Biogeographic transitions for tropical Butterflyfish around South Africa

Just to give an example of what I have in mind, I took the distribution range of the 14 species of tropical Butterflyfish (most of them from the genus Chaetodon) around South Africa. I excluded the one endemic C. marleyi as its distribution range (Maputo to Lambert's Bay) suggest that it is not tropical. Then, I recorded the presence (1) / absence (0) of each species in 20 locations along the east and south coasts. I then performed a logistic regression pooling the data from all the species. I obtained the graph below that gives the probability of occurrence of tropical Butterflyfish. The dots represents the presence/absence data in different locations and the red curve represents the regression model.

So, as a preparation for the next discussion group, we can try and interpret the graph. As guidelines, try and answer the question below:
(1) Considering the trend of the regression model, can you suggest the location I used for the "origin" (coordinate 0 on the x axis)? and the last location (x ~ 3500 km)
(2) Considering the position of T1, T2 and T3 on the graph, what do they represent in term of the occurrence of the Butterflyfish?
(3) What are the biogeographic interpretations one can make in term of species distribution using these three lines?
Try answer these questions and if you have any questions, please contact me by email or write a comment.
Enjoy!

Marine Biogeographic transitions on the east coast of South Africa

Biogeographic regions are one of the most important unit in biogeography. They are characterised by a specific history and specific environmental conditions that make their biota unique. At the boundary between two regions, there is a zone usually not well defined where species of both regions occur: the biogeographic transition zone.
I will start a small project on the marine biogeographic transition zone on the east coast of South Africa using coastal fish as model organism. The project consists first in having a discussion around biogeographic transitions in general (definition, implications and limits on questions related to biogeography) and then use the transition between subtropical and subtemperate coastal region in South Africa as a case study (with some homework for all involved).
I found a short but nice introduction to transition zone on a website that talk about the Durban transition zone, though it is on terrestrial environments (http://www.ceroi.net/reports/durban/issues/Terrestri/biogeog.htm).
If you are interested just send me an email and I'll organise the first meeting.

microsatellites for sparids

Congratulation to Kerry for her first publication!

The paper is online in the early view section of Molecular Ecology Resources.

http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1755-0998/earlyview

I am sure the paper will be useful for lots of people and highly cited !

High-throughput microsatellite marker development in two sparid species and verification of their transferability in the family Sparidae

K Reid, TB Hoareau and P Bloomer

Abstract:

Recently, 454 sequencing has emerged as a popular method for isolating microsatellites owing to cost-effectiveness and time saving. In this study, repeat-enriched libraries from two southern African endemic sparids (Pachymetopon blochii and Lithognathus lithognathus) were 454 GS-FLX sequenced. From these, 7370 sequences containing repeats (SCRs) were identified. A brief survey of 23 studies showed a significant difference between the number of SCRs when enrichment was performed

first before 454 sequencing. We designed primers for 302 unique fragments containing more than five repeat units

and suitable flanking regions. A fraction (<11%) of these loci were characterized with 18 polymorphic microsatellite loci (nine in each of the focal species) being described. Sanger sequencing of alleles confirmed that size variation was because of differences in the number of tandemrepeats. However, a case of homoplasy and sequencing errors in the 454 sequencing were identified. These newly developed and four previously isolated loci were successfully used to identify polymorphic markers in nine other economically important species, representative of sparid diversity. The combination of newly developed markers with data from previous sparid cross-species studies showed a significant negative correlation between genetic divergence to focal species and microsatellite transferability. The high level of transferability we described (48% amplification success and 32% polymorphism) suggests that the 302 microsatellite loci identified represent an excellent resource for future studies on sparids. Microsatellite marker development should commonly include tests of transferability to reduce costs and increase feasibility of population genetics studies in nonmodel organisms.

Journal Club Sessions (Semester 1)

Date	Name	Venue
12 Mar	Kerry	Tea room
19 Mar	Sarita	Tea room
26 Mar	Sam	Tea room
2 Apr	Arrie	Tea room
16 Apr	Thierry	Tea room
23 Apr	Emilie	Tea room
7 May	Ilkser	Tea room
14 May	Catherine	Tea room
21 May	Amanda	Tea room
28 May	Paulette	Tea room
4 June	Bianca	Tea room
11 June	Michael	Tea room
18 June	Angelika	Tea room
25 June	Carel	Tea room

The historical Biogeography of Mammalia

Today, Sarita will present a paper on historical biogeography of mammals. The authors proposed to identify the origins of the different groups of mammals by comparing nine different methods for reconstructing ancestral areas including data on phylogenies, divergence times and ancestral areas reconstructions. This approach shows that both dispersal and vicariance triggered diversification of mammals. Thanks Sarita.

From MS Springer, RW Meredith, JE Janecka and WJ Murphy, Philosophical Transactions of the Royale Society B, (2011) 366, 2478–2502 [doi:10.1098/rstb.2011.0023]


Title: The historical biogeography of Mammalia

Abstract. Palaeobiogeographic reconstructions are underpinned by phylogenies, divergence times and ancestral area reconstructions, which together yield ancestral area chronograms that provide a basis for proposing and testing hypotheses of dispersal and vicariance. Methods for area coding include multi-state coding with a single character, binary coding with multiple characters and string coding. Ancestral reconstruction methods are divided into parsimony versus Bayesian/likelihood approaches. We compared nine methods for reconstructing ancestral areas for placental mammals. Ambiguous reconstructions were a problem for all methods. Important differences resulted from coding areas based on the geographical ranges of extant species versus the geographical provenance of the oldest fossil for each lineage. Africa and South America were reconstructed as the ancestral areas for Afrotheria and Xenarthra, respectively. Most methods reconstructed Eurasia as the ancestral area for Boreoeutheria, Euarchontoglires and Laurasiatheria. The coincidence of molecular dates for the separation of Afrotheria and Xenarthra at approximately 100 Ma with the plate tectonic sundering of Africa and South America hints at the importance of vicariance in the early history of Placentalia. Dispersal has also been important including the origins of Madagascar’s endemic mammal fauna. Further studies will benefit from increased taxon sampling and the application of new ancestral area reconstruction methods.

Journal Club Sessions (Semester 1)

Date	Name	Venue
16 Jan	Arrie	7-34
23 Jan	Thierry	7-34
30 Jan	Emilie	7-34
6 Feb	Ilkser	7-34
13 Feb	Catherine	7-34
20 Feb	Amanda	Tea room / Office
27 Feb	Paulette	Tea room / Office
5 Mar	Carel	Tea room / Office
12 Mar	Kerry	Tea room / Office
19 Mar	Sarita	7-34
26 Mar	Sam	7-34
2 Apr	Arrie	7-34
16 Apr	Thierry	7-34
23 Apr	Emilie	7-34
7 May	Ilkser	7-34
14 May	Catherine	7-34
21 May	Angelika	7-34
28 May	Paulette	7-34

Microsatellite development in the Moorish Idol

Congratulation to Miekie for her nice poster on development of microsatellites in the Moorish Idol (Zanclus cornutus)! Good job!