Slide 1
Class III
DNA variation in Ecology and Evolution
III- Examples of application of molecular markers
Slide 2
Agama atra
Agama atra are rock-dwelling lizards with low dispersal capabilities. Two groups can
be distinguished within this species: (1) occupies the dry north-western regions of the
Northern Cape Province and comprises a large-sized animals with a long
breeding season, and (2) a group that occupies a more southern and eastern
distribution in South Africa and is smaller in size with a shorter breeding season.
The aim of this work is to investigate the phylogeographic pattern and infer historical
reasons for the present geographic distribution.
39 individuals were samples for 13 populations. DNA sequence information of two
mitochondrial genes were used for the phylogenetic reconstruction.
Image
http://www.capesnakes.org.za/index.php?full=1&set_albumName=jens&id=aaf&opti
on=com_gallery&Itemid=3&include=view_photo.php
Reference
MATTHEE CONRAD A. and FLEMMING ALEXANDER F. (2002) Population
fragmentation in the southern rock agama, Agama atra: more evidence for
vicariance in Southern Africa. Molecular Ecology 11, 465:471.
This work was carried out in the Zoology department, University of Stellenbosch.
Slide 3
Agama atra results
The phylogenetic reconstruction using different methods (maximum parsimony ML,
and maximum likelihood ML ) show congruent results. Three main lineages can be
identified, that show geographic distinctiveness; South Central, coinciding with the
Great Escarpment; North Central; and North in Namibia.
These lineages indicate that there is long-term restriction to gene flow between these
regions. Beside, the animals with large body size and prolonged breeding season
coincide with the North- Central clade, whereas the small animals with reduced
breeding season are restricted to the Southern central clade.
Using the rate of 0.5 –1 % change per million years for 16S rDNA, the clades
doverged 2-4 MY ago. The origin of the disjunct distributions could have been
originated from the cycles of dry- wet periods during glacial and interglacial periods
respectively, and some of these localities might have worked as refugia.
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Slide 4
Other rock dwelling species, a gecko and a rabbit show a similar pattern of
geographic distribution of maternal lineages. This is indicating a causal common
phenomenon affecting the biota. The appearance of geographical barriers and
divergent evolution in these isolated regions is called vicariance.
Images: http://www.tc.umn.edu/~gambl007/geckopics3a.htm
http://www.apus.ru/site.xp/049052056055124055054055053124.html
Slide 5
Tilapia hybrids in W Africa
Tilapias are closely related species that underwent a recent evolutionary radiation
during the Pleistocene. Many of these species show overlapping geographic
distribution and are utilized in aquaculture. Breeding programs in aquaculture usually
involve the hybridization between different phenotypes of even species obtain a
certain desired phenotype. Among the most utilized species are Oreochromis aureus
and Oreochromis niloticus. The geographic distribution of these species is shown in
the map: grey indicates O. niloticus and dashed line indicates O. aureus. Although
these species interbreed well in captivity, no hybrids were detected in the wild. In this
work, the authors utilize nuclear and mitochondrial variations along with the
morphological identification to test the hypothesis of gene flow between these two
species. For this, they utilized the variation at 30 allozyme loci (loci that code for
enzymes) and the DNA sequence information for cytochrome b and mitochondrial
DNA control region.
Samples were taken in locations in the Nile area and western Africa, O. aureus lives
in simpatry with O. niloticus.
Images
http://nis.gsmfc.org/photo/Oreochromis_aureus.jpg
http://64.95.130.5/Summary/SpeciesSummary.php?id=2
Reference
X. ROGNON and R . GUYOMARD (2003). Large extent of mitochondrial DNA
transfer from Oreochromis aureus to O. Niloticus in West Africa. Molecular
Ecology 12, 435-445.
Slide 6
Tilapia hybrids in W Africa
The slide shows partial results of the paper. The cluster in the 1st figure, on the left,
shows the clustering of population using genetic distance in allozyme polymorphisms
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between populations. We see that the three O. aureus population (from the Nile river,
from the Volta river in Niger river and from Senegal cluster together, whereas O.
niloticus shows to distinctive cluster: the top one is formed by population from the
Nile area, and the other cluster is formed by western Africa populations.
The cluster figure on the right shows the clustering of populations using mtDNA
polymorphisms. We see that the O. aureus population from Senegal clusters along
with O. niloticus from Senegal.
The clustering of all haplotypes shows the situation better: same haplotypes are
present in fish with O. niloticus and O. aureus phenotypes in the Niger and in
Senegal.
Slide 7
Hybridization of tilapias in W Africa
The main results are; shallow divergence between the haplotypes from Senegal,
regarless the species, and a strong divergence between O. niloticus from the Nile and
Western Africa. Two possible scenarios can explain this pattern;
1. ancestral retention
2. secondary contact followed by introgression
The first case: O. aureus could have originated from O. niloticus in western Africa.
This hypothesis agrees with mtDNA data but not with the deeper divergence observed
for protein data.
Thus, the most likely explanation is the replacement of mtDNA of one species by the
other.
Slide 8
Hybridization of tilapias in South Africa.
The map is showing the natural distribution of a few tilapia species in South Africa.
The Nile Tilapia O. niloticus is introduced in southern Africa for aquaculture and is
documented to have escaped into the natural environment in the Limpopo basin.
An investigation of the hybridization status of O. mossambicus in Southern Africa
with mtDNA control region gave surprising and unexpected results.
The network reconstruction including mtDNA control region of other parpatric
species revealed that there is hybridization or introgression with other native species.
The clusters indicate the group of belonging (species) and the colour represent
species. See, for instance, that the yellow genotypes (O. mossambicus) appear
clustering with the native species O. andersonii, O. karongae and the introduced
species O. aureus and O. niloticus.
See that it is possible to recognize 3 lineages within O. mossambicus.
Reference: unpublished data of D’Amato et al.
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María Eugenia D’Amato, M. Magdalena Esterhuyse, Ben C.W. van der Waal, D.
Brink and Filip A.M. Volckaert. Hybridization of the Mozambique tilapia
Oreochromis mossambicus in southern Africa evidenced by mitochondrial and
microsatellite DNA genotyping.
Slide 9
Phylogenetics of abalone
Gene families : Slide 17, Class I
The abalones are Gastropoda Molluscs that are distributed worldwide. The
phylogenetics of this group has been conflictive and phylogenies with 16S mtDNA
and lysine protein and other genes are not completely congruent.
The phylogenetic reconstruction presented here was performed with the DNA
sequence information of one highly conserved intron in the haemocyanine gene.
The heomocyanine is equivalent in function to the haemoglobin of mammals: binds
and transports oxygen to the tissues.
Hoemocyanines are a family of oxygen-binding proteins that evolved by duplication
and fusion (see Lieb and Markl, 2004). Gastropoda show tow isoforms that are
immunologically distinct, HtH1 and HtH2. These two forms duplicated approximately
350 Myr ago, before the divergence between limpets and abalones.
In the present work, the phylogeny is intended to be reconstructed from one intronic
and flanking exonic regions of the isoform HtH1. However, to avoid false clustering,
the authors have to prove that they sequenced the HtH1 form in all species. For this,
they used the ortholog HtH2 of one Haliotis species and another similar isoform in
Fisurellidae. The two isoforms show 65% identity within genome.
Images:
http://www.vetigastropoda.com/ABMAP/text/index.html
http://acd.ufrj.br/lamut/cropsite/cc01/cc01c.htm
References
Bernhard Lieb, Ju¨rgen Markl (2004). Evolution of molluscan hemocyanins as
deduced from DNA sequencing. Micron
Klaus Streit, Daniel L. Geiger and Bernhard Lieb (2006). Molecular Phylogeny and
the geographic origin of Haliotidae traced by haemocyanin sequences. Journal of
Molluscan Studies 72: 105-110.
Slide 10
Phylogenetics of abalone
The phylogenetic reconstruction shows that all Haliotis species cluster together, and
that the similarity between their HtH1 introns ranges from 80-95% sequence identity,
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therefore confirming that the sequences utilized in the phylogenetic reconstruction are
the paralogs.
Slide 11
Potential different adaptive values in different populations/ population structure
For population differentiation and Fst statistics See Slide 24, Class II
The threeline grunt Parapristipoma trilineatum is a fish species that lives in the coasts
of China and Japan. It is utilized in aquaculture, and it was imported to Japan because
of the higher growth rate of the Chinese form. The higher growth rate indicates
different quantitative traits and possibly different genetic composition. For this, the
population genetic structure of this species was investigated from 2 Chinese and 5
Japanese samples using 4 microsatellite loci.
The first table shows that the genetic variability in all population is similar in terms of
heterozygosity and number of alleles. Besides, the expected H (indicated He) do not
duffer significantly from the Ho (observed heterozygosity).
The second table shows an analysis of heterogeneity of allele frequency distributions
among populations (indicated by Fst and the probability that this its value differs
significantly from 0). The results show heterogeneity (population structure) between
the 2 Chinese populations, and between the Chinese and the Japanese populations.
The Japanese populations, however, are not differentiated and can be considered a
single stock for management.
Reference:
Keita Kumagai, Anna A. Barinova, Masamichi Nakajima, and Nobuhiko Taniguchi
(2004). Genetic Diversity Between Japanese and Chinese Threeline Grunt
(Parapristipoma trilineatum) Examined by Microsatellite DNA Markers. Mar.
Biotechnol. 6, 221–228.
Image: http://uni2004.hp.infoseek.co.jp/awajiikimono/sakanas11.jpg
Slide 12
Population differentiation in the threeline grunter
For microsatellites see Slide 20, Class I.
In this slide we see the pairwise Fst values between all population pairs. These values
were utilized as distances to construct a tree (UPGMA) that also reflects the
differences between the Chinese populations ( a deep divergence) and the differences
between the Japanese and Chinese samples.
Based on these results, recommendations are made to avoid escapees from the fish
farms as the introduced fish are distinctively different from the native fish and could
disrupt local adaptation.
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