The fossil calibration database - A new resource for divergence dating

Fossils provide the principal basis for temporal calibrations, which are critical to the accuracy of divergence dating analyses. Translating fossil data into minimum and maximum bounds for calibrations is the most important, and often least appreciated, step of divergence dating. Properly justified calibrations require the synthesis of phylogenetic, paleontological, and geological evidence and can be difficult for non-specialists to formulate. The dynamic nature of the fossil record (e.g., new discoveries, taxonomic revisions, updates of global or local stratigraphy) requires that calibration data be updated continually lest they become obsolete. Here, we announce the Fossil Calibration Database (http://fossilcalibrations.org), a new open-access resource providing vetted fossil calibrations to the scientific community. Calibrations accessioned into this database are based on individual fossil specimens and follow best practices for phylogenetic justification and geochronological constraint. The associated Fossil Calibration Series, a calibration-themed publication series at Palaeontologia Electronica, will serve as one key pipeline for peer-reviewed calibrations to enter the database.

Synthesizing and databasing fossil calibrations: divergence dating and beyond

Divergence dating studies, which combine temporal data from the fossil record with branch length data from molecular phylogenetic trees, represent a rapidly expanding approach to understanding the history of life. National Evolutionary Synthesis Center hosted the first Fossil Calibrations Working Group (3–6 March, 2011, Durham, NC, USA), bringing together palaeontologists, molecular evolutionists and bioinformatics experts to present perspectives from disciplines that generate, model and use fossil calibration data. Presentations and discussions focused on channels for interdisciplinary collaboration, best practices for justifying, reporting and using fossil calibrations and roadblocks to synthesis of palaeontological and molecular data. Bioinformatics solutions were proposed, with the primary objective being a new database for vetted fossil calibrations with linkages to existing resources, targeted for a 2012 launch.

Four mammal fossil calibrations: Balancing competing palaeontological and molecular considerations

With the introduction of relaxed-clock molecular dating methods, the role of fossil calibration has expanded from providing a timescale, to also informing the models for molecular rate variation across the phylogeny. Here I suggest fossil calibration bounds for four mammal clades, Monotremata (platypus and echidnas), Macropodoidea (kangaroos and potoroos), Caviomorpha-Phiomorpha (South American and African hystricognath rodents), and Chiroptera (bats). In each case I consider sources of uncertainty in the fossil record and provide a molecular dating analysis to examine how the suggested calibration priors are further informed by other mammal fossil calibrations and molecular data.

Influence of historical landscapes, drainage evolution and ecological traits on patterns of genetic diversity in Southeast Asian freshwater snakehead fishes

Snakehead fishes in the family Channidae are obligate freshwater fishes represented by two extant genera, the African Parachannna and the Asian Channa. These species prefer still or slow flowing water bodies, where they are top predators that exercise high levels of parental care, have the ability to breathe air, can tolerate poor water quality, and interestingly, can aestivate or traverse terrestrial habitat in response to seasonal changes in freshwater habitat availability. These attributes suggest that snakehead fishes may possess high dispersal potential, irrespective of the terrestrial barriers that would otherwise constrain the distribution of most freshwater fishes. A number of biogeographical hypotheses have been developed to account for the modern distributions of snakehead fishes across two continents, including ancient vicariance during Gondwanan break-up, or recent colonisation tracking the formation of suitable climatic conditions. Taxonomic uncertainty also surrounds some members of the Channa genus, as geographical distributions for some taxa across southern and Southeast (SE) Asia are very large, and in one case is highly disjunct. The current study adopted a molecular genetics approach to gain an understanding of the evolution of this group of fishes, and in particular how the phylogeography of two Asian species may have been influenced by contemporary versus historical levels of dispersal and vicariance. First, a molecular phylogeny was constructed based on multiple DNA loci and calibrated with fossil evidence to provide a dated chronology of divergence events among extant species, and also within species with widespread geographical distributions. The data provide strong evidence that trans-continental distribution of the Channidae arose as a result of dispersal out of Asia and into Africa in the mid–Eocene. Among Asian Channa, deep divergence among lineages indicates that the Oligocene-Miocene boundary was a time of significant species radiation, potentially associated with historical changes in climate and drainage geomorphology. Mid-Miocene divergence among lineages suggests that a taxonomic revision is warranted for two taxa. Deep intra-specific divergence (~8Mya) was also detected between C. striata lineages that occur sympatrically in the Mekong River Basin. The study then examined the phylogeography and population structure of two major taxa, Channa striata (the chevron snakehead) and the C. micropeltes (the giant snakehead), across SE Asia. Species specific microsatellite loci were developed and used in addition to a mitochondrial DNA marker (Cyt b) to screen neutral genetic variation within and among wild populations. C. striata individuals were sampled across SE Asia (n=988), with the major focus being the Mekong Basin, which is the largest drainage basin in the region. The distributions of two divergent lineages were identified and admixture analysis showed that where they co-occur they are interbreeding, indicating that after long periods of evolution in isolation, divergence has not resulted in reproductive isolation. One lineage is predominantly confined to upland areas of northern Lao PDR to the north of the Khorat Plateau, while the other, which is more closely related to individuals from southern India, has a widespread distribution across mainland SE Asian and Sumatra. The phylogeographical pattern recovered is associated with past river networks, and high diversity and divergence among all populations sampled reveal that contemporary dispersal is very low for this taxon, even where populations occur in contiguous freshwater habitats. C. micropeltes (n=280) were also sampled from across the Mekong River Basin, focusing on the lower basin where it constitutes an important wild fishery resource. In comparison with C. striata, allelic diversity and genetic divergence among populations were extremely low, suggesting very recent colonisation of the greater Mekong region. Populations were significantly structured into at least three discrete populations in the lower Mekong. Results of this study have implications for establishing effective conservation plans for managing both species, that represent economically important wild fishery resources for the region. For C. micropeltes, it is likely that a single fisheries stock in the Tonle Sap Great Lake is being exploited by multiple fisheries operations, and future management initiatives for this species in this region will need to account for this. For C. striata, conservation of natural levels of genetic variation will require management initiatives designed to promote population persistence at very localised spatial scales, as the high level of population structuring uncovered for this species indicates that significant unique diversity is present at this fine spatial scale.

Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny

Despite recent methodological advances in inferring the time-scale of biological evolution from molecular data, the fundamental question of whether our substitution models are sufficiently well specified to accurately estimate branch-lengths has received little attention. I examine this implicit assumption of all molecular dating methods, on a vertebrate mitochondrial protein-coding dataset. Comparison with analyses in which the data are RY-coded (AG → R; CT → Y) suggests that even rates-across-sites maximum likelihood greatly under-compensates for multiple substitutions among the standard (ACGT) NT-coded data, which has been subject to greater phylogenetic signal erosion. Accordingly, the fossil record indicates that branch-lengths inferred from the NT-coded data translate into divergence time overestimates when calibrated from deeper in the tree. Intriguingly, RY-coding led to the opposite result. The underlying NT and RY substitution model misspecifications likely relate respectively to “hidden” rate heterogeneity and changes in substitution processes across the tree, for which I provide simulated examples. Given the magnitude of the inferred molecular dating errors, branch-length estimation biases may partly explain current conflicts with some palaeontological dating estimates.

Geomolecular dating and the origin of placental mammals

In modern evolutionary divergence analysis the role of geological information extends beyond providing a timescale, to informing molecular rate variation across the tree. Here I consider the implications of this development. I use fossil calibrations to test the accuracy of models of molecular rate evolution for placental mammals, and reveal substantial misspecification associated with life history rate correlates. Adding further calibrations to reduce dating errors at specific nodes unfortunately tends to transfer underlying rate errors to adjacent branches. Thus, tight calibration across the tree is vital to buffer against rate model errors. I argue that this must include allowing maximum bounds to be tight when good fossil records permit, otherwise divergences deep in the tree will tend to be inflated by the interaction of rate errors and asymmetric confidence in minimum and maximum bounds. In the case of placental mammals I sought to reduce the potential for transferring calibration and rate model errors across the tree by focusing on well-supported calibrations with appropriately conservative maximum bounds. The resulting divergence estimates are younger than others published recently, and provide the long-anticipated molecular signature for the placental mammal radiation observed in the fossil record near the 66 Ma Cretaceous–Paleogene extinction event.

Big, bad, and beautiful: phylogenetic relationships of the horned frogs (Anura: Ceratophryidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Evolution and historical biogeography of the Eastern Atlantic skates

In my thesis, I tested the hypothesis that the diversification of the Eastern Atlantic skate faunas arose through vicariance rather than dispersal, using combined approach of molecular phylogeny reconstruction and zoogeography (namely historical biogeography). This analyses have been carried out independently on four Rajidae genera belonging to two different tribes: Rajini (Raja and Dipturus) and Amblyrajini (Rajella and Leucoraja). These taxa were selected because they displayed high species diversity and richness of endemic species in the Eastern Atlantic and Mediterranean. The verification of this hypothesis was carried out by reconstructing the best phylogenetic relationships among four genera and 26 species (including several endemism) based on mtDNA and nuDNA gene variation and several statistical approaches. Divergence times of taxa have been estimated based on molecular clock and fossil calibration to explain evolutionary patterns in the context of geological framework. Main issues are (i) the evidence that Eastern Atlantic skate evolution and displacement of species diversity occurred from pulsed geographical speciation (i.e. repeated series of parallel and independent speciation events) started in the Late Eocene-Early Miocene and they have occurred prevalently during Miocene; (ii) such relatively ancient origin of diversification has been allowed the sympatric displacement and evolution of several congeneric taxa likely because they have accumulated huge differences in the genomic and physiological/behavioural phenotypic traits; (iii) recently diverged sister species and taxa showed allopatric or parapatric evolution by the presence of oceanographic or hydrogeographical barriers which likely prevent large mixing between parapatric sister species.

Molecular phylogeny and historical zoogeography of four genera of Eastern Atlantic skates (Rajiformes, Rajidae)

The aim of this study was to reconstruct a solid phylogeny of four genera of the Rajidae family (Chondrichthyans: Batoidea) using a concatenated alignment of mtDNA genes. Then use the resultant tree to estimate divergence time between taxa based on molecular clock and fossil calibration and conduct biogeographic analysis. The intent was to prove that the actual distribution of species of Eastern Atlantic and Mediterranean skates is due to a series of vicariant events. The species considered belongs to two different tribe: Rajini (Raja and Dipturus) and Amblyrajini (Leucoraja and Rajella). The choice of this genera is due to their high presence in the area of interest and to the richness of endemic species. The results show that despite the ancient origin of Rajidae (97 MYA), the Eastern Atlantic and Mediterranean faunas originated more recently, during Middle Miocene-Late Pliocene, after the closure of connection between these areas and the Indo-Pacific ocean (15 MYA). The endemic species of the Mediterranean (Raja asterias, R. radula, R. polystigma and Leucoraja melitensis) originated after the Messinian salinity crisis (7-5 MYA), when the recolonization of the basin occurred, and are still maintained in allopatric distribution by the presence of biogeographic barriers. Moreover from 4 to 2.6 MYA we can observe the formation of sister species for Raja, Leucoraja and Rajella, one of which has a Northern distribution, and the other has a Southern distribution (R. clavata vs R. straeleni, L. wallacei vs L. naevus, R. fyllae vs R. caudaspinosa and R. kukujevi vs R. leopardus + R. barnardi). The Quaternary and present oceanographic discontinuities that occur along the western African continental shelf (e.g., Cape Blanc and the Angola–Benguela Front) might contribute to the maintenance of low or null levels of gene flow between these closely related siblings species. Also sympatric speciation must be invoked to explain the evolution of skates, for example for the division between R. leopardus and R. barnardi. The speciation processes followed a south-to-north pathways for Dipturus and a north-to-south pathways for Raja, Leucoraja and Rajella underling that the evolution of the genera occurred independently. In the end, it is conceivable that the evolutionary pathways of the tribes followed the costal line during the gondwana fragmentation. The results demonstrate that the evolution of this family is characterized by a series of parallel and independent speciation events, strictly correlated to the tectonic movement of continental masses and paleogeographic and paleoclimatic events and so can be explained by a panbiogeographical (vicariance) model.

The evolution of scarab beetles tracks the sequential rise of angiosperms and mammals

Extant terrestrial biodiversity arguably is driven by the evolutionary success of angiosperm plants, but the evolutionary mechanisms and timescales of angiosperm-dependent radiations remain poorly understood. The Scarabaeoidea is a diverse lineage of predominantly plant- and dung-feeding beetles. Here, we present a phylogenetic analysis of Scarabaeoidea based on four DNA markers for a taxonomically comprehensive set of specimens and link it to recently described fossil evidence. The phylogeny strongly supports multiple origins of coprophagy, phytophagy and anthophagy. The ingroup-based fossil calibration of the tree widely confirmed a Jurassic origin of the Scarabaeoidea crown group. The crown groups of phytophagous lineages began to radiate first (Pleurostict scarabs: 108 Ma; Glaphyridae between 101 Ma), followed by the later diversification of coprophagous lineages (crown-group age Scarabaeinae: 76 Ma; Aphodiinae: 50 Ma). Pollen feeding arose even later, at maximally 62 Ma in the oldest anthophagous lineage. The clear time lag between the origins of herbivores and coprophages suggests an evolutionary path driven by the angiosperms that first favoured the herbivore fauna (mammals and insects) followed by the secondary radiation of the dung feeders. This finding makes it less likely that extant dung beetle lineages initially fed on dinosaur excrements, as often hypothesized.

Chemostratigraphy of the Tamengo Formation (Corumba Group, Brazil) A contribution to the calibration of the Ediacaran carbon-isotope curve

The Corumba Group cropping out in the southern Paraguay Belt in Brazil is one of the most complete Ediacaran sedimentary archives of palaeogeographic climatic biogeochemical and biotic evolution in southwestern Gondwana The unit hosts a rich fossil record including acritarchs vendotaenids (Vendo taenia Eoholynia) soft-bodied metazoans (Corumbella) and skeletal fossils (Cloudina Titanotheca) The Tamengo Formation made up mainly of limestones and marls provides a rich bio- and chemostratigraphic record Several outcrops formerly assigned to the Cuiaba Group are here included in the Tamengo Formation on the basis of lithological and chemostratigraphical criteria High-resolution carbon isotopic analyses are reported for the Tamengo Formation showing (from base to top) (1) a positive delta(13)C excursion to +4 parts per thousand PDB above post-glacial negative values (2) a negative excursion to -3 5 parts per thousand associated with a marked regression and subsequent transgression (3) a positive excursion to +5 5 parts per thousand and (4) a plateau characterized by delta(13)C around +3 parts per thousand A U-Pb SHRIMP zircon age of an ash bed Interbedded in the upper part of the delta(13)C positive plateau yielded 543 +/- 3 Ma which is considered as the depositional age (Babinski et al 2008a) The positive plateau in the upper Tamengo Formation and the preceding positive excursion are ubiquitous features in several successions worldwide including the Nama Group (Namibia) the Dengying Formation (South China) and the Nafun and Ara groups (Oman) This plateau is constrained between 542 and 551 Ma thus consistent with the age of the upper Tamengo Formation The negative excursion of the lower Tamengo Formation may be correlated to the Shuram-Wonoka negative anomaly although delta(13)C values do not fall beyond -3 5 parts per thousand in the Brazilian sections Sedimentary breccias occur just beneath this negative excursion in the lower Tamengo Formation One possible interpretation of the origin of these breccias is a glacioeustatic sea-level fall but a tectonic interpretation cannot be completely ruled out Published by Elsevier B V

Tracking rates of ecotone migration due to salt-water encroachment using fossil mollusks in coastal South Florida

We determined the rate of migration of coastal vegetation zones in response to salt-water encroachment through paleoecological analysis of mollusks in 36 sediment cores taken along transects perpendicular to the coast in a 5.5 km2 band of coastal wetlands in southeast Florida. Five vegetation zones, separated by distinct ecotones, included freshwater swamp forest, freshwater marsh, and dwarf, transitional and fringing mangrove forest. Vegetation composition, soil depth and organic matter content, porewater salinity and the contemporary mollusk community were determined at 226 sites to establish the salinity preferences of the mollusk fauna. Calibration models allowed accurate inference of salinity and vegetation type from fossil mollusk assemblages in chronologically calibrated sediments. Most sediments were shallow (20–130 cm) permitting coarse-scale temporal inferences for three zones: an upper peat layer (zone 1) representing the last 30–70 years, a mixed peat-marl layer (zone 2) representing the previous ca. 150–250 years and a basal section (zone 3) of ranging from 310 to 2990 YBP. Modern peat accretion rates averaged 3.1 mm yr)1 while subsurface marl accreted more slowly at 0.8 mm yr)1. Salinity and vegetation type for zone 1 show a steep gradient with freshwater communities being confined west of a north–south drainage canal constructed in 1960. Inferences for zone 2 (pre-drainage) suggest that freshwater marshes and associated forest units covered 90% of the area, with mangrove forests only present along the peripheral coastline. During the entire pre-drainage history, salinity in the entire area was maintained below a mean of 2 ppt and only small pockets of mangroves were present; currently, salinity averages 13.2 ppt and mangroves occupy 95% of the wetland. Over 3 km2 of freshwater wetland vegetation type have been lost from this basin due to salt-water encroachment, estimated from the mollusk-inferred migration rate of freshwater vegetation of 3.1 m yr)1 for the last 70 years (compared to 0.14 m yr)1 for the pre-drainage period). This rapid rate of encroachment is driven by sea-level rise and freshwater diversion. Plans for rehydrating these basins with freshwater will require high-magnitude re-diversion to counteract locally high rates of sea-level rise.

Fossil associations from the middle and upper Eocene strata of the Pamplona Basin and surrounding areas (Navarre, western Pyrenees)

Fossil associations from the middle and upper Eocene (Bartonian and Priabonian) sedimentary succession of the Pamplona Basin are described. This succession was accumulated in the western part of the South Pyrenean peripheral foreland basin and extends from deep-marine turbiditic (Ezkaba Sandstone Formation) to deltaic (Pamplona Marl, Ardanatz Sandstone and Ilundain Marl formations) and marginal marine deposits (Gendulain Formation). The micropalaeontological content is high. It is dominated by foraminifera, and common ostracods and other microfossils are also present. The fossil ichnoasssemblages include at least 23 ichnogenera and 28 ichnospecies indicative of Nereites, Cruziana, Glossifungites and ?Scoyenia-Mermia ichnofacies. Body macrofossils of 78 taxa corresponding to macroforaminifera, sponges, corals, bryozoans, brachiopods, annelids, molluscs, arthropods, echinoderms and vertebrates have been identified. Both the number of ichnotaxa and of species (e. g. bryozoans, molluscs and condrichthyans) may be considerably higher. Body fossil assemblages are comparable to those from the Eocene of the Nord Pyrenean area (Basque Coast), and also to those from the Eocene of the west-central and eastern part of South Pyrenean area (Aragon and Catalonia). At the European scale, the molluscs assemblages seem endemic from the Pyrenean area, although several Tethyan (Italy and Alps) and Northern elements (Paris basin and Normandy) have been recorded. Palaeontological data of studied sedimentary units fit well with the shallowing process that throughout the middle and late Eocene occurs in the area, according to the sedimentological and stratigraphical data.