Phylogenomics and morphology of Celmisiinae (Asteraceae: Astereae): Taxonomic and evolutionary implications.

The tribe Astereae (Asteraceae) includes 36 subtribes and 252 genera, and is distributed worldwide in temperate and tropical regions. One of the subtribes, Celmisiinae Saldivia, has been recently circumscribed to include six genera and ca. 160 species, and is restricted to eastern Australia, New Zealand, and New Guinea. The species show an impressive range of growth habit, from small herbs and ericoid subshrubs to medium-sized trees. They live in a wide range of habitats and are often dominant in subalpine and alpine vegetation. Despite the well-supported circumscription of Celmisiinae, uncertainties have remained about their internal relationships and classification at genus and species levels. This study exploited recent advances in high-throughput sequencing to build a robust multi-gene phylogeny for the subtribe Celmisiinae. The target enrichment Angiosperms353 bait set and the hybpiper-nf and paragone-nf pipelines were used to retrieve, infer, and assemble orthologous loci from 75 taxa representing all the main putative clades within the subtribe. Because of the diploidised ploidy level in Celmisiinae, as well as missing data in the assemblies, uncertainty remains surrounding the inference of orthology detection. However, based on a variety of gene-family sets, coalescent and concatenation-based phylogenetic reconstructions recovered similar topologies. Paralogy and missing data in the gene-families caused some problems, but the estimated phylogenies were well-supported and well-resolved. The phylogenomic evidence supported Celmisiinae and three main clades: the Pleurophyllum clade (Pleurophyllum, Macrolearia and Damnamenia), mostly in the New Zealand Subantarctic Islands, Celmisia of mainland New Zealand and Australia, and Shawia (including 'Olearia pro parte' and Pachystegia) of New Zealand, Australia and New Guinea. The results presented here add to the accumulating support for the Angiosperms353 bait set as an efficient method for documenting plant diversity.

Correlated evolution in an ectomycorrhizal host-symbiont system.

Mechanisms of diversification in fungi are relatively poorly known. Many ectomycorrhizal symbionts show preference for particular host genera or families, so host-symbiont selection may be an important driver of fungal diversification in ectomycorrhizal systems. However, whether ectomycorrhizal hosts and symbionts show correlated evolutionary patterns remains untested, and it is unknown whether fungal specialisation also occurs in systems dominated by hosts from the same genus. We use metabarcoding of ectomycorrhizal fungi collected with hyphal ingrowth bags from Nothofagus forests across southern New Zealand to investigate host-symbiont specialisation and correlated evolution. We examine how ectomycorrhizal communities differ between host species and look for patterns of host-symbiont cophylogeny. We found substantial differences in ectomycorrhizal communities associated with different host taxa, particularly between hosts from different subgenera (Lophozonia and Fuscospora), but also between more closely related hosts. Twenty-four per cent of fungal taxa tested showed affiliations to particular hosts, and tests for cophylogeny revealed significant correlations between host relatedness and the fungal phylogeny that extended to substantial evolutionary depth. These results provide new evidence of correlated evolution in ectomycorrhizal systems, indicating that preferences among closely related host species may represent an important evolutionary driver for local lineage diversification in ectomycorrhizal fungi.

Zeta diversity differentiates factors driving community assembly of rare and common ectomycorrhizal fungi.

A fundamental goal in community ecology is to understand what factors drive community assembly processes. The factors affecting ectomycorrhizal fungal communities are unknown in many regions, particularly in the southern hemisphere. We investigate community assembly using ITS2 metabarcoding of ectomycorrhizal fungi sampled from 3943 hyphal ingrowth bags buried in 81 Nothofagus forests across New Zealand's South Island. By applying zeta diversity analysis and multisite generalized dissimilarity modelling (MS-GDM) we quantify the effects of 43 biotic and environmental variables on community turnover. Unlike traditional beta diversity analyses that are heavily influenced by rare species, the zeta diversity framework differentiates between factors driving turnover of rare and common species, providing a more complete picture of community dynamics. We found that community assembly was dominated by deterministic rather than stochastic processes and identified ecological factors affecting all taxa, as well as others that were specifically important to rare or common taxa. Soil variables were important drivers of turnover for all species, whereas ground cover variables, forest patch size, precipitation and host tree identity had greater effects on rarer species, and tree size and temperature effects were specific to more common species. Interestingly, the effect of temperature on common species is in line with recent evidence from other Kingdoms, pointing to possible generality, and highlighting the importance of considering common species. Applying these methods to fungi has allowed us to identify the distinct ecological processes that structure rare and common taxa during community assembly. This has important implications for understanding the functional effects of community responses to environmental change.

Does Evolutionary History Correlate with Contemporary Extinction Risk by Influencing Range Size Dynamics?

Extinction threatens many species yet is predicted by few factors across the plant tree of life (ToL). Taxon age is one factor that may associate with extinction if occupancy of geographic and adaptive zones varies with time, but evidence for such an association has been equivocal. Age-dependent occupancy can also influence diversification rates and thus extinction risk where new taxa have small range and population sizes. To test how age, diversification, and range size were correlated with extinction, we analyzed 639 well-sampled genera representing 8,937 species from across the plant ToL. We found a greater proportion of species were threatened by contemporary extinction in younger and faster-diversifying genera. When we directly tested how range size mediated this pattern in two large, well-sampled groups, our results varied. In conifers, potential range size was smaller in older species and was correlated with higher extinction risk. Age on its own had no direct effect on extinction when accounting for its influence on range size. In palm species, age was neither directly nor indirectly correlated with extinction risk. Our results suggest that range size dynamics may explain differing patterns of extinction risk across the ToL, with consequences for biodiversity conservation.

Homogeneous environmental selection dominates microbial community assembly in the oligotrophic South Pacific Gyre.

Oligotrophic subtropical gyres are the largest continuous biomes on Earth and play a key role in global biogeochemical cycles. Microbial communities govern primary production and carbon cycling in the oligotrophic South Pacific Gyre, yet the ecological processes which underpin microbial biogeography in the region remain understudied. We investigated microbial biogeography and community assembly processes at three depths over a ~2,000-km the transect was longitudinal, so ran from 32°S, 170°W to 32°S, 152°W). Thus the latitude (32°S) was constant. Microbial communities in the surface waters (15 and 50 m) were remarkably similar across the transect, whilst communities at the deep chlorophyll maximum were distinct from the surface waters and displayed greater compositional heterogeneity. An ecological null model approach indicated that homogeneous selection was the dominant community assembly process in both the surface waters (100%) and at the deep chlorophyll maximum (91.81%), although variable selection (2.34%) and stochastic processes (5.85%) had a minor influence at the deep chlorophyll maximum. Homogeneous selection (76.69%77.90%), dispersal limitation (15.00%-20.05%) and variable selection (3.01%-7.11%) influenced community assembly between the surface waters and the deep chlorophyll maximum. Seawater density and temperature, which were correlated, were the most important environmental modulators of the balance between stochastic and deterministic assembly processes. Our findings demonstrate remarkable similarity in microbial community composition across longitudinal scales in the oligotrophic South Pacific Gyre, underpinned by strong environmental selection which overwhelms the influence of ecological drift. These data significantly advance our understanding of microbial community dynamics in the oligotrophic subtropical gyres which dominate the Earth's surface.

Patterns of Reproductive Isolation in Eucalyptus-A Phylogenetic Perspective.

We assess phylogenetic patterns of hybridization in the speciose, ecologically and economically important genus Eucalyptus, in order to better understand the evolution of reproductive isolation. Eucalyptus globulus pollen was applied to 99 eucalypt species, mainly from the large commercially important subgenus, Symphyomyrtus. In the 64 species that produce seeds, hybrid compatibility was assessed at two stages, hybrid-production (at approximately 1 month) and hybrid-survival (at 9 months), and compared with phylogenies based on 8,350 genome-wide DArT (diversity arrays technology) markers. Model fitting was used to assess the relationship between compatibility and genetic distance, and whether or not the strength of incompatibility "snowballs" with divergence. There was a decline in compatibility with increasing genetic distance between species. Hybridization was common within two closely related clades (one including E. globulus), but rare between E. globulus and species in two phylogenetically distant clades. Of three alternative models tested (linear, slowdown, and snowball), we found consistent support for a snowball model, indicating that the strength of incompatibility accelerates relative to genetic distance. Although we can only speculate about the genetic basis of this pattern, it is consistent with a Dobzhansky-Muller-model prediction that incompatibilities should snowball with divergence due to negative epistasis. Different rates of compatibility decline in the hybrid-production and hybrid-survival measures suggest that early-acting postmating barriers developed first and are stronger than later-acting barriers. We estimated that complete reproductive isolation can take up to 21-31 My in Eucalyptus. Practical implications for hybrid eucalypt breeding and genetic risk assessment in Australia are discussed.

On the persistence of reproductive barriers in Eucalyptus: the bridging of mechanical barriers to zygote formation by F1 hybrids is counteracted by intrinsic post-zygotic incompatibilities.

BACKGROUND AND AIMS: Many previous studies conclude that pre-zygotic barriers such as mechanical isolation account for most reproductive isolation between pairs of taxa. However, the inheritance and persistence of barriers such as these after the first generation of hybridization is rarely quantified, even though it is a vital consideration in understanding gene flow potential. There is an asymmetrical pre-zygotic mechanical barrier to hybridization between Eucalyptus nitens and Eucalyptus globulus, which completely prevents small-flowered E. nitens pollen from mating with large E. globulus flowers, while the reverse cross is possible. We aimed to determine the relative importance of pre- and post-zygotic barriers in preventing gene flow following secondary contact between E. nitens and E. globulus, including the inheritance of barriers in advanced-generation hybrids. METHODS: Experimental crossing was used to produce outcrossed E. nitens, E. globulus and their F1, F2, BCg and BCn hybrids. The strength and inheritance of a suite of pre- and post-zygotic barriers were assessed, including 20-year survival, growth and reproductive capacity. KEY RESULTS: The mechanical barrier to hybridization was lost or greatly reduced in the F1 hybrid. In contrast, intrinsic post-zygotic barriers were strong and persistent. Line-cross analysis indicated that the outbreeding depression in the hybrids was best explained by epistatic loss. CONCLUSIONS: The removal of strong mechanical barriers between E. nitens and E. globulus allows F1 hybrids to act as a bridge for bi-directional gene flow between these species. However, strong and persistent post-zygotic barriers exist, meaning that wherever F1 hybridization does occur, intrinsic post-zygotic barriers will be responsible for most reproductive isolation in this system. This potential transient nature of mechanical barriers to zygote formation due to additive inheritance in hybrids appears under-appreciated, and highlights the often important role that intrinsic post-mating barriers play in maintaining species boundaries at zones of secondary contact.

Transient hybridization, not homoploid hybrid speciation, between ancient and deeply divergent conifers.

PREMISE OF THE STUDY: Homoploid hybrid speciation is receiving growing attention due the increasing recognition of its role in speciation. We investigate if individuals intermediate in morphology between the two species of the conifer genus Athrotaxis represent a homoploid hybrid species, A. laxifolia, or are spontaneous F1 hybrids. METHODS: A total of 1055 individuals of Athrotaxis cupressoides and A. selaginoides, morphologically intermediate individuals, and two putative hybrid swarms were sampled across the range of the genus and genotyped with 13 microsatellites. We used simulations to test the power of our data to identify the pure species, F1s, F2s, and backcross generations. KEY RESULTS: We found that Athrotaxis cupressoides and A. selaginoides are likely the most divergent congeneric conifers known, but the intermediates are F1 hybrids, sharing one allele each from A. cupressoides and A. selaginoides at six loci with completely species specific alleles. The hybrid swarms contain wide genetic variation with stronger affinities to the locally dominant species, A. selaginoides and A. selaginoides backcrosses outnumbering A. cupressoides backcrosses. In addition, we observed evidence for isolated advanced generation backcrosses within the range of the pure species. CONCLUSIONS: We conclude that, even though they can be large and long-lived, Athrotaxis hybrid swarms are on a trajectory of decline and will eventually be reabsorbed by the parental species. However, this process may take millennia and fossil evidence suggests that such events have occurred repeatedly since the early Quaternary. Given this timeline, our study highlights the many obstacles to homoploid hybrid speciation.

Trophic facilitation in forest restoration: Can Nothofagus trees use ectomycorrhizal fungi of the pioneer shrub Leptospermum?

The benefits of plant-to-plant facilitation in ecological restoration are well recognized, yet the potential for indirect trophic facilitation remains understudied. Nothofagus (southern beech; Nothofagaceae) is an iconic southern hemisphere tree genus that is frequently the focus of ecological restoration efforts. One aspect of Nothofagus ecology that may limit restoration success is the availability of appropriate ectomycorrhizal fungi. It has been suggested that pioneer dual-mycorrhizal hosts such as Leptospermum species (Myrtaceae) could facilitate Nothofagus establishment by providing fungal inoculum, but the capacity for Nothofagus to use Leptospermum ectomycorrhizal fungi is unknown. To investigate potential indirect facilitation, we conducted a common garden pot trial to determine if Nothofagus cliffortioides (mountain beech) can use symbionts from Leptospermum scoparium (manuka) ectomycorrhizal communities. Nothofagus and Leptospermum seedlings were grown in monoculture and mixed pairs with reciprocal "home" and "away" soil fungal inoculum. ITS2 metabarcoding of eDNA from hyphal ingrowth bags revealed that Nothofagus and Leptospermum inoculum contained different ectomycorrhizal fungal communities, but that half of the common ectomycorrhizal taxa identified were found in both soil types, suggesting generalist fungi exist. Nothofagus was able to form associations with some fungal species originating from Leptospermum inoculum, however, probable spore contamination meant that the proportion of root colonization associated with those species was ambiguous. Root ectomycorrhizal colonization rates were positively associated with seedling biomass, and there was some evidence of a home soil inoculum advantage in Nothofagus, but these effects were minor. Additionally, we found evidence that home inoculum provides a protective advantage against drought stress for Leptospermum seedlings. Our results indicate the potential for using Leptospermum to promote Nothofagus establishment in restoration plantings and highlight the possible benefits of considering fungal mutualists in ecological restoration projects.

Transferability of correlative and process-based species distribution models revisited: A response to Booth.

Here, we respond to Booth's criticism of our paper, "Predictive ability of a process-based versus a correlative species distribution model." Booth argues that our usage of the MaxEnt model was flawed and that the conclusions of our paper are by implication flawed. We respond by clarifying that the error Booth implies we made was not made in our analysis, and we repeat statements from the original manuscript which anticipated such criticisms. In addition, we illustrate that using BIOCLIM variables in a MaxEnt analysis as recommended by Booth does not change the conclusions of the original analysis. That is, high performance in the training data domain did not equate to reliable predictions in novel data domains, and the process model transferred into novel data domains better than the correlative model did. We conclude by discussing a hidden implication of our study, namely, that process-based SDMs negate the need for BIOCLIM-type variables and therefore reframe the variable selection problem in species distribution modeling.

The effect of single biome occupancy on the estimation of biome shifts and the detection of biome conservatism.

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.

Predictive ability of a process-based versus a correlative species distribution model.

Species distribution modeling is a widely used tool in many branches of ecology and evolution. Evaluations of the transferability of species distribution models-their ability to predict the distribution of species in independent data domains-are, however, rare. In this study, we contrast the transferability of a process-based and a correlative species distribution model. Our case study uses 664 Australian eucalypt and acacia species. We estimate models for these species using data from their native Australia and then assess whether these models can predict the adventive range of these species. We find that the correlative model-MaxEnt-has a superior ability to describe the data in the training data domain (Australia) and that the process-based model-TTR-SDM-has a superior ability to predict the distribution of the study species outside of Australia. The implication of this analysis, that process-based models may be more appropriate than correlative models when making projections outside of the domain of the training data, needs to be tested in other case studies.

Diversification in evolutionary arenas-Assessment and synthesis.

Understanding how and why rates of evolutionary diversification vary is a key issue in evolutionary biology, ecology, and biogeography. Evolutionary rates are the net result of interacting processes summarized under concepts such as adaptive radiation and evolutionary stasis. Here, we review the central concepts in the evolutionary diversification literature and synthesize these into a simple, general framework for studying rates of diversification and quantifying their underlying dynamics, which can be applied across clades and regions, and across spatial and temporal scales. Our framework describes the diversification rate (d) as a function of the abiotic environment (a), the biotic environment (b), and clade-specific phenotypes or traits (c); thus, d ~ a,b,c. We refer to the four components (a-d) and their interactions collectively as the "Evolutionary Arena." We outline analytical approaches to this framework and present a case study on conifers, for which we parameterize the general model. We also discuss three conceptual examples: the Lupinus radiation in the Andes in the context of emerging ecological opportunity and fluctuating connectivity due to climatic oscillations; oceanic island radiations in the context of island formation and erosion; and biotically driven radiations of the Mediterranean orchid genus Ophrys. The results of the conifer case study are consistent with the long-standing scenario that low competition and high rates of niche evolution promote diversification. The conceptual examples illustrate how using the synthetic Evolutionary Arena framework helps to identify and structure future directions for research on evolutionary radiations. In this way, the Evolutionary Arena framework promotes a more general understanding of variation in evolutionary rates by making quantitative results comparable between case studies, thereby allowing new syntheses of evolutionary and ecological processes to emerge.

The dimensionality of niche space allows bounded and unbounded processes to jointly influence diversification.

There are two prominent and competing hypotheses that disagree about the effect of competition on diversification processes. The first, the bounded hypothesis, suggests that species diversity is limited (bounded) by competition between species for finite ecological niche space. The second, the unbounded hypothesis, proposes that innovations associated with evolution render competition unimportant over macroevolutionary timescales. Here we use phylogenetically structured niche modelling to show that processes consistent with both of these diversification models drive species accumulation in conifers. In agreement with the bounded hypothesis, niche competition constrained diversification, and in line with the unbounded hypothesis, niche evolution and partitioning promoted diversification. We then analyse niche traits to show that these diversification enhancing and inhibiting processes can occur simultaneously on different niche dimensions. Together these results suggest a new hypothesis for lineage diversification based on the multi-dimensional nature of ecological niches that can accommodate both bounded and unbounded evolutionary processes.