DNA and Morphology Unite Two Species and 10 Million Year Old Fossils

Species definition and delimitation is a non-trivial problem in evolutionary biology that is particularly problematic for fossil organisms. This is especially true when considering the continuity of past and present species, because species defined in the fossil record are not necessarily equivalent to species defined in the living fauna. Correctly assigned fossil species are critical for sensitive downstream analysis (e.g., diversification studies and molecular-clock calibration). The marine snail genus Alcithoe exemplifies many of the problems with species identification. The paucity of objective diagnostic characters, prevalence of morphological convergence between species and considerable variability within species that are observed in Alcithoe are typical of a broad range of fossilised organisms. Using a synthesis of molecular and morphometric approaches we show that two taxa currently recognised as distinct are morphological variants of a single species. Furthermore, we validate the fossil record for one of these morphotypes by finding a concordance between the palaeontological record and divergence time of the lineage inferred using molecular-clock analysis. This work demonstrates the utility of living species represented in the fossil record as candidates for molecular-clock calibration, as the veracity of fossil species assignment can be more rigorously tested.     

Speciation in the fossil record

It is easy to claim that the fossil record says nothing about speciation because the biological species concept (which relies on interbreeding) cannot be applied to it and genetic studies cannot be carried out on it. However, fossilized organisms are often preserved in sufficient abundance for populations of intergrading morphs to be recognized, which, by analogy with modern populations, are probably biological species. Moreover, the fossil record is our only reliable documentation of the sequence of past events over long time intervals: the processes of speciation are generally too slow to be observed directly, and permanent reproductive isolation can only be verified with hindsight. Recent work has shown that some parts of the fossil record are astonishingly complete and well documented, and patterns of lineage splitting can be examined in detail. Marine plankton appear to show gradual speciation, with subsequent morphological differentiation of lineages taking up to 500000 years to occur. Marine invertebrates and vertebrates more commonly show punctuated patterns, with periods of rapid speciation followed by long-term stasis of species lineages.     

Amber microfossils: On the validity of species concept

Do terrestrial micro-organisms evolve morphologically? A recent concept suggests that morphological stasis over dozens of millions of years has persisted in microbial lineages. However, it is based on a weak fossil record. Indeed, it is already difficult to define a species with extant microbes, and this task is even harder when dealing with fossil micro-organisms. Based on research on fossils in amber, we highlighted the different problems that are raised when describing a new fossil species of micro-organisms and we discuss the concept of morphological stasis.     

A Middle-Late Eocene inflorescence of Caryophyllaceae from Tasmania, Australia

A new genus and species (Caryophylloflora paleogenica genus and species nova G. J. Jord. & Macphail) are proposed for a fossil inflorescence found in Middle-Late Eocene sediments at Locharbour, northeastern Tasmania, Australia. A parsimony analysis of 75 extant species of the order Caryophyllales and five outgroups placed the fossil within Caryophyllaceae, either subfamily Alsinoideae or Caryophylloideae. The analysis used molecular (rbcL and/or matK), morphological, and anatomical data for the extant species and morphological data for the fossil. Tests on extant species imply that the placement of the fossil should be convincing. The fossil appears to be of a lineage distinct from any extant Australian Caryophyllaceae. In situ pollen are consistent with the form species, Periporopollenites polyoratus. This relatively simple pollen type first appears in Australia and New Zealand in the Late Cretaceous, the oldest known record of the Caryophyllaceae. The last appearance of P. polyoratus in Australia is in the Oligocene, and extant Australian members of the Caryophyllaceae are best interpreted as having evolved from species that dispersed from elsewhere during the Neogene or Quaternary.     

THE SPECIES OF THE BIRDS-OF-PARADISE (PARADISAEIDAE): APPLYING THE PHYLOGENETIC SPECIES CONCEPT TO A COMPLEX PATTERN OF DIVERSIFICATION

Abstract The phylogenetic species concept is applied for the first time to a major radiation of birds, the birds-of-paradise (Paradisaeidae) of Australasia. Using the biological species concept, previous workers have postulated approximately 40–42 species in the family. Of these, approximately 13 are monotypic and 27 are polytypic with about 100 subspecies. Phylogenetic species are irreducible (basal) clusters of organisms (terminal taxa) that are diagnosably distinct from other such clusters. Within the context of this concept, approximately 90 species of paradisaeids are postulated to have diversified within Australasia. The phylogenetic species concept more accurately describes evolutionary diversity within the family and provides a better theoretical and empirical framework for analysing speciation, historical biogeography and patterns of morphological, behavioral and ecological diversification within this group than does the biological species concept.     

Human evolution at the Matuyama‐Brunhes boundary

The cranial morphology of fossil hominids between the end of the Early Pleistocene and the beginning of the Middle Pleistocene provides crucial evidence to understand the distribution in time and space of the genus Homo. This evidence is critical for evaluating the competing models regarding diversity within our genus. The debate focuses on two alternative hypotheses, one basically anagenetic and the other cladogenetic. The first suggests that morphological change is so diffused, slow, and steady that it is meaningless to apply species names to segments of a single lineage. The second is that the morphological variation observed in the fossil record can best be described as a number of distinct species that are not connected in a linear ancestor‐descendant sequence. Today much more fossil evidence is available than was in the past to test these alternative hypotheses, as well as intermediate variants. Special attention must be paid to Africa because this is the most probable continental homeland for both the origin of the genus Homo (around 2.5–2 Ma), 1 as well as the site, two million or so years later, of the emergence of the species H. sapiens. 2 However, the African fossil record is very poorly represented between 1 Ma and 600 ka. Europe furnishes recent discoveries in this time range around the Matuyama‐Brunhes chron boundary (780,000 years ago), a period for which, at present, we have no noteworthy fossil evidence in Africa or the Levant. Two penecontemporaneous sources of European fossil evidence, the Ceprano calvaria (Italy) 3 and the TD6 fossil assemblage of Atapuerca (Spain) 4 are thus of great interest for testing hypotheses about human evolution in the fundamental time span bracketed between the late Early and the Middle Pleistocene. This paper is based on a phenetic approach to cranial variation aimed at reviewing the Early‐to‐Middle Pleistocene trajectories of human evolution. The focus of the paper is on neither the origin nor the end of the story of the genus Homo, but rather its chronological and phylogenetic core. Elucidation of the evolutionary events that happened around 780 ka during the transition from the Early to Middle Pleistocene is one of the new frontiers for human paleontology, and is critical for understanding the processes that ultimately led to the origin of H. sapiens.     

On the placement of the Cretaceous orthopteran Brauckmannia groeningae from Brazil, with notes on the relationships of Schizodactylidae (Orthoptera, Ensifera)

The fossil orthopteran Brauckmannia groeningae Martins-Neto (Orthoptera, Ensifera) from the Early Cretaceous Crato Formation of Brazil, currently misplaced at both the genus and family level, is transferred to the family Schizodactylidae and assigned to the extant genus Schizodactylus Brullé; ergo, Brauckmannia enters synonymy under Schizodactylus and Brauckmanniidae enters synonymy under Schizodactylidae. Schizodactylus groeningae (Martins-Neto), comb. n. agrees in size and general habitus with extant members of the genus, but can be readily separated by the robust, subovoid form of the metatibiae and the distinctive morphology of the lateral metabasitarsal processes. This species represents the first fossil occurrence of Schizodactylidae and the only New World record of this ancient lineage. Phylogenetic relationships of the schizodactylids are reviewed and a sister-group relationship with Grylloidea advocated based on a reappraisal of morphological and molecular evidence.     

Dinoflagellate phylogeny revisited: reconciling morphological and molecular based phylogenies

Ultrastructural and molecular phylogenetic data suggest that dinoflagellates diverged as a lineage possibly as early as the Precambrian. However, the fossil record is problematic before the Mesozoic. From the mid Triassic, though, the fossil record of dinoflagellates is a rich source of information on Mesozoic-Cenozoic dinoflagellates, especially the gonyaulacoids and peridinioids. From the sequence of appearance of species and tabulation types and the impression of early morphological experimentation and later stabilization, the early Mesozoic radiation of dinoflagellates appears to be a real evolutionary event: indeed, dinoflagellate morphology as we know it today may originate in that event. This would explain why it is so difficult to interpret earlier fossils as dinoflagellates. However, that the dinoflagellate lineage existed in some form in the pre-Mesozoic is supported by biogeochemical data, early results of which indicate that certain early Paleozoic acanthomorph acritarchs may belong to the lineage.

A surprising degree of consistency is observed between ultrastructural (including tabulational), coarse biochemical and molecular sequence data. For example, sequence data provided by small subunit (SSU) rRNA support the hypothesis of progressive loss of histones within the dinoflagellates. Gymnodinioids have long been considered to be polyphyletic but are thought of generally as forerunners to the strongly thecate groups such as gonyaulacoids and peridinioids. In molecular trees they appear in both early-derived and late-derived positions, but mostly the latter. SSU data clearly support the gonyaulacoid/peridinioid ordinal separation, as does the fossil record. Prorocentroids are now thought to be the among the most derived dinoflagellates (and presumably the morphologically similar dinophysoids), but SSU sequences have so far failed to resolve the relationships of most gymnodinioids, peridinioids and prorocentroids (the so-called GPP complex) to one another. However, they do suggest the origin of prorocentroids from peridinioids rather than gonyaulacoids and that gymnodinioids probably had several origins.     

A phylogeny of Cenozoic macroperforate planktonic foraminifera from fossil data

We present a complete phylogeny of macroperforate planktonic foraminifer species of the Cenozoic Era (∼65 million years ago to present). The phylogeny is developed from a large body of palaeontological work that details the evolutionary relationships and stratigraphic (time) distributions of species‐level taxa identified from morphology (‘morphospecies’). Morphospecies are assigned to morphogroups and ecogroups depending on test morphology and inferred habitat, respectively. Because gradual evolution is well documented in this clade, we have identified many instances of morphospecies intergrading over time, allowing us to eliminate ‘pseudospeciation’ and ‘pseudoextinction’ from the record and thereby permit the construction of a more natural phylogeny based on inferred biological lineages. Each cladogenetic event is determined as either budding or bifurcating depending on the pattern of morphological change at the time of branching. This lineage phylogeny provides palaeontologically calibrated ages for each divergence that are entirely independent of molecular data. The tree provides a model system for macroevolutionary studies in the fossil record addressing questions of speciation, extinction, and rates and patterns of evolution.     

A geometric morphometric analysis of hominin upper first molar shape

Recent studies have revealed interesting differences in upper first molar morphology across the hominin fossil record, particularly significant between H. sapiens and H. neanderthalensis. Usually these analyses have been performed by means of classic morphometric methods, including the measurement of relative cusp areas or the angles defined between cusps. Although these studies have provided valuable information for the morphological characterization of some hominin species, we believe that the analysis of this particular tooth could be more conclusive for taxonomic assignment. In this study, we have applied geometric morphometric methods to explore the morphological variability of the upper first molar (M(1)) across the human fossil record. Our emphasis focuses on the study of the phenetic relationships among the European middle Pleistocene populations (designated as H. heidelbergensis) with H. neanderthalensis and H. sapiens, but the inclusion of Australopithecus and early Homo specimens has helped us to assess the polarity of the observed traits. H. neanderthalensis presents a unique morphology characterized by a relatively distal displacement of the lingual cusps and protrusion in the external outline of a large and bulging hypocone. This morphology can be found in a less pronounced degree in the European early and middle Pleistocene populations, and reaches its maximum expression with the H. neanderthalensis lineage. In contrast, modern humans retain the primitive morphology with a square occlusal polygon associated with a round external outline.     

The evolutionary history of the coral genus Acropora (Scleractinia, Cnidaria) based on a mitochondrial and a nuclear marker: reticulation, incomplete lineage sorting, or morphological convergence?

This study examines molecular relationships across a wide range of species in the mass spawning scleractinian coral genus Acropora. Molecular phylogenies were obtained for 28 species using DNA sequence analyses of two independent markers, a nuclear intron and the mtDNA putative control region. Although the compositions of the major clades in the phylogenies based on these two markers were similar, there were several important differences. This, in combination with the fact that many species were not monophyletic, suggests either that introgressive hybridization is occurring or that lineage sorting is incomplete. The molecular tree topologies bear little similarity to the results of a recent cladistic analysis based on skeletal morphology and are at odds with the fossil record. We hypothesize that these conflicting results may be due to the same morphology having evolved independently more than once in Acropora and/or the occurrence of extensive interspecific hybridization and introgression in combination with morphology being determined by a small number of genes. Our results indicate that many Acropora species belong to a species complex or syngameon and that morphology has little predictive value with regard to syngameon composition. Morphological species in the genus often do not correspond to genetically distinct evolutionary units. Instead, species that differ in timing of gamete release tend to constitute genetically distinct clades.     

Scientific drilling and biological evolution in ancient lakes: lessons learned and recommendations for the future

Scientific drilling to recover sediment core and fossil samples is a promising approach to increasing our understanding of species evolution in ancient lakes. Most lake drilling efforts to date have focused on paleoclimate reconstruction. However, it is clear from the excellent fossil preservation and high temporal resolution typical of lake beds that significant advances in evolutionary biology can be made through drill core studies coordinated with phylogenetic work on appropriate taxa. Geological records can be used to constrain the age of specific lakes and the timing of evolutionarily significant events (such as lake level fluctuations and salinity crises). Fossil data can be used to test speciation and biogeographic hypotheses and flesh out phylogenetic trees, using a better-resolved fossil record to estimate timing of phylogenetic divergences. The extraordinary preservation of many fossils in anoxic lake beds holds the hope of collecting fossil DNA from the same body fossils that improve our understanding of morphological character evolution and adaptation. Moreover, fossils allow calibration of molecular clocks, which are currently largely inferential. Lake Malawi Drilling Project results provide some guideposts on what might be expected in a drilling project for studies of evolution. The extreme variability in lake level and environmental history that most ancient lakes experience (exemplified by the Lake Malawi record) demonstrates that no one drilling locality is likely to provide a complete record of phylogenetic history for a radiating lineage. Evolutionary biologists should take an active role in the design of drilling projects, which typically have interdisciplinary objectives, to ensure their sampling needs will be met by whatever sites in a lake are ultimately drilled.     

Species,speciation and human evolution

Human evolution is considered from the perspective of the recognition concept of species, which views species as an epiphenomenon of shared fertilisation systems in sexually reproducing organisms. It is argued that this concept predicts the controversial pattern of punctuated equilibrium, and offers an understanding of the hominid fossil evidence in line with that pattern. Changes in the nature of the fertilization system in the human lineage over time are discussed in relation to the pattern of morphological continuity between proposed species.     

Correlates and catalysts of hominin evolution in Africa

Hominin evolution in the African Pliocene and Pleistocene was accompanied and mediated by changes in the abiotic and biotic spheres. It has been hypothesized that such environmental changes were catalysts of hominin morphological evolution and speciations. Whereas there is little doubt that ecological changes were relevant to shaping the trajectories of mammalian evolution, testing specific hypotheses with data from the fossil record has yielded ambiguous results regarding environmental disruption as a primary catalyst. Proposed mechanisms for abiotic and biotic causes of evolution are not always consistent with the timing and trends exhibited by the African fossil record of hominins and other mammals. Analyses of fossil and genetic data suggest that much of hominin evolution, and by extension mammalian evolution, was autocatalytic, driven by feedback loops within a species or lineage, irrespective of changes in the external environment.     

The Fossil Record of the Solanaceae Revisited and Revised—The Fossil Record of Rhamnaceae Enhanced

Solanaceae is a large cosmopolitan family of angiosperms that includes some 92–100 genera and 2300–2500 species. It has been the object of a great deal of attention because of its economic importance as a food source (tomatoes, potatoes, peppers), because it includes tobacco, and is source of drugs (alkaloids). However its fossil history has been elusive with relatively few seemingly reliable reports throughout Tertiary times and no solid bases for molecular dating models to pinpoint important events in its diversification and evolution. While the great diversity found within the family makes it difficult to find morphological characters that define it, in general, the flowers have an overall distinctive morphology with some diagnostic morphological characters. Thus, as is often the case, flowers are potentially the most reliable indicators of the family in the fossil record. There have been a number of reports of flowers representing Solanaceae in the Tertiary. Yet, we report here that upon reinvestigation only one taxon remains as a plausible representative of the family while one of the most notable and frequently cited fossil Solanaceae from the Tertiary of North America is clearly a member of the family Rhamnaceae consistent with the fossil leaf record.     

Towards a morphological metric of assemblage dynamics in the fossil record: a test case using planktonic foraminifera

With a glance, even the novice naturalist can tell you something about the ecology of a given ecosystem. This is because the morphology of individuals reflects their evolutionary history and ecology, and imparts a distinct ‘look’ to communities—making it possible to immediately discern between deserts and forests, or coral reefs and abyssal plains. Once quantified, morphology can provide a common metric for characterizing communities across space and time and, if measured rapidly, serve as a powerful tool for quantifying biotic dynamics. Here, we present and test a new high-throughput approach for analysing community shape in the fossil record using semi-three-dimensional (3D) morphometrics from vertically stacked images (light microscopic or photogrammetric). We assess the potential informativeness of community morphology in a first analysis of the relationship between 3D morphology, ecology and phylogeny in 16 extant species of planktonic foraminifera—an abundant group in the marine fossil record—and in a preliminary comparison of four assemblages from the North Atlantic. In the species examined, phylogenetic relatedness was most closely correlated with ecology, with all three ecological traits examined (depth habitat, symbiont ecology and biogeography) showing significant phylogenetic signal. By contrast, morphological trees (based on 3D shape similarity) were relatively distantly related to both ecology and phylogeny. Although improvements are needed to realize the full utility of community morphometrics, our approach already provides robust volumetric measurements of assemblage size, a key ecological characteristic.     

The most ancient bark beetle known: a new tribe,genus and species from Lebanese amber (Coleoptera,Curculionidae, Scolytinae)

Abstract Cylindrobrotus pectinatus gen. et sp.n. , a new scolytine species from Cretaceous Lebanese amber, is described. A new tribe, Cylindrobrotini trib.n. , is proposed for this unique species, which demonstrates an unusual combination of some archaic and many advanced characters. This finding suggests that the Scolytinae became a distinct lineage of Curculionoidea from the Lower Cretaceous. Fossil records are reviewed, and some remarks on the origin and taxonomic position of bark and ambrosia beetles are made. Some comments on the various phylogenetic interpretations of the last 30 years are given, particularly in respect of their correspondence with the fossil record. The early appearance of Scolytinae in the fossil record before other Curculionidae (which appeared in the Upper Cretaceous) can be used as evidence against the hypothesis of bark beetles as offspring of weevils. The question of the taxonomic rank of bark beetles (separate subfamily or family) and their placement among other groups of the superfamily remains unsolved.     

A well-preserved aneuretopsychid from the Jehol Biota of China (Insecta, Mecoptera, Aneuretopsychidae)

The Aneuretopsychidae is an unspeciose and enigmatic family of long-proboscid insects that presently consist of one known genus and three species from the Late Jurassic to Early Cretaceous of north-central Asia. In this paper, a new genus and species of fossil aneuretopsychid is described and illustrated, Jeholopsyche liaoningensisgen. et sp. n. Fossils representing this new taxon were collected from mid Early Cretaceous strata of the well known Jehol Biota in Liaoning Province, China. This finding documents the first formal record of fossil Aneuretopsychidae in China. In addition, this well-preserved and new material reveals previously unknown and detailed morphological structure of the mouthparts, antennae, head, thorax, legs and abdomen of this distinctive insect lineage.