Editing Molecular evolution (section)

==Genome architecture==
{{Main|Genome evolution}}

===Genome size===
{{Main|Genome size}}
Genome size is influenced by the amount of repetitive DNA as well as number of genes in an organism.  Some organisms, such as most bacteria, ''Drosophila'', and ''Arabidopsis'' have particularly compact genomes with little repetitive content or non-coding DNA.  Other organisms, like mammals or maize, have large amounts of repetitive DNA, long [[introns]], and substantial spacing between genes. The [[C-value paradox]]  refers to the lack of correlation between organism 'complexity' and genome size.  Explanations for the so-called paradox are two-fold.  First, repetitive genetic elements can comprise large portions of the genome for many organisms, thereby inflating DNA content of the haploid genome. Repetitive genetic elements are often descended from [[transposable elements]].

Secondly, the number of genes is not necessarily indicative of the number of developmental stages or tissue types in an organism.  An organism with few developmental stages or tissue types may have large numbers of genes that influence non-developmental phenotypes, inflating gene content relative to developmental gene families.

Neutral explanations for genome size suggest that when population sizes are small, many mutations become nearly neutral.  Hence, in small populations repetitive content and other [[junk DNA|'junk' DNA]] can accumulate without placing the organism at a competitive disadvantage.  There is little evidence to suggest that genome size is under strong widespread selection in multicellular eukaryotes.  Genome size, independent of gene content, correlates poorly with most physiological traits and many eukaryotes, including mammals, harbor very large amounts of repetitive DNA.

However, [[birds]] likely have experienced strong selection for reduced genome size, in response to changing energetic needs for flight.  Birds, unlike humans, produce nucleated red blood cells, and larger nuclei lead to lower levels of oxygen transport.  Bird metabolism is far higher than that of mammals, due largely to flight, and oxygen needs are high.  Hence, most birds have small, compact genomes with few repetitive elements.  Indirect evidence suggests that non-avian theropod dinosaur ancestors of modern birds<ref>{{cite journal | vauthors = Organ CL, Shedlock AM, Meade A, Pagel M, Edwards SV | title = Origin of avian genome size and structure in non-avian dinosaurs | journal = Nature | volume = 446 | issue = 7132 | pages = 180–184 | date = March 2007 | pmid = 17344851 | doi = 10.1038/nature05621 | s2cid = 3031794 | bibcode = 2007Natur.446..180O }}</ref> also had reduced genome sizes, consistent with endothermy and high energetic needs for running speed.  Many bacteria have also experienced selection for small genome size, as time of replication and energy consumption are so tightly correlated with fitness.

===Chromosome number and organization===
The ant ''Myrmecia pilosula'' has only a single pair of chromosomes<ref name=Crosland>{{cite journal | vauthors = Crosland MW, Crozier RH | title = Myrmecia pilosula, an Ant with Only One Pair of Chromosomes | journal = Science | volume = 231 | issue = 4743 | pages = 1278 | date = March 1986 | pmid = 17839565 | doi = 10.1126/science.231.4743.1278 | s2cid = 25465053 | bibcode = 1986Sci...231.1278C }}</ref> whereas the Adders-tongue fern  ''[[Ophioglossum]] reticulatum'' has up to 1260 chromosomes.<ref name="Grubben2004">{{cite book|author=Gerardus J. H. Grubben|title=Vegetables|url=https://archive.org/details/bub_gb_6jrlyOPfr24C|access-date=10 March 2013|year=2004|publisher=PROTA|isbn=978-90-5782-147-9|page=[https://archive.org/details/bub_gb_6jrlyOPfr24C/page/n404 404]}}</ref> The  [[List of organisms by chromosome count|number of chromosomes]] in an organism's genome does not necessarily correlate with the amount of DNA in its genome. The genome-wide amount of [[Genetic recombination|recombination]] is directly controlled by the number of chromosomes, with one [[Chromosomal crossover|crossover]] per chromosome or per chromosome arm, depending on the species.<ref>{{cite journal |last1=Pardo-Manuel de Villena |first1=Fernando |last2=Sapienza |first2=Carmen |title=Recombination is proportional to the number of chromosome arms in mammals |journal=Mammalian Genome |date=April 2001 |volume=12 |issue=4 |pages=318–322 |doi=10.1007/s003350020005|pmid=11309665 }}</ref>

Changes in chromosome number can play a key role in [[speciation]], as differing chromosome numbers can serve as a [[Reproductive isolation|barrier to reproduction]] in hybrids.  Human [[chromosome 2]] was created from a fusion of two chimpanzee chromosomes and still contains central [[telomeres]] as well as a vestigial second [[centromere]].  [[Polyploidy]], especially allopolyploidy, which occurs often in plants, can also result in reproductive incompatibilities with parental species.  ''Agrodiatus'' blue butterflies have diverse chromosome numbers ranging from n=10 to n=134 and additionally have one of the highest rates of speciation identified to date.<ref name="Butterflies">{{cite journal | vauthors = Kandul NP, Lukhtanov VA, Pierce NE | title = Karyotypic diversity and speciation in Agrodiaetus butterflies | journal = Evolution; International Journal of Organic Evolution | volume = 61 | issue = 3 | pages = 546–559 | date = March 2007 | pmid = 17348919 | doi = 10.1111/j.1558-5646.2007.00046.x | doi-access = free }}</ref>

[[Cilliate]] genomes house each gene in individual chromosomes.

===Organelles===
{{Main|Organelle}}
[[File:Animal cells SwissBioPics DL20221120.svg|thumb|150x150px|Animal cell showing organelles.]]
In addition to the [[Nuclear DNA|nuclear genome]], endosymbiont organelles contain their own genetic material. [[Mitochondrion|Mitochondrial]] and [[chloroplast]] DNA varies across taxa, but [[Membrane-bound protein (disambiguation)|membrane-bound protein]]s, especially [[electron transport chain]] constituents are most often encoded in the organelle.  Chloroplasts and [[Mitochondrion|mitochondria]] are maternally inherited in most species, as the organelles must pass through the [[Egg cell|egg]].  In a rare departure, some species of [[mussel]]s are known to inherit mitochondria from father to son.