species delimitation - species limits and character evolution

Species delimitationSpecies limits and character evolution

Rutger Vos @rvosa

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

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”


Common hogweedHeracleum sphondylium• Native to Western Europe• Used in folk remedies and

traditional recipes

Giant hogweedHeracleum mantegazzianum• Invasive, from Caucasus• Causes severe blisters,

possibly carcinogenic


“…I was much struck how entirely vague and arbitrary is the distinction between species and varieties” – Darwin, 1859


divergence,adaptation?


We have both practical as well as philosophicalreasons for attempting to define and delimit

species.Practical:• Distinguishing useful from harmful species• Defining and identifying endangered speciesPhilosophical:• Are species real? Are higher taxa?• How do species come about? How are they

maintained?

A quick review of species concepts

• Typological• Biological

• Evolutionary

• Phylogenetic

• Recognition

• Cohesion

TSC - LinnaeusDefinition: “a group of individuals that differ from

other groups by possessing constant diagnosticcharacters”. 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


• Typological

• Biological• Evolutionary

• Phylogenetic

• Recognition

• Cohesion

BSC - Dobzhansky, MayrMayr (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”?)



• Typological

• Biological

• Evolutionary• Phylogenetic

• Recognition

• Cohesion

ESC - George Gaylord Simpson, 1951Definition: “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



• Typological

• Biological

• Evolutionary

• Phylogenetic• Recognition

• Cohesion

PSC - Cracraft, 1983Definition: “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.



RSC - Paterson, 1985Definition: “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



• Typological

• Biological

• Evolutionary

• Phylogenetic

• Recognition

• Cohesion

CSC - Templeton, 1989Definition: “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


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.

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.

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

How specimens are inventoriedAlpha 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

How specimens are inventoriedBeta taxonomy: Classifying

higher taxa• Place the entities at the tips

(e.g. species) in a Linneanclassification

• Attempts to reconcile phylogeny and systematics

How specimens are inventoriedIdentification 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.

Assigning and delimiting species

Left: cryptic species

Right: adaptive radiation

Western/Eastern meadowlark Hawaiian silversword complex


• 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.

Assigning and delimiting speciesPhylogeny-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.


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.

Practical examplesDelimitation 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.

Practical examplesBarcode 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.

Practical examplesGorilla 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.

Practical examplesJavanese 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.


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

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

Thanks for listening!

species delimitation - species limits and character evolution

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