The complex history of the genus Ilex L. (Aquifoliaceae): evidence from the comparison of plastid and nuclear DNA sequences and from fossil data

 A plastid phylogeny of the genus Ilex based on three different loci (the atpB-rbcL spacer, trnL-trnF and rbcL) is compared with its nuclear phylogeny based on two different loci (the ribosomal ITS and the 5S RNA spacer). These two sets of molecular data are then compared to geographical and temporal data from the fossil record. The plastid phylogeny is strongly correlated with the geographic distribution of extant species. However, the nuclear phylogeny is strongly incongruent with the plastid phylogeny, suggesting frequent interlineage hybridizations. Moreover, the comparison of the ribosomal ITS tree and the 5S RNA spacer tree indicates also possible lineage sorting. Particularly interesting is the finding of two different Ilex lineages in the plastid American clade showing different biogeographic patterns in South America. One of them has a simple North American/South American biogeographical relationship. The other has complex biogeographical relationships, some species showing direct Asian/South American biogeographical relationships. During its history, the genus Ilex probably experienced frequent lineage sorting and interlineage hybridization with subsequent nuclear or cytoplasmic introgression, making the study of its history very complex. Received September 24, 2001; accepted August 19, 2002 Published online: November 28, 2002 Addresses of the authors: Jean-Fran?ois Manen (e-mail: manen@cjb.ville-ge.ch), Yamama Naciri-Graven, Conservatoire et Jardin Botaniques, Impératrice 1, CH-1292 Chambésy/Genève, Switzerland. Michael C. Boulter, Palaeobiology Research Unit, University of East London, Romford Road, London E15 4LZ, UK.     

Time to update the sectional classification of Ilex (Aquifoliaceae): New insights from Ilex phylogeny,morphology, and distribution

Resolving the infrageneric classification of species-rich genera has been challenging in plant taxonomy. Ilex L. is a subcosmopolitan genus with over 600 species of dioecious trees and shrubs. Many classification systems based on morphological data have been proposed during the past 250 years. However, these systems (such as Loesener's and Galle's systems) may not truly reflect Ilex's evolutionary trajectories because most of those system's infrageneric hierarchies are not monophyletic. In this study, we reconstructed a phylogeny of Ilex L. comprising 15 moderately to highly supported clades using rigorously identified samples (202 species) and closely authenticated gene sequences of three nuclear genes [internal transcribed spacer (ITS), external transcribed spacer (ETS), and nepGS]. The newly generated phylogenetic tree resembles essentially that of the nuclear tree of Manen et al., but shows conspicuous topological differences with the phylogeny of Yao et al. Closely scrutinizing morphological variation and distributional patterns of 202 species, this study found that most lineages of Ilex identified herein are well defined by a particular trait or a combination of morphological and distributional traits, displaying phylogeny–morphology–distribution conformity that has seldom been uncovered in previous studies. Given the general phylogeny–morphology–distribution conformity revealed in this genus, we put forward an updated sectional classification system for Ilex that temporarily contains 14 sections. The new classification will provide a robust framework for studying the evolution and diversification of this ecologically and economically important genus.     

North American Glyptodontines (Xenarthra, Mammalia) in the Upper Pleistocene of northern South America

The Glyptodontidae is one of the most conspicuous groups in the Pleistocene megafauna of the Americas. The Glyptodontinae were involved in the Great American Biotic Interchange (GABI) and their earliest records in North America are about 3.9 Ma, suggesting an earlier formation of the Panamanian landbridge. Taxonomically it is possible to recognize two Pleistocene genera of Glyptodontinae:Glyptodon (ca. 1.8 – 0.008 Ma), restricted to South America, andGlyptotherium (ca. 2.6 – 0.009 Ma), including records in both North and Central America. Here we present the first report of the genusGlyptotherium in South America, from the Late Pleistocene of several fossil localities in Falcón State, northwestern Venezuela. A comparative analysis of the material, represented by cranial and postcranial parts, including the dorsal carapace and caudal rings, suggests a close affinity withGlyptotherium cylindricum (Late Pleistocene of Central Mexico). This occurrence in the latest Pleistocene of the northernmost region of South America Supports the bidirectional faunal migration during the GABI and the repeated re-immigration from North America of South American clades, as has been reported in other members of the Cingulata (e.g., Pampatheriidae).      

The biogeography of Hoffmannseggia (Leguminosae, Caesalpinioideae, Caesalpinieae): a tale of many travels

Aim The flowering plant genus Hoffmannseggia consists of 21 species distributed amphitropically between the arid regions of the south‐western United States and adjacent Mexico, and west‐central South America. This pattern of geographical disjunction is shared by numerous other angiosperm genera and has been the subject of discussions for more than a century with various authors advocating a northern origin for particular taxa and others advocating a southern origin. This study uses a well‐supported phylogeny of a genus with numerous species in each area to address the issues of a northern or southern origin and the facility with which organisms move between the two continents. Location South‐western United States and northern Mexico, northern Chile and Argentina, southern Bolivia, and western Peru. Methods Using DNA sequence data from the nuclear and chloroplast genomes, we generated a phylogenetic hypothesis for all species of Hoffmannseggia rooted with Zuccagnia and Balsamocarpon. Geographical data were optimized on the resultant tree to assess the probable continent of origin for the genus, the pattern of disjunctions between North and South America, and species radiations within the genus. Main conclusions Hoffmannseggia arose in South America and initially split into a suffrutescent (somewhat woody) and an herbaceous clade. Within each of these major clades, there have been at least two exchanges between North and South America. There are no data to support an ancestral pan‐American range for Hoffmannseggia and we therefore ascribe the amphitropical disjunctions to long‐distance dispersal. The phylogeny clearly shows that all dispersals were from South to North America and they occurred at different times and thus the pattern is not the result of a single simultaneous set of dispersals.     

Biogeographic history of the butterfly subtribe Euptychiina (Lepidoptera,Nymphalidae, Satyrinae)

Peña, C., Nylin, S., Freitas, A. V. L. & Wahlberg, N. (2010). Biogeographic history of the butterfly subtribe Euptychiina (Lepidoptera, Nymphalidae, Satyrinae).—Zoologica Scripta, 39, 243–258. The diverse butterfly subtribe Euptychiina was thought to be restricted to the Americas. However, there is mounting evidence for the Oriental Palaeonympha opalina being part of Euptychiina and thus a disjunct distribution between it (in eastern Asia) and its sister taxon (in eastern North America). Such a disjunct distribution in both eastern Asia and eastern North America has never been reported for any butterfly taxon. We used 4447 bp of DNA sequences from one mitochondrial gene and four nuclear genes for 102 Euptychiina taxa to obtain a phylogenetic hypothesis of the subtribe, estimate dates of origin and diversification for major clades and perform a biogeographic analysis. Euptychiina originated 31 Ma in South America. Early Euptychiina dispersed from North to South America via the temporary connection known as GAARlandia during Eocene–Oligocene times. The current disjunct distribution of the Oriental Palaeonympha opalina is the result of a northbound dispersal of a lineage from South America into eastern Asia via North America. The common ancestor of Palaeonympha and its sister taxon Megisto inhabited the continuous forest belt across North Asia and North America, which was connected by Beringia. The closure of this connection caused the split between Palaeonympha and Megisto around 13 Ma and the severe extinctions in western North America because of the climatic changes of the Late Miocene (from 13.5 Ma onwards) resulted in the classic ‘eastern Asia and eastern North America’ disjunct distribution.     

Historical biogeography of the hyperdiverse hidden snout weevils (Coleoptera,Curculionidae, Cryptorhynchinae)

The first dated phylogeny of the weevil subfamily Cryptorhynchinae is presented within a framework of Curculionoidea. The inferred pattern and timing of weevil family relationships are generally congruent with previous studies, but our data are the first to suggest a highly supported sister-group relationship between Attelabidae and Belidae. Our biogeographical inferences suggest that Cryptorhynchinae s.s. originated in the Late Cretaceous (c. 86 Ma) in South America. Within the ‘Acalles group’ and the ‘Cryptorhynchus group’, several independent dispersal events to the Western Palaearctic via the Nearctic occurred in the Late Cretaceous and Early Paleogene. A second southern route via Antarctica may have facilitated the colonization of Australia in the Late Cretaceous (c. 82 Ma), where a diverse Indo-Australian clade probably emerged c. 73 Ma. In the Early Eocene (c. 50–55 Ma), several clades independently dispersed from Australia to proto-New Guinea, i.e. the tribe Arachnopodini s.l., the ‘Rhynchodes group’ and the genus Trigonopterus. New Zealand was first colonized in the Late Palaeocene (c. 60 Ma). Divergence time estimations and biogeographical reconstructions indicate that the colonization of New Guinea is older than expected from current geological reconstructions of the region.     

Revisiting the Great American Biotic Interchange through analyses of amphitropical bees

The Great American Biotic Interchange (GABI) is zoogeographic event characterized by the exchange of taxa between North and South America, typically associated with the rise of the Isthmus of Panama in the late Pliocene. Recent geologic evidence suggests the connections between North and South America may be much older, and that the interchange of organisms between the two continents could have therefore happened much earlier than 3 Ma. Most of the research investigating the GABI has come from tropical vertebrate taxa; little work has been done on invertebrates or on non‐tropical species. To investigate how the GABI shaped the distribution of arid‐adapted species, particularly those with amphitropical distributions (i.e. taxa found in South and North American xeric regions yet absent from the tropics), we examine the historical biogeography of the bee genus Diadasia using a hypothesis of Diadasia phylogenetic relationships. Nuclear and mitochondrial genetic loci are used to reconstruct a phylogeny of Diadasia, which is then used to estimate divergence dates and reconstruct ancestral area relationships. Our analyses suggest the divergence between North and South American Diadasia species occurred between 20.5 and 15 Ma, long before the formation of the Isthmus of Panama. This study is the first to show a Miocene connection for an amphitropically‐distributed insect group. It suggests that the biotic connection between continents is more complicated than previously thought and may have initiated long before the late Pliocene.     

Historical biogeography and phenotype‐phylogeny of Chroodiscus (lichenized Ascomycota: Ostropales: Graphidaceae)

Aim To analyse the historical biogeography of the lichen genus Chroodiscus using a phenotype‐based phylogeny in the context of continental drift and evolution of tropical rain forest vegetation. Location All tropical regions (Central and South America, Africa, India, Southeast Asia, north‐east Australia). Methods We performed a phenotype‐based phylogenetic analysis and ancestral character state reconstruction of 14 species of the lichen genus Chroodiscus, using paup * and mesquite ; dispersal–vicariance analysis (DIVA) and dispersal–extinction–cladogenesis (DEC) modelling to trace the geographical origin of individual clades; and ordination and clustering by means of pc‐ord , based on a novel similarity index, to visualize the biogeographical relationships of floristic regions in which Chroodiscus occurs. Results The 14 species of Chroodiscus show distinctive distribution patterns, with one pantropical and one amphi‐Pacific taxon and 12 species each restricted to a single continent. The genus comprises four clades. DIVA and DEC modelling suggest a South American origin of Chroodiscus in the mid to late Cretaceous (120–100 Ma), with subsequent expansion through a South American–African–Indian–Southeast Asian–Australian dispersal route and late diversification of the argillaceus clade in Southeast Asia. Based on the abundance of extant taxa, the probability of speciation events in Chroodiscus is shown to be extremely low. Slow dispersal of foliicolous rain forest understorey lichens is consistent with estimated phylogenetic ages of individual species and with average lengths of biological species intervals in fungi (10–20 Myr). Main conclusions The present‐day distribution of Chroodiscus can be explained by vicariance and mid‐distance dispersal through the interconnection or proximity of continental shelves, without the need for recent, trans‐oceanic long‐distance dispersal. Phylogenetic reconstruction and age estimation for Chroodiscus are consistent with the ‘biotic ferry’ hypothesis: a South American origin and subsequent eastward expansion through Africa towards Southeast Asia and north‐eastern Australia via the Indian subcontinent. The present‐day pantropical distributions of many clades and species of foliicolous lichens might thus be explained by eastward expansion through continental drift, along with the evolution of modern rain forests starting 120 Ma, rather than by the existence of a hypothetical continuous area of pre‐modern rain forest spanning South America, Africa and Southeast Asia during the mid and late Cretaceous.     

A tale of North and South America: time and mode of dispersal of the amphitropical genus Munroa (Poaceae,Chloridoideae)

Plant disjunctions have provided some of the most intriguing distribution patterns historically addressed by biogeographers. We evaluated the three hypotheses that have been postulated to explain these patterns [vicariance, stepping‐stone dispersal and long‐distance dispersal (LDD)] using Munroa, an American genus of grasses with six species and a disjunct distribution between the desert regions of North and South America. The ages of clades, cytology, ancestral characters and areas of distribution were investigated in order to establish relationships among species, to determine the time of divergence of the genus and its main lineages, and to understand further the biogeographical and evolutionary history of this genus. Bayesian inference recovered the North American M. pulchella as sister species to the rest. Molecular dating and ancestral area analyses suggest that Munroa originated in North America in the late Miocene–Pliocene (7.2 Mya; 8.2–6.5 Mya). Based on these results, we postulate that two dispersal events modelled the current distribution patterns of Munroa: the first from North to South America (7.2 Mya; 8.2–6.5 Mya) and the second (1.8 Mya; 2–0.8 Mya) from South to North America. Arid conditions of the late Miocene–Pliocene in the Neogene and Quaternary climatic oscillations in North America and South America were probably advantageous for the establishment of populations of Munroa. We did not find any relationship between ploidy and dispersal events, and our ancestral character analyses suggest that shifts associated with dispersal and seedling establishment, such as habit, reproductive system, disarticulation of rachilla, and shape and texture of the glume, have been important in these species reaching new areas. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 110–125.     

Integrated Fossil and Molecular Data Reveal the Biogeographic Diversification of the Eastern Asian-Eastern North American Disjunct Hickory Genus (Carya Nutt.)

The hickory genus (Carya) contains ca. 17 species distributed in subtropical and tropical regions of eastern Asia and subtropical to temperate regions of eastern North America. Previously, the phylogenetic relationships between eastern Asian and eastern North American species of Carya were not fully confirmed even with an extensive sampling, biogeographic and diversification patterns had thus never been investigated in a phylogenetic context. We sampled 17 species of Carya and 15 species representing all other genera of the Juglandaceae as outgroups, with eight nuclear and plastid loci to reconstruct the phylogeny of Carya. The phylogenetic positions of seven extinct genera of the Juglandaceae were inferred using morphological characters and the molecular phylogeny as a backbone constraint. Divergence times within Carya were estimated with relaxed Bayesian dating. Biogeographic analyses were performed in DIVA and LAGRANGE. Diversification rates were inferred by LASER and APE packages. Our results support two major clades within Carya, corresponding to the lineages of eastern Asia and eastern North America. The split between the two disjunct clades is estimated to be 21.58 (95% HPD 11.07-35.51) Ma. Genus-level DIVA and LAGRANGE analyses incorporating both extant and extinct genera of the Juglandaceae suggested that Carya originated in North America, and migrated to Eurasia during the early Tertiary via the North Atlantic land bridge. Fragmentation of the distribution caused by global cooling in the late Tertiary resulted in the current disjunction. The diversification rate of hickories in eastern North America appeared to be higher than that in eastern Asia, which is ascribed to greater ecological opportunities, key morphological innovations, and polyploidy.     

New information for Ilex phylogenetics based on the plastid psbA‐trnH intergenic spacer (Aquifoliaceae)

The aim of the present work was to clarify the origin and phylogenetic position of the species belonging to the genus Ilex (Aquifoliaceae), especially the South American species. Phylogenetic relationships of the genus Ilex were investigated using the plastid psbA‐trnH intergenic spacer and parsimony and Bayesian analyses. The psbA‐trnH intergenic spacer was shown to evolve slowly within Ilex, but a major gap present in this region was useful in the phylogenetic study of the genus. To obtain more potentially parsimonious characters, atpB‐rbcL intergenic spacer data were combined with those for psbA‐trnH. Many gaps present in the psbA‐trnH region were useful in the phylogenetic study of the genus Ilex. The topology of the trees showed that, in general, the clades are strongly related to geographical areas, a fact especially evident in certain different Asian lineages. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 182–193.     

Molecular phylogeny and historical biogeography of the genus Tuber, the 'true truffles'

Aim Various data sets and methods of analysis were combined to produce the first comprehensive molecular phylogeny of the genus Tuber and to analyse its biogeography. Location Europe, North Africa, China, Asia, North America. Methods Phylogenetic relationships among Tuber species were reconstructed based on a data set of internal‐transcribed spacer (ITS) sequences and various phylogenetic inference methods, specifically maximum parsimony, Bayesian analysis and neighbour joining. Tajima’s relative rate test showed that Tuber 18S rRNA, 5.8S rRNA, 5.8S‐ITS2 rRNA and β‐tubulin sequences evolved in a clock‐like manner. These genes, combined or not, were employed for molecular clock estimates after construction of linearized trees using mega 3.1. We reconstructed ancestral areas in the Northern Hemisphere by means of a dispersal–vicariance analysis (diva 1.1) based on current distribution patterns of the genus Tuber determined from the literature. Results The resulting molecular phylogeny divided the genus Tuber into five distinct clades, in agreement with our previously published studies. The Puberulum, Melanosporum and Rufum groups were diversified in terms of species and geographical distribution. In contrast, the Aestivum and Excavatum groups were less diversified and were located only in Europe or North Africa. Using a global molecular clock analysis, we estimated the divergence times for the origin of the genus and for the origin of several groups. diva inferred nine dispersal events and suggested that the ancestor of Tuber was originally present in Europe or was widespread in Eurasia. Equally optimal distributions were obtained for several nodes, suggesting different possible biogeographical patterns. Main conclusions Our analyses identified several discrepancies with the classical taxonomy of the genus, and we propose a new phylogenetic classification. According to molecular clocks, the radiation of the genus Tuber could have started between 271 and 140 Ma. Used in combination with the results obtained from time divergence estimates, this allows us to propose two equally probable scenarios of intra‐ and inter‐continental diversification of the genus according to the geographic distribution of the most recent common ancestor in Europe or Eurasia. The biogeographical patterns imply intra‐continental dispersal events between Europe and Asia and inter‐continental dispersal events between North America and Europe or Asia, which are compatible with land connections during the Tertiary.     

Rapid expansion and diversification into new niche space by fluvicoline flycatchers

The fluvicoline New World flycatchers (subfamily Fluvicolinae, family Tyrannidae) inhabit a broad range of forest and non‐forest habitats in all parts of the New World. Using a densely sampled phylogeny we depict the diversification and expansion of this group in time and space. We provide evidence that a shift in foraging behaviour allowed the group to rapidly expand in a wide range of tropical and subtropical habitats in South America. The results support that four main clades expanded into and specialized to distinct habitats and climates (closed to open, and warm to cold), respectively, and subsequently underwent vicariant speciation within their respective ecoregions. The group soon reached a significant species diversity over virtually all of South and North America, and with parallel trajectories of speciation slow‐down in all four clades. The genus Muscisaxicola is an exception, as it invaded the most inhospitable and barren environments in the Andes where they underwent rapid diversification in the Plio‐Pleistocene.     

Molecular Phylogenetics and Biogeography of the Caribbean-Centered <Emphasis Type="Italic">Croton</Emphasis> Subgenus <Emphasis Type="Italic">Moacroton</Emphasis> (Euphorbiaceae s.s.)

Initial molecular phylogenetic studies established the monophylly of the large genus Croton (Euphorbiaceae s.s.) and suggested that the group originated in the New World. A denser and more targeted sampling of Croton species points to a South American origin for the genus. The nuclear and chloroplast genomes indicate a different rooting for the phylogeny of Croton. Although we favor the rooting indicated by the chloroplast data our conclusions are also consistent with the topology inferred from the nuclear data. The satellite genera Cubacroton and Moacroton are embedded within Croton. These two genera are synonimized into Croton and a new subgenus, Croton subgenus Moacroton, is circumscribed to include them and their allied Croton species. Croton subgenus Moacroton is morphologically characterized by a primarily lepidote indumentum, bifid or simple styles, and pistillate flowers with sepals that are connate at the base. This newly circumscribed subgenus is found from North America to South America, and in contrast to the majority of Croton species most of its members are found in mesic habitats. The group is most diverse in the greater Caribbean basin. A molecular clock was calibrated to the phylogeny using the available Euphorbiaceae fossils. The timing and pattern of diversification of Croton is consistent with both the GAARlandia and Laurasian migration hypotheses. A single species, Croton poecilanthus from Puerto Rico, is placed incongruently by its nuclear and chloroplast genomes. The possibility of this species being of hybrid origin is discussed.      

The biogeography of Gunnera L.: vicariance and dispersal

Aim The genus Gunnera is distributed in South America, Africa and the Australasian region, a few species reaching Hawaii and southern Mexico in the North. A cladogram was used to (1) discuss the biogeography of Gunnera and (2) subsequently compare this biogeographical pattern with the geological history of continents and the patterns reported for other Southern Hemisphere organisms. Location Africa, northern South America, southern South America, Tasmania, New Zealand, New Guinea/Malaya, Hawaii, North America, Antarctica. Methods A phylogenetic analysis of twenty‐six species of Gunnera combining morphological characters and new as well as published sequences of the ITS region, rbcL and the rps16 intron, was used to interpret the biogeographical patterns in Gunnera. Vicariance was applied in the first place and dispersal was only assumed as a second best explanation. Results The Uruguayan/Brazilian Gunnera herteri Osten (subgenus Ostenigunnera Mattfeld) is sister to the rest of the genus, followed sequentially upwards by the African G. perpensa L. (subgenus Gunnera), in turn sister to all other, American and Australasian, species. These are divided into two clades, one containing American/Hawaiian species, the other containing all Australasian species. Within the Australasian clade, G. macrophylla Blume (subgenus Pseudogunnera Schindler), occurring in New Guinea and Malaya, is sister to a clade including the species from New Zealand and Tasmania (subgenus Milligania Schindler). The southern South American subgenus Misandra Schindler is sister to a clade containing the remaining American, as well as the Hawaiian species (subgenus Panke Schindler). Within subgenus Panke, G. mexicana Brandegee, the only North American species in the genus, is sister to a clade wherein the Hawaiian species are basal to all south and central American taxa. Main conclusions According to the cladogram, South America appears in two places, suggesting an historical explanation for northern South America to be separate from southern South America. Following a well‐known biogeographical pattern of vicariance, Africa is the sister area to the combined southern South America/Australasian clade. Within the Australasian clade, New Zealand is more closely related to New Guinea/Malaya than to southern South America, a pattern found in other plant cladograms, contradictory to some of the patterns supported by animal clades and by the geological hypothesis, respectively. The position of the Tasmanian G. cordifolia, nested within the New Zealand clade indicates dispersal of this species to Tasmania. The position of G. mexicana, the only North American species, as sister to the remaining species of subgenus Panke together with the subsequent sister relation between Hawaii and southern South America, may reflect a North American origin of Panke and a recolonization of South America from the north. This is in agreement with the early North American fossil record of Gunnera and the apparent young age of the South American clade.     

Geographical structure,narrow species ranges,and Cenozoic diversification in a pantropical clade of epiphyllous leafy liverworts

The evolutionary history and classification of epiphyllous cryptogams are still poorly known. Leptolejeunea is a largely epiphyllous pantropical liverwort genus with about 25 species characterized by deeply bilobed underleaves, elliptic to narrowly obovate leaf lobes, the presence of ocelli, and vegetative reproduction by cladia. Sequences of three chloroplast regions (rbcL, trnL‐F, psbA) and the nuclear ribosomal ITS region were obtained for 66 accessions of Leptolejeunea and six outgroup species to explore the phylogeny, divergence times, and ancestral areas of this genus. The phylogeny was estimated using maximum‐likelihood and Bayesian inference approaches, and divergence times were estimated with a Bayesian relaxed clock method. Leptolejeunea likely originated in Asia or the Neotropics within a time interval from the Early Eocene to the Late Cretaceous (67.9 Ma, 95% highest posterior density [HPD]: 47.9–93.7). Diversification of the crown group initiated in the Eocene or early Oligocene (38.4 Ma, 95% HPD: 27.2–52.6). Most species clades were established in the Miocene. Leptolejeunea epiphylla and L. schiffneri originated in Asia and colonized African islands during the Plio‐Pleistocene. Accessions of supposedly pantropical species are placed in different main clades. Several monophyletic morphospecies exhibit considerable sequence variation related to a geographical pattern. The clear geographic structure of the Leptolejeunea crown group points to evolutionary processes including rare long‐distance dispersal and subsequent speciation. Leptolejeunea may have benefitted from the large‐scale distribution of humid tropical angiosperm forests in the Eocene.     

A pre‐Miocene Irano‐Turanian cradle: Origin and diversification of the species‐rich monocot genus Gagea (Liliaceae)

The Irano‐Turanian (IT) floristic region is considered an important center of origin for many taxa. However, there is a lack of studies dealing with typical IT genera that also occur in neighboring areas. The species‐rich monocot genus Gagea Salisb. shows a center of diversity in IT region and a distribution in adjacent regions, therefore representing a good study object to investigate spatial and temporal relationships among IT region and its neighboring areas (East Asia, Euro‐Siberia, Himalaya, and Mediterranean). We aimed at (a) testing the origin of the genus and of its major lineages in the IT region, (b) reconstructing divergence times, and (c) reconstructing colonization events. To address these problems, sequences of the ribosomal DNA internal transcribed spacer (ITS) region of 418 individuals and chloroplast intergenic spacers sequences (psbA‐trnH, trnL‐trnF) of 497 individuals, representing 116 species from all sections of the genus and nearly its entire distribution area were analyzed. Divergence times were estimated under a random molecular clock based on nrITS phylogeny, which was the most complete data set regarding the representation of species and distribution areas. Ancestral distribution ranges were estimated for the nrITS data set as well as for a combined data set, revealing that Gagea most likely originated in southwestern Asia. This genus first diversified there starting in the Early Miocene. In the Middle Miocene, Gagea migrated to the Mediterranean and to East Asia, while migration into Euro‐Siberia took place in the Late Miocene. During the Pleistocene, the Arctic was colonized and Gagea serotina, the most widespread species, reached North America. The Mediterranean basin was colonized multiple times from southwestern Asia or Euro‐Siberia. Most of the currently existing species originated during the last 3 Ma.     

From Africa via Europe to South America: migrational route of a species‐rich genus of Neotropical lowland rain forest trees (Guatteria,Annonaceae)

Aim Several recent studies have suggested that a substantial portion of today’s plant diversity in the Neotropics has resulted from the dispersal of taxa into that region rather than by vicariance. In general, three routes have been documented for the dispersal of taxa onto the South American continent: (1) via the North Atlantic Land Bridge, (2) via the Bering Land Bridge, or (3) from Africa directly onto the continent. Here a species‐rich genus of Neotropical lowland rain forest trees (Guatteria, Annonaceae) is used as a model to investigate these three hypotheses. Location The Neotropics. Methods The phylogenetic relationships within the long‐branch clade of Annonaceae were reconstructed (using maximum parsimony, maximum likelihood and Bayesian inference) in order to gain insight in the phylogenetic position of Guatteria. Furthermore, Bayesian molecular dating and Bayesian dispersal–vicariance (Bayes‐DIVA) analyses were undertaken. Results Most of the relationships within the long‐branch clade of Annonaceae were reconstructed and had high support. However, the relationship between the Duguetia clade, the Xylopia–Artabotrys clade and Guatteria remained unclear. The stem node age estimate of Guatteria ranged between 49.2 and 51.3 Ma, whereas the crown node age estimate ranged between 11.4 and 17.8 Ma. For the ancestral area of Guatteria and its sister group, the area North America–Africa was reconstructed in 99% of 10,000 DIVA analyses, while South America–North America was found just 1% of the time. Main conclusions The estimated stem to crown node ages of Guatteria in combination with the Bayes‐DIVA analyses imply a scenario congruent with an African origin followed by dispersal across the North Atlantic Land Bridge in the early to middle Eocene and further dispersal into North and Central America (and ultimately South America) in the Miocene. The phylogenetically and morphologically isolated position of the genus is probably due to extinction of the North American and European stem lineages in the Tertiary.     

Identification of glacial refugia in south-eastern North America by phylogeographical analyses of a forest understorey plant, Trillium cuneatum

Aim We examine several hypotheses emerging from biogeographical and fossil records regarding glacial refugia of a southern thermophilic plant species. Specifically, we investigated the glacial history and post‐glacial colonization of a forest understorey species, Trillium cuneatum. We focused on the following questions: (1) Did T. cuneatum survive the Last Glacial Maximum (LGM) in multiple refugia, and (if so) where were they located, and is the modern genetic structure congruent with the fossil record‐based reconstruction of refugia for mesic deciduous forests? (2) What are the post‐glacial colonization patterns in the present geographical range? Location South‐eastern North America. Methods We sampled 45 populations of T. cuneatum throughout its current range. We conducted phylogeographical analyses based on maternally inherited chloroplast DNA (cpDNA haplotypes) and used TCS software to reconstruct intraspecific phylogeny. Results We detected six cpDNA haplotypes, geographically highly structured into non‐overlapping areas. With one exception, none of the populations had mixed haplotype composition. TCS analysis resulted in two intraspecific cpDNA lineages, with one clade subdivided further by shallower diversification. Main conclusions Our investigation revealed that T. cuneatum survived the LGM in multiple refugia, belonging to two (western, eastern) genealogical lineages geographically structured across south‐eastern North America. The western clade is confined to the south‐western corner of T. cuneatum’s modern range along the Lower Mississippi Valley, where fossil records document a major refugium of mesic deciduous forest. For the eastern clade, modern patterns of cpDNA haplotype distribution suggest cryptic vicariance, in the form of forest contractions and subsequent expansions associated with Pleistocene glacial cycles, rather than simple southern survival and subsequent northward colonization. The north–south partitioning of cpDNA haplotypes was unexpected, suggesting that populations of this rather southern thermophilic species may have survived in more northern locations than initially expected based on LGM climate reconstruction, and that the Appalachian Mountains functioned as a barrier to the dispersal of propagules originating in more southern refugia. Furthermore, our results reveal south‐west to north‐east directionality in historical migration through the Valley and Ridge region of north‐west Georgia.     

A tale of two clades: Comparative study of Glyptodon Owen and Glyptotherium Osborn (Xenarthra,Cingulata, Glyptodontidae)

Glyptodon and Glyptotherium represent the most conspicuous taxa of late Neogene and Pleistocene glyptodonts in South America and North America, respectively. The earliest records of Glyptodon in South America are 1.07 Ma (late early Pleistocene, Calabrian), although the possibility that “Paraglyptodon uquiensis” represents a Pliocene specimen of Glyptodon cannot be rejected. Glyptotherium originated from South American ancestry in northern South America or Central America about 3.9 Ma (early late Pliocene, Zanclean) or earlier. The diversity of South American Glyptodon is currently under study, but preliminary evidence would indicate that no more than three species (G. munizi, G. elongatus and G. reticulatus) are valid, plus a possible new Andean species. In turn, according to the updated taxonomy proposed herein, Glyptotherium includes two chronospecies. The earliest species, Gl. texanum, differs only slightly from the latest species, Gl. cylindricum. The relationship of Glyptodon and Glyptotherium has been problematical since the discovery of the North American lineage, at first identified as various species of Glyptodon and later considered a separate genus. Glyptodon is recognized as a natural group and recent taxonomic and phylogenetic revisions place all North American glyptodontines into Glyptotherium. In this paper, we propose a detailed morphological comparison between the southern South American species of Glyptodon and Glyptotherium in order to identify diagnostic differences and potential synapomorphies. Both genera can be distinguished mainly by differences in the skull, mandible, dentition, dorsal carapace, and caudal armor, Glyptodon being somewhat larger than Glyptotherium. Both clades show a highly conservative evolution, which could be interpreted as an anagenesis. The scarce records of glyptodonts in Central America show more morphological affinity with Glyptotherium than with Glyptodon.