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1.
A recent molecular clock analysis concluded that Gondwanan vicariance and out-of-India dispersal best explained the distribution of Crypteroniaceae and its allies (Conti et al. 2002). A reanalysis of their data using a different molecular dating technique and calibration point is congruent with an alternative hypothesis, namely dispersal between India, Africa, and South America long after the initial break-up of Gondwana.  相似文献   

2.
Inferring speciation rates from phylogenies   总被引:6,自引:0,他引:6  
Abstract It is possible to estimate the rate of diversification of clades from phylogenies with a temporal dimension. First, I present several methods for constructing confidence intervals for the speciation rate under the simple assumption of a pure birth process. I discuss the relationships among these methods in the hope of clarifying some fundamental theory in this area. Their performances are compared in a simulation study and one is recommended for use as a result. A variety of other questions that may, in fact, be the questions of primary interest (e.g., Has the rate of cladogenesis been declining?) are then recast as biological variants of the purely statistical question—Is the birth process model appropriate for my data? Seen in this way, a preexisting arsenal of statistical techniques is opened up for use in this area: in particular, techniques developed for the analysis of Poisson processes and the analysis of survival data. These two approaches start from different representations of the data—the branch lengths in the tree—and I explicitly relate the two. Aiming for a synoptic account of useful theory in this area, I briefly discuss some important results from the analysis of two distinct birth‐death processes: the one introduced into this area by Hey (1992) is refitted with some powerful statistical tools.  相似文献   

3.
The biogeographic and tectonic history of India   总被引:10,自引:0,他引:10  
Aim To present an up to date account of the Mesozoic history of India and its relationship to the other Gondwana continents and to Eurasia. Location Continents surrounding the Western Indian Ocean. Methods Utilization of recent evidence of continental relationships based upon research in stratigraphy, palaeomagnetism, palaeontology, and contemporary biotas. Results The physical data revealed a sequence of events as India moved northward: (1) India–Madagascar rifted from east Africa 158–160 Ma (million years ago), (2) India–Madagascar from Antarctica c. 130 Ma, (3) India–Seychelles from Madagascar 84–96 Ma, (4) India from Seychelles 65 Ma, (5) India began collision with Eurasia 55–65 Ma and (6) final suturing took place c. 42–55 Ma. However, data from fossil and contemporary faunas indicate that, throughout the late Cretaceous, India maintained exchanges with adjacent lands. There is an absence in the fossil record of peculiar animals and plants that should have evolved, had India undergone an extended period of isolation just before its contact with Eurasia. Main conclusions The depiction of India in late Cretaceous as an isolated continent is in error. Most global palaeomaps, including the most recent one, show India, as it moves northward, following a track far out in the Indian Ocean. But the evidence now indicates that India's journey into northern latitudes cannot have taken place under such isolated circumstances. Although real breaks among the lands were indicated by the physical data, faunal links were maintained by vagile animals that were able to surmount minor marine barriers. India, during its northward journey, remained close to Africa and Madagascar even as it began to contact Eurasia.  相似文献   

4.
With highly conserved morphology throughout the family, a tropical distribution, and no close living relatives, the trogons (Aves: Trogonidae) pose a difficult problem for systematists. Disjunct tropical distributions are often attributed to Gondwanan vicariance, but the fossil record for trogons is mostly from the Tertiary of Europe. This study examined support for the basal relationships among trogons using a combination of nuclear (RAG-1) and mitochondrial (ND2) DNA sequence data. Although some nodes could not be resolved with significant support, there is strong support for the basal position of three New World genera ( Pharomachrus , Euptilotis , and Priotelus ). This phylogenetic hypothesis differs markedly from previous studies of trogon relationships and taxonomic treatments. Biogeographically, it implies an origin and early vicariance events for the crown clade in the New World. Molecular divergence estimates place all of the basal nodes of the trogon phylogeny in the Oligocene, precluding a Gondwanan origin for modern trogons.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 725–738.  相似文献   

5.
Madagascar is home to numerous endemic species and lineages, but the processes that have contributed to its endangered diversity are still poorly understood. Evidence is accumulating to demonstrate the importance of Tertiary dispersal across varying distances of oceanic barriers, supplementing vicariance relationships dating back to the Cretaceous, but these hypotheses remain tentative in the absence of well-supported phylogenies. In the Papilio demoleus group of swallowtail butterflies, three of the five recognized species are restricted to Madagascar, whereas the remaining two species range across the Afrotropical zone and southern Asia plus Australia. We reconstructed phylogenetic relationships for all species in the P. demoleus group, as well as 11 outgroup Papilio species, using 60 morphological characters and about 4 kb of nucleotide sequences from two mitochondrial (cytochrome oxidase I and II) and two nuclear (wg and EF-1alpha) genes. Of the three endemic Malagasy species, the two that are formally listed as endangered or at risk represented the most basal divergences in the group, while the more common third endemic was clearly related to African P. demodocus. The fifth species, P. demoleus, showed little differentiation across southern Asia, but showed divergence from its subspecies sthenelus in Australia. Dispersal-vicariance analysis using cladograms derived from morphology and three independent genes indicated a Malagasy diversification of lime swallowtails in the middle Miocene. Thus, diversification processes on the island of Madagascar may have contributed to the origin of common butterflies that now occur throughout much of the Old World tropical and subtemperate regions. An alternative hypothesis, that Madagascar is a refuge for ancient lineages resulting from successive colonizations from Africa, is less parsimonious and does not explain the relatively low continental diversity of the group.  相似文献   

6.
Towards a panbiogeography of the seas   总被引:3,自引:0,他引:3  
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.  相似文献   

7.
A review of paleontological, phyletic, geophysical, and climatic evidence leads to a new scenario of land mammal dispersal among South America, Antarctica, and Australia in the Late Cretaceous to early Tertiary epochs. New fossil land vertebrate material has been recovered from all three continents in recent years. As regards Gondwana, the present evidence suggests that monotreme mammals and ratite birds are of Mesozoic origin, based on both geochronological and phyletic grounds. The occurrence of monotremes in the early Paleocene (ca. 62 Ma) faunas of Patagonia and of ratites in late Eocene (ca. 41-37 m.y.) faunas of Seymour Island (Antarctic Peninsula) probably is an artifact of a much older and widespread Gondwana distribution prior to the Late Cretaceous Epoch. Except for South American microbiotheres being australidelphians, marsupial faunas of South America and Australia still are fundamentally disjunct. New material from Seymour Island (Microbiotheriidae) indicates the presence there of a derived taxon that resides in a group that is the sister taxon of most Australian marsupials. There is no compelling evidence that dispersal between Antarctica and Australia was as recent as ca. 41 Ma or later. In fact, the derived marsupial and placental land mammal fauna of Seymour Island shows its greatest affinity with Patagonian forms of Casamayoran age (ca. 51–54 m.y.). This suggests an earlier dispersal of more plesiomorphic marsupials from Patagonia to Australia via Antarctica, and vicariant disjunction subsequently. This is consistent with geophysical evidence that the South Tasman Rise was submerged by 64 Ma and with geological evidence that a shallow water marine barrier was present from then onward. The scenario above is consistent with molecular evidence suggesting that australidelphian bandicoots, dasyurids, and diprotodontians were distinct and present in Australia at least as early as the 63-Ma-old australidelphian microbiotheres and the ancient but not basal australidelphian,Andinodelphys, in the Tiupampa Fauna of Bolivia. Land mammal dispersal to Australia typically has been considered to be at a low level of probability (e.g., by sweepstakes dispersal). This study suggests that the marsupial colonizers of Australia included already recognizable members of the Peramelina, Dasyuromorphia, and Diprotodontia, at least, and entered via a filter route rather than by a sweepstakes dispersal.To whom correspondence should be addressed.  相似文献   

8.
  1. The Spalacidae is a family of strictly subterranean rodents with a long evolutionary history. It is unclear how ecological changes have influenced the evolutionary history of these mammals, and the phylogenetic relationship of the subfamilies within Spalacidae is controversial.
  2. Through compiling fossil records, reconstructing molecular phylogeny from molecular data, determining the date of divergence, and analysing their geographical evolution based on molecular data and fossil taxa, we explore the origin and evolutionary process of Spalacidae in detail. Diversification within Spalacidae dates to the Late Oligocene, approximately 25 million years ago, based on molecular data.
  3. This family originated in South and East Asia in the Late Oligocene, and then split into four clades. The first clade includes Rhizomyinae, which was highly diversified in South Asia in the Early-to-Middle Miocene. Then Rhizomyinae from Asia migrated to northern Africa in multiple waves through the Afro-Eurasian land bridge. Its range largely contracted in the Late Miocene, notably in Central Asia. The second clade includes the extinct Tachyoryctoidinae, which was confined to East and Central Asia, and survived from the Late Oligocene to the Late Miocene. The third clade includes Spalacinae, which have remained around the Mediterranean region since the Late Oligocene with slight trend of northward expansion. The fourth clade is Myospalacinae. Ancient genera of this subfamily in East Asia dispersed eastward during the Late Miocene and reached northern China and south-east Russia.
  4. The general distribution pattern of Spalacidae has persisted since the Late Miocene. Extinction of Tachyoryctoidinae and clear range contraction of Rhizomyinae in Central and East Asia are likely to have resulted from increased aridification, while the slight northward expansion of Myospalacinae and Spalacinae since the Quaternary was probably a response to a similar northward expansion of suitable vegetation for these animals.
  相似文献   

9.
Abstract The theory of ‘punctuated equilibrium’ hypothesises that most morphological change in species takes place in rapid bursts triggered by speciation. Eldregde and Gould postulated the theory in 1972, as an alternative to the idea that morphological change slowly accumulates in the course of time, a then common belief they dubbed ‘phyletic gradualism’. Ever since its introduction the theory of punctuated equilibrium has been the subject of speculation rather than empirical validation. Here I present a method to detect punctuated evolution without reference to fossil data, based on the phenotypes of extant species and on their relatedness as revealed by molecular phylogeny. The method involves a general mathematical model describing morphological differentiation of two species over time. The two parameters in the model, the rates of punctual (cladogenetic) and gradual (anagenetic) change, are estimated from plots of morphological diversification against time since divergence of extant species.  相似文献   

10.
Grasses are widespread on every continent and are found in all terrestrial biomes. The dominance and spread of grasses and grassland ecosystems have led to significant changes in Earth′s climate, geochemistry, and biodiversity. The abundance of DNA sequence data, particularly chloroplast sequences, and advances in placing grass fossils within the family allows for a reappraisal of the family′s origins, timing, and geographic spread and the factors that have promoted diversification. We reconstructed a time-calibrated grass phylogeny and inferred ancestral areas using chloroplast DNA sequences from nearly 90% of extant grass genera. With a few notable exceptions, the phylogeny is well resolved to the subtribal level. The family began to diversify in the Early–Late Cretaceous (crown age of 98.54 Ma) on West Gondwana before the complete split between Africa and South America. Vicariance from the splitting of Gondwana may be responsible for the initial divergence in the family. However, Africa clearly served as the center of origin for much of the early diversification of the family. With this phylogenetic, temporal, and spatial framework, we review the evolution and biogeography of the family with the aim to facilitate the testing of biogeographical hypotheses about its origins, evolutionary tempo, and diversification. The current classification of the family is discussed with an extensive review of the extant diversity and distribution of species, molecular and morphological evidence supporting the current classification scheme, and the evidence informing our understanding of the biogeographical history of the family.  相似文献   

11.
Anthropogenic disturbances such as fishing, mining, oil drilling, bioprospecting, warming, and acidification in the deep sea are increasing, yet generalities about deep-sea biogeography remain elusive. Owing to the lack of perceived environmental variability and geographical barriers, ranges of deep-sea species were traditionally assumed to be exceedingly large. In contrast, seamount and chemosynthetic habitats with reported high endemicity challenge the broad applicability of a single biogeographic paradigm for the deep sea. New research benefiting from higher resolution sampling, molecular methods and public databases can now more rigorously examine dispersal distances and species ranges on the vast ocean floor. Here, we explore the major outstanding questions in deep-sea biogeography. Based on current evidence, many taxa appear broadly distributed across the deep sea, a pattern replicated in both the abyssal plains and specialized environments such as hydrothermal vents. Cold waters may slow larval metabolism and development augmenting the great intrinsic ability for dispersal among many deep-sea species. Currents, environmental shifts, and topography can prove to be dispersal barriers but are often semipermeable. Evidence of historical events such as points of faunal origin and climatic fluctuations are also evident in contemporary biogeographic ranges. Continued synthetic analysis, database construction, theoretical advancement and field sampling will be required to further refine hypotheses regarding deep-sea biogeography.  相似文献   

12.
Geographical affinities of the Cape flora, South Africa   总被引:1,自引:0,他引:1  
Aim The flora characteristic of the Cape Floristic Region (CFR) is dominated by a relatively small number of clades that have been proposed as ‘Cape clades’. These clades have variously been suggested to have African or Austral affinities. Here we evaluate the support for these conflicting hypotheses. In addition, we test the hypothesis that these clades share a common time of differentiation from their geographical neighbours. Location The Cape Floristic Region, South Africa Methods We use both published and unpublished phylogenetic information to investigate the geographical sister areas of the Cape clades as well as the timing and the direction of biogeographical disjunctions. Results Almost half of the Cape clades for which unambiguous sister areas could be established show a trans‐Indian Ocean disjunction. The earliest trans‐Indian Ocean disjunction dates from 80 Ma. Other disjunctions date from various times in the Cenozoic, and we suggest that the process of recruiting lineages into the Cape flora might be ongoing. Relatively few Cape clades show a sister relationship with South America and tropical Africa, despite their relative geographical proximity. Numerous Cape clades contain species also found on tropical African mountains; in all cases tested, these species are shown to be embedded within the Cape clades. While many Cape clades show a relationship with the Eurasian temperate flora, this is complicated by their presence in tropical Africa. The single case study addressing this to date suggests that the Cape clade is nested within a European grade. Main conclusions Although many Cape clades show Austral rather than African relationships, there are numerous other patterns suggestive of a cosmopolitan flora. This spatial variation is echoed in the temporal data, from which, although there is wide variance around the dates of disjunctions, it is clear the Cape flora has been assembled over a long time period. There is no simple hypothesis that can account for the geographical sources of the currently distinctive Cape flora. The phylogenetic positions of Afromontane members of Cape clades suggest a history of dispersal from the CFR, rather than the reverse.  相似文献   

13.
Distribution maps and notes are given for the 41 species of Parahebe sensu lata. The genus occurs in New Zealand, south-east Australia and New Guinea, with greatest diversity in New Zealand, especially in the Spenser Mountains region of South Island. A group of species with ciliate floral discs is found in north-east South Island, and also in eastern Papua New Guinea. This outer Australasian arc distribution is attributed to the group having originated before the break-up of Gondwana. Within New Zealand the P. catarraclae complex shows disjunction along the Alpine Fault, a plate boundary of the transform type. The disjunction is attributed to massive lateral displacement on the Fault during Tertiary time pulling apart plant populations. Parahebe sect. Paniculatae is newly described. The following new combinations are made: Parahebe brevistylis, P. macrantha, P. macrantha var. brachyphylla, P. raoulii, P. r. subsp. maccaskillii, P. r. subsp. pentasepala, P. lavaudiana, P. hulkeana, P. nivea, P. arenaria, P. velutina, P. blakelyi, P. arcuata, P. derwentiana subsp. maideniana, P. d. subsp. homalodonta, P. d. subsp. anisodonta and P. d. subsp. subglauca.  相似文献   

14.
GENIE implements a statistical framework for inferring the demographic history of a population from phylogenies that have been reconstructed from sampled DNA sequences. The methods are based on population genetic models known collectively as coalescent theory. AVAILABILITY: GENIE is available from http://evolve.zoo.ox.ac.uk. All popular operating systems are supported.  相似文献   

15.
16.
Oceanic dispersal has emerged as an important factor contributing to biogeographic patterns in numerous taxa. Chameleons are a clear example of this, as they are primarily found in Africa and Madagascar, but the age of the family is post-Gondwanan break-up. A Malagasy origin for the family has been suggested, yet this hypothesis has not been tested using modern biogeographic methods with a dated phylogeny. To examine competing hypotheses of African and Malagasy origins, we generated a dated phylogeny using between six and 13 genetic markers, for up to 174 taxa representing greater than 90 per cent of all named species. Using three different ancestral-state reconstruction methods (Bayesian and likelihood approaches), we show that the family most probably originated in Africa, with two separate oceanic dispersals to Madagascar during the Palaeocene and the Oligocene, when prevailing oceanic currents would have favoured eastward dispersal. Diversification of genus-level clades took place in the Eocene, and species-level diversification occurred primarily in the Oligocene. Plio-Pleistocene speciation is rare, resulting in a phylogeny dominated by palaeo-endemic species. We suggest that contraction and fragmentation of the Pan-African forest coupled to an increase in open habitats (savannah, grassland, heathland), since the Oligocene played a key role in diversification of this group through vicariance.  相似文献   

17.
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.  相似文献   

18.
Hundreds of studies have been dedicated to estimating speciation and extinction from phylogenies of extant species. Although it has long been known that estimates of extinction rates using trees of extant organisms are often uncertain, an influential paper by Rabosky (2010) suggested that when birth rates vary continuously across the tree, estimates of the extinction fraction (i.e., extinction rate/speciation rate) will appear strongly bimodal, with a peak suggesting no extinction and a peak implying speciation and extinction rates are approaching equality. On the basis of these results, and the realistic nature of this form of rate variation, it is now generally assumed by many practitioners that extinction cannot be understood from molecular phylogenies alone. Here, we reevaluated and extended the analyses of Rabosky (2010) and come to the opposite conclusion—namely, that it is possible to estimate extinction from molecular phylogenies, even with model violations due to heritable variation in diversification rate. Note that while it may be tempting to interpret our study as advocating the application of simple birth–death models, our goal here is to show how a particular model violation does not necessitate the abandonment of an entire field: use prudent caution, but do not abandon all hope.  相似文献   

19.
Aim Our aims were: (1) to reconstruct a molecular phylogeny of the cephalaspidean opisthobranch genus Bulla, an inhabitant of shallow sedimentary environments; (2) to test if divergence times are consistent with Miocene and later vicariance among the four tropical marine biogeographical provinces; (3) to examine the phylogenetic status of possible Tethyan relict species; and (4) to infer the timing and causes of speciation events. Location Tropical and warm‐temperate regions of the Atlantic, Indo‐West Pacific, Australasia and eastern Pacific. Methods Ten of the 12 nominal species of Bulla were sampled, in a total sample of 65 individuals, together with cephalaspidean outgroups. Phylogenetic relationships were inferred by Bayesian analysis of partial sequences of the mitochondrial cytochrome c oxidase I (COI) and 16S rRNA and nuclear 28S rRNA genes. Divergence times and rates of evolution were estimated using uncorrelated relaxed‐clock Bayesian methods with fossil calibrations (based on literature review and examination of fossil specimens), implemented in beast . The geographical pattern of speciation was assessed by estimating the degree of overlap between sister lineages. Results Four clades were supported: Indo‐West Pacific (four species), Australasia (one species), Atlantic plus eastern Pacific (three species) and Atlantic (two species), with estimated mean ages of 35–46 Ma. Nominal species were monophyletic, but deep divergences were found within one Indo‐West Pacific and one West Atlantic species. Species‐level divergences occurred in the Miocene or earlier. The age of a sister relationship across the Isthmus of Panama was estimated at 7.9–32.1 Ma, and the divergence of a pair of sister species on either side of the Atlantic Ocean occurred 20.4–27.2 Ma. Main conclusions Fossils suggest that Bulla originated in the Tethys realm during the Middle Eocene. Average ages of the four main clades fall in the Eocene, and far pre‐date the 18–19 Ma closure of the Tethys Seaway. This discrepancy could indicate earlier vicariant events, selective extinction or errors of calibration. Similarly, the transisthmian divergence estimate far pre‐dates the uplift of the Panamanian Isthmus at about 3 Ma. Speciation events occurred in the Miocene, consistent with tectonic events in the central Indo‐West Pacific, isolation of the Arabian Sea by upwelling and westward trans‐Atlantic dispersal. Differences in habitat between sister species suggest that ecological speciation may also have played a role. The basal position of the Australasian species supports its interpretation as a Tethyan relict.  相似文献   

20.
The southeast Australian coast potentially includes a complex biogeographic barrier, largely lacking exposed rocky shore that may limit the dispersal of rocky intertidal taxa and contribute to the maintenance of two biogeographic regions. Surprisingly, within the 300-km barrier region, several species considered exposed rocky shore specialists occurred within sheltered sites. We analysed COI sequence variation for 10 rocky intertidal invertebrate species, with a range of life histories, to test the hypotheses that larval type and habitat specificity are strong predictors of gene flow between biogeographic regions. Our data revealed that the southeast corner of Australia includes a strong barrier to gene flow for six of eight species with planktonic larvae, and a coalescence analysis of sequence differentiation (IM model) suggests that a barrier has existed since the Pleistocene. In contrast, two direct developers were not affected by the barrier. Our comparative approach and data from earlier studies (reviewed here) do not support the hypothesis that larval type predicts gene flow across this barrier, instead we found that the ability to utilize sheltered habitat provides a clearer explanation of the phylogeographic break. Indeed, the species that displayed little or no evidence of a phylogeographic break across the barrier each displayed unexpectedly relaxed habitat specificity.  相似文献   

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