Removal of a strong selective pressure allows for modification of traits previously requisite for survival, which may enable species to take advantage of new ecological opportunities. Globally many traits shared by grasses are a byproduct of strong selection due to mammalian herbivores and fire, including nondehiscence of senesced leaves. We used two genera of grasses (Danthoniiae), Chionochloa and Rytidosperma, that have radiated in New Zealand in the absence of mammalian herbivory and low fire frequency and have unusually high proportions (>50%) of species with dehiscent leaves to examine the ecological consequences of novel growth strategies. We integrate phylogenetic, niche modelling, and common garden studies to understand the evolutionary, biogeographic, and physiological consequences of leaf dehiscence. The Chionochloa and Rytidosperma phylogenies show a complex pattern of the development of dehiscence, with multiple lineages developing leaf dehiscence and several species or subspecies showing reversion to non-dehiscent states. Ecologically, the non-dehiscent species have broader physiological and geographical niches, likely representing continued adaptations to ancestral New Zealand habitats, while dehiscent species have narrower and distinctive niches in colder and wetter habitats. Both modelling and laboratory studies show that dehiscent species are more low temperature adapted than non-dehiscent species. Additionally, dehiscent species have lower quality leaves for herbivores, based on stoichiometry and silica content, suggesting that invertebrate and avian herbivory may have also been an important evolutionary factor in leaf-level traits in these genera. Both dehiscent and nondehiscent species have similar sensitivity to shading. Our results indicate that dehiscence evolved as species changed their defence strategies and allowed species to respond to the new ecological opportunity presented with the appearance of cold, wet alpine environments in the Pliocene-Pleistocene.

Genera with species of multiple ploidy levels provide models to understand successive rounds of whole genome duplication leading to intricate reticulate relationships of polyploid plant species. Here, we studied 17 polyploid taxa (species, subspecies, or varieties) in Azorella (Apiaceae) sections Schizeilema and Stilbocarpa that are mostly endemic to New Zealand. Using phylogenomic approaches, our goals were to resolve species relationships, determine the origins of the higher-level polyploids (6x and 10x), and assess the biogeography of the New Zealand Azorella species. Phylogenomic analysis of Anigosperms353 baits-captured Hyb-Seq data, together with comparison of phylogenies reconstructed using genome-skimming retrieved nrDNA and plastome sequences, showed that species diversification within New Zealand may relate to multiple origins from South America, which has been further shaped by additional rounds of polyploidy as well as hybridization or introgression. The two Azorella sections in New Zealand likely resulted from different biogeographic events from South America - one to the subantarctic islands (section Stilbocarpa) and a second to the South Island (section Schizeilema). In addition, within section Schizeilema, species have dispersed from the South Island (New Zealand) to Australia, the subantarctic islands, and the North Island (New Zealand). Our combined approach of phylogenomic analyses of plastome and nuclear locus-based data, together with SNP-based network approaches allowed us to determine the origins of some higher-level polyploids in New Zealand Azorella and revealed a more complex picture of historical and ongoing polyploidy and hybridization within these lineages.

Ecosourcing seed of 'local genetic stock' for ecological restoration has been practiced in New Zealand for about 50 years. However, we believe that it has become unnecessarily restrictive. Ecosourcing ensures plants used for restoration are adapted to local conditions and maintains current distributional patterns. It also restricts genetic diversity, confines species to their historic range, and reduces the conservation options for threatened species. For example, New Zealand tree species, the life form most frequently used in restoration plantings, have low population genetic differentiation and high net migration of alleles throughout their range. Therefore, very little is gained through restrictive ecosourcing of tree seed. Furthermore, avoidance of the danger of inbreeding depression and widening the scope for closer environmental matching, argues for larger rather smaller source areas. Climate change, extinctions across multiple trophic levels, habitat loss and fragmentation, spread of invasive species, and novel habitats have completely altered the contemporary biotic landscape. Conservation needs to engage with these changes if it is to protect and restore ecosystems. Restrictive ecosourcing is counter-productive as it limits utilising genotypic, phenotypic and ecotypic diversity, and thus the evolutionary potential of indigenous species and ecosystems. It also reduces opportunities to protect biodiversity when populations are small, and limits response to climate change. A new approach is needed. We recommend that phylogeographic patterns and biogeographic boundaries be used to set nine broad ecosourcing regions and, within these regions, phenotypic adaptation to particular environments be used as a guide to seed selection. This more relaxed approach to ecosourcing will improve restoration outcomes through increasing species and genetic diversity, reducing the detrimental effects of inbreeding and promoting the genetic rescue of populations of threatened species. Examples of adopting an eco-evolutionary approach to ecosourcing are provided for the early-successional coloniser Kunzea ericoides and late-successional conifer species.

Past climate changes have had large impacts on modern ecological patterns. Understanding if legacies are distinguishable in the climatic niches of extant and locally extinct taxa can provide insight into the importance of climate in extinction events. To better understand mid- to late-Cenozoic New Zealand plant extinctions, which are often attributed to Cenozoic climate cooling, we identify 13 con-familial extinct and extant New Zealand genus pairs, which have modern distributions in Australia. Using climatic niches derived from current geographic distributions in Australia, we compared (i) total niche breadth, (ii) niche overlap, and (iii) individual climate parameters, to investigate potential climate drivers of intrafamilial extinction and persistence patterns in New Zealand. A majority of New Zealand extinct genera (9 out of 13 pairs) do not indicate climate niche legacies consistent with susceptibility to extinction from changing climates, while the remaining four extinct/extant pairs show slight climatic niche legacies. Three extinct genera have warmer niches than their extant counterpart, which is consistent with extinction reflecting intolerance of cooling Cenozoic climates. The other genus pair with a climatic niche legacy has an extinct genus that is distinguished by a niche with smaller precipitation seasonality than its extant counterpart, suggesting that climate metrics other than temperature may also be important extinction drivers in some taxa. Our results show that the mechanisms of Cenozoic extinctions of New Zealand genera are likely more complex than taxa reaching environmental tolerances due to cooling climates. Comparisons of current climatic niches between extant and extinct sister taxa can provide useful insights into large-scale, long-term climatic legacies but more analyses, including trait and phylogeographic patterns, would lead to additional insights into alternative pathways of extinction.

Toothed leaf margins are common (∼36%) in the New Zealand indigenous flora, and are most abundant in cool forests with high rainfall. Toothed margins are often associated with hydathodes, specialised structures that release water and solutes to maintain positive xylem pressure. However, the presence of hydathodes is mainly known from herbaceous plants. Here we investigate the presence and morphology of hydathodes in indigenous woody species representing 25 families, 33 genera and 57 species, with toothed and entire leaf margins. We tested whether toothed leaf margins on predominantly evergreen species are associated with hydathodes. Two types of structures on leaves were recognised: laminar hydathodes, water pores larger than normal stomata and associated with veins, and hydathodes positioned at the terminus of leaf teeth serviced by principal veins. Laminar hydathodes occur more frequently, but not exclusively, on toothed leaves (on 61.8% of toothed species vs. 48.0% of entire-margined species). Leaf tooth hydathodes are complex structures with undifferentiated, porous tissue plugs linked to splayed vein termini of vessel elements and often form a distinctive cap on leaf teeth. Tooth hydathodes occur on ∼90% of the serrated leaves species sampled. Ontogenetic differences in hydathode occurrence were noted in Alectryon excelsus as leaf morphology changes with plant age from a serrated to a non-serrated form. Quintinia acutifolius showed a similar pattern between individuals with different leaf morphologies. In our sampled dataset, tree species with any type of hydathode occur in areas with a higher ratio of rainfall to potential evapotranspiration than tree species without hydathodes. This pattern was not observed in shrubs. The strong association between marginal hydathodes and toothed leaves in New Zealand trees, plus the association with higher rainfall environments, suggests that these structures function to release hydraulic water pressure in plants on periodically saturated soils in high rainfall zones.

The order Mycocaliciales (Ascomycota) comprises fungal species with diverse, often highly specialized substrate ecologies. Particularly within the genus Chaenothecopsis, many species exclusively occur on fresh and solidified resins or other exudates of vascular plants. In New Zealand, the only previously known species growing on plant exudate is Chaenothecopsis schefflerae, found on several endemic angiosperms in the family Araliaceae. Here we describe three new species; Chaenothecopsis matai Rikkinen, Beimforde, Tuovila & A.R. Schmidt, C. nodosa Beimforde, Tuovila, Rikkinen & A.R. Schmidt, and C. novae-zelandiae Rikkinen, Beimforde, Tuovila & A.R. Schmidt, all growing on exudates of endemic New Zealand conifers of the Podocarpaceae family, particularly on Prumnopitys taxifolia. Phylogenetic analyses based on ribosomal DNA regions (ITS and LSU) grouped them into a distinct, monophyletic clade. This, as well as the restricted host range, suggests that all three taxa are endemic to New Zealand. Copious insect frass between the ascomata contain ascospores or show an early stage of ascomata development, indicating that the fungi are spread by insects. The three new species represent the first evidence of Chaenothecopsis from any Podocarpaceae species and the first from any gymnosperm exudates in New Zealand.

Aim How mountains accumulate species diversity remains poorly understood, particularly the relative role of in situ cladogenesis compared with colonization from lower elevations. Here, we estimated the contributions of in situ cladogenesis and colonization in generating biodiversity of a large mountain plant radiation and determined the importance of niche adaptation and divergence in these processes. We expected cladogenesis would accompany novel habitats formed by mountain uplift, but colonization would become more important with time as dispersal opportunities accrue.Location New Zealand, Southern Alps.Taxon Veronica sect. Hebe (Plantaginaceae).Methods We estimated the most complete time-calibrated phylogeny to date for Veronica sect. Hebe to quantify rates of in situ cladogenesis and colonization of mountain habitat based on historical biogeographical models. We used environmental niche modelling to quantify species' climate niches and estimate niche disparity and divergence over time.Results In situ cladogenesis generated more species in the mountains than colonization from lowlands. Whereas cladogenesis slowed over time, colonization increased, especially in the alpine zone. Both adaptive ecological speciation along climate niche axes and non-adaptive, vicariant speciation contributed to cladogenesis. However, climate niche disparity through time became saturated, suggesting competition for niche space was important. Colonization brought more divergent species into mountain niches.Main Conclusions We suggest mountain diversity accumulates through three main stages: high cladogenesis after initial colonization, decreasing cladogenesis with increasing competition and increasing colonization after niches saturate, likely promoted by niche divergence. Combining lineage and mountain uplift trajectories, these stages provide a conceptual model to understand how diversity accumulates elsewhere. Assuming these deep-time findings apply to anthropogenic conditions, alpine specialists could struggle to outcompete colonizers facilitated by climate change, especially from generalist clades. Considering novel competitive interactions alongside niche traits and biogeographical processes will be crucial for predicting the fate of alpine biodiversity in a changing world.

All organisms must simultaneously tolerate the environment and access limiting resources if they are to persist. Otherwise they go extinct. Approaches to understanding environmental tolerance and resource competition have generally been developed independently. Consequently, integrating the factors that determine abiotic tolerance with those that affect competitive interactions to model species abundances and community structure remains an unresolved challenge. This is likely the reason why current models of community assembly do not accurately predict species abundances and dynamics. Here, we introduce a new synthetic framework that models both abiotic tolerance and biotic competition by using functional traits, which are phenotypic attributes that influence organism fitness. First, our framework estimates species carrying capacities that vary along abiotic gradients based on whether the phenotype tolerates the local environment. Second, it estimates pairwise competitive interactions as a function of multidimensional trait differences between species and determines which trait combinations produce the most competitive phenotypes. We demonstrate that our combined approach more than doubles the explained variance of species covers in a wetland community compared to the model of abiotic tolerances alone. Trait-based integration of competitive interactions and abiotic filtering improves our ability to predict species abundances across space, bringing us closer to more accurate predictions of biodiversity structure in a changing world.

Includes alignments and trees for the analysis found in Thomas et al. 2021, Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica; American Journal of Botany, Special Issue: Exploring Angiosperms353: a Universal Toolkit for Flowering Plant Phylogenomics. Alignments comprise subsets of Angiosperms353 genes given each filtering scheme (full, intersection, sortadate_BP, sortadate_TL) and gene type/subset (exons, introns, supercontigs), and for markers downloaded from GenBank, as explained in the Methods section of Thomas et al. 2021. Trees were included for each of these alignments from IQtree and Astral; SVDquartets tree was only estimated for the full set of supercontigs. Gene trees were generated with IQtree. Tree files are named differently than the final manuscript; refer to the number of genes specified in Fig 1 of Thomas et al, 2021 and specified in each filename to identify filtering scheme. Raw sequence reads are available on the Sequence Read Archive at http://www.ncbi.nlm.nih.gov/bioproject/715342.

Quantitative leaf mass per area reconstructions and prevalence of plicate vernation in broad-leaved Nothofagaceae fossils reveal that deciduousness was common in the middle to late Miocene of New Zealand. This functional type was subsequently lost, as modern-day New Zealand Nothofagaceae have small leaves that live for at least a year. Moreover, fully deciduous trees across all plant families are rare in the current New Zealand flora. Based on modern-day distribution in the Southern Hemisphere, broad-leaved deciduous Nothofagaceae occupy regions with consistently large seasonal differences in precipitation and cloud cover, relative to other functional types in the family (evergreen, small-leaved). Specifically, broad-leaved deciduous Nothofagaceae are in leaf in summer when cloud cover and precipitation are low, but are leafless in winter when cloud cover and precipitation is high. Notably, the seasonal difference in precipitation and cloud cover are more important in explaining deciduousness in Nothofagaceae than winter temperatures. Therefore, potential summer photosynthetic gains likely determine deciduousness in Nothofagaceae. Miocene palaeoclimate reconstructions reveal that New Zealand broad-leaved deciduous Nothofagaceae also thrived in a climate with larger seasonal precipitation differences than today, in an overall warmer climate. We suggest that deciduous Nothofagaceae in the New Zealand flora went extinct as the global climate cooled and summer photosynthetic gains diminished, as summers became progressively rainier and cloudier, favoring an evergreen habit.

Diversification of woody plant lineages in New Zealand has unfolded in complex physiographic, climatic, and environmental contexts. Many tree and shrub lineages have existed in New Zealand since the late Cenozoic when Forest was the dominant biome, subsequently diversifying (or continuing to diversify) during the Pliocene/Pleistocene as Open (below treeline) and Alpine biomes emerged. We examine the links between biomes occupied, traits, and diversification. In particular, whether traits are phylogenetically conserved or ecologically constrained and their relationship to biomes occupied. We focus on Melicytus, Myrsine and Pseudopanax which occur across Forest, Open, and Alpine biomes. Our approach combines measured traits and modelled niche traits of extant species to examine the importance of biome occupancy and biome shifts on trait evolution in these lineages. Our results demonstrate trait values are filtered by biomes in these lineages and can predict biomes occupied. However, few biome shifts were associated with trait evolution, typically only biome shifts into extreme environments (Alpine) involved trait innovations. In addition to biomes, trait evolution can also be influenced by species age, trait lability and broad climatic change. Integrating functional traits in a phylogenetic framework can identify how evolutionary and ecological features create modern biogeographic patterns in New Zealand.

Correlations of non-monocot woody angiosperm leaf traits to macroclimate are often used to reconstruct terrestrial paleoclimate under the assumption that macroclimate correlates with leaf phenotype are globally uniform, regardless of evolutionary history. Here, we evaluate if global trends in leaf trait variation with macroclimate are observed in the predominantly evergreen indigenous flora of New Zealand. A dataset of 557 indigenous woody dicot species and over 100,000 occurrences was employed to investigate community-level relationships of four leaf characters (leaf pubescence, margin teeth, area and length-to-width ratio) with geographic variation in temperature, precipitation, water deficit and solar radiation. Leaf area and the frequency of toothed leaves decline at higher latitudes in New Zealand. Variation in leaf pubescence and leaf teeth is associated primarily with measures of water availability, such as annual rainfall and annual water deficit; whereas leaf size is associated primarily with temperature. Variation in leaf length-to-width ratio was weakly correlated to climate parameters. The New Zealand relationship of leaf area with temperature aligns with global patterns, highlighting the importance of small leaves in limiting night-time chilling. The global negative correlation of leaf teeth with temperature is apparent in New Zealand trees and vines, but not in shrubs or all woody dicots combined. However, the primary correlate of leaf teeth in New Zealand is water availability, showing that the response of this trait to macroclimate is not globally uniform. The high occurrence of pubescent leaves in low rainfall and drought-prone environments in New Zealand suggests that the trait is associated with water retention in drier climates.

Biome conservatism is often regarded as common in diversifying lineages, based on the detection of low biome shift rates or high phylogenetic signal. However, many studies testing biome conservatism utilise a single-biome-per-species approach, which may influence the detection of biome conservatism. Meta-analyses show that biome shift rates are significantly lower (less than a tenth), when single biome occupancy approaches are adopted. Using New Zealand plant lineages, estimated biome shifts were also significantly lower (14–67% fewer biome shifts) when analysed under the assumption of a single biome per species. Although a single biome approach consistently resulted in lower biome shifts, it detected fewer instances of biome conservatism. A third of clades (3 out of 9) changed status in biome conservatism tests between single and multiple biome occupancy approaches, with more instances of significant biome conservatism when using a multiple biome occupancy approach. A single biome approach may change the likelihood of finding biome conservatism because it assumes biome specialisation within species, falsely recognises some biome shift types and fails to include other biome shift types. Our results indicate that the degree of biome fidelity assumed has a strong influence on analyses assessing biome shift rates, and biome conservatism testing. We advocate analyses that allow species to occupy multiple biomes.