Reasons to Believe

What Species Problem?

Most of us know what a species is. Or we think we do. So why is the scientific literature replete with papers trying to define and delimit species? Is there really a species problem?

In his book Life’s Engines, Paul Falkowski states that at the time Darwin wrote The Origin of Species, there was a clear definition of the word species in the context of plants and animals: a species “was an organism that could sexually reproduce viable offspring.” He offers an example to substantiate this definition:

Pigeons can reproduce viable offspring when mated with other pigeons, but the offspring of a cross between a pigeon and an eagle, if it were viable, could not reproduce. A cross between a male donkey and a female horse yields a mule, which is a sterile animal. Pigeons and eagles, horses and donkeys are all different, identifiable species.1

That seems straightforward. Mate two animals and their offspring must be viable and reproductively fertile. If they are not, you have failed because you tried to mate two true and distinct species. Still, I continue to run across articles that highlight the species problemand I see evidence in The Origin of Species that Darwin too struggled with delimiting and defining species. After all, not all matings of eagles produce fertile eagles, and besides, how does one distinguish infertile (specific individuals) from sterile (general for a whole class of progeny, like mules)?

Is There a Species Problem?

Reading about speciation and the species problem challenges one’s critical thinking skills and leaves my head spinning when trying to decide how best to describe the problem and the data to high school students. (It also reminds me why I became a molecular biologist rather than a biologist!) Surprisingly, I am finding just how complex this problem is. And it is surprising because I think each of us has a general idea, like Falkowski presented, of what different species are.

The species problem results from a wide range of approaches in defining how species are identified and how species function in nature; each different approach yields a different species concept. Despite Falkowski’s claim, Darwin even had two species concepts that he referred to in The Origin of Species: morphological and physiological species.2 But more than that, he articulated repeatedly the great difficulty that experts (naturalists) had in agreeing when a species was a species and not a subspecies or variation.3

Speciation and Macroevolution: Why Care about the Species Problem?

The species problem is at the heart of a major element of Darwinian evolution. One needs to be able to define and delimit species to articulate how they are evolving into other species in order for common descent, variation, and natural selection to account for all of life’s history and for macroevolutionary claims to be reasonable.

This was one area where Thomas Huxley, known as “Darwin’s bulldog” for ardently defending natural selection and macroevolution, deeply questioned Darwin’s claims. Huxley, a committed naturalist, embraced Darwin’s emphasis on natural selection because there was no better theory to replace it. But he doubted that natural selection alone could drive variations from one species to another and continually challenged Darwin on this. Huxley’s doubts arose from observations that artificial selection could not drive dog breeds beyond the production of dogs, and pigeon breeding resulted in only pigeons—even if they were of various species or kinds all originating from the rock pigeon.

Huxley was an evidentialist, as am I. We want evidence to support scientific claims or truth-claims of any kind. In light of the pronounced limitations achievable in artificial selection, the absence of fertile hybrids among distinct, living organisms, and the absence of transitional species in the fossil record, Huxley lacked evidence in support of natural selection’s ability to accomplish macro-changes. This left Huxley in a state of discomfort in accepting natural selection on variations as a sufficient mechanism accounting for all of life’s diversity of kinds.4

Species Concepts in Conflict

In the early 1940s, evolutionary biologist Ernst Mayr recognized, as Darwin had before, that different investigators approached species identification differently, and he characterized these different approaches as different species concepts. Mayr advocated a concept similar to that offered by Falkowski above, where a species consists of populations of organisms that can reproduce with one another and that are reproductively isolated from other such populations. Many biologists jointly credit Theodosius Dobzhansky and Mayr for emphasizing the need to consider reproductive isolation when studying species and speciation. Today, this concept is known as the biological species concept (BSC).

In contrast to the BSC, an ecological species concept recognizes a species as a group of similar organisms adapted to a particular environmental niche. The organisms may or may not be reproductively isolated from other similar organisms in other niches. And a given set of organisms may have cryptic species present within the same niche. In this case, a cryptic species of organisms may be isolated from another species, but not obviously so.

The genetic species concept (GSC) defines a species as a group of genetically compatible interbreeding natural populations that is genetically isolated from other such groups. This focus on genetic isolation, rather than reproductive isolation, distinguishes the GSC from the BSC.5

The GSC is one that is gaining ground because of our ability to quickly sequence and assemble large swaths of DNA and compare mitochondrial and nuclear DNA among various animals. If Darwin was right about common descent with modification occurring through variation and natural selection and its accounting for speciation and the relatedness of all life, then genomic analyses should help clarify the cryptic elements that are missing from analyses or classifications based on observable phenomena such as morphology, phenotype, and behavioral and reproductive isolation. Genomic analyses should help clarify and delineate the historical pathway of common descent and the relatedness of living organisms. The GSC approach applies our best science to the species problem.

Single Species of Giraffes Now Recognized as Four Species

Recent research highlighted in Science and Nature claims there are really four—not one—species of giraffes, a claim made on the grounds of the GSC.6 The researchers indicate that based on multilocus analyses of seven nuclear DNA sequences generated from 190 individuals, giraffes scattered throughout Africa cluster into four phylogenetic groups.

Their report raises several questions: Is data based on analyses of seven nuclear loci sufficient to provide a snapshot of evolutionary potential to be guided by natural selection, especially when the groups are not necessarily reproductively isolated? Does this interpretation of the data lead to a better understanding of speciation that helps build evidence for macroevolutionary (Darwinian) claims? Or is it merely identifying cryptic species and mating proclivities already present within a wide range of biodiverse possibilities within a given species?

Despite answers to these questions, at least one major problem with adopting the genetic species concept cannot be overlooked. Different sequence analyses yield different results. In this report, multilocus analyses yielded four distinct clusters when focused on seven nuclear segments, but mitochondrial DNA analysis of the same 190 giraffes seems to indicate six or more clusters, including two distinct groups within one of the four nuclear clusters. Other research drew the same conclusion of separate lineages for the Angolan and South African giraffes.7

Perhaps the more important question and issue at hand is really, Why isn’t our best science clarifying evolutionary pathways? If we’re going to use genetics, or more specifically genomics, to indicate evolutionary relatedness of various species (and not just specific genes or gene clusters or segments of mitochondrial or nuclear DNA), then we may need to wait for more complete whole genomes from more organisms and for greater computational power to solve the species problem. Yet even when whole genome analyses are conducted, the evolutionary relatedness is not clarified.

Maybe the problem isn’t with the genetic information, or a need for more sophisticated algorithms or greater computational power. Maybe the problem is with the underlying theory trying to delineate pathways of common descent across kinds that are not there.

Philosophy, Again

The complexity of the species problem is compounded because in the absence of evidence, one needs to realize how much may be hijacked into discussions of speciation and interpretation of relatedness due to a foregone conclusion that evolution (natural selection on variations) is the mechanism linking all living creatures to one another.

Additional attempts to solve the species problem, driven by just such a philosophical commitment to naturalism rather than to any body of evidence, seem even less helpful.

A 2007 paper by Kevin de Queiroz tries to solve the problem of conflicting species concepts by redefining a species according to the shared common element that is “fundamental to the way in which species are conceptualized.” The fundamental concept de Queiroz articulates “equates species with separately evolving metapopulation lineages, or more specifically, with segments of such lineages.” He later adds this observation:

Lineages do not have to be phenetically distinguishable, diagnosable, monophyletic, intrinsically reproductively isolated, ecologically divergent, or anything else to be considered species. They only have to be evolving separately from other lineages. If this proposal is accepted, then it is no longer appropriate to refer to the ideas in question as different species concepts.8

But this certainly is a circular definition of species generated from the same evolutionary paradigm it is invoked to support, leaving one wondering if this problem is being swept under the rug of evolutionary rhetoric like so many others. (See here for another related article.)

A Species Is a Species Is a Species

We know species is a taxonomic level: species, genus, family, order, class, phylum, kingdom. But we don’t always mean the same thing. The meaning of species is dependent on what type of organism we’re talking about. So when we talk about speciation, it’s critical that we realize that there’s an equivocation around the word species.

From a Darwinian evolutionary perspective, speciation refers to the process in which a given species becomes a genetically, phenotypically, and behaviorally distinct species, typically due to geographical isolation and resulting in reproductively independent populations. Certainly, biodiversity within species occurs and certain traits may be selected artificially by humans or naturally by environmental factors, honing a particular group to a particular environment. But it seems that evidence is still lacking to overcome the evidential hurdles that bothered Huxley more than 150 years ago—that the potential of variation and natural selection can account for the differences in kind and the history of all life on Earth.

In light of the 26 recognized species concepts that exist today, one has to wonder if resolving the species problem is possible or if trying to do so is even helpful for scientific advancement. Maybe we need a complete rethink.

Variability: Biodiversity or Differences between Species? 

It’s challenging to bring the discussion into the realm of adaptation of species—on the observations of preexisting molecular variations and capacities for molecular adaptation within individual organisms. But I think this is where we need to take the discussion. It is often as far as the evidence itself goes.

To put it another way, I wonder how many species of humans there might be if analyses were done on nuclear DNA and only seven loci were selected for multilocus analyses?

Is the species problem sort of like the problem of defining life? We know what a species or life is when we see it, but we fail to appreciate the diversity encompassed by each. When it’s differences in degree, it’s biodiversity. When it’s differences in kind, maybe it’s something more. Maybe it’s nature declaring the glory of God and giving obvious evidence to all who do not actively suppress the truth (Romans 1:19–22).



  1. Paul G. Falkowski, Life’s Engines: How Microbes Made Earth Habitable (Princeton, NJ: Princeton University Press, 2015), 92.
  2. Charles Darwin, The Origin of Species, 6th ed. (London, England: Murray, 1872), Kindle edition; Thomas Henry Huxley, review of The Origin of Species, by Charles Darwin, The Victorian Web, last modified May 10, 2014,
  3. Darwin, The Origin of Species.
  4. Huxley, review of The Origin of Species.
  5. Robert Baker and Robert Bradley, “Speciation in Mammals and the Genetic Species Concept,” Journal of Mammalogy 87 (August 2006): 643–62, doi:10.1644/06-MAMM-F-038R2.1.
  6. Julian Fennessy et al., “Multi-locus Analyses Reveal Four Giraffe Species Instead of One,” Current Biology 26 (September 2016): 2543–49, doi:10.1016/j.cub.2016.07.036.
  7. Ibid. and internal references.
  8. Kevin de Queiroz, “Species Concepts and Species Delimitation,” Systematic Biology 56 (September 2007): 879–86, doi:10.1080/10635150701701083.

Subjects: Challenges to Evolution, Critical Thinking, Natural Selection, Speciation