Morphological variation of species through time

Ten measurements, taken from each of 700 shells or four biologically distinct shallow marine gastropod species, were used to define the appropriate phenotypes in multidimensional space. Canonical discriminant analysis was performed on the data and a set of allocatory rules was derived. These allocatory rules, derived from extant specimens, were than applied to 644 fossil specimens of three of these biological species. Fossil individuals occupy the appropriate phenotypic space as defined by their modern descendants. The variation of fossil sample means about the modern means is illustrated. This variation is in the form of oscillations around the modern mean values and is correlated with climate. The distinction between taxonomic and biological species is discussed. The results of a number of previous studies are re-examined in the light of this discussion. It is argued that biological groupings can only be reliably determined when the appropriate data are available for extant organisms. Extant organisms, which have good fossil records, should therefore from the basis of paleontological evolutionary studies.     

Primate phylogeny: molecular evidence for a pongid clade excluding humans and a prosimian clade containing tarsiers

Unbiased readings of fossils are well known to contradict some of the popular molecular groupings among primates,particularly with regard to great apes and tarsiers.The molecular methodologies today are however flawed as they are based on a mistaken theoretical interpretation of the genetic equidistance phenomenon that originally started the field.An improved molecular method the ’slow clock’ was here developed based on the Maximum Genetic Diversity hypothesis,a more complete account of the unified changes in genotypes and phenotypes.The method makes use of only slow evolving sequences and requires no uncertain assumptions or mathematical corrections and hence is able to give definitive results.The findings indicate that humans are genetically more distant to orangutans than African apes are and separated from the pongid clade ～17.6 million years ago.Also,tarsiers are genetically closer to lorises than simian primates are.Finally,the fossil times for the radiation of mammals at the K/T boundary and for the Eutheria-Metatheria split in the Early Cretaceous were independently confirmed from molecular dating calibrated using the fossil split times of gorilla-orangutan,mouse-rat,and opossum-kangaroo.Therefore,the re-established primate phylogeny indicates a remarkable unity between molecules and fossils.     

Extinction and biogeography in the Caribbean: new evidence from a fossil riodinid butterfly in Dominican amber

We describe a new species of extinct riodinid butterfly, Voltinia dramba, from Oligo-Miocene Dominican amber (15-25 Myr ago). This appears to be the first butterfly to be taxonomically described from amber, and the first adult riodinid fossil. The series of five specimens represents probably the best-preserved fossil record for any lepidopteran. The phenomenon of extant Voltinia females ovipositing on arboreal epiphytes probably explains the discovery of multiple female V. dramba specimens in amber. Voltinia dramba appears to be one of many extinct butterfly species on Hispaniola. The northwestern Mexican distribution of the explicitly hypothesized sister species, the extant V. danforthi, supports the hypothesis that V. dramba reached Hispaniola by the 'proto-Greater Antillean arc', dating the divergence of V. dramba and V. danforthi to 40-50 Myr ago. This date is contemporaneous with the oldest known butterfly fossils, and implies a more ancient date of origin for many of the higher-level butterfly taxa than is often conceded.     

New specimens of the early Eocene stem group galliform Paraortygoides (Gallinuloididae), with comments on the evolution of a crop in the stem lineage of Galliformes

Two new specimens of the fossil stem group galliform Paraortygoides messelensis Mayr 2000 (Gallinuloididae) are described from the Middle Eocene of Messel in Germany, including a complete skeleton in which the hitherto unknown skull of this species is preserved. The shorter and more protruding crista deltopectoralis of the humerus, also for the first time visible in one of the new specimens, shows gallinuloidids to be the sister taxon of all other, extinct and extant, galliform birds. Gallinuloidids distinctly differ from modern Galliformes in several other plesiomorphic osteological features, mainly of the pectoral girdle, of which the absence of a spina interna on the sternum is here reported for the first time. It is assumed that major evolutionary transformations in the stem lineage of Galliformes are related to the evolution of a large crop, which appears to have been absent in gallinuloidids. The vegetarian food component of gallinuloidids thus probably mainly consisted of soft plant matter rather than coarse material such as seeds.     

Exploring the phylogeny of the marattialean ferns

The eusporangiate marattialean ferns represent an ancient radiation with a rich fossil record but limited modern diversity in the tropics. The long evolutionary history without close extant relatives has confounded studies of the phylogenetic origin, rooting and timing of marattialean ferns. Here we present new complete plastid genomes of six marattialean species and compiled a plastid genome dataset representing all of the currently accepted marattialean genera. We further supplemented this dataset by compiling a large dataset of mitochondrial genes and a phenotypic data matrix covering both extant and extinct representatives of the lineage. Our phylogenomic and total-evidence analyses corroborated the postulated position of marattialean ferns as the sister to leptosporangiate ferns, and the position of Danaea as the sister to the remaining extant marattialean genera. However, our results provide new evidence that Christensenia is sister to Marattia and that M. cicutifolia actually belongs to Eupodium. The apparently highly reduced rate of molecular evolution in marattialean ferns provides a challenge for dating the key phylogenetic events with molecular clock approaches. We instead applied a parsimony-based total-evidence dating approach, which suggested a Triassic age for the extant crown group. The modern distribution can best be explained as mainly resulting from vicariance following the breakup of Pangaea and Gondwana. We resolved the fossil genera Marattiopsis, Danaeopsis and Qasimia as members of the monophyletic family Marattiaceae, and the Carboniferous genera Sydneia and Radstockia as the monophyletic sister of all other marattialean ferns.     

Early origins of modern birds and mammals: molecules vs. morphology

Recent claims from molecular evidence that modern orders of birds and mammals arose in the Early Cretaceous, over 100 million years (Myr) ago, are contrary to palaeontological evidence. The oldest fossils generally fall in the time range from 70-50 Myr ago, with no earlier finds. If the molecular results are correct, then the first half of the fossil record of modern birds and mammals is missing. Suggestions that this early history was played out in unexplored parts of the world, or that the early progenitors were obscure forms, are unlikely. Intense collecting over hundreds of years has failed to identify these missing fossils. Control experiments, in the form of numerous Cretaceous-age fossil localities which yield excellently preserved lizards, salamanders, birds, and mammals, fail to show the modern forms. The most likely explanation is that they simply did not exist, and that the molecular clock runs fast during major radiations.     

The completeness of the fossil record of mesozoic birds: implications for early avian evolution

Many palaeobiological analyses have concluded that modern birds (Neornithes) radiated no earlier than the Maastrichtian, whereas molecular clock studies have argued for a much earlier origination. Here, we assess the quality of the fossil record of Mesozoic avian species, using a recently proposed character completeness metric which calculates the percentage of phylogenetic characters that can be scored for each taxon. Estimates of fossil record quality are plotted against geological time and compared to estimates of species level diversity, sea level, and depositional environment. Geographical controls on the avian fossil record are investigated by comparing the completeness scores of species in different continental regions and latitudinal bins. Avian fossil record quality varies greatly with peaks during the Tithonian-early Berriasian, Aptian, and Coniacian-Santonian, and troughs during the Albian-Turonian and the Maastrichtian. The completeness metric correlates more strongly with a 'sampling corrected' residual diversity curve of avian species than with the raw taxic diversity curve, suggesting that the abundance and diversity of birds might influence the probability of high quality specimens being preserved. There is no correlation between avian completeness and sea level, the number of fluviolacustrine localities or a recently constructed character completeness metric of sauropodomorph dinosaurs. Comparisons between the completeness of Mesozoic birds and sauropodomorphs suggest that small delicate vertebrate skeletons are more easily destroyed by taphonomic processes, but more easily preserved whole. Lagerst?tten deposits might therefore have a stronger impact on reconstructions of diversity of smaller organisms relative to more robust forms. The relatively poor quality of the avian fossil record in the Late Cretaceous combined with very patchy regional sampling means that it is possible neornithine lineages were present throughout this interval but have not yet been sampled or are difficult to identify because of the fragmentary nature of the specimens.     

New fossil species of ommatids (Coleoptera: Archostemata) from the Middle Mesozoic of China illuminating the phylogeny of Ommatidae

ABSTRACT: BACKGROUND: Ommatidae is arguably the "most ancestral" extant beetle family. Recent species of this group are only found in South America and Australia, but the fossil record reveals a much broader geographical distribution in the Mesozoic. Up to now, thirteen fossil genera with more than 100 species of ommatids have been described. However, the systematic relationships of the extant and extinct Ommatidae have remained obscure. RESULTS: In this study, four new species, Pareuryomma ancistrodonta sp. nov., Pareuryomma cardiobasis sp. nov., Omma delicata sp. nov., and Tetraphalerus decorosus sp. nov., are described. Based on well-preserved fossil specimens and previously published data the phylogenetic relationships of extant and extinct lineages of Ommatidae were analyzed for the first time cladistically. Based on the results we propose a new classification with six tribes of Ommatidae: Pronotocupedini, Notocupedini, Lithocupedini, Brochocoleini, Ommatini and Tetraphalerini. These taxa replace the traditional four subfamilies. CONCLUSION: There is good support for the monophyly of the ingroup. Notocupedini, as defined by Ponomarenko, are paraphyletic. Notocupoides + Eurydictyon are the sister group of the remaining fossil and extant ommatids. Together they form the clade Pronotocupedini. Notocupedini and Lithocupedini are the next two branches. The tribe Brochocoleini is the sister group of a clade comprising Tetraphalerini and Ommatini.     

Molecular dating in the genomic era

The comparison of DNA and protein sequences of extant species might be informative for reconstructing the chronology of evolutionary events on Earth. A phylogenetic tree inferred from molecular data directly depicts the evolutionary affinities of species and indirectly allows estimating the age of their origin and diversification. Molecular dating is achieved by assuming the molecular clock hypothesis, i.e., that the rate of change of nucleotide and amino acid sequences is on average constant over geological time. If paleontological calibrations are available, then absolute divergence times of species can be estimated. However, three major difficulties potentially hamper molecular dating : (1) a limited sample of genes and organisms, (2) a limited number of fossil references, and (3) pervasive variations of molecular evolutionary rates among genomes and species. To circumvent these problems, different solutions have been recently proposed. Larger data sets are built with more genes and more species sampled through the mining of an increasing number of genomes. Moreover, independent key fossils are identified to calibrate molecular clocks, and the uncertainty on their age is integrated in subsequent analyses. Finally, models of molecular rate variations are constructed, and incorporated in the so-called relaxed molecular clock approaches. As an illustration of these improvements, we mention that the debated age of the animal (bilaterian metazoans) diversification may have occurred between 642-761 million years ago (Mya), roughly 100 Ma before the Cambrian explosion. Among mammals, the initial diversification of major placental groups may have taken place around 100 Mya, well before the Cretaceous/Tertiary boundary marking the extinction of dinosaurs.     

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

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

Impact of increased character sampling on the phylogeny of Cetartiodactyla (Mammalia): combined analysis including fossils

The phylogenetic position of Cetacea (whales, dolphins and porpoises) is an important exemplar problem for combined data parsimony analyses because the clade is ancient and includes many well‐known and relatively complete fossil species. We combined data for 71 terminal taxa (43 extinct/28 extant) to test where Cetacea fits within Cetartiodactyla, and where various fossil hoofed mammals (e.g., ?entelodonts, “?anthracotheriids” and ?mesonychians) are positioned. We scored 635 phenotypic characters (osteology, dentition, soft tissue, behavior), approximately three times the number of characters in the last major analysis of this clade, and combined these with > 40 000 molecular characters, including new data from 10 genes. The analysis supported a topology consistent with the majority of recently published molecular studies. Cetacea was the extant sister taxon of Hippopotamidae, followed successively by Ruminantia, Suina and Camelidae. Several extinct taxa were phylogenetically unstable, upsetting resolution of the strict consensus and limiting branch support, but the positions of several key fossils were consistently resolved. The wholly extinct ?Mesonychia was more closely related to Cetacea than was any “artiodactylan.”“?Anthracotheriids” were paraphyletic, and, with the exception of one species, were more closely related to Hippopotamidae than to any other living taxon. The total evidence analysis overturned a highly nested position for Moschus supported by molecular data alone. The character partition that could be scored for the fossil taxa (osteological and dental characters) included more informative characters than most molecular partitions in our analysis, and had the fewest missing data. The osteological–dental data alone, however, did not support inclusion of cetaceans within crown “Artiodactyla.” Recently discovered ankle bones from fossil whales reinforced the monophyly of Cetartiodactyla but provided no particular evidence of derived similarities between hippopotamids and fossil cetaceans that were not shared with other “artiodactylans”. © The Willi Hennig Society 2007.     

Bone microstructure and developmental plasticity in birds and other dinosaurs

Patterns of bone microstructure have frequently been used to deduce dynamics and processes of growth in extant and fossil tetrapods. Often, the various types of primary bone tissue have been associated with different bone deposition rates and more recently such deductions have extended to patterns observed in dinosaur bone microstructure. These previous studies are challenged by the findings of the current research, which integrates an experimental neontological approach and a paleontological comparison. We use tetracycline labeling and morphometry to study the variability of bone deposition rates in Japanese quail (Coturnix japonica) growing under different experimental conditions. We compare resulting patterns in bone microstructure with those found in fossil birds and other dinosaurs. We found that a single type of primary bone varies significantly in rates of growth in response to environmental conditions. Ranging between 10-50 microm per day, rates of growth overlap with the full range of bone deposition rates that were previously associated with different patterns of bone histology. Bone formation rate was significantly affected by environmental/experimental conditions, skeletal element, and age. In the quail, the experimental conditions did not result in formation of lines of arrested growth (LAGs). Because of the observed variation of bone deposition rates in response to variation in environmental conditions, we conclude that bone deposition rates measured in extant birds cannot simply be extrapolated to their fossil relatives. Additionally, we observe the variable incidence of LAGs and annuli among several dinosaur species, including fossil birds, extant sauropsids, as well as nonmammalian synapsids, and some extant mammals. This suggests that the ancestral condition of the response of bone to environmental conditions was variable. We propose that such developmental plasticity in modern birds may be reduced in association with the shortened developmental time during the later evolution of the ornithurine birds.     

Geophilomorph centipedes from the Cretaceous amber of Burma

The only previously known Mesozoic fossils of the chilopod order Geophilomorpha are two species from the Late Jurassic and Late Cretaceous, both known from single specimens that cannot be assigned with precision to a family. Four specimens from the Late Cretaceous (earliest Cenomanian) amber of Burma include three that can be identified as conspecific, described here as Kachinophilus pereirai gen. nov. sp. nov. These specimens preserve greater morphological detail in comparison with other fossil geophilomorphs: the form and fine features of the head, the maxillary complex, the trunk sternites with associated glandular pores and the ultimate pair of legs defend the assignment of the species to the extant family Geophilidae, and most probably to a derived subgroup including well‐known extant genera such as Ribautia Brölemann, 1909. Confocal laser scanning microscopy supplements examination under incident and transmitted light to document details of high taxonomic relevance in the head and the forcipular segment. The modern appearance of this species and its membership among deeply nested extant clades are consistent with molecular estimates that most of the diversity of crown‐group Geophilomorpha originated before the Late Cretaceous.     

The fossil record and limb disparity of enantiornithines, the dominant flying birds of the Cretaceous

Morphometric and stratigraphic analyses that encompass the known fossil record of enantiornithine birds (Enantiornithes) are presented. These predominantly flighted taxa were the dominant birds of the second half of the Mesozoic; the enantiornithine lineage is known to have lasted for at least 60 million years (Ma), up until the end of the Cretaceous. Analyses of fossil record dynamics show that enantiornithine 'collectorship' since the 1980s approaches an exponential distribution, indicating that an asymptote in proportion of specimens has yet to be achieved. Data demonstrate that the fossil record of enantiornithines is complete enough for the extraction of biological patterns. Comparison of the available fossil specimens with a large data set of modern bird (Neornithes) limb proportions also illustrates that the known forelimb proportions of enantiornithines fall within the range of extant taxa; thus these birds likely encompassed the range of flight styles of extant birds. In contrast, most enantiornithines had hindlimb proportions that differ from any extant taxa. To explore this, ternary diagrams are used to graph enantiornithine limb variation and to identify some morphological oddities ( Otogornis , Gobipteryx ); taxa not directly comparable to modern birds. These exceptions are interesting – although anatomically uniform, and similar to extant avians in their wing proportions, some fossil enantiornithines likely had flight styles not seen among their living counterparts.     

Ancient DNA from an extinct Mediterranean micromammal—Hypnomys morpheus (Rodentia: Gliridae)—Provides insight into the biogeographic history of insular dormice

The dormice (Gliridae) are a family of rodents represented by relatively few extant species, though the family was much more species-rich during the Early Miocene. Intergeneric phylogenetic relationships among glirids in some cases remain unresolved, despite extensive molecular and morphological analyses. Uncertainty is greatest with respect to the relationships among fossil taxa and how extinct lineages are related to modern species. The fossil genus Hypnomys from the Balearic Islands (western Mediterranean Sea) includes the Late Pleistocene–Holocene species Hypnomys morpheus, which has variously been considered a close relative or subgenus of the extant Eliomys. In the present study, we sequenced ancient mitochondrial DNA from H. morpheus, which suggests a sister relationship with the extant members of Eliomys. In addition, the pairwise sequence variation between Hypnomys and Eliomys is higher than that observed between congeneric glirid species (e.g., many Graphiurus spp.), which allows us to reject the hypothesis that Hypnomys is a subgenus of Eliomys. Our molecular dating analyses suggest that Hypnomys and Eliomys diverged 13.67 million years ago (95% highest posterior density [HPD] = 7.39–20.07). The relatively early split between these genera together with the molar morphology of early representatives of Hypnomys points to a Middle-Late Miocene origin from a continental glirid with a complex molar pattern, such as Vasseuromys or a closely related genus.     

The Paleogene fossil record of birds in Europe

The Paleogene (Paleocene-Oligocene) fossil record of birds in Europe is reviewed and recent and fossil taxa are placed into a phylogenetic framework, based on published cladistic analyses. The pre-Oligocene European avifauna is characterized by the complete absence of passeriform birds, which today are the most diverse and abundant avian taxon. Representatives of small non-passeriform perching birds thus probably had similar ecological niches before the Oligocene to those filled by modern passerines. The occurrence of passerines towards the Lower Oligocene appears to have had a major impact on these birds, and the surviving crown-group members of many small arboreal Eocene taxa show highly specialized feeding strategies not found or rare in passeriform birds. It is detailed that no crown-group members of modern 'families' are known from pre-Oligocene deposits of Europe, or anywhere else. The phylogenetic position of Paleogene birds thus indicates that diversification of the crown-groups of modern avian 'families' did not take place before the Oligocene, irrespective of their relative position within Neornithes (crown-group birds). The Paleogene fossil record of birds does not even support crown-group diversification of Galliformes, one of the most basal taxa of neognathous birds, before the Oligocene, and recent molecular studies that dated diversification of galliform crown-group taxa into the Middle Cretaceous are shown to be based on an incorrect interpretation of the fossil taxa used for molecular clock calibrations. Several taxa that occur in the Paleogene of Europe have a very different distribution than their closest extant relatives. The modern survivors of these Paleogene lineages are not evenly distributed over the continents, and especially the great number of taxa that are today restricted to South and Central America is noteworthy. The occurrence of stem-lineage representatives of many taxa that today have a restricted Southern Hemisphere distribution conflicts with recent hypotheses on a Cretaceous vicariant origin of these taxa, which were deduced from the geographical distribution of the basal crown-group members.     

Morphological evidence for sister group relationship between flamingos (Aves: Phoenicopteridae) and grebes (Podicipedidae)

A recent molecular analysis strongly supported sister group relationship between flamingos (Phoenicopteridae) and grebes (Podicipedidae), a hypothesis which has not been suggested before. Flamingos are long-legged filter-feeders whereas grebes are morphologically quite divergent foot-propelled diving birds, and sister group relationship between these two taxa would thus provide an interesting example of evolution of different feeding strategies in birds. To test monophyly of a clade including grebes and flamingos, I performed a cladistic analysis of 70 morphological characters which were scored for 17 taxa. Parsimony analysis of these data supported monophyly of the taxon (Podicipedidae + Phoenicopteridae) and the clade received high bootstrap support. Previously overlooked morphological, oological and parasitological evidence is recorded which supports this hypothesis, and which makes the taxon (Podicipedidae + Phoenicopteridae) one of the best supported higher-level clades within modern birds. The phylogenetic significance of some fossil flamingo-like birds is discussed. The Middle Eocene taxon Juncitarsus is most likely the sister taxon of the clade (Podicipedidae + (Palaelodidae + Phoenicopteridae)) although resolution of its exact systematic position awaits revision of the fossil material. Contrary to previous assumptions, it is more parsimonious to assume that flamingos evolved from a highly aquatic ancestor than from a shorebird-like ancestor.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 140 , 157–169.     

New specimens of the Eocene Messelirrisoridae (Aves: Bucerotes), with comments on the preservation of uropygial gland waxes in fossil birds from Messel and the phylogenetic affinities of Bucerotes

Exceptionally well-preserved new specimens of the Messelirrisoridae (Aves: Bucerotes), which show previously unknown features of the osteology and feathering of these tiny birds, are described from the Middle Eocene of Messel in Germany. Most notably in one of the new specimens the wing and tail feathers are excellently preserved and even show the former color pattern of the tail. A cream-colored substance in some specimens most likely constitutes fossilized uropygial gland waxes. For the first time, the phylogenetic affinities of the Messelirrisoridae are evaluated in a cladistic analysis, based on 122 characters and 34 extant and fossil taxa. The results of this analysis support the earlier hypothesis that Messelirrisoridae are stem lineage Upupiformes, i.e. the sister taxon of the clade including extant hoopoes (Upupidae) and woodhoopoes (Phoeniculidae). The analysis further supports sister group relationship between Bucerotes (Upupiformes + Bucerotidae [hornbills]) and Piciformes (woodpeckers and allies), although it is detailed that one of the recently proposed apomorphies of the clade (Bucerotes + Piciformes) is absent in the Messelirrisoridae.     

A 15-Myr-old genetic bottleneck

Balancing selection preserves variation at the self-incompatibility locus (S-locus) of flowering plants for tens of millions of years, making it possible to detect demographic events that occurred prior to the origin of extant species. In contrast to other Solanaceae examined, SI species in the sister genera Physalis and Witheringia share restricted variation at the S-locus. This restriction is indicative of an ancient bottleneck that occurred in a common ancestor. We sequenced 14 S-alleles from the subtribe Iochrominae, a group that is sister to the clade containing Physalis and Witheringia. At least 6 ancient S-allele lineages are represented among these alleles, demonstrating that the Iochrominae taxa do not share the restriction in S-locus diversity. Therefore, the bottleneck occurred after the divergence of the Iochrominae from the lineage leading to the most recent common ancestor of Physalis and Witheringia. Using cpDNA sequences, 3 fossil dates, and a Bayesian-relaxed molecular clock approach, the crown group of Solanaceae was estimated to be 51 Myr old and the restriction of variation at the S-locus occurred 14.0-18.4 Myr before present. These results confirm the great age of polymorphism at the S-locus and the utility of loci under balancing selection for deep historical inference.