1. Taxonomic Units What is it that we are trying to do? Determine relationships among…? What do the terminal nodes represent? Often, they are supposed to represent some taxonomic unit, typically some group of species. “What is a species?”

2. Are species really ‘real’? Several competing species concepts. All differ in their assumptions and details but they generally agree on the following three main points: 1. Species consist of groups of interbreeding individuals that share a common ancestry. 2. Species are a fundamental unit of evolution. 3. Species are evolutionarily independent units. Different species follow different evolutionary trajectories through time. Taxonomic Units

3. A sampling of species concepts 1. Typological - A group of organisms in which individuals are members of the species if they sufficiently conform to certain fixed properties. ‘type specimens’ and ‘archetypes’ Clusters of variations or phenotypes within specimens (i.e. longer and shorter tails) would differentiate =species. “Classical" method of determining species, such as with Linnaeus. We now know that different phenotypes do not always constitute different species (e.g.: a 4-winged Drosophila born to a 2-winged mother is not a different species). Who defines what level of variation is acceptable? Doesn’t help define the mechanisms of speciation (evolution). Taxonomic Units

4. A sampling of species concepts 2. Morphological - A population or group of populations that differs morphologically from other populations. Useful when dealing with fossils Morphological criteria are often arbitrary Relies on ‘expert opinion’ What about cryptic species? What about sexual dimorphism? What about environmentally induced variation? Speciation mechanism is lacking. Taxonomic Units

5. A sampling of species concepts 3. Biological - “species are groups of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups” (Mayr 1963) Implies several possible isolation mechanisms and evolutionary processes. That “actually or potentially interbreeding” part bothers some people. How do we test this definition? Artificial conditions? Useless for fossils. Doesn’t apply to asexual species. Difficulties with hybridizing species Very popular and useful among vertebrate biologists (tiny percentage of all life) Taxonomic Units

6. A sampling of species concepts 4. Mate recognition - Similar to BSC but focuses on prezygotic isolating mechanisms. Often seen as the mirror image of BSC Focuses on the negative (isolating) vs. positive (interbreeding) Doesn’t apply to asexual species. Taxonomic Units

7. A sampling of species concepts 5. Ecological - A species is a group of organisms that occupy the same ecological niche Niche: The ecological niche of an organism depends not only on where it lives but also on what it does. By analogy, it may be said that the habitat is the organism's "address", and the niche is its "profession", biologically speaking. (Odum, 1959) BUT difficult to recognize, because many organisms occupy different niches due to adaptation or developmental changes Beierinck – “everything is everywhere…” Does the ecological species concept provide much resolving power for microbes? Taxonomic Units

8. A sampling of species concepts 6. Evolutionary - “a single lineage of ancestor-descendent populations which maintains its identity from other such lineages and which has its own evolutionary tendencies and historical fate” Focuses on evolutionary history Does not account for genomic hybrids, where genes have passed from one taxon to another, and the genetic make-up of individuals can be traced to different phylogenies or genealogies Completely sequenced microbial genomes have demonstrated that such hybrids are common: 5-15% of one bacterial species’ genomes can be attributed to acquisition from other species, making the evolutionary species concept practically irrelevant to prokaryotes 7. Phylogenetic - A group of organisms that shares an ancestor; a lineage that maintains its integrity with respect to other lineages through both time and space. A spinoff of the ESC aka the diagnostic species concept - an irreducible (basal) cluster of organisms, diagnosably distinct from other such clusters, and within which there is a parental pattern of ancestry and descent (Cracraft, 1989).

9. Many, many others Taxospecies Genospecies Natural Phylophenetic Genetic Cohesion Etc… Taxonomic Units

10. Others argue that species are not the important question. Evolution doesn’t work on species, it works on populations Evolutionarily significant units (ESU) – a population of organisms that is considered distinct for purposes of conservation. Sometimes called Operational Taxonomic Units (OTU) Can apply to any species, subspecies, geographic race, or population. Definitions of an ESU typically include at least one of the following criteria: Current geographic separation Genetic differentiation at neutral markers among ESUs caused by past restriction of gene flow Locally adapted phenotypic traits caused by differences in selection. Taxonomic Units