Tag Archives: Phylogenetics

Placental Phylogeny

Has this yet passed the scrutiny of our people?

Tarver, J. E., dos Reis, M., Mirarab, S., Moran, R. J., Parker, S., O’Reilly, J. E., King, B. L., O’Connell, M. J., Asher, R. J., Warnow, T., Peterson, K. J., Donoghue, P. C. J. & Pisani, D., 2016:

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference.

–Genome Biology and Evolution: Vol. 8, #2, pp. 330-344 [doi: 10.1093/gbe/evv261]



Placental mammals comprise three principal clades: Afrotheria (e.g., elephants and tenrecs), Xenarthra (e.g., armadillos and sloths), and Boreoeutheria (all other placental mammals), the relationships among which are the subject of controversy and a touchstone for debate on the limits of phylogenetic inference. Previous analyses have found support for all three hypotheses, leading some to conclude that this phylogenetic problem might be impossible to resolve due to the compounded effects of incomplete lineage sorting (ILS) and a rapid radiation. Here we show, using a genome scale nucleotide data set, microRNAs, and the reanalysis of the three largest previously published amino acid data sets, that the root of Placentalia lies between Atlantogenata and Boreoeutheria. Although we found evidence for ILS in early placental evolution, we are able to reject previous conclusions that the placental root is a hard polytomy that cannot be resolved. Reanalyses of previous data sets rec!

over Atlantogenata + Boreoeutheria and show that contradictory results are a consequence of poorly fitting evolutionary models; instead, when the evolutionary process is better-modeled, all data sets converge on Atlantogenata. Our Bayesian molecular clock analysis estimates that marsupials diverged from placentals 157-170 Ma, crown Placentalia diverged 86-100 Ma, and crown Atlantogenata diverged 84-97 Ma. Our results are compatible with placental diversification being driven by dispersal rather than vicariance mechanisms, postdating early phases in the protracted opening of the Atlantic Ocean.



Arthropod fossil data increase congruence of morphological and molecular phylogenies

Not vertebrates, but a good example of using fossils to increase congruence between morphological and molecular systematics.

– Laura

Arthropod fossil data increase congruence of morphological and molecular phylogenies

The relationships of major arthropod clades have long been contentious, but refinements in molecular phylogenetics underpin an emerging consensus. Nevertheless, molecular phylogenies have recovered topologies that morphological phylogenies have not, including the placement of hexapods within a paraphyletic Crustacea, and an alliance between myriapods and chelicerates. Here we show enhanced congruence between molecular and morphological phylogenies based on 753 morphological characters for 309 fossil and Recent panarthropods. We resolve hexapods within Crustacea, with remipedes as their closest extant relatives, and show that the traditionally close relationship between myriapods and hexapods is an artefact of convergent character acquisition during terrestrialisation. The inclusion of fossil morphology mitigates long-branch artefacts as exemplified by pycnogonids: when fossils are included, they resolve with euchelicerates rather than as a sister taxon to all other euarthropods.


EEB seminar 18th Sep, Per Lundberg “From individuals to phylogenies”

18th September, 3pm,

the Ecology and Evolutionary Biology wednesday seminar series kicks off with:

Prof. Per Lundberg, University of Lund, Sweden:

“From individuals to phylogenies”

I will present an eco-evolutionary model based on individual fitness functions from which adaptive radiations and entire phylogenies can be derived. I will demonstrate under what ecological conditions niche conservatism is expected and how that affects the phylogenetic signal in metacommunities emerging from a single lineage. This co-evolutionary theory recovers a number of empirical patterns relating to species coexistence, niche partitioning, sister species distributions, and the biogeography of adaptive radiations.

more on his research: http://www.teorekol.lu.se/staff/plundberg/plundberg.html

Place: Biocenter 3, room 2402 (Telkänpönttö)
Coffee at 14:45, talk at 15:15

PS: also mark in your calendars the upcoming seminars in the near future (a full program of the EEB seminar will be posted soon):

THURSDAY 26.9., 14:00 Corey Bradshaw, University of Adelaide, “Brave New Green World: Managing Threatened Carbon Pools from the Boreal to Australia”. Host: Mar Cabeza

2.10. 16:00 Jason Tylianakis, University of Canterbury, NZ, Global change and ecosystem functioning: the interplay of biodiversity, environmental context and species interactions. Host: Tomas Roslin

Thursday 3.10. Neil Metcalfe, University of Glasgow, “The origins and ecological consequences of variation in aggression and metabolic rate in fish” Host: Heikki Hirvonen

Tuesday 8.10. Alexander Schmidt, University of Goettingen, “Microorganisms in amber and their use in understanding terrestrial palaeoecosystems”, Host: Jouko Rikkinen

Kurtén Club 5.10.

Dear all,

tomorrow, Kate Carter will give a talk about

A constraint-based model for phylogeny reconstruction.

Time & Loc.:
16.00, 5.10.2010, C108 Physicum

Unfortunately, Kumpula Colloquim is held simultaneously; Kate is going to SVP meeting next week so this this was the only possible time for her pre-meeting presentation.
The ones who wished to attend the Colloquium, go to www.helsinki.fi/videot/ .


Kurtén Club 20.4.

Dear all,

This week Laura Säilä will be discussing her previous work on parareptilian phylogenetics and her new project with Neogene mammal supertrees, with a talk titled:

From traditional phylogenetics to Supertrees – examples and discussion

Time & Loc.:
16.00, 20.4.2010, C108 (Physicum)