DNA–DNA Hybridization Evidence for the Recent Origin of Marmots and Ground Squirrels (Rodentia: Sciuridae)

A molecular analysis, based on DNA/DNA hybridization experiments, examined seven species of the sciurid tribe Marmotini, in order to evaluate their evolutionary relationships. The branching pattern obtained from a neighbor-joining analysis and least-squares methods indicates that spermophiles and marmots are closely related. This result is in agreement with previous studies based on biochemical data which have suggested a Miospermophilus origin of Marmota (like Spermophilus), instead of the Protospermophilus origin usually proposed by paleontology. Using a molecular time scale calibrated by the fossil record of Sciurus (used here as an outgroup), we estimate the marmot/ground squirrel divergence at 6 My, at the same time as the major lineages of ground squirrels diverged from each other. Consequently, the species of Marmota appear as one of the numerous specialized forms derived from the explosive radiation of the Spermophilus lineage in the late Miocene.     

Phylogeny and Evolutionary History of the Ground Squirrels (Rodentia: Marmotinae)

Although ground squirrels (Spermophilus) and prairie dogs (Cynomys) are among the most intensively studied groups of mammals with respect to their ecology and behavior, a well-resolved phylogeny has not been available to provide a framework for comparative and historical analyses. We used complete mitochondrial cytochrome b sequences to construct a phylogeny that includes all 43 currently recognized species in the two genera, as well as representatives of two closely related genera (Marmota and Ammospermophilus). In addition, divergence times for ground squirrel lineages were estimated using Bayesian techniques that do not assume a molecular clock. All methods of phylogenetic analysis recovered the same major clades, and showed the genus Spermophilus to be paraphyletic with respect to both Marmota and Cynomys. Not only is the phylogeny at odds with previous hypotheses of ground squirrel relationships, but it suggests that convergence in morphology has been a common theme in ground squirrel evolution. A well-supported basal clade, including Ammospermophilus and two species in the subgenus Otospermophilus, diverged from all other ground squirrels an estimated 17.5 million years ago. Between 10 and 14 million years ago, a relatively rapid diversification gave rise to lineages leading to marmots and to several distinct groups of ground squirrels. The Eurasian ground squirrels diverged from their North American relatives during this period, far earlier than previously hypothesized. This period of diversification corresponded to warming climate and spread of grasslands in western North America and Eurasia. Close geographic proximity of related forms suggests that most species evolved in or near their current ranges.     

A Review of the Fossil Record of the Genus Itea (Iteaceae, Saxifragales) with Comments on its Historical Biogeography

Itea is a genus of about 20 species of trees and shrubs that are today native to southeastern North America, eastern Asia, and eastern Africa. In this paper, I review the fossil record of Itea, which is based on four types of fossils: diporate, psilate pollen attributed to Itea or the dispersed pollen genus Iteapollis; carpofossils representing fruits and seeds attributed to Itea europaea; flowers preserved in amber and assigned to Adenanthemum iteoides; and leaf impressions attributed to Itea. The distributions of these fossils indicate that Itea was present in western North America from the early Eocene to Miocene, in eastern North America beginning no later than the early Miocene, and in western Eurasia from the late Eocene to Pliocene. Only one datapoint is known from eastern Asia; it is early Miocene in age. Based on the fossil record, it can be inferred that Itea crossed between continents over both the Bering Land Bridge and North American Land Bridge, and that it reached Africa from Europe via Anatolia. Thus, it is predicted that the sole extant North American species, I. virginica, may be most closely related to the sole extant African species, I. rhamnoides. The potential application of Itea fossils to calibrating phylogenetic trees generated from molecular sequence data is also discussed.     

The Leporid Datum: a late Miocene biotic marker

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Exploring the Formation of a Disjunctive Pattern between Eastern Asia and North America Based on Fossil Evidence from Thuja (Cupressaceae)

Thuja, a genus of Cupressaceae comprising five extant species, presently occurs in both East Asia (3 species) and North America (2 species) and has a long fossil record from Paleocene to Pleistocene in the Northern Hemisphere. Two distinct hypotheses have been proposed to account for the origin and present distribution of this genus. Here we recognize and describe T. sutchuenensis Franch., a new fossil Thuja from the late Pliocene sediments of Zhangcun, Shanxi, North China, based on detailed comparisons with all living species and other fossil ones, integrate the global fossil records of this genus plotted in a set of paleomaps from different time intervals, which show that Thuja probably first appeared at high latitudes of North America in or before the Paleocene. This genus reached Greenland in the Paleocene, then arrived in eastern Asia in the Miocene via the land connection between East Asia and western North America. In the late Pliocene, it migrated into the interior of China. With the Quaternary cooling and drying, Thuja gradually retreated southwards to form today’s disjunctive distribution between East Asia and North America.     

Phylogeographic history of the woodwardioid ferns,including species from the Himalayas

The woodwardioid ferns are well-represented in the Northern Hemisphere, where they are disjunctly distributed throughout the warm temperate and subtropical regions of North America, Europe, and Asia. To infer the biogeographic history of the woodwardioid ferns, the phylogeny of Woodwardia was estimated using rbcL and rps4 sequences from divergent distribution regions including the Himalayas. Phylogenetic results support Woodwardia as a monophyletic group with Woodwardia areolatae and W. virginica as basal, these two species from eastern North America diverged early, which are sister clades to the remaining species from America, Europe, and Asia. Based on analyses of the fossil records of these species for divergence times, Woodwardia species were estimated to have diverged initially in the Paleogene of North America. After its New World origin, a greater diversification and expansion of Woodwardia occurred in eastern Eurasia, with the European arrival of Woodwardia radicans during the Middle Miocene. Compared to earlier reports, a migration back into North America via the Bering land bridge is consistent with these data.     

Origines du peuplement mammalien en Afrique du Nord durant le miocène terminal

The late Miocene North African mammalianassemblage is considered here from three viewpoints: survivals, extinctions, and immigrations. The Eurasiatic affinities of the large mammals slightly prevail over the Ethiopian affinities. Amongst the North African large mammals, 4 to 8 taxa are Eurasiatic immigrants, while 4 to 6 are of Subsaharian origin. Contrarily, the micromammalian fauna is highly endemic, with only one species, a murid (Paraethomys miocaenicus), considered here as being related to an Asiatic form (Karnimata darwini). Our study of Eurasian and African Miocene faunas reveals that during the late Astaracian-early Turolian interval, the Saharo-Arabic belt permitted very little latitudinal faunal exchanges. However, during the middle and late Turolian such faunal exchanges became frequent. The micromammal record unequivocally indicates that a brief period of faunal exchange occurred between Africa and western Europe at the end of the Miocene, corresponding with the Messinian Salinity Crisis. The increased intercontinental faunal exchange between Africa and Eurasia during the late Miocene coincides with, and counterbalances the extinction of more than 10 taxa at the Mio/Pliocene boundary.     

中国和其他全北界三趾马的头骨和头后骨骼形态比较(英文)

由于地理位置上处于北美和旧大陆西部之间,中国晚中新世的三趾马提供了重要的生物地层与生物地理信息。这些信息反映出晚中新世时期北美和欧亚大陆之间的动物群交流,同时也与当时的古环境变迁相关联。依据面部和牙齿形态以及肢骨比例,将中国的三趾马与欧亚大陆及北美的其他种类进行了对比。中国的三趾马可识别出两个分类类群,其中一个非系统发育意义上的类群包括 Hipparion dermatorhinum,H. weihoense,H. fossatum,H. hippidio-dus 和 H. coelophyes,这一类群与旧大陆西部的三趾马在形态上高度相似; 另一个为本土类群,包括 H. ptychodus,H. platyodus,H. tylodus,H. sefvei 和 H. plocodus,它们与其他地区的种类并无相似之处。前一个类群是中国北方草原型动物群中的典型分子,对欧亚大陆化石地点的生物地层对比相当重要; 后一类群与北美的三趾马( "Cormohipparion"属) 在面部形态上具有相似性,这些本土的三趾马是中国北方森林型动物群的分子。     

Phylogeny and geographical deployment of the Primates

A classification of the Primates into three suborders is adopted.The Paromyiformes, possibly derived from the Purgatorinae, illustrate an early radiation localized in time (Late Cretaceous-Eocene) and space (North America and Europe).The Strepsirhini pose phylogenetic problems: position of the Daubentoniidae; position of the Cheirogaleidae (possible Lorisoidea); interrelations of the Adapoidea, Lemuroidea and Lorisoidea. The cradle of the group was probably situated in Africa, which would have been the source of migrations towards Eurasia and Madagascar. It is not excluded that Madagascar could be the place of origin of the African Lorisoidea.The Haplorhini are divided into two sister-groups, early differentiated by geographical segregation on both sides of the Tethys. The Tarsiiformes, exclusively Laurasian, may have originated in North America, but their relationships with the Paromomyiformes remain problematical. The Simiiformes (= Anthropoidea) have almost certainly originated in Africa. A transatlantic migration towards the end of the Eocene constitutes the most probable hypothesis (here put forward) to explain the colonization of the neotropical region by the Platyrrhini. The Catarrhini, at first exclusively African (the question of the fossils from the Eocene of Burma remains open) have invaded Eurasia since the Miocene (arrivals at intervals since the middle Miocene) thanks to the new geographical connections resulting from the Alpine orogeny.     

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.     

When parasites persist: tapeworms survive host extinction and reveal waves of dispersal across Beringia

Investigations of intercontinental dispersal between Asia and North America reveal complex patterns of geographic expansion, retraction and isolation, yet historical reconstructions are largely limited by the depth of the record that is retained in patterns of extant diversity. Parasites offer a tool for recovering deep historical insights about the biosphere, improving the resolution of past community-level interactions. We explored biogeographic hypotheses regarding the history of dispersal across Beringia, the region intermittently linking Asia and North America, through large-scale multi-locus phylogenetic analyses of the genus Schizorchis, an assemblage of host-specific cestodes in pikas (Lagomorpha: Ochotonidae). Our genetic data support palaeontological evidence for two separate geographic expansions into North America by Ochotona in the late Tertiary, a history that genomic evidence from extant pikas does not record. Pikas descending from the first colonization of Miocene age persisted into the Pliocene, subsequently coming into contact with a second wave of Nearctic colonists from Eurasia before going extinct. Spatial and temporal overlap of historically independent pika populations provided a window for host colonization, allowing persistence of an early parasite lineage in the contemporary fauna following the extinction of its ancestral hosts. Empirical evidence for ancient ‘ghost assemblages'' of hosts and parasites demonstrates how complex mosaic faunas are assembled in the biosphere through episodes of faunal mixing encompassing parasite lineages across deep and shallow time.     

Phylogeny and biogeography of Fagus (Fagaceae) based on 28 nuclear single/low-copy loci

Fagus L. is a key component in temperate deciduous broadleaf forests of the Northern Hemisphere. However, its biogeographic history has not been examined under the framework of a fully resolved and reasonably time-calibrated phylogeny. In this study, we sequenced 28 nuclear single/low-copy loci (18 555 bp in total) of 11 Fagus species/segregates and seven outgroups. Phylogenetic trees were reconstructed using both concatenation-based (maximum parsimony, maximum likelihood, and Bayesian inference) and coalescent-based methods (StarBEAST2, ASTRAL). The monophyly of two subgenera (Fagus and Engleriana) and most sections was well supported, except for sect. Lucida, which was paraphyletic with respect to sect. Longipetiolata. We also found a major phylogenetic conflict among North American, East Asian, and West Eurasian lineages of subgen. Fagus. Three segregates that have isolated distribution (F. mexicana, F. multinervis, and F. orientalis) were independent evolutionary units. Biogeographic analysis with fossils suggested that Fagus could have originated in the North Pacific region in late early Eocene. Major diversifications coincided with a climate aberration at the Eocene/Oligocene boundary and the global cooling since mid-Miocene. The late Miocene accelerated global cooling and the Pleistocene glaciations would have driven beeches into East Asia, North America, and West Eurasia. Meanwhile, range reduction and extinction in high latitudes, central Asia, and western North America converged to form the beech modern distribution pattern. This study provides a first attempt to disentangle the biogeographic history of beeches in the context of a nearly resolved and time-calibrated phylogeny, which could shed new insights into the formation of the temperate biome in the Northern Hemisphere.     

Jaw muscles of new world squirrels

The jaw, suprahyoid, and extrinsic tongue muscles are described for eight species of New World squirrels, spanning more than an order of magnitude in body mass. Anatomical differences are discussed in the light of body size, natural history, and phylogeny. The relative sizes of different muscles, their orientations, and the shapes and positions of their areas of attachment vary but show few trends in relation to body size. The anatomical differences are likewise not readily explained by the mechanical requirements of the animals' diets, which are similar. The most marked anatomical differences occur in Sciurillus (the pygmy tree squirrel), as well as those genera—Glaucomys (the flying squirrel) and Tamias (the chipmunk)—that are taxonomically most distinct from the tree squirrels. sciurillus is noteworthy for its unusually small temporalis and an anterior deep masseter that is oriented to assist in retraction of the jaw. Tamias has a more vertically oriented temporalis and greater inclination in the anterior masseter muscles than the other squirrels, features that may be associated with its large diastema and relatively posteriorly situated cheek teeth, which in turn may relate to its having cheek pouches. Our results form a valuable database of information to be used in further studies of functional morphology and phylogeny. © 1995 Wiley-Liss, Inc.     

Late Miocene Microstonyx remains (Suidae, Mammalia) from Northern China

Several large suid cranial remains attributed to Microstonyx major are part of a new Hipparion Fauna collection from the Hezheng area, Northern China. The new material confirms the presence of Microstonyx in the late Miocene of the area. The Chinese form belongs to a small-sized eastern population with reduced premolar row and clear sexual bimodality. Statistical comparison shows that Microstonyx major was a polymorphic species and reinforces recognition of Hippopotamodon as a separate genus, defined by relatively stout premolars resulting from a different underlying pattern of allometric growth. The presence of Microstonyx in North China and the distinct suid assemblage that lived there suggest biogeographic connections between Northern China and Western Eurasia in contrast to isolation from Southern China and the Indian subcontinent. The suid fauna of the late Miocene of Northern China seems to have been restricted to the later, more humid phase represented by the Red Clay faunas.     

Analysis of DNA sequences of six chloroplast and nuclear genes suggests incongruence, introgression, and incomplete lineage sorting in the evolution of Lespedeza (Fabaceae)

The genus Lespedeza (Fabaceae) consists of 40 species disjunctively distributed in East Asia and eastern North America. Phylogenetic relationships of all Lespedeza species and closely related genera were reconstructed using maximum parsimony, maximum likelihood, and Bayesian analyses of sequence data from five chloroplast (rpl16, rpl32-trnL, rps16-trnQ, trnL-F, and trnK/matK) and one nuclear (ITS) DNA regions. All analyses yielded consistent relationships among major lineages. Our results suggested that Campylotropis, Kummerowia, and Lespedeza are monophyletic, respectively. Lespedeza is resolved as sister to Kummerowia and these two together are further sister to Campylotropis. Neither of the two subgenera, subgen. Lespedeza and subgen. Macrolespedeza, in Lespedeza based on morphological characters, is recovered as monophyletic. Within Lespedeza, the North American clade is retrieved as sister to the Asian clade. The nuclear and chloroplast markers showed incongruent phylogenetic signals at shallow-level phylogeny, which may point to either introgression or incomplete lineage sorting in Lespedeza. The divergence times within Lespedeza and among related genera were estimated using Bayesian approach with BEAST. It is assumed that following the divergence between Kummerowia and Lespedeza in Asia in the late Miocene, the ancestor of Lespedeza diverged into the North American and the Asian lineages. The North American ancestor quickly migrated to North America through the Bering land bridge in the late Miocene. The North American and Asian lineages started to diversify almost simultaneously in the late Miocene but resulted in biased numbers of species in two continents.     

Construction of the phylogenetic model for the genera of the tribe Arctiini (Lepidoptera,Arctiidae) with the SYNAP method

A new scheme of the phylogeny of the tribe Arctiini is proposed. The Western Mediterranean genus Atlantarctia is considered the most primitive one in the tribe; the rest of genera form two large clades Arctia-Pericallia and Gonerda-Platyprepia. The first clade is supposed to have been subjected to radiation in western Eurasia, and the second clade, in Asia and North America in the Palaeogene when the eastern part of Asia was isolated from western Eurasia. Subsequently, most probably in the Neogene-Pleistocene, representatives of both clades spread over the whole Eurasia and North America. The Arctiini fauna of the tundra zone, which includes the genera Acerbia and Pararctia, was formed in Asia and North America, whereas the subboreal fauna (both steppe and nemoral) originated in western Eurasia. The boreal genus Borearctia has most likely also originated in Asia.     

Divergence time estimation in Cichorieae (Asteraceae) using a fossil-calibrated relaxed molecular clock

Knowing the age of lineages is key to understanding their biogeographic history. We aimed to provide the best estimate of the age of Cichorieae and its subtribes based on available fossil evidence and DNA sequences and to interpret their biogeography in the light of Earth history. With more than 1,550 species, the chicory tribe (Cichorieae, Asteraceae) is distributed predominantly in the northern Hemisphere, with centres of distribution in the Mediterranean region, central Asia, and SW North America. Recently, a new phylogenetic hypothesis of Cichorieae based on ITS sequences has been established, shedding new light on phylogenetic relationships within the tribe, which had not been detected so far. Cichorieae possess echinolophate pollen grains, on the surface of which cavities (lacunae) are separated by ridges. These lacunae and ridges show patterns characteristic of certain groups within Cichorieae. Among the fossil record of echinolophate pollen, the Cichorium intybus-type is the most frequent and also the oldest type (22 to 28.4 million years old). By using an uncorrelated relaxed molecular clock approach, the Cichorieae phylogenetic tree was calibrated with this fossil find. According to the analysis, the tribe originated no later than Oligocene. The species-rich core group originated no later than Late Oligocene or Early Miocene and its subtribes diversified no later than Middle/Late Miocene or Early Pliocene—an eventful period of changing geological setting and climate in the Mediterranean region and Eurasia. The first dispersal from Eurasia to North America, which resulted in the radiation of genera and species in North America (subtribe Microseridinae), also occurred no later than Middle or Late Miocene, suggesting the Bering land bridge as the route of dispersal.     

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.     

Phylogeny and Phytogeography of Eupatorium (Eupatorieae, Asteraceae): Insights from Sequence Data of the nrDNA ITS Regions and cpDNA RFLP

Eupatorium were examined by sequencing the internal transcribed spacers (ITS) of nuclear ribosomal DNA and restriction site analysis of chloroplast DNA. Molecular data provided strong evidence that (1) this genus originated in North America, (2) the genus diverged into three morphological species groups, Eutrochium, Traganthes and Uncasia in North America, and (3) one of the North American Uncasia lineages migrated into temperate Europe and eastern Asia over the Bering land bridge. The estimated divergence times support a late Miocene to early Pliocene migration from North America to Eurasia via the Bering land bridge. A European species was sister to all of the eastern Asian species examined. The disjunct distribution pattern of the genus Eupatorium is incongruent with the classical Arcto-Tertiary geoflora concept. Received 13 September 1999/ Accepted in revised form 4 January 2000