Homology (biology)

For use of the term 'homologous in reference to chromosomes, see Homologous chromosomes. For use of
the term 'homologous in reference to behaviors, see
Homology (psychology).
In the context of biology, homology is the existence of

Ray Lankester dened the terms homogeny, meaning homology due to inheritance from a common ancestor, and homoplasy, meaning homology due to other
factors.[3][4]

2 Denition
Homology is a relationship dened between structures or DNA derived from a common ancestor.
Homologous[Etymology 1] traits of organisms are therefore
explained by descent from a common ancestor. The opposite of homologous organs are analogous organs which
do similar jobs in two taxa that were not present in the
last common ancestor but rather evolved separately. An
example of an analogous trait would be the wings of bats
and birds, which evolved independently in each lineage
separately after diverging from ancestors with forelimbs
not used as wings (terrestrial mammals and theropod dinosaurs, respectively).

The principle of homology: The biological derivation relationship (shown by colors) of the various bones in the forelimbs of
four vertebrates is known as homology and was one of Charles
Darwins arguments in favor of evolution.

It is important to distinguish between dierent hierarchical levels of homology in order to make informative
biological comparisons. In the above example, the bird
and bat wings are analogous as wings, but homologous
as forelimbs because the organ served as a forearm (not
a wing) in the last common ancestor of tetrapods.[5] Homology can also be described at the level of the gene. In
genetics homology can refer to both the gene (DNA) and
the corresponding protein product. It has been hypothesized that some behaviors might be homologous, based
on either shared behavior across related taxa or common
origins of the behavior in an individuals development,
though this remains controversial.

shared ancestry between a pair of structures, or genes, in

dierent species.[1] A common example of homologous
structures in evolutionary biology are the wings of bats
and the arms of primates.[1] Evolutionary theory explains
the existence of homologous structures adapted to different purposes as the result of descent with modication
from a common ancestor.
In the context of sexual dierentiationthe process of
development of the dierences between males and females from an undierentiated fertilized eggthe male
and female organs are homologous if they develop from
the same embryonic tissue.[2] A typical example is the
ovaries of female humans and the testicles of male
humans.[2]

3 Anatomical homology

Evolutionary ancestry means that structures evolved from

some structure in a common ancestor; for example, the
wings of bats and the arms of primates are homologous
in this sense. Developmental ancestry means that struc1 Etymology
tures arose from the same tissue in embryonal developThe word homology, coined in about 1656, derives from ment; the ovaries of female humans and the testicles of
the Greek homologos from homos same male humans are homologous in this sense.
and logos relation. In biology, two things are ho- Homology is dierent from analogy, which describes
mologous if they bear the same relationship to one an- the relation between characters that are apparently simother, such as a certain bone in various forms of the ilar yet phylogenetically independent. The wings of a
maple seed and the wings of an albatross are analogous
hand.
1

4 SEQUENCE HOMOLOGY
tion, many cladists consider homology to be synonymous
with synapomorphy.

3.2 Homologous structures in other phyla

Introductory discussions of homology commonly limit
themselves to the limbs of tetrapod vertebrates, occasionally touching on other structures, such as modied teeth
as in whales and elephants. However, homologies provide the fundamental basis for all aspects of biological
classication, although some of them may be highly counterintuitive. For example, within the arthropods, Brusca
and Brusca [10] provide the following homologies for the
rst 10 somites (embryonic segments) in several groups
of arthropods, but add that "...the subject of head appendage homology among the arthropods is quite unsettled and highly controversial...

3.3 Plants
Modications of primary leaves, stems, and roots occur
in many higher plants.
Examples:

4 Sequence homology
The wings of pterosaurs (1), bats (2) and birds (3) are analogous
as wings, but homologous as forelimbs.

but not homologous (they both allow the organism to

travel on the wind, but they didn't both develop from the
same structure). Analogy is commonly also referred to
as homoplasy, which is further distinguished into parallelism, reversal, and convergence.[6]
From the point of view of evolutionary developmental biology (evo-devo) where evolution is seen as the evolution
of the development of organisms, Rolf Sattler emphasized that homology can also be partial. New structures
can evolve through the combination of developmental
pathways or parts of them. As a result, hybrid or mosaic
structures can evolve that exhibit partial homologies. For
example, certain compound leaves of owering plants are
partially homologous both to leaves and shoots because
they combine some traits of leaves and shoots.[7][8]

3.1

Determining homology

Systematists identify two forms of homology: primary

homology is that initially conjectured by a researcher
based on similar structure or anatomical connections,
who states a hypothesis that two characters share an
ancestry; secondary homology is implied by parsimony
analysis, where a character that only occurs once on a tree
is taken to be homologous.[9] As implied in this deni-

A sequence alignment, produced by ClustalO, of mammalian

histone proteins.
Sequences are the amino acids for residues 120-180 of the proteins. Residues that are conserved across all sequences are highlighted in grey. Below the protein sequences is a key denoting conserved sequence (*), conservative mutations (:), semiconservative mutations (.), and non-conservative mutations (
).[11]

As with anatomical structures, homology between protein

or DNA sequences is dened in terms of shared ancestry.
Two segments of DNA can have shared ancestry because
of either a speciation event (orthologs) or a duplication
event (paralogs).[12]
Homology among proteins or DNA is often incorrectly
concluded on the basis of sequence similarity. The terms
percent homology and sequence similarity are often used interchangeably. As with anatomical structures, high sequence similarity might occur because of
convergent evolution, or, as with shorter sequences, because of chance. Such sequences are similar but not homologous. Sequence regions that are homologous are also

4.2

Paralogy

called conserved. This is not to be confused with conservation in amino acid sequences in which the amino acid
at a specic position has been substituted with a dierent
one with functionally equivalent physicochemical properties. One can, however, refer to partial homology where
a fraction of the sequences compared (are presumed to)
share descent, while the rest does not. For example, partial homology may result from a gene fusion event.

4.1

Orthology

Homologous sequences are orthologous if they are inferred to be descended from the same ancestral sequence
separated by a speciation event: when a species diverges
into two separate species, the copies of a single gene
in the two resulting species are said to be orthologous.
Orthologs, or orthologous genes, are genes in dierent
species that originated by vertical descent from a single
gene of the last common ancestor. The term ortholog
was coined in 1970 by Walter Fitch.[13]
For instance, the plant Flu regulatory protein is present
both in Arabidopsis (multicellular higher plant) and
Chlamydomonas (single cell green algae). The Chlamydomonas version is more complex: it crosses the membrane twice rather than once, contains additional domains
and undergoes alternative splicing. However it can fully
substitute the much simpler Arabidopsis protein, if transferred from algae to plant genome by means of gene engineering. Signicant sequence similarity and shared functional domains indicate that these two genes are orthologous genes,[14] inherited from the shared ancestor.
Orthology is strictly dened in terms of ancestry. Given
that the exact ancestry of genes in dierent organisms is
dicult to ascertain due to gene duplication and genome
rearrangement events, the strongest evidence that two
similar genes are orthologous is usually found by carrying
out phylogenetic analysis of the gene lineage. Orthologs
often, but not always, have the same function.[15]

3
sequence comparisons (heuristic) and those that use
phylogenetic methods. Sequence comparison methods
were rst pioneered by COGs,[16] now extended and
automatically enhanced by the eggNOG[17] database.
InParanoid[18] focuses on pairwise ortholog relationships. OrthoDB[19] appreciates that the orthology concept is relative to dierent speciation points by providing a hierarchy of orthologs along the species tree.
Other databases that provide eukaryotic orthologs include OrthoMCL,[20] OMA, Roundup,[21] OrthoMaM[22]
for mammals, OrthologID[23] and GreenPhylDB[24] for
plants.
Tree-based phylogenetic approaches aim to distinguish
speciation from gene duplication events by comparing
gene trees with species trees, as implemented in resources
such as TreeFam[25] and LOFT.[26] A third category of
hybrid approaches uses both heuristic and phylogenetic
methods to construct clusters and determine trees, for
example Ortholuge,[27] EnsemblCompara GeneTrees[28]
and HomoloGene.[29]

4.2 Paralogy
Homologous sequences are paralogous if they were created by a duplication event within the genome. If this
was a gene duplication event: if a gene in an organism is
duplicated to occupy two dierent positions in the same
genome, then the two copies are paralogous.
Paralogous genes often belong to the same species, but
this is not necessary: for example, the hemoglobin gene
of humans and the myoglobin gene of chimpanzees are
paralogs. Paralogs can be split into in-paralogs (paralogous pairs that arose after a speciation event) and outparalogs (paralogous pairs that arose before a speciation
event). Between-species out-paralogs are pairs of paralogs that exist between two organisms due to duplication
before speciation, whereas within-species out-paralogs
are pairs of paralogs that exist in the same organism,
but whose duplication event happened before speciation.
Paralogs typically have the same or similar function, but
sometimes do not: due to lack of the original selective
pressure upon one copy of the duplicated gene, this copy
is free to mutate and acquire new functions.

Orthologous sequences provide useful information in taxonomic classication and phylogenetic studies of organisms. The pattern of genetic divergence can be used to
trace the relatedness of organisms. Two organisms that
are very closely related are likely to display very similar
DNA sequences between two orthologs. Conversely, an
Paralogous sequences provide useful and dramatic inorganism that is further removed evolutionarily from ansight into some of the way genomes evolve. The
other organism is likely to display a greater divergence in
genes encoding myoglobin and hemoglobin are considthe sequence of the orthologs being studied.
ered to be ancient paralogs. Similarly, the four known
classes of hemoglobins (hemoglobin A, hemoglobin A2,
hemoglobin B, and hemoglobin F) are paralogs of each
4.1.1 Databases of orthologous genes
other. While each of these proteins serves the same baGiven their tremendous importance for biology and sic function of oxygen transport, they have already dibioinformatics, orthologous genes have been organized in verged slightly in function: fetal hemoglobin (hemoglobin
several specializeddatabases that provide tools to iden- F) has a higher anity for oxygen than adult hemoglobin.
tify and analyze orthologous gene sequences. These Function is not always conserved, however. Human
resources employ approaches that can be generally angiogenin diverged from ribonuclease, for example, and
classied into those that are based on all pairwise while the two paralogs remain similar in tertiary struc-

ture, their functions within the cell are now quite dierent.

7 See also

It is often asserted that orthologs are more functionally

similar than paralogs of similar divergence, but several
papers have challenged this notion.[30][31][32]

Cladistics

REFERENCES

Deep homology
OrthoDB

4.3

Ohnology

Ohnologous genes are paralogous genes that have originated by a process of whole-genome duplication (WGD).
The name was rst given in honour of Susumu Ohno by
Ken Wolfe.[33] Ohnologs/Ohnologues are interesting for
evolutionary analysis because they all have been diverging
for the same length of time since their common origin.

4.4

Xenology

Homologs resulting from horizontal gene transfer between two organisms are termed xenologs. Xenologs can
have dierent functions, if the new environment is vastly
dierent for the horizontally moving gene. In general,
though, xenologs typically have similar function in both
organisms. The term was coined by Walter Fitch.[13]

4.5

Gametology

Gametology denotes the relationship between homologous genes on nonrecombining, opposite sex chromosomes. Gametologs result from the origination of genetic sex determination and barriers to recombination between sex chromosomes. Examples of gametologs include CHDW and CHDZ in birds.

Homology between sexes and

forms

Main article: List of homologues of the human reproductive system

The term homology is sometimes applied to reproductive
structures that share a common embryonic origin, but become spectacularly dierent between the two sexes in the
adult. Those listed below are some of the more commonly cited examples.
Among insects, the stinger used by infertile female
worker bees is a modied ovipositor.

Homologies across phyla

For more details on this topic, see Deep homology.

Orthologous MAtrix (OMA)

Protein homology
TreeFam
Syntelog

8 Notes
[1] from Greek , 'to agree'

9 References
[1] Homology. Encyclopdia Britannica Online. Retrieved
2013-08-30.
[2] Hyde, Janet Shibley; DeLamater, John D. (June 2010),
Chapter 5, Understanding Human Sexuality (11th
ed.), New York: McGraw-Hill, p. 103, ISBN 9780073382821
[3] Bower, Frederick Orpen (1906). Plant Morphology.
Congress of Arts and Science: Universal Exposition, St.
Louis, 1904. Houghton, Miin. p. 64.
[4] Williams, David Malcolm; Forey, Peter L. (2004). Milestones in Systematics. CRC Press. p. 198. ISBN 0-41528032-X.
[5] Scotland, R. W. (2010). Deep homology: A view
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[6] Cf. Butler, A. B.: Homology and Homoplasty. In: Squire,
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[7] Sattler R (1984). Homology a continuing challenge.
Systematic Botany 9 (4): 38294. doi:10.2307/2418787.
JSTOR 2418787.
[8] Sattler, R. (1994). Homology, homeosis, and process
morphology in plants. In Hall, Brian Keith. Homology:
the hierarchical basis of comparative biology. Academic
Press. pp. 42375. ISBN 0-12-319583-7.
[9] Pinna, M. C. C. (1991). Concepts and Tests of Homology in the Cladistic Paradigm. Cladistics 7 (4): 367394.
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[10] Brusca, R.C. & Brusca, G.J. 1990. Invertebrates. Sinauer
Associates, Sunderland.: [i]-xviii, 1-922., P. 669
[11] Clustal FAQ #Symbols. Clustal. Retrieved 8 December
2014.

[12] Koonin EV (2005). Orthologs, paralogs, and evolutionary genomics. Annual Review of Genetics 39:
30938. doi:10.1146/annurev.genet.39.073003.114725.
PMID 16285863.

a multi-genome repository of orthologs and evolutionary distances. Bioinformatics (Oxford, England) 22

(16): 20446. doi:10.1093/bioinformatics/btl286. PMID
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[13] Fitch WM (June 1970). Distinguishing homologous

from analogous proteins. Systematic Zoology 19 (2): 99
113. doi:10.2307/2412448. PMID 5449325.

[22] OrthoMaM
Ranwez V, Delsuc F, Ranwez S, Belkhir K, Tilak
MK, Douzery EJ (2007). OrthoMaM: a database
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[14] Falciatore A, Merendino L, Barneche F et al. (January

2005). The FLP proteins act as regulators of chlorophyll synthesis in response to light and plastid signals in
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[15] Fang G, Bhardwaj N, Robilotto R, Gerstein MB (March
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2845645. PMID 20361041.
[16] COGs: Clusters of Orthologous Groups of proteins
Tatusov RL, Koonin EV, Lipman DJ (October 1997).
A genomic perspective on protein families. Science
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[17] eggNOG: evolutionary genealogy of genes: Nonsupervised Orthologous Groups
Muller J, Szklarczyk D, Julien P et al. (January
2010). eggNOG v2.0: extending the evolutionary
genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.
Nucleic Acids Research 38 (Database issue): D190
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19900971.
[18] Inparanoid: Eukaryotic Ortholog Groups
Ostlund G, Schmitt T, Forslund K et al. (January 2010).
InParanoid 7: new algorithms and tools for eukaryotic
orthology analysis. Nucleic Acids Research 38 (Database
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2808972. PMID 19892828.
[19] OrthoDB: The Hierarchical Catalog of Eukaryotic Orthologs
Waterhouse RM, Zdobnov EM, Tegenfeldt F, Li J,
Kriventseva EV (January 2011). OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011.
Nucleic Acids Research 39 (Database issue): D283
8. doi:10.1093/nar/gkq930. PMC 3013786. PMID
20972218.
[20] OrthoMCL: Identication of Ortholog Groups for Eukaryotic Genomes
Chen F, Mackey AJ, Stoeckert CJ, Roos DS (January 2006).
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups.
Nucleic Acids Research 34 (Database issue): D363
8. doi:10.1093/nar/gkj123. PMC 1347485. PMID
16381887.
[21] Roundup
Deluca TF, Wu IH, Pu J et al. (August 2006). Roundup:

[23] OrthologID
Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM,
DeSalle R (March 2006). OrthologID: automation
of genome-scale ortholog identication within a parsimony framework. Bioinformatics 22 (6): 699707.
doi:10.1093/bioinformatics/btk040. PMID 16410324.
[24] GreenPhylDB
Conte MG, Gaillard S, Lanau N, Rouard M, Prin C (January 2008). GreenPhylDB: a database for plant comparative genomics. Nucleic Acids Research 36 (Database issue): D9918. doi:10.1093/nar/gkm934. PMC 2238940.
PMID 17986457.
[25] TreeFam: Tree families database
Ruan J, Li H, Chen Z et al. (January 2008). TreeFam:
2008 Update. Nucleic Acids Research 36 (Database
issue): D73540. doi:10.1093/nar/gkm1005. PMC
2238856. PMID 18056084.
[26] TreeFam: Tree families database
van der Heijden RT, Snel B, van Noort V, Huynen MA
(2007). Orthology prediction at scalable resolution by
phylogenetic tree analysis. BMC Bioinformatics 8: 83.
doi:10.1186/1471-2105-8-83. PMC 1838432. PMID
17346331.
[27] Fulton DL, Li YY, Laird MR, Horsman BG, Roche FM,
Brinkman FS (2006). Improving the specicity of highthroughput ortholog prediction. BMC Bioinformatics 7:
270. doi:10.1186/1471-2105-7-270. PMC 1524997.
PMID 16729895.
[28] Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin
R, Birney E (February 2009). EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees
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[29] Sayers EW, Barrett T, Benson DA et al. (January
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PMC 3013733. PMID 21097890.
[30] Studer RA, Robinson-Rechavi M (May 2009). How
condent can we be that orthologs are similar, but paralogs dier?". Trends in Genetics 25 (5): 2106.
doi:10.1016/j.tig.2009.03.004. PMID 19368988.
[31] Nehrt NL, Clark WT, Radivojac P, Hahn MW
(June 2011). Testing the ortholog conjecture with

11

comparative functional genomic data from mammals. PLoS Computational Biology 7 (6): e1002073.
doi:10.1371/journal.pcbi.1002073.
PMC 3111532.
PMID 21695233.
[32] Eisen, Jonathan. Special Guest Post & Discussion Invitation from Matthew Hahn on Ortholog Conjecture Paper.
[33] Wolfe K (May 2000). Robustness--its not where
you think it is.
Nature Genetics 25 (1): 34.
doi:10.1038/75560. PMID 10802639.

10

Further reading

Carroll, Sean B. (2006). Endless Forms Most Beautiful. New York: W.W. Norton & Co. ISBN 0-29785094-6.
Carroll, Sean B. (2006). The making of the ttest:
DNA and the ultimate forensic record of evolution.
New York: W.W. Norton & Co. ISBN 0-39306163-9.
DePinna MC (1991).
Concepts and tests
of homology in the cladistic paradigm.
Cladistics 7 (4): 36794. doi:10.1111/j.10960031.1991.tb00045.x.
Dewey CN, Pachter L (April 2006). Evolution at
the nucleotide level: the problem of multiple wholegenome alignment. Human Molecular Genetics 15
(Spec No 1): R516. doi:10.1093/hmg/ddl056.
PMID 16651369.
Fitch WM (May 2000). Homology a personal view
on some of the problems. Trends in Genetics 16
(5): 22731. doi:10.1016/S0168-9525(00)020059. PMID 10782117.
Gegenbaur, G. (1898). Vergleichende Anatomie der
Wirbelthiere... Leipzig.
Haeckel, . (1866). Generelle Morphologie der Organismen. Bd 1-2. erlin.
Owen, R. (1847). On the archetype and homologies
of the vertebrate skeleton. London.
Mindell DP, Meyer A (2001). Homology evolving. Trends in Ecology and Evolution 16 (8): 434
40. doi:10.1016/S0169-5347(01)02206-6.
Kuzniar A, van Ham RC, Pongor S, Leunissen JA (November 2008). The quest for orthologs: nding the corresponding gene across
genomes. Trends Genet. 24 (11): 53951.
doi:10.1016/j.tig.2008.08.009. PMID 18819722.

EXTERNAL LINKS

11 External links
Brigandt, Ingo (2011) Essay: Homology. In: The
Embryo Project Encyclopedia. ISSN: 1940-5030.
http://embryo.asu.edu/handle/10776/1754

12
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