20
nga280 ELF3 EXP (rel) EXP (abs) OBS χ²
74/74 306/310 0,076 3,178 2 7,480 306/318 0,062 2,6 2 310/321 0,055 2,311 1 318/321 0,096 4,044 8 74/75 306/310 0,157 6,6 8 306/318 0,129 5,4 6 310/321 0,114 4,8 6 318/321 0,2 8,4 5 75/75 306/310 0,029 1,222 1 306/318 0,024 1 1 310/321 0,021 0,889 1 318/321 0,037 1,556 1
nga106 ICE9 EXP EXP (rel) EXP (abs) OBS χ²
104/106 117/117 0,310 0,155 6,5 8 0,727
117/120 0,690 0,345 14,5 14
106/106 117/117 0,310 0,155 6,5 5
117/120 0,690 0,345 14,5 15
nga106 AthGAPAb EXP (rel) EXP (abs) OBS χ²
104/106 123/123 0,056 2,5 4 1,914 123/132 0,3 13,5 13 132/132 0,144 6,5 6 106/106 123/123 0,056 2,5 1 123/132 0,3 13,5 14 132/132 0,144 6,5 7
nga106 AthZFPG EXP (rel) EXP (abs) OBS χ²
104/106 145/151 0,228 10,5 12 5,877 145/153 0,054 2,5 4 151/151 0,141 6,5 6 151/153 0,076 3,5 1 106/106 145/151 0,228 10,5 9 145/153 0,054 2,5 1 151/151 0,141 6,5 7 151/153 0,076 3,5 6
21
nga106 F2D22 EXP (rel) EXP (abs) OBS χ²
104/106 171/171 0,144 6,5 3 5,269 171/175 0,267 12 15 175/175 0,089 4 4 106/106 171/171 0,144 6,5 10 171/175 0,267 12 9 175/175 0,089 4 4
nga106 T15M6 EXP (rel) EXP (abs) OBS χ²
104/106 198/198 0,057 2,5 4 2,843 198/205 0,261 11,5 12 205/205 0,182 8 6 106/106 198/198 0,057 2,5 1 198/205 0,261 11,5 11 205/205 0,182 8 10
nga106 MSAT2.22 EXP (rel) EXP (abs) OBS χ²
104/106 221/221 0,25 11,5 11 0,087
221/223 0,25 11,5 12
106/106 221/221 0,25 11,5 12
221/223 0,25 11,5 11
nga106 01_N07 EXP (rel) EXP (abs) OBS χ²
104/106 230/232 0,159 6,5 5 7,743 230/235 0,134 5,5 8 232/232 0,098 4 6 232/235 0,110 4,5 2 106/106 230/232 0,159 6,5 8 230/235 0,134 5,5 3 232/232 0,098 4 2 232/235 0,110 4,5 7
nga106 01_G06 EXP (rel) EXP (abs) OBS χ²
104/106 296/296 0,25 9,5 10 0,526
296/302 0,25 9,5 11
106/106 296/296 0,25 9,5 9
296/302 0,25 9,5 8
22
nga106 ELF3 EXP (rel) EXP (abs) OBS χ²
104/106 306/310 0,131 5,5 7 4,104 306/318 0,107 4,5 3 310/321 0,095 4 2 318/321 0,167 7 8 106/106 306/310 0,131 5,5 4 306/318 0,107 4,5 6 310/321 0,095 4 6 318/321 0,167 7 6
ICE9 AthGAPAb EXP (rel) EXP (abs) OBS χ²
117/117 123/123 0,034 1,444 4 6,815 123/132 0,186 7,8 6 132/132 0,089 3,756 3 117/120 123/123 0,077 3,222 1 123/132 0,414 17,4 19 132/132 0,199 8,378 9
ICE9 AthZFPG EXP (rel) EXP (abs) OBS χ²
117/117 145/151 0,141 5,935 6 4,057 145/153 0,034 1,413 1 151/151 0,087 3,674 6 151/153 0,047 1,978 0 117/120 145/151 0,315 13,239 13 145/153 0,075 3,152 4 151/151 0,195 8,196 7 151/153 0,105 4,413 5
ICE9 F2D22 EXP (rel) EXP (abs) OBS χ²
117/117 171/171 0,089 3,666 3 1,851 171/175 0,165 6,768 6 175/175 0,055 2,256 4 117/120 171/171 0,199 8,178 9 171/175 0,368 15,098 15 175/175 0,123 5,033 4
23
ICE9 T15M6 EXP (rel) EXP (abs) OBS χ²
117/117 198/198 0,035 1,442 0 2,971 198/205 0,162 6,634 8 205/205 0,113 4,615 5 117/120 198/198 0,078 3,217 5 198/205 0,361 14,798 13 205/205 0,251 10,294 10
ICE9 MSAT2.22 EXP (rel) EXP (abs) OBS χ²
117/117 221/221 0,155 6,5 8 0,727
221/223 0,155 6,5 5
117/120 221/221 0,345 14,5 14
221/223 0,345 14,5 15
ICE9 01_N07 EXP (rel) EXP (abs) OBS χ²
117/117 230/232 0,098 3,828 3 6,891 230/235 0,083 3,239 4 232/232 0,060 2,355 0 232/235 0,068 2,650 5 117/120 230/232 0,219 8,538 8 230/235 0,185 7,225 7 232/232 0,135 5,254 8 232/235 0,152 5,911 4
ICE9 01_G06 EXP (rel) EXP (abs) OBS χ²
117/117 296/296 0,155 5,571 5 0,331
296/302 0,155 5,571 5
117/120 296/296 0,345 12,429 12
296/302 0,345 12,429 14
ICE9 ELF3 EXP (rel) EXP (abs) OBS χ²
117/117 306/310 0,081 3,162 6 4,574 306/318 0,066 2,587 3 310/321 0,059 2,299 1 318/321 0,103 4,024 3 117/120 306/310 0,181 7,053 5 306/318 0,148 5,770 5 310/321 0,132 5,129 6 318/321 0,230 8,976 10
24
AthGAPAb AthZFPG EXP (rel) EXP (abs) OBS χ²
123/123 145/151 0,051 2,283 1 8,102 145/153 0,012 0,543 2 151/151 0,031 1,413 2 151/153 0,017 0,761 0 123/132 145/151 0,274 12,326 14 145/153 0,065 2,935 3 151/151 0,170 7,630 6 151/153 0,091 4,109 4 132/132 145/151 0,132 5,935 6 145/153 0,031 1,413 0 151/151 0,082 3,674 5 151/153 0,044 1,978 2
AthGAPAb F2D22 EXP (rel) EXP (abs) OBS χ²
123/123 171/171 0,032 1,412 1 7,490 171/175 0,059 2,607 1 175/175 0,020 0,869 3 123/132 171/171 0,173 7,627 7 171/175 0,320 14,080 16 175/175 0,107 4,693 4 132/132 171/171 0,083 3,672 4 171/175 0,154 6,779 7 175/175 0,051 2,260 1
AthGAPAb T15M6 EXP (rel) EXP (abs) OBS χ²
123/123 198/198 0,013 0,556 0 1,454 198/205 0,058 2,556 3 205/205 0,040 1,778 2 123/132 198/198 0,068 3 3 198/205 0,314 13,8 15 205/205 0,218 9,6 9 132/132 198/198 0,033 1,444 2 198/205 0,151 6,644 5 205/205 0,105 4,622 5
25
AthGAPAb MSAT2.22 EXP (rel) EXP (abs) OBS χ²
123/123 221/221 0,056 2,5 3 3,049 221/223 0,056 2,5 2 123/132 221/221 0,3 13,5 16 221/223 0,3 13,5 11 132/132 221/221 0,144 6,5 4 221/223 0,144 6,5 9
AthGAPAb 01_N07 EXP (rel) EXP (abs) OBS χ²
123/123 230/232 0,035 1,444 2 4,641 230/235 0,030 1,222 1 232/232 0,022 0,889 0 232/235 0,024 1 1 123/132 230/232 0,190 7,8 6 230/235 0,161 6,6 9 232/232 0,117 4,8 5 232/235 0,132 5,4 5 132/132 230/232 0,092 3,756 5 230/235 0,078 3,178 1 232/232 0,056 2,311 3 232/235 0,063 2,6 3
AthGAPAb 01_G06 EXP (rel) EXP (abs) OBS χ²
123/123 296/296 0,056 2,111 2 0,702 296/302 0,056 2,111 2 123/132 296/296 0,3 11,4 11 296/302 0,3 11,4 13 132/132 296/296 0,144 5,489 6 296/302 0,144 5,489 4
AthGAPAb ELF3 EXP (rel) EXP (abs) OBS χ²
123/123 306/310 0,029 1,222 1 3,507 306/318 0,024 1 1 310/321 0,021 0,889 0 318/321 0,037 1,556 2 123/132 306/310 0,157 6,6 7 306/318 0,129 5,4 6 310/321 0,114 4,8 7 318/321 0,200 8,4 7 132/132 306/310 0,076 3,178 3 306/318 0,062 2,6 2 310/321 0,055 2,311 1 318/321 0,096 4,044 5
26
AthZFPG F2D22 EXP (rel) EXP (abs) OBS χ²
145/151 171/171 0,132 5,935 0 32,509 (<0.001) 171/175 0,243 10,957 18 175/175 0,081 3,652 3 145/153 171/171 0,031 1,413 0 171/175 0,058 2,609 2 175/175 0,019 0,870 3 151/151 171/171 0,082 3,674 9 171/175 0,151 6,783 2 175/175 0,050 2,261 2 151/153 171/171 0,044 1,978 4 171/175 0,081 3,652 2 175/175 0,027 1,217 0
AthZFPG T15M6 EXP (rel) EXP (abs) OBS χ²
145/151 198/198 0,052 2,283 2 7,032 198/205 0,239 10,5 12 205/205 0,166 7,304 6 145/153 198/198 0,012 0,543 1 198/205 0,057 2,5 4 205/205 0,040 1,739 0 151/151 198/198 0,032 1,413 2 198/205 0,148 6,5 4 205/205 0,103 4,522 7 151/153 198/198 0,017 0,761 0 198/205 0,080 3,5 3 205/205 0,055 2,435 3
AthZFPG MSAT2.22 EXP (rel) EXP (abs) OBS χ²
145/151 221/221 0,228 10,5 13 2,226 221/223 0,228 10,5 8 145/153 221/221 0,054 2,5 2 221/223 0,054 2,5 3 151/151 221/221 0,141 6,5 5 221/223 0,141 6,5 8 151/153 221/221 0,076 3,5 3 221/223 0,076 3,5 4
27
AthZFPG 01_N07 EXP (rel) EXP (abs) OBS χ²
145/151 230/232 0,145 5,935 7 6,042 230/235 0,122 5,022 6 232/232 0,089 3,652 3 232/235 0,100 4,109 4 145/153 230/232 0,034 1,413 0 230/235 0,029 1,196 1 232/232 0,021 0,870 2 232/235 0,024 0,978 1 151/151 230/232 0,090 3,674 5 230/235 0,076 3,109 3 232/232 0,055 2,261 1 232/235 0,062 2,543 3 151/153 230/232 0,048 1,978 1 230/235 0,041 1,674 1 232/232 0,030 1,217 2 232/235 0,033 1,370 1
AthZFPG 01_G06 EXP (rel) EXP (abs) OBS χ²
145/151 296/296 0,228 8,674 11 3,043 296/302 0,228 8,674 7 145/153 296/296 0,054 2,065 1 296/302 0,054 2,065 3 151/151 296/296 0,141 5,370 4 296/302 0,141 5,370 7 151/153 296/296 0,076 2,891 3 296/302 0,076 2,891 2
AthZFPG ELF3 EXP (rel) EXP (abs) OBS χ²
145/151 306/310 0,120 5,022 6 6,680 306/318 0,098 4,109 2 310/321 0,087 3,652 4 318/321 0,152 6,391 8 145/153 306/310 0,028 1,196 1 306/318 0,023 0,978 2 310/321 0,021 0,870 0 318/321 0,036 1,522 1 151/151 306/310 0,074 3,109 4 306/318 0,061 2,543 3 310/321 0,054 2,261 3 318/321 0,094 3,957 3 151/153 306/310 0,040 1,674 0 306/318 0,033 1,370 2 310/321 0,029 1,217 1 318/321 0,051 2,130 2
28
F2D22 T15M6 EXP (rel) EXP (abs) OBS χ²
171/171 198/198 0,033 1,412 2 3,188 198/205 0,151 6,493 4 205/205 0,105 4,517 6 171/175 198/198 0,061 2,606 3 198/205 0,279 11,988 13 205/205 0,194 8,339 8 175/175 198/198 0,020 0,869 0 198/205 0,093 3,996 5 205/205 0,065 2,780 2
F2D22 MSAT2.22 EXP (rel) EXP (abs) OBS χ²
171/171 221/221 0,144 6,5 5 1,359 221/223 0,144 6,5 8 171/175 221/221 0,267 12 13 221/223 0,267 12 11 175/175 221/221 0,089 4 5 221/223 0,089 4 3
F2D22 01_N07 EXP (rel) EXP (abs) OBS χ²
171/171 230/232 0,092 3,664 4 4,525 230/235 0,078 3,100 4 232/232 0,056 2,255 1 232/235 0,063 2,537 3 171/175 230/232 0,169 6,764 6 230/235 0,143 5,724 7 232/232 0,104 4,163 6 232/235 0,117 4,683 4 175/175 230/232 0,056 2,255 2 230/235 0,048 1,908 0 232/232 0,035 1,388 1 232/235 0,039 1,561 2
F2D22 01_G06 EXP (rel) EXP (abs) OBS χ²
171/171 296/296 0,144 5,344 4 2,932 296/302 0,144 5,344 7 171/175 296/296 0,267 9,867 13 296/302 0,267 9,867 9 175/175 296/296 0,089 3,289 2 296/302 0,089 3,289 2
29
F2D22 ELF3 EXP (rel) EXP (abs) OBS χ²
171/171 306/310 0,076 3,178 3 4,613 306/318 0,062 2,6 4 310/321 0,055 2,311 3 318/321 0,096 4,044 2 171/175 306/310 0,140 5,867 7 306/318 0,114 4,8 4 310/321 0,102 4,267 3 318/321 0,178 7,467 10 175/175 306/310 0,047 1,956 1 306/318 0,038 1,6 1 310/321 0,034 1,422 2 318/321 0,059 2,489 2
T15M6 MSAT2.22 EXP (rel) EXP (abs) OBS χ²
198/198 221/221 0,057 2,5 3 0,493 221/223 0,057 2,5 2 198/205 221/221 0,261 11,5 11 221/223 0,261 11,5 12 205/205 221/221 0,182 8 9 221/223 0,182 8 7
T15M6 01_N07 EXP (rel) EXP (abs) OBS χ²
198/198 230/232 0,036 1,477 0 11,538 230/235 0,030 1,25 2 232/232 0,022 0,909 3 232/235 0,025 1,023 0 198/205 230/232 0,166 6,795 7 230/235 0,140 5,75 7 232/232 0,102 4,182 2 232/235 0,115 4,705 4 205/205 230/232 0,115 4,727 6 230/235 0,098 4 2 232/232 0,071 2,909 3 232/235 0,080 3,273 5
T15M6 01_G06 EXP (rel) EXP (abs) OBS χ²
198/198 296/296 0,057 2,159 0 7,051 296/302 0,057 2,159 5 198/205 296/296 0,261 9,932 11 296/302 0,261 9,932 7 205/205 296/296 0,182 6,909 8 296/302 0,182 6,909 7
30
T15M6 ELF3 EXP (rel) EXP (abs) OBS χ²
198/198 306/310 0,030 1,25 1 3,465 306/318 0,024 1,023 2 310/321 0,022 0,909 0 318/321 0,038 1,591 2 198/205 306/310 0,137 5,75 7 306/318 0,112 4,705 4 310/321 0,100 4,182 4 318/321 0,174 7,318 6 205/205 306/310 0,095 4 3 306/318 0,078 3,273 3 310/321 0,069 2,909 4 318/321 0,121 5,091 6
MSAT2.22 01_N07 EXP (rel) EXP (abs) OBS χ²
221/221 230/232 0,159 6,5 3 15,587 (<0.05) 230/235 0,134 5,5 7 232/232 0,098 4 2 232/235 0,110 4,5 9 221/223 230/232 0,159 6,5 10 230/235 0,134 5,5 4 232/232 0,098 4 6 232/235 0,110 4,5 0
MSAT2.22 01_G06 EXP (rel) EXP (abs) OBS χ²
221/221 296/296 0,25 9,5 10 0,105
296/302 0,25 9,5 10
221/223 296/296 0,25 9,5 9
296/302 0,25 9,5 9
MSAT2.22 ELF3 EXP (rel) EXP (abs) OBS χ²
221/221 306/310 0,131 5,5 5 6,321 306/318 0,107 4,5 8 310/321 0,095 4 3 318/321 0,167 7 6 221/223 306/310 0,131 5,5 6 306/318 0,107 4,5 1 310/321 0,095 4 5 318/321 0,167 7 8
31
Table 59, 60 and 61: results from two loci pair comparisons, between 01_N07 and 01_G06 (59), 01_N07 and ELF3 (60), and 01_G06 and ELF3 (61).
01_N07 01_G06 EXP (rel) EXP (abs) OBS χ²
230/232 296/296 0,159 6,024 6 0,876 296/302 0,159 6,024 5 230/235 296/296 0,134 5,098 6 296/302 0,134 5,098 5 232/232 296/296 0,098 3,707 4 296/302 0,098 3,707 4 232/235 296/296 0,110 4,171 3 296/302 0,110 4,171 5
01_N07 ELF3 EXP (rel) EXP (abs) OBS χ²
230/232 306/310 0,083 3,322 2 38,218 (<0.001) 306/318 0,068 2,718 0 310/321 0,060 2,416 5 318/321 0,106 4,228 5 230/235 306/310 0,070 2,811 7 306/318 0,057 2,230 1 310/321 0,051 2,044 2 318/321 0,089 3,577 1 232/232 306/310 0,051 2,044 0 306/318 0,042 1,672 1 310/321 0,037 1,487 0 318/321 0,065 2,602 7 232/235 306/310 0,057 2,300 2 306/318 0,047 1,882 6 310/321 0,042 1,672 0 318/321 0,073 2,927 1
01_G06 ELF3 EXP (rel) EXP (abs) OBS χ²
32
nga280/nga106 EXP OBS χ² 74/104 Present 20 20 0 Absent 25 25 74/106 Present 40 40 0 Absent 5 5 75/104 Present 16 15 0,097 Absent 29 30 75/106 Present 32 32 2,43E-31 Absent 13 13
nga280/ICE9 EXP OBS χ² 74/117 Present 37,333 39 0,670 Absent 4,667 3 74/120 Present 25,778 27 0,150 Absent 16,222 15 75/117 Present 29,867 29 0,087 Absent 12,133 13 75/120 Present 20,622 19 0,251 Absent 21,378 23
nga280/AthGAPAb EXP OBS χ² 74/123 Present 28,444 29 0,029 Absent 16,556 16 74/132 Present 35,556 36 0,026 Absent 9,444 9 75/123 Present 22,756 23 0,005 Absent 22,244 22 75/132 Present 28,444 28 0,019 Absent 16,556 17
nga280/AthZFPG EXP OBS χ² 74/145 Present 22,609 22 0,033 Absent 22,391 23 74/151 Present 35,652 36 0,016 Absent 9,348 9 74/153 Present 10,435 10 0,024 Absent 34,565 35 75/145 Present 18,087 18 0,001 Absent 26,913 27 75/151 Present 28,522 29 0,022 Absent 16,478 16 75/153 Present 8,348 8 0,018 Absent 36,652 37
nga280/F2D22 EXP OBS χ² 74/171 Present 32,158 32 0,003 Absent 11,842 12 74/175 Present 27,812 28 0,003 Absent 16,188 16 75/171 Present 25,726 25 0,049 Absent 18,274 19 75/175 Present 22,250 22 0,006 Absent 21,750 22
nga280/MSAT2.22 EXP OBS X 74/221 Present 40 40 0 Absent 5 5 74/223 Present 20 19 0,09 Absent 25 26 75/221 Present 32 32 2,427E-31 Absent 13 13 75/223 Present 16 16 0 Absent 29 29
Tables 62, 63, 64, 65, 66, 67 and 68. Chi-square results from individual allele pairs comparisons, between nga280 and nga106 (62), nga280 and ICE9 (63), nga280 and AthGAPAb (64), nga280 and AthZFPG (65), nga280 and F2D22 (66), nga280 and T15M6 (67), and nga280 and MSAT2.22 (68).
33
nga280/ELF3 EXP OBS χ²
74/306 Present 17,778 18 0,005 Absent 24,222 24 74/310 Present 16,889 17 0,001 Absent 25,111 25 74/318 Present 20,444 21 0,029 Absent 21,556 21 74/321 Present 19,556 20 0,019 Absent 22,444 22 75/306 Present 14,222 16 0,336 Absent 27,778 26 75/310 Present 13,511 16 0,676 Absent 28,489 26 75/318 Present 16,356 13 1,128 Absent 25,644 29 75/321 Present 15,644 13 0,712 Absent 26,356 29
nga280/01_G06 EXP OBS χ² 74/296 Present 33,778 35 0,398 Absent 4,222 3 74/302 Present 16,889 18 0,132 Absent 21,111 20 75/296 Present 27,022 25 0,524 Absent 10,978 13 75/302 Present 13,511 14 0,027 Absent 24,489 24
nga106/ICE9 EXP OBS χ²
104/117 Present 21 22 0,095 Absent 21 20 104/120 Present 14,5 14 0,026 Absent 27,5 28 106/117 Present 42 42 0 Absent 0 0 106/120 Present 29 29 0 Absent 13 13
nga106/AthGAPAb EXP OBS χ² 104/123 Present 16 17 0,097 Absent 29 28 104/132 Present 20 19 0,09 Absent 25 26 106/123 Present 32 32 2,427E-31 Absent 13 13 106/132 Present 40 40 0 Absent 5 5
Tables 69, 70, 71, 72, 73 and 74. Chi-square results from individual allele pairs comparisons, between nga280 and 01_N07 (69), nga280 and 01_G06 (70), nga280 and ELF3 (71), nga106 and ICE9 (72), nga106 and AthGAPAb (73), and nga106 and AthZFPG (74).
nga106/AthZFPG EXP OBS χ² 104/145 Present 13 16 0,965 Absent 33 30 104/151 Present 20,5 19 0,198 Absent 25,5 27 104/153 Present 6 5 0,192 Absent 40 41 106/145 Present 26 26 0 Absent 20 20 106/151 Present 41 41 0 Absent 5 5 106/153 Present 12 12 0 Absent 34 34
34
nga106/ELF3 EXP OBS χ²
104/306 Present 10 10 0 Absent 32 32 104/310 Present 9,5 9 0,034 Absent 32,5 33 104/318 Present 11,5 11 0,030 Absent 30,5 31 104/321 Present 11 10 0,123 Absent 31 32 106/306 Present 20 20 0 Absent 22 22 106/310 Present 19 19 0 Absent 23 23 106/318 Present 23 23 0 Absent 19 19 106/321 Present 22 22 0 Absent 20 20
nga106/T15M6 EXP OBS χ² 104/198 Present 14 16 0,419 Absent 30 28 104/205 Present 19,5 18 0,207 Absent 24,5 26 106/198 Present 28 28 0 Absent 16 16 106/205 Present 39 39 0 Absent 5 5
nga106/F2D22 EXP OBS χ² 104/171 Present 18,5 18 0,023 Absent 26,5 27 104/175 Present 16 19 0,873 Absent 29 26 106/171 Present 37 37 0 Absent 8 8 106/175 Present 32 32 2,427E-31 Absent 13 13
nga106/01_N07 EXP OBS χ² 104/230 Present 12 13 0,118 Absent 29 28 104/232 Present 15 13 0,421 Absent 26 28 104/235 Present 10 10 0 Absent 31 31 106/230 Present 24 24 0 Absent 17 17 106/232 Present 30 30 0 Absent 11 11 106/235 Present 20 20 0 Absent 21 21
nga106/MSAT2.22 EXP OBS χ² 104/296 Present 23 23 0 Absent 23 23 104/302 Present 11,5 12 0,029 Absent 34,5 34 106/296 Present 46 46 0 Absent 0 0 106/302 Present 23 23 0 Absent 23 23
Tables 75, 76, 77, 78, 79 and 80. Chi-square results from individual allele pairs comparisons, between nga106 and F2D22 (75), nga106 and T15M6 (76), nga106 and MSAT2.22 (77), nga106 and 01_N07 (78), nga106 and 01_G06 (79), and nga106 and ELF3 (80).
35
Tables 81.82, 83, 84, 85, 86 and 87. Chi-square results from individual allele pairs comparisons, between ICE9 and AthGAPAb (81), ICE9 and AthZFPG (82), ICE9 and F2D22 (83), ICE9 and T15M6 (84), ICE9 and MSAT2.22 (85), ICE9 and 01_N07 (86), and ICE9 and 01_G06 (87).
ICE9/AthGAPAb EXP OBS χ² 117/123 Present 29,867 30 0,002 Absent 12,133 12 117/132 Present 37,333 37 0,027 Absent 4,667 5 120/123 Present 20,622 20 0,037 Absent 21,378 22 120/132 Present 25,778 28 0,496 Absent 16,222 14
ICE9/AthZFPG EXP OBS χ²
117/145 Present 23,739 24 0,007 Absent 18,261 18 117/151 Present 37,435 37 0,046 Absent 4,565 5 117/153 Present 10,957 10 0,113 Absent 31,043 32 120/145 Present 16,391 17 0,037 Absent 25,609 25 120/151 Present 25,848 25 0,072 Absent 16,152 17 120/153 Present 7,565 9 0,332 Absent 34,435 33
ICE9/F2D22 EXP OBS χ²
117/171 Present 33,711 33 0,084 Absent 7,289 8 117/175 Present 29,156 29 0,003 Absent 11,844 12 120/171 Present 23,277 24 0,052 Absent 17,723 17 120/175 Present 20,131 19 0,125 Absent 20,869 22
ICE9/T15M6 EXP OBS χ²
117/198 Present 26,091 26 0,001 Absent 14,909 15 117/205 Present 36,341 36 0,028 Absent 4,659 5 120/198 Present 18,015 18 0,000 Absent 22,985 23 120/205 Present 25,093 23 0,450 Absent 15,907 18
ICE9/MSAT2.22 EXP OBS χ² 117/221 Present 42 42 0 Absent 0 0 117/223 Present 21 20 0,095 Absent 21 22 120/221 Present 29 29 0 Absent 13 13 120/223 Present 14,5 15 0,026 Absent 27,5 27
ICE9/01_N07 EXP OBS χ²
117/230 Present 22,829 22 0,073 Absent 16,171 17 117/232 Present 28,537 28 0,038 Absent 10,463 11 117/235 Present 19,024 20 0,098 Absent 19,976 19 120/230 Present 15,763 15 0,062 Absent 23,237 24 120/232 Present 19,704 20 0,009 Absent 19,296 19 120/235 Present 13,136 11 0,524 Absent 25,864 28
ICE9/01_G06 EXP OBS χ²
36
Tables 88, 89, 90, 91, 92 and 93. Chi-square results from individual allele pairs comparisons, between ICE9 and ELF3 (88), AthGAPAb and AthZFPG (89), AthGAPAb and F2D22 (90), AthGAPAb and T15M6 (91), AthGAPAb and MSAT2.22 (92) and AthGAPAb and 01_N07 (93).
ICE9/ELF3 EXP OBS χ²
117/306 Present 18,571 19 0,019 Absent 20,429 20 117/310 Present 17,643 18 0,013 Absent 21,357 21 117/318 Present 21,357 21 0,013 Absent 17,643 18 117/321 Present 20,429 20 0,019 Absent 18,571 19 120/306 Present 12,823 10 0,926 Absent 26,177 29 120/310 Present 12,182 11 0,167 Absent 26,818 28 120/318 Present 14,747 15 0,007 Absent 24,253 24 120/321 Present 14,105 16 0,399 Absent 24,895 23
AthGAPAb/AthZFPG EXP OBS χ² 123/145 Present 18,087 20 0,338 Absent 26,913 25 123/151 Present 28,522 27 0,222 Absent 16,478 18 123/153 Present 8,348 9 0,063 Absent 36,652 36 132/145 Present 22,609 23 0,014 Absent 22,391 22 132/151 Present 35,652 37 0,245 Absent 9,348 8 132/153 Present 10,435 9 0,257 Absent 34,565 36
AthGAPAb/F2D22 EXP OBS χ² 123/171 Present 25,726 25 0,049 Absent 18,274 19 123/175 Present 22,250 24 0,278 Absent 21,750 20 132/171 Present 32,158 34 0,392 Absent 11,842 10 132/175 Present 27,812 28 0,003 Absent 16,188 16
AthGAPAb/T15M6 EXP OBS χ² 123/198 Present 19,911 21 0,109 Absent 24,089 23 123/205 Present 27,733 29 0,156 Absent 16,267 15 132/198 Present 24,889 25 0,001 Absent 19,111 19 132/205 Present 34,667 34 0,060 Absent 9,333 10
AthGAPAb/MSAT2.22 EXP OBS χ² 123/221 Present 32 32 2,427E-31 Absent 13 13 123/223 Present 16 13 0,873 Absent 29 32 132/221 Present 40 40 0 Absent 5 5 132/223 Present 20 20 0 Absent 25 25
37
AthGAPAb/01_G06 EXP OBS χ² 123/296 Present 27,022 28 0,122 Absent 10,978 10 123/302 Present 13,511 15 0,255 Absent 24,489 23 132/296 Present 33,778 34 0,013 Absent 4,222 4 132/302 Present 16,889 17 0,001 Absent 21,111 21
Tables 94, 95, 96, 97 and 98. Chi-square results from individual allele pairs comparisons, between AthGAPAb and 01_G06 (94), AthGAPAb and ELF3 (95), AthZFPG and F2D22 (96), AthZFPG and T15M6 (97), and AthZFPG and MSAT2.22 (98).
AthGAPAb/ELF3 EXP OBS χ² 123/306 Present 14,222 15 0,064 Absent 27,778 27 123/310 Present 13,511 15 0,242 Absent 28,489 27 123/318 Present 16,356 16 0,013 Absent 25,644 26 123/321 Present 15,644 16 0,013 Absent 26,356 26 132/306 Present 17,778 18 0,005 Absent 24,222 24 132/310 Present 16,889 18 0,122 Absent 25,111 24 132/318 Present 20,444 20 0,019 Absent 21,556 22 132/321 Present 19,556 20 0,019 Absent 22,444 22
AthZFPG/F2D22 EXP OBS χ² 145/171 Present 20,913 20 0,074 Absent 24,087 25 145/175 Present 18,087 26 5,789 (<0.025) Absent 26,913 19 151/171 Present 32,978 35 0,464 Absent 12,022 10 151/175 Present 28,522 27 0,222 Absent 16,478 18 153/171 Present 9,652 8 0,360 Absent 35,348 37 153/175 Present 8,348 7 0,267 Absent 36,652 38
AthZFPG/T15M6 EXP OBS χ² 145/198 Present 15,826 19 0,994 Absent 28,174 25 145/205 Present 22,043 22 0,000 Absent 21,957 22 151/198 Present 24,957 23 0,354 Absent 19,043 21 151/205 Present 34,761 35 0,008 Absent 9,239 9 153/198 Present 7,304 8 0,079 Absent 36,696 36 153/205 Present 10,174 10 0,004 Absent 33,826 34
38
F2D22/T15M6 EXP OBS χ² 171/198 Present 22,499 22 0,023 Absent 20,501 21 171/205 Present 31,338 31 0,013 Absent 11,662 12 175/198 Present 19,459 21 0,223 Absent 23,541 22 175/205 Present 27,103 28 0,080 Absent 15,897 15F2D22/MSAT2.22 EXP OBS χ² 171/221 Present 37 37 0 Absent 8 8 171/223 Present 18,5 19 0,023 Absent 26,5 26 175/221 Present 32 32 2,427E-31 Absent 13 13 175/223 Present 16 14 0,388 Absent 29 31
Tables 99, 100, 101, 102 and 103. Chi-square results from individual allele pairs comparisons, between AthZFPG and 01_N07 (99), AthZFPG and 01_G06 (100), AthZFPG and ELF3 (101), F2D22 and T15M6 (102) and F2D22 and MSAT2.22 (103)
AthZFPG/01_N07 EXP OBS χ² 145/230 Present 13,565 14 0,021 Absent 27,435 27 145/232 Present 16,957 17 0,000 Absent 24,043 24 145/235 Present 11,304 12 0,059 Absent 29,696 29 151/230 Present 21,391 23 0,253 Absent 19,609 18 151/232 Present 26,739 27 0,007 Absent 14,261 14 151/235 Present 17,826 18 0,003 Absent 23,174 23 153/230 Present 6,261 3 2,004 Absent 34,739 38 153/232 Present 7,826 7 0,108 Absent 33,174 34 153/235 Present 5,217 4 0,325 Absent 35,783 37
AthZFPG/01_G06 EXP OBS χ² 145/296 Present 21,478 22 0,029 Absent 16,522 16 145/302 Present 10,739 10 0,071 Absent 27,261 28 151/296 Present 33,870 34 0,005 Absent 4,130 4 151/302 Present 16,935 16 0,093 Absent 21,065 22 153/296 Present 9,913 9 0,114 Absent 28,087 29 153/302 Present 4,957 5 0,000 Absent 33,043 33
AthZFPG/ELF3 EXP OBS χ²
39
F2D22/01_N07 EXP OBS χ² 171/230 Present 19,252 21 0,306 Absent 20,748 19 171/232 Present 24,065 24 0,000 Absent 15,935 16 171/235 Present 16,043 18 0,398 Absent 23,957 22 175/230 Present 16,650 15 0,280 Absent 23,350 25 175/232 Present 20,813 21 0,004 Absent 19,187 19 175/235 Present 13,875 13 0,085 Absent 26,125 27Tables 104, 105, 106, 107, 108 and 109. Chi-square results from individual allele pairs comparisons, between F2D22 and 01_N07 (104), F2D22 and 01_G06 (105), F2D22 and ELF3 (106), T15M6 and MSAT2.22 (107), T15M6 and 01_N07 (108) and T15M6 and 01_G06 (109)
F2D22/01_G06 EXP OBS χ² 171/296 Present 30,422 33 1,229 Absent 6,578 4 171/302 Present 15,211 16 0,069 Absent 21,789 21 175/296 Present 26,311 26 0,013 Absent 10,689 11 175/302 Present 13,156 11 0,548 Absent 23,844 26
F2D22/ELF3 EXP OBS χ²
171/306 Present 16,444 18 0,242 Absent 25,556 24 171/310 Present 15,622 16 0,015 Absent 26,378 26 171/318 Present 18,911 20 0,114 Absent 23,089 22 171/321 Present 18,089 18 0,001 Absent 23,911 24 175/306 Present 14,222 13 0,159 Absent 27,778 29 175/310 Present 13,511 13 0,029 Absent 28,489 29 175/318 Present 16,356 17 0,042 Absent 25,644 25 175/321 Present 15,644 17 0,187 Absent 26,356 25 T15M6/01_N07 EXP OBS χ² 198/230 Present 15,273 16 0,055 Absent 25,727 25 198/232 Present 19,091 16 0,936 Absent 21,909 25 198/235 Present 12,727 13 0,008 Absent 28,273 28 205/230 Present 21,273 22 0,052 Absent 19,727 19 205/232 Present 26,591 27 0,018 Absent 14,409 14 205/235 Present 17,727 18 0,007 Absent 23,273 23
40
T15M6/ELF3 EXP OBS χ²
198/306 Present 12,727 14 0,183 Absent 29,273 28 198/310 Present 12,091 12 0,001 Absent 29,909 30 205/318 Present 14,636 14 0,042 Absent 27,364 28 205/321 Present 14 12 0,429 Absent 28 30 132/306 Present 17,727 17 0,052 Absent 24,273 25 132/310 Present 16,841 18 0,133 Absent 25,159 24 132/318 Present 20,386 19 0,183 Absent 21,614 23 132/321 Present 19,5 20 0,024 Absent 22,5 22
MSAT2.22/ELF3 EXP OBS χ² 221/306 Present 20 20 0 Absent 22 22 221/310 Present 19 19 0 Absent 23 23 221/318 Present 23 23 0 Absent 19 19 221/321 Present 22 22 0 Absent 20 20 223/306 Present 10 7 1,181 Absent 32 35 223/310 Present 9,5 11 0,306 Absent 32,5 31 223/318 Present 11,5 9 0,748 Absent 30,5 33 223/321 Present 11 13 0,493 Absent 31 29
Tables 110, 111, 112, 113 and 114. Chi-square results from individual allele pairs comparisons, between T15M6 and ELF3 (110), MSAT2.22 and 01_N07 (111), MSAT2.22 and 01_G06 (112), MSAT2.22 and ELF3 (113) and 01_N07 and 01_G06 (114).
MSAT2.22/01_N07 221/230 Present 24 24 0 Absent 17 17 221/232 Present 30 30 0 Absent 11 11 221/235 Present 20 20 0 Absent 21 21 223/230 Present 12 14 0,471 Absent 29 27 223/232 Present 15 16 0,105 Absent 26 25 223/235 Present 10 4 4,761 (<0.05) Absent 31 37
41
01_N07/ELF3 EXP OBS χ²
230/306 Present 11,150 10 0,164 Absent 28,850 30 230/310 Present 10,592 16 3,755 (<0.05) Absent 29,408 24 230/318 Present 12,822 7 3,891 (<0.05) Absent 27,178 33 230/321 Present 12,265 13 0,064 Absent 27,735 27 232/306 Present 13,937 11 0,950 Absent 26,063 29 232/310 Present 13,240 9 2,030 Absent 26,760 31 232/318 Present 16,028 20 1,643 Absent 23,972 20 232/321 Present 15,331 18 0,753 Absent 24,669 22 235/306 Present 9,292 16 6,309 (<0.025) Absent 30,708 24 235/310 Present 8,827 11 0,686 Absent 31,173 29 235/318 Present 10,685 9 0,363 Absent 29,315 31 235/321 Present 10,221 4 5,086 (<0.025) Absent 29,779 36
Tables 115 and 116. Chi-square results from individual allele pairs comparisons, between 01_N07 and ELF3 (115) and 01G06 and ELF3 (116)
01_G06/ELF3 EXP OBS χ²
