Unpacking boxes: Integration of molecular, morphological and ecological approaches reveals extensive patterns of reticulate evolution in box eucalypts

Morphological variation and its correlation with bioclimatic factors in Odorrana graminea sensu stricto

The large green cascade frog (Odorrana graminea sensu stricto) shows significant genetic differentiation in China, forming western, southern, and eastern clades. However, the morphological differentiation among the three clades is unclear, and the influence of bioclimatic factors on morphological variation among clades is unknown. Based on 20 morphological traits of 309 specimens from 28 localities, the present study explored the morphological differentiation and variation among clades and their correlation with bioclimatic factors through the multivariate statistical analysis. The results of the present study showed that O. graminea sensu stricto was divided into western, southern, and eastern morphological groups, and the gene flow between neighboring populations had caused an individual misidentification. With the three-step terrain and population distribution latitude and humidity, the annual mean temperature (Bio1) was significantly different between the southern and eastern–western clades; the maximum temperature of the hottest month (Bio5) was significantly different between the southern and western clades, and the mean temperature of the wettest quarter (Bio8) and the precipitation seasonality (Bio15) were significantly different between the eastern and western–southern clades. The southern clade that was affected by a high temperature had a smaller body size and larger sensory organs, and the eastern clade distributed in highly humid areas had a larger body size and smaller sensory organs. Moreover, the annual mean temperature range (Bio7) was the dominant factor in the morphological variation of O. graminea sensu stricto, and it had significant negative correlations with seven traits of male frogs and four traits of female frogs. The effect of precipitation factors on the morphological differentiation of each clade remained unclear. The local adaptation caused by climatic differences was the main reason for the morphological differentiation among clades. These findings will help us to understand amphibians’ abilities to adapt to environmental variation.

Sequential hybridization may have facilitated ecological transitions in the Southwestern pinyon pine syngameon

Multispecies interbreeding networks, or syngameons, have been increasingly reported in natural systems. However, the formation, structure, and maintenance of syngameons have received little attention. Through gene flow, syngameons can increase genetic diversity, facilitate the colonization of new environments, and contribute to hybrid speciation. In this study, we evaluated the history, patterns, and consequences of hybridization in a pinyon pine syngameon using morphological and genomic data to assess genetic structure, demographic history, and geographic and climatic data to determine niche differentiation. We demonstrated that Pinus edulis, a dominant species in the Southwestern US and a barometer of climate change, is a core participant in the syngameon, involved in the formation of two drought-adapted hybrid lineages including the parapatric and taxonomically controversial fallax-type. We found that species remain morphologically and genetically distinct at range cores, maintaining species boundaries while undergoing extensive gene flow in areas of sympatry at range peripheries. Our study shows that sequential hybridization may have caused relatively rapid speciation and facilitated the colonization of different niches, resulting in the rapid formation of two new lineages. Participation in the syngameon may allow adaptive traits to be introgressed across species barriers and provide the changes needed to survive future climate scenarios.

Evolutionary processes in an undescribed eucalypt: implications for the translocation of a critically endangered species

BACKGROUND AND AIMS

Knowledge of the evolutionary processes responsible for the distribution of threatened and highly localized species is important for their conservation. Population genomics can provide insights into evolutionary processes to inform management practices, including the translocation of threatened plant species. In this study, we focus on a critically endangered eucalypt, Eucalyptus sp. Cattai, which is restricted to a 40-km2 area of Sydney, Australia, and is threatened by increased urbanization. Eucalyptus sp. Cattai has yet to be formally described in part due to its suspected hybrid origin. Here, we examined evolutionary processes and species boundaries in E. sp. Cattai to determine whether translocation was warranted.

METHODS

We used genome-wide scans to investigate the evolutionary relationships of E. sp. Cattai with related species, and to assess levels of genetic health and admixture. Morphological trait and genomic data were obtained from seedlings of E. sp. Cattai propagated in a common garden to assess their genetic provenance and hybrid status.

KEY RESULTS

All analyses revealed that E. sp. Cattai was strongly supported as a distinct species. Genetic diversity varied across populations, and clonality was unexpectedly high. Interspecific hybridization was detected, and was more prevalent in seedlings compared to in situ adult plants, indicating that post-zygotic barriers may restrict the establishment of hybrids.

CONCLUSIONS

Multiple evolutionary processes (e.g. hybridization and clonality) can operate within one rare and restricted species. Insights regarding evolutionary processes from our study were used to assist with the translocation of genetically 'pure' and healthy ex situ seedlings to nearby suitable habitat. Our findings demonstrate that it is vital to provide an understanding of evolutionary relationships and processes with an examination of population genomics in the design and implementation of an effective translocation strategy.

The Syngameon Enigma

Despite their evolutionary relevance, multispecies networks or syngameons are rarely reported in the literature. Discovering how syngameons form and how they are maintained can give insight into processes such as adaptive radiations, island colonizations, and the creation of new hybrid lineages. Understanding these complex hybridization networks is even more pressing with anthropogenic climate change, as syngameons may have unique synergistic properties that will allow participating species to persist. The formation of a syngameon is not insurmountable, as several ways for a syngameon to form have been proposed, depending mostly on the magnitude and frequency of gene flow events, as well as the relatedness of its participants. Episodic hybridization with small amounts of introgression may keep syngameons stable and protect their participants from any detrimental effects of gene flow. As genomic sequencing becomes cheaper and more species are included in studies, the number of known syngameons is expected to increase. Syngameons must be considered in conservation efforts as the extinction of one participating species may have detrimental effects on the survival of all other species in the network.

Expansion of the rare Eucalyptus risdonii under climate change through hybridization with a closely related species despite hybrid inferiority

BACKGROUND AND AIMS

Hybridization is increasingly recognized as an integral part of the dynamics of species range expansion and contraction. Thus, it is important to understand the reproductive barriers between co-occurring species. Extending previous studies that argued that the rare Eucalyptus risdonii was expanding into the range of the surrounding E. amygdalina by both seed and pollen dispersal, we here investigate the long-term fitness of both species and their hybrids and whether expansion is continuing.

METHODS

We assessed the survival of phenotypes representing a continuum between the two pure species in a natural hybrid swarm after 29 years, along with seedling recruitment. The performance of pure species as well as of artificial and natural hybrids was also assessed over 28 years in a common garden trial.

KEY RESULTS

In the hybrid zone, E. amygdalina adults showed greater mortality than E. risdonii, and the current seedling cohort is still dominated by E. risdonii phenotypes. Morphologically intermediate individuals appeared to be the least fit. Similar results were observed after growing artificial first-generation and natural hybrids alongside pure species families in a common garden trial. Here, the survival, reproduction, health and growth of the intermediate hybrids were significantly less than those of either pure species, consistent with hybrid inferiority, although this did not manifest until later reproductive ages. Among the variable progeny of natural intermediate hybrids, the most E. risdonii-like phenotypes were the most fit.

CONCLUSIONS

This study contributes to the increasing number of reports of hybrid inferiority in Eucalyptus, suggesting that post-zygotic barriers contribute to the maintenance of species integrity even between closely related species. However, with fitness rapidly recovered following backcrossing, it is argued that hybridization can still be an important evolutionary process, in the present case appearing to contribute to the range expansion of the rare E. risdonii in response to climate change.

Coral Genus Differentiation Based on Direct Analysis in Real Time-High Resolution Mass Spectrometry-Derived Chemical Fingerprints

Coral reefs are one of the most biologically diverse ecosystems, and the accurate identification of the species is essential for diversity assessment and conservation. Current genus determination approaches are time-consuming and resource-intensive and can be highly subjective. To explore the hypothesis that the small-molecule profiles of coral are genus-specific and can be used as a rapid tool to catalogue and distinguish between coral genera, the small-molecule chemical fingerprints of the species Acanthastrea echinata, Catalaphyllia jardinei, Duncanopsammia axifuga, Echinopora lamellosa, Euphyllia divisa, Euphyllia paraancora, Euphyllia paradivisa, Galaxea fascicularis, Herpolitha limax, Montipora confusa, Monitpora digitata, Montipora setosa, Pachyseris rugosa, Pavona cactus, Plerogyra sinuosa, Pocillopora acuta, Seriatopora hystrix, Sinularia dura, Turbinaria peltata, Turbinaria reniformis, Xenia elongata, and Xenia umbellata were generated using direct analysis in real time-high resolution mass spectrometry (DART-HRMS). It is demonstrated here that the mass spectrum-derived small-molecule profiles for coral of different genera are distinct. Multivariate statistical analysis processing of the DART-HRMS data enabled rapid genus-level differentiation based on the chemical composition of the coral. Coral samples were analyzed with no sample preparation required, making the approach rapid and efficient. The resulting spectra were subjected to kernel discriminant analysis (KDA), which furnished accurate genus differentiation of the coral. Leave-one-out cross-validation (LOOCV) was carried out to determine the classification accuracy of each model and confirm that this approach can be used for coral genus attribution with prediction accuracies ranging from 86.67 to 97.33%. The advantages and application of the statistical analysis to DART-HRMS-derived coral chemical signatures for genus-level differentiation are discussed.

Major biogeographic barriers in eastern Australia have shaped the population structure of widely distributed Eucalyptus moluccana and its putative subspecies

We have investigated the impact of recognized biogeographic barriers on genetic differentiation of grey box (Eucalyptus moluccana), a common and widespread tree species of the family Myrtaceae in eastern Australian woodlands, and its previously proposed four subspecies moluccana, pedicellata, queenslandica, and crassifolia. A range of phylogeographic analyses were conducted to examine the population genetic differentiation and subspecies genetic structure in E. moluccana in relation to biogeographic barriers. Slow evolving markers uncovering long term processes (chloroplast DNA) were used to generate a haplotype network and infer phylogeographic barriers. Additionally, fast evolving, hypervariable markers (microsatellites) were used to estimate demographic processes and genetic structure among five geographic regions (29 populations) across the entire distribution of E. moluccana. Morphological features of seedlings, such as leaf and stem traits, were assessed to evaluate population clusters and test differentiation of the putative subspecies. Haplotype network analysis revealed twenty chloroplast haplotypes with a main haplotype in a central position shared by individuals belonging to the regions containing the four putative subspecies. Microsatellite analysis detected the genetic structure between Queensland (QLD) and New South Wales (NSW) populations, consistent with the McPherson Range barrier, an east-west spur of the Great Dividing Range. The substructure was detected within QLD and NSW in line with other barriers in eastern Australia. The morphological analyses supported differentiation between QLD and NSW populations, with no difference within QLD, yet some differentiation within NSW populations. Our molecular and morphological analyses provide evidence that several geographic barriers in eastern Australia, including the Burdekin Gap and the McPherson Range have contributed to the genetic structure of E. moluccana. Genetic differentiation among E. moluccana populations supports the recognition of some but not all the four previously proposed subspecies, with crassifolia being the most differentiated.

The functional roles of psyllid abundance and assemblage on bird-associated forest defoliation

Fluctuations in the abundance of insect herbivores and the severity of damage they cause to their hosts are key factors affecting tree health and trophic interactions. Bell miner associated dieback (BMAD) is a trophic cascade involving eucalypt trees, psyllids and bell miners. Bell miners are a territorial species of bird that reduce insectivorous bird diversity, thereby increasing psyllid abundances. The role of psyllids in BMAD is debated, primarily because psyllid host specificity, genus, defoliation potential and/or lerp composition have been conflated or unexplored. This study documented psyllid communities and canopy structure of four eucalypt hosts (Eucalyptus bridgesiana, E. caliginosa, E. propinqua and E. siderophloia) in BMAD and non-BMAD-affected forests in northern New South Wales. Psyllid abundances were significantly higher in BMAD-affected forests. However, psyllid assemblages did not differ between forest types which contrasts with an influential hypothesis concerning bell miner farming of psyllids that produce sugary lerps (Glycaspis species). Importantly, psyllid communities differed among species of eucalypt host. Hosts supporting higher abundances of Cardiaspina tended to have a stronger negative relationship between canopy health and psyllid abundances than other host trees. Cardiaspina were also found on older leaves and associated with more leaf damage than other psyllids. Unlike most other psyllid genera, Cardiaspina initiate premature foliar senescence leading to defoliation which ultimately changes the age structure of leaves of the canopies of affected trees. Our study supports the functional linkage between psyllid assemblages, their relative abundances and defoliation potential to bottom-up mechanisms behind a bird-associated trophic cascade.

Patterns of hybridization and cryptic introgression among one- and four-needled pinyon pines

BACKGROUND AND AIMS

Pinyon pine hybridization is widely acknowledged, but the frequency of and contributors to such interspecific mating remain largely unstudied. Pinus quadrifolia has three to four needles per fascicle, suggesting that it is a result of hybridization between the five-needled P. juarezensis and the single-needled P. monophylla. In this study we address the taxonomic validity of P. juarezensis, the hybrid origin of P. quadrifolia and the presence of hybridization and intermediate morphology as a result of interspecific hybridization in this complex.

METHODS

We address these questions by combining a genomic and morphological approach. We generated 1868 single nucleotide polymorphisms (SNPs) to detect genetic clusters using principal co-ordinates analyis, discriminant analysis of principal components, fastSTRUCTURE and ADMIXTURE analyses, and performed a morphological analysis of the leaves.

KEY RESULTS

We found that the five-needled pinyons did not differ genetically from the four-needled P. quadrifolia, reducing the status of P. juarezensis to P. quadrifolia. We also found no evidence that P. quadrifolia is of hybrid origin from P. juarezensis × P. monophylla but is instead a genetically distinct species with natural needle number variation that has yet to be explained. Hybridization does occur in this complex, but mostly between P. quadrifolia and P. californiarum, and less commonly between P. quadrifolia and P. monophylla. Interestingly, some hybrid derivatives were detected between both single-needled taxa, P. monophylla and P. californiarum, a hybrid combination that has not yet been proposed. Hybrids have intermediate morphology when they have similar genetic contributions from both parental species; however, when one parent contributes more, hybrid derivatives resemble the parent with higher genetic contribution, resulting in cryptic introgression.

CONCLUSIONS

Our detailed sampling across the distribution of this complex allows us to describe the patterns of hybridization among these taxa, resolves an ancient taxonomic conflict and provides insights into the challenges of exclusively using morphological traits when identifying these taxa with cryptic hybridization and variable morphology.

Extensive reticulate evolution within Fargesia (s.l.) (Bambusoideae: Poaceae) and its allies: Evidence from multiple nuclear markers

Reticulate evolution resulting from hybridization and introgression has been recognized as a creative source of species and diversification in bamboos. Previous phylogenetic studies revealed that Fargesia (s.l.) (Fargesia and Yushania) was divided into the Fargesia spathe clade and the non-spathe clade. Interestingly, the Fargesia spathe clade may have originated from hybridization among other clades within Fargesia (s.l.). Understanding the hybrid origin of this clade requires a robust phylogenetic framework in which major clades within Fargesia (s.l.) are resolved. Here, we used three nuclear genes to reconstruct the evolutionary history of Fargesia (s.l.) and its allies to identify putative patterns in the origin of the Fargesia spathe clade and to examine the extent to which reticulate evolution has occurred at the interspecific level in bamboos. Bashania species form a clade with Fargesia (s.l.), which is further divided into Group I and Group II. The Fargesia spathe clade, the Alpine Bashania clade, and Fargesia yajiangensis comprise Group I, while the Bashania fargesii clade and the remaining Fargesia (s.l.) species form Group II. Incongruence between the current nuclear-based and previous plastid phylogenies demonstrate several possible hybridization events among Fargesia (s.l.) species and related taxa, which have given rise to the Fargesia spathe clade, the Phyllostachys clade, and the Ampelocalamus clade. We also detected several putative hybrid species of Fargesia (s.l.). Our results show that reticulate evolution has played a prominent role in Fargesia (s.l.) evolution, which could, in part, account for the taxonomic difficulty associated with Fargesia (s.l.) and the alpine bamboos. The study also underscores the importance of hybridization in the evolution of bamboos, at both intergeneric and intrageneric levels.

Chloroplast genome analysis of box-ironbark Eucalyptus

Eucalyptus L'Hérit. (Myrtaceae) is a taxonomically complex and highly speciose genus that dominates much of Australia's woody vegetation. However, very little information is available about the molecular biology and chloroplast diversity of certain groups, such as Eucalyptus section Adnataria, which is found in many woodland habitats of eastern Australia. We report four new complete chloroplast genomes of Eucalyptus, including three genomes from species previously lacking any chloroplast reference sequences. Plastomes of E. albens, E. conica, E. crebra and E. melliodora assembled using a de novo approach were shown to be largely identical to each other, and similar in size and structure to previously published chloroplast genomes from Eucalyptus. A total of 132 genes (114 single-copy genes and 18 duplicated genes in the IR regions) were identified, and shown to be highly conserved in terms of gene order, content and organization. Slightly higher divergence in the intergenic spacers was identified through comparative genomic analyses. Chloroplast sequences of 35 additional individuals representing 12 species were assembled using a reference guided approach. Rates of nucleotide substitution varied among the protein coding genes, with 17 genes under possible positive selection, and 29 invariant genes. Phylogenetic analysis of either the whole reconstructed plastome sequences or the individual genes revealed extreme discordance with expected species boundaries or higher-level relationships. Plastome relationships were better predicted by geography than by nuclear DNA or taxonomic relationships, suggesting a substantial influence of gene flow over and above the effects of incomplete lineage sorting. These results provide resources for future research and valuable insights into the prevalence of interspecific gene flow among Eucalyptus species.

The molecular basis of differential morphology and bleaching thresholds in two morphs of the coral Pocillopora acuta

Processes of cnidarian evolution, including hybridization and phenotypic plasticity, have complicated the clear diagnosis of species boundaries within the phylum. Pocillopora acuta, a species of scleractinian coral that was recently split from the widespread Pocillopora damicornis species complex, occurs in at least two distinct morphs on the Great Barrier Reef. Contrasting morphology combined with evidence of differential bleaching thresholds among sympatrically distributed colonies suggest that the taxonomy of this recently described species is not fully resolved and may represent its own species complex. To examine the basis of sympatric differentiation between the two morphs, we combined analyses of micro- and macro-skeletal morphology with genome wide sequencing of the coral host, as well as ITS2 genotyping of the associated Symbiodinium communities. We found consistent differences between morphs on both the macro- and micro-skeletal scale. In addition, we identified 18 candidate functional genes that relate to skeletal formation and morphology that may explain how the two morphs regulate growth to achieve their distinct growth forms. With inconclusive results in endosymbiotic algal community diversity between the two morphs, we propose that colony morphology may be linked to bleaching susceptibility. We conclude that cryptic speciation may be in the early stages within the species P. acuta.

Unravelling mummies: cryptic diversity, host specificity, trophic and coevolutionary interactions in psyllid - parasitoid food webs

BACKGROUND

Parasitoids are hyperdiverse and can contain morphologically and functionally cryptic species, making them challenging to study. Parasitoid speciation can arise from specialisation on niches or diverging hosts. However, which process dominates is unclear because cospeciation across multiple parasitoid and host species has rarely been tested. Host specificity and trophic interactions of the parasitoids of psyllids (Hemiptera) remain mostly unknown, but these factors are fundamentally important for understanding of species diversity, and have important applied implications for biological control.

RESULTS

We sampled diverse parasitoid communities from eight Eucalyptus-feeding psyllid species in the genera Cardiaspina and Spondyliaspis, and characterised their phylogenetic and trophic relationships using a novel approach that forensically linked emerging parasitoids with the presence of their DNA in post-emergence insect mummies. We also tested whether parasitoids have cospeciated with their psyllid hosts. The parasitoid communities included three Psyllaephagus morphospecies (two primary and, unexpectedly, one heteronomous hyperparasitoid that uses different host species for male and female development), and the hyperparasitoid, Coccidoctonus psyllae. However, the number of genetically delimited Psyllaephagus species was three times higher than the number of recognisable morphospecies, while the hyperparasitoid formed a single generalist species. In spite of this, cophylogenetic analysis revealed unprecedented codivergence of this hyperparasitoid with its primary parasitoid host, suggesting that this single hyperparasitoid species is possibly diverging into host-specific species. Overall, parasitoid and hyperparasitoid diversification was characterised by functional conservation of morphospecies, high host specificity and some host switching between sympatric psyllid hosts.

CONCLUSIONS

We conclude that host specialisation, host codivergence and host switching are important factors driving the species diversity of endoparasitoid communities of specialist host herbivores. Specialisation in parasitoids can also result in heteronomous life histories that may be more common than appreciated. A host generalist strategy may be rare in endoparasitoids of specialist herbivores despite the high conservation of morphology and trophic roles, and endoparasitoid species richness is likely to be much higher than previously estimated. This also implies that the success of biological control requires detailed investigation to enable accurate identification of parasitoid-host interactions before candidate parasitoid species are selected as biological control agents for target pests.