Repeat intercontinental dispersal and Pleistocene speciation in disjunct Mediterranean and desert Senecio (Asteraceae)

To explore the biogeographic history of Mediterranean/arid plant disjunctions, Old and New World Senecio sect. Senecio were analyzed phylogenetically using nuclear ribosomal DNA sequences (ITS). A clade corresponding to sect. Senecio was strongly supported. Area optimization indicated this clade to be of southern African origin. The Mediterranean and southern African floras were not distinguishable as sources of the main New World lineage, estimated to have become established during the middle Pliocene. Another previously suspected recent dispersal to the New World from the Mediterranean was confirmed for the recently recognized disjunction in S. mohavensis. The loss of suitable land connections by the Miocene means that both New World lineages must represent long-distance dispersal, providing the first evidence of repeat intercontinental dispersal in a Mediterranean group. In contrast, migration within Africa may have utilized an East African arid corridor. Recent dispersal to northern Africa is supported for S. flavus, which formed part of a distinct southern African lineage. Novel pappus modifications in both disjunct species may have enabled dispersal by birds. An estimated early Pliocene origin of sect. Senecio coincides with the appearance of summer-dry climate. However, diversification from 1.6 BP highlights the importance of Pleistocene climate fluctuations for speciation.     

啄木鸟科内谱系生物地理学新探

啄木鸟群体共包含254种,但早期对啄木鸟的分类学研究局限于形态学、行为学和鸣唱法等方向,分子研究结果又彼此存在差异,因此啄木鸟分类系统目前还有争议。分子数据的大量累积为啄木鸟系统发育的研究提供了条件。利用从GenBank获取的ND2基因序列,对啄木鸟科179种啄木鸟采用NJ法、MP法以及ML法分别进行了分子进化树构建,同时用NJ法重建了Picumnus属分子进化树。此外又利用cytb基因序列采用NJ法对Dryobates属和Picoides属进行分子进化树重建。我们的结果显示,姬啄木亚科Picumnus属新大陆物种彼此的进化关系仍需进一步研究,而该属唯一一种旧大陆种P.innominatus,种内遗传差异在种间水平依然显著,这说明其种内遗传差异一直被低估了。在啄木鸟亚科内,Hemicircus属和Nesoctites属为姐妹关系,而Geocolaptes olivaceus插入了Campethera属支系中,并非与其构成姐妹群体。此外,一些姐妹群在新旧大陆上的分布,推测这种分布可能与第四纪冰川有关。啄木鸟从旧大陆向新大陆迁移,在第四纪冰川作用下不断发生分布范围的扩张与收缩,最终形成现存的分布格局。     

Quaternary Climate Change was Not an Engine of Diversification in New World Bats (Chiroptera)

Quaternary climate change has been hypothesized to have played a significant role in driving diversification rates in a variety of taxa. We test the hypothesis of increased rates of diversification during the Quaternary in nine groups of New World bats (Chiroptera). The fit of six models of diversification was determined for each group. None experienced an increase in net diversification, rejecting the Quaternary hypothesis. Instead, four groups experienced constant net diversification rates, suggesting no Quaternary climate change impact. Five groups are evolving under a density-dependent model of diversification, suggesting climate cycles may have reduced rates initiated during the Pliocene or late Miocene. The distribution of divergences between sister taxa is consistent with results obtained from avian lineages experiencing declining rates of Quaternary diversification, further discrediting this often invoked hypothesis. Our results suggest that Quaternary climate change did not increase diversification rates in New World bats.     

Recent oceanic long-distance dispersal and divergence in the amphi-Atlantic rain forest genus Renealmia L.f. (Zingiberaceae)

Renealmia L.f. (Zingiberaceae) is one of the few tropical plant genera with numerous species in both Africa and South America but not in Asia. Based on phylogenetic analysis of nuclear ribosomal internal transcribed spacer (ITS) and chloroplast trnL-F DNA, Renealmia is shown to be monophyletic with high branch support. Low sequence divergence found in the two genome regions (ITS: 0-2.4%; trnL-F: 0-1.9%) suggests recent diversification within the genus. Molecular divergence age estimates give further support to the recent origin of the genus and show that Renealmia has attained its amphi-Atlantic distribution by an oceanic long-distance dispersal event from Africa to South America during the Miocene or Pliocene (15.8-2.7 My ago). Some support is found for the hypothesis that speciation in neotropical Renealmia was influenced by the Andean orogeny. Speciation has been approximately simultaneous on both sides of the Atlantic, but increased taxon sampling is required to compare the speciation rates between the New World and Old World tropics.     

Age and historical biogeography of the pantropically distributed Spathelioideae (Rutaceae,Sapindales)

Aim The family Rutaceae (rue family) is the largest within the eudicot order Sapindales and is distributed mainly in the tropical and subtropical regions of both the New World and the Old World, with a few genera in temperate zones. The main objective of this study is to present molecular dating and biogeographical analyses of the subfamily Spathelioideae, the earliest branching clade (which includes eight extant genera), to interpret the temporal and spatial origins of this group, ascertaining possible vicariant patterns and dispersal routes and inferring diversification rates through time. Location Pantropics. Methods A dataset comprising a complete taxon sampling at generic level (83.3% at species level) of Spathelioideae was used for a Bayesian molecular dating analysis (beast ). Four fossil calibration points and an age constraint for Sapindales were applied. An ancestral area reconstruction analysis utilizing the dispersal–extinction–cladogenesis model and diversification rate analyses was conducted. Results Dating analyses indicate that Rutaceae and Spathelioideae are probably of Late Cretaceous origin, after which Spathelioideae split into a Neotropical and a Palaeotropical lineage. The Palaeotropical taxa have their origin inferred in Africa, with postulated dispersal events to the Mediterranean, the Canary Islands, Madagascar and Southeast Asia. The lineages within Spathelioideae evolved at a relatively constant diversification rate. However, abrupt changes in diversification rates are inferred from the beginning of the Miocene and during the Pliocene/Pleistocene. Main conclusions The geographical origin of Spathelioideae probably lies in Africa. The existence of a Neotropical lineage may be the result of a dispersal event at a time in the Late Cretaceous when South America and Africa were still quite close to each other (assuming that our age estimates are close to the actual ages), or by Gondwanan vicariance (assuming that our age estimates provide minimal ages only). Separation of land masses caused by sea level changes during the Pliocene and Pleistocene may have been triggers for speciation in the Caribbean genus Spathelia.     

Molecular phylogeny and biogeographic history of the piculets (Piciformes: Picumninae)

The subfamily Picumninae (piculets) includes 3 genera and 30 species of tiny and short-tailed woodpeckers with a pantropical distribution. Within the Picumninae, two cases of intercontinentally disrupted distributions at the genus level occur. The first one concerns the genus Sasia (one species in Africa and two in southeast Asia) while the second concerns Picumnus (one species in southeast Asia and 25 in South America). These disrupted distributions, as well as several morphological differences, have lead some authors to place the African representative of Sasia and the southeast Asian representative of Picumnus in their own monotypic genera ( Verreauxia and Vivia , respectively). To address the taxonomic status and biogeographic history of the piculets, we sequenced 2676 bp of DNA from one mitochondrial (ND2) and two nuclear markers (myoglobin intron 2 and β-fibrinogen intron 7). Monophyly of Picumninae could not be recovered with confidence, while monophyly of Sasia and Picumnus were always strongly supported. Molecular dating analyses revealed that the splits both between the African and Indo-Malayan Sasia and between the New World and Old World Picumnus occurred at ca 7.9 Myr BP. This time corresponds to the beginning of the formation of the northern Hemisphere ice sheets and the accompanying expansion of grasslands throughout the world. The spread of open areas in the northern parts of Eurasia and America prevented gene flow between tropical forest birds, such as the piculets, in Africa, southeast Asia and South America, respectively.     

Climate-influenced boreotropical survival and rampant introgressions explain the thriving of New World grapes in the north temperate zone

The north temperate region was characterized by a warm climate and a rich thermophilic flora before the Eocene, but early diversifications of the temperate biome under global climate change and biome shift remain uncertain. Moreover, it is becoming clear that hybridization/introgression is an important driving force of speciation in plant diversity. Here, we applied analyses from biogeography and phylogenetic networks to account for both introgression and incomplete lineage sorting based on geno...     

Climatic niche evolution in Smilacaceae (Liliales) drives patterns of species diversification and richness between the Old and New World

Geographical variation in species richness in plant groups is determined by the interplay between historical, evolutionary, and ecological processes. However, the processes underlying the striking disparity in species richness between Asia and the Americas remain poorly understood. Here, we synthesize global phylogenetic and macroecological data on the diversification of Smilacaceae, deciphering potential drivers underlying the species diversity pattern biased toward Asia. We compiled global distributions of all Smilacaceae species, and reconstructed the biogeographic history and niche evolution using a new time-calibrated phylogeny (eight genes, 135 species). Integrating these data sets, we estimated evolutionary histories and diversification rates for each region, and tested correlations among species diversification, niche evolution, and niche divergence. Smilacaceae probably originated during the Late Cretaceous/Early Palaeocene and began to diversify in middle to low latitudes in Central America and Eurasia during the Late Eocene. Both the Old and New World clades exhibited a steady, albeit slight, increase of species diversification from the Late Eocene to Early Miocene. However, the Old World clade experienced an abrupt increase in net diversification during the Late Miocene. Our findings also revealed that species diversification rates were positively correlated with ecological niche evolution and niche divergence. Niche shifts and climatic niche evolution since the Middle Miocene played crucial roles in species diversification dynamics within Smilacaceae. The high plant richness in Asia may be explained by greater diversification in this region, potentially promoted by heterogeneous environments.     

Canary Grasses (Phalaris,Poaceae): biogeography,molecular dating and the role of floret structure in dispersal

Canary grasses (Phalaris, Poaceae) include 21 species, widely spread throughout the temperate and subtropical regions of the world with two centres of diversity: the Mediterranean Basin and western North America. The genus contains annual and perennial, endemic, cosmopolitan, wild, and invasive species with diploid, tetraploid and hexaploid cytotypes. As such, Phalaris presents an ideal platform to study diversification via historic hybridization and polyploidy events, and geographical dispersal in grasses. We present the first empirical phylogeographic study for Phalaris testing current, intuitive hypotheses on the centres of origin, historic dispersal events and diversification within a geological timeframe. Bayesian methods (beast , version 1.6.2) were used to establish divergence dates, and dispersal–vicariance analyses (rasp , version 2.1b) were implemented for ancestral node reconstructions. Our phylogeographic results indicate that the genus emerged during the Miocene epoch [20.6–8.4 Ma (million years ago)] in the Mediterranean basin followed by dispersal and vicariance events to Africa, Asia and the Americas. We propose that a diploid ancestor of P. arundinacea migrated to western North America via the Bering Strait, where further diversification emerged in the New World. It appears that polyploidy played a major role in the evolution of the genus in the Old World, while diversification in the New World followed a primarily diploid pathway. Dispersal to various parts of the Americas followed different routes. Fertile florets with hairy protruding sterile lemmas showed significant correlation with wider geographical distribution.     

Melastomeae come full circle: biogeographic reconstruction and molecular clock dating

Rhexia, with 11 species in the Coastal Plain province of North America, is the only temperate zone endemic of the tropical eudicot family Melastomataceae. It is a member of the only pantropical tribe of that family, Melastomeae. Based on the chloroplast gene ndhF, we use a fossil-calibrated molecular clock to address the question of the geographic origin and age of Rhexia. Sequences from 37 species in 21 genera representing the tribe's geographical range were analyzed together with five outgroups. To obtain better clade support, another chloroplast region, the rpl16 intron, was added for 24 of the species. Parsimony analysis of the combined data and maximum-likelihood analysis of ndhF alone indicate that the deepest split is between Rhexia plus its sister group, a small Central American genus, and all other Melastomeae. Old World Melastomeae are monophyletic and nested within New World Melastomeae. Although likelihood-ratio tests of clock and nonclock substitution models for the full or moderately pruned datasets rejected the clock, these models yielded identical topologies (for 30 taxa) with few significantly different branch lengths as assessed by a Student's t-test. Age estimates obtained were 22 million years ago (Mya) for the divergence of Rhexia from its sister group, 12 Mya for the dispersal of Melastomeae from the New World to West Africa, and 1 Mya for the diversification of Melastoma in Southeast Asia. The only other genus of Melastomeae to have reached Southeast Asia from Africa or Madagascar is Osbeckia. The age and geographic distribution of fossils, which come from Miocene sites throughout Eurasia, suggest that Melastomeae once ranged from Eurasia across Beringia to North America from whence they reached South America and subsequently Africa and Southeast Asia. Climate deterioration led to their extinction in the Northern Hemisphere, with Rhexia possibly surviving in Coastal Plain refugia.     

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.     

Cross-hemisphere migration of a 25 g songbird

The northern wheatear (Oenanthe oenanthe) is a small (approx. 25 g), insectivorous migrant with one of the largest ranges of any songbird in the world, breeding from the eastern Canadian Arctic across Greenland, Eurasia and into Alaska (AK). However, there is no evidence that breeding populations in the New World have established overwintering sites in the Western Hemisphere. Using light-level geolocators, we demonstrate that individuals from these New World regions overwinter in northern sub-Sahara Africa, with Alaskan birds travelling approximately 14 500 km each way and an eastern Canadian Arctic bird crossing a wide stretch of the North Atlantic (approx. 3500 km). These remarkable journeys, particularly for a bird of this size, last between one to three months depending on breeding location and season (autumn/spring) and result in mean overall migration speeds of up to 290 km d(-1). Stable-hydrogen isotope analysis of winter-grown feathers sampled from breeding birds generally support the notion that Alaskan birds overwinter primarily in eastern Africa and eastern Canadian Arctic birds overwinter mainly in western Africa. Our results provide the first evidence of a migratory songbird capable of linking African ecosystems of the Old World with Arctic regions of the New World.     

The early Eocene birds of the Messel fossil site: a 48 million‐year‐old bird community adds a temporal perspective to the evolution of tropical avifaunas

Birds play an important role in studies addressing the diversity and species richness of tropical ecosystems, but because of the poor avian fossil record in all extant tropical regions, a temporal perspective is mainly provided by divergence dates derived from calibrated molecular analyses. Tropical ecosystems were, however, widespread in the Northern Hemisphere during the early Cenozoic, and the early Eocene German fossil site Messel in particular has yielded a rich avian fossil record. The Messel avifauna is characterized by a considerable number of flightless birds, as well as a high diversity of aerial insectivores and the absence of large arboreal birds. With about 70 currently known species in 42 named genus‐level and at least 39 family‐level taxa, it approaches extant tropical biotas in terms of species richness and taxonomic diversity. With regard to its taxonomic composition and presumed ecological characteristics, the Messel avifauna is more similar to the Neotropics, Madagascar, and New Guinea than to tropical forests in continental Africa and Asia. Because the former regions were geographically isolated during most of the Cenozoic, their characteristics may be due to the absence of biotic factors, especially those related to the diversification of placental mammals, which impacted tropical avifaunas in Africa and Asia. The crown groups of most avian taxa that already existed in early Eocene forests are species‐poor. This does not support the hypothesis that the antiquity of tropical ecosystems is key to the diversity of tropical avifaunas, and suggests that high diversification rates may be of greater significance.     

Climate‐driven rampant speciation of the Cape flora

Aim To test whether the radiation of the extremely rich Cape flora is correlated with marine‐driven climate change. Location Middle to Late Miocene in the south‐east Atlantic and the Benguela Upwelling System (BUS) off the west coast of South Africa. Methods We studied the palynology of the thoroughly dated Middle to Late Miocene sediments of Ocean Drilling Program (ODP) Site 1085 retrieved from the Atlantic off the mouth of the Orange River. Both marine upwelling and terrestrial input are recorded at this site, which allows a direct correlation between changes in the terrestrial flora and the marine BUS in the south‐east Atlantic. Results Pollen types from plants of tropical affinity disappeared, and those from the Cape flora gradually increased, between 10 and 6 Ma. Our data corroborate the inferred dating of the diversification in Aizoaceae c. 8 Ma. Main conclusions Inferred vegetation changes for the Late Miocene south‐western African coast are the disappearance of Podocarpus‐dominated Afromontane forests, and a change in the vegetation of the coastal plain from tropical grassland and thicket to semi‐arid succulent vegetation. These changes are indicative of an increased summer drought, and are in step with the development of the southern BUS. They pre‐date the Pliocene uplift of the East African escarpment, suggesting that this did not play a role in stimulating vegetation change. Some Fynbos elements were present throughout the recorded period (from 11 Ma), suggesting that at least some elements of this vegetation were already in place during the onset of the BUS. This is consistent with a marine‐driven climate change in south‐western Africa triggering substantial radiation in the terrestrial flora, especially in the Aizoaceae.     

On the time scale of New World primate diversification

New World primates comprise a diverse group of neotropical mammals that suddenly appeared in the Late Oligocene deposits of South America at around 26 million years ago (MYA). Platyrrhines seem to have separated from Old World anthropoids ca. 35 MYA, and their subsequent diversfication is not well documented in the fossil record. Therefore, molecular clock studies were conducted to unveil the temporal scenario for the evolution of the group. In this study, divergence times of all splits within platyrrhines until the generic level were investigated, using two different gene data sets under relaxed molecular clocks. Special attention was paid to the basal diversification of living platyrrhines and to the basal split of the modern Cebidae family, since these nodes were reported to be phylogenetically difficult to resolve. The results showed that analyses from various genomic regions are similar to estimates obtained by early single-gene studies. Living New World primates are descendants of ancestors that lived in the Early Miocene, at around 20 MYA, and modern Cebidae and Pitheciidae appeared ca. 16.9 and 15.6 MYA, respectively. The last common ancestor of living Atelidae is 12.4 million years old, making this clade the youngest New World primate family; at approximately the same time, modern Callitrichinae was evolving (11.8 MYA). The gap between the Platyrrhini/Catarrhini separation and the last common ancestor of living Platyrrhini may be as big as 20 million years. Paleontological and geoclimatological evidence corroborates that the sudden appearance of modern families may be a consequence of environmental changes during the Miocene.     

Pliocene diversification within the South American Forest falcons (Falconidae: Micrastur)

The Neotropics are one of the most species rich regions on Earth, with over 3150 species of birds. This unrivaled biodiversity has been attributed to higher proportions of mountain ranges, tropical rain forest or rain fall in the forest than in any other major biogeographic regions. Five primary hypotheses aim to explain processes of diversification within the Neotropics; (1) the Pleistocene refuge hypothesis, (2) the riverine barrier hypothesis, (3) the Miocene marine incursions hypothesis, (4) the ecological gradient hypothesis, and (5) the impact of the last Andean uplift serving as a barrier between eastern and western population Andean populations. We assessed these hypotheses to see which best explained the species richness of the forest-falcons (Micrastur), a poorly known lineage of birds that inhabit lowland and mid-elevation humid forest. Our analyses suggest all speciation events within the genus Micrastur probably occurred in the last 2.5-3.6 myrs, at or before the Pliocene/Pleistocene boundary, with the basal split within the genus being 7 myrs old. Hence our data allow us to formerly reject the classical Pleistocene refuge for Micrastur, Our divergence time estimates are younger that dates for the Miocene marine incursions, the riverine barrier and the Andean uplift hypotheses.     

Convergent evolution of sunbird pollination systems of Impatiens species in tropical Africa and hummingbird systems of the New World

The bird pollination systems of the New and Old Worlds evolved independently, and differ in many aspects. New World plants are often presented as those adapted to hovering birds while Old World plants to perching birds. Most Neotropical studies also demonstrate that in hummingbird species rich assemblages, only a small number of highly specialized birds exploits the most specialized plants with long corollas. Nevertheless, recent research on bird–plant pollination interactions suggest that sunbird pollination systems in the Old World have converged more with the highly specialized hummingbird pollination systems than previously thought. In this study we focus on the pollination systems of the bird pollination syndrome Impatiens species on Mt. Cameroon, West Africa. We show that despite the high diversity of sunbirds on Mt. Cameroon, only Cyanomitra oritis appear to be important pollinator of all Impatiens species. This asymmetry indicates the absence of pair wise co‐evolution and points to a diffuse co‐evolutionary process resulting in guilds of highly specialized plants and birds; a situation well known from hummingbirds and specialized plant communities of the New World. Additionally, the herbaceous habits of Impatiens species, the frequent adaptations to pollination by hovering birds, and the habitat preference for understory in tropical forests or epiphytic growth, resemble the highly specialized Neotropical plants. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 127–133.     

Rivers,not refugia,drove diversification in arboreal,sub‐Saharan African snakes

The relative roles of rivers versus refugia in shaping the high levels of species diversity in tropical rainforests have been widely debated for decades. Only recently has it become possible to take an integrative approach to test predictions derived from these hypotheses using genomic sequencing and paleo‐species distribution modeling. Herein, we tested the predictions of the classic river, refuge, and river‐refuge hypotheses on diversification in the arboreal sub‐Saharan African snake genus Toxicodryas. We used dated phylogeographic inferences, population clustering analyses, demographic model selection, and paleo‐distribution modeling to conduct a phylogenomic and historical demographic analysis of this genus. Our results revealed significant population genetic structure within both Toxicodryas species, corresponding geographically to river barriers and divergence times from the mid‐Miocene to Pliocene. Our demographic analyses supported the interpretation that rivers are indications of strong barriers to gene flow among populations since their divergence. Additionally, we found no support for a major contraction of suitable habitat during the last glacial maximum, allowing us to reject both the refuge and river‐refuge hypotheses in favor of the river‐barrier hypothesis. Based on conservative interpretations of our species delimitation analyses with the Sanger and ddRAD data sets, two new cryptic species are identified from east‐central Africa. This study highlights the complexity of diversification dynamics in the African tropics and the advantages of integrative approaches to studying speciation in tropical regions.