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GENOMICS AND BACTERIAL SPECIES CONCEPTS AND GENOME CO-ADAPTATION - Coggle…
GENOMICS AND BACTERIAL SPECIES CONCEPTS AND GENOME CO-ADAPTATION
what is a species?
we can define species based on genetics
things can be morphologically/phenotypically similar but genetically different and vv
convergent evolution
species concepts
interbreeding
biological species concept
species are groups of interbreeding natural populations that are reproductively isolated from other such groups (Mayr 1995)
genetic or phenotypic cohesion
genotypic cluster species concept
a species is a [morphologically or genetically] distinguishable group of individuals that has few or no intermediates when in contact with other such clusters (Mallet 1995)
recognition species concept
a species is the most inclusive population of individual biparental organisms which shares a common fertilisation system (Paterson 1985)
cohesion species concept
a species is the most inclusive population of individuals having the potential for phenotypic cohesion through intrinsic cohesion mechanisms (Templetom 1989)
evolutionary cohesion
ecological species concept
a species is a lineage (or closely related set of lineages) which occupies an adaptive zone minimally different from that of any other lineage in its range and which evolves separately from all lineages outside its range (Van Valen 1976)
evolutionary species concept
a species is a single lineage of ancestral descendant populations or organisms which maintains its identity from other such lineages and which has its own evolutionary tendencies and historical fate (Wiley 1978, modified from Simpson 1961)
evolutionary history
phylogenetic species concept 1
a phylogenetic species is an irreducible (basal) cluster of organisms that is diagnosable distinct from other such clusters, and within which there is a paternal pattern of ancestry and descent (Cracraft 1989)
phylogenetic species concept 2
a species is the smallest [exclusive] monophyletic group of common ancestry (de Queiroz and Donoghue 1988)
phylogenetic species concept 3 or genealogical species concept
a species is a basal, exclusive group of organisms all of whose genes coalesced more recently with each other than with those of any organisms outside the group, and that contains no exclusive group within it (Baum and Donoghue 1995; Shaw 1998)
barriers to recombination
adaptive barriers
selection against hybrid genotypes
hybrid plumage will not be successful when finding a mate
mechanistic barrers
factors promoting DNA specificity (chromosomal incompatibility)
ecological barriers
consequence of physical separation of populations
a gull in the uk cannot mate with a gull in Australia
fuzzy species
distinct species with overlapping ecology
but can get strange intermediate strains
Fuzzy species among recombinogenic bacteria
Campylobacter
MLST - multi locus sequence typing
10 years ago there was no technology for sequencing large numbers of genomes
instead sequence 7 genes in PCR (1000bp each)
look at sequence variation and give it an arbitrary allele number
if they have the same number they are the same gene
a particular allelic profile would be given the name sequence type (ST)
revealed interspecies hybrids
interspecies hybrids indicates horizontal gene transfer betwin
coli
and
jejuni
despeciation
horizontal gene transfer was very common in
campylobacter
indicated a larger number of SNPs
forces of recombination bringing the species together was much higher than regular forces of recombination
in the future different
campylobacter
species could return to being one species?
can be promoted by hybrid/mosaic gene flow
Campylobacter
genotyping to determine the source of human infection
hybridisation has implications for species concepts
introgressed alleles in
campylobacter
are usually associated with agriculture
consistent with a scenario where expansion into a shared agricultural niche promoted descpeciation
clearly bacterial species do not behave according to mayrs species concept model
ecology
introgression - movement of DNA from one population to another
ecology can have a major effect on species
genomics: a tree does not show discrete clades for
C. coli
clade 1
agriculture
C. coli
have hybrid ancestry
every vertical column is assigned to either coli or jejuni
black = pure jejuni
white = pure coli
stripy pattern proves hybridisation
in plotting genomic divergence you see that most of the genes have little genomic divergence
Progressive genome-wide introgression in agricultural Campylobacter coli
ecology and introgression
introgression occurs across a great genetic distance
introgression might aid adaptation to novel environments but might be disruptive
does the new agricultural niche promote introgression?
does epistasis limit introgression?
epistasis
epistasis is the interaction of genes where the phenotype of one depends on the other
genes are connected
recombination paradox
the lateral transfer of genes among bacteria has opposing effects, conferring
beneficial adaptations
whilst introducing
disharmony in coadapted genomes
the prevailing outcome depends upon the fitness cost of disrupting established epistatic gene networks
quantifying HGT again
chromosome painting
to identify regions of different ancestry - we can identify where different bits of the genome have recombined
quantifies gene flow, identifying regions of atypical ancestry in the genome
donor clonal complexes
co-adaptation (epistasis) and introgression
epistasis is the interaction of genes where the phenotype of one depends on the other
modelling coadaptation
epistatic sites change more frequently than average
mutations that are fixed just occur on one branch
epistatic sites are found together on multiple branches
genes that depend on one another tend to be close
epistatic interactions between painted SNPs
most epistatic interactions found between recombines and antic SNPs
very unexpected
fitness is reduced during initial HGT
if HGT continues fitness may increase again
eventually fitness may become higher than original pop
an evolutionary scenario for the observed patterns of covariation and introgression in natural C. coli populations
The landscape of coadaptation in
Vibrio parahaemolyticus
SuperDCA for genome-wide epistasis analysis
BIOLOGICAL SPECIES CONCEPT CANNOT APPLY TO BACTERIA AS THEY BEHAVE VERY DIFFERENTLY