Incorporating Fossils into Molecular Analysis for Evolutionary Insights

All is not lost for fossils – incorporating them into molecular analysis reveals important evolutionary insights.

Evolution is descent with modification. Through time this process produces a tree like structure of relationships among all living organisms. Understanding these phylogenetic relationships between organisms is a prerequisite of almost all evolutionary studies (Delsuc et al 2005, Zhang et al 2012). It provides the foundations for evolutionary biology and many other disciplines such biogeography, studies of biodiversity, evolutionary development, comparative genomics and crop breeding. Since the first representation of a phylogeny by Darwin in an origin of species, scientists have strived to reconstruct the tree of life. New technologies are bringing the completion this goal closer than ever before.

Traditionally most phylogenies were inferred from DNA-fragments. However, due to a lack of informative sites in the genome, many of these plant phylogenies remain unresolved at any evolutionary scales. A major advancement in the field is phylogenomics, it offers a new and exciting solution to this problem (Delsuc et al 2005, Eisen 1998). Phylogenomics uses genomic data to infer species relationships. It also allows us to gain an understanding of the processes of molecular evolution (Phillipe et al 2005).   By making use of vast amounts of sequence data as well as gene order, insertions and deletions phylogenomics can potentially resolve species relationships (Rokas and Holland 2000). By examining entire genomes, you expand the number of characters looked at. This overcomes the limitations of previous phylogenetic studies, in particular the stochastic error that arose due to the sampling of only a few genes (Delsuc et al 2005). Phylogenomics therefore provides an opportunity to better understand the evolutionary relationships of plants and generate a more robust picture of the tree of life.

The rapid improvement of next generation sequencing technology as well as the development of statistical methods has meant the gathering and analysis of genomic data has become much more convenient and cost effective. This has greatly expanded the use of genomic data in plant phylogenies (Barrett et al 2016, Gao et al 2010, Yu et al 2018). For example, as of November 2019 more than 3500 records of whole plastid genomes have been deposited on GenBank.  The number of studies involving plant phylogenomics has also risen dramatically since 2015 as shown in Figure 1. Phylogenomics has undoubtedly served as an effective tool for uncovering relationships of hard to distinguish plant groups including the: Asteraceae (Siniscalchi et al 2019); Saxifragales (Dong et al 2018); Liverworts (Yu et al 2019) and Lauraceae (Song et al 2019). Furthermore, it has discovered insight into the evolution of gene content and architecture in plant lineages (Labiak et al 2017). It has also helped to develop understanding of speciation. For example, phylogenomics was used to show the importance of allopatry for generating the increased diversity of plant species in eastern Asia compared with eastern north America (Li et al 2019). Phylogenomics has helped to reveal spatial patterns in genetic diversity, Bell et al 2018 used the method to identify distinct genetic structure of shrub and herbs between the northern and central mountains in the Australian alpine national Park.

Figure 1: Publications relating to plant phylogenomics, as identified through web of science, using the search term ‘plant phylogenomics’ on 13 December 2019. Of the results only papers that involved genomic data being used to construct a plant phylogeny were selected.

Due to the increase in sequencing power and the subsequent increase in the number of novel findings that have come from phylogenomics, many phylogenesists have become mesmerised with this new field. However, their hope that by simply using larger datasets the problems of incongruence could be overcome is false. The reality is far more complex.  For example, Kliendorf et al 2019 demonstrated the uncertainty present in phylogenies generated using genomic data of the rapidly speciating lineages of Haiwaiin cyrtandra. Rydin et al 2017 attempted to construct a phylogeny of Rubiaceae using mitochondrial genome data, but found many conflicting and potentially correct trees. This highlighted that merely adding more sequences is not enough to resolve inconsistencies. Two factors contribute significantly to the difficulty of reconstructing phylogenetic relationships from genetic data. Firstly, if speciation events are closely spaced in time the amount of phylogenetic signal is often small. This leads to short internal branches that are difficult to resolve. The second reason occurs if speciation events are ancient. Terminal branches tend to be long and multiple substitutions occurring at the same position are common. Incorrect phylogenetic relationships are generated in both cases. The best-known example of this misleading effect is long branch attraction. This is where two or more lineages have much longer branches than normal and so tend to group together irrespective of their relationship. The addition of more gene sequences does not solve the problem. Improved statistical methods go someway to overcome these limitations, but some incongruence remains.

Part of the problem in reconstructing phylogenies accurately from genomic data, is that they can only be inferred from extant species. Throughout the course of evolution branches from phylogenetic trees are lost; as genes, morphological characteristics and species become extinct. This makes it difficult to accurately reconstruct relationships based upon molecular data alone. Fossils can be used to help solve this problem. Fossils give us a window into the past, not possible through the study of any extant species. Because of this they possess, several characteristics which make them important for helping to construct accurate phylogenetic relationships. Fossils preserve combinations of characteristics not present among living clades. This means they can potentially modify relationships of homology and the polarity of evolution of traits (Edgecome 2010). They can also occupy unique positions within phylogenetic trees. These are places where by simply using data from extant species the relationships between species would be difficult to determine. For example, in the middle of ancient and rapid radiations or in between long branches that often separate morphologically distant extant species. Fossils morphology also may often represent the common ancestors of extant lineages due to lack of subsequent evolution on the extinct lineage. Fossils can therefore expect to have a strong impact on helping to resolve the relationships of plant lineages.

A number of recent studies have used fossils to resolve longstanding conflicts between morphological and molecular trees. For example, Cairo et al 2018 looked at the placement of angiosperms and gnetales in the seed plant phylogeny. Morphological data sets link gnetales with the angiosperms, however molecular analysis group them with the conifers. When they included fossil taxa in the morphological phylogenies they found it weakened the support for the relationship between the angiosperms and gnetales. Other examples include Parry et al 2016; Simoes et al 2018 and Miyushita et al 2019. However, given the fact that most relationships between lineages are constructed from molecular data this seems irrelevant. But it is important to remember that morphology will be the only way in which to incorporate fossils into trees with extant taxa. So, these results demonstrate the ability of fossils to resolve unclear relationships in phylogenetic trees. Koch and Parry et al 2019, developed predictive models that demonstrated that the relative impact of taxa on a phylogeny could be predicted before analysis. Using this they showed that fossil data can provide a unique role in inferring phylogenetic relationships.

Incorporating information preserved in fossil record into phylogenies also allows improved dating. This has recently led to the development of methods that integrate the phylogenetic placement of fossils into the dating process. This overcomes some of the limitations of previous methods. Standard practice up to now has been to date phylogenies using relaxed-clock models, where molecular rates of evolution are estimated from multiple points in the fossil record (Yang and Rannala 2006). However these methods suffer from several limitations including the fact that the calibration fossil must be associated with a fixed point in the tree but fossils cannot be dated to a high degree of accuracy and so this leads to uncertainty in the dating estimates. More modern methods use morphological data to infer fossils positions in phylogonies and so lead to better estimates of dates (Heath et al 2014, Gavryvchkina et al 2014). This have been used to more accurately date phylogenies when compared to other methods (Puschel et al 2019).

Accurate dating of trees can improve understanding of evolutionary processes through time. Mandel et al 2019 constructed a phylogenetic tree of the Astaracaeae using phylogenomics which was dated using fossils. This showed that the family underwent a series of rapid radiations during the Eocene that coincided with a cooling period. These radiating lineages then gave rise to 95% of the extant species of the family. Phylogenomics along with accurate fossil dating can also be used to look at what aspects of plants genomes may have led to subsequent diversification. Cai et al 2019 used a fossil dated phylogony of Malpighiales to find that widespread ancient genome duplications coincided with the Eocene climate upheaval. This in turn lent support to the hypothesis that polyploidisation promotes adaption and enhanced the plant lineages survival during periods of rapid change. These examples show the importance of accurately dated phylogenies in helping us understand the macroevolutionary processes that generate species diversity.

The fossil record also plays an important role in understanding the geographic assembly of biodiversity through time as they give a definitive location of the past distributions of plants not possible through the study of extant species. So by combining this information with phylogenetic trees you can look at how past biogeography of species has changes through time. For example, Xiang et al 2019 used fossil and molecular data to investigate the historical biogeography of the Hamamelidaceae. Importantly most of the fossils were found outside of extant species lineages and so exact knowledge of the past locations would not have been possible without fossil evidence. Their analysis indicates the extant lineages originated in tropical Asia and then dispersed around the globe in 20 seperate events. The study demonstrates how fossil data can be used to expand knowledge of assembly and evolution of angio-sperm dominated tropical forests. The location of fossil plants can be combined with their morphology to see how traits of plants evolved over time and in different locations. Jia et al 2018 used the first fossil of the genus Cedrelospermum discovered in the Tibetan plateau to investigate the biogeographic history and morphological evolution of the genus. Most previous fossils have been found in Northern America and Europe. This supports the hypothesis that the genus migrated to Asia from north America across the bearing land bridge. The morphology of the fossil suggests the evolutionary trend from obtuse to acute wings of the fruit.

Fossils preserve the morphology of extinct plants, morphology which can only be inferred from studies of extant plants. One of the key features preserved in plant fossils are diagnostic features of plant development. This means they can possess information on the origin of evolutionary innovations. This is particularly relevant for evolutionary innovations that may have occurred in extant lineages that are poorly represented and so phylogenomics offers little help. An example of this is found in the evolution of wood across plant lineages. In extant lineages wood is only found in the seed plants. However, the fossil record shows that woody growth has evolved multiple times over the course of evolution of vascular plants. Wood in extant plants is controlled by a polar auxin regulatory pathway, the physiological fingerprint of which can be seen in the plant fossils. This supports the hypothesis that there have been multiple acquisitions of wood but that they have been mediated by the same developmental pathway (Rothwell et al 2014). This shows how fossils can be used to uncover the history of plant development, which would not have been possible based solely upon developmental studies and phylogenomics of living plants.

The integration of fossils with phylogenomics is even more important in light of new techniques that expand our current understanding of fossils. Most plant fossils are not preserved whole, but instead are in the form of minute fragments of well preserved tissue. These fragments can be very difficult to identify which limits their usefulness. The realisation that they contain complex biomolecules that can remain relatively unaltered for millions of years, could revolutionise our understanding of the fossil record. Many plant components are resilient to change over geological timescales and are abundant in the fossil record. State of the art spectroscopy techniques such as Fourier-transform infrared spectroscopy (FTIR) have allowed the characterisation of the chemical composition of these components. This has been done on spores (Lomax 2012), pollen (Steemans 2010) and fossil resin (Seyfulla 2015). Being able to derive the biochemical characteristics of preserved fossil fragments is important. This is because it allows the identification of the fossils taxa, which traditionally would have been based upon morphological characters that are recognised in in relatively complete macrofossils. Unique phylogenetic signals can be obtained from even exceptionally old plant components (Amijaya et al 2006). This has been used to establish the relationship between several gymnosperms the Nilssoniales, Bennettitales and Cycadales. Which lended support hypothesis derived from genomic data (Vajda et al 2019). The technique also offers unique insights into the molecular structure of ancient plants. Qu et al 2019 used FTIR to examine fossil and extant royal fern specimens. They looked at 13C values and showed that the metabolic pathways of carbon assimilation since the Jurassic were unchanged. It also shed light on the function of ancient plant cellular organelles during mitosis. This demonstrates the ability of these techniques in studying the evolution and behaviour of ancient cells. With new techniques being developed to study fossils in greater detail, there exists an exciting opportunity to combine these with pylogenomics to develop new insight into the evolution of the plant kingdom.

Phylogenomics is not a panacea. It can offer an almost unparalled way of investigating the relationships between plants which has led to many exciting discoveries. However, it should be remembered that the plants alive on earth today only represent a fraction of those that have existed on earth. Simply sequencing more genes cannot replace this lost part of the tree of life. Fossils offer a window into the past timing and location of events. They can also give us an insight into the morphology of extinct lineages. The scientific community needs to recognise this. The combination of phylogenomics and fossil data has the potential to revolutionise our understanding of both the plant tree of life and the evolutionary processes that have created it.

References

Barrett, C. F., Baker, W. J., Comer, J. R., Conran, J. G., Lahmeyer, S. C., Leebens‐Mack, J. H., … Davis, J. I. (2016). Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots. New Phytologist, 209(2), 855–870. doi: 10.1111/nph.13617

Bell, N., Griffin, P. C., Hoffmann, A. A., & Miller, A. D. (2018). Spatial patterns of genetic diversity among Australian alpine flora communities revealed by comparative phylogenomics. Journal of Biogeography, 45(1), 177–189. doi: 10.1111/jbi.13120

Cai, L., Xi, Z., Amorim, A. M., Sugumaran, M., Rest, J. S., Liu, L., & Davis, C. C. (2019). Widespread ancient whole-genome duplications in Malpighiales coincide with Eocene global climatic upheaval. New Phytologist, 221(1), 565–576. doi: 10.1111/nph.15357

Delsuc, F., Brinkmann, H., & Philippe, H. (2005). Phylogenomics and the reconstruction of the tree of life. Nature Reviews Genetics, 6(5), 361–375. doi: 10.1038/nrg1603

Eisen, J. A. (1998). Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis. Genome Research, 8(3), 163–167. doi: 10.1101/gr.8.3.163

Frontiers | Phylogenomics Yields New Insight Into Relationships Within Vernonieae (Asteraceae) | Plant Science. (n.d.). Retrieved December 18, 2019, from https://www.frontiersin.org/articles/10.3389/fpls.2019.01224/full

Gao, L., Su, Y.-J., & Wang, T. (2010). Plastid genome sequencing, comparative genomics, and phylogenomics: Current status and prospects. Journal of Systematics and Evolution, 48(2), 77–93. doi: 10.1111/j.1759-6831.2010.00071.x

Gavryushkina, A., Welch, D., Stadler, T., & Drummond, A. J. (2014). Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration. PLOS Computational Biology, 10(12), e1003919. doi: 10.1371/journal.pcbi.1003919

Heath, T. A., Huelsenbeck, J. P., & Stadler, T. (2014). The fossilized birth–death process for coherent calibration of divergence-time estimates. Proceedings of the National Academy of Sciences, 111(29), E2957–E2966. doi: 10.1073/pnas.1319091111

Jia, L.-B., Su, T., Huang, Y.-J., Wu, F.-X., Deng, T., & Zhou, Z.-K. (2019). First fossil record of Cedrelospermum (Ulmaceae) from the Qinghai–Tibetan Plateau: Implications for morphological evolution and biogeography. Journal of Systematics and Evolution, 57(2), 94–104. doi: 10.1111/jse.12435

Kleinkopf, J. A., Roberts, W. R., Wagner, W. L., & Roalson, E. H. (2019). Diversification of Hawaiian Cyrtandra (Gesneriaceae) under the influence of incomplete lineage sorting and hybridization. Journal of Systematics and Evolution, 57(6), 561–578. doi: 10.1111/jse.12519

Koch, N. M., & Parry, L. A. (2019). Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses. BioRxiv, 723882. doi: 10.1101/723882

Labiak, P. H., & Karol, K. G. (2017). Plastome sequences of an ancient fern lineage reveal remarkable changes in gene content and architecture. American Journal of Botany, 104(7), 1008–1018. doi: 10.3732/ajb.1700135

Mandel, J. R., Dikow, R. B., Siniscalchi, C. M., Thapa, R., Watson, L. E., & Funk, V. A. (2019). A fully resolved backbone phylogeny reveals numerous dispersals and explosive diversifications throughout the history of Asteraceae. Proceedings of the National Academy of Sciences, 116(28), 14083–14088. doi: 10.1073/pnas.1903871116

Miyashita, T., Coates, M. I., Farrar, R., Larson, P., Manning, P. L., Wogelius, R. A., … Currie, P. J. (2019). Hagfish from the Cretaceous Tethys Sea and a reconciliation of the morphological–molecular conflict in early vertebrate phylogeny. Proceedings of the National Academy of Sciences, 116(6), 2146–2151. doi: 10.1073/pnas.1814794116

Parry, L. A., Edgecombe, G. D., Eibye-Jacobsen, D., & Vinther, J. (2016). The impact of fossil data on annelid phylogeny inferred from discrete morphological characters. Proceedings of the Royal Society B: Biological Sciences, 283(1837), 20161378. doi: 10.1098/rspb.2016.1378

(PDF) Allopatric Speciation in Asia Contributed to the Diversity Anomaly between Eastern Asia and Eastern North America: Evidence from Anchored Phylogenomics of Stewartia (Theaceae). (n.d.). Retrieved December 18, 2019, from ResearchGate website: https://www.researchgate.net/publication/334719086_Allopatric_Speciation_in_Asia_Contributed_to_the_Diversity_Anomaly_between_Eastern_Asia_and_Eastern_North_America_Evidence_from_Anchored_Phylogenomics_of_Stewartia_Theaceae

(PDF) First fossil record of Cedrelospermum (Ulmaceae) from the Qinghai-Tibetan Plateau: Implications for morphological evolution and biogeography. (n.d.). Retrieved December 19, 2019, from https://www.researchgate.net/publication/325605963_First_fossil_record_of_Cedrelospermum_Ulmaceae_from_the_Qinghai-Tibetan_Plateau_Implications_for_morphological_evolution_and_biogeography

(PDF) Plant phylogenomics based on genome-partitioning strategies: Progress and prospects. (n.d.). Retrieved December 18, 2019, from ResearchGate website: https://www.researchgate.net/publication/326094923_Plant_phylogenomics_based_on_genome-partitioning_strategies_Progress_and_prospects

(PDF) Plastid phylogenomics improve phylogenetic resolution in the Lauraceae. (n.d.). Retrieved December 18, 2019, from ResearchGate website: https://www.researchgate.net/publication/335380583_Plastid_phylogenomics_improve_phylogenetic_resolution_in_the_Lauraceae

Philippe, H., Delsuc, F., Brinkmann, H., & Lartillot, N. (2005). Phylogenomics. Annual Review of Ecology, Evolution, and Systematics, 36(1), 541–562. doi: 10.1146/annurev.ecolsys.35.112202.130205

Püschel, H. P., O’Reilly, J. E., Pisani, D., & Donoghue, P. C. J. (n.d.). The impact of fossil stratigraphic ranges on tip-calibration, and the accuracy and precision of divergence time estimates. Palaeontology, n/a(n/a). doi: 10.1111/pala.12443

Qu, Y., McLoughlin, N., van Zuilen, Mark. A., Whitehouse, M., Engdahl, A., & Vajda, V. (2019). Evidence for molecular structural variations in the cytoarchitectures of a Jurassic plant. Geology, 47(4), 325–329. doi: 10.1130/G45725.1

Rokas, A., & Holland, P. W. H. (2000). Rare genomic changes as a tool for phylogenetics. Trends in Ecology & Evolution, 15(11), 454–459. doi: 10.1016/S0169-5347(00)01967-4

Rothwell, G. W., Wyatt, S. E., & Tomescu, A. M. F. (2014). Plant evolution at the interface of paleontology and developmental biology: An organism-centered paradigm. American Journal of Botany, 101(6), 899–913. doi: 10.3732/ajb.1300451

Rydin, C., Wikström, N., & Bremer, B. (2017). Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny. American Journal of Botany, 104(10), 1522–1532. doi: 10.3732/ajb.1700255

Simões, T. R., Caldwell, M. W., Tałanda, M., Bernardi, M., Palci, A., Vernygora, O., … Nydam, R. L. (2018). The origin of squamates revealed by a Middle Triassic lizard from the Italian Alps. Nature, 557(7707), 706–709. doi: 10.1038/s41586-018-0093-3

Vajda, V., Pucetaite, M., McLoughlin, S., Engdahl, A., Heimdal, J., & Uvdal, P. (2017). Molecular signatures of fossil leaves provide unexpected new evidence for extinct plant relationships. Nature Ecology & Evolution, 1(8), 1093–1099. doi: 10.1038/s41559-017-0224-5

Xiang, X., Xiang, K., Ortiz, R. D. C., Jabbour, F., & Wang, W. (2019). Integrating palaeontological and molecular data uncovers multiple ancient and recent dispersals in the pantropical Hamamelidaceae. Journal of Biogeography, 46(11), 2622–2631. doi: 10.1111/jbi.13690

Xiang, X., Xiang, K., Ortiz, R. D. C., Jabbour, F., & Wang, W. (n.d.). Integrating palaeontological and molecular data uncovers multiple ancient and recent dispersals in the pantropical Hamamelidaceae. Journal of Biogeography, n/a(n/a). doi: 10.1111/jbi.13690

Yang, Z., & Rannala, B. (2006). Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Molecular Biology and Evolution, 23(1), 212–226. doi: 10.1093/molbev/msj024

Yu, Y., Yang, J.-B., Ma, W.-Z., Pressel, S., Liu, H.-M., Wu, Y.-H., & Schneider, H. (n.d.). Chloroplast phylogenomics of liverworts: a reappraisal of the backbone phylogeny of liverworts with emphasis on Ptilidiales. Cladistics, n/a(n/a). doi: 10.1111/cla.12396

Zhang, N., Zeng, L., Shan, H., & Ma, H. (2012). Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiosperms. New Phytologist, 195(4), 923–937. doi: 10.1111/j.1469-8137.2012.04212.x