Integrative, next-generation, collaborative vascular plant systematics in New Zealand

Systematics is a synthetic science which focuses on species delimitation, taxonomy, classification, and phylogeny, with an additional aim of understanding underlying evolutionary and biogeographic patterns and processes. Systematic research has many downstream benefits including underpinning conservation management, biosecurity and health.  In this short overview article, I will give a brief synopsis of integrative systematics, in which multiple data sets are used to robustly test species limits in a statistical framework, and illustrate why I think we need integrative systematics in New Zealand. I will then discuss examples from my own systematics research, especially on the flowering plant families Plantaginaceae (Ourisia, Plantago, Veronica) and Boraginaceae (Myosotis), as well as from other vascular plant systematics research being done by colleagues in New Zealand and elsewhere. Through these examples, I will show how using an integrative systematics approach to analysing morphological, molecular, cytological and other data sets can aid species delimitation and new species discovery, and allow inferences into questions regarding such diverse themes as diversification, variability and conservation of threatened species, polyploidy (whole genome duplication) and biogeography of New Zealand vascular plants.  I will also argue that the future of systematics should not only be integrative, but also next-generation and collaborative, and that such forward-looking, cooperative research – and the institutional and governmental investment to support it – is essential for New Zealand

Species delimitation and phylogeny of a New Zealand plant species radiation

<p>Abstract</p> <p>Background</p> <p>Delimiting species boundaries and reconstructing the evolutionary relationships of late Tertiary and Quaternary species radiations is difficult. One recent approach emphasizes the use of genome-wide molecular markers, such as amplified fragment length polymorphisms (AFLPs) and single nucleotide polymorphisms (SNPs), to identify distinct metapopulation lineages as taxonomic species. Here we investigate the properties of AFLP data, and the usefulness of tree-based and non-tree-based clustering methods to delimit species and reconstruct evolutionary relationships among high-elevation <it>Ourisia </it>species (Plantaginaceae) in the New Zealand archipelago.</p> <p>Results</p> <p>New Zealand <it>Ourisia </it>are shown to comprise a geologically recent species radiation based on molecular dating analyses of ITS sequences (0.4–1.3 MY). Supernetwork analyses indicate that separate tree-based clustering analyses of four independent AFLP primer combinations and 193 individuals of <it>Ourisia </it>produced similar trees. When combined and analysed using tree building methods, 15 distinct metapopulations could be identified. These clusters corresponded very closely to species and subspecies identified on the basis of diagnostic morphological characters. In contrast, Structure and PCO-MC analyses of the same data identified a maximum of 12 and 8 metapopulations, respectively. All approaches resolved a large-leaved group and a small-leaved group, as well as a lineage of three alpine species within the small-leaved group. We were unable to further resolve relationships within these groups as corrected and uncorrected distances derived from AFLP profiles had limited tree-like properties.</p> <p>Conclusion</p> <p><it>Ourisia </it>radiated into a range of alpine and subalpine habitats in New Zealand during the Pleistocene, resulting in 13 morphologically and ecologically distinct species, including one reinstated from subspecies rank. Analyses of AFLP identified distinct metapopulations consistent with morphological characters allowing species boundaries to be delimited in <it>Ourisia</it>. Importantly, Structure analyses suggest some degree of admixture with most species, which may also explain why the AFLP data do not exhibit sufficient tree-like properties necessary for reconstructing some species relationships. We discuss this feature and highlight the importance of improving models for phylogenetic analyses of species radiations using AFLP and SNP data.</p

Is genome downsizing associated with diversification in polyploid lineages of Veronica?

[EN] The study of genome size evolution in a phylogenetic context in related polyploid and diploid lineages can help us to understand the advantages and disadvantages of genome size changes and their effect on diversification. Here, we contribute 199 new DNA sequences and a nearly threefold increase in genome size estimates in polyploid and diploid Veronica (Plantaginaceae) (to 128 species, c. 30% of the genus) to provide a comprehensive baseline to explore the effect of genome size changes. We reconstructed internal transcribed spacer (ITS) and trnL-trnL-trnF phylogenetic trees and performed phylogenetic generalized least squares (PGLS), ancestral character state reconstruction, molecular dating and diversification analyses. Veronica 1C-values range from 0.26 to 3.19 pg. Life history is significantly correlated with 1C-value, whereas ploidy and chromosome number are strongly correlated with both 1C- and 1Cx-values. The estimated ancestral Veronica 1Cx-value is 0.65 pg, with significant genome downsizing in the polyploid Southern Hemisphere subgenus Pseudoveronica and two Northern Hemisphere subgenera, and significant genome upsizing in two diploid subgenera. These genomic downsizing events are accompanied by increased diversification rates, but a ‘core shift’ was only detected in the rate of subgenus Pseudoveronica. Polyploidy is important in the evolution of the genus, and a link between genome downsizing and polyploid diversification and species radiations is hypothesized

Polyploidy on Islands: Its Emergence and Importance for Diversification.

Whole genome duplication or polyploidy is widespread among floras globally, but traditionally has been thought to have played a minor role in the evolution of island biodiversity, based on the low proportion of polyploid taxa present. We investigate five island systems (Juan Fernández, Galápagos, Canary Islands, Hawaiian Islands, and New Zealand) to test whether polyploidy (i) enhances or hinders diversification on islands and (ii) is an intrinsic feature of a lineage or an attribute that emerges in island environments. These island systems are diverse in their origins, geographic and latitudinal distributions, levels of plant species endemism (37% in the Galapagos to 88% in the Hawaiian Islands), and ploidy levels, and taken together are representative of islands more generally. We compiled data for vascular plants and summarized information for each genus on each island system, including the total number of species (native and endemic), generic endemicity, chromosome numbers, genome size, and ploidy levels. Dated phylogenies were used to infer lineage age, number of colonization events, and change in ploidy level relative to the non-island sister lineage. Using phylogenetic path analysis, we then tested how the diversification of endemic lineages varied with the direct and indirect effects of polyploidy (presence of polyploidy, time on island, polyploidization near colonization, colonizer pool size) and other lineage traits not associated with polyploidy (time on island, colonizer pool size, repeat colonization). Diploid and tetraploid were the most common ploidy levels across all islands, with the highest ploidy levels (>8x) recorded for the Canary Islands (12x) and New Zealand (20x). Overall, we found that endemic diversification of our focal island floras was shaped by polyploidy in many cases and certainly others still to be detected considering the lack of data in many lineages. Polyploid speciation on the islands was enhanced by a larger source of potential congeneric colonists and a change in ploidy level compared to overseas sister taxa

Polyploidy on Islands: Its Emergence and Importance for Diversification.

Whole genome duplication or polyploidy is widespread among floras globally, but traditionally has been thought to have played a minor role in the evolution of island biodiversity, based on the low proportion of polyploid taxa present. We investigate five island systems (Juan Fernández, Galápagos, Canary Islands, Hawaiian Islands, and New Zealand) to test whether polyploidy (i) enhances or hinders diversification on islands and (ii) is an intrinsic feature of a lineage or an attribute that emerges in island environments. These island systems are diverse in their origins, geographic and latitudinal distributions, levels of plant species endemism (37% in the Galapagos to 88% in the Hawaiian Islands), and ploidy levels, and taken together are representative of islands more generally. We compiled data for vascular plants and summarized information for each genus on each island system, including the total number of species (native and endemic), generic endemicity, chromosome numbers, genome size, and ploidy levels. Dated phylogenies were used to infer lineage age, number of colonization events, and change in ploidy level relative to the non-island sister lineage. Using phylogenetic path analysis, we then tested how the diversification of endemic lineages varied with the direct and indirect effects of polyploidy (presence of polyploidy, time on island, polyploidization near colonization, colonizer pool size) and other lineage traits not associated with polyploidy (time on island, colonizer pool size, repeat colonization). Diploid and tetraploid were the most common ploidy levels across all islands, with the highest ploidy levels (>8x) recorded for the Canary Islands (12x) and New Zealand (20x). Overall, we found that endemic diversification of our focal island floras was shaped by polyploidy in many cases and certainly others still to be detected considering the lack of data in many lineages. Polyploid speciation on the islands was enhanced by a larger source of potential congeneric colonists and a change in ploidy level compared to overseas sister taxa

Travel Tales of a Worldwide Weed: Genomic Signatures of Plantago major L. Reveal Distinct Genotypic Groups With Links to Colonial Trade Routes

Retracing pathways of historical species introductions is fundamental to understanding the factors involved in the successful colonization and spread, centuries after a species’ establishment in an introduced range. Numerous plants have been introduced to regions outside their native ranges both intentionally and accidentally by European voyagers and early colonists making transoceanic journeys; however, records are scarce to document this. We use genotyping-by-sequencing and genotype-likelihood methods on the selfing, global weed, Plantago major, collected from 50 populations worldwide to investigate how patterns of genomic diversity are distributed among populations of this global weed. Although genomic differentiation among populations is found to be low, we identify six unique genotype groups showing very little sign of admixture and low degree of outcrossing among them. We show that genotype groups are latitudinally restricted, and that more than one successful genotype colonized and spread into the introduced ranges. With the exception of New Zealand, only one genotype group is present in the Southern Hemisphere. Three of the most prevalent genotypes present in the native Eurasian range gave rise to introduced populations in the Americas, Africa, Australia, and New Zealand, which could lend support to the hypothesis that P. major was unknowlingly dispersed by early European colonists. Dispersal of multiple successful genotypes is a likely reason for success. Genomic signatures and phylogeographic methods can provide new perspectives on the drivers behind the historic introductions and the successful colonization of introduced species, contributing to our understanding of the role of genomic variation for successful establishment of introduced taxa.publishedVersio

Travel Tales of a Worldwide Weed: Genomic Signatures of Plantago major L. Reveal Distinct Genotypic Groups With Links to Colonial Trade Routes

Retracing pathways of historical species introductions is fundamental to understanding the factors involved in the successful colonization and spread, centuries after a species’ establishment in an introduced range. Numerous plants have been introduced to regions outside their native ranges both intentionally and accidentally by European voyagers and early colonists making transoceanic journeys; however, records are scarce to document this. We use genotyping-by-sequencing and genotype-likelihood methods on the selfing, global weed, Plantago major, collected from 50 populations worldwide to investigate how patterns of genomic diversity are distributed among populations of this global weed. Although genomic differentiation among populations is found to be low, we identify six unique genotype groups showing very little sign of admixture and low degree of outcrossing among them. We show that genotype groups are latitudinally restricted, and that more than one successful genotype colonized and spread into the introduced ranges. With the exception of New Zealand, only one genotype group is present in the Southern Hemisphere. Three of the most prevalent genotypes present in the native Eurasian range gave rise to introduced populations in the Americas, Africa, Australia, and New Zealand, which could lend support to the hypothesis that P. major was unknowlingly dispersed by early European colonists. Dispersal of multiple successful genotypes is a likely reason for success. Genomic signatures and phylogeographic methods can provide new perspectives on the drivers behind the historic introductions and the successful colonization of introduced species, contributing to our understanding of the role of genomic variation for successful establishment of introduced taxa.info:eu-repo/semantics/publishedVersio

Biogeography and systematics of Ourisia (Plantaginaceae)

textThis dissertation examines the biogeography, taxonomy, species relationships, and morphological evolution of the genus Ourisia (Plantaginaceae; Scrophulariaceae s.l.). Ourisia is distributed in subalpine to alpine habitats of South America, New Zealand, and Tasmania. This classic austral biogeographic pattern displayed by numerous extant plants and animals has been attributed to either Gondwanan vicariance or long-distance dispersal. To test these hypotheses for Ourisia, a molecular phylogenetic approach was used to reconstruct the evolutionary history of most species of Ourisia based on two chloroplast and two nuclear DNA markers using parsimony and Bayesian methods. Parametric bootstrapping rejected both the Gondwana biogeographic hypothesis and an Australasian origin for the genus. Instead, Ourisia likely arose in the southern Andes, and subsequently spread to the north-central Andes and to New Zealand and Tasmania via long-distance dispersal. These results corroborate other recent molecular phylogenetic studies that have highlighted the important role of dispersal in the evolutionary history of many other high-elevation plants in the Southern Hemisphere. The molecular phylogeny also elucidated interesting biogeographic trends within both South America and New Zealand, which are discussed in light of the geological history of each region. A detailed morphological study of herbarium specimens resulted in the first comprehensive monograph of Ourisia. Twenty-seven total species were recognized from South America (15), Tasmania (1), and New Zealand (11). A new infrageneric classification for Ourisia was proposed based on habit. The three suffruticose southern Andean species comprise subg. Suffruticosa, while the remaining 24 herbaceous species make up subg. Ourisia. This infrageneric classification contrasts with that of Poeppig and Endlicher, who delimited the two subgenera within Ourisia based largely on calyx symmetry. Separate and combined phylogenetic analyses of 21 morphological characters in addition to the molecular data for 29 of the 33 species and varieties of Ourisia plus the outgroup supported the monophyly and sister relationship of the herbaceous and suffruticose subgenera. Six other morphological characters, including leaf attachment, presence of an inflated hypogynous disc, seed type, ovary vestiture, (internal) calyx vestiture, and inflorescence structure, also support this circumscription. Evolution of these and other characters, in addition to species relationships, were also addressed.Biological Sciences, School o