Although temporal calibration is widely recognized as critical for obtaining accurate divergence-time estimates using molecular dating methods, few studies have evaluated the variation resulting from different calibration strategies. Depending on the information available, researchers have often used primary calibrations from the fossil record or secondary calibrations from previous molecular dating studies. In analyses of flowering plants, primary calibration data can be obtained from macro- and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g., pollen). Fossil data can vary substantially in accuracy and precision, presenting a difficult choice when selecting appropriate calibrations. Here, we test the impact of eight plausible calibration scenarios for Nothofagus (Nothofagaceae, Fagales), a plant genus with a particularly rich and well-studied fossil record. To do so, we reviewed the phylogenetic placement and geochronology of 38 fossil taxa of Nothofagus and other Fagales, and we identified minimum age constraints for up to 18 nodes of the phylogeny of Fagales. Molecular dating analyses were conducted for each scenario using maximum likelihood (RAxML + r8s) and Bayesian (BEAST) approaches on sequence data from six regions of the chloroplast and nuclear genomes. Using either ingroup or outgroup constraints, or both, led to similar age estimates, except near strongly influential calibration nodes. Using "early but risky" fossil constraints in addition to "safe but late" constraints, or using assumptions of vicariance instead of fossil constraints, led to older age estimates. In contrast, using secondary calibration points yielded drastically younger age estimates. This empirical study highlights the critical influence of calibration on molecular dating analyses. Even in a best-case situation, with many thoroughly vetted fossils available, substantial uncertainties can remain in the estimates of divergence times. For example, our estimates for the crown group age of Nothofagus varied from 13 to 113 Ma across our full range of calibration scenarios. We suggest that increased background research should be made at all stages of the calibration process to reduce errors wherever possible, from verifying the geochronological data on the fossils to critical reassessment of their phylogenetic position.

Aim The mesic biome, encompassing both rain forest and open sclerophyllous forests, is central to understanding the evolution of Australia's terrestrial biota and has long been considered the ancestral biome of the continent. Our aims are to review and refine key hypotheses derived from palaeoclimatic data and the fossil record that are critical to understanding the evolution of the Australian mesic biota. We examine predictions arising from these hypotheses using available molecular phylogenetic and phylogeographical data. In doing so, we increase understanding of the mesic biota and highlight data deficiencies and fruitful areas for future research.Location The mesic biome of Australia, along the eastern coast of Australia, and in the south-east and south-west, including its rain forest and sclerophyllous, often eucalypt-dominated, habitats.Methods We derived five hypotheses based on palaeoclimatic and fossil data regarding the evolution of the Australian mesic biota, particularly as it relates to the mesic biome. We evaluated predictions formulated from these hypotheses using suitable molecular phylogenies of terrestrial plants and animals and freshwater invertebrates.Results There was support for the ancestral position of mesic habitat in most clades, with support for rain forest habitat ancestry in some groups, while evidence of ancestry in mesic sclerophyllous habitats was also demonstrated for some plants and herpetofauna. Contraction of mesic habitats has led to extinction of numerous lineages in many clades and this is particularly evident in the rain forest component. Species richness was generally higher in sclerophyllous clades than in rain forest clades, probably due to higher rates of net speciation in the former and extinction in the latter. Although extinction has been prominent in rain forest communities, tropical rain forests appear to have experienced extensive immigration from northern neighbours. Pleistocene climatic oscillations have left genetic signatures at multiple levels of divergence and with complex geographical structuring, even in areas with low topographical relief and few obvious geographical barriers.Main conclusions Our review confirms long-held views of the ancestral position of the Australian mesic biome but also reveals new insights into the complexity of the processes of contraction, fragmentation, extinction and invasion during the evolution of this biome.

Gondwanan rainforest lineages contribute significantly to modern rainforest community assembly and often co-occur in widely separated assemblages far from their early fossil records. Understanding how and where lineages from ancient Gondwanan assemblages co-occur today has implications for the conservation of global rainforest vegetation, including in the Old World tropics.

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The Pliocene epoch (5.3-2.6 Ma) represents the most recent geological interval in which global temperatures were several degrees warmer than today and is therefore considered our best analog for a future anthropogenic greenhouse world. However, our understanding of Pliocene climates is limited by poor age control on existing terrestrial climate archives, especially in the Southern Hemisphere, and by persistent disagreement between paleo-data and models concerning the magnitude of regional warming and/or wetting that occurred in response to increased greenhouse forcing. To address these problems, here we document the evolution of Southern Hemisphere hydrocli-mate from the latest Miocene to the middle Pliocene using radiomet-rically-dated fossil pollen records preserved in speleothems from semiarid southern Australia. These data reveal an abrupt onset of warm and wet climates early within the Pliocene, driving complete biome turnover. Pliocene warmth thus clearly represents a discrete interval which reversed a long-term trend of late Neogene cooling and aridification, rather than being simply the most recent period of greater-than-modern warmth within a continuously cooling trajec-tory. These findings demonstrate the importance of high-resolution chronologies to accompany paleoclimate data and also highlight the question of what initiated the sustained interval of Pliocene warmth. paleoclimate | pollen | speleothems | aridification | Neogene

Aim We tested an entrenched concept -that the Australian rain forest flora is essentially a Gondwanan relict. We also assessed the role of regional-level sourcesink dynamics in the assembly of this flora. Location Eastern Australia.Methods To avoid potential biases inherent in selective studies undertaken to date, we used an analytical, whole-of-flora approach integrated with the fossil record. We identified disjunctions between woody Australian rain forest plant taxa and relatives on other land masses. To test the strength of the fossil evidence for the regional antiquity of this flora, we evaluated the proportion of these disjunct clades represented in the Australian fossil record, and to minimize the effects of biases in this record, we compared late Quaternary (i.e. late Pleistocene and Holocene, 126-0 ka), Pliocene and late Oligocene-early Miocene Australian pollen records interpreted as tropical rain forest. Using within-species disjunctions as a proxy, we assessed the role of recent immigration from Asia into Australia. To assess the role of source-sink dynamics, we performed comparative analyses of disjunctions in major rain forest categories representing a north-south/climatic gradient.Results Southern Australian, cool temperate (microthermal) rain forests contain many floristic disjunctions with Gondwanan fragments and most of these clades have Gondwanan fossils. Disjunct clades in Australian mesothermal rain forest mostly occur in Asia/Malesia and a low proportion of these clades show preNeogene records. Many clades in lowland tropical and 'dry' rain forest show disjunctions with Asia/Malesia and few have Australian fossil records. Rates of recent immigration from Asia/Malesia are high in these northern forests, and outweigh rates of recent emigration approximately nine-fold. The late Quaternary fossil record has many more rain forest angiosperms than Oligocene-Miocene and Pliocene floras, consistent with extensive late Cenozoic immigration.Main conclusions The microthermal rain forests are largely Gondwanan relicts, but there is progressively greater, and more recent contribution from Asia/ Malesia into more northern, and more lowland tropical rain forests. This variation reflects a strong gradient in geographic and ecological proximity between these forests and source floras in Asia/Malesia, and is consistent with a source-sink size model of immigration driven by late Cenozoic contractions and expansions of Australian rain forest.

Since the late Miocene, plants using the C4 photosynthetic pathway have increased to become major components of many tropical and subtropical ecosystems. However, the drivers for this expansion remain under debate, in part because of the varied histories of C4 vegetation on different continents. Australia hosts the highest dominance of C4 vegetation of all continents, but little is known about the history of C4 vegetation there. Carbon isotope ratios of plant waxes from scientific ocean drilling sediments off north‐western Australia reveal the onset of Australian C4 expansion at ~3.5 Ma, later than in many other regions. Pollen analysis from the same sediments reveals increasingly open C3‐dominated biomes preceding the shift to open C4‐dominated biomes by several million years. We hypothesize that the development of a summer monsoon climate beginning in the late Pliocene promoted a highly seasonal precipitation regime favorable to the expansion of C4 vegetation.

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