Floral odour chemistry defines species boundaries and underpins strong reproductive isolation in sexually deceptive orchids

Background and AimsThe events leading to speciation are best investigated in systems where speciation is ongoing or incomplete, such as incipient species. By examining reproductive barriers among incipient sister taxa and their congeners we can gain valuable insights into the relative timing and importance of the various barriers involved in the speciation process. The aim of this study was to identify the reproductive barriers among sexually deceptive orchid taxa in the genus Chiloglottis.MethodsThe study targeted four closely related taxa with varying degrees of geographic overlap. Chemical, morphological and genetic evidence was combined to explore the basis of reproductive isolation. Of primary interest was the degree of genetic differentiation among taxa at both nuclear and chloroplast DNA markers. To objectively test whether or not species boundaries are defined by the chemistry that controls pollinator specificity, genetic analysis was restricted to samples of known odour chemistry.Key ResultsFloral odour chemical analysis was performed for 600+ flowers. The three sympatric taxa were defined by their specific chiloglottones, the semiochemicals responsible for pollinator attraction, and were found to be fully cross-compatible. Multivariate morphometric analysis could not reliably distinguish among the four taxa. Although varying from very low to moderate, significant levels of genetic differentiation were detected among all pairwise combinations of taxa at both nuclear and chloroplast loci. However, the levels of genetic differentiation were lower than expected for mature species. Critically, a lack of chloroplast DNA haplotype sharing among the morphologically indistinguishable and most closely related taxon pair confirmed that chemistry alone can define taxon boundaries.ConclusionsThe results confirmed that pollinator isolation, mediated by specific pollinator attraction, underpins strong reproductive isolation in these taxa. A combination of large effective population sizes, initial neutral mutations in the genes controlling floral scent, and a pool of available pollinators likely drives diversity in this system

Organelle DNA haplotypes reflect crop-use characteristics and geographic origins of Cannabis sativa

Comparative sequencing of cannabis individuals across 12 chloroplast and mitochondrial DNA loci revealed 7 polymorphic sites, including 5 length variable regions and 2 single nucleotide polymorphisms. Simple PCR assays were developed to assay these polymorphisms, and organelle DNA haplotypes were obtained for 188 cannabis individuals from 76 separate populations, including drug-type, fibre-type and wild populations. The haplotype data were analysed using parsimony, UPGMA and neighbour joining methods. Three haplotype groups were recovered by each analysis method, and these groups are suggestive of the crop-use characteristics and geographical origin of the populations, although not strictly diagnostic. We discuss the relationship between our haplotype data and taxonomic opinions of cannabis, and the implications of organelle DNA haplotyping to forensic investigations of cannabis

Socio-seasonal changes in scent-marking habits in the carnivorous marsupial Dasyurus maculatus at communal latrines

Scat DNA analyses and monthly monitoring were used to elucidate patterns of latrine use in a free-ranging population of a rare Australian marsupial carnivore, the spotted-tailed quoll (Dasyurus maculatus) Kerr. In all, 132 latrines were identified at large complex outcrops and on bedrock in drainage lines, creeks and rivers at a single woodland site in south-eastern mainland Australia. Annual cyclic variation in scat deposition was found over the two years that latrines were monitored. Peaks in scat deposition on latrines coincided with seasonal social behaviours and differed between sites on outcrops and sites along drainage lines. A marked increase in scat deposition on latrines in drainage lines was recorded during the mating season and at outcrop latrines when females were nursing young. Genetic analyses of scats collected over one breeding season revealed that multiple individuals of both sexes defaecated at latrines. The communal use of latrines during the mating season along with the seasonal patterns of scat deposition demonstrates that latrines are important scent-marking sites that facilitate social communication among individuals of this solitary-living species. The collective evidence indicates that latrines play a major role in aiding reproduction and interindividual spacing

A heterogeneity test for fine-scale genetic structure

For organisms with limited vagility and/or occupying patchy habitats, we often encounter nonrandom patterns of genetic affinity over relatively small spatial scales, labelled fine-scale genetic structure. Both the extent and decay rate of that pattern can be expected to depend on numerous interesting demographic, ecological, historical, and mating system factors, and it would be useful to be able to compare different situations. There is, however, no heterogeneity test currently available for fine-scale genetic structure that would provide us with any guidance on whether the differences we encounter are statistically credible. Here, we develop a general nonparametric heterogeneity test, elaborating on standard autocorrelation methods for pairs of individuals. We first develop a 'pooled within-population' correlogram, where the distance classes (lags) can be defined as functions of distance. Using that pooled correlogram as our null-hypothesis reference frame, we then develop a heterogeneity test of the autocorrelations among different populations, lag-by-lag. From these single-lag tests, we construct an analogous test of heterogeneity for multilag correlograms. We illustrate with a pair of biological examples, one involving the Australian bush rat, the other involving toadshade trillium. The Australian bush rat has limited vagility, and sometimes occupies patchy habitat. We show that the autocorrelation pattern diverges somewhat between continuous and patchy habitat types. For toadshade trillium, clonal replication in Piedmont populations substantially increases autocorrelation for short lags, but clonal replication is less pronounced in mountain populations. Removal of clonal replicates reduces the autocorrelation for short lags and reverses the sign of the difference between mountain and Piedmont correlograms

Sex ratio bias and shared paternity reduce individual fitness and population viability in a critically endangered parrot

Sex‐biased mortality can lead to altered adult sex ratios (ASRs), which may in turn lead to harassment and lower fitness of the rarer sex and changes in the mating system. Female critically endangered swift parrots (Lathamus discolor) suffer high predation while nesting due to an introduced mammalian predator, the sugar glider (Petaurus breviceps). High predation on females is causing severe population decline alongside strongly biased adult sex ratios (≥73% male). Our 6‐year study showed that 50.5% of critically endangered swift parrot nests had shared paternity although the birds remained socially monogamous. Shared paternity increased significantly with the local rate of predation on breeding females, suggesting that rates of shared paternity increased when the ASR became more biased. Nests that were not predated produced fewer fledglings as the local ASR became more male‐biased possibly due to higher interference during nesting from unpaired males. Population viability analyses showed that part of the predicted decline in the swift parrot population is due to reduced reproductive success when paternity is shared. The models predicted that the population would decline by 89.4% over three generations if the birds maintained the lowest observed rate of shared paternity. This compares with predicted population reductions of 92.1–94.9% under higher rates of shared paternity. We conclude that biases in the ASR, in this case caused by sex‐specific predation from an introduced predator, can lead to changes in the mating system and negative impacts on both individual fitness and long‐term population viability.This research was funded by an Australian Research Council Discovery Grant (DP140104202)

Orchid conservation: from theory to practice

Background: Given the exceptional diversity of orchids (26,000+ species), improving strategies for the conservation of orchids will benefit a vast number of taxa. Furthermore, with rapidly increasing numbers of endangered orchids, and low success rates in orchid conservation translocation programs worldwide, it is evident that our progress in understanding the biology of orchids is not yet translating into widespread effective conservation. Scope: We highlight unusual aspects of the reproductive biology of orchids that can have important consequences for conservation programs such as specialisation of pollination systems, low fruit set but high seed production, and the potential for long-distance seed dispersal. Further, we discuss the importance of their reliance on mycorrhizal fungi for germination, including quantifying the incidence of specialised versus generalised mycorrhizal associations in orchids. In light of leading conservation theory and the biology of orchids, we provide recommendations for improving population management and translocation programs. Conclusions: Major gains in orchid conservation can be achieved by incorporating knowledge of ecological interactions, for both generalist and specialist species. For example, habitat management can be tailored to maintain pollinator populations, and conservation translocation sites selected based on confirmed availability of pollinators. Similarly, use of efficacious mycorrhizal fungi in propagation will increase the value of ex-situ collections, and likely increase the success of conservation translocations. Given the low genetic differentiation between populations of many orchids, experimental genetic mixing is an option to increase fitness of small populations, although caution is needed where cytotypes or floral ecotypes are present. Combining demographic data and field experiments will provide knowledge to enhance management and translocation success. Finally, high per-fruit fecundity means that orchids offer powerful but overlooked opportunities to propagate plants for experiments aimed at improving conservation outcomes. Given the uncertainty of future environmental change, experimental approaches also offer powerful ways to build more resilient populations.grants from the Wimmera Catchment Management Authority (National Landcare Program), Department of Land Water and Primary Industry community grants, Grampians Threatened Species Hub, Saving our Species funding NSW Office of Environment and Heritage, and the Office of the threatened Species Commissioner to N.

Converting quadratic entropy to diversity: Both animals and alleles are diverse, but some are more diverse than others

The use of diversity metrics has a long history in population ecology, while population genetic work has been dominated by variance-derived metrics instead, a technical gap that has slowed cross-communication between the fields. Interestingly, Rao’s Quadratic Entropy (RQE), comparing elements for ‘degrees of divergence’, was originally developed for population ecology, but has recently been deployed for evolutionary studies. We here translate RQE into a continuous diversity analogue, and then construct a multiply nested diversity partition for alleles, individuals, populations, and species, each component of which exhibits the behavior of proper diversity metrics, and then translate these components into [0,1]—scaled form. We also deploy non-parametric statistical tests of the among-stratum components and novel tests of the homogeneity of within-stratum diversity components at any hierarchical level. We then illustrate this new analysis with eight nSSR loci and a pair of close Australian marsupial (Antechinus) congeners, using both ‘different is different’ and ‘degree of difference’ distance metrics. The total diversity in the collection is larger than that within either species, but most of the within-species diversity is resident within single populations. The combined A. agilis collection exhibits more diversity than does the combined A. stuartii collection, possibly attributable to localized differences in either local ecological disturbance regimes or differential levels of population isolation. Beyond exhibiting different allelic compositions, the two congeners are becoming more divergent for the arrays of allele sizes they possess.PES was supported by the USDA National Institute of Food and Agriculture Hatch Project 1005333, and the New Jersey Agricultural Experiment Station, Hatch project NJ17160; SCB was supported by Australian Research Council Future Fellowship FT130100043. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

How does ecological disturbance influence genetic diversity?

Environmental disturbance underpins the dynamics and diversity of many of the ecosystems of the world, yet its influence on the patterns and distribution of genetic diversity is poorly appreciated. We argue here that disturbance history may be the major

Niche Perspectives on Plant-Pollinator Interactions

Ecological niches are crucial for species coexistence and diversification, but the niche concept has been underutilized in studying the roles of pollinators in plant evolution and reproduction. Pollination niches can be objectively characterized using pollinator traits, abundance, and distributions, as well as network topology. We review evidence that floral traits represent adaptations to pollination niches, where tradeoffs in trait deployment reinforce niche specialization. In turn, specialized pollination niches potentially increase speciation rates, foster species coexistence, and constrain species range limits. By linking studies of adaptation with those on speciation and coexistence, the pollination niche provides an organizing principle for research on plant reproduction, and conceptually unites these studies with fields of biology where the niche perspective is already firmly established.T.V.N. was supported by an incentive grant from the National Research Foundation of South Africa (109547). S.D.J. was supported by the South African Research Chairs Programme (NRF grant 46372). We thank Nathan Muchhala, Jeff Ollerton, Supreet Sahoo, Thomas Semple, Robert Raguso, Lynn Watson, and Stella Watts for providing images, and Jeff Ollerton and an anonymous reviewer for comments that improved the final manuscript

New species of Tulasnella associated with terrestrial orchids in Australia

Recent studies using sequence data from eight sequence loci and coalescent-based species delimitation methods have revealed several species-level lineages of Tulasnella associated with the orchid genera Arthrochilus, Caleana, Chiloglottis, and Drakaea in Australia. Here we formally describe three of those species, Tulasnella prima, T. secunda, and T. warcupii spp. nov., as well as an additional Tulasnella species associated with Chiloglottis growing in Sphagnum, T. sphagneti sp. nov. Species were identified by phylogenetic analyses of the ITS with up to 1.3 % sequence divergence within taxa and a minimum of 7.6 % intraspecific divergence. These new Tulasnella (Tulasnellaceae, Cantharellales) species are currently only known from orchid hosts, with each fungal species showing a strong relationship with an orchid genus. In this study, T. prima and T. sphagneti associate with Chiloglottis, while T. secunda associates with Drakaea and Caleana, and T. warcupii associates with Arthrochilus oreophilu