Relaxed molecular clock provides evidence for long-distance dispersal of Nothofagus (southern beech)

Nothofagus (southern beech), with an 80-million-year-old fossil record, has become iconic as a plant genus whose ancient Gondwanan relationships reach back into the Cretaceous era. Closely associated with Wegener's theory of “Kontinentaldrift”, Nothofagus has been regarded as the “key genus in plant biogeography”. This paradigm has the New Zealand species as passengers on a Moa's Ark that rafted away from other landmasses following the breakup of Gondwana. An alternative explanation for the current transoceanic distribution of species seems almost inconceivable given that Nothofagus seeds are generally thought to be poorly suited for dispersal across large distances or oceans. Here we test the Moa's Ark hypothesis using relaxed molecular clock methods in the analysis of a 7.2-kb fragment of the chloroplast genome. Our analyses provide the first unequivocal molecular clock evidence that, whilst some Nothofagus transoceanic distributions are consistent with vicariance, trans-Tasman Sea distributions can only be explained by long-distance dispersal. Thus, our analyses support the interpretation of an absence of Lophozonia and Fuscospora pollen types in the New Zealand Cretaceous fossil record as evidence for Tertiary dispersals of Nothofagus to New Zealand. Our findings contradict those from recent cladistic analyses of biogeographic data that have concluded transoceanic Nothofagus distributions can only be explained by vicariance events and subsequent extinction. They indicate that the biogeographic history of Nothofagus is more complex than envisaged under opposing polarised views expressed in the ongoing controversy over the relevance of dispersal and vicariance for explaining plant biodiversity. They provide motivation and justification for developing more complex hypotheses that seek to explain the origins of Southern Hemisphere biota.     

Panbiogeography of Nothofagus (Nothofagaceae): analysis of the main species massings

Aim The aim of this paper is to analyse the biogeography of Nothofagus and its subgenera in the light of molecular phylogenies and revisions of fossil taxa. Location Cooler parts of the South Pacific: Australia, Tasmania, New Zealand, montane New Guinea and New Caledonia, and southern South America. Methods Panbiogeographical analysis is used. This involves comparative study of the geographic distributions of the Nothofagus taxa and other organisms in the region, and correlation of the main patterns with historical geology. Results The four subgenera of Nothofagus have their main massings of extant species in the same localities as the main massings of all (fossil plus extant) species. These main massings are vicariant, with subgen. Lophozonia most diverse in southern South America (north of Chiloé I.), subgen. Fuscospora in New Zealand, subgen. Nothofagus in southern South America (south of Valdivia), and subgen. Brassospora in New Guinea and New Caledonia. The main massings of subgen. Brassospora and of the clade subgen. Brassospora/subgen. Nothofagus (New Guinea–New Caledonia–southern South America) conform to standard biogeographical patterns. Main conclusions The vicariant main massings of the four subgenera are compatible with largely allopatric differentiation and no substantial dispersal since at least the Upper Cretaceous (Upper Campanian), by which time the fossil record shows that the four subgenera had evolved. The New Guinea–New Caledonia distribution of subgenus Brassospora is equivalent to its total main massing through geological time and is explained by different respective relationships of different component terranes of the two countries. Global vicariance at family level suggests that Nothofagaceae/Nothofagus evolved largely as the South Pacific/Antarctic vicariant in the breakup of a world‐wide Fagales ancestor.     

Biogeographic mirages? Molecular evidence for dispersal‐driven evolution in Hydrobiusini water scavenger beetles

Water beetles of the tribe Hydrobiusini are globally distributed in the northern hemisphere and all austral continents except Antarctica. A remarkable clade also occurs in the Hawaiian Islands. The phylogenetic relationships among genera were recently investigated using a combination of molecules and morphology. Here, we use this phylogenetic framework to address the biogeographic evolution of this group using Bayesian fossil‐based divergence times, and model‐based maximum likelihood ancestral range estimations. We recover an origin of the tribe in the Cretaceous ca. 100 Ma. Our biogeographic analyses support an origin of the tribe in Laurasia followed by the colonization of Australia. However, a Gondwanan origin of the group cannot be ruled out when considering the fossil record. The timeframe of the tribe's evolution as well as the model‐based approach of ancestral range estimation favour a scenario invoking multiple transoceanic dispersal events over a Gondwana vicariance hypothesis. The Hawaiian radiation originated from long‐distance dispersal to now‐submerged islands, paired with dispersal to new islands as they formed.     

Molecular clocks keep dispersal hypotheses afloat: evidence for trans‐Atlantic rafting by rodents

Aim In order to resolve disputed biogeographical histories of biota with Gondwanan continental distributions, and to assess the null hypothesis of vicariance, it is imperative that a robust geological time‐frame be established. As an example, the sudden and coincident appearance of hystricognath rodents (Rodentia: Hystricognathi) on both the African and South American continents has been an irreconcilable controversy for evolutionary biologists, presenting enigmas for both Gondwanan vicariance and Late Eocene dispersal hypotheses. In an attempt to resolve this discordance, we aim to provide a more robust phylogenetic hypothesis and improve divergence‐date estimates, which are essential to assessing the null hypothesis of vicariance biogeography. Location The primary centres of distribution are in Africa and South America. Methods We implemented parsimony, maximum‐likelihood and Bayesian methods to generate a phylogeny of 37 hystricognath taxa, the most comprehensive taxonomic sampling of this group to date, on the basis of two nuclear gene regions. To increase phylogenetic resolution at the basal nodes, these data were combined with previously published data for six additional nuclear gene regions. Divergence dates were estimated using two relaxed‐molecular‐clock methods, Bayesian multidivtime and nonparametric rate smoothing. Results Our data do not support reciprocal monophyly of African and South American lineages. Indeed, Old World porcupines (i.e. Hystricomorpha) appear to be more closely related to New World lineages (i.e. Caviomorpha) than to other Old World families (i.e. Bathyergidae, Petromuridae and Thryonomyidae). The divergence between the monophyletic assemblage of South American lineages and its Old World ancestor was estimated to have occurred c. 50 Ma. Main conclusions Our phylogenetic hypothesis and divergence‐date estimates are strongly at odds with Gondwanan‐vicariance isolating mechanisms. In contrast, our data suggest that transoceanic dispersal has played a significant role in governing the contemporary distribution of hystricognath rodents. Molecular‐clock analyses imply a trans‐Tethys dispersal event, broadly confined to the Late Cretaceous, and trans‐Atlantic dispersal within the Early Eocene. Our analyses also imply that the use of the oldest known South American rodent fossil as a calibration point has biased molecular‐clock inferences.     

The ghosts of Gondwana and Laurasia in modern liverwort distributions

Recent advances in phylogenetics and, in particular, molecular dating, indicate that transoceanic dispersal has played an important role in shaping plant and animal distributions, obscuring any effect of tectonic history. Taxonomic sampling in biogeographic studies is, however, systematically biased towards vertebrates and higher plants and the possibility remains that a much stronger signature of ancient vicariance might be evident among other organisms, particularly among basal land plants. Here, an explicit Bayesian model‐based approach was used to investigate global‐scale biogeographic patterns among liverwort genera and to determine whether the patterns identified are consistent with the expectations of vicariance or dispersal scenarios. The distribution of each genus was mapped onto the phylograms describing the floristic affinities among areas in order to define the synapomorphic transitions supporting the observed groupings. The probabilities of change in a branch were calculated by implementing the Markov model of BayesTraits. The consistent ambiguity in ancestral state reconstructions returned by the unconstrained, two‐rate model indicated that the overall signal in the data was weak, leading us to test the performance of competing, explicit models. The analyses resolved clades of geographic areas that are mostly consistent with the kingdoms traditionally identified for plants and animals, but with strikingly lower rates of endemism. The major split observed in the phylograms is into almost entirely Laurasian and Gondwanan clades. Other patterns recovered by the analyses, including Wallace's line and the South Atlantic Disjunction, have also traditionally been interpreted in terms of vicariance. These observations contrast with the idea that, in spore‐dispersed organisms like bryophytes and pteridophytes, dispersal obscures evidence of vicariance. However, some discrepancies between the liverwort trees and expectations from a continental drift scenario were observed, such as the sister‐group relationship of the Australian and New Zealand floras, which is supported by the co‐occurrence of many genera, often endemic to these two areas. Together with an interpretation of the results within a phylogenetic context, our analyses suggest that patterns, which are at first sight consistent with an ancient vicariance hypothesis, may, in fact, conceal a complex mixture of relictual distributions and more recent, asymmetrical dispersal events. Our results provide a framework for testing specific evolutionary hypotheses concerning the extremely low levels of endemism in bryophytes and in particular, the significance of dispersal and cryptic diversification.     

Worldwide long‐distance dispersal favored by epizoochorous traits in the biogeographic history of Omphalodeae (Boraginaceae)

Biogeographic dispersal is supported by numerous phylogenetic results. In particular, transoceanic dispersal, rather than vicariance, is suggested for some plant lineages despite current long distances between America and Europe. However, few studies on the biogeographic history of plants have also studied the role of diaspore syndromes in long‐distance dispersal (LDD). Species of the tribe Omphalodeae (Boraginaceae) offer a suitable study system because the species have a wide variety of diaspore traits related to LDD and different lineages conform to patched worldwide distributions on three distant continents (Europe, America and New Zealand). Our aim is to reconstruct the biogeographical history of the Omphalodeae and to investigate the role of diaspore traits favoring LDD and current geographic distributions. To this end, a time‐calibrated phylogeny with 29 of 32 species described for Omphalodeae was reconstructed using biogeographical analyses (BioGeoBEARS, Lagrange) and models (DEC and DIVA) under different scenarios of land connectivity. Character‐state reconstruction (SIMMAP) and diversification rate estimations of the main lineages were also performed. The main result is that epizoochorous traits have been the ancestral state of LDD syndromes in most clades. An early diversification age of the tribe is inferred in the Western Mediterranean during late Oligocene. Colonization of the New World by Omphalodeae, followed by fast lineage differentiation, took place sometime in the Oligocene‐Miocene boundary, as already inferred for other angiosperm genera. In contrast, colonization of remote islands (New Zealand, Juan Fernández) occurred considerably later in the Miocene‐Pliocene boundary.     

Orthoglymma wangapeka gen.n., sp.n. (Coleoptera: Carabidae: Broscini): a newly discovered relict from the Buller Terrane,north‐western South Island,New Zealand,corroborates a general pattern of Gondwanan endemism

Orthoglymma Liebherr, Marris, Emberson, Syrett & Roig‐Juñent gen.n. (Coleoptera: Carabidae: Broscini) is described to accommodate the single type species Orthoglymma wangapeka Liebherr, Marris, Emberson, Syrett & Roig‐Juñent sp.n., known from the Wangapeka Track, Kahurangi National Park, north‐western South Island, New Zealand. Orthoglymma wangapeka sp.n. is analysed cladistically along with a comprehensive array of 42 other broscine generic terminals and four out‐group taxa, using information obtained from 73 morphological characters, and placed as adelphotaxon to the remainder of subtribe Nothobroscina, a clade distributed in New Zealand, southern South America and Australia. Based on fossil evidence for Carabidae, the occurrence of Orthoglymma wangapeka sp.n. on the Buller Terrane, a geological feature once situated on the eastern margin of Gondwana, and early cladistic divergence of Orthoglymma from the remaining Nothobroscina, Orthoglymma wangapeka sp.n. is interpreted as a Gondwanan relict. The New Zealand arthropod fauna is reviewed to identify other taxa in existence at the time of Cretaceous vicariance of New Zealand and Australia. These candidate Gondwanan taxa, all of which are specified using fossil data or molecular divergence‐based estimates, are analysed biogeographically. Where phylogenetic hypotheses are available, primordial distributions are optimized using event‐based, dispersal‐vicariance (DIVA) analysis. The hypothesized Gondwanan‐aged taxa demonstrate inordinate fidelity to the Gondwanan‐aged geological terranes that constitute the western portions of New Zealand, especially in the South Island. Persistence of these relicts through a hypothesized ‘Oligocene drowning’ event is the most parsimonious explanation for the concentration of Gondwanan relicts in the Nelson, Buller and Fiordland districts of the South Island. Geographic patterns of Gondwanan‐aged taxa are compared with distributions of taxa hypothesized to have colonized New Zealand across the Tasman Sea from Australia and New Caledonia, subsequent to Cretaceous vicariance. These post‐Gondwanan taxa exhibit very different patterns of distribution and diversification in New Zealand, including: (i) abundant endemism in Northland, and the islands and peninsulas of the North Island; (ii) species geographically restricted to areas underlain by the youngest Rakaia and Pahau geological terranes; and (iii) species exhibiting exceedingly widespread geographic distributions spanning geological terranes of disparate ages.

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Molecular dating of the 'Gondwanan' plant family Proteaceae is only partially congruent with the timing of the break-up of Gondwana

Aim  The flowering plant family Proteaceae is putatively of Gondwanan age, with modern and fossil lineages found on all southern continents. Here we test whether the present distribution of Proteaceae can be explained by vicariance caused by the break-up of Gondwana.
Location  Africa, especially southern Africa, Australia, New Zealand, South America, New Caledonia, New Guinea, Southeast Asia, Sulawesi, Tasmania.
Methods  We obtained chloroplast DNA sequence data from the rbc L gene, the rbc L- atp B spacer, and the atp B gene from leaf samples of forty-five genera collected from the field and from living collections. We analysed these data using Bayesian phylogenetic and molecular dating methods, with five carefully selected fossil calibration points to obtain age estimates for the nodes within the family.
Results  Four of eight trans-continental disjunctions of sister groups within our sample of the Proteaceae post-date the break-up of Gondwana. These involve independent lineages, two with an Africa-Australia disjunction, one with an Africa–South America disjunction, and one with a New Zealand–Australasia disjunction. The date of the radiation of the bird-pollinated Embothriinae corresponds approximately to the hypothesized date of origin of nectar-feeding birds in Australia.
Main conclusions  The findings suggest that disjunct distributions in Proteaceae result from both Gondwanan vicariance and transoceanic dispersal. Our results imply that ancestors of some taxa dispersed across oceans rather than rafting with Gondwanan fragments as previously thought. This finding agrees with other studies of Gondwanan plants in dating the divergence of Australian, New Zealand and New Caledonian taxa in the Eocene, consistent with the existence of a shared, ancestral Eocene flora but contrary to a vicariance scenario based on accepted geological knowledge.     

MOLECULAR CLOCKS PROVIDE NEW INSIGHTS INTO THE EVOLUTIONARY HISTORY OF GALEICHTHYINE SEA CATFISHES

Intercontinental distributions in the southern hemisphere can either be the result of Gondwanan vicariance or more recent transoceanic dispersal. Transoceanic dispersal has come into vogue for explaining many intercontinental distributions; however, it has been used mainly for organisms that can float or raft between the continents. Despite their name, the Sea Catfishes (Ariidae) have limited dispersal ability, and there are no examples of nearshore ariid genera with a transoceanic distribution except for Galeichthys where three species occur in southern Africa and one in the Peruvian coast. A previous study suggested that the group originated in Gondwana, and that the species arrived at their current range after the breakup of the supercontinent in the Early Cretaceous. To test this hypothesis, we infer molecular phylogenies (mitochondrial cytochrome b , ATP synthase 8/6, 12S, and 16S; nuclear rag2 ; total ∼4 kb) and estimate intercontinental divergence via molecular clocks (penalized-likelihood, Bayesian relaxed clock, and universal clock rates in fishes). Age ranges for cladogenesis of African and South American lineages are 15.4–2.5 my, far more recent than would be suggested by Gondwanan vicariance; thus, the distribution of galeichthyines must be explained by dispersal or more recent vicariant events. The nested position of the Peruvian species ( Galeichthys peruvianus ) within the African taxa is robust, suggesting that the direction of the dispersal was from Africa to South America. The progenitor of the Peruvian species likely arrived at its current distribution with the aid of ocean currents, and several scenarios are discussed.     

Biological disjunction along the West Caledonian fault,New Caledonia: a synthesis of molecular phylogenetics and panbiogeography

This paper documents a newly discovered pattern of biological disjunction between NW and SE New Caledonia. The disjunction occurs in 87 (mapped) taxa, including plants, moths and lizards, and correlates spatially with the West Caledonian fault. This fault is controversial; some geologists interpret it as a major structure, others deny that it exists. It may have undergone 150–200 km of lateral movement and it is suggested that this has caused the biological disjunction by pulling populations apart. The disjunction matches similar dextral disjunctions of taxa along transform faults in New Zealand, New Guinea, California and Indonesia. Major biogeographic patterns – whether centres of diversity, boundaries of allopatric taxa or disjunctions – all include taxa with many different degrees of differentiation. Studies using a clock model of evolution will therefore interpret a biogeographic pattern as the result of many disparate events. However, this line of reasoning reaches the untenable conclusion that biogeographic patterns, including normal allopatry, are always caused by chance dispersal, never by vicariance. A more productive approach, avoiding the pitfalls of a fossil‐based molecular clock, involves a close examination of molecular clades, comparative biogeography and tectonics. The New Caledonia example documented here shows that this can lead to novel, testable predictions. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 158 , 470–488.     

The age and biogeography of Citrus and the orange subfamily (Rutaceae: Aurantioideae) in Australasia and New Caledonia

The geological history of Australasia, New Caledonia, and Southeast Asia, has been complex, resulting in competing biogeographic hypotheses for taxa found here. Alternative hypotheses-Gondwanan vicariance, rafting terranes, long-distance dispersal-may be distinguished by different predicted divergence times between disjunct sister taxa. Taxa within Rutaceae subfamily Aurantioideae are ideal for testing these hypotheses because of their distributions. Therefore, the ages of Rutaceae and Aurantioideae were estimated using molecular dating. One data set comprised 51 sequences of rbcL and atpB with sampling across rosids and three fossil calibrations: crown Fabales+Fagales+Rosales (>94 Ma), Fabaceae (>51 Ma) and stem Ailanthus, Simaroubaceae (>52 Ma). Another data set comprised 81 Aurantioideae using >8 kb of chloroplast sequence and secondary calibration. Confidence in estimated divergence times was explored by varying the root age, dating method (strict, local, and relaxed clocks), and inclusion of internal calibrations. We conclude that the Rutaceae crown diverged in the Eocene (36.4-56.8 Ma, mean 47.6), whereas the Aurantioideae crown originated in the early Miocene (12.1-28.2 Ma, mean 19.8). This young age suggests that Gondwanan vicariance does not explain the distributions of extant Aurantioideae. Taxa found in New Caledonia may have arrived by separate transoceanic dispersal events.     

Inferring biogeographic history from molecular phylogenies

The present study illustrates a method for analysing the biogeography of a group that is based on the group's phylogeny but does not invoke founder dispersal or centre of origin. The case studies presented include groups from many different parts of the world, but most are from the south‐west Pacific. The idea that basal groups are ancestral is not valid as a generalization. Neither the basal group, nor the oldest fossil represents the centre of origin, the time of origin or the ancestral ecology. Basal groups comprise less diverse sister groups and their distributions occur around centres of differentiation in already widespread ancestors, and not centres of origin for the whole group. Thus, the sequence of nodes in a phylogeny may indicate the spatial sequence of differentiation in a widespread ancestor rather than a series of founder dispersal events. Allocation of clades to a priori geographic areas, such as the continents, in the initial stages of biogeographic analysis has often involved incorrect assumptions of sympatry. This has led to the idea that the ‘areas of sympatry’ were centres of origin. Areas other than those defined by the taxa themselves need not be used in analysis. The fossil‐calibrated molecular clock, with dates transmogrified from minimum to maximum dates, has been used to test for vicariance. Recent work in population genetics, however, indicates that allopatry is caused by vicariance rather than founder dispersal, and so vicariance can instead be used to test the clock. Deriving evolutionary chronology by calibrating spatial vicariance in molecular clades with associated tectonic events is more reasonable than relying on the fossil record to give maximum (absolute) dates. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 757–774.     

Out of Africa: Biogeography and diversification of the pantropical pond skater genus Limnogonus Stål, 1868 (Hemiptera: Gerridae)

Gondwanan vicariance, long‐distance dispersal (LDD), and boreotropical migration have been proposed as alternative hypotheses explaining the pantropical distribution pattern of organisms. In this study, the historical biogeography of the pond skater genus Limnogonus was reconstructed to evaluate the impact of biogeographical scenarios in shaping their modern transoceanic disjunction. We sampled almost 65% of recognized Limnogonus species. Four DNA fragments including 69 sequences were used to reconstruct a phylogram. Divergence time was estimated using a Bayesian relaxed clock method and three fossil calibrations. Diversification dynamics and ancestral area reconstruction were investigated by using maximum likelihood and Bayesian approaches. Our results showed the crown group of Limnogonus originated and diversified in Africa in the early Eocene (49 Ma, HPD: 38–60 Ma), subsequently expanding into other regions via dispersal. The colonization of the New World originated from the Oriental Region probably via the Bering Land Bridge in the late Eocene. Two split events between the Old World and New World were identified: one between Neotropics and Oriental region around the middle Oligocene (30 Ma, HPD: 22–38 Ma), and the other between Neotropics and Africa during the middle Miocene (14 Ma, HPD: 8–21 Ma). The evolutionary history of Limnogonus involved two biogeographical processes. Gondwanan vicariance was not supported in our analyses. The diversification of Limnogonus among Africa, Oriental, and Neotropical regions corresponded with the age of land bridge connection and dispersed as a member associated with the broad boreotropical belt before local cooling (34 Ma). The current transoceanic disjunctions in Limnogonus could be better explained by the disruption of “mixed‐mesophytic” forest belt; however, the direct transoceanic LDD between the Neotropics and Africa could not be ruled out. In addition, the “LDD” model coupled with island hopping could be a reasonable explanation for the diversification of the Oriental and Australian regions during the Oligocene.     

Patterns of animal dispersal, vicariance and divsrsification in the Holarctic

We analysed patterns of animal dispersal, vicariance and diversification in the Holarctic based on complete phylogenies of 57 extant non‐marine taxa, together comprising 770 species, documenting biogeographic events from the Late Mesozoic to the present. Four major areas, each corresponding to a historically persistent landmass, were used in the analyses: eastern Nearctic (EN), western Nearctic (WN), eastern Palaeoarctic (EP) and western Palaeoarctic (WP). Parsimony‐based tree fitting showed that there is no significantly supported general area cladogram for the dataset. Yet, distributions are strongly phylogenetically conserved, as revealed by dispersal‐vicariance analysis (DIVA). DIVA‐based permutation tests were used to pinpoint phylogenetically determined biogeographic patterns. Consistent with expectations, continental dispersals (WP?EP and WN?EN) are significantly more common than palaeocontinental dispersals (WN?EP and EN?WP), which in turn are more common than disjunct dispersals (EN?EP and WN?WP). There is significant dispersal asymmetry both within the Nearctic (WN→EN more common than EN→WN) and the Palaeoarctic (EP→WP more common than WP→EP). Cross‐Beringian faunal connections have traditionally been emphasized but are not more important than cross‐Atlantic connections in our data set. To analyse changes over time, we sorted biogeographic events into four major time periods using fossil, biogeographic and molecular evidence combined with a ‘branching clock’. These analyses show that trans‐Atlantic distributions (EN‐WP) were common in the Early‐Mid Tertiary (70‐20 Myr), whereas trans‐Beringian distributions (WN‐EP) were rare in that period. Most EN‐EP disjunctions date back to the Early Tertiary (70‐45 Myr), suggesting that they resulted from division of cross‐Atlantic rather than cross‐Beringian distributions. Diversification in WN and WP increased in the Quaternary (< 3 Myr), whereas in EP and EN it decreased from a maximum in the Early‐Mid Tertiary.     

Towards a panbiogeography of the seas

A contrast is drawn between the concept of speciation favoured in the Darwin–Wallace biogeographic paradigm (founder dispersal from a centre of origin) and in panbiogeography (vicariance or allopatry). Ordinary ecological dispersal is distinguished from founder dispersal. A survey of recent literature indicates that ideas on many aspects of marine biology are converging on a panbiogeographic view. Panbiogeographic conclusions supported in recent work include the following observations: fossils give minimum ages for groups and most taxa are considerably older than their earliest known fossil; Pacific/Atlantic divergence calibrations based on the rise of the Isthmus of Panama at 3 Ma are flawed; for these two reasons most molecular clock calibrations for marine groups are also flawed; the means of dispersal of taxa do not correlate with their actual distributions; populations of marine species may be closed systems because of self‐recruitment; most marine taxa show at least some degree of vicariant differentiation and vicariance is surprisingly common among what were previously assumed to be uniform, widespread taxa; mangrove and seagrass biogeography and migration patterns in marine taxa are best explained by vicariance; the Indian Ocean and the Pacific Ocean represent major biogeographic regions and diversity in the Indo‐Australian Archipelago is related to Indian Ocean/Pacific Ocean vicariance; distribution in the Pacific is not the result of founder dispersal; distribution in the south‐west Pacific is accounted for by accretion tectonics which bring about distribution by accumulation and juxtaposition of communities; tectonic uplift and subsidence can directly affect vertical distribution of marine communities; substantial parallels exist between the biogeography of terrestrial and marine taxa; biogeographically and geologically composite areas are tractable using panbiogeographic analysis; metapopulation models are more realistic than the mainland/island dispersal models used in the equilibrium theory of island biogeography; and regional biogeography is a major determinant of local community composition. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 84 , 675–723.     

Fossil Ericaceae from New Zealand: Deconstructing the use of fossil evidence in historical biogeography

The Australasian Ericaceae epitomize many problems in understanding the biogeography of the southern hemisphere, especially the relative contributions of Gondwanan vicariance and dispersal. Late Cretaceous fossil pollen of the family suggests extreme antiquity of the group in Australasia, but recent phylogenetic evidence suggests much younger histories for most of the groups in that region. This paper documents two new species of latest Oligocene-Early Miocene macrofossils of Ericaceae from New Zealand. Cyathodophyllum novae-zelandiae G.J.Jord. & Bannister gen. and sp. nov. is the oldest record of the tribe Styphelieae, but is of a clade now extinct in New Zealand, possibly related to the Tasmanian genus Cyathodes. Richeaphyllum waimumuensis G.J.Jord. & Bannister sp. nov. is a member of Richeeae, but it is ambiguous as to whether it is a member of the impressive modern New Zealand radiation in Dracophyllum. These fossils emphasize the fact that at least some of the fossil pollen of Ericaceae may have been derived from extinct lineages and therefore should not be used as evidence for the antiquity of any modern New Zealand clade of Ericaceae. New fossils and/or detailed analysis of fossil and extant pollen may help resolve such uncertainty.     

Southern hemisphere biogeography inferred by event-based models: plant versus animal patterns

The Southern Hemisphere has traditionally been considered as having a fundamentally vicariant history. The common trans-Pacific disjunctions are usually explained by the sequential breakup of the supercontinent Gondwana during the last 165 million years, causing successive division of an ancestral biota. However, recent biogeographic studies, based on molecular estimates and more accurate paleogeographic reconstructions, indicate that dispersal may have been more important than traditionally assumed. We examined the relative roles played by vicariance and dispersal in shaping Southern Hemisphere biotas by analyzing a large data set of 54 animal and 19 plant phylogenies, including marsupials, ratites, and southern beeches (1,393 terminals). Parsimony-based tree fitting in conjunction with permutation tests was used to examine to what extent Southern Hemisphere biogeographic patterns fit the breakup sequence of Gondwana and to identify concordant dispersal patterns. Consistent with other studies, the animal data are congruent with the geological sequence of Gondwana breakup: (Africa(New Zealand(southern South America, Australia))). Trans-Antarctic dispersal (Australia <--> southern South America) is also significantly more frequent than any other dispersal event in animals, which may be explained by the long period of geological contact between Australia and South America via Antarctica. In contrast, the dominant pattern in plants, (southern South America(Australia, New Zealand)), is better explained by dispersal, particularly the prevalence of trans-Tasman dispersal between New Zealand and Australia. Our results also confirm the hybrid origin of the South American biota: there has been surprisingly little biotic exchange between the northern tropical and the southern temperate regions of South America, especially for animals.     

Macroevolutionary patterns in the diversification of parrots: effects of climate change,geological events and key innovations

Aim Parrots are thought to have originated on Gondwana during the Cretaceous. The initial split within crown group parrots separated the New Zealand taxa from the remaining extant species and was considered to coincide with the separation of New Zealand from Gondwana 82–85 Ma, assuming that the diversification of parrots was mainly shaped by vicariance. However, the distribution patterns of several extant parrot groups cannot be explained without invoking transoceanic dispersal, challenging this assumption. Here, we present a temporal and spatial framework for the diversification of parrots using external avian fossils as calibration points in order to evaluate the relative importance of the influences of past climate change, plate tectonics and ecological opportunity. Location Australasian, African, Indo‐Malayan and Neotropical regions. Methods Phylogenetic relationships were investigated using partial sequences of the nuclear genes c‐mos, RAG‐1 and Zenk of 75 parrot and 21 other avian taxa. Divergence dates and confidence intervals were estimated using a Bayesian relaxed molecular clock approach. Biogeographic patterns were evaluated taking temporal connectivity between areas into account. We tested whether diversification remained constant over time and if some parrot groups were more species‐rich than expected given their age. Results Crown group diversification of parrots started only about 58 Ma, in the Palaeogene, significantly later than previously thought. The Australasian lories and possibly also the Neotropical Arini were found to be unexpectedly species‐rich. Diversification rates probably increased around the Eocene/Oligocene boundary and in the middle Miocene, during two periods of major global climatic aberrations characterized by global cooling. Main conclusions The diversification of parrots was shaped by climatic and geological events as well as by key innovations. Initial vicariance events caused by continental break‐up were followed by transoceanic dispersal and local radiations. Habitat shifts caused by climate change and mountain orogenesis may have acted as a catalyst to the diversification by providing new ecological opportunities and challenges as well as by causing isolation as a result of habitat fragmentation. The lories constitute the only highly nectarivorous parrot clade, and their diet shift, associated with morphological innovation, may have acted as an evolutionary key innovation, allowing them to explore underutilized niches and promoting their diversification.     

Salmonella enterica Serovar Typhimurium Exploits Inflammation to Compete with the Intestinal Microbiota

Most mucosal surfaces of the mammalian body are colonized by microbial communities (“microbiota”). A high density of commensal microbiota inhabits the intestine and shields from infection (“colonization resistance”). The virulence strategies allowing enteropathogenic bacteria to successfully compete with the microbiota and overcome colonization resistance are poorly understood. Here, we investigated manipulation of the intestinal microbiota by the enteropathogenic bacterium Salmonella enterica subspecies 1 serovar Typhimurium (S. Tm) in a mouse colitis model: we found that inflammatory host responses induced by S. Tm changed microbiota composition and suppressed its growth. In contrast to wild-type S. Tm, an avirulent invGsseD mutant failing to trigger colitis was outcompeted by the microbiota. This competitive defect was reverted if inflammation was provided concomitantly by mixed infection with wild-type S. Tm or in mice (IL10^−/−, VILLIN-HA^CL4-CD8) with inflammatory bowel disease. Thus, inflammation is necessary and sufficient for overcoming colonization resistance. This reveals a new concept in infectious disease: in contrast to current thinking, inflammation is not always detrimental for the pathogen. Triggering the host's immune defence can shift the balance between the protective microbiota and the pathogen in favour of the pathogen.     

Tectonic blocks and molecular clocks

Evolutionary timescales have mainly used fossils for calibrating molecular clocks, though fossils only really provide minimum clade age constraints. In their place, phylogenetic trees can be calibrated by precisely dated geological events that have shaped biogeography. However, tectonic episodes are protracted, their role in vicariance is rarely justified, the biogeography of living clades and their antecedents may differ, and the impact of such events is contingent on ecology. Biogeographic calibrations are no panacea for the shortcomings of fossil calibrations, but their associated uncertainties can be accommodated. We provide examples of how biogeographic calibrations based on geological data can be established for the fragmentation of the Pangaean supercontinent: (i) for the uplift of the Isthmus of Panama, (ii) the separation of New Zealand from Gondwana, and (iii) for the opening of the Atlantic Ocean. Biogeographic and fossil calibrations are complementary, not competing, approaches to constraining molecular clock analyses, providing alternative constraints on the age of clades that are vital to avoiding circularity in investigating the role of biogeographic mechanisms in shaping modern biodiversity.This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.