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Supporting Information Fitzpatrick et al. 10.1073/pnas.0809990106 SI Methods likely to lead to 2 and 3, which in turn leads to 4. We can assess Testing the Directionality of Evolutionary Transitions. BayesDiscrete these possible evolutionary transitions by examining the tran- (www.evolution.rdg.ac.uk) (1) uses discrete binary data (0 and 1) sition parameters leading away from value 1. For example, the to assess all possible transitions between 2 traits. Traits assigned as evolutionary pathway of value 1 to 2 to 4 indicates that changes binary variables create 4 possible values (1 value per species) that in trait 2 preceded changes in trait 1, because the value 1 traits can be described as [trait 1,trait 2] as follows: [0,0], [0,1], [1,0], [1,1]. [0,0] shifted to value 2 traits [0,1]. Applying this logic, we can BayesDiscrete allows forward and reverse transitions between these assess the other possible evolutionary transitions described in 4 values, so there are 8 possible transitions between values: 4 our example above. forward and 4 reverse. Each transition parameter (q) is assigned a We assessed the frequency that transition parameters where unique numerical code describing the direction of change between set equal to zero using a reversible-jump Markov chain Monte Carlo (RJ MCMC) method, which explores the entire parameter 2 states. For example, q represents a transition from value 1 to 1,2 space. We selected a subsample of trees from the 2 million value 2, and q represents the reverse transition from state 2 to 2,1 generations produced from our MrBayes analysis. After a state 1. BayesDiscrete assumes that transitions involving simulta- burn-in of 1 million generations, we sampled 500 trees at neous change in 2 traits do not occur (i.e., transitions from [0,0] to intervals of 20,000 generations. This analysis controls for phy- [1,1] or from [0,1] to [1,0]). The 4 trait values and 8 transition logenetic uncertainty by assessing transitions among a broad parameters are illustrated in Scheme 1 subset of trees generated from our MrBayes analysis. We ran the RJ MCMC chain for 5,050,000 iterations, with a burn-in of 50,000 iterations. The chain was sampled every 100th iteration, creating a posterior distribution of 50,000 sample points, from which we determined the mean Ϯ SE transition parameter value, and the proportion of samples where the transition parameter was assigned to zero. Transition parameters less likely to have occurred are frequently assigned to zero, whereas those that are likely are assigned non-zero values. The strength of each tran- sition parameter was also assessed by using the average value of each transition parameter. In general, transitions are considered likely when Z Ͻ 0.10, meaning that Ͻ10% of the iterations from the MC are assigned to zero (1). However, following refs. 2, 3, we also used a more conservative approach to assess trait evolution, which accounts for nonsignificance that may result from low statistical power due to small phylogenies (4). In this approach, we considered Evolutionary pathways from ancestral to derived values can nonsignificant (Z Ͼ 0.10) transitions to be likely evolutionary be determined by assessing the probability of a certain tran- transitions if the nonsignificant transition parameter (q value) sition parameter having occurred relative to another. For was higher than that of the lowest parameter that yielded a example, if value 1 was the ancestral trait and value 4 was the significant transition. However, when examining sperm size derived state, then the evolutionary transition from the an- and speed, we considered q1,2 to be a likely transition, because cestral to the derived state could have occurred in 1 of 3 ways: comparisons of the q1,2 to q1,3 suggested that q1,2 was the most (i) value 1 to 2 to 4, (ii) value 1 to 3 to 4, (iii) value 1 is equally likely transition from the ancestral to the intermediate state. 1. Pagel M, Meade A (2006) Bayesian analysis of correlated evolution of discrete charac- 11. Taylor MI, Morley JI, Rico C, Balshine S (2003) Evidence for genetic monogamy and ters by reversible-jump Markov chain Monte Carlo. Am Naturalist 167:808–825. female-biased dispersal in the biparental mouthbrooding cichlid Eretmodus cyanos- 2. Kolm N, Goodwin NB, Balshine S, Reynolds JD (2006) Life history evolution in cichlids tictus from Lake Tanganyika. Mol Ecol 12:3173–3177. 2: Directional evolution of the trade-off between egg number and egg size. J Evol Biol 12. Yanagisawa Y (1985) Parental strategy of the cichlid fish Perissodus microlepis, with 19:76–84. particular reference to intraspecific brood ‘framing out.’ Environ Biol Fish 12:241–249. 3. Kolm N, Stein RW, Mooers AO, Verspoor JJ, Cunningham EJA (2007) Can sexual 13. Egger B, Obermu¨ ller B, Phiri H, Sturmbauer C, Sefc KM (2006) Monogamy in the selection drive female life histories? A comparative study of galliform birds. J Evol Biol maternally mouthbrooding Lake Tanganyika cichlid fish Tropheus moorii. Proc R Soc 20:627–638. London Ser B 273:1797–1802. 4. Rolland C, Danchin E, de Fraipont M (1998) The evolution of coloniality in birds in 14. Yanagisawa Y (1986) Parental care in a monogamous cichlid Xenotilapia flavipinnis in relation to food, habitat, predation, and life-history traits: A comparative analysis. Am Lake Tanganyika. Jap J Ichthyol 34:82–90. Naturalist 151:514–529. 15. Ochi H, Yanagisawa Y (1999) Sand-transfer behavior outside the nest by guarding 5. Koblmuller S, Salzburger W, Sturmbauer C (2004) Evolutionary relationships in the sand- parents of the Tanganyikan cichlid, Neolamprologus caudopunctatus. Ichthyol Res dwelling cichlid lineage of lake Tanganyika suggest multiple colonization of rocky habi- 46:419–422. tats and convergent origin of biparental mouthbrooding. J Mol Evol 58:79–96. 16. Yamagishi S, Kohda M (1996) Is the cichlid fish Julidochromis marlieri polyandrous? 6. Day JJ, Santini S, Garcia-Moreno J (2007) Phylogenetic relationships of the Lake Ichthyol Res 43:469–471. Tanganyika cichlid tribe Lamprologini: The story from mitochondrial DNA. Mol Phy- 17. Taborsky M (1985) Breeder-helper conflict in a cichlid fish with broodcare helpers: An logenet Evol 45:629–642. experimental analysis. Behav 95:45–75. 7. Nylander JAA (2004) MrModeltest v2. Program distributed by the author. (Evolution- 18. Takemon Y, Nakanishi N (1998) Reproductive success in female Neolamprologus ary Biology Centre, Uppsala University, Sweden). mondabu (Cichlidae): Influence of substrate types. Environ Biol Fish 52:261–269. 8. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under 19. Heg D, Bachar Z, Taborsky M (2005) Cooperative breeding and group structure in the mixed models. Bioinformatics 19:1572–1574. Lake Tanganyika cichlid Neolamprologus savoryi. Ethology 111:1017–1043. 9. Kuwamura T (1997) Parental care. Fish Communities in Lake Tanganyika, eds 20. Awata S, Munehara H, Kohda M (2005) Social system and reproduction of helpers in a Kawanabe H, Hori M, Nagoshi M (Kyoto Univ Press, Kyoto, Japan), pp 59–86. cooperatively breeding cichlid fish (Julidochromis ornatus) in Lake Tanganyika: Field 10. Morley JI, Balshine S (2002) Faithful fish: Territory and mate defence favour monogamy observations and parentage analyses. Behav Ecol Sociobiol 58:506–516. in an African cichlid fish. Behav Ecol Sociobiol 52:326–331. Fitzpatrick et al. www.pnas.org/cgi/content/short/0809990106 1of9 21. Awata S, Heg D, Munehara H, Kohda M (2006) Testis size depends on social status and 27. Fitzpatrick JL, Desjardins JK, Milligan N, Montgomerie R, Balshine S (2007) Reproduc- the presence of male helpers in the cooperatively breeding cichlid Julidochromis tive-tactic-specific variation in sperm swimming speeds in a shell-brooding cichlid. Biol ornatus. Behav Ecol 17:372–379. Reprod 77:280–284. 22. Sato T (1994) Active accumulation of spawning substrate: A determinant of extreme 28. Rossiter A, Yamagishi S (1997) Intraspecific plasticity in the social system and mating polygyny in a shell-brooding cichlid fish. Anim Behav 48:669–678. behaviour of a lek-breeding cichlid fish. Fish Communities in Lake Tanganyika, eds 23. Sato T, Hirose M, Taborsky M, Kimura S (2004) Size-dependent male alternative Kawanabe H, Hori M, Nagoshi M (Kyoto Univ Press, Kyoto, Japan), pp 293–318. reproductive tactics in the shell-brooding cichlid fish Lamprologus callipterus in Lake 29. Haesler MP, Simone I, Taborsky M (2005) Unusual testes morphology and its implica- Tanganyika. Ethology 110:49–62. tions for the reproductive biology of the lekking cichlid Ophthalmotilapia ventralis 24. Katoh R, Munehara H, Kohda M (2005) Alternative male mating tactics of the substrate (Cichlidae, Teleostei). Annual Conference of the Swiss Societies of Botany, Mycology brooding cichlid Telmatochromis temporalis in Lake Tanganyika. Zool Sci 22:555–561. and Zoology, p 19. 25. Mboko SK, Kohda M (1999) Piracy mating by large males in a monogamous substrate- 30. Wickler W (1962) ‘Egg-dummies’ as natural releasers in mouth-brooding cichlids. breeding cichlid in Lake Tanganyika. J Ethol 17:51–55. Nature 194:1092–1093. 26. Ota K, Kohda M (2006) Description of alternative male reproductive tactics in a 31. Dierkes P, Taborsky M, Kohler U (1999) Reproductive parasitism of broodcare helpers shell-brooding cichlid, Telmatochromis vittatus, in Lake Tanganyika. J Ethol 24:9–15. in a cooperatively breeding fish. Behav Ecol 10:510–515. Fitzpatrick et al. www.pnas.org/cgi/content/short/0809990106 2of9 Fig. S1. Transition representation illustrating the evolutionary pathways from the ancestral to the derived state for sperm length (a) and sperm swimming speed (b). Sperm swimming speed was measured at 0.5 min postactivation. Intermediate states are represented in the middle of each transition representation. Forward transitions are depicted with black arrows and back transitions with gray arrows.
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    RESEARCH FOR THE MANAGEMENT OF THE FISHERIES ON LAKE GCP/RAF/271/FIN-TD/Ol(En) TANGANYIKA GCP/RAF/271/FIN-TD/01 (En) January 1992 TOWARDS A REGIONAL INFORMATION BASE FOR LAKE TANGANYIKA RESEARCH by J. Eric Reynolds FINNISH INTERNATIONAL DEVELOPMENT AGENCY FOOD AND AGRICULTURE ORGANIZATION OF THE UNITED NATIONS Bujumbura, January 1992 The conclusions and recommendations given in this and other reports in the Research for the Management of the Fisheries on Lake Tanganyika Project series are those considered appropriate at the time of preparation. They may be modified in the light of further knowledge gained at subsequent stages of the Project. The designations employed and the presentation of material in this publication do not imply the expression of any opinion on the part of FAO or FINNIDA concerning the legal status of any country, territory, city or area, or concerning the determination of its frontiers or boundaries. PREFACE The Research for the Management of the Fisheries on Lake Tanganyika project (Tanganyika Research) became fully operational in January 1992. It is executed by the Food and Agriculture organization of the United Nations (FAO) and funded by the Finnish International Development Agency (FINNIDA). This project aims at the determination of the biological basis for fish production on Lake Tanganyika, in order to permit the formulation of a coherent lake-wide fisheries management policy for the four riparian States (Burundi, Tanzania, Zaïre and Zambia). Particular attention will be also given to the reinforcement of the skills and physical facilities of the fisheries research units in all four beneficiary countries as well as to the buildup of effective coordination mechanisms to ensure full collaboration between the Governments concerned.
  • Hered 347 Master..Hered 347 .. Page702

    Hered 347 Master..Hered 347 .. Page702

    Heredity 80 (1998) 702–714 Received 3 June 1997 Phylogeny of African cichlid fishes as revealed by molecular markers WERNER E. MAYER*, HERBERT TICHY & JAN KLEIN Max-Planck-Institut f¨ur Biologie, Abteilung Immungenetik, Corrensstr. 42, D-72076 T¨ubingen, Germany The species flocks of cichlid fish in the three great East African Lakes, Victoria, Malawi, and Tanganyika, have arisen in each lake by explosive adaptive radiation. Various questions concerning their phylogeny have not yet been answered. In particular, the identity of the ancestral founder species and the monophyletic origin of the haplochromine cichlids from the East African lakes have not been established conclusively. In the present study, we used the anonymous nuclear DNA marker DXTU1 as a step towards answering these questions. A 280 bp-fragment of the DXTU1 locus was amplified by the polymerase chain reaction from East African lacustrine species, the East African riverine cichlid species Haplochromis bloyeti, H. burtoni and H. sparsidens, and other African cichlids. Sequencing revealed several indels and substitutions that were used as cladistically informative markers to support a phylogenetic tree constructed by the neighbor-joining method. The topology, although not supported by high bootstrap values, corresponds well to the geographical distribution and previous classifica- tion of the cichlids. Markers could be defined that: (i) differentiate East African from West African cichlids; (ii) distinguish the riverine and Lake Victoria/Malawi haplochromines from Lake Tanganyika cichlids; and (iii) indicate the existence of a monophyletic Lake Victoria cichlid superflock which includes haplochromines from satellite lakes and East African rivers. In order to resolve further the relationship of East African riverine and lacustrine species, mtDNA cytochrome b and control region segments were sequenced.