W11L2 speciation : concept and decimation

Question 1

The idea of species pre-Darwin

Answer 1

• majority of ancient thinker held to the idea if essentialism or creationism: organism where static and never change over time
• term have meaning similar to species was use in the past
  -in 1735, created the ideas of species and genus in the formalize taxonomic system but struggle with the ideas that species were not immutable (able to change)

Question 2

Darwin and the idea of species

Answer 2

-Darwin book doesn’t really touch on speciation much at all.
-Darwin own ideas of species were unclear and Change over time

Question 3

species post Darwin

Answer 3

• Darwin work alter how biologist viewed species: the ability to change overtime to suit their environment via natural selection

Question 4

The age of biological species concept

Answer 4

-The BSC is attributed to Mayr but similar ideas has existed prior

Question 5

Species concept vs. species delimitation

Answer 5

-Species concepts are attempts at defining the term “species” in a rigorous and consistent way
-Species delimitation is the practical process of identifying species in nature

Question 6

problem with carrying out species delimitation

Answer 6

Sympatric species demonstrate isolation, but what about those in allopatry
-taxonomist almost never use experimental inbreeding for delimitation process
-Asexual organism (no sex)
-Gene flow and introgression (are two species really isolated ? Substantial evidence of introgression)
-horizontal gene transfer (gene flow without reproduction)

Question 7

Modified BSC by Coyne & Orr (2004)

Answer 7

• distinct species are characterized by substantial but not necessary complete reproductive isolation

Question 8

Alternative species concept

Answer 8

— The BSC is commonly accepted by many scientist, it is controversial among both biologist and philosopher
-up to 23 other species concept
-Some major category are : biological, evolutionary and cohesion,…

Question 9

Evolutionary species concept (EvSC)

Answer 9

“A species is a simple 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”
- developed due to paleontology and fossil record. No breeding information

Question 10

Advantages and disadvantage of EvSC

Answer 10

Advantages:
* Can deal with a single lineage evolving through time being considered a single species, as long as it doesn’t branch
* ie. species are only created when divergence between two contemporaneous populations occurs (cladogenesis)
Disadvantages:
* Amount of divergence needed before species can be distinguished is essentially arbitrary
* Unclear how to deal with gene flow between species

Question 11

Genotypic cluster species concept (GCSC)

Answer 11

-A species is a [morphologically or genetically] distinguishable group of individuals that has few or no intermediates when in contact with other such clusters
- very similar to BSC, proposed because BSC is untesable

Question 12

Advantages and dis advantages of GCSC

Answer 12

Advantages:
* Independent of theories of speciation—it is a way to recognize/delimit species without assuming how species are produced
Disadvantages:
* How much genetic differentiation is allowed?
Populations that differ in only one or two genomic loci might occur due to population-specific selection, where heterozygotes in each population might be unfit.
* Clustering can be multi-level—where do you draw the line at a “species”?

Question 13

Cohesion species concept (CSC)

Answer 13

-A species in the most inclusive population of individuals having the potential for phenotypic cohesion through intrinsic cohesion mechanisms

Question 14

What is cohesion mechanism

Answer 14

• Genetic exchangeability: those that allow gene flow between members of the species (eg. sexual reproduction),
• Demographic exchangeability: “the factors that define the fundamental [ecological] niche and limits of spread of new genetic variants through genetic drift and natural selection”

Question 15

Advantages and disadvantage of cohesion species concept

Answer 15

Advantages:
• Emphasises the factors that keep individuals of a species together, rather than what keeps separate species apart
• Demographic exchangeability can apply to asexual organisms
Disadvantages:
• Demographic exchangeability criterion could define sympatric, genetically diverged “species” where one outcompetes the other due to a similar ecological niche, as the same species

Question 16

Does speciation occur in bacteria

Answer 16

-Bacteria (and archaea) are clonally reproducing organisms, so cannot meet the reproductive isolation criteria of the BSC, nor many other species concepts
-speciation biologist tend to ignore asexual species
-The best fit model for bacteria is the cohesion species concept through demographic exchange ability criterion

Question 17

Bacteria classification method

Answer 17

-Origionaly, classified by phenotype (morphology and metabolism)
-spare sampling lead to uncontroversial demarcation of species
-Now, gene or genome sequencing is the most common method
-deep sampling in certain Claude’s has led to ambiguity in separating lineages into distinct species

Question 18

Are bacteria really asexual

Answer 18

While bacteria don’t truly sexually reproduce, most or all taxa can recombine their genome with outside sources of genetic material
Conjugation
* DNA directly transferred between relatively closely related cells
Transduction
* DNA transferred through a viral vector
Transformation
* Uptake of naked DNA from the environment
This means “gene flow” is typically non-zero within populations, although when it is close enough to the mutation rate, it is thought to not be a driving force in speciation

Question 19

Periodic selection and bacterial ecotypes

Answer 19

-Ecotype is a set of strains using the same or vary similar ecological niches. An adaptive mutant from the same ecotype can drive other strain to extrication but cannot do the same for other ecotype
-Periodic selection of adaptive mutations purges diversity within an ecotype and makes each ecotype more genetically similar
-Selection is generally efficient because bacterial population sizes are very large; limited effect of drift
-This is generally called the stable ecotype model of bacterial speciation

Question 20

Selective sweeps vs recombination in bacteria

Answer 20

• genome wide sweep lead to no genomic diversity
  -narrow sweep with recombination lead to moderate to large genomic diversity
  -genome wide sweep with horizontal gene transfer: diversity between ecotype but not within

Question 21

ecotype vs geotype

Answer 21

-Often assumed that bacteria can ubiquitously disperse—ie. they can get anywhere and everywhere, eventually
-Some bacteria are severely restricted in their dispersal, such as geothermal taxa and those line in dee underground rock
-can the ecotype model hold if bacteria in the same ecotype cannot disperse?
-bacterial population that are geographically isolated largely diverge due to genetic drift- these are geotypes

Question 22

Uncultured microbes and metagenomics

Answer 22

Metagenomics involves high-throughput sequencing of DNA from bulk environmental samples, typically to identify microbes
* Metagenome-assembled genomes (MAGs) are complete or near-complete genomes assembled solely through metagenomic analyses
-It has been estimated that 99% of microbes cannot be isolated as pure lab cultures
* As such, the majority of known microbial diversity is based on 16S rRNA sequence and/or MAGs

Question 23

Delimiting bacterial species using genomics

Answer 23

-Even given a theoretical understanding of how bacteria might speciate, delimiting species in practice is very hard
-Operational taxonomic units (OTUs) are groupings of related organisms based on sequence identity (typically ~97%), usually from a single gene
* This sidesteps the problem of defining species by replacing it with the OTU framework
* For metagenomics and microbial diversity analyses, this is the commonly used method
* Measuring ecotypes is practically impossible given the multi-dimensional landscape of ecological niches
High (>95%) Average Nucleotide Identity (ANI) across conserved single-copy genes has been proposed as a universal species threshold

Question 24

Aren’t sequence identity thresholds arbitrary?

Answer 24

Probably!
Choices for delimitation are often based on practicality, and convention and community inertia often win out in the long run
Ultimately, bacterial systematics must adapt to sequence-only samples or risk falling behind as the amount of metagenomic sequence increases exponentially