An enhanced calibration of a recently released megatree for the analysis of phylogenetic diversity

Calibração aperfeiçoada de uma megatree lançada recentemente para a análise da diversidade filogenética

M. Gastauer J. A. A. Meira-Neto About the authors

Abstract

Dated or calibrated phylogenetic trees, in which branch lengths correspond to evolutionary divergence times between nodes, are important requirements for computing measures of phylogenetic diversity or phylogenetic community structure. The increasing knowledge about the diversification and evolutionary divergence times of vascular plants requires a revision of the age estimates used for the calibration of phylogenetic trees by the bladj algorithm of the Phylocom 4.2 package. Comparing the recently released megatree R20120829.new with two calibrated vascular plant phylogenies provided in the literature, we found 242 corresponding nodes. We modified the megatree (R20120829mod.new), inserting names for all corresponding nodes. Furthermore, we provide files containing age estimates from both sources for the updated calibration of R20120829mod.new. Applying these files consistently in analyses of phylogenetic community structure or diversity serves to avoid erroneous measures and ecological misinterpretation.

Keywords:
R20120829.new; phylogenetic community analysis; ecological misinterpretation; phylogenetic diversity; evolutionary divergence times; phylogenetic dispersion; phylogeny of vascular plants

Resumo

Árvores filogenéticas datadas, ou calibradas, em que os comprimentos dos ramos correspondem ao tempo evolutivo de divergência entre os nós, são importantes requisitos para calcular medidas de diversidade filogenética ou de estrutura filogenética de comunidades. O conhecimento crescente sobre a diversificação e sobre o tempo de divergência evolutiva das plantas vasculares fez necessária uma revisão das estimativas de idades dos nós que são utilizadas para a calibração de árvores filogenéticas por meio do algoritmo bladj do pacote Phylocom 4.2. Comparando a mega-árvore R20120829.new, recentemente publicada, e outras duas filogenias calibradas de plantas vasculares, encontramos 242 nós correspondentes. Modificamos esta mega-árvore (R20120829mod.new), inserindo todos os nomes dos nós correspondentes. Além disso, providenciamos dois arquivos com todas as estimativas das idades para uma calibração mais atualizada. Utilizando esses arquivos de maneira consistente nas análises de diversidade ou de estrutura filogenética de comunidades, evita-se incorreções nas datações e imprecisões na interpretação de informações ecológicas.

Palavras-chave:
R20120829.new; análise filogenética de comunidades; má interpretação ecológica; diversidade filogenética; tempo de divergência evolutiva; dispersão filogenética; filogenia de plantas vasculares

1 Introduction

Dated or calibrated phylogenetic trees, in which branch lengths correspond to evolutionary divergence times, are important requirements for computing measures of phylogenetic diversity (Faith, 1992Faith, D.P., 1992. Conservation evaluation and phylogenetic diversity. Biological Conservation, vol. 61, no. 1, pp. 1-10. http://dx.doi.org/10.1016/0006-3207(92)91201-3.
http://dx.doi.org/10.1016/0006-3207(92)9...
) or phylogenetic community structure (Webb et al., 2002Webb, C.O., Ackerly, D.D., Mcpeek, M.A. and Donoghue, M.J., 2002. Phylogenies and community ecology. Annual Review of Ecology and Systematics, vol. 33, no. 1, pp. 475-505. http://dx.doi.org/10.1146/annurev.ecolsys.33.010802.150448.
http://dx.doi.org/10.1146/annurev.ecolsy...
; Gastauer and Meira-Neto, 2014Gastauer, M. and Meira-Neto, J.A.A., 2014. Interactions, environmental sorting and chance: phylostructure of a tropical forest assembly. Folia Geobotanica, vol. 49, no. 3, pp. 443-459. http://dx.doi.org/10.1007/s12224-013-9181-1.
http://dx.doi.org/10.1007/s12224-013-918...
). The importance of correct calibration has been highlighted to avoid ecological misinterpretation, i.e., the outcome of a correctly calibrated tree indicates a phylogenetic community structure different from the outcome of a wrongly calibrated tree (Gastauer and Meira-Neto, 2013Gastauer, M. and Meira-Neto, J.A.A., 2013. Avoiding inaccuracies in tree calibration and phylogenetic community analysis using Phylocom 4.2. Ecological Informatics, vol. 15, no. 1, pp. 85-90. http://dx.doi.org/10.1016/j.ecoinf.2013.03.005.
http://dx.doi.org/10.1016/j.ecoinf.2013....
), but achieving an updated calibration is still not an easy task. Furthermore, constantly increasing knowledge about the phylogenetic relationships among vascular plants, especially angiosperms (Smith et al., 2011Smith, S.A., Beaulieu, J.M., Stamatakis, A. and Donoghue, M.J., 2011. Understanding Angiosperm diversification using small and large phylogenetic trees. American Journal of Botany, vol. 98, no. 3, pp. 404-414. http://dx.doi.org/10.3732/ajb.1000481. PMid:21613134.
http://dx.doi.org/10.3732/ajb.1000481...
), and about the diversification times of different clades (i.e., Magallón and Castillo, 2009Magallón, S. and Castillo, A., 2009. Angiosperm diversification through time. American Journal of Botany, vol. 96, no. 1, pp. 349-365. http://dx.doi.org/10.3732/ajb.0800060. PMid:21628193.
http://dx.doi.org/10.3732/ajb.0800060...
; Lemaire et al., 2011Lemaire, B., Huysmans, S., Smets, E. and Merckx, V., 2011. Rate accelerations in nuclear 18S rDNA of mycoheterotrophic and parasitic angiosperms. Journal of Plant Research, vol. 124, no. 5, pp. 561-576. http://dx.doi.org/10.1007/s10265-010-0395-5. PMid:21188459.
http://dx.doi.org/10.1007/s10265-010-039...
; Magallón et al., 2013Magallón, S., Hilu, K.W. and Quandt, D., 2013. Land plant evolutionary timeline: gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates. American Journal of Botany, vol. 100, no. 3, pp. 556-573. http://dx.doi.org/10.3732/ajb.1200416. PMid:23445823.
http://dx.doi.org/10.3732/ajb.1200416...
) require regular revisions of the database used to achieve updated tree calibrations.

The rapid increase in information results in the periodic release of new, updated megatrees, i.e., phylogenetic hypotheses containing all euphyllophyte families (GitHub, 2014GITHUB, 2014 [viewed 3 January 2014]. [online]. Available from: https://github.com/camwebb/tree-of-trees/tree/master/megatrees
https://github.com/camwebb/tree-of-trees...
). For phylogenetic community analyses or the computation of phylogenetic diversity measures, these megatrees may be pruned down to a user-supplied list of species by the phylomatic function of the Phylocom 4.2 package (Webb and Donoghue, 2005Webb, C.O. and Donoghue, M.J., 2005. Phylomatic: tree assembly for applied phylogenetics. Molecular Ecology Notes, vol. 5, no. 1, pp. 181-183. http://dx.doi.org/10.1111/j.1471-8286.2004.00829.x.
http://dx.doi.org/10.1111/j.1471-8286.20...
). By this procedure, all species are inserted as terminals, and branches of the megatree without terminals are cut. Internal node names are maintained. For the calibration of such community trees, the bladj algorithm from the Phylocom package is run (Webb et al., 2008Webb, C.O., Ackerly, D.D. and Kembel, S.W., 2008. Phylocom: software for the analysis of phylogenetic community structure and character evolution. Bioinformatics, vol. 24, no. 18, pp. 2098-2100. http://dx.doi.org/10.1093/bioinformatics/btn358. PMid:18678590.
http://dx.doi.org/10.1093/bioinformatics...
). This algorithm recognizes the names of internal nodes and dates them according to clade dating information provided in a separate ages file. Not matched internal nodes are smoothed by mean dates between fixed divergence times.

The Phylocom package includes the wikstrom.ages file, which provides the minimum age estimates for 176 internal nodes within the angiosperms proposed by Wikström et al. (2001)WIKSTRÖM, N., Savolainen, V. and Chase, M.W., 2001. Evolution of angiosperms: calibrating the family tree. Proceedings. Biological Sciences, vol. 268, no. 1482, pp. 2211-2220. http://dx.doi.org/10.1098/rspb.2001.1782. PMid:11674868.
http://dx.doi.org/10.1098/rspb.2001.1782...
. Revised age estimates are available (e.g. Bell et al., 2010Bell, C.D., Soltis, D.E. and Soltis, P.S., 2010. The age and diversification of the angiosperms re-revisited. American Journal of Botany, vol. 97, no. 8, pp. 1296-1303. http://dx.doi.org/10.3732/ajb.0900346. PMid:21616882.
http://dx.doi.org/10.3732/ajb.0900346...
), but still not incorporated within the Phylocom package.

Therefore, the aim of this note is to outline how community trees derived from the megatree R20120829.new, recently released for phylogenetic community analysis and the computation of phylogenetic diversity among vascular plants, are calibrated in the most updated way. For that, we identified and provided recent age estimates from literature of a maximum number of internal nodes that are distributed over the entire megatree.

2 Material and Methods

We compared the topology of R20120829.new with two comprehensive revisions about vascular plant diversification (Hedges and Kumar, 2009Hedges, S.B. and Kumar, S., 2009. The time tree of life. New York: Oxford University Press.; Bell et al., 2010Bell, C.D., Soltis, D.E. and Soltis, P.S., 2010. The age and diversification of the angiosperms re-revisited. American Journal of Botany, vol. 97, no. 8, pp. 1296-1303. http://dx.doi.org/10.3732/ajb.0900346. PMid:21616882.
http://dx.doi.org/10.3732/ajb.0900346...
). Corresponding nodes, i.e., nodes with the same descending clades or taxa, were identified. If not already named by the authors of R20120829.new, these corresponding nodes were named within the plain text archive of the megatree.

Age estimates from both revisions were pooled to provide updated ages files for tree calibration. In several cases, two or three subsequent nodes within the same lineage were estimated to identical ages by literature. In these cases, the bladj algorithm calibrates the node that appears first in the ages file and ignores age estimates for the other node(s), smoothing by mean dates between fixed divergence times. This causes distortions of the tree altering patterns of phylogenetic diversity, because the subsequent node(s) is/are always fixed to more recent divergence times than hypothetically assumed by literature. To avoid that, we corrected the age estimates of the most recent node of the sequence by –0.1 Myr, while in case of three subsequent nodes with identical age estimations, the oldest one is corrected by +0.1 Myr. Due to this procedure, the topology of R20120829.new is conserved.

To illustrate advances in tree calibration, age estimates of these corresponding nodes were used to calibrate a hypothetic community phylogeny that contains two species from each monophyletic family from R20120829.new. Resulting trees are visualized with FigTree v1.4.2.

3 Results and Discussion

Bell et al. (2010)Bell, C.D., Soltis, D.E. and Soltis, P.S., 2010. The age and diversification of the angiosperms re-revisited. American Journal of Botany, vol. 97, no. 8, pp. 1296-1303. http://dx.doi.org/10.3732/ajb.0900346. PMid:21616882.
http://dx.doi.org/10.3732/ajb.0900346...
revised Wikstrom’s age estimates by dating an angiosperm phylogeny using a relaxed molecular clock calibrated by 36 fossils considered as minimum ages of the most recent common ancestor. They used two slightly different approaches to estimate node ages, one in which they included these minimum age constraints from fossil data into an exponential distribution (BEASTa analysis in the paper’s terminology) and one in which they used a lognormal distribution (BEASTb), two different ages files are provided. This results in two sets of calibration points labeled as ages_exp and ages_logn available from the authors in the Supplementary Material* *Supplementary Material: http://www.leep.ufv.br/pt-BR/noticia/pesquisadores-da-floresta-escola-lancam-artigo-cientifico-sobre-computacao-da-diversidade-filogenetica ; either of them might be used to arrive at a revised calibration of the angiosperm clade in a user-specific community tree, given the user is aware of the possible shortcomings and pitfalls of both types of approaches. Furthermore, age estimates for gymnosperms and ferns, among other clades, have been compiled by Hedges and Kumar (2009)Hedges, S.B. and Kumar, S., 2009. The time tree of life. New York: Oxford University Press..

We identified 242 corresponding nodes (Table 1). Of these nodes, 26 were identified by comparing gymnosperm and fern clades from Hedges and Kumar (2009)Hedges, S.B. and Kumar, S., 2009. The time tree of life. New York: Oxford University Press. with R20120829.new. The other nodes represented correspondences between Bell et al. (2010)Bell, C.D., Soltis, D.E. and Soltis, P.S., 2010. The age and diversification of the angiosperms re-revisited. American Journal of Botany, vol. 97, no. 8, pp. 1296-1303. http://dx.doi.org/10.3732/ajb.0900346. PMid:21616882.
http://dx.doi.org/10.3732/ajb.0900346...
and R20120829.new. Node names lacking in the plain text archive of the megatree were added. This modified R20120829mod.new is available in the Supplementary Material*.

Table 1
Age estimates (ages_exp1 and ages_logn2) of corresponding nodes between R20120829.new and vascular plant phylogenies provided by Hedges and Kumar (2009)Hedges, S.B. and Kumar, S., 2009. The time tree of life. New York: Oxford University Press. as well as Bell et al. (2010)Bell, C.D., Soltis, D.E. and Soltis, P.S., 2010. The age and diversification of the angiosperms re-revisited. American Journal of Botany, vol. 97, no. 8, pp. 1296-1303. http://dx.doi.org/10.3732/ajb.0900346. PMid:21616882.
http://dx.doi.org/10.3732/ajb.0900346...
using syntax of R20120829mod.new and their comparison to former age estimates given by Wikström et al. (2001WIKSTRÖM, N., Savolainen, V. and Chase, M.W., 2001. Evolution of angiosperms: calibrating the family tree. Proceedings. Biological Sciences, vol. 268, no. 1482, pp. 2211-2220. http://dx.doi.org/10.1098/rspb.2001.1782. PMid:11674868.
http://dx.doi.org/10.1098/rspb.2001.1782...
, wikstrom.ages). Nodes with age estimates according to Hedges and Kumar (2009)Hedges, S.B. and Kumar, S., 2009. The time tree of life. New York: Oxford University Press. are marked with asterisks*.

Age estimates of all 242 nodes are available as ages files from the authors (Table 1). Four groups of subsequent nodes within the same lineages were estimated to have identical ages by Bell et al. (2010)Bell, C.D., Soltis, D.E. and Soltis, P.S., 2010. The age and diversification of the angiosperms re-revisited. American Journal of Botany, vol. 97, no. 8, pp. 1296-1303. http://dx.doi.org/10.3732/ajb.0900346. PMid:21616882.
http://dx.doi.org/10.3732/ajb.0900346...
. As shown in Table 2, we corrected the age estimates by + or –0.1 Myr to avoid distortion of the community tree.

Table 2
Subsequent nodes in R20120829mod.new with identical age estimates according to Bell et al. (2010)Bell, C.D., Soltis, D.E. and Soltis, P.S., 2010. The age and diversification of the angiosperms re-revisited. American Journal of Botany, vol. 97, no. 8, pp. 1296-1303. http://dx.doi.org/10.3732/ajb.0900346. PMid:21616882.
http://dx.doi.org/10.3732/ajb.0900346...
exponential distribution (BEASTa) or lognormal distribution (BEASTb) of minimum age constraints plus corrected diversification time in ages_exp and ages_logn (available from Supplementary Material*).

Calibrating the modified version R20120829mod.new with provided ages files produces a phylogeny that differs substantially from the original file (R20120829.new) calibrated with the age estimates from Wikström et al. (2001)WIKSTRÖM, N., Savolainen, V. and Chase, M.W., 2001. Evolution of angiosperms: calibrating the family tree. Proceedings. Biological Sciences, vol. 268, no. 1482, pp. 2211-2220. http://dx.doi.org/10.1098/rspb.2001.1782. PMid:11674868.
http://dx.doi.org/10.1098/rspb.2001.1782...
, especially regarding gymnosperms and ferns (Figures 1 and 2), because these clades were previously not covered by the wikstrom.ages file. Important to note is that difference in trees results from varying divergence times, while tree topology is maintained. Such differences indicate that phylogenetic community analyses can generate relatively different results depending on the chosen databases, which can lead to ecological misinterpretation if based on incorrect data (Gastauer and Meira-Neto, 2013Gastauer, M. and Meira-Neto, J.A.A., 2013. Avoiding inaccuracies in tree calibration and phylogenetic community analysis using Phylocom 4.2. Ecological Informatics, vol. 15, no. 1, pp. 85-90. http://dx.doi.org/10.1016/j.ecoinf.2013.03.005.
http://dx.doi.org/10.1016/j.ecoinf.2013....
).

Figure 1
Hypothetical trees of a community composed of two species from all monophyletic families from APG III (APG III, 2009ANGIOSPERM PHYLOGENY GROUP – APG III, 2009. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society, vol. 161, no. 2, pp. 105-121. http://dx.doi.org/10.1111/j.1095-8339.2009.00996.x.
http://dx.doi.org/10.1111/j.1095-8339.20...
) that were inserted in the original megatree R20120829.new that was calibrated by agesclIII (see Gastauer and Meira-Neto, 2013Gastauer, M. and Meira-Neto, J.A.A., 2013. Avoiding inaccuracies in tree calibration and phylogenetic community analysis using Phylocom 4.2. Ecological Informatics, vol. 15, no. 1, pp. 85-90. http://dx.doi.org/10.1016/j.ecoinf.2013.03.005.
http://dx.doi.org/10.1016/j.ecoinf.2013....
for details, upper tree) and R20120829mod.new calibrated by ages_exp (lower tree).
Figure 2
Hypothetical community trees containing two species of all monophyletic families from APG III (APG III, 2009ANGIOSPERM PHYLOGENY GROUP – APG III, 2009. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society, vol. 161, no. 2, pp. 105-121. http://dx.doi.org/10.1111/j.1095-8339.2009.00996.x.
http://dx.doi.org/10.1111/j.1095-8339.20...
) and resulting from insertion in the original megatree R20120829.new that was calibrated by agesclIII (see Gastauer and Meira-Neto, 2013Gastauer, M. and Meira-Neto, J.A.A., 2013. Avoiding inaccuracies in tree calibration and phylogenetic community analysis using Phylocom 4.2. Ecological Informatics, vol. 15, no. 1, pp. 85-90. http://dx.doi.org/10.1016/j.ecoinf.2013.03.005.
http://dx.doi.org/10.1016/j.ecoinf.2013....
for details, upper tree) and R20120829mod.new calibrated by ages_logn (lower tree).

4 Conclusions

Differences in tree branch calibrations may produce different results regarding phylogenetic diversity and/or change the ecological interpretation of measures of phylogenetic community structure. Our goal was to gather and make available the most updated vascular plant phylogeny as well as updated minimum divergence times, as available from the recent literature. For that, we recommend the consistent application of the R20120829mod.new file in combination with ages_exp or ages_logn (available in the Supplementary Material*). This ensures a more inclusive and updated calibration of phylogenetic trees including not only angiosperms, but also gymnosperms and ferns, due to a higher number of internal nodes being dated, distributed among the entire tree of euphyllophytes. Furthermore, users have the possibility to choose between underlying statistical extrapolation of age estimates in their studies of evolutionary ecology, phylogenetic comparisons and analysis of most recent common ancestor analysis in plants.

Acknowledgements

We are grateful to the Floresta-Escola Environmental Science Center, SECTES-MG, CNPq, FAPEMIG and CAPES for grants and scholarships.

References

  • ANGIOSPERM PHYLOGENY GROUP – APG III, 2009. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society, vol. 161, no. 2, pp. 105-121. http://dx.doi.org/10.1111/j.1095-8339.2009.00996.x
    » http://dx.doi.org/10.1111/j.1095-8339.2009.00996.x
  • Bell, C.D., Soltis, D.E. and Soltis, P.S., 2010. The age and diversification of the angiosperms re-revisited. American Journal of Botany, vol. 97, no. 8, pp. 1296-1303. http://dx.doi.org/10.3732/ajb.0900346 PMid:21616882.
    » http://dx.doi.org/10.3732/ajb.0900346
  • Faith, D.P., 1992. Conservation evaluation and phylogenetic diversity. Biological Conservation, vol. 61, no. 1, pp. 1-10. http://dx.doi.org/10.1016/0006-3207(92)91201-3
    » http://dx.doi.org/10.1016/0006-3207(92)91201-3
  • Gastauer, M. and Meira-Neto, J.A.A., 2013. Avoiding inaccuracies in tree calibration and phylogenetic community analysis using Phylocom 4.2. Ecological Informatics, vol. 15, no. 1, pp. 85-90. http://dx.doi.org/10.1016/j.ecoinf.2013.03.005
    » http://dx.doi.org/10.1016/j.ecoinf.2013.03.005
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    » http://dx.doi.org/10.1007/s12224-013-9181-1
  • GITHUB, 2014 [viewed 3 January 2014]. [online]. Available from: https://github.com/camwebb/tree-of-trees/tree/master/megatrees
    » https://github.com/camwebb/tree-of-trees/tree/master/megatrees
  • Hedges, S.B. and Kumar, S., 2009. The time tree of life. New York: Oxford University Press.
  • Lemaire, B., Huysmans, S., Smets, E. and Merckx, V., 2011. Rate accelerations in nuclear 18S rDNA of mycoheterotrophic and parasitic angiosperms. Journal of Plant Research, vol. 124, no. 5, pp. 561-576. http://dx.doi.org/10.1007/s10265-010-0395-5 PMid:21188459.
    » http://dx.doi.org/10.1007/s10265-010-0395-5
  • Magallón, S. and Castillo, A., 2009. Angiosperm diversification through time. American Journal of Botany, vol. 96, no. 1, pp. 349-365. http://dx.doi.org/10.3732/ajb.0800060 PMid:21628193.
    » http://dx.doi.org/10.3732/ajb.0800060
  • Magallón, S., Hilu, K.W. and Quandt, D., 2013. Land plant evolutionary timeline: gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates. American Journal of Botany, vol. 100, no. 3, pp. 556-573. http://dx.doi.org/10.3732/ajb.1200416 PMid:23445823.
    » http://dx.doi.org/10.3732/ajb.1200416
  • Smith, S.A., Beaulieu, J.M., Stamatakis, A. and Donoghue, M.J., 2011. Understanding Angiosperm diversification using small and large phylogenetic trees. American Journal of Botany, vol. 98, no. 3, pp. 404-414. http://dx.doi.org/10.3732/ajb.1000481 PMid:21613134.
    » http://dx.doi.org/10.3732/ajb.1000481
  • Webb, C.O. and Donoghue, M.J., 2005. Phylomatic: tree assembly for applied phylogenetics. Molecular Ecology Notes, vol. 5, no. 1, pp. 181-183. http://dx.doi.org/10.1111/j.1471-8286.2004.00829.x
    » http://dx.doi.org/10.1111/j.1471-8286.2004.00829.x
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    » http://dx.doi.org/10.1146/annurev.ecolsys.33.010802.150448
  • Webb, C.O., Ackerly, D.D. and Kembel, S.W., 2008. Phylocom: software for the analysis of phylogenetic community structure and character evolution. Bioinformatics, vol. 24, no. 18, pp. 2098-2100. http://dx.doi.org/10.1093/bioinformatics/btn358 PMid:18678590.
    » http://dx.doi.org/10.1093/bioinformatics/btn358
  • WIKSTRÖM, N., Savolainen, V. and Chase, M.W., 2001. Evolution of angiosperms: calibrating the family tree. Proceedings. Biological Sciences, vol. 268, no. 1482, pp. 2211-2220. http://dx.doi.org/10.1098/rspb.2001.1782 PMid:11674868.
    » http://dx.doi.org/10.1098/rspb.2001.1782

Publication Dates

  • Publication in this collection
    19 Apr 2016
  • Date of issue
    Jul-Sep 2016

History

  • Received
    02 Oct 2014
  • Accepted
    31 Mar 2015
Instituto Internacional de Ecologia R. Bento Carlos, 750, 13560-660 São Carlos SP - Brasil, Tel. e Fax: (55 16) 3362-5400 - São Carlos - SP - Brazil
E-mail: bjb@bjb.com.br