Most people have heard of family trees and know that they are used to illustrate family histories or genealogies. A child’s drawing of a family pedigree showing the relationships of his/her immediate family is a well-known classroom exercise at schools. We also use this family tree concept in evolutionary biology to learn more about the histories of biological organisms.
Taxonomy is the field of biology that focuses on describing and naming organisms, and determining how they are related. Early taxonomists relied heavily on the external appearance of organisms (e.g. shape, colour, size, number and appearance of body parts such as scales) to classify them. Nowadays, more advanced methods, namely phylogenetics using DNA sequences, are available to taxonomists.
Phylogenetics, an area of research that deals with the study of evolutionary relationships among groups of organisms, seeks to establish the genetic relationships existing between populations or species. These relationships are revealed mainly through molecular sequence data (i.e. the organisation of amino acid bases in parts of the DNA molecule). This can be used in conjunction with morphological data to characterise a species. Phylogenetics compares specific characters of species under the assumption that species with similar characters are genetically closely-related.
Systematic biology aims to delimit species and reconstruct phylogenetic relationships through time. Unfortunately, history is not something we can see. It happens only once, but fortunately for us it leaves behind clues which taxonomists use to reconstruct evolutionary history. DNA accumulates mutations over time and these are inherited from one generation to the next. This means that DNA molecules contain historical genetic material. Species that have the same mutations share a recent common ancestor.
Genetic data has become especially useful for determining the relationships between species, and groups of related species (i.e. genera), and identifying cryptic species that are virtually identical to other species in appearance. A species is defined as a large group of organisms on the same evolutionary trajectory that is capable of mating and producing fertile offspring.
Modern phylogeneticists use information extracted from genetic material, mainly DNA, to look for differences in single-position sites (bases or amino acids) after aligning several such sequences.
If a taxonomist is working on geckos, a group of small-bodied nocturnal lizards usually found in or around stones or rocks, the following procedure is followed in order to obtain genetic information. Firstly, DNA is extracted from liver or muscle tissue in a ‘genetics’ or ‘molecular’ laboratory. A polymerase chain reaction (PCR) is then applied to amplify a specific gene region using specialised machines.
PCR products, which are in liquid form, are then loaded into an automated DNA sequencer machine. The liquid runs through a glass-fiber capillary, and the different nucleotides (A: Adenine, G: Guanine, C: Cytosine, T: Thymine) fluoresce in different colours. The sequencer is able to interpret the colours into text files containing only nucleotide sequences, and these we use for analysis using phylogenetic computer programs.
The DNA sequences can be aligned with other such sequences to identify matching sequences and mutations that make them distinct. Sequence alignments allow us to quantify differences in the sequences that can be easily visualised through phylogenies (including ‘family tree’ diagrams) using specific computer programs designed for this purpose. This allows us to learn how much variation there is within and between species. The term ‘phylogeny’ refers to such relationships, representing evolutionary relationships in one or more populations of an organism. Phylogenies are widely used in evolutionary biology as they are considered to be an approximation of species relationships.
In a recent study that investigated phylogenetic relationships within a group of endemic flat geckos (genus Afroedura) we incorporated genetic data that indicated that populations from different hills, which were thought to belong to one wide-ranging species, were actually cryptic species. Individuals from various populations were similar in external appearance, but represented different genetic lineages, or put differently, they represent separate species. Even though there are genetic differences between them, morphological similarities show that at one point these populations were part of a super-population.
Species are the cornerstone of biology. Their correct delimitation is essential because when species boundaries are properly estimated the number of real entities in nature that are evolving individually, i.e. species, can be correctly inferred. Modern taxonomic revisions using DNA data have led to the recognition of numerous additional species, many of them cryptic species. Examination of multiple genetic datasets, combined with morphological or ecological information, is now standard for modern taxonomic revisions.
Bibliography
Conradie, W., Measey, G.J., Branch, W.R., Tolley, K.A. 2012. Revised phylogeny of African sand lizards (Pedioplanis), with the description of two new species from south-western Angola. African Journal of Herpetology 61: 91–112.
Makhubo, B.G., Tolley, K.A. & Bates, M.F. 2015. Molecular phylogeny of the Afroedura nivaria (Reptilia: Gekkonidae) species complex in South Africa provides insight on cryptic speciation. Molecular Phylogenetics and Evolution 82: 31–42.
Rissler, L.J., Hijmans, R.J., Graham, C.H., Moritz, C., Wake, D.B. 2006. Phylogeographic lineages and species comparisons in conservation analyses: a case study of California Herpetofauna. The American Naturalist 167: 655–666.
Wiens, J.J. & Penkrot, T.A. 2002. Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus). Systematic Biology 51: 69–91.
The structure of part of a DNA double helix. (Photo: Wikimedia Commons).
Chemical structure of DNA. Nucleic acid double helices will only form between two strands of complementary sequences where the bases are matched into A-T or G-C pairs. (Photo: Wikimedia Commons)
A sequence alignment of four Afroedura amotolica (Amatola Flat Gecko) samples from geckos collected from two different hills. Similar bases are highlighted in green below the consensus sequence. Note changes in bases 03, 23, 25 and 28 highlighted in yellow.
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