of landscape genetics.
Defining Units of Conservation
Species are the typical focus of conservation, but just conserving species will not adequately protect intraspecific diversity, which is the basis of evolutionary potential. How are species and their constituent populations organized across their range? How should they best be protected? Fisheries biologists frequently try to distinguish stocks of fish for improved management – that is, uncovering “units of conservation” – a good example of which is the work of Zhivotovsky et al. (2015) on how a massive salmonid fish known as the taimen is organized around the Russian Far East.
Hybridization
Genetics is critical for measurement of hybridization between species. In many countries, hybrids are not protected by law. The ongoing controversy over listing the red wolf as an endangered “species” versus dropping protection because it is merely a hybrid of gray wolves and coyotes is one that pivots on new and ever more definitive genetic analyses published every few years (see Cahill et al. 2016). Hybridization is also a real threat to many rare species, and genetic methods enable us to detect the extent of the problem. Very occasionally hybrids can be used to restore depleted species (Edwards et al. 2013).
“Genes that Matter”
Most genetic analyses are based on “markers” with no known connection to the actual fitness. Which specific genes and alleles are actually tied to a particular challenge the species is facing? These genetic signatures of adaptation are critical for choosing the best individuals for rescuing a species, particularly in a changing world where certain alleles might be more advantageous. A good example is the use of scans of the entire genome of the endangered Przewalski’s horse of Mongolia to identify informative genetic markers to monitor and select for during captive breeding (Der Sarkissian et al. 2015).
Phylogenetic Prioritization
Knowing how one species is related to another is useful for at least three reasons. The first is identification of distinct lineages in need of protection (e.g. cryptic cave fish: Niemiller et al. 2013). The second is understanding a species’ relative phylogenetic distinctiveness (e.g. for prioritizing lineages of freshwater mussels for protection: Jones et al. 2015). The third is mapping areas of their world where evolutionary distinctiveness is concentrated (Jetz et al. 2014).
Trade
Molecular genetics has been helpful for identifying the sources and identity of traded species, for example in the case of elephant ivory (Wasser et al. 2015), caviar from endangered sturgeon (Fain et al. 2013), and mahogany in the timber trade (Degen et al. 2013).
Diagnosing Disease
Disease is a primary threat to many species but it is often difficult to diagnose based solely on external symptoms. Screening for the DNA of possible disease agents has revolutionized diagnosis and treatment, for example for many amphibians (e.g. Collins 2013) and Tasmanian devils (Morris et al. 2015).
Environmental DNA
Environmental DNA, or eDNA, is DNA collected from environmental samples such as soil, water, or even air rather than directly sampled from an individual organism. Such eDNA usually originates from shed skin cells that accumulate in an organism’s environment via feces, mucus, gametes, shed skin, carcasses, and hair. Sometimes, eDNA can be extracted from the meals found in guts of blood‐sucking or predator arthropods. Samples of the environment where organisms of interest might live can be analyzed with DNA sequencing methods, known as metagenomics, for rapid measurement and monitoring of species richness and community composition. eDNA is particularly useful for detecting rare species without having to capture them. The approach may eventually be able to tell us about population size and dynamics and species geographic distribution, but the methods are still under development. A helpful overview on the uses and limitations of eDNA is provided by Cristescu and Hebert (2018).
Genetic Engineering
We now are approaching a new era in which we can provide endangered species with new traits that enable them to deal with the threats they are facing. For example, scientists have transferred two genes from wheat into the American chestnut, conferring upon the chestnut resistance to a fungal blight that nearly eradicated it across the vast range in which it was a dominant species (Powell 2014). Genetic engineering may also generate novel genes that can be introduced into populations of invasive exotic species so that they limit their own numbers, a distinct possibility now for dealing with the scourge of endemic island species everywhere: black rats (Campbell et al. 2015). Genetic engineering falls within the realm of “synthetic biology” and offers extraordinary opportunities to address some seemingly intractable conservation issues (Piaggio et al. 2017) while also posing new ethical quandaries. Some straightforward applications include transplanting genes for resistance to white‐nose syndrome into bats and to chytrid fungus into amphibians, or giving corals that are vulnerable to bleaching carefully selected genes from nearby corals that are more tolerant of heat and acidity. More controversial would be eliminating populations of feral cats and dogs by producing generations that are genetically programmed to be sterile. The same is envisioned for eradicating mosquitoes without pesticides, including in areas where mosquitoes vector diseases that hobble endangered species, as in the case of birds in Hawaii. Perhaps most daunting, intriguing, and controversial of all is the possibility to resurrect extinct species through synthetic biology, grafting fragments of their DNA harvested from museum specimens into similar, extant surrogate species to recreate admixtures that largely appear and function as the original species once did (Shapiro 2017). This is being done using Asian elephants to snip into their genome functional and distinctive genes from extinct mammoths to recreate something resembling the latter to release upon the Siberian tundra to help clear woody vegetation, deepen penetration of freezing temperatures into the permafrost, and help slow the melting of the Arctic (Campbell and Whittle 2017).
CASE STUDY 5.1 Galápagos Giant Tortoises
The Galápagos Archipelago in Ecuador is home to many unusual species, including Darwin’s finches, marine and land iguanas, and, perhaps their most famous inhabitants, giant tortoises. These animals are indeed giants, weighing up to 400 kg. Giant tortoises were found on most continents during the Pleistocene but now persist only on two groups of remote oceanic islands: the Galápagos and the Seychelles. Only in the Galápagos do multiple populations survive, although only some 10 species of the original 15 still survive in the wild. A major reason for their endangerment is that an estimated 200,000 tortoises were taken from wild populations starting in the seventeenth century when buccaneers and whalers collected tortoises as a source of fresh meat.
Although they have been studied for centuries, recent research on Galápagos tortoises based on modern molecular genetic techniques has catapulted our understanding, starting with a 10‐year‐long effort to survey every remaining tortoise population, archiving blood samples and extracting DNA from some 5000 individual tortoises. DNA sequencing in mitochondria as well as microsatellites was undertaken to shed light on relationships among populations and to assist with designing captive breeding programs.
What has been learned? This research revealed a new species of giant tortoise (Poulakakis et al. 2015). On the largest island of Santa Cruz people have long known of a small and nondescript population of tortoises at a remote site named Cerro Fatal. Genetic analyses revealed that the Cerro Fatal tortoises are more different
