The classification of individual species is often necessary to obtain protection and funding for conservation purposes. This presentation explains the process of taxonomic classifications and how modern genomic sequencing techniques are important considerations in the classification process.

1. Ateneo de Davao University
Davao City, Philippines
March 9, 2018
Taxonomy and the Conservation of Endangered Species
By
Shannon Bohle

2. "What's in a name? That which we call a rose by any other name would smell as sweet.”
- William Shakespeare (1564-1616)

3. How Does Taxonomy Work?
Carl Linnaeus (1707-1788)
"father of modern taxonomy"
Linnaeus
Linnaean
Binomial
Classification
KINGDOM
PHYLUM
CLASS
ORDER
FAMILY
GENUS
SPECIES
Philippine eagle
(Pithecophaga jefferyi)

4. What is Taxonomy?
TAXONOMY
is part of a larger science called Systematics.

5. Here Lies
the Imprecise
Nature of Words
Nothing is certain in life but death and tax(onomi)es

6. How Does Taxonomy Work?
Charles Darwin (1809-1902)
Author of On the Origin of Species (1859)
Darwin
“Thus between A & B immense gap
of relation, C & B the finest gradation,
B & D rather greater distinction.
Thus genera would be formed.”
Observing phenotypical similarities
between species, Darwin linked
Linnaean taxonomy with
the processes of evolution and
extinction.
“I think [the] case must be that one
generation then should be as many
living as now.
To do this & to have many species in
same genus (as is) requires extinction.”

7. (Source: Mayr, Axel. "On the Importance of Being Ernst Mayr." PLoS Biology, vol 3, no. 5, 2005, pp. e152. doi:10.1371/journal.pbio.0030152. Image credit: University of Konstanz).
How Does Taxonomy Work?
Mayr
Ernst Mayr (1904-2005)
Author of Systematics and the Origin of Species (1942)
“Darwin did not think that species were real in the philosophical sense,
but rather that they were the result of the human predilection to
perceive discontinuity among continuously varying individuals. Most
biologists nowadays disagree with Darwin's view of species, largely
because of Mayr's ‘biological species concept.’
Together with Dobzhansky, Mayr developed this definition of species
‘as groups of interbreeding populations in nature, unable to exchange
genes with other such groups living in the same area.’ Barriers to gene
flow between species—termed reproductive isolating
mechanisms—keep biological species distinct through processes
such as species-specific mate choice and hybrid sterility.”
Excellent news.
This solidifies my hierarchy.

8. Speciation Reversal
02 March 2018
The dynamic nature of evolution tells us that
organisms will change.
DNA sequencing technology helps identify genotype
clusters and their changes with precision.
Nevertheless, we do not yet have the ability to predict
the stability of a species based upon its genome.
Under stress (both environmental or genomic),
a species can go extinct, evolve new traits, migrate,
hybridize, or experience a reversal in order to survive.
One explanation for speciation reversal is that
“species [especially hybrid species] have no
guarantee of permanence. Two genotypic clusters
might be stable for a long time, yet when
ecological circumstances change, gene flow may
exceed some threshold, eventually resulting in a
single genotypic cluster that absorbs both species.
There are several examples of species fusion in the
literature, for example in Darwin’s finches and
cichlid fish” (Mallet, James. “Hybrid Speciation.”
Nature, vol. 446, no. 15, 2007, pp.279-283.)

9. What is a Species?
A Competition of Concepts
Since the turn of the century, the problem of fertile hybrids are apparent.
Oh no.
My hierarchy must be
to include fertile hybrids.
Extended
Linnaean
Trinomial
Classification
KINGDOM
Subkingdom
PHYLUM
Sub Phylum
CLASS
Sub Class
ORDER
Sub Order
FAMILY
Sub Family
GENUS
Sub Genus
SPECIES
Sub Species
extended
“There is no universally accepted
definition of species.”
Introduction to Conservation Genetics.
2nd ed. (Cambridge UP, 2010).
Yet at least one viable definition appears in 2009:
“Species can be defined as distinguishable groups
of genotypes that remain distinct in the face of
potential or actual hybridization and gene flow. This
is similar to Darwin’s usage of species to divide
biodiversity by means of gaps or troughs in the
distributions of phenotypes and genotypes. ‘Hybrid
speciation’ implies that hybridization has had a
principal role in the origin of a new species . . . The
fraction of species that hybridize is variable, but on
average around 10% of animal and 25% of plant
species are known to hybridize with at least one
other species” (Mallet, James. “Hybrid Speciation.”
Nature, vol. 446, no. 15, 2007, pp.279-283.)

10. What is a Subspecies & How Does it Impact Conservation?
Phylogenetic Species Philosophy – Subspecies does not matter
Increased conservation funding is needed.
Loss of a subspecies might be “acceptable” within the
larger species concept.
Additional legislative protections may be required to
continue to protect individual subspecies or unidentified
species.

11. Philippine Eagle
-
Philippine eagle
(Pithecophaga jefferyi)
Critically Endangered (IUCN)
The Philippine eagle is a member of the Accipitridae family.
In it, 9 are critically endangered, 4 are endangered,
237 species are threatened, and 23 are vulnerable.
(Source: http://animaldiversity.org/accounts/Accipitridae/).
A History of Sub Family Misidentification
In 1919, a study of the phenotypical features of the Philippine eagle,
specifically the morphology of the skeleton, led to its misclassification
into the Harpiinae subfamily.
DNA genotyping correctly placed it in the Circaetinae subfamily in 2005.

12. Sub Species of the Philippine Eagle
-
According to Amauf, et al., “There are many cases where the level
of conservation concern depends heavily on taxonomic decisions.”
Amauf, Anita, et al. “Species or Subspecies? The Dilemma of Taxonomic Ranking of Some South-East Asian Hawk-Eagles (Genus Spizaetus).”
Bird Conservation International, vol. 15, no. 1, 2005, pp. 99–117, doi:10.1017/S0959270905000080.
Philippine eagle
(Pithecophaga jefferyi)
“Subspecies are included only exceptionally in conservation
efforts, mostly regional or local in scale.”
“Taxa restricted to islands have been raised from subspecies
to species level to intensify conservation.”
Notably, “the application of the Biological Species Concept
(BSC: Mayr 1963) or the Phylogenetic Species Concept (PSC:
Cracraft 1983) would result in a considerably different number
of species.”

13. BSC Versus PSC Methodology
Biological Species Concept
Most commonly used, but cannot account for hybridization and speciation reversal. However, it is difficult to test populations to see if they can interbreed and,
under it, sub species are often deemed a “low priority” whereas they could be a high priority if classed as a species
“The biological species concept classifies species as a group of actually or potentially interbreeding individuals. This means that any two individuals (well
a male and female) within the group could breed and produce fertile offspring. This is definition is commonly used but there are some issues with it, and
situations it can't be used in.
1) Not all species sexually reproduce
2) It can't be applied to the fossil record”
Phylogenetic Species Concept
Causes additional legislation but prevents oversight of subspecies
“The phylogenetic approach is now commonly used instead of the above, especially with increased
knowledge of genetics. By comparing DNA sequences it can be found which individuals have a
common ancestor (an organism the whole group evolved from). This (monophyletic) group can be
classed as a species. This species classification system is better as it:
1) Can be applied to asexual organisms
2) Can be used for extinct species if DNA is available
3) Does not need to test the population to see if they can interbreed as this can be very difficult
However it is subjective - the scientist has to decide how recent a common ancestor to use (as all
individuals have a common ancestor at some point in evolution). Usually the most recent common
ancestor of a population, that can be distinguished from other populations, is used.”
Source: https://www.mytutor.co.uk/answers/381/A-Level/Biology/What-is-the-difference-beween-biological-species-concept-and-the-phylogentic-approach-to-defining-species

14. PSC Applied to Two Sub Species of the Philippine Eagle
-
In 2005, using PSC, “our data indicate a clear genetic distinction between the
two subspecies S. p. philippensis and S. p. pinskeri, suggesting that they should be
treated as distinct species.”
(Amauf, Anita, et al. “Species or Subspecies? The Dilemma of Taxonomic Ranking of Some South-East Asian
Hawk-Eagles (Genus Spizaetus).” Bird Conservation International, vol. 15, no. 1, 2005, pp. 99–117,
doi:10.1017/S0959270905000080).
* Spizaetus philippensis / Nisaetus pinskeri – new species, 2014
* Spizaetus pinskeri / Nisaetus pinskeri - new species, 2014
Both are labeled “Endangered” due to human-caused deforestation, hunting &
farming according to the International Union for Conservation of Nature and Natural Resources (IUCN)
(http://www.iucnredlist.org/details/45015567/0 , http://www.iucnredlist.org/details/22734083/0)
Philippine eagle
(Pithecophaga jefferyi)

15. Classification and Legal Protection - – IUCN Red List (2012)

16. Classification and Legal Protection – IUCN Red List (2012)

17. "What's in a name? That which we call a rose by any other name would smell as sweet.”
- William Shakespeare (1564-1616) Clearly, a name matters a
lot, as Shakespeare knew
when he wrote Romeo
and Juliet, a tragedy
about marriage between
rival families – it can lead
to tragedy in drama and
species joining in
conservation.
Genome sequencing can
be done quickly today.
This Nature article argues
that PSC (used by the
IUBS) should be chosen
instead of BSC (used
by the IUCN)
to determine
endangered species.
Considering what
happened with the
Philippine eagle
subspecies,
it is easy to see why.
Learn more about
IUBS’s PhyloCode
(https://www.ohio.edu/phylocode/)