Conserving Biodiversity: A Phylogenetic Perspective

Conserving Biodiversity: A Phylogenetic Perspective
H. S. Kathriarachchi
Department of Plant Sciences, University of Colombo

I dedicate this Presidential Address to my wonderful teachers with gratitude; who inspired me, to learn and understand the fascinating things in the nature while truly enjoying them.

Systematics and phylogenetics in biodiversity conservation:

The systematics partly overlaps with taxonomy and was originally used to describe the system of classification prescribed by early biologists. Simply the term Systematics can be defined as the “Science of the diversity of organisms”. It involves the discovery, description, and interpretation of biological diversity, as well as the synthesis of information on diversity as a classification system. The modern concept of ‘Systematics’ is broader, and it involves a wider scope incorporating Taxonomy, Phylogeny and the Evolution as major components. Taxonomy is the process of classification including identification and nomenclature. Phylogeny includes divergence or development of all groups in terms of mode, time, and place. The process of evolution will study the sources of variability, organization of genetic variability in populations, differentiation of populations, reproductive isolation and the origin of species. Considering all these we now accept the modern concept of systematics which has a strong phylogenetic approach. Phylogenetic systematics has made the discipline predictive and explanatory. Biodiversity is the incredible variety of life that surrounds us, including all of the earth’s plants, animals, and micro-organisms, the communities they form and the habitats in which they live and have evolved in as well as the natural processes they facilitate. It is clear that systematic knowledge merge all of biology by establishing a conceptual framework for interpreting features, activities, and distribution of species and then grouping of these taxa. Systematic discoveries, data and interpretations are essential components to conserve and manage the earth’s biotic wealth. Thus, the phylogenetic systematics is directly relevant to biodiversity science and can have enormous practical value in guiding conservation efforts, enhancing sustainability and improving human welfare. In this talk I will briefly outline some selected activities in which phylogenetics have been directly relevant to biodiversity conservation. My emphasis on floristics reflects the intended focus of this talk, however, most of the scientific facts that I discuss apply more broadly across the tree of life.

Discovering and documenting undetected diversity

Starting from Linnaeus, we have made a remarkable achievement and extraordinary understanding of the earth’s biodiversity today through the discovering and documenting over 1.5 million species. This is still only a small proportion of earth’s unbelievable biotic wealth: millions
of species still waiting to be discovered. Major component of undescribed organisms are microbes including achaea, bacteria, fungi and algae. Our current best estimate for the number of vascular plant species known to science is approximately 390,900, of which approximately 369,400 are angiosperms. The Plant List managed by the Royal Botanic Gardens Kew provides the current most comprehensive global list of all known plant species, including vascular plants and bryophytes (mosses, liverworts and hornworts). The native flora of Sri Lanka has about 7,000 species of mosses, ferns and flowering plants. Nearly one fourth of the angiosperms of Sri Lanka are endemic and highly concentrated in the humid southwestern quarter of the country, which includes moist low country and the montane zones. Species inventories produced through comprehensive biodiversity surveys are essential to discover undetected biodiversity. The task of documentation and organization of biodiversity today is largely a task assigned to systematists including phylogenetisits and evolutionary biologists. We have recently conducted a compressive floristic survey on montane forests in Sri Lanka; some of these areas have remained unexplored for hundreds of years. Floristic inventories conducted in Piduruthalagala, Namunukula, Kikiliyamana and Adam’s Peak mountains have resulted in the discovery of at least one new species, brought to light that three (03) species recorded as probably extinct were re-discovered and found over 20 critically endangered plants. Quantitative floristic surveys of these montane forests further revealed some important findings on floristic structure and richness and community assemblages addressing both species richness (alpha diversity) and habitat heterogeneity (beta diversity). Information on beta diversity is important when developing multiple-use management plans because most of the endemic plant species have restricted habitats.
When addressing species discoveries we cannot overlook DNA barcoding. Today, DNA barcodes are becoming an integral tool for the identification of species and for understanding the evolutionary and ecological relationships and then documenting biodiversity. In this procedure species identification is performed using DNA sequences from a small fragment of the genome, with the aim of contributing powerfully to taxonomic and biodiversity research. Although it is extraordinary contentious to define a species and delimit a species, it is still vital to discover species and document them accurately. Species richness provides a more practical metric for distinguishing habitats and monitoring ecosystem’s health. They are the fundamental natural unit of biodiversity. The majority of the studies relating to taxonomy, physiology, biochemistry and population dynamics are conducted at the species level. Species discoveries are important to understand how human activities that destroy ecosystems at an ever increasing rate and the impacts on extinction.

Use of the phylogenetic species concept

When describing and naming new taxa, traditionally taxonomists played the major role while at present phylogenetists have become increasingly involved in this process. The phylogenetic species concept defined a species is the least inclusive taxon recognized in a formal phylogenetic classification. Monophyly is the basic idea behind the phylogenetic species concept and it has been assumed that, the populations of each species should share a common ancestor. This is the underlying theory of ‘Cladistics’ and now we often use this concept to discover and delimit species by creating phylogenetic trees. The phylogenetic species concept has been used to recognize most of the new species in well worked or working taxa and directly determines the evolutionary history that we seek to preserve. This concept can be used across the domains of life to detect species and record them in a diverse array of fields, not only in the field of biodiversity. A recent research on the Colletotrichum leaf disease in rubber in Sri Lanka has recorded for the first time that C. simmondsii, C. nymphaeae, C. laticiphilum and C. citri belonging to the C. acutatum complex as the causative organisms in Sri Lanka. Here we have used three gene regions to discover these new records to Sri Lanka. A preliminary study conducted on Sri Lankan Garcinia revealed that the vegetative morphological characters were useful to detect species limits and these results have been successfully used to develop a field identification key. Numerous detailed phylogenetic studies performed using combination of several genes or DNA regions and non-coding regions have provided more insights to phylogenetic reconstruction at different taxonomic levels i.e. family or generic level classifications and revealed more specific information about today’s biodiversity. A combination of five gene regions provided a clear understanding of the family, Phyllanthaceae and which was used in producing the fully revised phylogenetic classification for this taxonomically complex pantropical plant family. In that study we favor the inclusion of four other plant genera (Breynia, Glochidion, Phyllanthodendron, Recherchonia and Sauropus) to the large genus Phyllanthus and presently the monophyletic genus Phyllanthus comprises an estimated 1200 species or more, making it one of the ‘giant’ plant genera among the angiosperms. These findings further offer opportunities to discover phylogenetic affiliations and the placements of several enigmatic species. Andrachne cuneifolia a rare endemic of the serpentine and limestone floras of the Caribbean and a globally threatened species is a good example. Here we showed clearly this taxon belongs to the genus Phyllanthus, subgenus Xylophylla and the species was determined as Phyllanthus cuneifolius (Britton) Croizat. More significant findings are now emerging from, native Sri Lankan flora through some of our collaborative research work. A phylogenetic study conducted on Sri Lankan bamboo using multiple chloroplast DNA sequences supported Kuruna, a new temperate woody bamboo (Poaceae, Bambusoideae) genus from Sri Lanka. This genus represents the twelfth major lineage of temperate woody bamboos in the global phylogeny and is well distinguished by vegetative and reproductive characters. This study tested the monophyly of Sri Lankan temperate woody bamboos, placed them in the correct genus and performed a taxonomic revision for this group including a newly described bamboo species Kuruna serrulata recorded from the Hadapan Ella in Sri Lanka. Today, cryptic species (two or more distinct species, morphologically indistinguishable and classified as a single species) complexes in most types of organisms and habitats from deep sea to arctic plants have newly discovered and eventually incorporated to biodiversity at an increasing rate providing openings to study speciation mechanisms and conservation management.
For past 2-3 decades DNA sequencing data together with the phylogenetic approach have opened up new horizons in species discovery and biodiversity conservation. However, now we are in a transforming era of DNA sequencing technologies. High-throughput genomic sequencing revolutionized our understating on all types of biodiversity studies from phylogenomics, systematics, barcoding, population genetics and ecological research. As detailed above phylogenetic understanding contributes greatly to discover, describe and organize knowledge on biodiversity and these advances largely improve the science of biogeography and ecology.

Drivers of diversification and evolutionary patterns

The biodiversity that we see today is a product of past evolutionary processes. The future of the biodiversity largely also depends on contemporary evolution. Therefore, phylogenetic and evolutionary studies will definitely facilitate the prediction of the responses of biodiversity to changing environments. Phylogeneticists seek to uncover the possible mechanisms that have driven evolutionary radiation; character changes, climate changes or the spread of lineages to new areas. An enormous amount of phylognetic and biogeographic data are now available to investigate the processes driving species diversity. These studies on plants and animals demonstrate that tropical regions promoted diversification for almost all groups of organisms, due to the large extent of tropical environments, together with greater climatic stability. Dated and interspecies and broad scale phylogenies provide more conclusive results about the rate of evolution and species extinctions, patterns of diversification and the nature of radiation. Intraspecific phylogeographical studies have begun to complement this picture at much finer temporal and spatial scales. Detail phylogenetic analyses clearly show that, at present, the loss of biodiversity is mainly focused on large, long-lived, slowly reproducing taxa, having specialized habitats and high endemism. These trends suggest that widespread weed species will dominate while specialized adaptations are being lost rapidly. Biologists show a greater concern for the reasons that have led to species diversification and the conservation of rare species and endemics, especially those areas that have been marked as global biodiversity ‘hotspots’ as they can conserve a larger proportion of the planet’s biodiversity. Apart from the above applications of phylogenetics, there is a growing interest that reveals major ecological niches are more conserved through evolutionary history, thus integrating phylogenetic data into studies of community assembly and structure. Phylogenetic niche conservation concept is studying the trends of species to either maintain or shift their ecological niches. These tendencies have an impact on phylogenetic composition of both local communities and on regional species pools. Phylogenetic relatedness of communities is now studied in detail and used to infer the relative importance of habitat filtering, competitive interactions etc. These findings demonstrate that adaptations to climate change have not readily been accomplished in all plant lineages.
Another collaborative research project is progressing and involves the use of an integrated approach to understand the drivers of diversification of the angiosperm genus Memecylon in the family Melastomataceae. Memecylon has about 400 species distributed widely in the Old World
tropics occupying a variety of habitats. The high proportion of Memecylon species are regional endemics. In this project we are using the next generation sequencing (NGS) technique and attempt to produce the robust dated global molecular phylogeny for Memecylon including Sri Lankan Memecylon species and use the results for an ancestral area reconstruction. Results revealed that Memecylon originated most likely in Africa followed by migrations into South and Southeast Asia. In the same study we test the Sri Lankan Memecylon for Ecological Niche Modelling using geo-reference data and climatic variables for narrow endemic, wide endemic, and non-endemic species. Niche suitability was tested for Sri Lankan species and projections were made for 2070 and this shows that there is a reduction of suitable habitats. Here we successfully integrate detail phylogenetic studies, ancestral reconstruction with niche modeling to uncover the drivers of diversification of this plant group and predict the niche suitability in present and future. Patterns of diversification in this type of species-rich clades provide insight into the processes that generates biological diversity. These studies highlight the significance of phylogenetic knowledge together with historical biogeography in elucidating global biodiversity patterns. They also have implications for the future of biodiversity.

Phylogenetic diversity as a measure of biodiversity

Phylogenetic diversity (PD) in general is a biodiversity measure based on evolutionary relationships between species and represents one of the components of biodiversity. The whole idea was to integrate information on the phylogenetic positions of species and the evolutionary processes (e.g., speciation, radiation) into conservation. Feature diversity refers to the relative number of different features represented among species or other taxa. The phylogenetic diversity measure provides a way to measure biodiversity at the level of features. The feature diversity of species and communities is difficult to estimate directly, but can be predicted by the phylogenetic relationships among the species. Following that the PD of a set of species is simply the sum of the phylogenetic branch-lengths among those species in order to predict underlying patterns of diversity, frequently defined by geographical proximity. Phylogenetic diversity captures the shared ancestry of species, and is increasingly being recognized as a valuable conservation measure. Simply put, the total number of species in a given locality is a poor indicator of PD. However, regionally, PD frequently correlated closely with species richness. Variation in speciation events and extinction rates and the biogeographic history of lineages can result in significant deviations. Using PD, we can identify sets of species / areas that maximize evolutionary potential. PD is considered as a promising measure to assess the biodiversity, but is yet ambiguous. It can be related to processes such as extinction, biotic invasion, ecosystem functioning, and even ecosystem services. The ‘Rarity concept’ in terms of PD is ‘phylogenetic rarity’, which can be measured as uniqueness or phylogenetic distinctiveness. The extinction of a highly distinct species from an old and species-poor clade has a higher impact on biodiversity. It might also stir contradictory questions as to whether the ‘hotspots’ which are the centers of endemism might also be the centers for high levels of PD. It is argued that phylogenetically distinct species are likely to also have distinct functional traits and therefore PD can be used as a proxy for functional diversity.
From a community perspective, there are studies indicating that an increase in PD of a community increases the evolutionary potential to adapt to environmental changes. Today we are well aware that when conserving biodiversity it is necessary not only to maximize the number of taxa that are conserved, but also that we should aim at conserving sets of species that include as much ‘evolutionary history’ as possible in order to guarantee the maintenance of high levels of biological diversity. Limited resources for conservation highlight the need for placing priorities on species or other taxa. Consequently, applications of PD-based measures include the identification of key biodiversity sites of global significance for biodiversity conservation because it better reflects the diversity of unique traits that might exist within an area.

Synopsis and looking into future

Biodiversity is a complex multidimensional concept that includes scales in space and time, and entities such as species, traits, evolutionary units and phylogenetic relationships are a few of these. Recent research on biodiversity mainly focused on community assembly and phylogenetic-based determinants of biodiversity and shifted the emphasis away from simple measures of species diversity. Broadly, it is clear that biologists have been interested in the phylogenetic component of biodiversity for two main reasons: i) to explicitly incorporate species differences, rather than merely species numbers, into conservation prioritization and ii) to provide insight into the structure, and distribution patterns of ecological communities. In summary, here I attempted to explain the importance of phylogenetics in conserving biodiversity, specifically, discovering and detecting biodiversity, the use of the phylogenetic species concept, understanding the drivers of diversification and evolutionary patterns and the use of phylogenetic diversity as a measure of biodiversity. The advent of novel next-generation sequencing (NGS) technologies provides the opportunity to greatly scale up the numbers of individuals, populations and species sampled, potentially merging intraspecific and interspecific approaches to phylogenetic inferences and immensely contribute to biodiversity conservation. Integrative approaches incorporating evolution and phylogenetics could aid in decision making, even while much of the biodiversity still remains unknown and undescribed. Synthesizing findings on patterns of species distribution, traits, and phylogenetic diversity could open up a range of new questions; the answers to which are essential in order to understand the future of biodiversity in terms of changes in ecosystem function and losses of evolutionary history. The basic premise is that phylogenies provide new approaches to quantify and understand biodiversity through inferring evolutionary and ecological patterns and processes of biodiversity. In the future more accurate and specific data will be available for most of the lesser known taxa. Most of the conservation options and priorities will drive towards maximizing phylogenetic history, and preserving the tree of life.