CHROMOSOMES AND SPECIATION

CAN CHROMOSOMAL EVENTS PROMOTE THE FORMATION OF NEW SPECIES?

EVOLUTIONARY MODEL

If the evolution model is correct, then the changes in chromosomal structure and number which are occasionally observed in humans and other species are potential sources of new genetic information and mediators of reproductive isolation. The evolutionary model would predict that chromosomal changes would be involved in hybrid sterility and the reproductive isolation of populations. The evolutionary model would predict that over long periods of time, multiple copies of genes would allow the descendents of polyploids to utilize the extra copies to achieve greater complexity.

CREATIONISM MODEL

If creationism and intelligent design are true, chromosomal changes would not be expected to be associated with speciation or increases in complexity.

INTELLIGENT DESIGN

If intelligent design is true, chromosomal changes would not be expected to be associated with increases in complexity. The genes which are located in duplicated portions of the genome should not be integral to the development of novel complex structures.

CHROMOSOMAL REARRANGEMENTS
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).


MOSQUITOES
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).

FRUIT FLIES
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).
MAMMALS

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, 2000).
POLYPLOIDY
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, 1993).
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).

TELEOSTS
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).