Assessing a Bayesian Approach for Detecting Exotic Hybrids between Plantation and Native Eucalypts

Eucalyptus globulus is grown extensively in plantations outside its native range in Australia. Concerns have been raised that the species may pose a genetic risk to native eucalypt species through hybridisation and introgression. Methods for identifying hybrids are needed to enable assessment and management of this genetic risk. This paper assesses the efficiency of a Bayesian approach for identifying hybrids between the plantation species E. globulus and E. nitens and four at-risk native eucalypts. Range-wide DNA samples of E. camaldulensis, E. cypellocarpa, E. globulus, E. nitens, E. ovata and E. viminalis, and pedigreed and putative hybrids (n = 606), were genotyped with 10 microsatellite loci. Using a two-way simulation analysis (two species in the model at a time), the accuracy of identification was 98% for first and 93% for second generation hybrids. However, the accuracy of identifying simulated backcross hybrids was lower (74%). A six-way analysis (all species in the model together) showed that as the number of species increases the accuracy of hybrid identification decreases. Despite some difficulties identifying backcrosses, the two-way Bayesian modelling approach was highly effective at identifying F1s, which, in the context of E. globulus plantations, are the primary management concern

Diversification in evolutionary arenas : Assessment and synthesis

Understanding how and why rates of evolutionary diversification vary is a central issue in evolutionary biology and ecology. The concept of adaptive radiation has attracted much interest, but is metaphorical and verbal in nature, making it difficult to quantitatively compare different evolutionary lineages or geographic regions. In addition, the causes of evolutionary stasis are relatively neglected. Here we review the central concepts in the evolutionary diversification literature and bring these together by proposing a general framework for estimating 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 conceptual model that open up new avenues for research, and present a case study on conifers, for which we parameterise the general model. We also discuss three conceptual examples based on existing literature: the Lupinus radiation in the Andes in the context of emerging ecological opportunity and fluctuating fragmentation due to climatic oscillation; oceanic island radiations in the context of archipelago isolation and 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 large niches, lack of competition, and high-rates of niche evolution differentially promote diversification, but these results go further by quantifying the statistical interactions between variables representing these three drivers. The conceptual examples illustrate how using the synthetic Evolutionary Arena framework results in highlighting gaps in current knowledge, and thus help to identify 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

Meiosis and beyond – understanding the mechanistic and evolutionary processes shaping the germline genome

The separation of germ cell populations from the soma is part of the evolutionary transition to multicellularity. Only genetic information present in the germ cells will be inherited by future generations, and any molecular processes affecting the germline genome are therefore likely to be passed on. Despite its prevalence across taxonomic kingdoms, we are only starting to understand details of the underlying micro‐evolutionary processes occurring at the germline genome level. These include segregation, recombination, mutation and selection and can occur at any stage during germline differentiation and mitotic germline proliferation to meiosis and post‐meiotic gamete maturation. Selection acting on germ cells at any stage from the diploid germ cell to the haploid gametes may cause significant deviations from Mendelian inheritance and may be more widespread than previously assumed. The mechanisms that affect and potentially alter the genomic sequence and allele frequencies in the germline are pivotal to our understanding of heritability. With the rise of new sequencing technologies, we are now able to address some of these unanswered questions. In this review, we comment on the most recent developments in this field and identify current gaps in our knowledge

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

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

Range reshuffling: Climate change, invasive species, and the case of Nothofagus forests in Aotearoa New Zealand

Aim: The impact of climate change on forest biodiversity and ecosystem services will be partly determined by the relative fortunes of invasive and native forest trees under future conditions. Aotearoa New Zealand has high conservation value native forests and one of the world's worst invasive tree problems. We assess the relative effects of habitat redistribution on native Nothofagus and invasive conifer (Pinaceae) species in New Zealand as a case study on the compounding impacts of climate change and tree invasions. Location: Aotearoa New Zealand. Methods: We use species distribution models (SDMs) to predict the current and future distribution of habitat for five native Nothofagus species and 13 invasive conifer species under two 2070 climate scenarios. We calculate habitat loss/gain for all species and examine overlap between the invasive and native species now and in future. Results: Most species will lose habitat overall. The native species saw large changes in the distribution of habitat with extensive losses in North Island and gains mostly in South Island. Concerningly, we found that most new habitat for Nothofagus was also suitable for at least one invasive species. However, there were refugia for the native species in the wetter parts of the climate space. Main Conclusion: If the predicted changes in habitat distribution translate to shifts in forest distribution, it would cause widespread ecological disruption. We discuss how acclimation, adaptation and biotic interactions may prevent/delay some changes. But we also highlight that the poor establishment capacity of Nothofagus, and the contrasting ability of the conifers to invade, will present persistent conservation challenges in areas of both new habitat and forest retreat. Pinaceae are problematic invaders globally, and our results highlight that control of invasions and active native forest restoration will likely be key to managing forest biodiversity under future climates.ISSN:1366-9516ISSN:1472-464

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 (m & amacr;nuka) 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.ISSN:2045-775

Multiple origins of mountain biodiversity in New Zealand's largest plant radiation

Funder: Gates Cambridge Trust; Id: http://dx.doi.org/10.13039/501100005370Funder: Linnean Society of London; Id: http://dx.doi.org/10.13039/501100001264Funder: Marsden Fund; Id: http://dx.doi.org/10.13039/501100009193Funder: Newnham College, University of Cambridge; Id: http://dx.doi.org/10.13039/501100000663Funder: Society of Systematic Biologists; Id: http://dx.doi.org/10.13039/100006069Funder: Swedish Research Council; Id: http://dx.doi.org/10.13039/501100004359AbstractAimHow 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.LocationNew Zealand, Southern Alps.TaxonVeronica sect. Hebe (Plantaginaceae).MethodsWe 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.ResultsIn 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 ConclusionsWe 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.</jats:sec

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 emerg