Beyond species description

Beyond Species Description
Shreeram Ghimire
M.Sc. Zoology Program
Amrit Science Campus, Thamel, Kathmandu

Species Evolution (sub-species concept)
• Evolutionary theory must explain macroevolution, the origin of new
taxonomic groups
• Speciation, or the origin of new species, is central to macroevolution
since all higher taxa originate with a new species which is novel
enough to be the first member
• Fossil record provides evidence for two patterns of speciation:
• Anagenesis (phyletic evolution) – transformation of an unbranched lineage of
organisms to a different state (the new species)
• Cladogenesis (branching evolution) – budding of one or more species from a
parent species that continues to exist

Anagenesis and cladogenesis
A
B
B C D E F
A

What is Species?
• Species = Latin for “kind” or “appearance”
• Linnaeus described species in terms of their morphology
• Modern taxonomists also consider genetic makeup and
functional and behavioural differences when describing
species

What is sub-species?
• The term subspecies refers to a unity of populations of a
species living in a subdivision of the species' global range and varies
from other populations of the same species by morphological
characteristics (Mayr, E. 1982, Monroe, B.L. 1982).
• The term is abbreviated subsp. in botany or ssp. in zoology
The plural is the same as the singular: subspecies.
• In zoology, under the International Code of Zoological Nomenclature ,
the subspecies is the only taxonomic rank below that of species that
can receive a name.

African leopard (Panthera pardus
pardus), the
nominotypical leopard subspecies
native to Africa
Sumatran tiger (P. tigris sondaica), a tiger subspecies
native to the Sunda islands

• While the scientific name of a species is a binomen, the scientific name
of a subspecies is a trinomen - a binomen followed by a subspecific
name. A tiger's binomen is Panthera tigris, so for a Sumatran tiger the
trinomen is, for example, Panthera tigris sumatrae. Subspecies is
generally abbreviated as "ssp." in zoology, but is not used in scientific
name.
• In zoological nomenclature, when a species is split into subspecies, the
originally described population is retained as the "nominotypical
subspecies“ (ICZN Art. 47) or "nominate subspecies", which repeats the
same name as the species. For example, Motacilla alba alba (often
abbreviated M. a. alba) is the nominotypical subspecies of the white
wagtail (Motacilla alba).

Motacilla alba Motacilla alba alba

Monotypic and Polytypic species
• In biological terms, rather than in relation to nomenclature,
a polytypic species has two or more genetically and phenotypically
divergent subspecies, races, or more generally
speaking, populations that differ from each other so that a separate
description is warranted (Mayr, E., 1970). These distinct groups do not
interbreed as they are isolated from another, but which can
interbreed and have fertile offspring, e.g. in captivity. Example:
Sparrows
• In a monotypic species, all populations exhibit the same genetic and
phenotypical characteristics. Example: Indian One Horned Rhinoceros

Phenotypic Plasticity
• Phenotypic plasticity refers to some of the changes in an organism's
behavior, morphology and physiology in response to a unique
environment (Price, T.D., Qvarnström, A., and Irwin, D.E., 2003).
• Phenotypic plasticity encompasses all types of environmentally
induced changes (e.g. morphological, physiological, behavioral,
phenological) that may or may not be permanent throughout an
individual's lifespan.
• Generally, phenotypic plasticity is more important for immobile
organisms (e.g. plants) than mobile organisms (e.g. most animals), as
mobile organisms can often move away from unfavorable
environments (Schlichting, C.D., 1986).

• Polyphenism: The special case when differences in environment
induce discrete phenotypes.
• Phenotypic plasticity is the ability of one genotype to produce more
than one phenotype when exposed to different environments.
• Phenotypic plasticity has been taken as important part of ecosystem
when environmental change happens over relatively short periods of
time.
• Example: Specklewood Butterflies have two morphs-one with three
dots in hindwing and other with two dots. The existence of these
subspecies is due to variation in morphology down a gradient
corresponding to a geographic cline. The males of this species exhibit
two types of mate locating behaviors: territorial defense and
patrolling.

Factors
• Temperature: Ectothermic animals respond to change in their thermal
environment.
• Geography: altitudinal variations alter seasonal changes, photoperiods and
surrounding bio-diversity which in turn cause phenotypic plasticity various
species.
• Inter-relation with other organisms: example-parasitism. House mice
infected with intestinal nematodes experience decreased rates of glucose
transport in the intestine. To compensate for this, mice increase the total
mass of mucosal cells, cells responsible for glucose transport, in the
intestine. This allows infected mice to maintain the same capacity
for glucose uptake and body size as uninfected mice.
• Nutrition: animals must process a greater total volume of poor-quality food
to extract the same amount of energy as they would from a high-quality
diet. Many species respond to poor quality diets by increasing their food
intake, enlarging digestive organs, and increasing the capacity of the
digestive tract. Example: Mongolian Gerbils etc.

Significance
• Relation with Evolution: Plasticity is usually thought to be an evolutionary
adaptation to environmental variation that is reasonably predictable and occurs
within the lifespan of an individual organism, as it allows individuals to 'fit' their
phenotype to different environments (Gabriel, W. 2005 and Garland, T. and Kelly,
S.A. 2006). In the presence of a predator, bluegill sunfish, the freshwater snails
make their shell shape more rotund and reduce growth. This makes them more
crush-resistant and better protected from predation.
• Relation with Climate Change: Phenotypic plasticity is a key mechanism with
which organisms can cope with a changing climate, as it allows individuals to
respond to change within their lifetime (Williams et.al., 2006). The North
American red squirrel (Tamiasciurus hudsonicus) has experienced an increase in
average temperature over this last decade of almost 2 °C. This increase in
temperature has caused an increase in abundance of white spruce cones, the
main food source for winter and spring reproduction. In response, the mean
lifetime parturition (delivery) date of this species has advanced by 18 days.

The Genus Concept
• In the hierarchy of biological classification, genus comes above species and
below family. In binomial nomenclature, the genus name forms the first
part of the binomial species name for each species within the genus.
• The standards for genus classification are not strictly codified, so different
authorities often produce different classifications for genera. There are
some general practices used, however, including the idea that a newly
defined genus should fulfill these three criteria to be descriptively useful:
• Monophyly: phylogenetic analysis should clearly demonstrate both monophyly and
validity as a separate lineage
• Distinctness: genetic distinctness
• Reasonable Compactness
(Sigward, J. D., Sutton, M. D., Bennett, K. D. 2018)

• The term "genus" comes from the Latin genus (origin, type, group,
race). Linnaeus popularized its use in his 1753 Species Plantarum.
• The gray wolf's scientific name is Canis lupus, with Canis (Lat. "dog")
being the generic name shared by the wolf's close relatives
and lupus (Lat. "wolf") being the specific name particular to the wolf. A
botanical example would be Hibiscus arnottianus, a particular species
of the genus Hibiscus native to Hawaii.
• In zoological usage, taxonomic names, including those of genera, are
classified as "available" or "unavailable". Available names are those
published in accordance with the International Code of Zoological
Nomenclature and not otherwise suppressed by subsequent decisions
of the International Commission on Zoological Nomenclature (ICZN);
the earliest such name for any taxon (for example, a genus) should
then be selected as the "valid" (i.e., current or accepted) name for the
taxon in question.

• Homonyms: Within the same kingdom, one generic name can apply to
one genus only. However, many names have been assigned (usually
unintentionally) to two or more different genera. For example,
the platypus belongs to the genus Ornithorhynchus although George
Shaw named it Platypus in 1799 (these two names are thus synonyms).
However, the name Platypus had already been given to a group
of ambrosia beetles by Johann Friedrich Wilhelm Herbst in 1793. A
name that means two different things is a homonym. Since beetles and
platypuses are both members of the kingdom Animalia, the name
could not be used for both. Johann Friedrich Blumenbach published
the replacement name Ornithorhynchus in 1800.
• Aotus is the generic name of both golden peas and night monkeys.

• Genus size: The number of species in genera varies considerably
among taxonomic groups. For instance, among (non-avian) reptiles,
which have about 1180 genera, the most (>300) have only 1 species,
~360 have between 2 and 4 species, 260 have 5-10 species, ~200
have 11-50 species, and only 27 genera have more than 50
species. However, some insect genera such as the bee
genera Lasioglossum and Andrena have over 1000 species each.
• Accepted genera: approximately 510,000 as at end 2016, increasing at
some 2,500 per year (Rees, T. at.al. 2017).

Taxonomic Keys
• A taxonomic key is a device, which when properly constructed and used,
enables a user to identify an organism. Keys are devices consisting of a
series of contrasting or contradictory statements or propositions requiring
the identifier to make comparisons and decisions based on statements in
the key as related to the material to be identified.
• There are two types of keys: (a) Dichotomous and (b) Poly clave (also
called Multiple Access or Synoptic)
• Dichotomous keys allow the user to determine the identity of items using
a sequence of alternative choices. Dichotomous keys always give two,
mutually exclusive choices in parallel statements. The pair of statements is
referred to as a couplet and each 1/2 of a couplet is a lead. At each couplet
of a dichotomous key the user is presented with two choices about a
specific character present in the group of organisms, a specific character
state is described for each lead. Sometimes the characters
are quantitative (i.e., measurements) and sometimes the characters
are qualitative (e.g., texture).

• Polyclave Keys are tools used to help identify unknown objects or species.
The keys are generated using interactive computer programs. Polyclave
keys use a process of elimination. The user is presented with a series of
choices that describe features of the species they wish to identify. The user
then checks off a list of character states present in the organism they wish
to study. The program looks to match those character states with all the
species they can possibly match. If a species does not have that character
state it is eliminated from the list. The more character states listed the
more species that are eliminated. This allows the rapid elimination of large
numbers of species that the specimen cannot be. The process continues
until only one species (or a short list of species) remains. This allows the
user to eliminate lots of potential species and identify the species or at
least a short list of possible species. This continues until only one species is
left. If all went well, and the key fits your group of organisms, that is the
name of the species you have located. Even the best keys have their
limitations, so make sure you verify your identification using multiple tools
(image verification, herbarium specimens, expert identification, etc.).

Polyclave way of Identification Dichotomous way of Identification

Evolutionary Systematics
• Evolutionary systematics or Darwinian classification is a branch of biological
classification that seeks to classify organisms using a combination
of phylogenetic relationship (shared descent), progenitor-descendant relationship
(serial descent), and degree of evolutionary change.
• This type of taxonomy may consider whole taxa rather than single species, so that
groups of species can be inferred as giving rise to new groups (Mayr, Ernst and
Bock, W.J., 2002).
• Evolutionary taxonomy differs from strict pre-Darwinian Linnaean
taxonomy(producing orderly lists only), in that it builds evolutionary trees. While
in phylogenetic nomenclature each taxon must consist of a single ancestral node
and all its descendants, evolutionary taxonomy allows for groups to be excluded
from their parent taxa (e.g. dinosaurs are not considered to include birds, but to
have given rise to them), thus permitting paraphyletic taxa (Grant, V. 2003 and
Aubert, D. 2015).

Historical Background
• Evolutionary Systematics arose as a result of influence of the theory of
evolution on Linnaean taxonomy. Linnaean taxonomy refers to rank-based
scientific classification. Linnaean classification oppose cladistics classification
concept.
• In this type of classification, the animals and plants are orderly placed into
dendrogram. Dendrogram is a tree diagram, which shows taxonomic
relationships.
• The concept arose after study of transmutation of species by various scientists
like Louis M de Maupertuis (1751), Erasmus Darwin (1796) and J B Lamarck
(1809).
• The concept was formally mentioned in the book ‘the Origin of Species’ by
Charles Darwin in 1859.
• T H Huxley scientifically argued that birds are descendants of dinosaurs after
study of fossils of Archaeopteryx.

Tree of Life
• It is a tool to present the evolution of life and describe the relationships
between organisms. In other words, it represents genealogical
relationships. The idea was firstly published the book ‘the origin of
species’ by Charles Darwin in 1859. Seven years later, German Zoologist
Ernst Haeckel drew up a more comprehensive tree.
• Tree of life is created by compiling the comprehensive phylogenetic
databases rooted at the last universal common ancestor of life on earth.
• Typical example of database represented by tree of life is ‘Open Tree of
Life’. It is an open digital database published in 2015.
• Lamarck produced first branching tree of animals in his book ‘Philosophie
Zoologique’ which is upside down tree starting with worms and ending
with mammals.

Haeckel tree of life
• Haeckel published his concept in the book ‘General
Morphology of Organisms’ in 1866.
• The root of tree symbolizes a common primordial
ancestor from which all other forms emerged.
• He developed his tree over almost 1000 pages based
on paleontological, embryological and systematic
data.
• During his work, he also coined the term ecology
describing it as the whole science of the relations of
the organism to the environment.

Phenetics
• The way to classify organisms based on overall similarity in morphology
i.e. observable traits, regardless of their phylogeny or evolutionary
relation.
• Phenetics is termed as numerical taxonomy or taximetrics.
• Phenetics is the techniques of clustering and ordination of organisms by
reducing the variation to a manageable level. The variations are
measured by dozens of variables, and then presenting them as two- or
three-dimensional graphs.
• Phenetics classifies organisms in two ways: artificial and natural
• Artificial classification: It is based on one or few easily observable
characters. Linnaeus used this type of classification.

• Natural Classification: the classification is based on similarities.
Hooker and Bentham used this type of classification.
• Operational Taxonomic Units (OTUs): it is a practical definition
to group individuals by similarity, equivalent to but not
necessarily in line with classical Linnaean taxonomy or modern
evolutionary taxonomy. Nowadays, OUT refers to clusters of
organisms, grouped by DNA sequence similarity of a specific
taxonomic marker gene.
• Phenogram: it is a branching diagrammatic tree used
in phenetic classification to illustrate the degree of similarity
among taxa.

Cladistics
• The method of classifying organisms by categorizing them in groups based on
the most recent common ancestor.
• The classification correlates with synapomorphies that can be traced to most
recent common ancestor and are not present in more distant groups and
ancestors.
• Synapomorphy: characteristics present in an ancestral species and shared
exclusively by its evolutionary descendants
• The method was firstly used by German Entomologist Willi Hennig, who referred
it as phylogenetic systematics.
• In the 1990s, the development of effective polymerase chain
reaction techniques allowed the application of cladistic methods to biochemical
and molecular genetic traits of organisms, vastly expanding the amount of data
available for phylogenetics.
• Cladistic can be studied in three different way of characteristics: Plesiomorphy,
apomorphy and homoplay

Cladogram
• The outcome of a cladistics is a cladogram. Cladogram is a tree
shaped diagram which is interpreted to represent the best hypothesis
of phylogenetic relationships. Cladogram is also coined as
dendrogram.
• Every cladogram is based on a particular dataset analyzed with a
particular method. Datasets are tables consisting of molecular,
morphological, ethological and/or other characters and a list
of operational taxonomic units (OTUs), which may be genes,
individuals, populations, species, or larger taxa that are presumed to
be monophyletic and therefore to form, all together, one large clade;
phylogenetic analysis infers the branching pattern within that clade.

Plesiomorphy
• A plesiomorphy ("close form") or ancestral state is a character state
that a taxon has retained from its ancestors. When two or more taxa
that are not nested within each other share a plesiomorphy, it is
a symplesiomorphy (from syn-, "together"). Symplesiomorphies do
not mean that the taxa that exhibit that character state are necessarily
closely related. For example, Reptilia is traditionally characterized by
(among other things) being cold-blooded (i.e., not maintaining a
constant high body temperature), whereas birds are warm-blooded.
Since cold-bloodedness is a plesiomorphy, inherited from the common
ancestor of traditional reptiles and birds, and thus a symplesiomorphy
of turtles, snakes and crocodiles (among others), it does not mean that
turtles, snakes and crocodiles form a clade that excludes the birds.

Apomorphy
• An apomorphy is a character that is different from the form found in an
ancestor, i.e., an innovation, that sets the clade apart from other clades.
• Autoapomorphy: autapomorphy is a distinctive feature, known as
a derived trait, that is unique to a given taxon. That is, it is found only in
one taxon, but not found in any others or outgroup taxa, not even those
most closely related to the focal taxon. Typical example is snake in reptilian
group.
• Synapomorphy: synaphomorphy is a characteristic present in an ancestral
species and shared exclusively (in more or less modified form) by its
evolutionary descendants. Typical example is tetrapod character among
different groups in reptiles.

Homoplasy
• The character state that is shared by two or more organisms but is absent
from their common ancestor or from a later ancestor in the lineage leading
to one of the organisms.
• Both mammals and birds are able to maintain a high constant body
temperature (i.e., they are warm-blooded). However, the accepted
cladogram explaining their significant features indicates that their common
ancestor is in a group lacking this character state, so the state must have
evolved independently in the two clades. Warm-bloodedness is separately
a synapomorphy of mammals (or a larger clade) and of birds (or a larger
clade), but it is not a synapomorphy of any group including both these
clades.

• Monophyly: In cladistics, a monophyletic group, or clade, is a group of
organisms that consists of all the descendants of a common ancestor. The
clade is characterized by one or more apomorphies i.e. derived character
states present in the first member of the taxon, inherited by its
descendants and not inherited by any other taxa.
• Paraphyly: A paraphyletic assemblage is one that is constructed by taking
a clade and removing one or more smaller clades. Removing one clade
produces a singly paraphyletic assemblage, removing two produces a
doubly paraphylectic assemblage, and so on. A paraphyletic assemblage is
characterized by one or more plesiomorphies.
• Polyphyly: A polyphyletic assemblage is one which is neither
monophyletic nor paraphyletic. A polyphyletic assemblage is
characterized by one or more homoplasies.

Phenetics vs. Cladistics
• Phenetics concept was firstly described by Peter Sneath and
Robert Sokal in 1963 as a principle of numerical taxonomy.
Cladistics was described by Willi Hennig in 1966 as
phylogenetic systematic.
• Phenetic methods construct phenogram by considering the
current states of characters without regard to the evolutionary
history. Cladistic methods construct cladograms rely on
assumptions about ancestral relationships as well as on current
data.
• Phenetic method is termed as distance method while Cladistic
method is termed as character-state method.

Molecular Systematics
• Molecular systematics is the use of molecular genetics to study the
evolution of relationships among individuals and species.
• Molecular biology has revolutionized the field of systematics. DNA
evolves by mutations being incorporated in the DNA and fixed in
populations. This will lead to divergence of DNA sequences in different
species. Although diverged, we can refer to two DNA sequences
as homologous. Divergence of DNA nicely demonstrates descent with
modification as a definition of evolution. For this reason, DNA should be
an excellent tool for inferring phylogenies: large number of homologous
characters that should be less subject to convergent evolution than other
characters that might lead to a confusion of grade and clade.
• Molecular approaches to systematics for us to think about the rates of
molecular evolution. If DNA or proteins evolved at a constant rate in all
species, then one could use estimates of sequence divergence to build
very reliable phylogenies.

• Mitochondrial DNA (mtDNA) is a pivotal tool in evolutionary and
population genetics including molecular ecology. The control region of
the mitochondrial DNA (mtDNA) due to its elevated mutation rate, lack
of recombination and maternal inheritance serve as a biomarker
in phylogenetic studies.
• The molecular clock is figurative term for a technique that uses the
mutation rate of biomolecules to deduce the time in prehistory when
two or more life forms diverged. The biomolecular data used for such
calculations are usually nucleotide sequences for DNA or amino acid
sequences for proteins. Instead of measuring seconds, minutes and
hours, says Hedges, the molecular clock measures the number of
changes, or mutations, which accumulate in the gene sequences of
different species over time.

उद्यमेन हि हिध्यन्ति कार्ााहि न मनोरथैः।
न हि िुप्तस्य हििंिस्य प्रहिशन्ति मुखे मृगा: ।।

Beyond species description

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