Andrew H Thornhill | University of California, Berkeley (original) (raw)

Papers by Andrew H Thornhill

Australian Journal of Botany, 2012

Australian Systematic Botany, 2015

Methods in Ecology and Evolution, 2015

Ecology and Evolution, 2015

Northern Australia, Papua New Guinea and New Caledonia all boast unique endemic rainforest and sa... more Northern Australia, Papua New Guinea and New Caledonia all boast unique endemic rainforest and savanna flora, but also share a large number and diversity of common plant taxa. The knowledge and understanding of these floras and their evolutionary histories has to date been largely compiled through morphological comparisons. Advances in molecular phylogenetics, however, now allows us to use genetic data to gain deeper insights into diversity and the evolutionary processes driving floristic community assembly and speciation. In this talk we will present vascular plant ‘area’ phylogenies for northern Australia, Papua New Guinea and New Caledonia and attempt to use them to identify patterns of phylogenetic diversity and endemism within and between the areas. The three phylogenies will also be combined and divergence dates estimated to gain an improved understanding of the evolutionary history of the floras and their component species.

Frontiers in Genetics, 2015

Fergusonina flies (Diptera: Fergusoninidae) and Fergusobia nematodes (Tylenchida: Neotylenchidae)... more Fergusonina flies (Diptera: Fergusoninidae) and Fergusobia nematodes (Tylenchida: Neotylenchidae) together form galls on plants in the Myrtaceae in a unique insect-nematode mutualism. Each fly/nematode association is specific and induces formation of a specific type of gall, for example, shoot buds, axial or terminal leaf buds, leaf blades, or flower buds. The Fergusonina/Fergusobia pairs have been reared from seven genera within the Myrtaceae including Angophora, Corymbia, Eucalyptus, Leptospermum, Melaleuca, Metrosideros, and Syzygium (Taylor et al. 2005; Taylor et al. 2007) indicating a broad distribution across the Myrtaceae lineages. Phylogenetic analysis of the Fergusonina flies is compared to that for its plants hosts in the Myrtaceae in order to test hypotheses of coevolution, particularly with regard to cospeciation and host-tracking. Phylogenetic analysis coupled with divergence time analysis of both Myrtaceae hosts and the Fergusonina flies suggest that the crown radiatio...

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, Jan 19, 2015

Evolutionary and genetic knowledge is increasingly being valued in conservation theory, but is ra... more Evolutionary and genetic knowledge is increasingly being valued in conservation theory, but is rarely considered in conservation planning and policy. Here, we integrate phylogenetic diversity (PD) with spatial reserve prioritization to evaluate how well the existing reserve system in Victoria, Australia captures the evolutionary lineages of eucalypts, which dominate forest canopies across the state. Forty-three per cent of remaining native woody vegetation in Victoria is located in protected areas (mostly national parks) representing 48% of the extant PD found in the state. A modest expansion in protected areas of 5% (less than 1% of the state area) would increase protected PD by 33% over current levels. In a recent policy change, portions of the national parks were opened for development. These tourism development zones hold over half the PD found in national parks with some species and clades falling entirely outside of protected zones within the national parks. This approach of u...

Vicariance or long-distance dispersal tested using a molecular clock.Up to six potential vicarian... more Vicariance or long-distance dispersal tested using a molecular clock.Up to six potential vicariance events.Three overland dispersals via new land connections.Thirteen disjunctions due to long-distance dispersal and establishment.Uncertain cause of disjunction in Myrtaceae taxa on long branches of the phylogeny.The angiosperm family Myrtaceae has extant and fossil taxa from all southern continents and is assumed to be of Gondwanan origin. Many modern groups contain sister taxa that have disjunct transoceanic distributions, which can be interpreted as a result of either vicariance or long-distance dispersal and establishment (LDDE). Further, some Myrtaceae groups occur on Pacific islands with enigmatic geological histories. We tested hypotheses of vicariance and LDDE by estimating divergence times using a relaxed molecular clock calibrated with 12 fossils. In total, 88 genera and 202 species were sampled, representing both subfamilies and all tribes of Myrtaceae. We reconstructed the family as Gondwanan in origin. Of the 22 geographically disjunct sister groups in our study, up to six are potentially explained as the product of vicariance, three resulting from overland dispersal via new land connections, and 13 due to LDDE events. Nine of the 13 hypothesized LDDE events occurred in fleshy-fruited taxa. Our results indicate that most of the transoceanic distribution patterns in Myrtaceae have occurred since the Miocene due to LDDE, whereas inferred vicariance events all occurred before the Late Eocene. There are many instances of sister relationships between species-poor and species-rich groups in Myrtaceae, and at least three occurrences of geographically isolated taxa on long branches of the phylogeny (Arillastrum, Myrtus, and Tepualia), whose modern-day distributions are difficult to explain without additional fossil or geological evidence.

Biological Journal of the Linnean Society, 2014

ABSTRACT A unique obligate mutualism occurs between species of Fergusonina Malloch flies (Diptera... more ABSTRACT A unique obligate mutualism occurs between species of Fergusonina Malloch flies (Diptera: Fergusoninidae) and nematodes of the genus Fergusobia Currie (Nematoda: Neotylenchidae). These mutualists together form different types of galls on Myrtaceae, mainly in Australia. The galling association is species-specific, and each mutualism in turn displays host specificity. This tritrophic system represents a compelling arena to test hypotheses about coevolution between the host plants, parasitic nematodes and the fergusoninid flies, and the evolution of these intimate mutualisms. We have a basic knowledge of the interactions between the host plant, fly and nematode in this system, but a more sophisticated understanding will require a much more intensive and coordinated research effort. Summaries of the known Fergusonina/Fergusobia species associations and gall type terminology are presented. This paper identifies the key advantages of the system and questions to be addressed, and proposes a number of predictions about the evolutionary dynamics of the system given our understanding of the biology of the mutualists. Future research will profitably focus on (1) gall cecidogenesis and phenology, (2) the interaction between the fly larva and the nematode in the gall, and between the adult female fly and the parasitic nematode, (3) the means by which the fly and nematode life cycles are coordinated, (4) a targeted search of groups in the plant family Myrtaceae that have not yet been identified as gall hosts, and (5) establishment and comparison of the phylogenetic relationships of the host plants, fly species and nematodes. Recently derived phylogenies and divergence time estimation studies of the Diptera and the Myrtaceae show that the fly family Fergusoninidae is less than half the age of the Myrtaceae, discounting the hypothesis of cospeciation and coradiation of the fly/nematode mutualism and the plants at the broadest levels. However, cospeciation may have occurred at shallower levels in the phylogeny, following the establishment of the fly/nematode mutualism on the Myrtaceae. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, ●●, ●●–●●.

Molecular Phylogenetics and Evolution, 2013

The identification and application of reliable fossil calibrations represents a key component of ... more The identification and application of reliable fossil calibrations represents a key component of many molecular studies of evolutionary timescales. In studies of plants, most paleontological calibrations are associated with macrofossils. However, the pollen record can also inform age calibrations if fossils matching extant pollen groups are found. Recent work has shown that pollen of the myrtle family, Myrtaceae, can be classified into a number of morphological groups that are synapomorphic with molecular groups. By assembling a data matrix of pollen morphological characters from extant and fossil Myrtaceae, we were able to measure the fit of 26 pollen fossils to a molecular phylogenetic tree using parsimony optimisation of characters. We identified eight Myrtaceidites fossils as appropriate for calibration based on the most parsimonious placements of these fossils on the tree. These fossils were used to inform age constraints in a Bayesian phylogenetic analysis of a sequence alignment comprising two sequences from the chloroplast genome (matK and ndhF) and one nuclear locus (ITS), sampled from 106 taxa representing 80 genera. Three additional analyses were calibrated by placing pollen fossils using geographic and morphological information (eight calibrations), macrofossils (five calibrations), and macrofossils and pollen fossils in combination (12 calibrations). The addition of new fossil pollen calibrations led to older crown ages than have previously been found for tribes such as Eucalypteae and Myrteae. Estimates of rate variation among lineages were affected by the choice of calibrations, suggesting that the use of multiple calibrations can improve estimates of rate heterogeneity among lineages. This study illustrates the potential of including pollen-based calibrations in molecular studies of divergence times.

Nature Communications, 2011

Fire is a major modifier of communities, but the evolutionary origins of its prevalent role in sh... more Fire is a major modifier of communities, but the evolutionary origins of its prevalent role in shaping current biomes are uncertain. Australia is among the most fire-prone continents, with most of the landmass occupied by the fire-dependent sclerophyll and savanna biomes. In contrast to biomes with similar climates in other continents, Australia has a tree flora dominated by a single genus, Eucalyptus, and related Myrtaceae. A unique mechanism in Myrtaceae for enduring and recovering from fire damage likely resulted in this dominance. Here, we find a conserved phylogenetic relationship between post-fire resprouting (epicormic) anatomy and biome evolution, dating from 60 to 62 Ma, in the earliest Palaeogene. Thus, fire-dependent communities likely existed 50 million years earlier than previously thought. We predict that epicormic resprouting could make eucalypt forests and woodlands an excellent long-term carbon bank for reducing atmospheric CO2 compared with biomes with similar fire regimes in other continents.

Nature Communications, 2014

Understanding spatial patterns of biodiversity is critical for conservation planning, particularl... more Understanding spatial patterns of biodiversity is critical for conservation planning, particularly given rapid habitat loss and human-induced climatic change. Diversity and endemism are typically assessed by comparing species ranges across regions. However, investigation of patterns of species diversity alone misses out on the full richness of patterns that can be inferred using a phylogenetic approach. Here, using Australian Acacia as an example, we show that the application of phylogenetic methods, particularly two new measures, relative phylogenetic diversity and relative phylogenetic endemism, greatly enhances our knowledge of biodiversity across both space and time. We found that areas of high species richness and species endemism are not necessarily areas of high phylogenetic diversity or phylogenetic endemism. We propose a new method called categorical analysis of neo- and paleo-endemism (CANAPE) that allows, for the first time, a clear, quantitative distinction between centres of neo- and paleo-endemism, useful to the conservation decision-making process.

Plos One, 2014

The largest digitized dataset of land plant distributions in Australia assembled to date (750,741... more The largest digitized dataset of land plant distributions in Australia assembled to date (750,741 georeferenced herbarium records; 6,043 species) was used to partition the Australian continent into phytogeographical regions. We used a set of six widely distributed vascular plant groups and three non-vascular plant groups which together occur in a variety of landscapes/habitats across Australia. Phytogeographical regions were identified using quantitative analyses of species turnover, the rate of change in species composition between sites, calculated as Simpson's beta. We propose six major phytogeographical regions for Australia: Northern, Northern Desert, Eremaean, Eastern Queensland, Euronotian and South-Western. Our new phytogeographical regions show a spatial agreement of 65% with respect to previously defined phytogeographical regions of Australia. We also confirm that these new regions are in general agreement with the biomes of Australia and other contemporary biogeographical classifications. To assess the meaningfulness of the proposed phytogeographical regions, we evaluated how they relate to broad scale environmental gradients. Physiographic factors such as geology do not have a strong correspondence with our proposed regions. Instead, we identified climate as the main environmental driver. The use of an unprecedentedly large dataset of multiple plant groups, coupled with an explicit quantitative analysis, makes this study novel and allows an improved historical bioregionalization scheme for Australian plants. Our analyses show that: (1) there is considerable overlap between our results and older biogeographic classifications; (2) phytogeographical regions based on species turnover can be a powerful tool to further partition the landscape into meaningful units; (3) further studies using phylogenetic turnover metrics are needed to test the taxonomic areas.

Diversity and Distributions, 2014

Aim To map spatial patterns of species richness, species endemism and species turnover of the eu... more Aim
To map spatial patterns of species richness, species endemism and species turnover of the eucalypts; to propose a biogeographical regionalization of eucalypts based on species turnover; and to identify the environmental correlates of these patterns.

Location
Australia and Malesia.

Methods
We analysed 798 eucalypt species (Angophora, Corymbia and Eucalyptus) with distributions across Australia and Malesia using square cells with a resolution of 100 9 100 km. Species richness, endemism and species turnover were calculated. Phytogeographical regions were identified using an agglomerative cluster analysis derived from a matrix of pairwise Simpson’s beta (bsim) dissimilarity values. Eleven environmental variables were used to analyse the environmental correlates of species turnover. Non-metric multidimensional scaling (NMDS) of the bsim, Getis-Ord Gi* hotspot spatial statistics and an ordination of the bsim -NMDS were used to investigate the environmental drivers at the continental level and for each of the phytogeographical regions.

Results
We identified three centres of species richness and fourteen of endemism, of which several are newly identified. The main centres of species richness agree with previous studies. Six major eucalypt phytogeographical regions are proposed based on the species turnover: monsoon, tropical/subtropical, south-east, south-west, Eremaean north and Eremaean south. These findings are supported by significant environmental differences of the NMDS vectors and the Gi* statistics. The environmental drivers of species turnover are broadly consistent with the continental patterns of summer and winter rainfall below and above the Tropic of Capricorn.

Main conclusions
The proposed phytogeographical regions are similar to the Australian biomes. Climate is the main driver of the phytogeographical regions, varying from region to region. Comprehensive bioregionalization frameworks and phytogeography updates, as proposed here, are fundamental for enhancing our understanding of the spatial distribution of biodiversity and therefore benefit global biogeography and help planners to identify regions of high conservation relevance.