No abstract

Phylogenetics has become a powerful tool in many areas of biology. Land plants are the most important primary producers of terrestrial ecosystems and have colonized various habitats on Earth. In the past two decades, tremendous progress has been made in our understanding of phylogenetic relationships at all taxonomic levels across all land plant groups by employing DNA sequence data. Here, we review the progress made in large-scale phylogenetic reconstructions of land plants and assess the current situation of phylogenetic studies of land plants. We then emphasize directions for future study. At present, the phylogenetic framework of land plants at the order and familial levels has been well built. Problematic deep-level relationships within land plants have also been well resolved by phylogenomic analyses. We pointed out five major aspects of molecular phylogenetics of land plants, which are nowadays being studied and will continue to be goals moving forward. These five aspects include: (1) constructing the genus- and species-level phylogenies for land plant groups, (2) updating the classification systems by combining morphological and molecular data, (3) integrating fossil taxa into phylogenies derived from living taxa, (4) resolving deep-level and/or rapidly divergent phylogenetic relationships using phylogenomic data, and (5) building big trees using the supermatrix method. We hope that this review paper will promote the development of plant molecular phylogenetics and other related areas.

Phylogenetic analyses can provide an accurate identification for endangered species, which is a prerequisite for their conservation. Understanding how threats shape the current realized niche of declining species can effectively improve conservation policies. In this study, we used molecular data to identify the real Eleutharrhena macrocarpa, a critically endangered species in Yunnan, China. A niche reduction approach was used to model its range change by predicting the historic and current distributions. Our subfamily-wide phylogenetic analyses based on five plastid DNA regions indicate that the E. macrocarpa with pinnate-nerved leaves is real and is a member of Tiliacoreae, whereas the so-called E. macrocarpa with triplinerved leaves is actually Haematocarpus subpeltatus, which is for the first time reported to be distributed in China. Our subsequent analyses of Tiliacoreae using seven plastid and two nuclear DNA regions further support Eleutharrhena as a distinctly monotypic genus and as sister to Pycnarrhena. Among the four prevalent barcodes in plants, three plastid DNA fragments (rbcL, matK, trnH-psbA) failed to discriminate E. macrocarpa from Pycnarrhena; however, nuclear ribosomal internal transcribed spacer (ITS) regions could well recognize this endangered species. The distributional range of E. macrocarpa has undergone a dramatic contraction over the last 100 years and may further shrink southwestwards in the future. This dramatic range contraction might be associated with habitat loss due to increasing drought and expansion of rubber plantation. We point out the need for in situ conservation of E. macrocarpa populations, and suggest to establish a large nature reserve in southern and western Yunnan to effectively protect E. macrocarpa and other declining species that exhibit similar distribution and habitat requirements. This study highlights the significance of taxonomy and molecular phylogenetics in biological conservation.