Molecular Ecology


Molecular ecology is a field of biology that uses molecular genetic data to address ecological questions in disciplines as varied as genomics, biogeography, conservation genetics, and behavioural ecology. The majority of studies in molecular ecology use data that are based on deoxyribonucleic acid (DNA) sequences, an approach that has been greatly enhanced in recent years by the advent of next‐generation sequencing, which collectively refers to methods that allow researchers to simultaneously sequence up to several thousand genes from a very small amount of starting DNA. In addition to DNA sequences, researchers can compare individuals and populations by characterising different versions of a particular gene (known as alleles) based on their sizes. By using molecular markers such as DNA sequences or allele sizes, researchers can quantify the genetic diversity within populations and the genetic similarity among populations. This in turn allows them to address specific questions pertaining to the ecology and evolution of species.

Key Concepts:

  • Molecular ecology uses molecular genetic data to address ecological questions.

  • A variety of molecular markers can be used to genetically characterise species and populations.

  • Next‐generation sequencing has greatly enhanced our ability to collect large amounts of genetic data at relatively low cost.

  • Molecular genetic data from natural populations allow researchers to quantify the genetic diversity within populations, and the genetic similarity among populations.

  • Genetic diversity is required for the long‐term survival of populations and species, and is influenced by a range of different factors.

  • Gene flow among populations strongly influences their genetic similarity.

  • Landscape genetics helps researchers to understand barriers to gene flow across a series of landscapes.

  • Eco‐genomics is a field of study that seeks to understand the genetic mechanisms behind adaptation and natural selection.

  • Behavioural molecular ecology uses highly variable molecular markers to differentiate individuals and to assign parentage.

  • Phylogeography uses molecular genetic data to infer some of the ways in which historical events and processes have shaped the current distributions of species.

Keywords: genetic diversity; genetic differentiation; gene flow; polymerase chain reaction; DNA sequencing; microsatellites; phylogeography; behavioural ecology; landscape genetics; eco‐genomics

Figure 1.

Part of the DNA sequence that comprises the mitochondrial genome of the common green darner dragonfly (Anax junius). Each large peak represents an individual base, and the corresponding sequence is written along the top of the image.

Figure 2.

A DNA sequence that includes a microsatellite repeat motif that was isolated from the cattail Typha latifolia (Ciotir et al., ). The microsatellite, which is (AT)12 – in other words twelve repeats of the motif ‘AT’ – is underlined. The number of ‘AT’ repeats at each allele is the main determinant of the allele length. The flanking sequences in bold show the DNA sequences to which the primers anneal when this microsatellite allele is being amplified during PCR.

Figure 3.

An electropherogram, from which the sizes of microsatellite alleles can be determined through comparison to size standards, which are DNA fragments of known sizes. In this figure, the allele sizes represent an individual that is heterozygous at this particular locus, with one allele of approximately 174 bp in length, and the second allele approximately 176 bp in length. Within the sequences amplified at this particular locus is a microsatellite motif ‘AT’. The difference between the sizes of these two alleles results from one additional ‘GC’ repeat in the 176 bp allele compared to the 174 bp allele. The relative fluorescent units (rfu) on the y axis refers to the intensity of the DNA fragment: when more DNA is loaded on the genotyping machine, the rfu (peak size) will increase.

Figure 4.

Results of a structure analysis that was done on orchids sampled from nine sites in Ontario. Each colour represents a genetic cluster, or lineage. In this example, orchids were sampled from nine sites, but Structure analysis concluded that they comprised four genetic lineages (denoted as red, blue, green and yellow). Each genetic cluster was recovered from two or more sites (e.g. the yellow genetic cluster was found in sites 8 and 9). Individuals are represented by vertical lines, and these can be most clearly identified for individuals with mixed genetic ancestry, and which are therefore made up of two different colours, for example, individuals that are half red and half blue comprise roughly 50% the blue genetic lineage, and 50% the red genetic lineage (which is seen in several individuals from each of sites 2 and 3).

Figure 5.

The current distribution of lineages in subpopulations A, B, C and D have been influenced by historical processes that occurred over different time scales. What was originally a single interbreeding population (step one) was divided by a desert that arose approximately 100 000 years ago (step two). The effect of this desert was to restrict gene flow between populations A and B, which over time led to the split between these populations that is illustrated by the first phylogenetic tree (the closer together groups are on the tree, the more closely related they are). More recently, the populations were further subdivided by an urban landscape that arose approximately 1000 years ago, which further restricted gene flow. The second phylogenetic tree shows that populations A and C are now split, as are populations B and D, although the relative recency of that split means that A and C remain more similar to one another than to B and D, and vice versa.



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Further Readings

Allan GJ and Max TL (2010) Molecular genetic techniques and markers for ecological research. Nature Education Knowledge 3: 2.

Allendor FW, Hohenlohe PA and Luikart G (2010) Genomics and the future of conservation genetics. Nature Reviews Genetics 11: 697–709.

Andrew RL, Bernatchez L, Bonin A et al. (2013) A road map for molecular ecology. Molecular Ecology 22: 2605–2626.

Diepeveen E and Salzburger W (2012) Two decades of molecular ecology: where are we and where are we heading? Molecular Ecology 23: 5656–5659.

Ellegren H (2014) Genome sequencing and population genomics in non‐model organisms. Trends in Ecology and Evolution 29: 51–63.

Freeland JR, Kirk H and Petersen S (2011) Molecular Ecology, 2nd edn. Chichester: Wiley & Sons.

Kirk H and Freeland JR (2011) Applications and implications of neutral versus non‐neutral markers in molecular ecology. International Journal of Molecular Sciences 12: 3966–3988.

Monsen‐Collar KJ and Dolcemascolo P (2010) Using molecular techniques to answer ecological questions. Nature Education Knowledge 3: 1.

Storfer A, Murphy MA, Spear SF, Holderegger AR and Waits LP (2010) Landscape genetics: where are we now? Molecular Ecology 19: 3496–3514.

Yoccoz NG (2012) The future of environmental DNA in ecology. Molecular Ecology 21(S1): 2031–2038.

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Freeland, Joanna R(Oct 2014) Molecular Ecology. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0003268.pub2]