It's biology's most fundamental question, and we still don't have a single answer.
You've likely heard that a species is a group of organisms that can breed and produce fertile offspring. This classic definition, known as the biological species concept, works well for many animals. But what about bacteria, which reproduce asexually? Or organisms that hybridize freely in nature? Or fossils, which we can't test for reproduction? Suddenly, the simple definition falls apart.
This is the species problem—the long-standing failure of biologists to agree on a single definition of what a species actually is. It is one of the most persistent and controversial puzzles in science. Despite decades of debate, scientists have proposed at least 30 different definitions, each with its own strengths and blind spots. This isn't just academic squabbling; how we define a species affects everything from how we measure the planet's biodiversity to which creatures we fight to protect from extinction.
At its heart, the species problem is the challenge that different ways of defining species carve up the tree of life in different, often inconsistent ways. A group of organisms might be considered one species under one definition and multiple species under another 6 .
Different species concepts divide the tree of life in inconsistent ways, creating confusion in classification and conservation efforts.
Conservation funding, legal protections, and biodiversity estimates all depend on how we define species boundaries.
Biologists have developed a plethora of species concepts, each focusing on different criteria 1 6 :
One of the oldest definitions, it groups organisms based on physical similarity. It's practical but can miss hidden diversity or confuse different species that look alike.
Defines species as groups of interbreeding populations that are reproductively isolated from others. It's powerful for animals but useless for asexual organisms like many bacteria and plants 2 .
Defines a species as the smallest group of individuals that share a common ancestor and form a distinct branch on the family tree. This can identify fine-scale differences but may lead to "taxonomic inflation" by splitting familiar species into many smaller ones 1 .
Focuses on a species' adaptation to a specific niche or environment.
The confusion is compounded because the word "species" is used in three different ways: as a rank in classification (like "genus" or "family"), as a specific taxon (like Homo sapiens), and as a term for an evolving entity in nature 2 . This one word does a lot of heavy lifting, and the context isn't always clear.
This isn't just a philosophical debate. The lack of a universal standard has tangible consequences 6 .
When ornithologists began using the Phylogenetic Species Concept instead of the Biological Species Concept, the number of bird species suddenly jumped by nearly 10%. Similar splits have occurred in other animal groups.
For conservationists, this creates a moving target. Listing a species as "endangered" triggers legal protections and funding, often in the millions of dollars for recovery efforts. If a single species is split into two, the resources required to protect them double. The species problem, therefore, moves from the pages of scientific journals directly into the courtroom and the conservation plan 6 .
If we can't agree on a definition by looking at static organisms, perhaps we can understand species by watching them evolve in real time. Long-term evolution experiments do just that, offering a unique window into the dynamic processes that lead to diversification.
In 1988, biologist Richard Lenski started a simple experiment that would become a cornerstone of evolutionary science. He founded 12 populations of E. coli bacteria from a single ancestor and began growing them in a low-nutrient glucose medium. Every day, a small sample from each population is transferred to fresh medium, allowing the bacteria to continue growing and evolving. Generations fly by in hours, and the populations have now surpassed 80,000 generations—a span that would take paleontologists millions of years to study in fossils 4 .
| Aspect | Detail |
|---|---|
| Start Date | February 24, 1988 |
| Number of Populations | 12, all founded from the same ancestor |
| Generations (as of 2024) | Over 80,000 |
| Key Method | Daily serial transfer of 1% of each population |
| "Frozen Fossil Record" | Samples frozen every 500 generations for future study |
This monumental experiment has yielded profound insights 4 :
All 12 populations showed similar patterns of fitness improvement, showing evolution can be directed by environment.
Citrate utilization evolved in only one population after 31,000 generations, highlighting the role of chance.
All populations evolved larger cell sizes, demonstrating visible evolutionary change.
| Type of Change | Description | Significance |
|---|---|---|
| Fitness Increase | All populations grew ~70% faster by 20,000 generations. | Shows continuous, predictable adaptation to a constant environment. |
| Citrate Utilization | One population evolved to use citrate as a food source under aerobic conditions. | Demonstrates the role of historical contingency in opening new evolutionary niches. |
| Mutation Rate | Six populations evolved elevated mutation rates ("hypermutators"). | Reveals that the ability to evolve can itself be an evolved trait. |
| Cell Size | All populations showed a significant increase in cell size. | Illustrates parallel morphological evolution across independent lines. |
While the LTEE shows evolution within a species, long-term field studies have captured the moment a new lineage emerges. For over 40 years, Peter and Rosemary Grant have studied Darwin's finches on the isolated Galápagos island of Daphne Major 3 .
In 1981, a male large cactus finch—a species not native to the island—arrived and mated with two local medium ground finches. Their offspring, a new hybrid lineage, were reproductively and ecologically isolated from both parent species. They were larger, had unique beak shapes, and sang a distinctive song that ensured they mated only with each other 3 .
Dubbed the "Big Bird" lineage, these finches represent a new species forming in real time. This rare documented case shows how hybridization and natural selection, driven by a competitive environment, can swiftly create a reproductively isolated group—a process called speciation that is central to many definitions of a species 3 .
Given the conceptual chaos, how do practicing biologists actually identify and classify species in the field and lab? They use a polyphasic approach, combining multiple lines of evidence 1 5 .
| Tool or Concept | Function | Applicability |
|---|---|---|
| DNA Barcoding | Uses a short, standard gene sequence (e.g., COI for animals) as an identifier. | Quick, efficient for distinguishing known species; can struggle with very recently diverged groups 1 . |
| 16S rRNA Sequencing | Compares the sequence of this ribosomal RNA gene, which evolves slowly. | The gold standard for identifying and classifying prokaryotes (bacteria and archaea) 1 5 . |
| DNA-DNA Hybridization | Measures the overall genetic similarity between two organisms by comparing their whole genomes. | Historically used to define bacterial species (≥70% similarity threshold) 5 . |
| Average Nucleotide Identity (ANI) | A modern, precise method that compares all shared genes between two genomes. | Increasingly used for prokaryotic species delimitation, with a sharp genetic "gap" at 85-95% identity suggesting a species boundary 1 . |
| Morphological Analysis | The classical method of comparing physical traits like size, shape, and color. | Essential for field biology, paleontology, and for initial descriptions; can be misleading if used alone 1 . |
With so many concepts and tools, is the species problem solvable? Many biologists now advocate for a hierarchical framework 6 . In this view, there is one core theoretical concept—the Evolutionary Species Concept—which sees a species as a lineage evolving separately from others. This abstract idea is then operationalized using the various other concepts as "tools in a toolbox." A botanist might use morphological and ecological data to identify a plant species, while a microbiologist would rely on genetic data. The operational tool depends on the organism, but the overarching goal is the same: to identify a distinct evolutionary lineage 6 .
This pragmatic approach allows for flexibility without sacrificing scientific rigor. It acknowledges that the dazzling diversity of life may be too complex to be captured by a single, simple definition. The species, it turns out, is not a flawed concept, but a multidimensional one.
Morphological & Ecological Data
Biological & Phylogenetic Concepts
Genetic & Genomic Approaches
The species problem is a beautiful reminder that nature is messy and resists our neat classifications. It forces biologists to remain humble and curious. The ongoing debate is not a sign of failure, but a vibrant, essential part of scientific inquiry. As long-term experiments continue to reveal evolution in action and new genetic tools offer ever-finer looks at life's code, our understanding of life's fundamental unit will only deepen. The definition may never be perfect, but the quest to find it continues to drive science forward, shaping how we understand, count, and protect the magnificent biodiversity of our planet.