Basic concepts of evolution

Chromosome and gene

To introduce the chromosome and gene, we have to start from DNA. DNA is short for DesoxyriboNucleic Acid, and it is the basic storage of entire genetic information. In general, DNA comprises of a long chain of base pairs in which each pair is a carrier of some genetic information. The genetic information is stored as DNA, and exists in the nucleus of an organism cell which is known as the genome. The genome is further separated into a few chromosomes. Note that, for some organisms, they might have a single chromosome in the nucleus, other than the genome. Compared with a chromosome, a gene or allele refers to a series of base pairs which is determined by the phenotypical traits, and its locations on the chromosome are called locus. In evolution, different genotypes can be created by changing an allele on a locus of a genotype, and the phenotype is the genotype’s physical realisation, where it reflects specific behaviours of the genotype. Figure 4.2 illustrates chromosome and gene of an organism.

Figure 4.2: Chromosome and gene of an organism, a cell contains a genome (a few chromosomes) or a single chromosome depending on the type of organism. Genetic information is stored on DNA, and DNA comprises of a long chain of base pairs. A set of base pairs is called a gene, which controls organism’s physical traits. The position of gene is known as locus (GENCODYS, 2010).

Cell reproduction

The types of cell reproduction are amitosis, mitosis and meiosis. Amitosis is for a eukaryotic cell division but without nuclear envelope breakdown, chromosomes condensed and visible spindle are formed. Opposite to amitosis, mitosis divides eukaryotic cells into two involving nuclear envelope breakdown, chromosomes condensed and visible spindle are formed. Among these cell reproduction types, meiosis is a major type for an organism with sexual reproduction, and it is important as it allows parent genetic information to be mixed for offspring (Starr, 2007). Meiosis is facilitated in two major steps (Toole and Toole, 1999; Starr, 2007) as shown in Figure 4.3: In the first step, paternal and maternal chromosomes of a diploid cell, are aligned and formed as homologous chromosomes, where a diploid cell refers a cell that contains two sets of chromosomes and each set is inherited from each parent. Note

Chromatid self copied Form tetrad Two chromatids Crossover at chiasmata Cell division Cell division Cell division 4 Gametes

Meiosis step I Meiosis step II Homologous

Chromosomes

Interphase

Figure 4.3: Detailed process of meiosis: A diploid cell contains paternal and maternal chromosomes, or called chromatids (single pair). In the interphase, chromatids are self copied. In the first step of meiosis, chromosomes are aligned and formed as homologous chromosomes – tetrad. The paris of chromatids are joint at random crossing points – chiasmata. In the second step of meiosis, chromatids are first divided into two cells, and further divided into four sets of chromosomes stored in gametes.

that a diploid cell has both the paternal and maternal genomes, and these genomes are self copied formed as two chromatids. As each chromatid has two pairs of homologous chromosomes, in this case, it is called tetrad. Then the pairs of chromatids are joint at a few random crossing points, known as chiasmata, and the exchanged parts between the chiasmata is called crossing over. In this way, it allows the paternal and maternal genetic information to be mixed. Subsequently, these mixed chromatids are obtained at the end of the first step. In the second step, these chromatids are first divided into two cells, and further divided into four sets of chromosomes stored in four separated cells – gametes. Since each cell only has one set of chromosomes (the mixed genome), it is called haploid.

Haploidy and diploidy cells

Although there are not only haploid and diploid (cells) creatures, these two are related to higher-level creature evolutions. For example, human beings are diploid creatures, but the gamete is haploid since meiosis exists. However, when the mating process occurs, two gametes are merged and produce a new diploid cell, where paternal and maternal genomes are inherited simultaneously. Subsequently, a new child grows from the new diploid cell, and its development process is known as ontogenesis. Compared with the diploidy creatures, in the haploid creatures, the genome is directly copied to a new cell, and the new cell is further developed in the ontogenesis process. In this way, the responses of the genome in ontogenesis are all passed to the offspring, most of EAs are based on this process (Langeheine, 2005). On the other hand, in the diploid creatures, their phenotypes are dependant on the mixed maternal and paternal genomes, and so are not fully correlated to a former genome.

Mutations

Mutation is an important mechanism to drive evolution, and involves vari- ations in the evolutionary process. Mutation can occur at the gene level, chromosome level or the genome level. This section focuses on the first two levels as these concepts are close to EAs. The smallest mutation happens at the gene level, where partial base pairs are replaced by other base pairs in the DNA. However, this might not change the phenotypical traits. On the chromosome level, the mutation can occur on a single chromosome, or two or more chromosomes. On a single chromosome, one or more genes might be deleted, and these genes will no longer be in the genome. In addition, the

order of some genes on a chromosome can be reversed (180◦) and reinserted in

the chromosome itself. For two chromosomes, where these two chromosomes need to be initially homologous, but later non-homologous, the mutation is usually classified as duplication and translocation. In a duplication muta- tion, a segment of one chromosome is inserted into the other chromosome

– this segment is omitted from the first chromosome and it is duplicated in the second chromosome. Similar to the crossing over, the genetic material changes since the duplication causes the genetic material position to shift on chromosomes, and this phenomenon is known as translocation (Toole and Toole, 1999).

Ontogenesis

Ontogenesis is a relatively complex process which involves the conversion of the DNA stored genetic information into phenotypical traits under a particular environment. In terms of a genome, it can carry a large amount of genetic information, but not all the information can be used to encode the phenotype. Put simply, a genotype to phenotype mapping can be summarised as the following two major steps: First, to guide a protein synthesis, the DNA attached genetic information will convert to a special substance called messenger RNA (RiboNucleic Acid), and this process is known as transcription. Second, the messenger RNA will instruct the amino acids to form different proteins, and these proteins are the sources to produce and control traits of an organism or creature.