The expansion of conservation genetics

Key Points

  • Conservation biology is considered to be a 'crisis discipline', and therefore requires an arsenal of approaches and techniques to ensure that educated, rapid decisions about endangered species and threatened areas are made.

  • The expansion of genomic technologies in data acquisition, storage and analysis has assisted in increasing the efficiency of the field of conservation genetics and in helping conservation decision-making.

  • Conservation genetics leads us to a better picture of pattern and process in endangered species, and allows the use of pattern and process in conservation decision-making.

  • The most important applications of conservation genetics in the future will be those that incorporate both pattern and process into a cohesive approach to decision-making.

  • A wide range of unconventional sources for DNA is used in conservation work; this includes faeces, feathers, fur, sloughed-off skin, plants from herbarium sheets and clever direct-biopsy approaches that minimize invasiveness.

  • One approach that will be increasingly important in the expansion of conservation genetics concerns recent efforts to form centralized DNA barcode databases and DNA registries.

  • Conservation genetics itself needs to be placed in the context of the difficulties of working across political boundaries, amidst economic challenges and in the face of the complexity of using science to inform management decisions.

Abstract

The 'crisis discipline' of conservation biology has voraciously incorporated many technologies to speed up and increase the accuracy of conservation decision-making. Genetic approaches to characterizing endangered species or areas that contain endangered species are prime examples of this. Technical advances in areas such as high-throughput sequencing, microsatellite analysis and non-invasive DNA sampling have led to a much-expanded role for genetics in conservation. Such expansion will allow for more precise conservation decisions to be made and, more importantly, will allow conservation genetics to contribute to area- and landscape-based decision-making processes.

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Figure 1: Map of conservation priority areas based on levels of human disturbance across all terrestrial landscapes.
Figure 2: Cetacean conservation genetics.
Figure 3: Ex situ conservation genetics: the Amazon parrot example.

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Acknowledgements

The authors thank M. Russello for assistance in preparing figure 3e and acknowledge the continued support to the Conservation Genetics Program from the American Museum of Natural History (AMNH) Center for Biodiversity Conservation. R.D. thanks the Louis and Dorothy Cullman Program for Molecular Systematics at the AMNH.

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Correspondence to Rob DeSalle.

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FURTHER INFORMATION

Bacterial Nomenclature Up-to-Date

Glossary

SYSTEMATICS

The field of biology concerned with the diversity of life on Earth. Systematics is usually viewed as having two components — phylogenetics and taxonomy.

RANDOMLY AMPLIFIED POLYMORPHIC DNA

(RAPD). DNA fragments that are generated by PCR using one or two randomly selected oligonucleotides or primers and are polymorphic in size.

MINISATELLITES

Regions of DNA in which repeat units of 6–100 bp are arranged in tandem arrays that are 0.5–30 kb in length

RESTRICTION-FRAGMENT-LENGTH POLYMORPHISM

(RFLP). A fragment-length variant of a DNA sequence that is generated through the gain or loss of a restriction site due to a DNA substitution.

ALLOZYMES

Co-dominant nuclear DNA markers that consist of enzymes that differ in their mobility on a charged gel.

PARAPHYLETIC

A term applied to a clade of organisms that includes the most recent common ancestor of all of its members, but not all of the descendants of that most recent common ancestor.

AMPLIFIED-FRAGMENT-LENGTH POLYMORPHISM

(AFLP). A DNA marker generated by digestion of genomic DNA with two restriction enzymes to create many DNA fragments, followed by ligation of specific sequences of DNA (adaptors) to the ends of these fragments, amplification by PCR (using primers corresponding to the adaptors plus random combinations of three additional bases at the end) and visualization of the fragments by gel electrophoresis.

MICROSATELLITES

Co-dominant nuclear DNA markers that consist of sets of short, repeated nucleotide sequences.

INTER-SIMPLE-SEQUENCE REPEAT

(ISSR). DNA fragments found between adjacent, oppositely oriented microsatellites. DNA is amplified by PCR, separated by gel electrophoresis and scored for the presence or absence of fragments.

SUBSPECIES

A physically distinct subunit of a species.

EVOLUTIONARILY SIGNIFICANT UNIT

(ESU). A population of organisms that is reproductively isolated from other populations of the same species, and represents an important component in the evolutionary legacy of the species.

INBREEDING DEPRESSION

Reduction in fitness or vigour caused by one or more generations of inbreeding.

BREEDING EFFECTIVE POPULATION SIZE

The number of individuals that make up the breeding population in an idealized population.

MINIMUM VIABLE POPULATION SIZE

An estimate of the smallest number of individuals in a population that is capable of maintaining that population without significant manipulation.

WRIGHT'S INBREEDING COEFFICIENTS

Measures of inbreeding in a sub-population first devised by Sewall Wright to describe the amount of homozygosity in a population due to inbreeding. Measures of inbreeding at different hierarchical levels of comparison can be obtained using this approach.

COALESCENCE-THEORY-BASED ANALYSIS

A means of investigating the shared genealogical history of genes. A genealogy is constructed backwards in time, starting with the present-day sample. Lineages coalesce when they have a common ancestor.

POPULATION-VIABILITY ANALYSIS

(PVA). The process of identifying threats faced by a species and incorporating these threats into an estimation of the likelihood of persistence of a species for a given time in the future.

POPULATION-AGGREGATION ANALYSIS

(PAA). Provides a straightforward criterion for demarcating a phylogenetic break between aggregates of individuals. An aggregate is said to be distinct when an attribute or combination of attributes in one aggregate is fixed and different from an attribute or combination of attributes in another aggregate.

CLADISTIC DIVERSITY

A measurement that ranks areas for biodiversity-conservation priorities based on information in cladograms or phylogenetic trees. Also called phylogenetic diversity.

AREAS OF ENDEMISM

Geographical areas where maximal numbers of endemic species exist.

CETACEAN

An aquatic mammal of the order Cetacea, including whales, porpoises and dolphins.

MITOCHONDRIAL D-LOOP

The highly variable, non-coding, portion of the mammalian mitochondrial genome. A D-loop is the configuration found during DNA replication of chloroplast and mitochondrial chromosomes wherein the origin of replication is different on the two strands. The first structure formed is a displacement loop or D-loop.

SPECIES-SURVIVAL PROGRAMS

Programmes established by the American Zoo and Aquarium Association to ensure the survival of selected wild or captive species through cooperative genetic and demographic management.

CONVENTION ON IMPORTATION AND TRADE OF ENDANGERED SPECIES OF WILD FLORA AND FAUNA

(CITES). A convention first started in 1973 and established amongst participating nations to restrict the international commerce of plant and animal species harmed by international trade.

MANAGEMENT UNIT

(MU). A population, stock or group of stocks of a species that are aggregated for the purposes of achieving a desired conservation objective.

SEMISPECIES

An emerging species in the early stages of speciation.

INCIPIENT SPECIES

A newly formed species pair.

ENDANGERED SPECIES ACT

(ESA). A US congressional act established in 1973 that articulates guidelines and rules for the protection of species on the brink of extinction.

NATURAL; NATURALNESS

A thing is natural if it is not made by humans. Naturalness is the degree to which something is natural.

NATURAL IMPERATIVES

An essential and urgent duty to restore some aspect of the environment to its 'natural' state.

CONVENTION OF THE PARTIES

Also known as the Conference of the Parties to the Convention on Biological Diversity. An international organization dedicated to fostering conservation, sustainable use and equitable benefit-sharing concerning biological diversity.

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DeSalle, R., Amato, G. The expansion of conservation genetics. Nat Rev Genet 5, 702–712 (2004). https://doi.org/10.1038/nrg1425

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