Majid SajeelM.Sc. ZoologySemester_iv

R# 09030814-023

University of Gujrat

TAXONOMICAL COLLECTION AND IDENTIFICATION

Systematics

Introduction• All the classification is based upon the

comparison of specimens that represent population and species

• Determination the species-specific characteristics by comparing it with the members of their similar species

• Electron microscope• Warburg apparatus• Ultracentrifuges

Collection must be borrowed from museumusually insufficient in certain crucial areas does not provide the biological information broad geographic scope

Systematic collection

Value of Collection

• Museums center of documentation permanent record particularly for the localities

Collections are reference tools, just as necessary as the books in the library, which are

not in continuous use yet, must be available when needed

Purpose of Scientific Collection

• old style typologically oriented taxonomist• current thinking the ordering of populationan adequate sample of every population

should be connected and preserveddealing with the size, population, coloration,

or polymorphism, large sample from numerous localities are needed

Example: fishes

Scope of Collection

• The late Admiral H. Lyenes Interested in Cisticola, a genus of African warblers46 speciesmade a series of collecting trips to nearly every corner

of Africa. He combined the collecting of the specimens with a

detail study of the ecology, habits, songs, and nest construction of these birds.

Result was that the genus Cisticola, formerly is reasonably well understood

Where and How To Collect

• A collection trip must be carefully plannedi. geographic informationii. distribution of vegetation typesiii. Altitudesiv. types of seasonsv. information on means of public and private

transportationvi. the availabilities of health care

Attention • geographically variable species• geographic isolation• seasonal variations• allopatric populations categorical status is uncertain

(species or subspecies)• New techniques are continually being developed • Use of mist nests for bird’s collection• “black light” (ultraviolet lamps) for insect collecting• Different kind of traps• baits• poisons

Collection of Specimens

• Classical image of systematic collection is that of preserved whole specimens

• specimens may bedried skins of mammals or birdsinsects mounted on the pinsreptiles, amphibians, fishes, and invertebrates are preserved in alcohol or another liquid preservative.

Biological Information

• Additional information• permanent records:films of courtship display and other aspects of

behaviorrecordings of the vocalization of the animals

(tapes, spectrograms)collections, or photographs, or cast of the work

of animals (nests, galls, spider webs, tracks).

Preservation of Specimens

• Least subject to deteriorationthrough the action of

insects pestsMoldOxidationbleaching by sun lightdrying outprotein decay etc

Anatomical, Tissue, And Molecular Material

• Anatomic• Histological• cytological (chromosomal)• biochemical molecular research• new techniques

1. Electrophoresis2. DNA Hybridization

Labeling

• A specimen that is not accurately labeled is worthless

• it is more important than specimen• exact locality of a collection• distinct populations living as little as half a

kilometer apartgeodetic mapsaltitude

Identification

Sorting Of Collections

• first rough sorting in the field• Entomologist may keep specimens in separate

containers• oceanographic expeditions collection is sorted

immediately b/c diff. species require diff. preservation methods

• Identification up to family or Genus, then shipped to specialists….(Linnaeus thinking)*

Determination Labels

• Each species should be labeled when this identification is made

• Label should give the scientific nameboth generic and specificauthor namealong with the name of the determinerthe year in which identification is madeIn bird and mammal collections these names

are usually written in pencil

Process of Identification

• Even a rank beginner can try to identify a specimen by telling us that is a bird, a spider, grasshopper, or a butterfly

• Then He/she tries keys and manuals • Trouble with most common kind of animals• general textbooks• Handbooks• All literature a species should be identified

character by character

Comparison with the Type

• Type specimens are most authentic source• But routine identification should be there• In the course of a monographic study of a

group All type specimens should be reexamined

Identification of Birds through DNA Barcodes

DNA Barcode

• Short DNA sequences from a standardized region of the genome provide a DNA barcode for identifying species

New master key for identifying speciesOne whose power will rise with increased

taxon coverageWith faster, cheaper sequencing

Which Region is barcode…

• Sequence diversity in a 648-bp region of the mitochondrial gene

“cytochrome c oxidase I (COI)”• Discriminating bird species

one of the largest and best-studied vertebrate groups

• Researchers determined COI barcodes for 260 species of North American birds straightforward

rRNA in history• The use of nucleotide sequence differences in

a single gene to investigate evolutionary relationships by Carl Woese

• He recognized that sequence differences in a conserved gene, ribosomal RNA, could be used to infer phylogenetic relationships

• rRNA, often do not differ among closely related organisms

• providing insights as far back as the origin of cellular life

mtDNA in history

• Mitochondrial DNA (mtDNA) phylogenetic studies of animalsevolves much more rapidly than nuclear DNAdifferences between closely related species rapid “pace of sequence change” so difference in population gene pole

DNA barcode

• short region of mtDNA• consistently differentiated• vouchered specimens would make this

sequence an identifier for species• Deep sequence divergences between 13,000

closely related pairs of animal species• Investigation by testing GeneBank

Results analysis

260 bird species had a different COI sequence(s)none was shared between species

COI sequences in the 130 species represented by two or more individuals were either identicalmost similar to other sequences of the same species

• neighbor-joining (NJ) tree: showed shallow intra-specificdeep inter-specific divergences

• The intra-specific K2P distances in these exceptional species were

3.7%–7.2%, 9- to 17-fold higher than the average

distance.

Material and method

• Mitochondrial pseudo-genes can complicate PCR-based studies of mitochondrial gene diversity

• Researchers used protocols to reduce pseudo-genes impacts

• employing primers with high universality, and amplifying a relatively long PCR product because most pseudo-genes are short

Primers

• 749-bp region near the 5 terminus of the COI ′gene was amplified using primers

BirdF1-TTCTCCAACCACAAAGACATTGGCACBirdR1-ACGTGGGAGATAATTCCAAATCCTG

Material needed• 10 μL of H2O,• 749-bp region near the 5 terminus′• primers • The 50-μl PCR reaction mixes included 40 μl of

ultrapure water• 1.0 U of Taq polymerase• 2.5 μl of MgCl2

• 4.5 μl of 10× PCR buffer• 0.5 μl of each primer (0.1 mM)• 0.25 μl of each dNTP (0.05 mM)• 0.5–3.0 μl of DNA.

What to do…???

• PCR• Gel electrophorasis• Sequencing• Gene recovery did not contain insertions,

deletions, nonsense, or stop codons, supporting the absence of nuclear pseudo-genes amplification

• Analysis through GeneBank

Thank you