Using the fossil record to estimate the age of the last common ancestor of extant primates

Divergence times estimated from molecular data often considerably predate the earliest known fossil representatives of the groups studied. For the order Primates, molecular data calibrated with various external fossil dates uniformly suggest a mid-Cretaceous divergence from other placental mammals, some 90 million years (Myr) ago, whereas the oldest known fossil primates are from the basal Eocene epoch (54-55 Myr ago). The common ancestor of primates should be earlier than the oldest known fossils, but adequate quantification is needed to interpret possible discrepancies between molecular and palaeontological estimates. Here we present a new statistical method, based on an estimate of species preservation derived from a model of the diversification pattern, that suggests a Cretaceous last common ancestor of primates, approximately 81.5 Myr ago, close to the initial divergence time inferred from molecular data. It also suggests that no more than 7% of all primate species that have ever existed are known from fossils. The approach unites all the available palaeontological methods of timing evolutionary events: the fossil record, extant species and clade diversification models.     

Parallel adaptive radiations in two major clades of placental mammals

Higher level relationships among placental mammals, as well as the historical biogeography and morphological diversification of this group, remain unclear. Here we analyse independent molecular data sets, having aligned lengths of DNA of 5,708 and 2,947 base pairs, respectively, for all orders of placental mammals. Phylogenetic analyses resolve placental orders into four groups: Xenarthra, Afrotheria, Laurasiatheria, and Euarchonta plus Glires. The first three groups are consistently monophyletic with different methods of analysis. Euarchonta plus Glires is monophyletic or paraphyletic depending on the phylogenetic method. A unique nine-base-pair deletion in exon 11 of the BRCA1 gene provides additional support for the monophyly of Afrotheria, which includes proboscideans, sirenians, hyracoids, tubulidentates, macroscelideans, chrysochlorids and tenrecids. Laurasiatheria contains cetartiodactyls, perissodactyls, carnivores, pangolins, bats and eulipotyphlan insectivores. Parallel adaptive radiations have occurred within Laurasiatheria and Afrotheria. In each group, there are aquatic, ungulate and insectivore-like forms.     

Cretaceous eutherians and Laurasian origin for placental mammals near the K/T boundary

Estimates of the time of origin for placental mammals from DNA studies span nearly the duration of the Cretaceous period (145 to 65 million years ago), with a maximum of 129 million years ago and a minimum of 78 million years ago. Palaeontologists too are divided on the timing. Some support a deep Cretaceous origin by allying certain middle Cretaceous fossils (97-90 million years old) from Uzbekistan with modern placental lineages, whereas others support the origin of crown group Placentalia near the close of the Cretaceous. This controversy has yet to be addressed by a comprehensive phylogenetic analysis that includes all well-known Cretaceous fossils and a wide sample of morphology among Tertiary and recent placentals. Here we report the discovery of a new well-preserved mammal from the Late Cretaceous of Mongolia and a broad-scale phylogenetic analysis. Our results exclude Cretaceous fossils from Placentalia, place the origin of Placentalia near the Cretaceous/Tertiary (K/T) boundary in Laurasia rather than much earlier within the Cretaceous in the Southern Hemisphere, and place afrotherians and xenarthrans in a nested rather than a basal position within Placentalia.     

Late Cretaceous relatives of rabbits, rodents, and other extant eutherian mammals.

Extant eutherian mammals and their most recent common ancestor constitute the crown group Placentalia. This taxon, plus all extinct taxa that share a more recent common ancestor with placentals than they do with Metatheria (including marsupials), constitute Eutheria. The oldest well documented eutherian-dominated fauna in the world is Dzharakuduk, Uzbekistan. Among eutherians that it yields is Kulbeckia, an 85-90-Myr-old member of Zalambdalestidae (a family of Late Cretaceous Asian eutherians). This extends Zalambdalestidae back by some 10 million years from sites in the Gobi Desert, Mongolia. A phylogenetic analysis of well described Late Cretaceous eutherians strongly supports Zalambdalestidae, less strongly supports 'Zhelestidae' (a Late Cretaceous clade related to Tertiary ungulates), but does not support Asioryctitheria (a group of Late Cretaceous Asian eutherians). A second analysis incorporating placentals from clades that include rodents (Tribosphenomys), lagomorphs (Mimotona) and archaic ungulates (Protungulatum and Oxyprimus) strongly supports Zalambdalestidae in a clade with Glires (rabbits, rodents and extinct relatives) and less strongly 'Zhelestidae' within a clade that includes archaic ungulates ('condylarths'). This argues that some Late Cretaceous eutherians belong within the crown group Placentalia. The ages of these taxa are in line with molecularly based estimates of 64-104 Myr ago (median 84 Myr ago) for the superordinal diversification of some placentals, but provide no support for a Late Cretaceous diversification of extant placental orders.     

The earliest known eutherian mammal

The skeleton of a eutherian (placental) mammal has been discovered from the Lower Cretaceous Yixian Formation of northeastern China. We estimate its age to be about 125 million years (Myr), extending the date of the oldest eutherian records with skull and skeleton by about 40 50 Myr. Our analyses place the new fossil at the root of the eutherian tree and among the four other known Early Cretaceous eutherians, and suggest an earlier and greater diversification of stem eutherians that occurred well before the molecular estimate for the diversification of extant placental superorders (104 64 Myr). The new eutherian has limb and foot features that are known only from scansorial (climbing) and arboreal (tree-living) extant mammals, in contrast to the terrestrial or cursorial (running) features of other Cretaceous eutherians. This suggests that the earliest eutherian lineages developed different locomotory adaptations, facilitating their spread to diverse niches in the Cretaceous.     

Molecular phylogenetics and the origins of placental mammals

The precise hierarchy of ancient divergence events that led to the present assemblage of modern placental mammals has been an area of controversy among morphologists, palaeontologists and molecular evolutionists. Here we address the potential weaknesses of limited character and taxon sampling in a comprehensive molecular phylogenetic analysis of 64 species sampled across all extant orders of placental mammals. We examined sequence variation in 18 homologous gene segments (including nearly 10,000 base pairs) that were selected for maximal phylogenetic informativeness in resolving the hierarchy of early mammalian divergence. Phylogenetic analyses identify four primary superordinal clades: (I) Afrotheria (elephants, manatees, hyraxes, tenrecs, aardvark and elephant shrews); (II) Xenarthra (sloths, anteaters and armadillos); (III) Glires (rodents and lagomorphs), as a sister taxon to primates, flying lemurs and tree shrews; and (IV) the remaining orders of placental mammals (cetaceans, artiodactyls, perissodactyls, carnivores, pangolins, bats and core insectivores). Our results provide new insight into the pattern of the early placental mammal radiation.     

Single origin of Malagasy Carnivora from an African ancestor

The Carnivora are one of only four orders of terrestrial mammals living in Madagascar today. All four (carnivorans, primates, rodents and lipotyphlan insectivores) are placental mammals with limited means for dispersal, yet they occur on a large island that has been surrounded by a formidable oceanic barrier for at least 88 million years, predating the age of origin for any of these groups. Even so, as many as four colonizations of Madagascar have been proposed for the Carnivora alone. The mystery of the island's mammalian origins is confounded by its poor Tertiary fossil record, which leaves us with no direct means for estimating dates of initial diversification. Here we use a multi-gene phylogenetic analysis to show that Malagasy carnivorans are monophyletic and thus the product of a single colonization of Madagascar by an African ancestor. Furthermore, a bayesian analysis of divergence ages for Malagasy carnivorans and lemuriforms indicates that their respective colonizations were temporally separated by tens of millions of years. We therefore conclude that a single event, such as vicariance or common dispersal, cannot explain the presence of both groups in Madagascar.     

The delayed rise of present-day mammals

Did the end-Cretaceous mass extinction event, by eliminating non-avian dinosaurs and most of the existing fauna, trigger the evolutionary radiation of present-day mammals? Here we construct, date and analyse a species-level phylogeny of nearly all extant Mammalia to bring a new perspective to this question. Our analyses of how extant lineages accumulated through time show that net per-lineage diversification rates barely changed across the Cretaceous/Tertiary boundary. Instead, these rates spiked significantly with the origins of the currently recognized placental superorders and orders approximately 93 million years ago, before falling and remaining low until accelerating again throughout the Eocene and Oligocene epochs. Our results show that the phylogenetic 'fuses' leading to the explosion of extant placental orders are not only very much longer than suspected previously, but also challenge the hypothesis that the end-Cretaceous mass extinction event had a major, direct influence on the diversification of today's mammals.     

Dating the origin of the Orchidaceae from a fossil orchid with its pollinator

Since the time of Darwin, evolutionary biologists have been fascinated by the spectacular adaptations to insect pollination exhibited by orchids. However, despite being the most diverse plant family on Earth, the Orchidaceae lack a definitive fossil record and thus many aspects of their evolutionary history remain obscure. Here we report an exquisitely preserved orchid pollinarium (of Meliorchis caribea gen. et sp. nov.) attached to the mesoscutellum of an extinct stingless bee, Proplebeia dominicana, recovered from Miocene amber in the Dominican Republic, that is 15-20 million years (Myr) old. This discovery constitutes both the first unambiguous fossil of Orchidaceae and an unprecedented direct fossil observation of a plant-pollinator interaction. By applying cladistic methods to a morphological character matrix, we resolve the phylogenetic position of M. caribea within the extant subtribe Goodyerinae (subfamily Orchidoideae). We use the ages of other fossil monocots and M. caribea to calibrate a molecular phylogenetic tree of the Orchidaceae. Our results indicate that the most recent common ancestor of extant orchids lived in the Late Cretaceous (76-84 Myr ago), and also suggest that the dramatic radiation of orchids began shortly after the mass extinctions at the K/T boundary. These results further support the hypothesis of an ancient origin for Orchidaceae.     

Origin of extant domesticated sunflowers in eastern North America

Eastern North America is one of at least six regions of the world where agriculture is thought to have arisen wholly independently. The primary evidence for this hypothesis derives from morphological changes in the archaeobotanical record of three important crops--squash, goosefoot and sunflower--as well as an extinct minor cultigen, sumpweed. However, the geographical origins of two of the three primary domesticates--squash and goosefoot--are now debated, and until recently sunflower (Helianthus annuus L.) has been considered the only undisputed eastern North American domesticate. The discovery of 4,000-year-old domesticated sunflower remains from San Andrés, Tabasco, implies an earlier and possibly independent origin of domestication in Mexico and has stimulated a re-examination of the geographical origin of domesticated sunflower. Here we describe the genetic relationships and pattern of genetic drift between extant domesticated strains and wild populations collected from throughout the USA and Mexico. We show that extant domesticates arose in eastern North America, with a substantial genetic bottleneck occurring during domestication.     

A lamprey from the Cretaceous Jehol biota of China

Widespread nowadays in freshwater and coastal seas of the cold and temporal zones, lampreys are a jawless vertebrate group that has been in existence for more than 300 million years but left a meagre fossil record. Only two fossil lamprey species, namely Mayomyzon pieckoensis and Hardistiella montanensis, have been recognized with certainty from North American Carboniferous marine deposits. Here we report a freshwater lamprey from the Early Cretaceous epoch (about 125 million years ago) of Inner Mongolia, China. The new taxon, Mesomyzon mengae, has a long snout, a well-developed sucking oral disk, a relatively long branchial apparatus showing branchial basket, seven gill pouches, gill arches and impressions of gill filaments, about 80 myomeres and several other characters that are previously unknown or ambiguous. Our finding not only indicates Mesomyzon's closer relationship to extant lampreys but also reveals the group's invasion into a freshwater environment no later than the Early Cretaceous. The new material furthers our understanding of ancient lampreys, bridges the gap between the Carboniferous ones and their recent relatives, and adds to our knowledge of the evolutionary history of lampreys.     

A stem batrachian from the Early Permian of Texas and the origin of frogs and salamanders

The origin of extant amphibians (Lissamphibia: frogs, salamanders and caecilians) is one of the most controversial questions in vertebrate evolution, owing to large morphological and temporal gaps in the fossil record. Current discussions focus on three competing hypotheses: a monophyletic origin within either Temnospondyli or Lepospondyli, or a polyphyletic origin with frogs and salamanders arising among temnospondyls and caecilians among the lepospondyls. Recent molecular analyses are also controversial, with estimations for the batrachian (frog-salamander) divergence significantly older than the palaeontological evidence supports. Here we report the discovery of an amphibamid temnospondyl from the Early Permian of Texas that bridges the gap between other Palaeozoic amphibians and the earliest known salientians and caudatans from the Mesozoic. The presence of a mosaic of salientian and caudatan characters in this small fossil makes it a key taxon close to the batrachian (frog and salamander) divergence. Phylogenetic analysis suggests that the batrachian divergence occurred in the Middle Permian, rather than the late Carboniferous as recently estimated using molecular clocks, but the divergence with caecilians corresponds to the deep split between temnospondyls and lepospondyls, which is congruent with the molecular estimates.     

Earliest evidence for efficient oral processing in a terrestrial herbivore

Herbivores can increase their digestion rate by mechanically reducing particle size through oral trituration. Groups of terrestrial vertebrates with the greatest capacity to reduce tough plant foods orally are also the most abundant and diverse, as exemplified by ornithopod dinosaurs during the Mesozoic and extant artiodactyl and perissodactyl mammals. Thus, the effective oral processing of high-fibre plant material seems to represent an evolutionary innovation of both functional and macroevolutionary significance. However, evidence for oral processing is poorly documented in the fossil record, especially during the initial stages of terrestrial vertebrate diversification. Here we report on the basal anomodont Suminia getmanovi, the only known Palaeozoic vertebrate in which unequivocal specializations in its cranium and teeth for high-fibre herbivory are well preserved. We propose that the capacity to comminute tough plant foods was critical to the diversification of anomodonts, the most diverse, widely dispersed and abundant group of Palaeozoic terrestrial vertebrates, and to the onset of modern terrestrial ecosystems.     

Dual origin of tribosphenic mammals

Marsupials, placentals and their close therian relatives possess complex (tribosphenic) molars that are capable of versatile occlusal functions. This functional complex is widely thought to be a key to the early diversification and evolutionary success of extant therians and their close relatives (tribosphenidans). Long thought to have arisen on northern continents, tribosphenic mammals have recently been reported from southern landmasses. The great age and advanced morphology of these new mammals has led to the alternative suggestion of a Gondwanan origin for the group. Implicit in both biogeographic hypotheses is the assumption that tribosphenic molars evolved only once in mammalian evolutionary history. Phylogenetic and morphometric analyses including these newly discovered taxa suggest a different interpretation: that mammals with tribosphenic molars are not monophyletic. Tribosphenic molars evolved independently in two ancient (holotherian) mammalian groups with different geographic distributions during the Jurassic/Early Cretaceous: an australosphenidan clade endemic to Gondwanan landmasses, survived by extant monotremes; and a boreosphenidan clade of Laurasian continents, including extant marsupials, placentals and their relatives.     

Fossil evidence for an ancient divergence of lorises and galagos

Morphological, molecular, and biogeographic data bearing on early primate evolution suggest that the clade containing extant (or 'crown') strepsirrhine primates (lemurs, lorises and galagos) arose in Afro-Arabia during the early Palaeogene, but over a century of palaeontological exploration on that landmass has failed to uncover any conclusive support for that hypothesis. Here we describe the first demonstrable crown strepsirrhines from the Afro-Arabian Palaeogene--a galagid and a possible lorisid from the late middle Eocene of Egypt, the latter of which provides the earliest fossil evidence for the distinctive strepsirrhine toothcomb. These discoveries approximately double the previous temporal range of undoubted lorisiforms and lend the first strong palaeontological support to the hypothesis of an ancient Afro-Arabian origin for crown Strepsirrhini and an Eocene divergence of extant lorisiform families.     

石珊瑚起源的形态学和分子系统学研究

石珊瑚是现代最重要的造礁动物,在地质史的过去和现在都非常重要。石珊瑚的起源一直是珊瑚研究中颇有争议的重大问题：石珊瑚究竟是起源于古生代的皱壁珊瑚、一种石珊瑚形珊瑚,还是一类软体海葵,目前还很难下定论。建立在现代石珊瑚及其化石的形态学特征基础上的传统研究手段和新兴的分子系统学分析手段,是研究石珊瑚起源问题的2种主要方法。用分子生物学方法测定了珊瑚的18S rDNA,构建了珊瑚纲珊瑚的系统发育树,对当前国际上争论纷纷的有关石珊瑚起源问题进行了形态学和分子系统学的比较研究,以期为更好地解决石珊瑚起源问题提供思路。     

Ferns diversified in the shadow of angiosperms

The rise of angiosperms during the Cretaceous period is often portrayed as coincident with a dramatic drop in the diversity and abundance of many seed-free vascular plant lineages, including ferns. This has led to the widespread belief that ferns, once a principal component of terrestrial ecosystems, succumbed to the ecological predominance of angiosperms and are mostly evolutionary holdovers from the late Palaeozoic/early Mesozoic era. The first appearance of many modern fern genera in the early Tertiary fossil record implies another evolutionary scenario; that is, that the majority of living ferns resulted from a more recent diversification. But a full understanding of trends in fern diversification and evolution using only palaeobotanical evidence is hindered by the poor taxonomic resolution of the fern fossil record in the Cretaceous. Here we report divergence time estimates for ferns and angiosperms based on molecular data, with constraints from a reassessment of the fossil record. We show that polypod ferns (> 80% of living fern species) diversified in the Cretaceous, after angiosperms, suggesting perhaps an ecological opportunistic response to the diversification of angiosperms, as angiosperms came to dominate terrestrial ecosystems.     

Highly specialized mammalian skulls from the Late Cretaceous of South America

Dryolestoids are an extinct mammalian group belonging to the lineage leading to modern marsupials and placentals. Dryolestoids are known by teeth and jaws from the Jurassic period of North America and Europe, but they thrived in South America up to the end of the Mesozoic era and survived to the beginnings of the Cenozoic. Isolated teeth and jaws from the latest Cretaceous of South America provide mounting evidence that, at least in western Gondwana, dryolestoids developed into strongly endemic groups by the Late Cretaceous. However, the lack of pre-Late Cretaceous dryolestoid remains made study of their origin and early diversification intractable. Here we describe the first mammalian remains from the early Late Cretaceous of South America, including two partial skulls and jaws of a derived dryolestoid showing dental and cranial features unknown among any other group of Mesozoic mammals, such as single-rooted molars preceded by double-rooted premolars, combined with a very long muzzle, exceedingly long canines and evidence of highly specialized masticatory musculature. On one hand, the new mammal shares derived features of dryolestoids with forms from the Jurassic of Laurasia, whereas on the other hand, it is very specialized and highlights the endemic, diverse dryolestoid fauna from the Cretaceous of South America. Our specimens include only the second mammalian skull known for the Cretaceous of Gondwana, bridging a previous 60-million-year gap in the fossil record, and document the whole cranial morphology of a dryolestoid, revealing an unsuspected morphological and ecological diversity for non-tribosphenic mammals.     

Whole fossil plants of <Emphasis Type="Italic">Ephedra</Emphasis> and their implications on the morphology,ecology and evolution of Ephedraceae (Gnetales)

Although there are many reports of fossil Ephedraceae,whole plant fossil record remains rare.Due to a lack of trust on partially preserved fossil materials,scholars working on molecular clock proposed a recent origin of Ephedra and cast doubt on the earlier origin time of Ephedraceae.To better the understanding on this interesting group,here we report whole plants of Ephedra hongtaoi sp.nov.(Ephedraceae,Gnetales) from the Yixian Formation (Early Cretaceous) in western Liaoning,China.These whole plants of Ep...     

Primitive Early Eocene bat from Wyoming and the evolution of flight and echolocation

Bats (Chiroptera) represent one of the largest and most diverse radiations of mammals, accounting for one-fifth of extant species. Although recent studies unambiguously support bat monophyly and consensus is rapidly emerging about evolutionary relationships among extant lineages, the fossil record of bats extends over 50 million years, and early evolution of the group remains poorly understood. Here we describe a new bat from the Early Eocene Green River Formation of Wyoming, USA, with features that are more primitive than seen in any previously known bat. The evolutionary pathways that led to flapping flight and echolocation in bats have been in dispute, and until now fossils have been of limited use in documenting transitions involved in this marked change in lifestyle. Phylogenetically informed comparisons of the new taxon with other bats and non-flying mammals reveal that critical morphological and functional changes evolved incrementally. Forelimb anatomy indicates that the new bat was capable of powered flight like other Eocene bats, but ear morphology suggests that it lacked their echolocation abilities, supporting a 'flight first' hypothesis for chiropteran evolution. The shape of the wings suggests that an undulating gliding-fluttering flight style may be primitive for bats, and the presence of a long calcar indicates that a broad tail membrane evolved early in Chiroptera, probably functioning as an additional airfoil rather than as a prey-capture device. Limb proportions and retention of claws on all digits indicate that the new bat may have been an agile climber that employed quadrupedal locomotion and under-branch hanging behaviour.