The Taxonomic Basis of Subspecies Listed as Threatened and Endangered under the Endangered Species Act

Executive Summary

The US Endangered Species Act (ESA) protects species and subspecies that are in serious decline. 

The United States Fish and Wildlife Service (USFWS) relies on the experts who study particular organisms to decide what should count as a species or a subspecies. As a result, there is no single definition of subspecies across plants and animals, and these designations have been subjected to various levels of debate and controversy. 

Of the 170 subspecies listed as threatened or endangered, most were described decades ago using relatively primitive taxonomic methods. 

In this paper, authors Robert M. Zink and Luke B. Klicka examine—according to modern standards—the validity of subspecies currently listed. Their findings suggest that about one-third are valid, one-third are not, and one-third have not been tested. 

This is important because preserving a subspecies is expensive. Millions of dollars are being spent to preserve subspecies that do not merit conservation protection by modern standards.

The authors recommend that the USFWS reevaluate listed subspecies to determine whether they are taxonomically distinct and qualified to be listed under the ESA. Any future listing of a subspecies should be preceded by a modern assessment of the subspecies’ distinctiveness—that is, its taxonomic validity. They also recommend that the USFWS convene a panel of experts to agree on minimal criteria for listing subspecies, irrespective of the type of organism.

If the USFWS decides to follow these recommendations, it will free up funds to focus on the endangered species and subspecies that need the most protection.


More than 170 subspecies are listed as threatened or endangered under the US Endangered Species Act. Most of these subspecies were described decades ago using relatively primitive taxonomic methods. The status quo in government agencies is to accept all named subspecies as taxonomically valid. The US Fish and Wildlife Service basically defaults to taxonomists working with specific groups of organisms, and as a result there is no single definition of subspecies across plants and animals. However, the Integrated Taxonomic Information System maintained by the US Fish and Wildlife Service makes judgments about the validity of subspecies without providing supporting evidence. We find that subspecies designations repeatedly lack empirical and theoretical consistency, ranging from arbitrary divisions of single character clines to strongly supported evolutionary units. Valid tests today usually entail molecular analyses of variation within and among populations, including tests for significant differences between samples of the putative endangered subspecies and its nearest geographic relatives. Evaluation of data gathered since subspecies were described suggests that about one-third are valid, one-third are not, and one-third have not been tested. Therefore, it should not be assumed that because a subspecies is listed, it is taxonomically valid. Some new molecular methods (next-generation sequencing) will find differences between most if not all geographically separated populations, and it remains to be seen how these populations, whether named as subspecies or not, will be adjudicated under the Endangered Species Act. It will also be useful to explore whether listed subspecies are ecologically significant. A unified scheme to prioritize listed entities on the basis of their level of taxonomic and ecological significance is yet to be proposed or accepted.

Introduction to the Endangered Species Act and Taxonomic Categories

The legislative basis for much of the conservation effort in the United States is the Endangered Species Act (ESA), passed in 1973 and modified in 1978, 1982, and 1988. Given its title, one might expect it to apply only to species, but in fact it also can be used to list subspecies and distinct population segments (vertebrates only) as threatened or endangered. Listing decisions usually come about when either a U.S. citizen or organization, or the Fish and Wildlife Service itself, determines that the population size of one of these taxonomic entities places it in danger of extinction (endangered) or in almost as much peril (threatened). The species or subspecies is placed on a list of candidate species, and the Fish and Wildlife Service is directed to use the best available scientific or commercial data in making a ruling as to whether the taxon merits listing as endangered or threatened. In this paper we examine the taxonomic category or rank of subspecies. In particular, we determine whether modern tests of subspecies limits have confirmed the validity of listed subspecies, most of which were described more than a half-century ago.

Taxonomic Background and the Concept of Subspecies

Taxonomy and Concepts of Species and Subspecies

Systematists, taxonomists, and evolutionary biologists have struggled to define the term species for a century and a half. The biological species concept recognizes a species as a diagnosable distinct population or group of populations that is reproductively isolated from other such populations or groups. Lineage concepts, on the other hand, such as the phylogenetic species concept, recognize diagnosable populations or groups of populations as species irrespective of whether they can hybridize with other such groups (Cracraft 1983). That is, diagnosable subspecies of biological species would more than likely be considered phylogenetic species (Barrowclough et al. 2016). Many other species concepts have been offered, including recent ones that search for congruence among multiple loci or character sets: so-called species-delimitation approaches (Malaney et al. 2017). Several methods automate the process of converting data on molecular variation with and between populations into estimates of numbers of species (e.g., Luo et al. 2018).

Below the level of the species, the biological species concept considers geographically differing populations to be subspecies when they are distinguishable by phenotypic or genotypic characters and are (or are presumed to be) capable of hybridizing. In general, most lineage views of species do not consider subspecies, because diagnostically distinct populations that are (or are presumed to be) reproductively compatible would be considered species (de Queiroz 2007). Thus, the debate about species concepts is somewhat tangential to determining the geographic limits of populations proposed for listing, although some authors (e.g., Haig et al. 2006; Mallet 2007) have confused the relationship between species and subspecies concepts and the relevance of these concepts to conservation. Species are usually considered more important than the lower taxonomic ranks, and typically conservationists’ question is to list or not to list them, whereas with subspecies, the question is often whether they are taxonomically valid in the first place. See contrasting views of wolf (Canis lupus) species and subspecies taxonomy in which the same data were considered (National Academies of Sciences, Engineering, and Medicine 2019; Cronin et al. 2015).

What Exactly Is a Subspecies?

A subspecies is a formal taxonomic category that is specified by three Latin names: the genus name, the species name, and the subspecies name. Subspecies are described in different ways depending on the organism. Definitions of subspecies range from whatever a taxonomist says is valid to multi-character genetic and morphological assessments (Zink 1997). Some favor a rule in which 75% of individuals in a subspecies must be separable from 99% in another subspecies—clearly an arbitrary standard. Taylor et al. (2017) suggest that “a subspecies is a population, or collection of populations, that appears to be a separately evolving lineage with discontinuities resulting from geography, ecological specialization, or other forces that restrict gene flow to the point that the population or collection of populations is diagnosably distinct.” For butterflies, Braby et al. (2012) concluded that “definition of subspecies be restricted to extant animal groups that comprise evolving populations representing partially isolated lineages of a species that are allopatric, phenotypically distinct, and have at least one fixed diagnosable character state, and that these character differences are (or are assumed to be) correlated with evolutionary independence according to population genetic structure.” We believe that this definition provides sufficient criteria for recognizing a subspecies as valid and potentially qualified to be listed under the ESA should it become threatened or endangered. However, the subspecies category has been used in different ways by taxonomists in the same groups and in different groups. That is, the expectation from the definition proposed by Taylor et al. (2017) is evolutionary independence of subspecies, whereas the 75% rule carries no such connotation. This is a fundamentally important difference. The lack of consistency is presumably the reason the US Fish and Wildlife Service (USFWS) has no set definition of subspecies, instead relying on peer-reviewed literature that reflects the views of taxonomists in different groups. It would be beneficial to all involved if the USFWS would at least provide a minimal set of criteria for determining whether a subspecies is listable.

Historical Views on Subspecies

Issues surrounding subspecies have drawn considerable attention. In 1992, National Academy scientist John C. Avise wrote,

Taxonomic assignments inevitably shape perceptions of biological diversity. Therefore, it is disconcerting that many subspecies and species descriptions trace to very limited information, often gathered in the last century, on the distributions of a small number of (usually morphological) traits with unknown genetic basis. Yet once a Latin binomial or trinomial is in the literature, the group of organisms to which it refers almost automatically assumes an aura of reality that may or may not be commensurate with its true evolutionary distinctiveness. Given the overriding importance of taxonomy on biodiversity recognition and management, increased attention should be devoted to taxonomic assessments (from molecular as well as other data). . . . Population managers should therefore keep an open mind regarding taxonomic realignments, particularly for populations within the majority of species that have remained poorly studied.

Avise’s sentiment could not be truer today, and it is not unique. In 1953, Wilson and Brown wrote, “The subspecies concept is the most critical and disorderly area of modern systematic theory.” Mayr (1970) wrote, “This concept of the subspecies is fallacious. Species are not composites of uniform subtypes—subspecies—but consist of an almost infinite number of local populations, each in turn (in sexual species) consisting of genetically different individuals. . . . The better the geographic variation of a species is known, the more difficult it becomes to delimit subspecies and the more obvious it becomes that many such delimitations are quite arbitrary.” Remsen (2005) commented on avian subspecies, “Is it any wonder, therefore, that the roster of formal subspecies, most described before the advent of statistical methods in ornithology, contains many names that refer only to arbitrary points on clines, average differences between populations, or zones of intergradation . . . rather than to discrete entities?” Barrowclough (1982) wrote, “It seems curious that qualitative examination of color or a few skin measurements of a few specimens, often without statistical tests for clines or without adequate sampling of intermediate geographic areas, frequently results in trinomials, while the authors of large, quantitative studies frequently avoid them. This strongly suggests to me that most subspecies are not to be taken too seriously.” Zink (2004) wrote, “A massive reorganization of classifications is required so that the lowest ranks, be they species or subspecies, reflect evolutionary diversity. Until such reorganization is accomplished, the subspecies rank will continue to hinder progress in taxonomy, evolutionary studies and especially conservation.” Lastly, Burbrink et al. (in press) state succinctly: “We argue that the use of subspecies is indefensible on philosophical and empirical grounds.”

Of course, there are (at least) two sides to all issues. Patten and Remsen (2017) discount the concerns of Wilson and Brown (1953): “Wilson and Brown’s point of view was easy to understand because in that era many subspecies were being described for trivial or inconsistent reasons and with no little effort to establish standards.” Actually, Patten and Remsen (2017) inadvertently cast suspicion on subspecies listed under the ESA because, as we note below, 137 of the 176 subspecies (80%) were described before Wilson and Brown’s paper appeared. As we also note below, many avian biologists support the recognition of subspecies, both as a tool for evolutionary research (Winker 2010) and for use in conservation decisions.

Nonetheless, it is difficult to state the problem any better than Avise did three decades ago. What Avise did not accomplish, however, was to provide the details that support his argument. That is, every taxonomic description of a new subspecies provides some kind of supporting data for its recognition and significance, including the number of specimens examined, the number and location of sampling sites and the extent of the range examined, the number and types of characters, and statistical methods for analyzing character data. The pertinent question is whether these descriptions of subspecies, many adduced with century-old “technology,” are acceptable at face value today without assessments using modern technology. It seems obvious that conservationists should evaluate whether new technologies tend to validate or confirm the reality of a subspecies. We provide such an evaluation below.

Subspecies Studies: Some Good and Some Bad

Rigorous application of subspecies names has not historically been the status quo. Consider the Rio Grande subspecies (Meleagris gallopavo intermedia) of the North American wild turkey. The subspecific part of the scientific name, intermedia, was justified by the author (Sennett 1879) because it was his opinion that the turkey’s appearance was “intermediate” between two other subspecies. Exactly where it starts and stops being intermediate was not documented by the author, which understandably confounds placement of subspecies boundaries. There can be no better example of Mayr’s (1970) caricature of some subspecies than this turkey subspecies. Unless, perhaps, it is the subspecies of white-tailed deer(Odocoileus virginianus leucurus) from the Columbia River area that was described on the basis of a single specimen, which was later consumed by the hunter who harvested it.

There are several examples in which subspecies correspond to genetically or morphologically defined units that have experienced evolutionarily independent histories and therefore qualify for listing under the ESA. For example, the spotted owl (Strix occidentalis) has three subspecies: the northern spotted owl (S. o. caurina), California spotted owl (S. o. occidentalis), and Mexican spotted owl (S. o. lucida). Barrowclough et al. (2006; 2011) show that each subspecies is genetically distinct, with a narrow hybrid zone between northern and California spotted owls. Given their evolutionary independence, these subspecies are worthy of separate conservation status, and one could easily consider each one a species. Vázquez-Miranda et al. (2019) show that subspecies of the LeConte’s thrasher (Toxostoma lecontei) found in the Vizcaino Desert of Baja California, and populations to the north, are genetically distinct and qualify as units worthy of conservation status. Catanach et al. (2021) provide a textbook example of how a subspecies should be tested with modern methods. They examined the status of the hawk Accipter straitus venator from Puerto Rico using ultra-conserved elements (nuclear DNA), mitochondrial DNA (mtDNA), and morphology. Their study shows that the specimens from the island formed a discrete genetic cluster, and in fact they suggest A. s. venator be raised to a full species. The fact that the population is on an island reduces the chances that there will be clinal variation as a result of gene flow linking adjacent populations, as is often the case with widely distributed species on a continent.

These are three examples of subspecies that would be of interest to evolutionary biologists seeking to explain how and when differentiation arose. They are, however, in the minority of described subspecies. At the other end of the continuum, Benedict et al. (2019) used molecular methods to test subspecies limits in Heermann’s kangaroo rat (Dipodomys heermanni), including the federally listed D. h. morroensis, and concluded “that D. h. morroensis is not genetically or morphologically distinct, with no support for monophyly of D. h. morroensis in any of the molecular analyses.” (Monophyly would be the situation in which all populations trace to a single common ancestor.) Other examples are provided in the supplementary information.

Integrated Taxonomic Information System

The USFWS maintains a website called the Integrated Taxonomic Information System (ITIS) where subspecies are classified as valid or invalid.1ITIS: Integrated Taxonomic Information System (home page), accessed May 31, 2022, According to the USFWS, “ITIS taxonomy is based on the latest scientific consensus available, and is provided as a general reference source for interested parties.” The page refers to some publications, but the evidence for subspecies validity is not given, and the evaluations cannot be verified. When there is no critical evaluation of a subspecies, the status quo is assumed and the subspecies is classified as valid as long as it is included in one or more taxonomic checklists.

Scientific Societies and Their Views on Subspecies

Taxonomists struggle to come up with consistent ways to delimit subspecies (Taylor et al. 2017). In fact, several authoritative bodies have avoided the subspecies conundrum by ignoring subspecies altogether. The authors of a compilation of mammalian taxonomy note that “subspecies have not yet been addressed here due to their inconsistent historical usages in mammalogy, although future efforts are likely to compile subspecies information for the purposes of species-level synonymy.”2“About the Mammal Diversity Database,” Mammal Diversity Database website, accessed May 31, 2022, In ornithology, the committee tasked with providing a taxonomic classification last used subspecies in its 1957 list (AOU 1957); and Zink (2004) and Phillimore and Owens (2006) find that a low percentage of avian subspecies are supported by modern methods of molecular systematics, in support of Remsen’s (2005) sentiments.

Thus, there is no agreed-upon list of subspecies, even for taxonomically well-studied groups such as birds and mammals, because (1) there is no agreed-upon general definition of subspecies and (2) many subspecies have been found to be invalid upon modern reanalysis (see below). Thus, it is easy to understand why the USFWS does not have a consistent set of criteria for subspecies recognition and rather defers to taxonomists in a particular group. We suggest that it should be the purview of taxonomists in different fields to find common ground for defining subspecies to be used in ESA listing decisions.

At Least Two Perceived Uses of Subspecies

The Rio Grande wild turkey is a useful segue to considering what characteristics subspecies ought to possess. As Remsen (2005) notes, many subspecies are arbitrary divisions of clines, and it is easy to partition a cline in different ways, and sometimes different characters have different clines that lead to yet different subspecies limits. Remsen (2005) and Taylor et al. (2017) also make it clear that a “good” subspecies should be a discrete entity. That is, a discrete taxonomic entity should have diagnostic boundaries defined by concordant patterns of morphology or genetics, which would qualify the entities as the basic, or lowest, taxonomic unit. Thus, the owls and thrasher discussed earlier are good examples of qualified subspecies. However, others suggest that subspecies are by definition not discretely differentiated populations or groups of independently evolving populations but have “fuzzy” edges owing either to ongoing introgression (gene flow) or to insufficient time having elapsed since the cessation of genetic exchange (the so-called lag effect). In the former case the evolving unit is geographically larger than each participating subspecies. Nonetheless, this is an oft-cited justification for subspecies: a subspecies designation signifies that “something interesting is going on” that could be of interest to ecologists or evolutionary biologists.

Winker (2010) considers subspecies a gold mine of testable hypotheses in evolutionary biology. Indeed, this can be an important function of subspecies, but such subspecies should not be construed as worthy of conservation status under the ESA—only those that are discretely differentiated should be considered worthy of conservation status. The reason is that otherwise, there will be thousands of such arbitrarily defined subspecies that could be accorded taxonomic trinomials and therefore qualify for listing. For example, the author of the Rio Grande wild turkey subspecies could have erected very different subspecies boundaries, depending on the definition of “intermediate”, and such subspecies could be of interest to evolutionary biologists (to direct study toward understanding the causes of geographic variation) but not to taxonomists.

To be clear, we do not argue against preserving “evolutionarily interesting” parts of species ranges, but—given the need to prioritize support—they should be less important than genuinely evolutionarily distinct units (Taylor et al. 2017). In conservation decisions, the status quo is to accept a subspecies if it has a formal taxonomic name, irrespective of whether its attributes have been tested since its description. This results in the potential to name thousands of arbitrarily defined subspecies, when in fact they are not important elements of biodiversity at the lowest taxonomic level.

Tests of Subspecies

What Constitutes a Strong Test of Subspecies Limits?

A strong test of a listed subspecies, as envisioned by Taylor et al. (2017), would include the comparison of statistically adequate samples from throughout listed subspecies with samples of other subspecies, preferably those geographically adjacent. Listed subspecies should have at least two geographically spaced samples (if possible), allowing a researcher to test whether each sample is more closely related to the other than to samples from other subspecies. There should be no sampling gaps that would give the illusion of real genetic or morphological discontinuities (see Rising 2001) owing simply to geographic distance between sampling localities. Evidence of taxonomic distinctiveness ought to be gathered from several character systems, with preference perhaps given to modern molecular methods. All data must be publicly available, and the analyses must be clearly described. The data should show concordant geographic splits in multiple character systems (Barrowclough 1982), which would confirm a hypothesis of evolutionary independence; it is inappropriate to delete characters with conflicting patterns. This sets a high bar for taxonomic descriptions of subspecies.

Molecular methods have revolutionized tests of subspecies and their evolutionary independence (Avise 1992). The foundation of the ESA rests on the assumption that listed entities are evolutionarily independent. If one examines morphological characters, which are almost certainly under strong selection, one does not expect a single evolutionary history to emerge. The reason is that characters often respond idiosyncratically to opposing environmental dimensions, and therefore picking one morphological character to draw subspecies boundaries leads to a lack of evolutionary consistency. Only when a suite of morphological or genetic characters all show the same pattern can one safely infer that the pattern reflects the history of population subdivision.

Molecular characters used to date are usually considered to be “selectively neutral”—that is, not influenced unduly by natural selection—and hence the only reason for congruent geographic patterns is that they reflect a common underlying evolutionary history. Therefore, if a population or group of populations is evolving independently, one expects correspondence among a host of neutral genetic characters. Patten and Remsen (2017) failed to understand this basic point when they claimed that neutral genetic characters should not be expected to map to subspecies boundaries. The point they missed is that subspecies as described by several generations of morphological taxonomists do not map to evolutionarily independent groupings. Thus, it is not surprising that most subspecies lack molecular genetic support. It is not the genetics that failed; it is the morphological characters that contain ambiguous and conflicting information and fail to recover evolutionary entities.

Is There Such a Thing as Too Much Resolving Power with Modern Genetic Methods?

The El Segundo blue butterfly (Euphilotes battoides allyni) is a federally listed subspecies found along the coast of southern California. Dupuis et al. (2020) used a sophisticated molecular analysis and found that this subspecies is distinct. However, north and south along the coast are six additional, equally distinct genetic clusters. Should all be accorded the same protection? Either there are too few subspecies of E. battoides or the newer techniques will find minor differences of statistical importance irrespective of subspecies boundaries—differences of dubious biological significance.

The federally listed butterfly Lange’s metalmark (Apodemia mormo langei) occupies a narrow range. MtDNA studies found it to be reciprocally monophyletic, supporting its listing (Proshek et al. 2015), although the researchers remark, “Placed in the context of the entire species complex, A. m. langei is no more genetically distinctive than most populations in California, and other populations exist in this region that exhibit higher mitochondrial and nuclear divergence.” In this case, the subspecies framework does not capture the evolutionary pattern. Saglam et al. (2017) used nuclear genomics to test subspecies limits in two trout, Oncorhynchus clarkii seleniris and O. c. henshawi, which were ambiguous with mtDNA. Their analyses found that both subspecies were highly distinctive. Given the potential resolving power of new techniques, it will be possible to find what appear to be local isolates but in fact are the result of isolation by distance (see below). That is, local family groups could give the illusion of genetic gaps. Hence, although the heightened resolving power of next-generation sequencing methods is unprecedented, the results should be interpreted cautiously.

A subspecies of great interest to conservation biologists is the southwestern willow flycatcher (Empidonax traillii extimus). In the only authoritative statement on subspecies in North America, the American Ornithologists’ Union (1957) Checklist, this subspecies was not accepted, although it had been described nine years earlier (Phillips 1948). Data sets on mtDNA, amplified fragment length polymorphisms, niche modeling, and song vocalizations supported the AOU’s decision to not designate E. t. extimus as a valid subspecies (Zink 2015; 2016; see Mahoney et al. 2020). But when Ruegg et al. (2021) analyzed variation in 105,000 single nucleotide polymorphisms (SNPs) from 175 individuals, they concluded that the subspecies was valid.

There are concerns about Ruegg et al.’s (2021) sampling and data analysis, however. For example, they used a principal component analysis to conclude that there were seven “main clusters.” They used these groupings to choose SNPs that best discriminated among these clusters, which borders on a circular procedure. Also, there are sampling gaps between E. t. extimus and the subspecies to the north (E. t. adastus), there are no samples from the southern extent of the range in Mexico (see below), and there is no assessment of isolation by distance. The samples from California, within the range of E. t. extimus, do not group with those in the eastern part of the subspecies’ range. Thus, Ruegg et al. (2021) clearly found geographic differentiation in genetic variation throughout the range of the species, but whether the data recover the limits of E. t. extimus as described by Phillips (1948) is unclear.

Thus, the so-called next-generation sequencing methods need to be interpreted with caution so as not to confuse sampling and genetic gaps (see below) and so as not to cherry-pick SNPs that favor one hypothesis over another. That is, one might exclude characters that suggest a different pattern, whereas overall differentiation should be assessed across all characters (e.g., SNPs). That is, conflicting characters should be a part of the analysis so as not to bias the result to a preconceived conclusion. Needless to say, assigning individuals to preordained subspecies is a flawed procedure.

Economics and Subspecies: The Cost of Invalid Subspecies

Preserving rigorously defined subspecies listed under the ESA is a justifiable cost to society, given the often-stated goal of preserving biodiversity (Leopold 1989). These subspecies have evolved over thousands or tens of thousands of years and represent potentially unique adaptations to their local environments. They are an important part of our biodiversity heritage, and we owe it to future generations to see to their preservation. The listing of arbitrarily defined subspecies, in contrast, serves only to draw resources from species and subspecies that merit protection.

Costs of preservation vary widely within and among different groups of organisms (Gordon et al. 2020). At the level of full species, the average cost of preserving a bird species in the United States is $2,571,017, with a wide range of variation. One of the costliest vertebrate species is the delta smelt (Hypomesus transpacificus), whose annual cost of preservation is about $39 million. According to Gordon et al. (2020), mammals cost 8–26 times more on average to conserve than plants, and bird species cost 5–30 times more to conserve than plants and 6–14 times more than aquatic invertebrates. Bias toward “charismatic” species is also well documented (Courchamp et al. 2018). Thus, spending money on ill-defined taxa is inappropriate.

Preserving subspecies also carries a hefty price tag. The coastal California gnatcatcher (Polioptila californica californica) is listed as threatened. Its range includes the densely populated area of southern California from Palos Verde Peninsula south to the border with Baja California (and farther south to the end of Baja California Sur, where it becomes relatively common). The validity of the subspecies has been challenged (Zink et al. 2000; 2013; 2015) and defended (McCormack and Maley 2015), and recent genomics data show that it is not evolutionarily distinct and hence not a valid subspecies (Vázquez-Miranda et al. 2022). Its listing has prevented the development of coastal sage scrub habitat, and the USFWS has suggested that excluding this habitat has come at a cost of at least $1 billion (Gordon 2018). Fortunately, much of the land occupied by the coastal California gnatcatcher is currently preserved by habitat conservation plans (Winchell and Doherty 2018), and gnatcatcher populations are apparently genetically connected (Vandergast et al. 2019). This subspecies is essentially a symbol for an entire biome: coastal sage scrub. However, there is no current legislation like the ESA for biomes. Obviously, other subspecies occupying less densely populated areas would carry a much lower price tag.

Review of Subspecies Listed under the ESA

Most ESA-listed subspecies were described before 1950 (137 of 175), and 150 (86%) were described before 1966 (see figure 1), using methods that involved assessments of morphological variation. It was not until 1966 that the first molecular methods appeared that could be used to test subspecies limits. These molecular methods were a major improvement because they allowed the actual genetic basis for subspecies distinctiveness to be measured quantitatively. Knowing the relationship between patterns of actual genetic differentiation and subspecies limits greatly aids efforts to clarify the validity of subspecies.

The molecular methods used evolved from relatively crude assessment of distinguishing alleles at protein-coding loci (allozyme electrophoresis) to studies involving thousands of base-pairs at the DNA level. Most molecular examinations (n = 92) of subspecies limits used mtDNA (n = 67), and some were combinations of mtDNA and microsatellites (n = 19) or mtDNA and nuclear DNA (n = 14). Evaluations of listed subspecies vary widely in their sampling size, from a single individual to over 100 samples. Given the variation in the areal extent of listed subspecies’ distributions, a diversity in sampling size is not surprising; however, the relative percentage of the distribution covered by sampling also varies widely. Clearly, “point samples” are insufficient, and a valid test requires at least two samples within each subspecies so that the relationships within and between subspecies can be assessed. However, gaining permission to acquire the necessary samples of threatened and endangered subspecies to perform modern sequencing methods and close sampling gaps may prove difficult. Although these difficulties should not be ignored, in several cases researchers were able to include only a single population represented by one individual, thus making inferences of population distinctiveness difficult.

Figure 1. Distribution of years in which subspecies listed under the endangered species act were described. Arrow “A” marks the beginning of the use of allozymes in studying genetic variation in natural populations, and arrow “B” marks the beginning of the use of mitochondrial DNA.

We examined 165 listed subspecies to determine how many were supported by modern analyses (see table 1: 11 have been removed the USFWS in ITIS; As noted earlier, a valid test would include multiple samples within the subspecies and comparisons with adjacent samples. Seven subspecies have been removed from the list because, according to the ITIS website, they have been elevated to species or there was a data error in the description. We found that the bulk of the remaining subspecies are distributed relatively equally among three categories: supported, not supported, and not tested (figure 2). This summary suggests that a listed subspecies has a fifty-fifty chance of being significant.

Figure 2. Distribution of results of evaluation of listed vertebrate subspecies. “Not tested” means samples from listed subspecies were not compared with samples from adjacent subspecies, there were too few samples, or samples were not examined.

We found that the ITIS classification rather strongly departs from our summary. More than 40 of the 51 subspecies (78%) that were not supported by our evaluation were considered valid on the ITIS website.

Role of Introductions in Obscuring Historical Units

Tursi et al. (2013) found that the Lower Keys marsh rabbit (Sylvilagus palustris hefneri) was not distinct from other subspecies, and that introductions might be required to maintain populations. They identified areas from which rabbits could be translocated to keep genetic integrity to the greatest degree possible. In many other cases, modern molecular methods are used to choose populations to serve as sources for reintroductions.

What if a narrowly distributed subspecies goes extinct? The San Joaquin woodrat (Neotoma fuscipes riparia) is found in a small area in the Central Valley of California. It is closely related to adjacent populations of different subspecies. If it is determined that the woodrat’s ecological role is important, perhaps individuals from adjacent populations could be transplanted. Granted, this would not reconstitute the genetic integrity of the lost populations, but the transplants might fill the woodrat’s ecological role. Similar examples exist with the dusky seaside sparrow (Ammospiza maritima nigrescens) and the Florida panther (Puma concolor couguar), where preserving the animal’s ecological role at the expense of historical taxonomic integrity appears to be the goal.

Summary and Future Considerations


The molecular methods used to test subspecies have evolved greatly over the past few decades, owing to a large increase in resolving power. With the new potential to describe genomes of individuals, some issues should be recognized. First, if sampling is not evenly spaced, sampling gaps will give the illusion of discrete taxonomic boundaries (figure 3). Also, if a gap in the range is caused by anthropogenic elimination of intermediate areas, the populations might appear distinct, albeit not from natural evolutionary processes. Subspecies limits cannot be tested without a clear and rigorous sampling protocol.

It is possible for a subspecies that is not evolutionary distinct (a category that includes many subspecies) to be ecologically important—perhaps important enough to merit listing. Examples might include keystone species such as large carnivores: the Florida panther, for instance. However, providing quantitative data of ecological importance might be as large a task as documenting taxonomic distinctiveness. The lack of consistency among subspecies definitions used in ESA listings is a major failing of taxonomists. To further the use of taxonomic work in conservation decisions, this failing ought to be addressed.

Figure 3. A. Clinal gradient in genetics showing three groups. B. The effects either of not sampling from region 2, and mistaking isolation by distance for discrete groups, or of region 2 being extirpated because of anthropogenic factors, which will give the illusion of discrete groups that could be classified taxonomically.

The Path Forward

Given the high cost of subspecies preservation and the fact that roughly 50% of subspecies tested are supported by modern methods, it should be unacceptable to list a subspecies under the ESA without modern analyses following the criteria given earlier. Taylor et al. (2017) developed a set of quantitative criteria for use in cetacean subspecies taxonomy. These criteria are unlikely to be broadly applicable, but they could form a template for taxonomists of different groups of organisms to work from. Therefore, it should be incumbent upon the USFWS to undertake valid surveys of the listed subspecies to determine whether they are taxonomically distinct and qualified to be evolutionary units under the ESA. That is, it should not be assumed that because a subspecies exists in a checklist, it is evolutionarily significant. In addition, USFWS should seek consensus among taxonomists who work on different groups or organisms to agree on a list of minimal criteria for a subspecies to be listed under the ESA so that listing decisions are transparent.

Table 1. Review of subspecies listed under the US Endangered Species Act


* The Integrated Taxonomic Information System considers the subspecies invalid. (In most cases, the basis for an invalid conclusion is a change in the scientific name of the described subspecies.)
Note: This list does not include other subspecies already considered invalid by the Integrated Taxonomic Information System: Aerodramus vanikorensis bartschi, Bufo hemiophrys baxteri, Drymarchon corais couperi, Epicrates monensis monensis, Epioblasma torulosa gubernaculum, Epioblasma torulosa rangiana, Epioblasma obliquata obliquata, Epioblasma torulosa torulosa, Epioblasma obliquata perobliqua, Epioblasma florentina florentina, Gasterosteus aculeatus williamsoni, Lasiurus cinereus semotus, Oxyloma haydeni kanabensis.


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CGO scholars and fellows frequently comment on a variety of topics for the popular press. The views expressed therein are those of the authors and do not necessarily reflect the views of the Center for Growth and Opportunity or the views of Utah State University.