The document discusses the advancements in molecular systematics and biodiversity, emphasizing the need to classify organisms based on evolutionary relationships using molecular data. It highlights the limitations of traditional classification methods and advocates for the implementation of DNA barcoding to assess biodiversity accurately. The paper outlines the potential of modern techniques in revealing hidden diversity among species, particularly in less-studied groups, and the importance of databases for managing genetic data.

1. MOLECULAR SYSTEMATICS AND BIODIVERSITY
PRESENTED TO: DR. MUHAMMAD TAHIR
PRESENTED BY: SARWAR ALLAH DITTA
COURSE CODE: Z-8118
PHD SEMESTER-I
DEPARTMENT OF ZOOLOGY, GOVERNMENT COLLEGE UNIVERSITY LAHORE

2. Naturalistic Systematic
Around the 18th century,
naturalists sought to classify
nature in a way that reflected
nature, rather than the way
humans use nature.
Of course, there was
disagreement about what
constituted a “natural”
system, or even if a “natural”
system was necessary.
From the early history of human being, he has been
classified the organisms for getting more and more
benefits and information

3. Linnaean System
Three Kingdoms of
nature: Plants,
Animals, Protista.
Within each Kingdom,
organisms were
organized into nested
hierarchies.

4. Domains • More recently, a new
taxonomic level has been
added above Kingdoms:
Domains.
• Living things are divided
into three non-hierarchical
Domains:
• Bacteria
• Archaea
• Eukarya
Domains
Domain
Kingdoms
within
Domain
Eukarya

5. Classifying Organisms
Systematists develop
classifications based
on evolutionary
relationships. They
tend to look at:
Anatomy - a
traditional method.
molecular data - to
examine genetic
similarities and
differences.

6. It is impossible to describe biological
diversity with traditional approaches.
Molecular methods are the way forward —
especially, perhaps, in the form of DNA
barcodes.
Multidisciplinary characterization of
biological and genetic resources at
biochemical, cytological and molecular
level; identification of potential
genotypes of economic and other
interest; conservation of genes and
nucleotides in DNA libraries.

7. For 200 years taxonomists have recognized two
living species of elephant, the African and the
Indian. According to molecular evidence,
however, this understanding is wrong.
Although the details are still under discussion, two
or maybe three groups of ‘African’ elephant are
as distinct from each other as either is from the
Indian, and so may constitute distinct taxonomic
groups — a finding with implications for
conservation. This kind of discovery, using
molecular markers, epitomizes a sea change
occurring in taxonomy.

8. A proposal, published by Hebert et al. in
Proceedings of the Royal Society, for a DNA-
based barcoding system for all animal species.
Hebert et al. now formally suggest that a
molecular barcode inventory should be made
of known animal taxa, and that this data-base
should become the basis of biodiversity
assessment and taxon identification.

9. For taxa with large body sizes, such as
vertebrates, the catalogue may be essentially
complete. For smaller taxa (with bodies 0.5–10
mm long) that is far from the case.
For instance, there are some 1 million described
species of arthropods (insects and allies), but
estimates of actual diversity range from 3
million to 30 million.
Only 20,000 species of nematode (roundworms)
have been described out of a predicted million
or so

10. For the smallest organisms — the bacteria,
archaea and single-celled eukaryotes — we
may be ignorant of over 99% of actual
diversity.
It is not feasible to catalogue that diversity by
traditional methods based on taxon-by-taxon,
specimen-by-specimen morphological
description.
Instead, emerging technologies must be
harnessed to the task.

11. All cellular organisms have the highly conserved
small subunit ribosomal RNA (SSU) gene,
which can be isolated specifically even from
bulk samples of ‘environmental DNA’.
By surveying SSU gene sequences in a sample, it
is possible to identify how many different taxa
are present, and assess their relationships to
previously described and sequenced groups.

12. All environments sampled yield the same pattern:
many of the constituent microorganisms come
from major groups unknown to traditional
microbiology, and the diversity of prokaryotes
is probably 100 times higher than was
previously expected.
Similar SSU gene surveys of communities of
eukaryotic microbes, such as marine
picoplankton, also suggest that traditional,
descriptive methods have sampled only the tip
of diversity.

13. There may be over 100
million extant species
on Earth, but only a tiny
proportion of them have
been described.
The scale of the
descriptive deficit varies
widely for different
groups of organisms

15. Thus a DNA sequence can be used to both
identify and classify an organism, much as
a barcode identifies supermarket
products.
It is now accepted in bacteriology that taxa can be
identified using sequence data, and rules of thumb for
defining taxa based on sequence difference are
developing.
The taxa so defined have
been termed 'phylo-
types‘ or 'molecular
operational taxonomic
units'.

16. • Hebert et al. extend this idea to non-microbes, and
propose that a database of DNA barcodes for
identification of all animal taxa should be established.
• The gene region that is being used as the standard
barcode for almost all animal groups is a 648 base-pair
region in the mitochondrial cytochrome c oxidase 1
gene (“CO1”).
• COI is proving highly effective in identifying birds,
butterflies, fish, flies and many other animal groups.
• COI is not an effective barcode region in plants
because it evolves too slowly, but two gene regions in
the chloroplast, matK and rbcL, have been approved as
the barcode regions for plants.

17. In a survey of moths collected around Guelph,
Ontario, the authors show that the COI
barcode can in most cases yield a reliable
assignment to previously identified and
sequenced species.
Other insect specimens were correctly assigned
to the superfamily level,
Hebert et al. claim that in general the approach
can identify which phylum a sequence derives
from.

18. Many potential barcode sequences already exist in public
databases: about 12,000 COI sequences, over 20,000
SSU gene sequences (from all organisms),
and more than 50,000 sequences from the ‘ribosomal
internal transcribed spacer segment’ (from higher
eukaryotes).
Barcode of Life Database (BOLD) was created and is
maintained by University of Guelph in Ontario. It
offers researchers a way to collect, manage, and
analyze DNA barcode data.
Consortium for the Barcode of Life-CBOL's Data Analysis
Working Group has created the Barcode of Life Data
Portal which offers researchers new and more flexible
ways to store, manage, analyze and display their barcode
data.

19. Nonetheless, a taxonomic genomics programme
should yield huge benefits for biodiversity science
and ecology, much as the sequencing of
genomes has benefited other areas of biology.
As was the case with the initial work of Hebert and
colleagues, the first stages of such a programme
will need identified specimens to represent known
diversity and link barcodes to biology.
Subsequently, barcoding of environmental samples
or collections of unidentified specimens will reveal
novelties: flocks of taxa where one species was
expected, or divergent taxa with possible novel
biology.

20. One of the advantages of this approach is that the
raw data — the DNA sequence — can be
stored in data-bases and accessed through the
Internet for comparison and reanalysis.
Another is that debate about what usefully defines
a taxon, how many taxa there are and what
taxon diversity means will become a data-rich
science, rather than resembling theological
speculation as to how many angels can dance
on the head of a pin.

21. Sequence statistics
Species coverage (formally
described)
Barcode clusters for
animals (BINs) 550,825 Animals 189,919
All Sequences 6,951,393 Plants 66,836
Barcode Sequences 6,042,516 Fungi & Other Life 21,224

22. Animals: 440555 Public BINs
Acanthocephala [64]
Annelida [6553]
Arthropoda [379269]
Brachiopoda [36]
Bryozoa [293]
Chaetognatha [68]
Chordata [32706]
Cnidaria [1043]
Cycliophora [0]
Echinodermata [1764]
Gnathostomulida [10]
Hemichordata [7]
Mollusca [15505]
Nematoda [724]
Nemertea [262]
Other Life: 3179 Public BINs
Heterokontophyta [373]
Rhodophyta [2806]
Onychophora [130]
Platyhelminthes [676]
Porifera [485]
Priapulida [2]
Rotifera [690]
Sipuncula [107]
Tardigrada [156]
Xenoturbellida [5]

23. One of the advantages of
this approach is that the
raw data — the DNA
sequence — can be stored
in databases and
accessed through the
Internet for comparison
and reanalysis.

24. Techniques used in Molecular Systematic
Allozyme electrophoresis,
Restriction fragment length polymorphisms (RFLP),
Single-stranded conformational polymorphisms (SSCP),
Amplified fragment length polymorphism (AFLP),
Random amplified polymorphic DNA (RAPD).
Sequencing is generally the most appropriate for studies at
interspecific levels and higher . However, questions of intraspecific
population structure, species limits, and species diagnosis often can
be effectively addressed using time-honored techniques like
The best strategy for certain problems will often use one or more of
these in combination with sequencing.

25. DNA sequences are often used in constructing phylogenetic
trees. Ancestral DNA may be inferred from living species. In rare
instances, DNA may be recovered from fossils.

26. Summary
• Modern Systematic seeks to classify organisms
according to evolutionary relationships.
• Anatomical and molecular data are used to infer
relatedness between modern organisms.
• Different Molecular techniques are used to find
more biodiversity.

27. References
Blaxter, M. (2003). Molecular systematics: counting
angels with DNA. Nature, 421(6919), 122.
http://v3.boldsystems.org/index.php/Public_BarcodeIndex
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