Segments of chromosomes can be duplicated, deleted, translocated, and
inverted. All of these types of chromosomal changes are known to occur
within human populations. When comparing the genome of one species to
another, many observed differences can be attributed to segments of chromosomes
which have been duplicated, deleted, translocated, and inverted. These
chromosomal arrangements are implicated in the reproductive isolation
of populations and the formation of new species. The first steps in this
speciation would occur when a population accumulates alleles which increase
its fitness in its specific environment (as opposed to the environments
of other populations of the species). If a chromosomal inversion subsequently
occurs near or includes this adaptive locus, it would deter recombination
with the parental chromosomes since hybrids would be at a disadvantage.
Chromosomal rearrangements (which include fissions and fusions) could
effectively isolate two populations although there would be difficulty
in establishing a population which the new chromosomal type at first.
Eventually, a population with genes that adapt it to a specific environment
would be reproductively isolated from related populations.
In insects, chromosomal changes have been implicated in the recent speciation
of fruit fly and mosquito species groups (Ayala, 2005). The large salivary
chromosomes of flies make them ideal for the study of chromosomal inversions.
Because inversions are more difficult to study in most other species,
their frequency is probably underestimated (Kirkpatrick, 2006).
Most of the segmental duplications on human chromosome 16 have resulted from a specific locus LCR16a organized into 17 blocks which compose more than 10% of the euchromatic portion of the chromosome. Each of the ape species has also experienced intrachromosomal duplications (15–200 kb in size) originating from this region. Old World monkeys possess only one LCR16a block.About 450 regions have been identified as contributing to multiple segmental duplications within ape genomes (Johnson, 2006). In ancestral anthropoid primates, a segmental duplication occurred in the chromosomal region 1q22 region. Two new genes unique to anthropoid primates resulted from this duplication (Kuryshev, 2006). Segmental duplications seem to have been occurring at a rate of 4 to 5 million bases per million years in human and chimp lineages (Britten, 2006). Some genomic areas which have undergone segmental duplications are hotspots for copy number variations (CNVs) which can affect human phenotype and disease susceptibility. Many of the same regions in the chimp genome are sites of CNVs which contribute to genetic diversity among chimps (Perry, 2006). For example, a reduced copy number of the CCL3L1 gene is linked to increased HIV infection risk (Perry, 2006).
Microinversions can alter genomes and can be found in diverse genomes, including those of chimps and humans. Typically a species accumulates one microinversion per megabase every 66 million years (Chaisson, 2006).
In the past several thousand years, the mosquito species complex related
to Anopheles gambiae has diversified and chromosomal rearrangements are
implicated in their diversification (Ayala, 2005).
The mosquito genus Anopheles has been intensively studied because of its
role in spreading malaria. There are nearly 500 known species in the genus,
of which at least 170 are difficult to distinguish from other species
which are almost identical. These 170 species are classified into 30 species
complexes. The following paragraph contains an analysis of the species
complex of the malaria host A. gambiae (Ayala, 2005).
At least 6 thousand years ago, Anopheles arabiensis migrated from the
Middle East to Africa where it gave rise to a new species, Anopheles quadriannulatus.
Three chromosomal inversions help to reproductively isolate these species.
Anopheles quadriannulatus populations diverged into two separate species
(A. quadriannulatus A and A. quadriannulatus B ) which subsequently diverged
again produce to Anopheles bwambae and Anopheles melas from one lineage
and A. gambiae from a second lineage. These seven species are nearly identical
morphologically and thus the chromosomal inversions which separate these
species are important for their identification. Less than four thousand
years ago, Anopheles quadriannulatus adapted to human hosts and habitats
other than rainforests to become the A. gambiae which is so devastating
because of the malaria it can carry. Anopheles quadriannulatus and A.
gambiae are reproductively isolated because of genes located within two
inversions on the X chromosome. A. gambiae, A. arabiensis, and A. melas
have all produced populations which are in the process of diverging through
sympatric speciation and are all accumulating chromosomal inversions which
distinguish them (Ayala, 2005).
Drosophila pseudoobscura and Drosophila persimilis can hybridize in nature
although it only occurs occasionally. It seems that chromosomal inversions
which lead to sterility after interbreeding are the main source of reproductive
isolation (Noor, 2001). D. persimilis and D. pseudoobscura can occur in
the same areas. Although hybrid females are fertile, hybrid males are
sterile. Most of the genes which reproductively isolate these species
(including hybrid sterility, courtship dysfunction, and sexual isolation)
are located in chromosomal regions which have undergone inversions since
the parental species differentiated. It is thought that these species
shared a common ancestor 500,000 years ago (Ayala, 2005). Within 20 years
after being introduced to the New World, D. subobscura populations in
different habitats are already developing inversions (Kirkpatrick, 2006).
Allopatric isolation is the key to speciation in many species of birds.
Nevertheless, there are examples of closely related birds which differ
in chromosome number or the presence of chromosomal inversions, suggesting
that chromosomal changes can promote speciation as well (Grant, 1997).
A number of interchromosomal and intrachromosomal rearrangements have
occurred between mouse and rat genomes (Zhao, 2004). Mus terricolor and
Mus booduga are a pair of sibling species of field mice which coexist
in India. While the chromosomes of Mus booduga are similar to the ancestral
state, Mus terricolor populations can be divided into three separate chromosomal
species (labeled I, II, and III) which vary in the chromosome structure.
Within populations of these species, additional chromosomal changes (such
as chromosomal fusions and inversions) which still allow fertile hybridization
with chromosomally typical individuals (Sharma, 2003).
The genus of African mole rats Fukomys (Rodentia: Bathyergidae) is not
only one of the most species-rich genera of rodents, it is among the mammalian
genera in which chromosomal number displays the greatest variation (2n=
40 through 78). Given the chromosomal variation of known species, and
the likely identification of cryptic species based on chromosomal variations,
chromosomal changes seem to be a major factor in the speciation of this
group (Van Daele, 2007).
Pericentric inversions are known which distinguish the Sumatran and
Borneo subspecies of orangutans (Ayala, 2005). The numerous inversions
which separate human and chimp chromosomes and the fusion of two ancestral
ape chromosomes into human chromosome 2 may have been important in the
reproductive isolation of ancestral hominids from other apes (Ayala, 2005).
About 300 chromosomal rearrangements seem to have occurred since the divergence
of the human and mouse genomes (Nimura, 2003).
Other examples of speciation which has involved chromosomal rearrangements
are known ranging from yeast to sunflowers (Mallet, 2006; Ayala, 2005).
Transposable elements can cause chromosomal inversions. Some of these
chromosomal changes are species specific and may play a role in speciation
in species as diverse as yeast, fruit flies (such as Drosophila buzzatii),
and humans (such as the LINE-1 element which caused a species-specific
inversion on the Y chromosome) (Evgen, 2000).
Some species have genetic mechanisms which inactivate the transposable
elements which have inserted into their genome. When species hybridize,
it has been observed that the viability of hybrids can be decreased due
to activation of these transposable elements which disrupt the genome.
In the Drosophila virilis species group, the families of transposable
elements which have been shown to cause chromosomal abnormalities (such
as inversions, translocations, and deletions) in inter-species hybrids
include the Ulysses, Helena, Paris, Telemac, and Penelope families (Evgen,
Is polyploidy possible? There are many modern species which have arisen
through more recent polyploidy events ranging from microorganisms to vertebrates.
For example, chromosome comparisons indicate that polyploidy has occurred
in microscopic yeast. The number and arrangement of multiple copies of
genes indicate that a tetraploid genome duplication resulted in yeast
after the divergence of the genus Saccharomyces from Kluyveromyces (Wolfe,
1997; Ohno from Muller, 1998).
In the early 1900s, the botanist deVries observed a primrose (Oenthura
gigas) with a polyploidy chromosome count which could not be crossed with
its parent species O. lamarkianon (Campbell, 2003). Among plants, polyploidy
is most common among flowering plants (where it may be the cause of half
of all species) and ferns. Many species utilized by humans (wheat, tobacco,
potato, banana, strawberry, and coffee, for example) are polyploidy. Allopolyploidy
seems to occur more frequently than autopolyploidy (Ayala, 2005).
Polyploid events seem to be responsible for 2 to 4% of the new species
of flowering plants and 7% the new species of ferns (Otto, 2000; Coyne,
2007). Given that more than 99% of fern species are estimated to be polyploidy,
polyploidy seems to have been important in the early diversification of
ferns in addition to an important mechanisms for new speciation (Otto,
2000; Starr, 2006).
The frequency of polyploidy varies with environmental conditions (with
temperature being an important variable), parental genotype, and whether
or not the parents were hybrids (in which case the frequency of polyploidy
increases). Given that under certain circumstances the incidence of polyploidy
increases, the possibility of a polyploidy population which could interbreed
would also increase (Otto, 2000).
Although polyploidy does not occur as frequently in animals as in plants,
hundreds of separate polyploidy events are known modern and ancient events.
Polyploidy is common (42%) among decapod crustaceans whose diploid chromosome
counts vary from 54 to 376.
Polyploidy is more common among asexual/parthenogenetic species, hermaphroditic
species (such as plants), and in species which determine gender with a
Y chromosome (rather than an X to Y ratio) and without dosage compensation
(Otto, 2000). Examples of polyploid worms and planarians are thought to
have originated from hermaphroditic parent species and polyploidy shrimp,
sow bugs, moths, beetles, fish, and amphibians are thought to have originated
from parthenogenic species (Ayala, 2005).
The fish family Salmonidae seems to have arisen after an autotetraploid
event and considerable chromosome variation has occurred since. In the
family, chromosome numbers vary from 74 to 170 (Phillips, 2001). The common
carp (Cyprinus carpio, 2n=104) is a tetraploid species compared to the
grass carp (Ctenopharyngodon, 2n=52) (Ohno from Muller, 1998). Tetraploid
hybrids of red crucian carp (Carassius auratus) and common carp (Cyprinus
carpio) are known and were fertile (Liu, 2001). Salmon and catastomids
are tetraploid, unlike other fish in their order. (Hoyle, 1998; Lundin,
In amphibians, Xenopus laevis possesses 36 chromosomes while X. ruwensoriensis
possesses 108. Virtually all of the species in the subfamily Xenopodinae
are polyploid (Flajnik, 1991; Wu, 2003). In the frog genus Ceratophyrs,
C. calcarata possesses 26 chromosomes, C. ornata is known with both diploid
(26) and octoploid (104) individuals, and C. dorsata possesses 104 chromosomes.
In the genus Odontophrynus, diploid (2n=22) and tetraploid (2n= 44) are
known. The same diploid and tetraploid counts are known in the genus Pleurodema.
Diploid and tetraploid species are known in the genus Hyla and Phyllomedusa
(Chiarelli, 1973). Triploid chickens are not uncommon and there is one
line of chickens which often produces triploid offspring (20% of embryos
and 8-12% of hatchlings) (Solari, 1994). It is possible that the increased
cell volume of polyploid frogs affects their vocalization and underlies
the relative frequency of polyploidy in frogs (Otto, 2000).
Polyploidy typically increases cell volume, slows developmental time,
increases overall body size (in invertebrates and plants but not vertebrates),
and in plants is often associated with a change of flowering time (Otto,
2000). A mutation is more likely to be beneficial in a polyploidy since
the original alleles would still be intact. Changes in the tissue expression
ranges and developmental timing of duplicate genes is known in organisms
as diverse as yeast and vertebrates (such as fish and frogs) (Otto, 2000).
Only a fraction of the original duplicate genes are ultimately retained
(8% in yeast after 100 million years, 72% in maize after 11 million years,
77% in the frog Xenopus in 30 million years, and 33% in vertebrates after
540 million years) (Otto, 2000).
POLYPLOIDY IN ANCESTRAL VERTEBRATES
A great deal of evidence suggests that two such genome duplications occurred
before the evolution of the jawed vertebrates from primitive chordate
ancestors. Tunicates have 6% DNA content as mammals (Lundin, 1993). The
genome of tunicates, about 160 million base pairs, is about 20 times smaller
than that of humans. The predicted 15,000-16,000 genes is a number similar
to that found in other nonvertebrates (such as fruit flies, 14,000, and
nematodes, 19,000). The tunicate genome is intermediate in many ways between
invertebrates and vertebrates (Dehal, 2002). . A few hundred tunicate
genes are more similar to those of protostomes than to those of vertebrates.
Tunicates have 6 FGF genes (compared to 1-2 in protostomes and 22 in mammals),
5 Smad genes (which include TGF-ß and bone morphogenetic proteins;
8 genes of this family are known in mammals), and 10 T-box genes (mammals
have 18) (Dehal, 2002).
From the analysis of Hox sequences in hagfish, it appears that at least
one of the genome duplications early in vertebrate evolution occurred
before craniates evolved and it seems that additional duplications occurred
in hagfish after this. The second genome duplication event occurred in
the gnathostome lineage after its divergence from that of lampreys, although
additional duplications may have susequently occurred in lampreys(Stadler,
2004; Hahn, 1998; Escriva, 2002; Hoyle, 1998). The following pattern is
frequently observed in comparative genomics in which vertebrates have
four homologs of single invertebrate genes.
There are a number of cases in which a single invertebrate gene is homolgous
to four vertebrate genes. This is observed in Hox clusters, syndecan,
myc, BMP (5-8), EGFR/ERBB2-4, ENGR, GPC, ID, JAK (non-receptor kinases),
MEF (MADS box enhancing factors), NOTCH, Src kinases, and Src-related
kinases. There are a number of gene families in which three vertebrate
genes are homologous to a single invertebrate gene, perhaps after one
member was lost; these include aldoase, Alzheimer -amyloid protease inhibitors,
ankyrin, Bruton's tyrosine kinase, cadherin, calmodulin, caudal homeobox
genes, collagen type IV, cathepsin (cystein protease), Dlx homeobox proteins,
E2A transcription factors, exrin, glioblastoma family zinc fingers, hedgehog,
insulin receptors, integrin chains, laminin chains, laminin chains, MyoD
transcription facots, myosin heavy chains, nitric oxide synthases, Pbx
homeobox, Raf kinases, Ras, retinoblastoma, retinoic acid receptors, Stat,
tenascin, and Wnt (wingless signalling factors (Spring, 1997). The observation
that shared regions between human chromosomes indicate large-scale duplication,
has allowed the positions of additional genes (such as PBX and NOTCH family
members) to be predicted and located (Katsanis, 1996). Regions of human
chromosomes 1, 6, 9, and 19 are homologous and contain trilogues and tetraloges
(such as notch, PBX, heat shock proteins, retinoid receptors, tenascin,
calcium channels, collagen alpha chians, ABC transporters, complement
proteins (Ohno from Muller, 1998 ; Lundin, 1993).
The comparative analysis of the genomes of teleosts and other vertebrates
indicate that genome duplications have occurred at the base of the teleost
lineage. The teleost lineage was subsequently characterized by substantial
gene loss from this polyploidy event and, at least in the teleost Fugu,
there are relatively few new genes which have evolved from duplications
since then. In contrast, the lineage which led to humans developed many
new genes from duplications and thus many human genes are younger than
those found in Fugu (Vandepoele, 2004). Additional copies of a number
of genes (such as bHLH, interleukin, and Sox genes) are located in chromosome
regions which seem to have undergone duplication in teleosts (Chiang,
2001; Ledent, 2001; Galay-Burgos, 2004, Bowles, 2000; Magor, 2001).