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Journal club + *Evol Comp Meth (for those marked with *)

Dear Class!

This year we will read papers on DNA techniques and analysis, phylogeography and phylogeny in areas related to your MSc thesis. For those who have to do the comparative course I suggest to work on novel problems, perhaps you can present it at TDK if successful :-)

Please download the four papers obligatory for all of you. Also, download all papers under your name. Select the ones you like, write me a mail with your choice by 3rd of April.

We would have two meetings, one in mid-April, and two in early May.

The April meeting will be short. We would discuss the four papers obligatory for all of you.

Please note: links to articles do not work from out of campus.

for all students:

  1. Ancient DNA (all students) here
  2. Plea for DNA taxonomy here
  3. Widespread loss of sexually selected traits here
  4. Nonlinear relationships and phylogenetically independent contrasts here

By the May meetings you should have read the four other papers of your choice (some students have more to read). You will have 15 minutes to summarize those articles. Please use the video projector for you presentation.

Your are required to sum up the papers in writing, 2-4 pages to be submitted by e-mail.
Regarding the "DNA techniques" papers you can write a single sentence on the aim of the study and then discribe the methods used. Results can be given in a single sentence.
The Phylogeny papers: aim and methods of the study in a few sentences and then discribe anything new, interesting results.

A few students have to read more than 4 papers because they can skipp the phylogeny problems and focus on their diploma thesis. Please read and discuss those papers. However, review only 4 papers in writing. Alternatively (and preferebly :-) summerise all papers as a single essay. Bit more difficult but a good start up for you thesis.


Form of the assignment:
YOUR NAME
Assignment for the Journal Club, Kabai's class, 2006
Title, authors and source of the article
text

As I will put your assignment on the Internet, please do not republish any figures, do not copy-paste sentences, avoid plagiarism.

Comparative: while working on the project I expect you to have consultations with me or Aniko at least on 2 occasions. Please see us first in April to discuss how to start the job. The analysis will take some time, but remember, this is a full course for credits.

Feel free to contact me with any questions. Have fun with it!

Best wishes, Peter (peter.kabai###gmail.com, replace ### with superdot)

 

Bokán Kata: Apes

DNA techniques (pick four of these):

  1. Dispersed Male Networks in Western Gorillas here
  2. Queuing and queue-jumping: long-term patterns of reproductive skew in male savannah baboons, Papio cynocephalus here
  3. Are genes of human intelligence related to the
    metabolism of thyroid and steroids hormones? here
  4. A complete species-level phylogeny of the Hylobatidae based on mitochondrial ND3–ND4 gene sequences here
  5. Possible multiple origins of replication in primate mitochondria: Alternative role of tRNA sequences here
  6. Ontogeny and phylogeny in papionin primates here
  7. Alu insertion loci and platyrrhine primate phylogeny here
  8. Molecular cladistic markers in New World monkey
    phylogeny (Platyrrhini, Primates) here
  9. Phylogenetic relationships among Lemuridae (Primates): evidence from mtDNA here
  10. A mobile element based phylogeny of Old World monkeys here

Fanaczán Anikó: spiders

DNA techniques (pick two of these):

  1. Satellite DNA here
  2. Barcoding here
  3. Evolution of silk proteins here
  4. Variation in spider silk gene here
  5. Diet studied by DNA (1) here
  6. Diet studied by DNA (2) here

Phylogeny (pick two of these):

  1. Phylogeny of web construction here
  2. Systematics of African.. here
  3. Phylogeny of Central European wolf spiders here
  4. Phylogeography here
  5. Phylogeny of jumping spiders here

Comparative (elective for you):

Foraging strategy and metabolic rate in spiders here
For phylogenetic tree you can start from here: http://tolweb.org/Entelegynae/2651

(also: Metabolic rates... here)

Although not obligatory for you, it might be interesting to re-analyse the data in "foraging strategy..." (or "Metabolic rates") using independent contrasts. Please let me know about your decision, because others might take this job if you don't.


* Gavalda Kinga and Kiss Georgina Lujza: horses

Please do not share any of these papers.

DNA techniques (pick two-two of these):

  1. Linkage map here
  2. Horse Y chromosome here
  3. DNA from a frozen tomb here KINGA
  4. Spanish donkeys here
  5. MHC phylogeny here
  6. Horse genomics here KINGA

Phylogeny (pick two-two of these):

  1. mtDNA and evolution of domestic horses here + comments here
  2. Italian breeds here KINGA
  3. Lipizzan pedigrees here
  4. Andalusian pedigree here
  5. Iberian horses here
  6. Lusitano maternal lineage here
  7. THE ORIGINS OF SEXUAL DIMORPHISM IN BODY SIZE IN UNGULATES here KINGA

Comparative: (not for Georgina)

Please read this on the evolution of sex dimorphism in body size in Ungulates. The authors suggest that sex dimorphism evolved after the shift from monogamy to polygyny after the shift from living in closed to living in open habitat.
I would be interested to know, whether the degree of sex. size dimorphism is also related to dimorphism in specific weapons used by males during competing for females. The assignment is not without risk, because the atuhors do not provide raw data. Please let me know what you think.

 

Gyenes Nóra: flycatchers

DNA techniques (pick two of these):

  1. Female control of reproductive skew in cooperatively breeding brown jayshere
  2. Manipulation of male quality in wild tits: effects on paternity loss here
  3. Characterization of polymorphic microsatellite loci in a neotropical wood-quail here
  4. Part-Time Mate Guarding Affects Paternity in Male Reed Buntings here
  5. Extra-pair paternity in birds: explaining variation between
    species and populations here

Phylogeny (pick two of these):

  1. Speciation in flycathers here
  2. Inheritance of size and shape here
  3. Sexually selected trait here
  4. Genome size and longevity here + comments here
  5. Behavioural flexibility predicts species richness in birds here

 

Kemencei Zita: cat communication

DNA techniques and analysis (pick two of these):

  1. Japanese population here
  2. Latin American population here
  3. Lions pop.gen. here
  4. Molecular phylogenetic inference from saber-toothed cat fossils here
  5. Molecular phylogeny of the extinct cave lion Panthera leo spelaea here

Cat behaviour (read five of these):

  1. Object play here
  2. Object discrimination here
  3. Anticipation here
  4. Food preference here
  5. Home range here
  6. Ontogeny here
  7. Paw preference here
  8. Taste here
  9. Social group here
  10. Species-specific call here
  11. Housing here

 

*Kiss Alexa: Glia

DNA techniques and whatever (pick two of these + bring 2 of your own library):

  1. Dynamics of CNS Barriers: Evolution,
    Differentiation, and Modulation     here
  2. Glia in Droso here
  3. Knock-out here
  4. Antisense as a neuroscience tool and therapeutic agent here

Phylogeny and comparative:

I have not found anything relevant to your topic. Make a literature search yourself, or work with me on human data if that is fine with you. The paper you need to read for the human problem is this one. Your job would be to modify the tree and do a comparative analysis using this new tree. Please, see me to discuss how to go on.

 

Kiss Georgina Lujza: see papers to select from at Kinga's list. (You are not required to do the comparative part)

 

*Kopena Renáta: lizard

DNA techniques and Phylogeny (pick four of these):

  1. Karyological and genetic variation in Middle Eastern lacertid lizards here
  2. Delimiting Species Using DNA here
  3. Horn evolution here
  4. Lacerta vivipara here
  5. Polymorphic characters here
  6. The phylogeny of squamate reptiles here
  7. Loss of sex. selected characters here
  8. Evol. of sex. dischrom. here
  9. Decoupled evolution of display morphology and display behaviour in phrynosomatid lizards here
  10. Variation in speed, gait characteristics and microhabitat use in lacertid lizards here
  11. PHYLOGENY AND PHYLOGEOGRAPHY OF THE LIOLAEMUS DARWINII COMPLEX here

Comparative:

Perhaps you can use the tree in The phylogeny of squamate reptiles here to do some simple comparative analysis.

A more interesting possibility would be to re-analyse data on pheromones (here) using the tree published here (I have just received an e-print from the author and had no time to read it yet.) The authors of the pheromone study found that "The number of precloacal pores correlated positively with altitude and negatively with latitude, suggesting that lizards produce more secretions under harsh environments." However, independent contrasts were not used.


Kovács Anikó: biodiversity in cultivated fields

Please pick at least two of these

  1. Correlates of extinction risk and hunting pressure in gamebirds here
  2. A molecular genetic approach for forensic animal species identification here
  3. The calculus of biodiversity here
  4. Considering evolutionary processes in conservation biology here
  5. Biodiversity conservation: Does phylogeny matter? here
  6. Conservation genetics: where are we now? here

Also, bring articles from your own collection, so that the sum of papers to be reviewed would be 6.


*Kovács Szilvia: imperial eagle genetics

DNA techniques (pick or bring a few from your own collection, read 4 articles):

  1. A non-invasive test for sex identification in Short-toed Eagle here
  2. Social mating system affects the frequency of extra-pair paternity in house wrens here

Phylogeny (pick two of these):

  1. MtDNA genetic diversity and population history here
  2. Phylogeny of eagles, Old World vultures, and other Accipitridae based on nuclear and mitochondrial DNA here
  3. The evolution of plumage polymorphism in birds of prey and owls: the apostatic selection hypothesis revisited here
  4. Gene pool variability of a golden eagle here

Comparative

Males are smaller than females in many raptor species. I would be interested to learn about the evolution of female or male biased sexual dimorphism in birds of prey. Perhaps you could use the tree from the "Phylogeny of eagles..." here, and we can get body weight data from the Internet. Please let me know what you think.


*Kulcsár Anna: Papilloma and plumage

DNA techniques (pick two of these):

  1. microsatellites here
  2. avian papillomaviruses here (external): http://www.biomedcentral.com/1471-2180/2/19
  3. Male tail streamer length predicts fertilization success here
  4. Manipulation of male quality in wild tits here
  5. Determining the reproductive behaviour of individual
    brown-headed cowbirds using microsatellite DNA markers     here
  6. Extra-pair paternity in monogamous and polygynous Savannah sparrows, Passerculus sandwichensis here

Phylogeny (pick two of these):

  1. Phylogenetic relationships of finches and allies here
  2. The Old World Sparrows (Genus Passer) Phylogeography here
  3. Melanin-based plumage coloration and flight displays here
  4. MELANIN-BASED BLACK PLUMAGE COLORATION IS RELATED TO REPRODUCTIVE INVESTMENT IN CARDUELINE FINCHES here

Comparative:

It could be very educational (and not too time consuming :-) for you to re-analyse some of the studies done by Verocs. You can get the tree and data from her. Alternatively, we can cook up some other projects for you. There are two excellent trees (finches and sparrows) to work with. Might be more interesting to work on a novel problem, but it would take more of your time.


Mátrai Eszter: tigers

Eszter, you can work on the papers you collected. Please let me which four you would review.

Várkonyi Emese Éva: intelligence of marine mammals

DNA techniques and phylogeny (pick two of these):

  1. RAPD typing of north-east Atlantic minke whale here
  2. Phylogeny of mysticete whales here
  3. Molecular Phylogenetic Examination of the Delphinoidea Trichotomy here
  4. Cytochrome b and Bayesian inference of whale phylogeny here
  5. Low Genetic Variation Among Killer Whales here
  6. Low worldwide genetic diversity in the killer whale
    (Orcinus orca): implications for demographic
    history     here

Intelligence, communication, social behaviour (pick at least two of these):

  1. Social evolution in toothed whales here
  2. Cultural transmission within maternal lineages here
  3. Quantitative tools for comparing animal communication systems: here
  4. Pitfalls in the categorization of behaviour: a comparison of dolphin whistle classification methods here
  5. Evolution of the brain and intelligence here
  6. The biology and evolution of music here
  7. The fallacy of ‘signature whistles’ in bottlenose dolphins here
  8. Do sperm whales share coda vocalizations? here
  9. Culture in whales and dolphins here

fun stuff: http://www.hhmi.org/news/suzuki20060321.html