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Keywords:

  • angiosperm;
  • community ecology;
  • gymnosperm;
  • life form;
  • phylogenetic signal

Abstract

  1. Top of page
  2. Abstract
  3. Material and methods
  4. Results
  5. Discussion
  6. Acknowledgements
  7. References
  8. Supporting Information

Diversity and membership of species in a biological community result from the interplay between evolutionary and ecological processes. Plant ecologists often rely on family-level phylogenies to address various issues of community assembly because phylogenies resolved at the species or genus level are generally not available. Here, we present an updated time-calibrated family-level phylogeny that includes all families of extant seed plants (i.e., angiosperms and gymnosperms) in the world, and use the phylogeny to show patterns of genus and species richness and life forms of all seed plant families in the world across the phylogeny. In addition, we use the phylogeny to examine whether life forms (woody vs. herbaceous) of seed plant families in the world are non-randomly distributed across the phylogeny. Our study shows that life forms exhibit significant phylogenetic signal across the phylogeny of seed plants.

Diversity and membership of species in a biological community result from the interplay between evolutionary and ecological processes (Ricklefs, 1987). Phylogenies, especially when calibrated with a dimension of time, can illuminate our knowledge of evolutionary histories of biological communities at multiple temporal and spatial scales (Pennington et al., 2006). For example, phylogenies permit a re-evaluation of the relative roles of plate tectonics and long-distance dispersal in the assembly of regional and continental biota at a global scale (Crisp et al., 2004) on one hand and permit an examination of phylogenetic relatedness of species and provide insights into the assembly of biological communities at a local scale on the other hand (Webb et al., 2002). Since Campbell O. Webb laid a cornerstone for phylogenetic community ecology by providing an approach for analyzing phylogenetic structure of biological communities a decade ago (Webb, 2000; Webb et al., 2002), the use of phylogenies to investigate patterns of community structure has blossomed. For example, based on the Thomson Reuters' Web of Science (accessed on January 3, 2014; searched using the key words “phylogen*” and “community ecology”), only 177 articles on phylogenetic community ecology were published over the 10 years from 1991 to 2000; however, over 500 articles on phylogenetic community ecology were published in the last 2 years (2012 and 2013) alone.

Seed plants are dominant in all major terrestrial biomes and ecosystems across the globe (Ricklefs, 2008). For trees alone, 1 ha of tropical forest may hold more than 650 species (Coley & Kursar, 2014), of which ∼300 may be tree species of >10 cm diameter at breast height (Pitman et al., 2002). A local or regional flora can often have several thousand seed plant species (Zhu, 2012) even in temperate regions (Cooperative Group of the Flora of Anhui, 1986–1992). Although a phylogeny that includes all plant species of a local community may be generated using gene sequences, it is currently impractical, if not impossible, to generate a species-level phylogeny based on molecular data for a study including numerous floras, which each may have hundreds or thousands of species, due to lack of gene sequences for all species in the floras. As a result, plant ecologists often use a family-level phylogeny (supertree) as a backbone to assemble their phylogenies and to attach genera and species in the floras to their respective families in the supertree phylogeny.

Davies et al. (2004) and APG III (2009) are the only published phylogenies that include all or nearly all families of angiosperms. These two phylogenies have been frequently used as backbones to generate smaller phylogenies for specific studies in the past decade (see examples in Appendix S1 in Supplementary Material). Branch lengths in Davies et al.'s (2004) phylogeny were time-calibrated; however, family delineations in their phylogeny followed APG II (2003) and some families of angiosperms are not included in the phylogeny. APG II (2003) is an earlier version of APG III (2009) and thus is outdated. For example, Davies et al. (2004) recognized 440 families whereas APG III (2009) recognized 413 families. In addition, new gene sequences for a large number of angiosperm species have been available from GenBank (http://www.ncbi.nlm.nih.gov/genbank) since the publication of the phylogeny of Davies et al. (2004) and the new molecular data have substantially changed memberships among families and branch lengths of families and higher clades (e.g., Bell et al., 2010; Qiu et al., 2010; Soltis et al., 2011; Zhang et al., 2012; Zanne et al., 2014). APG III (2009) provided a topology for angiosperm orders with member families of each order indicated but it did not provide branch lengths in the topology and memberships of families within orders. A phylogeny that has not been calibrated with an absolute dimension of time for families and higher clades becomes a less powerful tool although it still contains information of relative recency of common ancestry and is useful to investigate how closely ecology or geography correlates with relationships (Pennington et al., 2006). In order to better use the phylogeny of APG III (2009), it has become a fairly standard practice to use Phylomatic and the branch length adjustment (BLADJ) algorithm implemented in Phylocom (Webb et al., 2008) to assign plant clade age estimates from Wikström et al. (2001) to branches in the APG III phylogeny (e.g., Duarte et al., 2012; Giehl & Jarenkow, 2012; Carboni et al., 2013; Seger et al., 2013). The use of the APG III phylogeny in conjunction with clade age estimates from Wikström et al. (2001) is presumably better than the use of the APG III phylogeny alone. However, the file with clade age estimates of Wikström et al. (2001) in Phylocom (http://phylodiversity.net/phylocom/) includes only 120 clades at the family level or less than 30% of the 413 families recognized by APG III (2009). Furthermore, as Beaulieu et al. (2012) point out, no study has critically evaluated the assumption of BLADJ approach. Thus, it is uncertain how reliable branch lengths generated by BLADJ are. The family-level phylogenies published in Davies et al. (2004) and APG III (2009) have played an important role in advancing our knowledge of how evolutionary processes have driven diversity patterns and memberships of angiosperms within and between biological assemblages, but both are outdated.

Several recent studies have provided time-calibrated phylogenies and ages for angiosperm families since APG III (2009) but none of them have included all families of angiosperms. For example, Bell et al. (2010) provided dates for 335 of the 413 families of APG III (2009); similarly, Soltis et al. (2011) provided a phylogeny for 330 families. Smith et al. (2011) provided a phylogeny for angiosperms (available from http://datadryad.org/resource/doi:10.5061/dryad.8790) but this phylogeny is not time-calibrated. More recently, Zanne et al. (2014) provided a species-level phylogeny for 32 223 land plant species. This phylogeny was built based on seven gene regions (i.e., 18S rDNA, 26S rDNA, ITS, matK, rbcL, atpB, and trnL-F), which include, as Zanne et al. (2014) point out, “both slowly evolving regions that have been broadly sampled across the clade (e.g., rbcL, 18S rDNA) and more quickly evolving regions that have been densely sampled for species-level phylogenetic studies (e.g., ITS, trnL-F).” The maximum-likelihood estimates in the phylogeny were time-scaled based on 39 fossil calibrations. Both minimum and maximum age constraints were utilized for each fossil calibration. Thus, Zanne et al.'s (2014) phylogeny was built based on multi-gene molecular and fossil data. The phylogeny includes 31 029 species of seed plants, 30 447 of which are angiosperms. Orders and families were constrained according to APG III (2009) with some exceptions; for example, Lophiocarpaceae was recognized in APG III but was merged with Phytolaccaceae in Zanne et al. (2014). The phylogeny from Zanne et al. (2014) is the largest and most up-to-date time-calibrated species-level phylogeny of seed plants. However, because this phylogeny includes only 7933 (51.6%) of the 15 363 genera of seed plants (Zanne et al., 2014) and only 11.2% of ∼277 600 species of seed plants based on the APweb (Stevens, 2013), the use of this phylogeny in analyses of plant community at the genus and species levels is substantially limited. Nevertheless, although the phylogeny does not include all angiosperm families, a complete time-calibrated family-level phylogeny for seed plants can be created by adding missing angiosperm families to the phylogeny provided by Zanne et al. (2014), using additional information from other sources.

Family-level phylogenies have been frequently used in functional trait analyses (e.g., Fortunel et al., 2012; Knapp et al., 2012; Qi et al., 2014) but to our knowledge there are no studies that have examined whether there is significant phylogenetic signal for a given functional trait across a phylogeny that includes all families of seed plants. The major objective of this article is to use an updated time-calibrated family-level phylogeny that includes all families of extant seed plants in the world to examine whether life forms (woody vs. herbaceous) of seed plant families are non-randomly distributed across the phylogeny. We focus on life forms of plants because they are an important functional trait for both regional and local assemblages of plants but whether there is significant phylogenetic signal in life forms across a phylogeny that includes all families of seed plants has not been examined.

Material and methods

  1. Top of page
  2. Abstract
  3. Material and methods
  4. Results
  5. Discussion
  6. Acknowledgements
  7. References
  8. Supporting Information

We first generated a phylogenetic backbone by extracting one species per family from the species-level phylogeny of Zanne et al. (2014). We compared families in the genus file of Zanne et al. (2014; i.e., Spermatophyta_Genera.csv) with families in the phylogeny file of Zanne et al. (2014; i.e., Vascular_Plants_rooted.dated.tre) and found that six families (i.e., Apodanthaceae, Cynomoriaceae, Emblingiaceae, Haptanthaceae, Octoknemaceae, and Rafflesiaceae) which are present in the former file are absent from the latter file. We checked the current literature, including APweb (Stevens, 2013), and found that all the families included in Zanne et al. (2014) except for Haptanthaceae are recognized by the current literature. Thus, we included them in the family-level phylogeny. Haptanthaceae is a monotypic family including a single species (Haptanthus hazlettii, an enigmatic Central American tree). Based on molecular data (the barcoding region of rbcL), Shipunov & Shipunova (2011) showed that a lineage including both Haptanthus and Buxus is sister to a lineage with three other genera (i.e., Pachysandra, Sarcococca, and Styloceras) of the family Buxaceae. Furthermore, APweb (Stevens, 2013) includes Haptanthus in Buxaceae. Accordingly, we included Haptanthus in Buxaceae in our study. When we compared genera and families of seed plants in the genus list provided by Zanne et al. (2014) with other sources, we found that the family Petenaeaceae, which includes a monotypic genus (Petenaea), is missing from their genus list and phylogeny. This family is recognized in the current literature (e.g., Stevens, 2013); accordingly, we included Petenaeaceae in our study. As a result, we expanded the incomplete family-level phylogeny extracted from Zanne et al. (2014) into a complete family-level phylogeny of extant seed plants in the world by including the six additional families. The placement of these additional families in the phylogeny was based on the current literature, which was shown in Appendix S2 (Supplementary Material).

Data of plant life forms (woody, herbaceous, mixed) were compiled based on various sources, such as Wu et al. (1994–2013) and the APweb (Stevens, 2013). We also documented the genus and species richness of each family. The number of genera for each family was documented based on Zanne et al. (2014) except for Petenaeaceae (see above), and the number of species for each family was documented based on the APweb (Stevens, 2013). Generic richness was divided into five classes (A, 1 genus; B, 2–5; C, 6–20; D, 21–100; E, >100); species richness was also divided into five classes (A, 1–10 species; B, 11–50; C, 51–200; D, 201–1000; E, >1000). Seed plant families were put in five taxonomic groups: Gymnosperms, Monocotyledoneae, Magnoliidae, Superrosidae, and Superasteridae. Twenty-four families, which do not belong to any of these groups (Fig. 1), were put in the “unclassified” group.

image

Figure 1. Phylogeny for all the 437 families of seed plants in the world. See details and Newick version of the phylogeny in Appendix S3. Branch lengths are in millions of years. The numbers 1 through 5 indicate five major groups of seed plants: Gymnosperms, Monocotyledoneae, Magnoliidae, Superrosidae, and Superasteridae (families in the same group are shown in the same color; unclassified families are shown in black color). Tip branches are shown in three colors (blue, red, and green), which represent different life forms (woody, herbaceous, and mixed, respectively). Generic richness is indicated by five colors in circle symbols on branch tips (A, 1 genus; B, 2–5; C, 6–20; D, 21–100; E, >100), and species richness is indicated by five colors in square symbols (A, 1–10 species; B, 11–50; C, 51–200; D, 201–1000; E, >1000). Photo credit: 1, Abies beshanzuensis var. ziyuanensis of the Pinaceae family, Chinese Virtual Herbarium (courtesy Yan Liu); 2, Tulipa sp. of the Liliaceae family, http://www.google.com/imgres; 3, Manglietia grandis of the Magnoliaceae family, Huang et al. (2013; courtesy Wei-Bang Sun); 4, Rosa sp. of the Rosaceae family, http://www.google.com/imgres; 5, Rhododendron delavayi of the Ericaceae family, Huang et al. (2013; courtesy Xiang Chen).

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We applied two approaches to determine whether different life forms of seed plants are randomly distributed across the family-level phylogeny. First, we conducted a Chi-square analysis (Zar, 1984) on the contingency table of three life forms and six plant groups. Second, we used two indices of phylogenetic signal, Blomberg's K (Blomberg et al., 2003) and Pagel's λ (Pagel, 1999), to determine whether significant phylogenetic signal of life forms occurs for seed plant families. These two indices are commonly used to assess phylogenetic signal of a focal trait with respect to a phylogeny (e.g., Shrestha et al., 2014). For both indices, a value of 0 indicates a random distribution of life forms with respect to the phylogeny whereas a value of 1 indicates that the evolution of this trait matches expectations under the Brownian motion model of evolution. Woody, mixed, and herbaceous families were coded as 1, 2, and 3, respectively, in the analyses. Phylogenetic signal was assessed for the entire data set with all families as well as for a subset of the data, which excluded the category of mixed life forms. We tested whether observed values significantly differ from those expected at random by comparing observed values with those generated by a null model in which species identities were randomly shuffled 999 times across the tips of the phylogeny. We used the R function “phylosig” in the R package “phytools” (Revell, 2012) for the assessment of phylogenetic signal.

Results

  1. Top of page
  2. Abstract
  3. Material and methods
  4. Results
  5. Discussion
  6. Acknowledgements
  7. References
  8. Supporting Information

The resulting phylogeny, which is available in Appendix S3, included all the 437 families of seed plants in the world (12 families of gymnosperms, 425 families of angiosperms; Fig. 1). Of the 437 families, 112 are monotypic at the genus level; 86 each have only two or three genera. The vast majority of the families with one to three genera are endemic to one continent or restricted to one or few biomes (Wielgorskaya, 1995; Takhtajan, 1997; Mabberley, 2008); thus, their distribution patterns likely reflect the imprint of evolutionary histories. Species and genus richness of each family was shown in Fig. 1. The numbers of species and genera are strongly correlated (Fig. 2).

image

Figure 2. Relationship between the numbers of genera and species in the 437 seed plant families of the world.

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Proportions of life forms were significantly non-randomly distributed among taxonomic groups (χ2 = 148.9, d.f. = 10, P < 0.001; Fig. 3). When all three life forms (i.e., woody, herbaceous, mixed) were included in an analysis assessing phylogenetic signal, values of Blomberg's K and Pagel's λ were significantly larger than 0 (0.475 and 0.668, respectively; P < 0.001 in both cases). When families in the category of mixed life forms were excluded from an analysis, values of Blomberg's K and Pagel's λ were not only significantly larger than 0 (0.517 and 0.675, respectively; P < 0.001 in both cases) but also greater than those of the analysis based on all three life forms. Thus, these results are consistent with that of Chi-square analysis, and all these results indicate that the trait of life forms exhibited significant phylogenetic signal across the family-level phylogeny of seed plants.

image

Figure 3. The number of families (above each bar) and proportions of three life forms (woody in black, herbaceous in dark gray, and mixed in light gray) for each taxonomic group (1, gymnosperms; 2, monocotyledoneae; 3, magnoliidae; 4, superrosidae; 5, superasteridae; 6, unclassified).

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Discussion

  1. Top of page
  2. Abstract
  3. Material and methods
  4. Results
  5. Discussion
  6. Acknowledgements
  7. References
  8. Supporting Information

Unlike the family-level phylogenies provided by Davies et al. (2004) and APG III (2009) which include only angiosperms, the family-level phylogeny used in our study included both gymnosperms and angiosperms. For angiosperms, the phylogeny used in our study may be considered as an updated version of the phylogeny of Davies et al. (2004) because delineations of and memberships among families reflect the current knowledge of angiosperms and all angiosperm families were included in the phylogeny; the phylogeny may be also considered as an updated version of the phylogeny of APG III (2009) because memberships among families in the phylogeny were established and time-calibrated branch lengths were provided. However, because all phylogenies are hypotheses and subject to change when new data become available, we view the phylogeny used in our study as a work in progress, which can and will change as new studies are published. Nevertheless, because the phylogeny used in our study was based on the phylogeny of Zanne et al. (2014), which was generated using seven gene regions, which included both slowly and relatively quickly evolving regions, and reliable fossil data, we believe that memberships among clades (including families) in the family-level phylogeny used in our study are robust for ecological studies.

Ideally, all phylogenetic community studies would use time-calibrated species-level phylogenies that would be built based on molecular data in conjunction with fossil data. However, considering that through tremendous efforts of biologists across the world over the past decades, only less than 20% of seed plant species have been sequenced (see above; also see Beaulieu et al., 2012). A time-calibrated phylogeny including all species of seed plants may not be available within next decades, if not centuries. Thus, ecologists, particularly those who work with large data sets covering broad spatial scales and extents, have to rely on phylogenies built at higher taxonomic ranks such as family-level phylogenies. A species-level phylogeny would presumably be more informative than a genus-level or family-level phylogeny; however, if species in study samples are widely spread across major clades such as orders and families, rather than restricted to a few clustered major clades, of a phylogeny, ecological patterns based on a family-level phylogeny may not differ substantially from those based on a species-level phylogeny because traits evolved at deep divisions of major clades may play a more important role than those evolved within genera or families in driving ecological and biogeographical patterns, at least in some cases. As shown in the present study, life forms of seed plants are significantly non-randomly distributed and phylogenetic signal of life forms is significant across the family-level phylogeny of seed plants.

Many biological and functional traits are restricted to one or few major clades (e.g., orders and families) on one hand and are commonly shared by member taxa within the clades on the other hand. For example, the order Fagales, which includes seven families (i.e., Nothofagaceae, Fagaceae, Myricaceae, Juglandaceae, Casuarinaceae, Ticodendraceae, and Betulaceae) and dominant trees in many broad-leaved forests across the world, is a monophyletic and woody clade. All families of the Fagales possess a combination of the following traits: unisexual flowers with reduced perianth, inferior ovary with one or two ovules per locule, pollen tube entering the ovule via the chalaza, lack of nectaries, and indehiscent 1-seeded fruits (Judd et al., 2002). Within the Fagales, only members of the family Nothofagaceae possess the trait that fruits are associated with a conspicuous cupule. Of the remaining families of the Fagales, all except for Fagaceae possess triporoporate pollen. Of the families with triporoporate pollen, Juglandaceae are sister to Myricaceae and both have aromatic glands and 1-ortotropous ovule but they are distinguished from each other by many traits such as the former have compound leaves whereas the latter have simple leaves. This clade is then sister to the clade with Betulaceae, Ticodendraceae, and Casuarinaceae, which share pollen grains with the exine having tiny spines in rows. Betulaceae are sister to Ticodendraceae, which both have two-ranked leaves and clusters of sclerids in the bark; this clade is then sister to Casuarinaceae, which have many traits (e.g., leaves whorled) that are lacking in their sister clade (Judd et al., 2002; Judd & Olmstead, 2004). In addition to unique trait character states associated with each family or higher clade, broad-scale geographic distributions may differ substantially among families, even for some closely related ones. For examples, in the case of the order Fagales, Nothofagaceae are more closely related with Fagaceae than any other families within the order but the former are restricted to the Southern Hemisphere whereas the latter are nearly restricted to the Northern Hemisphere. This pattern of geographic distributions of the two families reflects their different evolutionary histories. Thus, a family-level phylogeny may be appropriate for phylogenetic analyses of biological and functional traits, as shown in the present study for the trait of life forms.

Over a hundred studies have used different versions of family-level phylogenies of angiosperms to address various issues of community assembly at a wide range of spatial scales. For example, He et al. (2009) used a phylogeny based on APG II (2003) to examine the trade-offs between leaf persistence and leaf productivity in grassland biomes in China; Kooyman et al. (2011) and Giehl & Jarenkow (2012) used the APG III phylogeny in conjunction with clade ages from Wikström et al. (2001) to determine differences in phylogenetic relatedness in woody floras between tropical and subtropical regions in Australia and South America; Qian et al. (2013) used the APG III phylogeny to investigate changes in phylogenetic relatedness of regional tree assemblages along latitudinal gradients in North America; Li et al. (2014) and Qian et al. (2014) both used the APG phylogeny to investigate changes in phylogenetic relatedness of angiosperm assemblages along elevational gradients in China; Cavender-Bares et al. (2006) used the phylogeny of Davies et al. (2004) to investigate phylogenetic structure of local plant communities in Florida, USA, and Cadotte et al. (2008) used the same phylogeny to investigate the effect of biodiversity on plant productivity. Over the last 3 years (2011 through 2013) alone, at least 46 studies utilized Davies et al.'s (2004) and/or APG III (2009) family-level phylogenies of angiosperms to address issues of community assembly (see Appendix S1 in Supplementary Material). All previous studies based on family-level phylogenies of angiosperms have successfully found significant ecological and biogeographical patterns with respect to phylogenies used, suggesting that evolutionary processes have played a role in assembly of biological communities. Phylogenetic community ecology has been a research focus of many ecologists, which is reflected by an exponential increase in the number of published articles in this field (Qian & Jiang, 2014). It is expected that the updated time-calibrated family-level phylogeny of seed plants used in our study would be a useful tool for many plant ecologists addressing issues of community assembly.

Acknowledgements

  1. Top of page
  2. Abstract
  3. Material and methods
  4. Results
  5. Discussion
  6. Acknowledgements
  7. References
  8. Supporting Information

We are grateful to Yin-Long QIU (University of Michigan, USA) and an anonymous reviewer for their helpful comments.

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  2. Abstract
  3. Material and methods
  4. Results
  5. Discussion
  6. Acknowledgements
  7. References
  8. Supporting Information
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Supporting Information

  1. Top of page
  2. Abstract
  3. Material and methods
  4. Results
  5. Discussion
  6. Acknowledgements
  7. References
  8. Supporting Information

Additional supporting information may be found in the online version of this article:

FilenameFormatSizeDescription
jse12086-sm-0001-SuppApp-S1.doc39KAppendix S1. A list of selected papers which were published over the last 3 years and used family-level phylogenies of angiosperms to address ecological issues.
jse12086-sm-0002-SuppApp-S2.doc32KAppendix S2. The placement of six additional families into the family-level phylogeny generated based on Zanne et al. (2014).
jse12086-sm-0003-SuppApp-S3.doc41KAppendix S3. Newick version of the family-level phylogeny of seed plants in the world.

Please note: Wiley Blackwell is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.