Phylogenetics review. Trees are the basis for biodiversity (taxonomy, systematics, measuring and mapping) Trees are hard to estimate

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1 Phylogenetics review Trees are the basis for biodiversity (taxonomy, systematics, measuring and mapping) Sheppard software Trees are hard to estimate Trees don't start after species form. Genealogy occurs at all levels, from individuals who share the same (looking) alleles all the way down to the origin of life. What do these trees look like? - two axes of variation: (1) topology and (2) edge lengths of the 4554 spp Bininda-Emonds et al However, in all that diversity ~40% of ~4500 mammals are in a single 'Order': Rodentia (~25 orders total) And several orders (Monotremata, Dermoptera, Tubulendentata, Philodota) have <10 species. ~4500 spp 4

2 ~4 species 2 species 1 species ~4500 spp Allocebus.trichotis Microcebus.berthae Microcebus.myoxinus Microcebus.griseorufus Microcebus.murinus Microcebus.bongolavensis Microcebus.ravelobensis Microcebus.danfossi Microcebus.tavaratra Microcebus.jollyae Microcebus.simmonsi Microcebus.lehilahytsara Microcebus.rufus Microcebus.mittermeieri Microcebus.mamiratra Microcebus.sambiranensis Mirza.coquereli Mirza.zaza Cheirogaleus.crossleyi Cheirogaleus.medius Cheirogaleus.major Cheirogaleus.sibreei Lepilemur.ankaranensis Lepilemur.dorsalis Lepilemur.sahamalazensis Lepilemur.septentrionalis Lepilemur.edwardsi Lepilemur.leucopus Lepilemur.randrianasoli Phaner.furcifer Phaner.pallescens Avahi.cleesei Avahi.occidentalis Avahi.unicolor Avahi.laniger Propithecus.candidus Propithecus.perrieri Propithecus.diadema Propithecus.edwardsi Propithecus.coquereli Propithecus.tattersalli Propithecus.coronatus Propithecus.deckeni Propithecus.verreauxi Indri.indri Eulemur.albifrons Eulemur.sanfordi Eulemur.fulvus Eulemur.rufus Eulemur.cinereiceps Eulemur.collaris Eulemur.rubriventer Eulemur.mongoz Eulemur.coronatus Eulemur.macaco Hapalemur.alaotrensis Hapalemur.griseus Hapalemur.occidentalis Hapalermur.meridionalis Hapalemur.aureus Prolemur.simus Lemur.catta Varecia.rubra Varecia.variegata Daubentonia.madagascariensis 6 Purvis, 2000 These are called 'hollow curves' most species of mammal are rodents - and likewise, most animals are insects, most insects are Coleoptera (beetles); most birds are songbirds, most songbirds are Corvids (or Fringillids); most plants are angiosperms, most angiosperms are Orchids; most fish are in the Perciform order, in the Percidae itself. order most rodents are murids (rats and mice) family species seem evolutionarily clumped...some clades are very big, and some are very small most murids are Rattus genus

3 What should biodiversity look like? i.e. What is the expectation? Well, species come from other species (Yule or Markov model - many names..) YULE: all lineages equally likely to give rise to new species but because , this is often an exponential process YULE TREES D. pseudoobscura D. persimilis D. miranda D. lowei D. athabasca D. subobscura D. ambigua An unbalanced tree (Drosophila) S. auromalus hispidus S. varius S. obesus S. ater klauberi S. australis S. ater slevini A balanced tree (chuckwallas) ( (Petren and Case, 1997)

4 Trees should show evolutionary clumping (same topology for simple coalescent as for Yule trees!) You can measure the topology of a tree in many ways. The most common is Colless' index: difference in sister clade sizes Within species Among species max possible on fully unbalanced tree Coalescent tree Yule tree The basic principle of the coalescent is that alleles come from other alleles, and diverge (baring recombination) in a tree-like manner. (parenthesis: the coalescent redux, again) So samples of alleles are connected by a genealogy = a tree a coalescent 'event' (note red is ancestral) 15

5 Some (biodiversity-related) properties of coalescent (gene) trees 1. A very stochastic process 2. Most 'events' occur nearer the present 3. Events occur more slowly in large populations 4. The topology is the "Yule" expectation The coalescent is a very stochastic process The time between coalescent events is very noisy. These are trees simulated under a stochastic version of the coalescent with an identical N (population size) and k (number of samples). this looks like 2 spp! 17 So different genes in a populations can have very different histories, just due to random variation Most events occur near the present, when there are the most copies of alleles around: But, because most events occur near the present: time to event ~4N/(k(k-1)) For any given locus (even without selection), the gene tree will look like there have been deep splits = qualitative breaks time to event ~ 2N Good thing: We can recover deeper splits from a small sample of individuals Bad thing: this is the expected shape of a gene tree: one might think there are 2 (or 3) species here!

6 So, good species are those where MANY of the genes show the SAME break, due to cessation of gene flow HOFFMAN, J. I., MATSON, C. W., AMOS, W., LOUGHLIN, T. R. & BICKHAM, J. W. Deep genetic subdivision within a continuously distributed and highly vagile marine mammal, the Steller's sea lion (Eumetopias jubatus). Molecular Ecology 15 (10), loci (microsatellites) split follows geography Gene A Gene C Stellar s Sea lion Gene B Western Alaska but not: population one population two Southeast Alaska Gene D Fig. 3 Neighbour-joining tree showing genetic relationships among 668 Steller's sea lions based on Slatkin's linearized FST at the rookery level Many surveys of published species trees show them to show more clumping than even the Yule expectation (we'll test the Lemur tree in lab) Without proof: within-species and across species topologies should be similar, though branch lengths should be different... Something else is going on. In diversification, success breeds success 23 "trait" that spurs diversification is inherited by the diversifying lineage: diversification accelerates (Vrba, Gould, etc.) 24

7 tested correlates of diversification morphology! small size: carnivores (Gittleman, Purvis-98)!! early age of 1rst reproduction: various (Marzluff, Dial-91)!! dichromatism: birds (Barraclough-95)!! feather ornaments: bird subspecies (Møller-98)!! latex(resin) canals: angiosperms (Farrell-91)! +ve corr.! nectar spurs: various angiosperms (Hodges-95)! NO corr! hypocone (molar): mammals (Hunter-95)!! herbaceousness+biotic pollination: plants (Dodd et al-99)!! zygomorphic flowers (Sargent, 2004) [SFU grad] pharyngeal jaws in fish (Wainright et al., 2012)!! carnivorous parasitism: insects (Wiegmann-93)!! small size: birds, primates, all things!!! (AØM, G&P, Owens, Bennett -90's, Purvis-02)!! eyes: all taxa (de Queiroz-00) lots of vertebrae: squamate reptiles (Bergmann-12)!! tested correlates ecology!! large fragmented ranges: birds (Owens, Bennett-99)!! good dispersal capability: birds (O,B)!! monoecious-ness: plants (Heilbuth-2001) [SFU grad]!! High UV habitat: plants (Davies et al., 2004)! +ve corr.! "fast life history": birds (OB)!! evolutionary flexibility: plants (Dodd, Silvertown, Chase-99)! NO corr behaviour! angiosperm feeding: beetles (Farrell-98)!! plant feeding: all insects (Mitter, Farrell-88)!! multiple mating: insects (Arnqvist-00)!! behavioural flexibility (& brain size): birds (Sol -2003)!! colonial breeding: birds (AØM-95) What do these trees look like? - two axes of variation: (1) topology and (2) edge lengths We can use the same Null Model(s) for diversification as we did for topology... Nigel Dennis