Question: Can gene squences be used to reconstruct bacterial phylongeny
About the article "Bacteria", section "Origin and early evolution".

Candidate passages:
Gene flow is the exchange of genes between populations, which are usually of the same species.
Examples of gene flow within a species include the migration and then breeding of organisms, or the exchange of pollen.
Gene transfer between species includes the formation of hybrid organisms and horizontal gene transfer.
Migration into or out of a population can change allele frequencies, as well as introducing genetic variation into a population.
Immigration may add new genetic material to the established gene pool of a population.
Conversely, emigration may remove genetic material.
Population genetic models can be used to reconstruct the history of gene flow between populations. 
The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, about 4 billion years ago.
For about 3 billion years, all organisms were microscopic, and bacteria and archaea were the dominant forms of life.
Although bacterial fossils exist, such as stromatolites, their lack of distinctive morphology prevents them from being used to examine the history of bacterial evolution, or to date the time of origin of a particular bacterial species.
However, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage.
Bacteria were also involved in the second great evolutionary divergence, that of the archaea and eukaryotes.
Here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea.
This involved the engulfment by proto-eukaryotic cells of alpha-proteobacterial symbionts to form either mitochondria or hydrogenosomes, which are still found in all known Eukarya (sometimes in highly reduced form, e.g.
in ancient "amitochondrial" protozoa).
Later on, some eukaryotes that already contained mitochondria also engulfed cyanobacterial-like organisms.
This led to the formation of chloroplasts in algae and plants.
There are also some algae that originated from even later endosymbiotic events.
Here, eukaryotes engulfed a eukaryotic algae that developed into a "second-generation" plastid.
This is known as secondary endosymbiosis.
Study systems.
Viruses and bacteriophages.
Bacteriophages have played and continue to play a key role in bacterial genetics and molecular biology.
Historically, they were used to define gene structure and gene regulation.
Also the first genome to be sequenced was a bacteriophage.
However, bacteriophage research did not lead the genomics revolution, which is clearly dominated by bacterial genomics.
Only very recently has the study of bacteriophage genomes become prominent, thereby enabling researchers to understand the mechanisms underlying phage evolution.
Bacteriophage genome sequences can be obtained through direct sequencing of isolated bacteriophages, but can also be derived as part of microbial genomes.
Analysis of bacterial genomes has shown that a substantial amount of microbial DNA consists of prophage sequences and prophage-like elements.
A detailed database mining of these sequences offers insights into the role of prophages in shaping the bacterial genome. 
Bacterial display (or bacteria display or bacterial surface display) is a protein engineering technique used for in vitro protein evolution.
Libraries of polypeptides displayed on the surface of bacteria can be screened using flow cytometry or iterative selection procedures (biopanning).
This protein engineering technique allows us to link the function of a protein with the gene that encodes it.
Bacterial display can be used to find target proteins with desired properties and can be used to make affinity ligands which are cell-specific.
This system can be used in many applications including the creation of novel vaccines, the identification of enzyme substrates and finding the affinity of a ligand for its target protein.
Bacterial display is often coupled with magnetic-activated cell sorting (MACS) or fluorescence-activated cell sorting (FACS) techniques.
Competing methods for protein evolution "in vitro" are phage display, ribosome display, yeast display, and mRNA display.
Bacteriophage display is the most common type of display system used although bacterial display is becoming increasingly popular as technical challenges are overcome.
Bacterial display combined with FACS also has the advantage that it is a real-time technique. 
In addition to highly conserved primer binding sites, 16S rRNA gene sequences contain hypervariable regions that can provide species-specific signature sequences useful for bacterial identification.
As a result, 16S rRNA gene sequencing has become prevalent in medical microbiology as a rapid and cheap alternative to phenotypic methods of bacterial identification.
Although it was originally used to identify bacteria, 16S sequencing was subsequently found to be capable of reclassifying bacteria into completely new species, or even genera.
It has also been used to describe new species that have never been successfully cultured.