DIFFERENTIATION AND SYSTEMATICS IN THE LONG-TAILED GROUND SQUIRREL, SPERMOPHILUS UNDULATUS (SCIURIDAE, RODENTIA) Marina V. Tsvirka, Vladimir P. Korablev,

Slides:



Advertisements
Similar presentations
RAPD markers Larisa Gustavsson (Garkava)
Advertisements

Genetics differentiation and systematic of peripheral populations of East Asian endemic rodent Myospalax psilurus (Rodentia, Spalacidae) M.V. Tsvirka,
APPLICATION OF MOLECULAR MARKERS IN THE STUDIES OF PHYLOGENY AND PHYLOGEOGRAPHY: ADVANCES, PITFALLS AND PERSPECTIVES OF DEVELOPMENT Abramson N.I., Kostygov.
Diversity of two forms of silver crucian carp Carassius auratus gibelio based on mitochondrial DNA analysis Diversity of two forms of silver crucian carp.
Amorphophallus titanum Largest unbranched inflorescence in the world Monecious and protogynous Carrion flower (fly/beetle pollinated) Indigenous to the.
Sampling distributions of alleles under models of neutral evolution.
1 General Phylogenetics Points that will be covered in this presentation Tree TerminologyTree Terminology General Points About Phylogenetic TreesGeneral.
Classification of Living Things. 2 Taxonomy: Distinguishing Species Distinguishing species on the basis of structure can be difficult  Members of the.
GENETICAL FEATURES OF CHROMOSOMAL FORM «C» OF MICROTUS MAXIMOWICZII FROM THE RUSSIAN FAR EAST GENETICAL FEATURES OF CHROMOSOMAL FORM «C» OF MICROTUS MAXIMOWICZII.
The Barcode Gap Speciation or Phylogeography? BANBURY 3 ? Graham Stone, Richard Challis, James Nicholls, Jenna Mann, Sonja Preuss Mark Blaxter Institute.
Molecular Evolution Revised 29/12/06
14 Molecular Evolution and Population Genetics
Introduction to Computational Biology Topics. Molecular Data Definition of data  DNA/RNA  Protein  Expression Basics of programming in Matlab  Vectors.
Molecular Markers DNA & PROTEINS –mtDNA = often used in systematics; in general, no recombination = uniparental inheritance –cpDNA = often used in systematics;
Dispersal models Continuous populations Isolation-by-distance Discrete populations Stepping-stone Island model.
Human Migrations Saeed Hassanpour Spring Introduction Population Genetics Co-evolution of genes with language and cultural. Human evolution: genetics,
Topic : Phylogenetic Reconstruction I. Systematics = Science of biological diversity. Systematics uses taxonomy to reflect phylogeny (evolutionary history).
Phylogenetic trees Sushmita Roy BMI/CS 576
MOLECULAR GENETIC RELATIONSHIPS OF THE ZOKORS (RODENTIA, MYOSPALACINAE): ANALYSIS OF D-LOOP REGION POLIMORPHISM Tsvirka Marina 1, Pavlenko Marina 1, Korablev.
- Delphine MUTHS & Jérôme BOURJEA - Connectivity of Marine Protected Areas in South-Western Indian Ocean: Using population genetics of reef fish to contribute.
DISCREPANCY IN NUCLEAR, MITOCHONDRIAL AND KARYOLOGICAL CHARACTERISTICS OF MUS MUSCULUS SUBSPECIES IN PRIMORYE HYBRID ZONE IN PRIMORYE HYBRID ZONE Spiridonova.
Morphological and genetic diversity of the larch populations on the Kuril Island I.Yu. Adrianova Group of Plant Molecular Genetics Institute of Biology.
Chapter 3 -- Genetics Diversity Importance of Genetic Diversity Importance of Genetic Diversity -- Maintenance of genetic diversity is a major focus of.
Multiple Sequence Alignments and Phylogeny.  Within a protein sequence, some regions will be more conserved than others. As more conserved,
GENETIC FINGERPRINT ESTABLISHED FOR THE SELECTED ALFALFA GENOTYPES USING MOLECULAR MARKERS.
Terminology of phylogenetic trees
A MOLECULAR APPROACH TO INVESTIGATE TUBERCULOSIS CASES IN A GOTHIC POPULATION FROM GHERĂSENI NECROPOLIS, BUZĂU COUNTY 1 Molecular Biology Center, Interdisciplinary.
Molecular phylogenetics
Molecular evidence for endosymbiosis Perform blastp to investigate sequence similarity among domains of life Found yeast nuclear genes exhibit more sequence.
Speciation history inferred from gene trees L. Lacey Knowles Department of Ecology and Evolutionary Biology University of Michigan, Ann Arbor MI
Phylogenetics and Coalescence Lab 9 October 24, 2012.
Bioinformatics 2011 Molecular Evolution Revised 29/12/06.
Molecular phylogenetics 4 Level 3 Molecular Evolution and Bioinformatics Jim Provan Page and Holmes: Sections
Announcements Urban Forestry project starts this week. Go through protocol. We'll be sending you off on your own. Please act responsibly. Peer review of.
Introduction to Phylogenetics
PHYLOGEOGRAPHY OF THE BOBWHITES Damon Williford, Randy W. DeYoung, Leonard A. Brennan, Fidel Hernández Caesar Kleberg Wildlife Research Institute Texas.
Calculating branch lengths from distances. ABC A B C----- a b c.
Lecture 17: Phylogenetics and Phylogeography
Chapter 10 Phylogenetic Basics. Similarities and divergence between biological sequences are often represented by phylogenetic trees Phylogenetics is.
Why do trees?. Phylogeny 101 OTUsoperational taxonomic units: species, populations, individuals Nodes internal (often ancestors) Nodes external (terminal,
Introduction to Phylogenetic trees Colin Dewey BMI/CS 576 Fall 2015.
Phylogeny & the Tree of Life
Estimating genetic diversity (  within populations  =  a function of the number of polymorphic sites in a population (S) “Watterson’s theta”
Ayesha M.Khan Spring Phylogenetic Basics 2 One central field in biology is to infer the relation between species. Do they possess a common ancestor?
Phylogenetic analysis of flatfish species (Teleostei, Pleuronectiformes) based on cytochrome oxidase 1 (Co-1) and cytochrome b (Cyt-b) genes Sharina S.N.,
Classification Biology I. Lesson Objectives Compare Aristotle’s and Linnaeus’s methods of classifying organisms. Explain how to write a scientific name.
Phylogenetic trees. 2 Phylogeny is the inference of evolutionary relationships. Traditionally, phylogeny relied on the comparison of morphological features.
Gene flow and speciation. Mechanism for speciation Allopatric speciation Sympatric speciation.
Population Structure and Genetic Diversity in South Tunisian Hedysarum
Evolutionary history of gorillas inferred from complete mitochondrial DNA sequences Das R1, Hergenrother SD1, Lurie-Marino M1, Soto-Calderón ID2,3, Anthony.
Phylogenetic basis of systematics
Inferring phylogenetic trees: Distance methods
Phylogeny & the Tree of Life
C.J. Kyle, C.C. Wilson  Forensic Science International 
Linkage and Linkage Disequilibrium
The 6th SPPS PhD conference, 2-5 September, 2010, Espoo, Finland
Goals of Phylogenetic Analysis
Patterns in Evolution I. Phylogenetic
Are my haplotypes sensitive enough?
Parsimony is Computationally Intensive
Why Models of Sequence Evolution Matter
Track the Split of Crocodile Sub Populations
Chapter 19 Molecular Phylogenetics
Evolutionary Origin of the Medaka Y Chromosome
Ethiopian Mitochondrial DNA Heritage: Tracking Gene Flow Across and Around the Gate of Tears  Toomas Kivisild, Maere Reidla, Ene Metspalu, Alexandra Rosa,
Development of a real-time PCR assay for the specific detection and identification of Streptococcus pseudopneumoniae using the recA gene  V. Sistek, M.
Volume 13, Issue 23, Pages (December 2003)
Phylogenetic Trees Jasmin sutkovic.
But what if there is a large amount of homoplasy in the data?
Phylogenetic tree representation of a neighbor-joining analysis of several species of piroplasms. Phylogenetic tree representation of a neighbor-joining.
Presentation transcript:

DIFFERENTIATION AND SYSTEMATICS IN THE LONG-TAILED GROUND SQUIRREL, SPERMOPHILUS UNDULATUS (SCIURIDAE, RODENTIA) Marina V. Tsvirka, Vladimir P. Korablev, Marina V. Pavlenko Institute of Biology and Soil Science FEB RAS, Vladivostok, 690022, Russia

Map of the ground squirrels distribution in the Palaearctic region

two geographical forms PROBLEM Genus Spermophilus Subgenus Urocitellus Species Spermophilus undulatus Subspecies S. u. undulatus, S. u. intercedens, S. u. menzbieri, S. u. jacutensis, S. u. stramineus, S. u. eversmanni two geographical forms “eastern” “western” (Vorontsov et al., 1980; Frisman, Vorontsov, 1989) (Gromov, Erbaeva, 1995)

? Map of S. undulatus distributions species or semispecies western form eastern form hybrid zone ? species or semispecies

Morphometric data (Popkov, 1978) Morphotypical study (Linetskiy, Linetskaya 1989) Karyological data (Korablev, 1988)

THE AIM IS to better understand species subdivision in S. undulatus , and ultimately speciation, in Spermophilus.

THE MAIN TASKS ARE To study genetic variability and differentiation of S. undulatus based on nuclear (RAPD) and mitochondrial (D-loop) DNA. To assess genetic divergence and phylogenetic relationships among subspesies of S. undulatus. To specify the taxonomic rank of eversmanni (independent species S. eversmanni or subspecies of S. undulatus) based on the data obtained

Map of sampling localities MATERIALS Map of sampling localities western form eastern form S. relictus, S. dauricus and S. parryi, S. taurensis and S. xanthoprymnus were chosen for comparative analyses, Tamias sibiricus was chosen as outgroup taxon.

Mitochondrial DNA analysis METHODS RAPD-PCR analysis 166 binary characters including the molecular markers Ten arbitrary decanucleotide primers Calculation of genetic distances (Nei, 1972) Reconstructions: NJ and UPGMA with bootstrap estimation of branching robustness in TREECONW 1.3 b (Van de Peer, De Wacher, 1994 ) Mitochondrial DNA analysis 5’ end of the D-loop (518 bp) Calculation of genetic distances based on Kimura two-parametric (K2P) estimator. Reconstructions: NJ, MP, ML and UPGMA with bootstrap estimation of branching robustness in MEGA 4.0 (Tamura et al., 2007)

Sequencing of the D-loop L15702 CAACGWAGYATAATATTYCGACC H15917 Primer Sequence (5' - 3') RAPD OPA-02 TGCCGAGCTG OPC-02 GTGAGGCGTC OPC-05 GATGACCGCC OPC-09 CTCACCGTCC OPC-12 TCGGCGATAG OPC-20 ACTTCGCCAC OPD-05 TGAGCGGACA OPE-20 AACGGTGACC POC-10 TGTCTGGCTG OPC-16 CACACTCCAG Sequencing of the D-loop L15702 CAACGWAGYATAATATTYCGACC H15917 CGGAATTCCATTTTTGGTTTACAAG polymorphic profiles monomorphic profiles

RESULTS Electrophoregrams of S. undulatus obtained using primers OPD-05 and OPE-20 “eastern” form common for all of subspecies eversmanni menzbiery Marker loci are indicated by arrows.

Genetic variability among S. undulatus subspecies RAPD analysis Genetic variability among S. undulatus subspecies N Np A / P intercedens menzbieri jacutensis eversmanni 166 126 0.42/0.15 0.48/0.23 0.45/0.27 0.38/0.17 N – total number of loci, Np – number of polymorphic loci, A – allele frequencies, Р – percentage of polymorphic loci (as the proportion of loci polymorphic within each population tested).

Parameters of genetic differentiation on RAPD analysis   n DN p (Ex) intercedens / menzbieri 10 0.7 1.00 menzbieri / jacutensis 12 0.8 intercedens / jacutensis 0.6 eversmanni / “eastern” form 19 0.40 0.00 S. parryi / S. relictus 6 0.41 S. dauricus / S. relictus 0.42 S. dauricus / S. parryi 0.46 n- number of samples, DN - genetic distances (Nei, 1972), p (Ex) - probability (exact test for interpopulation differentiation (Raymond and Rousset, 1995).

NJ and UPGMA trees based on RAPD data “eastern” form eversmanni UPGMA “eastern” form eversmanni

mt DNA data 519 nucleotides; 92 variable sites, 56 parsimony informative; Mean pairwise transition/transversion ratios was 1.284. 1 2 3 4 5 6 1. S. u. jacutensis - 2. S. u. interscedens 0.043 3. S. u. menzbieri 0.0 5 0.22 4. S. u. eversmanni 0. 113 0.107 0.115 5. S. xanthoprymnus 0.159 0.165 0.142 6. S. taurensis 0.175 0.160 0.166 0.162 0.134 Estimates of mean divergence between main lineages of Spermophilus given as genetic distances

NJ and UPGMA trees based on KP2 distances calculated from mtDNA data

Genetic distances for nuclear (RAPD) and mitochondrial (mtDNA) genomes within “eastern” populations 0.026-0.06 0.022-0.05 within eversmanni - 0.029 between eversmanni and “eastern” form 0.39-0.41 0.116 between distinct species of Spermophilus 0.41-0.46 0.134

CONCLUSIONS Both nuclear and mitochondrial DNA analyses showed that the subspecies of “eastern” form were close to each other and far from subspecies of “western” form. 2. Our molecular genetic data showed an important level of genetic divergence between the animals from Altai (S. u. eversmanni) and Far East of Russia (S. u. intercedens, S. u. menzbieri, S. u. jacutensis), similar to those observed between different Spermophilus species (S. relictus, S. dauricus, S. parryi, S. xanthoprymnus, S. taurensis). 3. The results confirm a distinct taxonomic position of eversmanni. It should be considered as a species taxon within Urocitellus group.

THANKS FOR YOUR ATTENTION ACKNOWLEDGMENTS The study was supported by the RFBR (grant nos. 06-04-39015) and FEBRAS (grant nos. 09-III-В-138). THANKS FOR YOUR ATTENTION