1. Majid Sajeel M.Sc. Zoology Semester_iv R# 09030814-023 University of Gujrat TAXONOMICAL COLLECTION AND IDENTIFICATION Systematics

2. 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

3. Collection must be borrowed from museum  usually insufficient  in certain crucial areas  does not provide the biological information  broad geographic scope

4. Systematic collection

5. 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

6. Purpose of Scientific Collection old style  typologically oriented taxonomist current thinking  the ordering of population  an adequate sample of every population should be connected and preserved  dealing with the size, population, coloration, or polymorphism, large sample from numerous localities are needed  Example: fishes

7. Scope of Collection The late Admiral H. Lyenes  Interested in Cisticola, a genus of African warblers  46 species  made 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

8. Where and How To Collect A collection trip must be carefully planned i.geographic information ii.distribution of vegetation types iii.Altitudes iv.types of seasons v.information on means of public and private transportation vi.the availabilities of health care

9. 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

10. Collection of Specimens Classical image of systematic collection is that of preserved whole specimens specimens may be  dried skins of mammals or birds  insects mounted on the pins  reptiles, amphibians, fishes, and invertebrates are preserved in alcohol or another liquid preservative.

11. Biological Information Additional information permanent records:  films of courtship display and other aspects of behavior  recordings of the vocalization of the animals (tapes, spectrograms)  collections, or photographs, or cast of the work of animals (nests, galls, spider webs, tracks).

12. Preservation of Specimens Least subject to deterioration  through the action of insects pests Mold Oxidation bleaching by sun light drying out protein decay etc

13. Anatomical, Tissue, And Molecular Material Anatomic Histological cytological (chromosomal) biochemical molecular research new techniques 1.Electrophoresis 2.DNA Hybridization

14. 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 apart  geodetic maps  altitude

15. Identification

16. 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)*

17. Determination Labels Each species should be labeled when this identification is made Label should give the scientific name  both generic and specific  author name  along with the name of the determiner  the year in which identification is made  In bird and mammal collections these names are usually written in pencil

18. 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

19. 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

20. Identification of Birds through DNA Barcodes

21. DNA Barcode Short DNA sequences from a standardized region of the genome provide a DNA barcode for identifying species  New master key for identifying species  One whose power will rise with increased taxon coverage  With faster, cheaper sequencing

22. 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

23. 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

24. mtDNA in history Mitochondrial DNA (mtDNA)  phylogenetic studies of animals  evolves much more rapidly than nuclear DNA  differences between closely related species  rapid “pace of sequence change”  so difference in population gene pole

25. 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

26. 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 identical most similar to other sequences of the same species

28. neighbor-joining (NJ) tree: showed  shallow intra-specific  deep 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.

30. 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

31. Primers 749-bp region near the 5′ terminus of the COI gene was amplified using primers  BirdF1-TTCTCCAACCACAAAGACATTGGCAC  BirdR1-ACGTGGGAGATAATTCCAAATCCTG

32. Material needed 10 μL of H 2 O, 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 MgCl 2 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.

33. 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