Genome evolution is the process by which a genome
changes in structure (sequence) or size over time. The study of genome
evolution involves multiple fields such as structural analysis of the
genome, the study of genomic parasites, gene and ancient genome duplications, polyploidy, and comparative genomics.
Genome evolution is a constantly changing and evolving field due to the
steadily growing number of sequenced genomes, both prokaryotic and
eukaryotic, available to the scientific community and the public at
large.
Circular representation of the Mycobacterium leprae genome created using JCVI online genome tools.
History
Since the first sequenced genomes became available in the late 1970s, scientists have been using comparative genomics to study the differences and similarities between various genomes. Genome sequencing has progressed over time to include more and more complex genomes including the eventual sequencing of the entire human genome in 2001.
By comparing genomes of both close relatives and distant ancestors the
stark differences and similarities between species began to emerge as
well as the mechanisms by which genomes are able to evolve over time.
Prokaryotic and eukaryotic genomes
Prokaryotes
The principal forces of evolution in prokaryotes and their effects on archaeal and bacterial genomes. The horizontal line shows archaeal and bacterial genome size on a logarithmic scale (in megabase pairs)
and the approximate corresponding number of genes (in parentheses).The
effects of the main forces of prokaryotic genome evolution are denoted
by triangles that are positioned, roughly, over the ranges of genome
size for which the corresponding effects are thought to be most
pronounced.
Prokaryotic genomes have two main mechanisms of evolution: mutation and horizontal gene transfer. A third mechanism, sexual reproduction,
is prominent in eukaryotes and also occurs in bacteria. Prokaryotes
can acquire novel genetic material through the process of bacterial conjugation
in which both plasmids and whole chromosomes can be passed between
organisms. An often cited example of this process is the transfer of
antibiotic resistance utilizing plasmid DNA. Another mechanism of genome evolution is provided by transduction whereby bacteriophages introduce new DNA into a bacterial genome. The main mechanism of sexual interaction is natural genetic transformation
which involves the transfer of DNA from one prokaryotic cell to another
though the intervening medium. Transformation is a common mode of DNA
transfer and at least 67 prokaryotic species are known to be competent
for transformation.
Genome evolution in bacteria is well understood because of the
thousands of completely sequenced bacterial genomes available. Genetic
changes may lead to both increases or decreases of genomic complexity
due to adaptive genome streamlining and purifying selection.
In general, free-living bacteria have evolved larger genomes with more
genes so they can adapt more easily to changing environmental
conditions. By contrast, most parasitic bacteria have reduced genomes as
their hosts supply many if not most nutrients, so that their genome
does not need to encode for enzymes that produce these nutrients
themselves.
E.coli largely contains only exons in genes. However, it does contain a small amount of self-splicing introns (Group II).
Eukaryotes
Eukaryotic genomes are generally larger than that of the prokaryotes. While the E. coli genome is roughly 4.6Mb in length, in comparison the Human genome is much larger with a size of approximately 3.2Gb.
The eukaryotic genome is linear and can be composed of multiple
chromosomes, packaged in the nucleus of the cell. The non-coding
portions of the gene, known as introns, which are largely not present in prokaryotes, are removed by RNA splicing before translation
of the protein can occur. Eukaryotic genomes evolve over time through
many mechanisms including sexual reproduction which introduces much
greater genetic diversity to the offspring than the usual prokaryotic
process of replication in which the offspring are theoretically genetic
clones of the parental cell.
Genome size is usually measured in base pairs (or bases in single-stranded DNA or RNA). The C-value
is another measure of genome size. Research on prokaryotic genomes
shows that there is a significant positive correlation between the C-value of prokaryotes and the amount of genes that compose the genome. This indicates that gene number is the main factor influencing the size of the prokaryotic genome. In eukaryotic
organisms, there is a paradox observed, namely that the number of genes
that make up the genome does not correlate with genome size. In other
words, the genome size is much larger than would be expected given the
total number of protein coding genes.
Genome size can increase by duplication, insertion, or polyploidization. Recombination can lead to both DNA loss or gain. Genomes can also shrink because of deletions. A famous example for such gene decay is the genome of Mycobacterium leprae, the causative agent of leprosy. M. leprae has lost many once-functional genes over time due to the formation of pseudogenes. This is evident in looking at its closest ancestor Mycobacterium tuberculosis. M. leprae
lives and replicates inside of a host and due to this arrangement it
does not have a need for many of the genes it once carried which allowed
it to live and prosper outside the host. Thus over time these genes
have lost their function through mechanisms such as mutation causing
them to become pseudogenes. It is beneficial to an organism to rid
itself of non-essential genes because it makes replicating its DNA much
faster and requires less energy.
An example of increasing genome size over time is seen in
filamentous plant pathogens. These plant pathogen genomes have been
growing larger over the years due to repeat-driven expansion. The
repeat-rich regions contain genes coding for host interaction proteins.
With the addition of more and more repeats to these regions the plants
increase the possibility of developing new virulence factors through
mutation and other forms of genetic recombination. In this way it is
beneficial for these plant pathogens to have larger genomes.
Chromosomal evolution
Chromosome fusion, leading to a reduced number of chromosomes (here a fused human chromosome 2, with 2 separate chromosomes still present in chimpanzees and other apes).
The evolution of genomes can be impressively shown by the
change of chromosome number and structure over time. For instance, the
ancestral chromosomes corresponding to chimpanzee chromosomes 2A and 2B fused to produce human chromosome 2.
Similarly, the chromosomes of more distantly related species show
chromosomes that have been broken up into more parts over the course of
evolution. This can be demonstrated by Fluorescence in situ hybridization.
Gene duplication is the process by which a region of DNA coding for a gene is duplicated. This can occur as the result of an error in recombination or through a retrotransposition event. Duplicate genes are often immune to the selective pressure
under which genes normally exist. As a result, a large number of
mutations may accumulate in the duplicate gene code. This may render the
gene non-functional or in some cases confer some benefit to the
organism.
Whole genome duplication
Similar
to gene duplication, whole genome duplication is the process by which
an organism's entire genetic information is copied, once or multiple
times which is known as polyploidy.
This may provide an evolutionary benefit to the organism by supplying
it with multiple copies of a gene thus creating a greater possibility of
functional and selectively favored genes. However, tests for enhanced
rate and innovation in teleost fishes with duplicated genomes compared
with their close relative holostean fishes (without duplicated genomes)
found that there was little difference between them for the first 150
million years of their evolution.
In 1997, Wolfe & Shields gave evidence for an ancient duplication of the Saccharomyces cerevisiae (Yeast) genome.
It was initially noted that this yeast genome contained many individual
gene duplications. Wolfe & Shields hypothesized that this was
actually the result of an entire genome duplication in the yeast's
distant evolutionary history. They found 32 pairs of homologous
chromosomal regions, accounting for over half of the yeast's genome.
They also noted that although homologs were present, they were often located on different chromosomes. Based on these observations, they determined that Saccharomyces cerevisiae underwent a whole genome duplication soon after its evolutionary split from Kluyveromyces,
a genus of ascomycetous yeasts. Over time, many of the duplicate genes
were deleted and rendered non-functional. A number of chromosomal
rearrangements broke the original duplicate chromosomes into the current
manifestation of homologous chromosomal regions. This idea was further
solidified in looking at the genome of yeast's close relative Ashbya gossypii.
Whole genome duplication is common in fungi as well as plant species.
An example of extreme genome duplication is represented by the Common
Cordgrass (Spartina anglica) which is a dodecaploid, meaning that it contains 12 sets of chromosomes, in stark contrast to the human diploid structure in which each individual has only two sets of 23 chromosomes.
Transposable elements
are regions of DNA that can be inserted into the genetic code through
one of two mechanisms. These mechanisms work similarly to
"cut-and-paste" and "copy-and-paste" functionalities in word processing
programs. The "cut-and-paste" mechanism works by excising DNA from one
place in the genome and inserting itself into another location in the
code. The "copy-and-paste" mechanism works by making a genetic copy or
copies of a specific region of DNA and inserting these copies elsewhere
in the code.The most common transposable element in the human genome is the Alu sequence, which is present in the genome over one million times.
Spontaneous mutations often occur which can cause various changes in the genome. Mutations can either change the identity of one or more nucleotides, or result in the addition or deletion of one or more nucleotide bases. Such changes can lead to a frameshift mutation,
causing the entire code to be read in a different order from the
original, often resulting in a protein becoming non-functional. A mutation in a promoter region, enhancer region or transcription factor binding region can also result in either a loss of function, or an up or downregulation in the transcription
of the gene targeted by these regulatory elements. Mutations are
constantly occurring in an organism's genome and can cause either a
negative effect, positive effect or neutral effect (no effect at all).
The proS loci in Mycobacterium leprae and M. tuberculosis, showing 3 pseudogenes (indicated by crosses) in M. leprae that still represent functional genes in M. tuberculosis. Homologous genes are indicated by identical colors and vertical, hatched bars. Modified after Cole et al. 2001.
Often a result of spontaneous mutation, pseudogenes
are dysfunctional genes derived from previously functional gene
relatives. There are many mechanisms by which a functional gene can
become a pseudogene including the deletion or insertion of one or
multiple nucleotides. This can result in a shift of reading frame, causing the gene to no longer code for the expected protein, introduce a premature stop codon or a mutation in the promoter region.
Often cited examples of pseudogenes within the human genome include the once functional olfactory
gene families. Over time, many olfactory genes in the human genome
became pseudogenes and were no longer able to produce functional
proteins, explaining the poor sense of smell humans possess in
comparison to their mammalian relatives.
Similarly, bacterial pseudogenes commonly arise from adaptation of free-living bacteria to parasitic
lifestyles, so that many metabolic genes become superfluous as these
species become adapted to their host. Once a parasite obtains nutrients
(such as amino acids or vitamins) from its host it has no need to produce these nutrients itself and often loses the genes to make them.
Exon shuffling is a mechanism by which new genes are created. This can occur when two or more exons
from different genes are combined or when exons are duplicated. Exon
shuffling results in new genes by altering the current intron-exon
structure. This can occur by any of the following processes: transposon mediated shuffling, sexual recombination or non-homologous recombination (also called illegitimate recombination).
Exon shuffling may introduce new genes into the genome that can be
either selected against and deleted or selectively favored and
conserved.
Genome reduction and gene loss
Many
species exhibit genome reduction when subsets of their genes are not
needed anymore. This typically happens when organisms adapt to a
parasitic life style, e.g. when their nutrients are supplied by a host.
As a consequence, they lose the genes needed to produce these nutrients.
In many cases, there are both free living and parasitic species that
can be compared and their lost genes identified. Good examples are the
genomes of Mycobacterium tuberculosis and Mycobacterium leprae, the latter of which has a dramatically reduced genome (see figure under pseudogenes above).
Another beautiful example are endosymbiont species. For instance, Polynucleobacter necessarius was first described as a cytoplasmic endosymbiont of the ciliate Euplotes aediculatus. The latter species dies soon after being cured of the endosymbiont. In the few cases in which P. necessarius is not present, a different and rarer bacterium apparently supplies the same function. No attempt to grow symbiotic P. necessarius
outside their hosts has yet been successful, strongly suggesting that
the relationship is obligate for both partners. Yet, closely related
free-living relatives of P. necessarius have been identified. The
endosymbionts have a significantly reduced genome when compared to their
free-living relatives (1.56 Mbp vs. 2.16 Mbp).
A major question of evolutionary biology is how genomes change to create new species. Speciation requires changes in behavior, morphology, physiology, or metabolism
(or combinations thereof). The evolution of genomes during speciation
has been studied only very recently with the availability of next-generation sequencing technologies. For instance, cichlid fish
in African lakes differ both morphologically and in their behavior. The
genomes of 5 species have revealed that both the sequences but also the
expression pattern of many genes has quickly changed over a relatively
short period of time (100,000 to several million years). Notably, 20% of
duplicate gene pairs have gained a completely new tissue-specific expression pattern, indicating that these genes also obtained new functions. Given that gene expression is driven by short regulatory sequences,
this demonstrates that relatively few mutations are required to drive
speciation. The cichlid genomes also showed increased evolutionary rates
in microRNAs which are involved in gene expression.
Gene expression
Mutations
can lead to changed gene function or, probably more often, to changed
gene expression patterns. In fact, a study on 12 animal species
provided strong evidence that tissue-specific gene expression was
largely conserved between orthologs in different species. However,
paralogs within the same species often have a different expression
pattern. That is, after duplication of genes they often change their
expression pattern, for instance by getting expressed in another tissue
and thereby adopting new roles.
Composition of nucleotides (GC content)
The genetic code is made up of sequences of four nucleotide bases: Adenine, Guanine, Cytosine and Thymine,
commonly referred to as A, G, C, and T. The GC-content is the
percentage of G & C bases within a genome. GC-content varies greatly
between different organisms.
Gene coding regions have been shown to have a higher GC-content and the
longer the gene is, the greater the percentage of G and C bases that
are present. A higher GC-content confers a benefit because a
Guanine-Cytosine bond is made up of three hydrogen bonds
while an Adenine-Thymine bond is made up of only two. Thus the three
hydrogen bonds give greater stability to the DNA strand. So, it is not
surprising that important genes often have a higher GC-content than
other parts of an organism's genome.
For this reason, many species living at very high temperatures such as
the ecosystems surrounding hydrothermal vents, have a very high
GC-content. High GC-content is also seen in regulatory sequences such as
promoters which signal the start of a gene. Many promoters contain CpG islands,
areas of the genome where a cytosine nucleotide occurs next to a
guanine nucleotide at a greater proportion. It has also been shown that
a broad distribution of GC-content between species within a genus shows
a more ancient ancestry. Since the species have had more time to
evolve, their GC-content has diverged further apart.
Evolving translation of genetic code
Amino acids are made up of three base long codons and both Glycine and Alanine
are characterized by codons with Guanine-Cytosine bonds at the first
two codon base positions. This GC bond gives more stability to the DNA
structure. It has been hypothesized that as the first organisms evolved
in a high-heat and pressure environment they needed the stability of
these GC bonds in their genetic code.
Novel genes can arise from non-coding DNA. De novo origin of (protein-coding) genes only requires two features, namely the generation of an open reading frame, and the creation of a transcription factor binding site. For instance, Levine and colleagues reported the origin of five new genes in the D. melanogaster genome from noncoding DNA. Subsequently, de novo origin of genes has been also shown in other organisms such as yeast, rice and humans. For instance, Wu et al. (2011) reported 60 putative de novo human-specific genes all of which are short consisting of a single exon (except one). In bacteria, 'grounded' prophages
(i.e. integrated phage that cannot produce new phage) are buffer zones
which would tolerate variations thereby increasing the probability of de
novo gene formation. These grounded prophages and other such genetic elements are sites where genes could be acquired through horizontal gene transfer (HGT).
Origin of life and the first genomes
In
order to understand how the genome arose, knowledge is required of the
chemical pathways that permit formation of the key building blocks of
the genome under plausible prebiotic conditions. According to the RNA world
hypothesis free-floating ribonucleotides were present in the primitive
soup. These were the fundamental molecules that combined in series to
form the original RNA
genome. Molecules as complex as RNA must have arisen from small
molecules whose reactivity was governed by physico-chemical processes.
RNA is composed of purine and pyrimidine nucleotides, both of which are necessary for reliable information transfer, and thus Darwinian natural selection and evolution. Nam et al.
demonstrated the direct condensation of nucleobases with ribose to give
ribonucleosides in aqueous microdroplets, a key step leading to
formation of the RNA genome. Also, a plausible prebiotic process for
synthesizing pyrimidine and purine ribonucleotides leading to genome
formation using wet-dry cycles was presented by Becker et al.
OS/2 (Operating System/2) is a series of computer operating systems, initially created by Microsoft and IBM under the leadership of IBM software designer Ed Iacobucci. As a result of a feud between the two companies over how to position OS/2 relative to Microsoft's new Windows 3.1 operating environment, the two companies severed the relationship in 1992 and OS/2 development fell to IBM exclusively. The name stands for "Operating System/2", because it was introduced as part of the same generation change release as IBM's "Personal System/2 (PS/2)" line of second-generation personal computers. The first version of OS/2 was released in December 1987 and newer versions were released until December 2001.
OS/2 was intended as a protected-mode successor of PC DOS targeting the Intel 80286 processor. Notably, basic system calls were modeled after MS-DOS calls; their names even started with "Dos" and it was possible to create "Family Mode" applications – text mode applications that could work on both systems. Because of this heritage, OS/2 shares similarities with Unix, Xenix, and Windows NT.
Up to $990 million per year was spent developing OS/2 and its
replacement. OS/2 sales were largely concentrated in networked computing
used by corporate professionals; however, by the early 1990s, it was
overtaken by Microsoft Windows NT. While OS/2 was arguably technically
superior to Microsoft Windows 95, OS/2 failed to develop much
penetration in the mass market consumer and stand-alone desktop PC
segments.
IBM discontinued its support for OS/2 on December 31, 2006.
Since then, OS/2 has been developed, supported and sold by two
different third-party vendors under license from IBM – first by Serenity
Systems as eComStation since 2001, and later by Arca Noae LLC as ArcaOS since 2017.
Development
1985–1990: Joint IBM–Microsoft development
Logo of OS/2 1.x
OS/2 1.0 featured a text-mode interface similar to MS-DOS.
The development of OS/2 began when IBM and Microsoft signed the "Joint Development Agreement" in August 1985. It was code-named "CP/DOS" and it took two years for the first product to be delivered.
OS/2 1.0 (1987)
OS/2 1.0 was announced in April 1987 and released in December. The original release only ran in text mode, and a GUI was introduced with OS/2 1.1 about a year later. OS/2 features an API for controlling the video display (VIO) and handling keyboard and mouse events so that programmers writing for protected mode need not call the BIOS
or access hardware directly. Other development tools included a subset
of the video and keyboard APIs as linkable libraries so that family mode
programs are able to run under MS-DOS, and, in the OS/2 Extended Edition v1.0, a database engine called Database Manager or DBM (this was related to DB2, and should not be confused with the DBM family of database engines for Unix and Unix-like operating systems). A task-switcher named Program Selector was available through the Ctrl-Esc hotkey
combination, allowing the user to select among multitasked text-mode
sessions (or screen groups; each can run multiple programs).
Communications and database-oriented extensions were delivered in 1988, as part of OS/2 1.0 Extended Edition: SNA, X.25/APPC/LU 6.2, LAN Manager, Query Manager, SQL.
OS/2 1.1 was the first version to feature the Presentation Manager GUI.
OS/2 1.1 (1988)
The promised user interface, Presentation Manager, was introduced with OS/2 1.1 in October 1988. It had a similar user interface to Windows 2.1, which was released in May of that year. (The interface was replaced in versions 1.2 and 1.3 by a look closer in appearance to Windows 3.0.)
The Extended Edition of 1.1, sold only through IBM sales
channels, introduced distributed database support to IBM database
systems and SNA communications support to IBM mainframe networks.
OS/2 1.2 (1989)
In 1989, Version 1.2 introduced Installable Filesystems and, notably, the HPFSfilesystem. HPFS provided a number of improvements over the older FAT file system, including long filenames and a form of alternate data streams called Extended Attributes. In addition, extended attributes were also added to the FAT file system.
Installation Disk A of Microsoft OS/2 1.3 (3½-inch floppy disk)
The Extended Edition of 1.2 introduced TCP/IP and Ethernet support.
OS/2- and Windows-related books of the late 1980s acknowledged
the existence of both systems and promoted OS/2 as the system of the
future.
1990: Breakup
OS/2 1.3 (1990)
The collaboration between IBM and Microsoft unravelled in 1990, between the releases of Windows 3.0 and OS/2 1.3. During this time, Windows 3.0 became a tremendous success, selling millions of copies in its first year. Much of its success was because Windows 3.0 (along with MS-DOS) was bundled with most new computers. OS/2, on the other hand, was available only as an additional stand-alone software package. In addition, OS/2 lacked device drivers for many common devices such as printers, particularly non-IBM hardware.
Windows, on the other hand, supported a much larger variety of
hardware. The increasing popularity of Windows prompted Microsoft to
shift its development focus from cooperating on OS/2 with IBM to
building its own business based on Windows.
Several technical and practical reasons contributed to this
breakup. The two companies had significant differences in culture and
vision. Microsoft favored the open hardware system approach that
contributed to its success on the PC. IBM sought to use OS/2 to drive
sales of its own hardware, and urged Microsoft to drop features, such as
fonts, that IBM's hardware did not support. Microsoft programmers also became frustrated with IBM's bureaucracy and its use of lines of code to measure programmer productivity. IBM developers complained about the terseness and lack of comments in Microsoft's code, while Microsoft developers complained that IBM's code was bloated.
The two products have significant differences in API. OS/2 was announced when Windows 2.0 was near completion, and the Windows API already defined. However, IBM requested that this API be significantly changed for OS/2.
Therefore, issues surrounding application compatibility appeared
immediately. OS/2 designers hoped for source code conversion tools,
allowing complete migration of Windows application source code to OS/2
at some point. However, OS/2 1.x did not gain enough momentum to allow
vendors to avoid developing for both OS/2 and Windows in parallel.
OS/2 1.3 was the final 16-bit only version of OS/2, and the last to be sold by Microsoft.
OS/2 1.x targets the Intel 80286 processor and DOS fundamentally does not. IBM insisted on supporting the 80286 processor, with its 16-bit segmented memory
mode, because of commitments made to customers who had purchased many
80286-based PS/2s as a result of IBM's promises surrounding OS/2. Until release 2.0 in April 1992, OS/2 ran in 16-bit protected mode and therefore could not benefit from the Intel 80386's much simpler 32-bitflat memory model and virtual 8086 mode features. This was especially painful in providing support for DOS applications. While, in 1988, Windows/386 2.1 could run several cooperatively multitasked DOS applications, including expanded memory (EMS) emulation, OS/2 1.3, released in 1991, was still limited to one 640 kB "DOS box".
Given these issues, Microsoft started to work in parallel on a
version of Windows which was more future-oriented and more portable. The
hiring of Dave Cutler, former VAX/VMS
architect, in 1988 created an immediate competition with the OS/2 team,
as Cutler did not think much of the OS/2 technology and wanted to build
on his work on the MICA project at Digital rather than creating a "DOS plus". His NT OS/2 was a completely new architecture.
IBM grew concerned about the delays in development of OS/2 2.0.
Initially, the companies agreed that IBM would take over maintenance of
OS/2 1.0 and development of OS/2 2.0, while Microsoft would continue
development of OS/2 3.0. In the end, Microsoft decided to recast NT OS/2
3.0 as Windows NT, leaving all future OS/2 development to IBM. From a
business perspective, it was logical to concentrate on a consumer line
of operating systems based on DOS and Windows, and to prepare a new
high-end system in such a way as to keep good compatibility with
existing Windows applications. While it waited for this new high-end
system to develop, Microsoft would still receive licensing money from
Xenix and OS/2 sales. Windows NT's OS/2 heritage can be seen in its
initial support for the HPFS filesystem,
text mode OS/2 1.x applications, and OS/2 LAN Manager network support.
Some early NT materials even included OS/2 copyright notices embedded in
the software.
One example of NT OS/2 1.x support is in the WIN2K resource kit. Windows NT could also support OS/2 1.x Presentation Manager and AVIO applications with the addition of the Windows NT Add-On Subsystem for Presentation Manager.
1990–1996: Post-breakup
OS/2 2.0 and DOS compatibility (1992)
OS/2 2.0 was the first 32-bit release of OS/2, and the first to feature the Workplace Shell.
OS/2 2.0 was released in April 1992. At the time, the suggested retail price was US$195, while Windows retailed for $150.
OS/2 2.0 provided a 32-bit API for native programs, though the OS
itself still contained some 16-bit code and drivers. It also included a
new OOUI (object-oriented user interface) called the Workplace Shell.
This was a fully object-oriented interface that was a significant
departure from the previous GUI. Rather than merely providing an
environment for program windows (such as the Program Manager), the
Workplace Shell provided an environment in which the user could manage
programs, files and devices by manipulating objects on the screen. With
the Workplace Shell, everything in the system is an "object" to be
manipulated.
OS/2 2.0 was touted by IBM as "a better DOS than DOS and a better Windows than Windows".
It managed this by including the fully-licensed MS-DOS 5.0, which had
been patched and improved upon. For the first time, OS/2 was able to run
more than one DOS application at a time. This was so effective that it
allowed OS/2 to run a modified copy of Windows 3.0, itself a DOS extender, including Windows 3.0 applications.
Because of the limitations of the Intel 80286
processor, OS/2 1.x could run only one DOS program at a time, and did
this in a way that allowed the DOS program to have total control over
the computer. A problem in DOS mode could crash the entire computer. In
contrast, OS/2 2.0 could leverage the virtual 8086 mode of the Intel 80386 processor to create a much safer virtual machine
in which to run DOS programs. This included an extensive set of
configuration options to optimize the performance and capabilities given
to each DOS program. Any real-mode operating system (such as 8086 Xenix) could also be made to run using OS/2's virtual machine capabilities, subject to certain direct hardware access limitations.
The OS/2 2.0 upgrade box
Like most 32-bit environments, OS/2 could not run protected-mode DOS programs using the older VCPI interface, unlike the Standard mode of Windows 3.1; it only supported programs written according to DPMI. (Microsoft discouraged the use of VCPI under Windows 3.1, however, due to performance degradation.)
Unlike Windows NT, OS/2 always allowed DOS programs the
possibility of masking real hardware interrupts, so any DOS program
could deadlock the machine in this way. OS/2 could, however, use a hardware watchdog
on selected machines (notably IBM machines) to break out of such a
deadlock. Later, release 3.0 leveraged the enhancements of newer Intel 80486 and Intel Pentium processors—the Virtual Interrupt Flag (VIF), which was part of the Virtual Mode Extensions (VME)—to solve this problem.
OS/2
2.1 was released in 1993. This version of OS/2 achieved compatibility
with Windows 3.0 (and later Windows 3.1) by adapting Windows user-mode
code components to run inside a virtual DOS machine
(VDM). Originally, a nearly complete version of Windows code was
included with OS/2 itself: Windows 3.0 in OS/2 2.0, and Windows 3.1 in
OS/2 2.1. Later, IBM developed versions of OS/2 that would use whatever
Windows version the user had installed previously, patching it on the
fly, and sparing the cost of an additional Windows license.
It could either run full-screen, using its own set of video drivers, or
"seamlessly," where Windows programs would appear directly on the OS/2
desktop. The process containing Windows was given fairly extensive
access to hardware, especially video, and the result was that switching
between a full-screen WinOS/2 session and the Workplace Shell could
occasionally cause issues.
Because OS/2 only runs the user-mode system components of Windows, it is incompatible with Windows device drivers (VxDs) and applications that require them.
Multiple Windows applications run by default in a single Windows
session – multitasking cooperatively and without memory protection –
just as they would under native Windows 3.x. However, to achieve true
isolation between Windows 3.x programs, OS/2 can also run multiple
copies of Windows in parallel, with each copy residing in a separate
VDM. The user can then optionally place each program either in its own
Windows session – with preemptive multitasking and full memory
protection between sessions, though not within them – or
allow some applications to run together cooperatively in a shared
Windows session while isolating other applications in one or more
separate Windows sessions. At the cost of additional hardware resources,
this approach can protect each program in any given Windows session
(and each instance of Windows itself) from every other program running
in any separate Windows session (though not from other programs running in the same Windows session).
Whether Windows applications are running in full-screen or
windowed mode, and in one Windows session or several, it is possible to
use DDE between OS/2 and Windows applications, and OLE between Windows applications only.
IBM's OS/2 for Windows product (codename Ferengi), also
known as "OS/2, Special Edition", was interpreted as a deliberate
strategy "of cashing in on the pervasive success of the Microsoft
platform" but risked confusing consumers with the notion that the
product was a mere accessory or utility running on Windows such as Norton Desktop for Windows
when, in fact, it was "a complete, modern, multi-tasking, pre-emptive
operating system", itself hosting Windows instead of running on it.
Available on CD-ROM or 18 floppy disks, the product documentation
reportedly suggested Windows as a prerequisite for installing the
product, also being confined to its original FAT partition, whereas the
product apparently supported the later installation of Windows running
from an HPFS partition, particularly beneficial for users of larger hard
drives. Windows compatibility, relying on patching specific memory
locations, was reportedly broken by the release of Windows 3.11,
prompting accusations of arbitrary changes to Windows in order to
perpetrate "a deliberate act of Microsoft sabotage" against IBM's
product.
OS/2 Warp 3 (1994)
Wordmark of OS/2 Warp 3.0
OS/2 Warp Connect 3.0, showing the Windows 3.1 Program Manager, QBASIC in a DOS window, and the LaunchPad (bottom center)
Released in 1994, OS/2 version 3.0 was labelled as OS/2 Warp
to highlight the new performance benefits, and generally to freshen the
product image. "Warp" had originally been the internal IBM name for the
release: IBM claimed that it had used Star Trek
terms as internal names for prior OS/2 releases, and that this one
seemed appropriate for external use as well. At the launch of OS/2 Warp
in 1994, Patrick Stewart was to be the Master of Ceremonies; however Kate Mulgrew of the then-upcoming series Star Trek: Voyager substituted for him at the last minute.
OS/2 Warp offers a host of benefits over OS/2 2.1, notably broader hardware support, greater multimedia capabilities, Internet-compatible networking, and it includes a basic office application suite known as IBM Works.
It was released in two versions: the less expensive "Red Spine" and the
more expensive "Blue Spine" (named for the color of their boxes). "Red
Spine" was designed to support Microsoft Windows
applications by utilizing any existing installation of Windows on the
computer's hard drive. "Blue Spine" includes Windows support in its own
installation, and so can support Windows applications without a Windows
installation. As most computers were sold with Microsoft Windows
pre-installed and the price was less, "Red Spine" was the more popular
product. OS/2 Warp Connect—which has full LAN client support built-in—followed in mid-1995. Warp Connect was nicknamed "Grape".
In OS/2 2.0, most performance-sensitive subsystems, including the
graphics (Gre) and multimedia (MMPM/2) systems, were updated to 32-bit
code in a fixpack, and included as part of OS/2 2.1. Warp 3 brought
about a fully 32-bit windowing system, while Warp 4 introduced the
object-oriented 32-bit GRADD display driver model.
In 1991, IBM started development on an intended replacement for OS/2 called Workplace OS.
This was an entirely new product, brand new code, that borrowed only a
few sections of code from both the existing OS/2 and AIX products. It
used an entirely new microkernel code base, intended (eventually) to
host several of IBM's operating systems (including OS/2) as microkernel
"personalities". It also included major new architectural features
including a system registry, JFS, support for UNIX graphics libraries,
and a new driver model.
Workplace OS was developed solely for POWER platforms, and IBM intended to market a full line of PowerPCs in an effort to take over the market from Intel.
A mission was formed to create prototypes of these machines and they
were disclosed to several corporate customers, all of whom raised issues
with the idea of dropping Intel.
Advanced plans for the new code base would eventually include replacement of the OS/400
operating system by Workplace OS, as well as a microkernel product that
would have been used in industries such as telecommunications and
set-top television receivers.
A partially functional pre-alpha version of Workplace OS was demonstrated at Comdex, where a bemused Bill Gates stopped by the booth. The second and last time it would be shown in public was at an OS/2 user group in Phoenix, Arizona; the pre-alpha code refused to boot.
It was released in 1995. But with $990 million being spent per
year on development of this as well as Workplace OS, and no possible
profit or widespread adoption, the end of the entire Workplace OS and
OS/2 product line was near.
OS/2 Warp 4 (1996)
Firefox 3.5.4 for OS/2 Warp 4
Wordmark of OS/2 Warp 4
OS/2 Warp 4 desktop after installation
In 1996, Warp 4 added Java and speech recognition software.
IBM also released server editions of Warp 3 and Warp 4 which bundled
IBM's LAN Server product directly into the operating system
installation. A personal version of Lotus Notes
was also included, with a number of template databases for contact
management, brainstorming, and so forth. The UK-distributed free demo CD-ROM of OS/2 Warp essentially contained the entire OS and was easily, even accidentally, cracked,
meaning that even people who liked it did not have to buy it. This was
seen as a backdoor tactic to increase the number of OS/2 users, in the
belief that this would increase sales and demand for third-party
applications, and thus strengthen OS/2's desktop numbers.
This suggestion was bolstered by the fact that this demo version had
replaced another which was not so easily cracked, but which had been
released with trial versions of various applications. In 2000, the July edition of Australian Personal Computer
magazine bundled software CD-ROMs, included a full version of Warp 4
that required no activation and was essentially a free release. Special
versions of OS/2 2.11 and Warp 4 also included symmetric multiprocessing (SMP) support.
OS/2 sales were largely concentrated in networked computing used
by corporate professionals; however, by the early 1990s, it was
overtaken by Microsoft Windows NT. While OS/2 was arguably technically
superior to Microsoft Windows 95,
OS/2 failed to develop much penetration in the consumer and stand-alone
desktop PC segments; there were reports that it could not be installed
properly on IBM's own Aptiva series of home PCs. Microsoft made an offer in 1994 where IBM would receive the same terms as Compaq
(the largest PC manufacturer at the time) for a license of Windows 95,
if IBM ended development of OS/2 completely. IBM refused and instead
went with an "IBM First" strategy of promoting OS/2 Warp and disparaging
Windows, as IBM aimed to drive sales of its own software as well as
hardware. By 1995, Windows 95 negotiations between IBM and Microsoft,
which were already difficult, stalled when IBM purchased Lotus SmartSuite, which would have directly competed with Microsoft Office.
As a result of the dispute, IBM signed the license agreement 15 minutes
before Microsoft's Windows 95 launch event, which was later than their
competitors and this badly hurt sales of IBM PCs. IBM officials later
conceded that OS/2 would not have been a viable operating system to keep
them in the PC business.
1996–2001: Downsizing
A project was launched internally by IBM to evaluate the looming
competitive situation with Microsoft Windows 95. Primary concerns
included the major code quality issues in the existing OS/2 product
(resulting in over 20 service packs, each requiring more diskettes than
the original installation), and the ineffective and heavily matrixed
development organization in Boca Raton (where the consultants reported
that "basically, everybody reports to everybody") and Austin.
That study, tightly classified as "Registered Confidential" and
printed only in numbered copies, identified untenable weaknesses and
failures across the board in the Personal Systems Division as well as
across IBM as a whole. This resulted in a decision being made at a level
above the Division to cut over 95% of the overall budget for the entire
product line, end all new development (including Workplace OS),
eliminate the Boca Raton development lab, end all sales and marketing
efforts of the product, and lay off over 1,300 development individuals
(as well as sales and support personnel). $990 million had been spent in
the last full year. Warp 4 became the last distributed version of OS/2.
2001–2006: Discontinuation and end-of-life
Although a small and dedicated community remains faithful to OS/2,
OS/2 failed to catch on in the mass market and is little used outside
certain niches where IBM traditionally had a stronghold. For example,
many bank installations, especially automated teller machines, run OS/2 with a customized user interface; French SNCF national railways used OS/2 1.x in thousands of ticket selling machines. Telecom companies such as Nortel used OS/2 in some voicemail systems. Also, OS/2 was used for the host PC used to control the Satellite Operations Support System equipment installed at NPR member stations from 1994 to 2007, and used to receive the network's programming via satellite.
Although IBM began indicating shortly after the release of Warp 4
that OS/2 would eventually be withdrawn, the company did not end
support until December 31, 2006,
with sales of OS/2 stopping on December 23, 2005. The latest IBM OS/2
Warp version is 4.52, which was released for both desktop and server
systems in December 2001.
IBM is still delivering defect support for a fee. IBM urges customers to migrate their often highly complex applications to e-business
technologies such as Java in a platform-neutral manner. Once
application migration is completed, IBM recommends migration to a
different operating system, suggesting Linux as an alternative.
ArcaOS is the most recent OS/2-based operating system developed outside of IBM.
After IBM discontinued development of OS/2, various third parties
approached IBM to take over future development of the operating system.
The OS/2 software vendor Stardock made such a proposal to IBM in 1999, but it was not followed through by the company. Serenity Systems succeeded in negotiating an agreement with IBM, and began reselling OS/2 as eComStation in 2001. eComStation is now sold by XEU.com, the most recent version (2.1) was released in 2011. In 2015, Arca Noae, LLC announced that they had secured an agreement with IBM to resell OS/2. They released the first version of their OS/2-based operating system in 2017 as ArcaOS. As of 2023, there have been multiple releases of ArcaOS, and it remains under active development.
Petitions for open source
Many people hoped that IBM would release OS/2 or a significant part of it as open source. Petitions were held in 2005 and 2007, but IBM refused them, citing legal and technical reasons.
It is unlikely that the entire OS will be open at any point in the
future because it contains third-party code to which IBM does not have
copyright, and much of this code is from Microsoft. IBM also once
engaged in a technology transfer with Commodore, licensing Amiga technology for OS/2 2.0 and above, in exchange for the REXX scripting language.
This means that OS/2 may have some code that was not written by IBM,
which can therefore prevent the OS from being re-announced as
open-sourced in the future. On the other hand, IBM donated Object REXX for Windows and OS/2 to the Open Object REXX project maintained by the REXX Language Association on SourceForge.
There was a petition, arranged by OS2World, to open parts of the OS. Open source operating systems such as Linux have already profited from OS/2 indirectly through IBM's release of the improved JFSfile system,
which was ported from the OS/2 code base. As IBM didn't release the
source of the OS/2 JFS driver, developers ported the Linux driver back
to eComStation and added the functionality to boot from a JFS partition.
This new JFS driver has been integrated into eComStation v2.0, and
later into ArcaOS 5.0.
Summary of releases
Release dates refer to the US English editions unless otherwise noted.
Date
Version
December 1987
OS/2 1.0
November 1988
OS/2 1.1
October 1989
OS/2 1.2
December 1990
OS/2 1.3
October 1991
OS/2 2.0 LA (Limited Availability)
April 1992
OS/2 2.0
October 1992
OS/2 2.00.1
May 1993
OS/2 2.1
November 1993
OS/2 for Windows
February 1994
OS/2 2.11
July 1994
OS/2 2.11 SMP
October 1994
OS/2 Warp 3
May 1995
OS/2 Warp Connect
December 1995
OS/2 Warp, PowerPC Edition
February 1996
OS/2 Warp Server 4
September 1996
OS/2 Warp 4
September 1996
OS/2 Warp Server Advanced SMP
November 1997
WorkSpace On-Demand 1.0
October 1998
WorkSpace On-Demand 2.0
April 1999
OS/2 Warp Server for e-Business (version 4.50)
November 2000
OS/2 Convenience Pack 1 (version 4.51)
November 2001
OS/2 Convenience Pack 2 (version 4.52)
Features and technology
User interface
The
graphic system has a layer named Presentation Manager that manages
windows, fonts, and icons. This is similar in functionality to a
non-networked version of X11 or the Windows GDI. On top of this lies the Workplace Shell (WPS) introduced in OS/2 2.0. WPS is an object-orientedshell
allowing the user to perform traditional computing tasks such as
accessing files, printers, launching legacy programs, and advanced
object oriented tasks using built-in and third-party application objects
that extended the shell in an integrated fashion not available on any
other mainstream operating system. WPS follows IBM's Common User Access user interface standards.
WPS represents objects such as disks, folders, files, program objects, and printers using the System Object Model
(SOM), which allows code to be shared among applications, possibly
written in different programming languages. A distributed version called
DSOM allowed objects on different computers to communicate. DSOM is
based on CORBA. The object oriented aspect of SOM is similar to, and a direct competitor to, Microsoft's Component Object Model,
though it is implemented in a radically different manner; for instance,
one of the most notable differences between SOM and COM is SOM's
support for inheritance (one of the most fundamental concepts of OO
programming)—COM does not have such support. SOM and DSOM are no longer
being developed.
The multimedia capabilities of OS/2 are accessible through Media Control Interface commands.
The last update (bundled with the IBM version of Netscape Navigator plugins) added support for MPEG files. Support for newer formats such as PNG, progressive JPEG, DivX, Ogg, and MP3
comes from third parties. Sometimes it is integrated with the
multimedia system, but in other offers it comes as standalone
applications.
The TCP/IP stack is based on the open sourceBSD stack as visible with SCCSwhat
compatible tools. IBM included tools such as ftp and telnet and even
servers for both commands. IBM sold several networking extensions
including NFS support and an X11 server.
Drivers
Hardware
vendors were reluctant to support device drivers for alternative
operating systems including OS/2, leaving users with few choices from a
select few vendors. To relieve this issue for video cards, IBM licensed a
reduced version of the Scitech display drivers, allowing users to choose from a wide selection of cards supported through Scitech's modular driver design.
Virtualization
OS/2 has historically been more difficult to run in a virtual machine than most other legacy x86 operating systems because of its extensive reliance on the full set of features of the x86 CPU; in particular, OS/2's use of ring 2 prevented it from running in early versions of VMware. Newer versions of VMware provide official support for OS/2, specifically for eComStation.
VirtualPC from Microsoft (originally Connectix)
has been able to run OS/2 without hardware virtualization support for
many years. It also provided "additions" code which greatly improves
host–guest OS interactions in OS/2. The additions are not provided with
the current version of VirtualPC, but the version last included with a
release may still be used with current releases. At one point, OS/2 was a
supported host for VirtualPC in addition to a guest. Note that OS/2
runs only as a guest on those versions of VirtualPC that use
virtualization (x86 based hosts) and not those doing full emulation
(VirtualPC for Mac).
VirtualBox from Oracle Corporation (originally InnoTek, later Sun)
supports OS/2 1.x, Warp 3 through 4.5, and eComStation as well as
"Other OS/2" as guests. However, attempting to run OS/2 and eComStation
can still be difficult, if not impossible, because of the strict
requirements of VT-x/AMD-V hardware-enabled virtualization and only
ACP2/MCP2 is reported to work in a reliable manner.
ArcaOS supports being run as a virtual machine guest inside VirtualBox, VMware ESXi and VMWare Workstation. It ships with VirtualBox Guest Additions, and driver improvements to improve performance as a guest operating system.
The difficulties in efficiently running OS/2 have, at least once, created an opportunity for a new virtualization company. A large bank in Moscow
needed a way to use OS/2 on newer hardware that OS/2 did not support.
As virtualization software is an easy way around this, the company
desired to run OS/2 under a hypervisor.
Once it was determined that VMware was not a possibility, it hired a
group of Russian software developers to write a host-based hypervisor
that would officially support OS/2. Thus, the Parallels, Inc. company and their Parallels Workstation product was born.
Security niche
OS/2 has few native computer viruses; while it is not invulnerable by design, its reduced market share appears to have discouraged virus writers.
There are, however, OS/2-based antivirus programs, dealing with DOS
viruses and Windows viruses that could pass through an OS/2 server.
Problems
Some problems were classic subjects of comparison with other operating systems:
Synchronous input queue (SIQ): if a GUI application was not servicing its window messages,
the entire GUI system could get stuck and a reboot was required. This
problem was considerably reduced with later Warp 3 fixpacks and refined
by Warp 4, by taking control over the application after it had not
responded for several seconds.
No unified object handles (OS/2 v2.11 and earlier): The
availability of threads probably led system designers to overlook
mechanisms which allow a single thread to wait for different types of
asynchronous events at the same time, for example the keyboard and the
mouse in a "console" program. Even though select was added later,
it only worked on network sockets. In case of a console program,
dedicating a separate thread for waiting on each source of events made
it difficult to properly release all the input devices before starting
other programs in the same "session". As a result, console programs
usually polled the keyboard and the mouse alternately, which resulted in
wasted CPU and a characteristic "jerky" reactivity to user input. In
OS/2 3.0 IBM introduced a new call for this specific problem.
Historical uses
OS/2 has been widely used by Iran Export Bank (Bank Saderat Iran) in
their teller machines, ATMs and local servers (over 35,000 working
stations). As of 2011, the bank moved to virtualize and renew their
infrastructure by moving OS/2 to Virtual Machines running over Windows.
OS/2 was widely used by Brazilian banks. Banco do Brasil had a peak 10,000 machines running OS/2 Warp in the 1990s. OS/2 was used in automated teller machines until 2006. The workstations and automated teller machines and attendant computers have been migrated to Linux.
An ATM in Australia revealing during a reboot that it is based on OS/2 Warp
OS/2 has been used in the banking industry. Suncorp bank in Australia still ran its ATM network on OS/2 as late as 2002. ATMs at Perisher Blue used OS/2 as late as 2009, and even the turn of the decade.
OS/2 was widely adopted by accounting professionals and auditing companies. In mid-1990s native 32-bit accounting software were well developed and serving corporate markets.
OS/2 ran the faulty baggage handling system at Denver International Airport.
The OS was eventually scrapped, but the software written for the system
led to massive delays in the opening of the new airport. The OS itself
was not at fault, but the software written to run on the OS was. The
baggage handling system was eventually removed.
OS/2 was used by radio personality Howard Stern. He once had a 10-minute on-air rant about OS/2 versus Windows 95 and recommended OS/2. He also used OS/2 on his IBM 760CD laptop.
OS/2 was used as part of the Satellite Operations Support System (SOSS) for NPR's Public Radio Satellite System.
SOSS was a computer-controlled system using OS/2 that NPR member
stations used to receive programming feeds via satellite. SOSS was
introduced in 1994 using OS/2 3.0, and was retired in 2007, when NPR
switched over to its successor, the ContentDepot.
OS/2 was used to control the SkyTrain automated light rail system in Vancouver, Canada until the late 2000s when it was replaced by Windows XP.
OS/2 was used in the London UndergroundJubilee Line Extension
Signals Control System (JLESCS) in London, England. This control system
delivered by Alcatel was in use from 1999 to 2011 i.e. between
abandonment before opening of the line's unimplemented original
automatic train control system and the present SelTrac
system. JLESCS did not provide automatic train operation only manual
train supervision. Six OS/2 local site computers were distributed along
the railway between Stratford and Westminster, the shunting tower at Stratford Market Depot, and several formed the central equipment located at Neasden Depot. It was once intended to cover the rest of the line between Green Park and Stanmore but this was never introduced.
OS/2 has been used by The Co-operative Bank
in the UK for its domestic call centre staff, using a bespoke program
created to access customer accounts which cannot easily be migrated to
Windows.
OS/2 has been used by the Stop & Shop supermarket chain (and has been installed in new stores as recently as March 2010).
OS/2 has been used on ticket machines for Tramlink in outer-London.
OS/2 was used in checkout systems at Safeway supermarkets.
OS/2 was used by Trenitalia,
both for the desktops at Ticket Counters and for the Automatic Ticket
Counters up to 2011. Incidentally, the Automatic Ticket Counters with
OS/2 were more reliable than the current ones running a flavor of
Windows.
OS/2 was used as the main operating system for Abbey National
General Insurance motor and home direct call centre products using the
PMSC Series III insurance platform on DB2.2 from 1996 to 2001.
Awards
BYTE
in 1989 listed OS/2 as among the "Excellence" winners of the BYTE
Awards, stating that it "is today where the Macintosh was in 1984: It's a
development platform in search of developers". The magazine predicted
that "When it's complete and bug-free, when it can really use the 80386,
and when more desktops sport OS/2-capable PCs, OS/2
will—deservedly—supersede DOS. But even as it stands, OS/2 is a
milestone product".
In March 1995 OS/2 won seven awards
InfoWorld Product of the Year.
Five Awards at CeBIT.
PC Professional Magazine - Innovation of the Year award.
CHIP Magazine named OS/2 Warp the Operating System of the Year.
DOS International named OS/2 Warp the Operating System of the Year.
1+1 Magazine awarded it with the Software Marketing Quality award.
Industrie Forum awarded it with its Design Excellence.
