Lecture slides for the program orientation Evolutionary Biology at the Institute of Biology Leiden, the Netherlands. Thursday, September 7th, 2017. Lecture notes are here: https://docs.google.com/document/d/e/2PACX-1vRIv5mKK1fjBby--u97emC7hrqXUbxFQZe63P1FpguuhHLG6xykbwXKeKXCUE5W-LSpakXYCI621xCK/pub

1. Species delimitation
Species limits and character evolution
Rutger Vos @rvosa

2. Outline
• Why care about species delimitation?
• A quick review of species concepts
• Applying species concepts
• How specimens are inventoried
• Assigning and delimiting species
• Practical examples
• Summary

3. Why care about species delimitation?
“On my way to De
Parade I came across
this forest of giants,
hogweed. For some time
now, I’ve been intrigued
by the amazing smell of
the green seeds of these,
and the possibility of
using them in an exciting
composition. One feels
tiny among these
monsters of sometimes 3
meters tall, unbelievable
these plants!”
- Chef of the popular, highly recommended, Amsterdam restaurant “Choux”

4. Why care about species delimitation?

5. Why care about species delimitation?
Common hogweed
Heracleum sphondylium
• Native to Western Europe
• Used in folk remedies and
traditional recipes
Giant hogweed
Heracleum mantegazzianum
• Invasive, from Caucasus
• Causes severe blisters,
possibly carcinogenic

6. Why care about species delimitation?
“…I was much struck how entirely
vague and arbitrary is the
distinction between species and
varieties” – Darwin, 1859

7. Why care about species delimitation?
divergence,
adaptation?

8. Why care about species delimitation?
We have both practical as well as philosophical
reasons for attempting to define and delimit
species.
Practical:
• Distinguishing useful from harmful species
• Defining and identifying endangered species
Philosophical:
• Are species real? Are higher taxa?
• How do species come about? How are they
maintained?

9. A quick review of species concepts
• Typological
• Biological
• Evolutionary
• Phylogenetic
• Recognition
• Cohesion
TSC - Linnaeus
Definition: “a group of individuals that differ from
other groups by possessing constant diagnostic
characters”. Based on collecting and describing a
“type” specimen for a given species.
Problems with the TSC:
• Polymorphism within populations
• Geographic variation among populations
• Sibling or cryptic species
Note: this overview is not exhaustive or definitive

10. A quick review of species concepts
• Typological
• Biological
• Evolutionary
• Phylogenetic
• Recognition
• Cohesion
BSC - Dobzhansky, Mayr
Mayr (1940): “species are groups of actually or
potentially interbreeding natural populations that
are reproductively isolated from other such
groups.”
Dobzhansky (1937): “species are the largest and
most inclusive reproductive community of sexual
and cross-fertilizing individuals that share a
common gene pool.”
Problems with the BSC:
• Not applicable to asexual species
• Reproductive isolation is often incomplete
• Difficult to verify (“potentially interbreeding”?)
Note: this overview is not exhaustive or definitive

11. A quick review of species concepts
• Typological
• Biological
• Evolutionary
• Phylogenetic
• Recognition
• Cohesion
ESC - George Gaylord Simpson, 1951
Definition: “an evolutionary species is a lineage
evolving separately from others with its own
unitary evolutionary role and tendencies.” Initially
developed to define fossil species.
Problems with the ESC:
• How to define independent roles and tendencies?
• Does not provide a mechanism
Note: this overview is not exhaustive or definitive

12. A quick review of species concepts
• Typological
• Biological
• Evolutionary
• Phylogenetic
• Recognition
• Cohesion
PSC - Cracraft, 1983
Definition: “the smallest diagnosable monophyletic
group of populations within which there is a
parental pattern of ancestry and descent.” Two
recent extensions are the internodal species
concept and the genealogical species concept.
Problems with the PSC:
• What characters to use?
• What level of divergence constitutes a species?
• Gene trees versus species trees.
• Does not address mechanism.
Note: this overview is not exhaustive or definitive

13. A quick review of species concepts
RSC - Paterson, 1985
Definition: “the most inclusive population of
biparental organisms that share a common
fertilization system.”
Focuses on mate-recognition systems:
• Courtship displays
• Timing of reproductive events
• Neuroendocrine signals (e.g. pheromones)
• Design of copulatory organs
• Gamete compatibility (i.e. sperm and egg
proteins)
Problems with the RSC:
• Not applicable to asexual species
• Recognition systems often go awry (i.e.,
hybridization occurs)
• Typological
• Biological
• Evolutionary
• Phylogenetic
• Recognition
• Cohesion
Note: this overview is not exhaustive or definitive

14. A quick review of species concepts
• Typological
• Biological
• Evolutionary
• Phylogenetic
• Recognition
• Cohesion
CSC - Templeton, 1989
Definition: “the most inclusive population of
organisms having the potential for cohesion
through intrinsic cohesive mechanisms.”
Two classes of cohesive mechanisms:
1. Genetic cohesive mechanisms - gene flow and
stabilizing selection function to maintain species
integrity.
2. Ecological cohesive mechanisms -
abundance, demographic stability, strengths of
interactions with other species, etc.
Problems with the CSC:
• Studying cohesive mechanisms is labour intensive
Note: this overview is not exhaustive or definitive

15. Applying species concepts
“There has been real progress made in thinking about species
concepts, which now makes some general agreement seem
possible. […] As evidence of some of this progress, there seems to
be general agreement among almost all participants that species are
lineages.”
Wiens, 2007
• Indeed, the post-Darwin species concepts reviewed (Biological,
Evolutionary, Phylogenetic, Recognition and Cohesion) all imply that
species are lineages.
• The different concepts just deal with the maintenance and
persistence of independent lineages through different time
scales.

16. Applying species concepts
Concept Conspecifics Characters Time Sex
Typological ✔ ❌
Biological ✔ ✔
Evolutionary ✔
Phylogenetic ✔ ✔
Recognition ✔ ✔
Cohesion ✔
Necessarily involves…
Because there is no direct need to observe or experiment with
conspecifics (useful for rare or extinct species) and no limitation to only
sexually reproducing groups, a place like Naturalis will mostly concern
itself with typological/phylogenetic species concepts when organizing its
specimen collections.

17. How specimens are inventoried
Naturalis has tens of millions of
specimens in its collection. To make
sense out of these, several
taxonomic procedures are applied:
• Description – associating a
published description, identification
key, and type specimen with an
available name
• Classification – ordering
organisms into groups based on
similarities and differences in
characters
• Identification – assigning a
specimen to a previously named
and classified group

18. How specimens are inventoried
Alpha taxonomy:
Describing new species
• Identify its type specimen
in a collection
• Pick a name according to
nomenclature rules
• Describe its morphology in
highly structured language
• Place it in an identification
key in relation to relatives
• (Optional) take photos
and/or DNA sequences

19. How specimens are inventoried
Beta taxonomy: Classifying
higher taxa
• Place the entities at the tips
(e.g. species) in a Linnean
classification
• Attempts to reconcile
phylogeny and systematics

20. How specimens are inventoried
Identification of specimens
• Comparison of specimen
with reference material,
descriptions, and keys
• Reference material:
o Morphological
characters from physical
specimens, images, etc.
o Molecular data from
DNA barcodes,
genomes, etc.

21. Assigning and delimiting species
Left: cryptic
species
Right: adaptive
radiation
Western/Eastern meadowlark Hawaiian silversword complex

22. Assigning and delimiting species
• Cryptic species might be reciprocally monophyletic at the
molecular level but polyphyletic in their morphology.
• Adaptive radiations vice versa: distinct morphologies, but
incomplete lineage sorting in their genes.

23. Assigning and delimiting species
Phylogeny-based delimitation
The general idea is that a gene
tree shows two distinct
processes of lineage
accumulation:
1. Inter-species birth/death
diversification
2. Intra-species coalescent
processes
The trick is to find the inflection
point, e.g. in a lineage-through-
time plot.

24. Assigning and delimiting species
PCA-based delimitation
For complex, incompletely
sorted cases, a lot of data
may have to be brought to
bear on the delimitation
problem.
One common approach to
deal with the volume and
dimensionality of the data
is to reduce it using
principal component
analysis, which can be
applied to both molecular
and morphological data.

25. Practical examples
Delimitation methods applied to European beetles
Four phylogenetic delimitation
methods were applied to
5,290 COI barcodes for 1,870
European beetle species:
• BIN – BoLD’s default
clustering method
• ABGD – Automatic
Barcode Gap Discover
• GMYC – Generalized
Mixed Yule Coalescent
• PTP – Poisson Tree
Process
Each method recovers about
90% of the input species (but
different ones). Simple
consensus among methods
approximates these further.

26. Practical examples
Barcode delimitation in European butterflies
The COI barcode for 41,583
specimens, previously identified as
4,977 species was sequenced and
gene trees were constructed. A
special pipeline assessed mono-,
para-, or polyphyly in the gene
trees.
Non-monophyletic species showed
low genetic distances to nearest
neighbors or high levels of
intraspecific variability.
In ~20% of non-monophyletic
species, lineages either allopatric or
parapatric — i.e. where species
delimitation is subjective and
dependent on the species concept.

27. Practical examples
Gorilla subspecies
Using previously published reference
data and our own results we are
currently using PCAs of SNPs to
identify the population origin of a
19th century museum specimen.

28. Practical examples
Javanese butterflies

29. Practical examples
Javanese butterflies
Using a custom pipeline for extracting salient image features (not characters)
and finding commonly occurring (pseudo-homologous) ones, a large data set
was created.

30. Practical examples
Javanese butterflies
Based on no morphological expertise
(pure algorithms) genera and species
can be distinguished. However, some
specimens, such as gynandromorphs,
present problems.

31. Summary
• Species are lineages, and species concepts deal
with the maintenance of their independence
• Taxonomy (species description and classification)
carries some pre-Darwinian, typological baggage
• Hence, morphological species identification and
delimitation limps on these two perspectives
• Molecular species delimitation methods are often
phylogenetic, and are rapidly advancing
• Growing amounts of available data show species
boundaries to be special snowflakes

32. Thanks for
listening!