Geographic patterns and climatic correlates of deep evolutionary legacies for angiosperm assemblages in China

Deep evolutionary histories can play an important role in assembling species into communities, but few studies have explored the effects of deep evolutionary histories on species assembly of angiosperms (flowering plants). Here we explore patterns of family divergence and diversification times (stem and crown ages, respectively) and phylogenetic fuses for angiosperm assemblages in 100 × 100 km grid cells across geographic and ecological gradients in China. We found that both family stem and crown ages of angiosperm assemblages are older in southeastern China with warm and humid climates than in northwestern China with cold and dry climates; these patterns are stronger for family stem ages than for family crown ages; families in colder and drier climates are more closely related across the family-level angiosperm phylogeny; and family phylogenetic fuses are, on average, longer for angiosperm assemblages in warm and humid climates than in cold and dry climate. We conclude that the fact that deep evolutionary histories, which were measured as family stem and crown ages and family phylogenetic fuses in this study, have shown strong geographic and ecological patterns suggests that deep evolutionary histories of angiosperms have profound effects on assembling angiosperm species into ecological communities.     

Woody plants optimise stomatal behaviour relative to hydraulic risk

Stomatal response to environmental conditions forms the backbone of all ecosystem and carbon cycle models, but is largely based on empirical relationships. Evolutionary theories of stomatal behaviour are critical for guarding against prediction errors of empirical models under future climates. Longstanding theory holds that stomata maximise fitness by acting to maintain constant marginal water use efficiency over a given time horizon, but a recent evolutionary theory proposes that stomata instead maximise carbon gain minus carbon costs/risk of hydraulic damage. Using data from 34 species that span global forest biomes, we find that the recent carbon‐maximisation optimisation theory is widely supported, revealing that the evolution of stomatal regulation has not been primarily driven by attainment of constant marginal water use efficiency. Optimal control of stomata to manage hydraulic risk is likely to have significant consequences for ecosystem fluxes during drought, which is critical given projected intensification of the global hydrological cycle.     

Regulation of jasmonate metabolism and activation of systemic signaling in Solanum nigrum: COI1 and JAR4 play overlapping yet distinct roles

? Understory plants are subjected to highly intermittent light availability and their leaf gas exchanges are mediated by delayed responses of stomata and leaf biochemistry to light fluctuations. In this article, the patterns in stomatal delays across biomes and plant functional types were studied and their effects on leaf carbon gains and water losses were quantified. ? A database of more than 60 published datasets on stomatal responses to light fluctuations was assembled. To interpret these experimental observations, a leaf gas exchange model was developed and coupled to a novel formulation of stomatal movement energetics. The model was used to test whether stomatal delays optimize light capture for photosynthesis, whilst limiting transpiration and carbon costs for stomatal movement. ? The data analysis showed that stomatal opening and closing delays occurred over a limited range of values and were strongly correlated. Plant functional type and climate were the most important drivers of stomatal delays, with faster responses in graminoids and species from dry climates. ? Although perfectly tracking stomata would maximize photosynthesis and minimize transpiration at the expense of large opening costs, the observed combinations of opening and closure times appeared to be consistent with a near-optimal balance of carbon gain, water loss and movement costs.     

Post-Eocene climate change, niche conservatism, and the latitudinal diversity gradient of New World birds

Aim The aim of this study was to test a variant of the evolutionary time hypothesis for the bird latitudinal diversity gradient derived from the effects of niche conservatism in the face of global climate change over evolutionary time. Location The Western Hemisphere. Methods We used digitized range maps of breeding birds to estimate the species richness at two grain sizes, 756 and 12,100 km². We then used molecular phylogenies resolved to family to quantify the root distance (RD) of each species as a measure of its level of evolutionary development. Birds were classified as ‘basal’ or ‘derived’ based on the RD of their family, and richness patterns were contrasted for the most basal and most derived 30% of species. We also generated temperature estimates for the Palaeogene across the Western Hemisphere to examine how spatial covariation between past and present climates might make it difficult to distinguish between ecological and evolutionary hypotheses for the current richness gradient. Results The warm, wet tropics support many species from basal bird clades, whereas the northern temperate zone and cool or dry tropics are dominated by species from more recent, evolutionarily derived clades. Furthermore, crucial to evaluating how niche conservatism among birds may drive the hemispherical richness gradient, the spatial structure of the richness gradient for basal groups is statistically indistinguishable from the overall gradient, whereas the richness gradient for derived groups is much shallower than the overall gradient. Finally, modern temperatures and the pattern of climate cooling since the Eocene are indistinguishable as predictors of bird species richness. Main conclusions Differences in the richness gradients of basal vs. derived clades suggest that the hemispherical gradient has been strongly influenced by the differential extirpation of species in older, warm‐adapted clades from parts of the world that have become cooler in the present. We propose that niche conservatism and global‐scale climate change over evolutionary time provide a parsimonious explanation for the contemporary bird latitudinal diversity gradient in the New World, although dispersal limitation of some highly derived clades probably plays a secondary role.     

How mountains shape biodiversity: The role of the Andes in biogeography,diversification, and reproductive biology in South America's most species‐rich lizard radiation (Squamata: Liolaemidae)

Testing hypotheses on drivers of clade evolution and trait diversification provides insight into many aspects of evolutionary biology. Often, studies investigate only intrinsic biological properties of organisms as the causes of diversity, however, extrinsic properties of a clade's environment, particularly geological history, may also offer compelling explanations. The Andes are a young mountain chain known to have shaped many aspects of climate and diversity of South America. The Liolaemidae are a radiation of South American reptiles with over 300 species found across most biomes and with similar numbers of egg‐laying and live‐bearing species. Using the most complete dated phylogeny of the family, we tested the role of Andean uplift in biogeography, diversification patterns, and parity mode of the Liolaemidae. We find that the Andes promoted lineage diversification and acted as a species pump into surrounding biomes. We also find strong support for the role of Andean uplift in boosting the species diversity of these lizards via allopatric fragmentation. Finally, we find repeated shifts in parity mode associated with changing thermal niches, with live‐bearing favored in cold climates and egg‐laying favored in warm climates. Importantly, we find evidence for possible reversals to oviparity, an evolutionary transition believed to be extremely rare.     

Frugivore gape size and the evolution of fruit size and shape in southern hemisphere floras

Abstract The present study uses differences among frugivore faunas of the southern hemisphere landmasses to test whether frugivore characteristics have influenced the evolution of fruit traits. Strong floristic similarities exist among southern landmasses; for example, 75% of New Zealand vascular plant genera also have species in Australia. However, plants in Australia and South America have evolved in the presence of a range of mammalian frugivores, whereas those in New Zealand, New Caledonia and the Pacific Islands have not. In addition, the avian frugivores in New Zealand and New Caledonia are generally smaller than those of Australia. If frugivore characteristics have influenced the evolution of fruit traits, predictable differences should exist between southern hemisphere fruits, particularly fruit size and shape. Fruit dimensions were measured for 77 New Zealand species and 31 Australian species in trans‐Tasman genera. New Zealand fruits became significantly more ellipsoid in shape with increasing size. This is consistent with frugivore gape size imposing a selective pressure on fruit ingestability. This result is not a product of phylogenetic correlates, as fruit length and width scaled isometrically for Australian species in genera shared with New Zealand. Within‐genus contrasts between New Zealand and Australian species in 20 trans‐Tasman genera showed that New Zealand species have significantly smaller fruits than their Australian counterparts. Within‐genus contrasts between New Zealand and South American species in nine genera gave the same result; New Zealand species had significantly smaller fruits than their South American counterparts. No difference was found in fruit size or shape between New Zealand and New Caledonia congeneric species from 12 genera. These results are consistent with the broad characteristics of the frugivore assemblage influencing the evolution of fruit size and shape in related species. The smaller‐sized New Zealand frugivore assemblage has apparently influenced the evolution of fruit size of colonizing taxa sometimes within a relatively short evolutionary timeframe.     

Relationships between gas-exchange characteristics and stomatal structural modifications in some desert grasses under high salinity

Two populations, one from lesser saline Derawar Fort (DF) and the other from highly saline Ladam Sir (LS) in the Cholistan desert, for each of the five grass species, Aeluropus lagopoides, Cymbopogon jwarancusa, Lasiurus scindicus, Ochthochloa compressa, and Sporobolus ioclados were examined to investigate the influence of salinity on structural and functional characteristics of stomata. Salinity tolerance in A. lagopoides mainly depended on controlled transpiration rate (E) and high water-use efficiency (WUE), which was found to be regulated by fewer and smaller stomata on both leaf surfaces as well as stomatal encryption by epidermal invaginations. C. jwarancusa had sunken stomata on the abaxial surface only, which largely reflected a reduced E, but less affected stomatal conductance (g _s) or WUE. L. scindicus had fewer but larger stomata along with hairs/trichomes which may function to avoid water loss through transpiration, and hence, to attain a high WUE. In O. compressa stomata were found only on the abaxial surface and these were completely encrypted by epidermal invaginations as well as a dense covering of microhairs, which was associated with a low E and high WUE under salinity stress. In S. ioclados, the traits of increased stomatal density and decreased stomatal area may be critical for stomatal regulation under salt-prone environments. High stomatal regulation depended largely on stomatal density, area, and degree of encryption under salinity, which is of great ecophysiological significance for plants growing under osmotic stresses.     

Historical biogeography and the origin of stomatal distributions in Banksia and Dryandra (Proteaceae) based on their cpDNA phylogeny

Banksia and Dryandra have undergone extensive speciation and adaptive radiation, especially in Australia's isolated Southwest Botanical Province. We derive a phylogeny for these groups based on cpDNA sequences and use it to reconstruct their historical biogeography and evolution of leaf traits thought to be adapted to drought and/or nutrient poverty. Slowly evolving regions (trnL intron, trnL/trnF spacer) are used to resolve large-scale relationships; faster evolving regions (rp116 intron, psbA/trnH and trnT/trnL spacers) are used to resolve relationships among closely related species. Banksia is paraphyletic with respect to Dryandra. The lineage underwent a basal split into two clades (here named /Cryptostomata and /Phanerostomata), and four infrageneric taxa supported by morphological cladistic analyses (series Spicigerae, Abietinae, Tetragonae, and Banksia) are not monophyletic. Dispersal-vicariance analysis resolves a southwestern Australian origin for the lineage, with two later expansions to the east followed by vicariance events. Stomatal crypts arose with the /Cryptostomata, which is characterized by tough, long-lived leaves and common in southwestern Australia. Sequestering of stomata also arose multiple times in /Phanerostomata, which is characterized by softer, short-lived leaves and common in moister coastal areas, via inrolling of the margins of narrow leaves and restricting stomata to shallow pits. The hypothesis that sclerophylly preadapted the plants to xeromorphy is supported in the case of shallow stomatal pits and deep stomatal crypts, but not narrow, needle-like leaves.     

Climate signals in Palaeozoic land plants

The Palaeozoic is regarded as a period in which it is difficult to recognize climate signals in land plants because they have few or no close extant relatives. In addition early, predominantly axial, representatives lack the features, e.g. leaf laminae, secondary growth, used later as qualitative and quantitive measures of past climates. Exceptions are stomata, and the preliminary results of a case study of a single taxon present throughout the Devonian, and analysis of stomatal complex anatomy attempt to disentangle evolutionary, taxonomic, habitat and atmospheric effects on stomatal frequencies. Ordovician-Silurian vegetation is represented mainly by spores whose widespread global distribution on palaeocontinental reconstructions with inferred climates suggest that the producers were independent of major climate variables, probably employing the physiology and behavioural strategies of extant bryophytes, further characterized by small size. Growth-ring studies, first possible on Mid-Devonian plants, have proved most informative in elucidating the climate at high palaeolatitudes in Late Permian Gondwana. Changes in the composition of Carboniferous-Permian low-latitude wetland vegetation are discussed in relation to tectonic activity and glaciation, with most confidence placed on the conclusion that major extinctions at the Westphalian-Stephanian boundary in Euramerica resulted from increased seasonality created by changes in circulation patterns at low latitudes imposed by the decrease of glaciations in most parts of Gondwana.     

Climate‐driven mitochondrial selection: A test in Australian songbirds

Diversifying selection between populations that inhabit different environments can promote lineage divergence within species and ultimately drive speciation. The mitochondrial genome (mitogenome) encodes essential proteins of the oxidative phosphorylation (OXPHOS) system and can be a strong target for climate‐driven selection (i.e., associated with inhabiting different climates). We investigated whether Pleistocene climate changes drove mitochondrial selection and evolution within Australian birds. First, using phylogeographic analyses of the mitochondrial ND2 gene for 17 songbird species, we identified mitochondrial clades (mitolineages). Second, using distance‐based redundancy analyses, we tested whether climate predicts variation in intraspecific genetic divergence beyond that explained by geographic distances and geographic position. Third, we analysed 41 complete mitogenome sequences representing each mitolineage of 17 species using codon models in a phylogenetic framework and a biochemical approach to identify signals of selection on OXPHOS protein‐coding genes and test for parallel selection in mitolineages of different species existing in similar climates. Of 17 species examined, 13 had multiple mitolineages (range: 2–6). Climate was a significant predictor of mitochondrial variation in eight species. At least two amino acid replacements in OXPHOS complex I could have evolved under positive selection in specific mitolineages of two species. Protein homology modelling showed one of these to be in the loop region of the ND6 protein channel and the other in the functionally critical helix HL region of ND5. These findings call for direct tests of the functional and evolutionary significance of mitochondrial protein candidates for climate‐associated selection.     

Contrasting responses of leaf stomatal characteristics to climate change: a considerable challenge to predict carbon and water cycles

Stomata control the cycling of water and carbon between plants and the atmosphere; however, no consistent conclusions have been drawn regarding the response of stomatal frequency to climate change. Here, we conducted a meta‐analysis of 1854 globally obtained data series to determine the response of stomatal frequency to climate change, which including four plant life forms (over 900 species), at altitudes ranging from 0 to 4500 m and over a time span of more than one hundred thousand years. Stomatal frequency decreased with increasing CO₂ concentration and increased with elevated temperature and drought stress; it was also dependent on the species and experimental conditions. The response of stomatal frequency to climate change showed a trade‐off between stomatal control strategies and environmental factors, such as the CO₂ concentration, temperature, and soil water availability. Moreover, threshold effects of elevated CO₂ and temperature on stomatal frequency were detected, indicating that the response of stomatal density to increasing CO₂ concentration will decrease over the next few years. The results also suggested that the stomatal index may be more reliable than stomatal density for determination of the historic CO₂ concentration. Our findings indicate that the contrasting responses of stomata to climate change bring a considerable challenge in predicting future water and carbon cycles.     

THE CUTICLE OF DREPANOPHYCUS SPINAEFORMIS,A LONG-RANGING DEVONIAN LYCOPOD FROM NEW YORK AND EASTERN CANADA

The presence of paracytic stomata and paired guard cells on specimens presumed to be Drepanophycus spinaeformis Göppert from eastern Canada and New York State supports the conclusion of Banks and Grierson that the species is not a reliable index of Lower Devonian strata. The interpretation of stomatal morphology demonstrates that the species lived in Early, Middle, and Late Devonian time and that slender specimens are distinct from zosterophylls such as Sawdonia that had anomocytic stomata and a single guard cell. Knowledge of the stomata also permits a reinterpretation of the stomatal apparatus as first described by Lang. Siegenian specimens of the genus apparently represent the oldest occurrence of paired guard cells and of paracytic stomata.     

Large-scale patterns of stomatal traits in Tibetan and Mongolian grassland species

We aimed to disentangle the influence of environmental variables on the spatial patterns in stomatal occurrence and stomatal traits. We surveyed the stomatal occurrence and the stomatal length (SL), density (SD) and index (SI) of 99 species in 150 grassland sites on the Tibetan and Inner Mongolian Plateau to explore their spatial patterns and evaluate the influence of climate. Of all species studied, two thirds were amphistomatous. The species from the Tibetan Plateau had larger but fewer stomata than those from Inner Mongolia. Among the climate factors examined, temperature and insolation affected SD, SI and SL, whereas the CO₂ partial pressure and the relative humidity affected SD. The climatic variables showed similar effects on the spatial variation of the adaxial and abaxial stomatal traits. We conclude that the low temperature and high insolation at high altitudes may be responsible for the larger and fewer stomata in plants on the Tibetan Plateau. The stomatal parameters that are presented here can be used to model the gas exchanges at the ecosystem scale.     

Comparison of temperate and tropical rainforest tree species: photosynthetic responses to growth temperature

Little is known about the differences in physiology between temperate and tropical trees. Australian rainforests extend from tropical climates in the north to temperate climates in the south over a span of 33° latitude. Therefore, they provide an opportunity to investigate differences in the physiology of temperate and tropical trees within the same vegetation type. This study investigated how the response of net photosynthesis to growth temperature differed between Australian temperate and tropical rainforest trees and how this correlated with differences in their climates. The temperate species showed their maximum rate of net photosynthesis at lower growth temperatures than the tropical species. However, the temperate species showed at least 80% of maximum net photosynthesis over a 12-16°C span of growth temperature, compared with a span of 9-11°C shown by the tropical species. The tropical species showed both larger reductions in maximum net photosynthesis at low growth temperatures and larger reductions in the optimum instantaneous temperature for net photosynthesis with decreasing growth temperature than the temperate species. The ability of the temperate species to maintain maximum net photosynthesis over a greater span of growth temperatures than the tropical species is consistent with the greater seasonal and day-to-day variation in temperature of the temperate climate compared with the tropical climate.     

Patterns of diversification in New Zealand Stylidiaceae

Phylogenetic analysis of ITS and rbcL sequences show that New Zealand Stylidiaceae fall into two distinct lineages differing in species richness. Each lineage represents a unique dispersal event to New Zealand occurring at different times during the evolutionary history of the family. One lineage comprises seven species of Forstera and Phyllachne, while the other consists solely of Oreostylidium subulatum. The origin of the Forstera/Phyllachne lineage in New Zealand is equivocal; either a South American or a Tasmanian origin is equally parsimonious. Possible sister groups are F. bellidifolia in Tasmania and P. uliginosa in South America. Oreostylidium subulatum has an Australian origin. In our analyses O. subulatum is nested in a clade composed entirely of species of Stylidium, almost all of which are endemic to Australia. Species of Phyllachne share a cushion habit with the outgroup Donatia (Donatiaceae) that may have preadapted them to alpine environments in New Zealand. The New Zealand Stylidiaceae have small, white, actinomorphic flowers that are well adapted to the unspecialized pollinator fauna. Forstera and Phyllachne share this trait with Donatia; however, the small, white flowers of Oreostylidium are a dramatic departure from the colorful, highly specialized flowers of Stylidium.     

Environment, area, and diversification in the species-rich flowering plant family Iridaceae

Phylogenetic analyses provide a means to explore evolutionary explanations for regional variation in species richness. The environment might also explain much of the previously unexplained imbalance of phylogenetic trees. We use data on geographic distribution and phylogenetic affinity to examine correlates of species richness among genera of irises (family: Iridaceae). Irises display strong phylogenetic imbalance, with a few clades containing a disproportionate number of species, most notably those found in the dry Mediterranean climate of the Cape of South Africa. The abiotic environment and area are strong predictors of iris species richness, but environment alone is insufficient to explain the high diversity of Cape clades. One possible explanation is that the interaction between biological traits and environment resulted in the unusually high diversification rates in the region.     

Ecophysiological responses of two closely related Magnoliaceae genera to seasonal changes in subtropical China

Aims Plants use a variety of hydraulic strategies to adapt to seasonal drought that differ by species and environmental conditions. The early-diverging Magnoliaceae family includes two closely related genera with contrasting leaf habits, Yulania (deciduous) and Michelia (evergreen), which naturally inhabit temperate and tropical regions, respectively. Here, we evaluate the hydraulic strategy of species from both genera that have been ex situ conserved in a subtropical region to determine how they respond to the novel cool–dry season climatic pattern.Methods We measured ecophysiological traits in five Michelia and five Yulania species conserved in the South China Botanical Garden in both wet and dry season conditions and monitored the whole-year sap flow for four of these species.Important findings We found that Magnoliaceae species that have been ex situ conserved in a subtropical climate did not suffer from excessive water stress due to the mild drought conditions of the dry season and the ecophysiological adjustments the species made to avoid this stress, which differed by leaf habit. Specifically, deciduous species completely shed their leaves during the dry season, while evergreen species decreased their turgor loss points, dry mass based photosynthetic rates, stomatal conductance and specific leaf areas (SLAs) compared to wet season measurements. In comparing the two distinct leaf habits during the wet season, the leathery-leaved evergreen species had higher leaf hydraulic conductance and leaf to sapwood area ratios than the papery-leaved deciduous species, while the deciduous species had greater hydraulic conductivity calculated on both a stem and leaf area basis, dry mass based photosynthetic rates, leaf nutrients, SLAs and stomatal sizes than the evergreen species. Interestingly, species from both genera maintained similar sap flow in the wet season. Both photosynthetically active radiation and vapour pressure deficit affected the diurnal patterns of sap flow in the wet season, while only vapour pressure deficit played a dominant role in the dry season. This study reveals contrasting hydraulic strategies in Yulania and Michelia species under subtropical seasonal conditions, and suggests that these ecophysiological adjustments might be affected more by leaf habit than seasonality, thus reflecting the divergent evolution of the two closely related genera. Furthermore, we show that Magnoliaceae species that are ex situ conserved in a subtropical climate are hydraulically sound, a finding that will inform future conservation efforts of this ancient family under the threat of climatic change.     

Leaf fossils of Banksia (Proteaceae) from New Zealand: An Australian abroad

Fossils can shed new light on plant biogeography and phylogeny. Pinnately lobed leaves from the Oligo-Miocene Newvale lignite mine, South Island, New Zealand are the first extra-Australian leaf fossils of the charismatic genus Banksia (Proteaceae), and they are assigned to a new species, B. novae-zelandiae. Comparison with extant taxa shows that the fossils are best regarded as an extinct stem relative of Banksia because their available features are either plesiomorphic for the genus (notably, the stomata are superficially placed, not sunken in balloon-like pits as in many extant species) or lack evidence of synapomorphies that would enable them to be placed in the crown group. Banksia novae-zelandiae does, however, exhibit two cuticular features that are unique or highly derived for Banksia. These are rugulate subsidiary cell ornamentation and the presence of complex papillae that extensively cover the abaxial leaf surface. The fossils add to the widespread records of the pinnately lobed leaf form in Banksia in Australia beginning in the late Paleocene. This form is now limited to species confined to sclerophyllous heathlands of Mediterranean climate in southwestern Australia. Banksia novae-zelandiae could be part of a lineage that had a long history in New Zealand, perhaps dating to the early Paleogene.     

Variation in the structure and development of foliar stomata in the Euphorbiaceae

The structure and ontogeny of foliar stomata were studied in 50 species of 28 genera belonging to 17 tribes of the family Euphorbiaceae. The epidermal cells are either polygonal, trapezoidal, or variously elongated in different directions and diffusely arranged. The epidermal anticlinal walls are either straight, arched or sinuous. The architecture of cuticular striations varies with species. The mature stomata are paracytic (most common), anisocytic, anomocytic and diacytic. Occasionally a stoma may be tetracytic, cyclocytic or with a single subsidiary cell. The ontogeny of paracytic stomata is mesogenous dolabrate or trilabrate, mesoperigenous dolabrate; that of diacytic stomata is mesogenous dolabrate, whereas that of anisocytic stomata is mesogenous trilabrate; rarely an anisocytic stoma may be mesoperigenous. Hemiparacytic stomata are mesoperigenous unilabrate; tetracytic stomata are mesoperigenous dolabrate and anomocytic stomata perigenous. Abnormalities encountered include four types of contiguous stomata, stomata with a single or both guard cells aborted and persistent stomatal initials. Cytoplasmic connections between the guard cells of two adjacent stomata or the guard cell of a stoma and an adjacent epidermal/subsidiary cell, or both types occurring in a species, were noticed. The stomatal development, distribution, diversity and basic stomatal type with reference to systematics are discussed.     

Biogeography of the Australian monsoon tropics

Aim This paper reviews the biogeography of the Australian monsoon tropical biome to highlight general patterns in the distribution of a range of organisms and their environmental correlates and evolutionary history, as well as to identify knowledge gaps. Location Northern Australia, Australian Monsoon Tropics (AMT). The AMT is defined by areas that receive more than 85% of rainfall between November and April. Methods Literature is summarized, including the origin of the monsoon climate, present‐day environment, biota and habitat types, and phylogenetic and geographical relationships of selected organisms. Results Some species are widespread throughout the AMT while others are narrow‐range endemics. Such contrasting distributions correspond to present‐day climates, hydrologies (particularly floodplains), geological features (such as sandstone plateaux), fire regimes, and vegetation types (ranging from rain forest to savanna). Biogeographical and phylogenetic studies of terrestrial plants (e.g. eucalypts) and animals (vertebrates and invertebrates) suggest that distinct bioregions within the AMT reflect the aggregated effects of landscape and environmental history, although more research is required to determine and refine the boundaries of biogeographical zones within the AMT. Phylogenetic analyses of aquatic organisms (fishes and prawns) suggest histories of associations with drainage systems, dispersal barriers, links to New Guinea, and the existence of Lake Carpentaria, now submerged by the Gulf of Carpentaria. Complex adaptations to the landscape and climate in the AMT are illustrated by a number of species. Main conclusions The Australian monsoon is a component of a single global climate system, characterized by a dominant equator‐spanning Hadley cell. Evidence of hot, seasonally moist climates dates back to the Late Eocene, implying that certain endemic elements of the AMT biota have a long history. Vicariant differentiation is inferred to have separated the Kimberley and Arnhem Land bioregions from Cape York Peninsula/northern Queensland. Such older patterns are overlaid by younger events, including dispersal from Southeast Asia, and range expansions and contractions. Future palaeoecological and phylogenetic investigations will illuminate the evolution of the AMT biome. Understanding the biogeography of the AMT is essential to provide a framework for ecological studies and the sustainable development of the region.