Distribution of living Cupressaceae reflects the breakup of Pangea.
ABSTRACT: Most extant genus-level radiations in gymnosperms are of Oligocene age or younger, reflecting widespread extinction during climate cooling at the Oligocene/Miocene boundary [?23 million years ago (Ma)]. Recent biogeographic studies have revealed many instances of long-distance dispersal in gymnosperms as well as in angiosperms. Acting together, extinction and long-distance dispersal are likely to erase historical biogeographic signals. Notwithstanding this problem, we show that phylogenetic relationships in the gymnosperm family Cupressaceae (162 species, 32 genera) exhibit patterns expected from the Jurassic/Cretaceous breakup of Pangea. A phylogeny was generated for 122 representatives covering all genera, using up to 10,000 nucleotides of plastid, mitochondrial, and nuclear sequence per species. Relying on 16 fossil calibration points and three molecular dating methods, we show that Cupressaceae originated during the Triassic, when Pangea was intact. Vicariance between the two subfamilies, the Laurasian Cupressoideae and the Gondwanan Callitroideae, occurred around 153 Ma (124-183 Ma), when Gondwana and Laurasia were separating. Three further intercontinental disjunctions involving the Northern and Southern Hemisphere are coincidental with or immediately followed the breakup of Pangea.
Project description:Since around 200?Ma, the most notable event in the process of the breakup of Pangea has been the high speed (up to 20?cm yr(-1)) of the northward drift of the Indian subcontinent. Our numerical simulations of 3-D spherical mantle convection approximately reproduced the process of continental drift from the breakup of Pangea at 200?Ma to the present-day continental distribution. These simulations revealed that a major factor in the northward drift of the Indian subcontinent was the large-scale cold mantle downwelling that developed spontaneously in the North Tethys Ocean, attributed to the overall shape of Pangea. The strong lateral mantle flow caused by the high-temperature anomaly beneath Pangea, due to the thermal insulation effect, enhanced the acceleration of the Indian subcontinent during the early stage of the Pangea breakup. The large-scale hot upwelling plumes from the lower mantle, initially located under Africa, might have contributed to the formation of the large-scale cold mantle downwelling in the North Tethys Ocean.
Project description:Monitor lizards are emblematic reptiles that are widely distributed in the Old World. Although relatively well studied in vertebrate research, their biogeographic history is still controversial. We constructed a molecular dataset for 54 anguimorph species, including representatives of all families with detailed sampling of the Varanidae (38 species). Our results are consistent with an Asian origin of the Varanidae followed by a dispersal to Africa 41 (49-33) Ma, possibly via an Iranian route. Another major event was the dispersal of monitors to Australia in the Late Eocene-Oligocene 32 (39-26) Ma. This divergence estimate adds to the suggestion that Australia was colonized by several squamate lineages prior to the collision of the Australian plate with the Asian plate starting 25 Ma.
Project description:In addition to their devastating effects on global biodiversity, mass extinctions have had a long-term influence on the history of life by eliminating dominant lineages that suppressed ecological change. Here, we test whether the end-Permian mass extinction (252.3 Ma) affected the distribution of tetrapod faunas within the southern hemisphere and apply quantitative methods to analyze four components of biogeographic structure: connectedness, clustering, range size, and endemism. For all four components, we detected increased provincialism between our Permian and Triassic datasets. In southern Pangea, a more homogeneous and broadly distributed fauna in the Late Permian (Wuchiapingian, ?257 Ma) was replaced by a provincial and biogeographically fragmented fauna by Middle Triassic times (Anisian, ?242 Ma). Importantly in the Triassic, lower latitude basins in Tanzania and Zambia included dinosaur predecessors and other archosaurs unknown elsewhere. The recognition of heterogeneous tetrapod communities in the Triassic implies that the end-Permian mass extinction afforded ecologically marginalized lineages the ecospace to diversify, and that biotic controls (i.e., evolutionary incumbency) were fundamentally reset. Archosaurs, which began diversifying in the Early Triassic, were likely beneficiaries of this ecological release and remained dominant for much of the later Mesozoic.
Project description:True seals (crown Phocidae) originated during the late Oligocene-early Miocene (approx. 27-20 Ma) in the North Atlantic/Mediterranean region, with later (middle Miocene, approx. 16-11 Ma) dispersal events to the South Atlantic and South Pacific. Contrasting with other pinnipeds, the fossil record of phocids from the North Pacific region is scarce and restricted to the Pleistocene. Here we present the oldest fossil record of crown phocids, monachines (monk seals), from the North Pacific region. The specimens were collected from the upper Monterey Formation in Southern California and are dated to 8.5-7.1 Ma, predating the previously oldest known record by at least 7 Ma. This record provides new insights into the early biogeographic history of phocids in the North Pacific and is consistent with a northward dispersal of monk seals (monachines), which has been recognized for other groups of marine mammals. Alternatively, this finding may correspond with a westward dispersal through the Central American Seaway of some ancestor of the Hawaiian monk seal. This record increases the taxonomic richness of the Monterey pinniped assemblage to five taxa, making it a fairly diverse fossil assemblage, but also constitutes the oldest record of sympatry among all three extant pinniped crown clades.
Project description:The accretion of the Indian subcontinent to Eurasia triggered a massive faunal and floral exchange, with Gondwanan taxa entering into Asia and vice versa. The traditional view on the Indian-Asian collision assumes contact of the continental plates during the Early Eocene. Many biogeographic studies rely on this assumption. However, the exact mode and timing of this geological event is still under debate. Here we address, based on an extensive phylogenetic analysis of rhacophorid tree frogs, if there was already a Paleogene biogeographic link between Southeast Asia and India; in which direction faunal exchange occurred between India and Eurasia within the Rhacophoridae; and if the timing of the faunal exchange correlates with one of the recently suggested geological models. Rhacophorid tree frogs showed an early dispersal from India to Asia between 46 and 57 Ma, as reconstructed from the fossil record. During the Middle Eocene, however, faunal exchange ceased, followed by increase of rhacophorid dispersal events between Asia and the Indian subcontinent during the Oligocene that continued until the Middle Miocene. This corroborates recent geological models that argue for a much later final collision between the continental plates. We predict that the Oligocene faunal exchange between the Indian subcontinent and Asia, as shown here for rhacophorid frogs, also applies for other nonvolant organisms with an Indian-Asian distribution, and suggest that previous studies that deal with this faunal interchange should be carefully reinvestigated.
Project description:Although continents were coalesced into the single landmass Pangea, Late Triassic terrestrial tetrapod assemblages are surprisingly provincial. In eastern North America, we show that assemblages dominated by traversodont cynodonts are restricted to a humid 6° equatorial swath that persisted for over 20 million years characterized by "semiprecessional" (approximately 10,000-y) climatic fluctuations reflected in stable carbon isotopes and sedimentary facies in lacustrine strata. More arid regions from 5-20 °N preserve procolophonid-dominated faunal assemblages associated with a much stronger expression of approximately 20,000-y climatic cycles. In the absence of geographic barriers, we hypothesize that these variations in the climatic expression of astronomical forcing produced latitudinal climatic zones that sorted terrestrial vertebrate taxa, perhaps by excretory physiology, into distinct biogeographic provinces tracking latitude, not geographic position, as the proto-North American plate translated northward. Although the early Mesozoic is usually assumed to be characterized by globally distributed land animal communities due to of a lack of geographic barriers, strong provinciality was actually the norm, and nearly global communities were present only after times of massive ecological disruptions.
Project description:Next generation sequencing technologies hold great potential for many biological questions. While mainly used for genomic sequencing, they are also very promising for gene expression profiling. Sequencing of cDNA does not only provide an estimate of the absolute expression level, it can also be used for the identification of allele specific gene expression.We developed PanGEA, a tool which enables a fast and user-friendly analysis of allele specific gene expression using the 454 technology. PanGEA allows mapping of 454-ESTs to genes or whole genomes, displaying gene expression profiles, identification of SNPs and the quantification of allele specific gene expression. The intuitive GUI of PanGEA facilitates a flexible and interactive analysis of the data. PanGEA additionally implements a modification of the Smith-Waterman algorithm which deals with incorrect estimates of homopolymer length as occuring in the 454 technologyTo our knowledge, PanGEA is the first tool which facilitates the identification of allele specific gene expression. PanGEA is distributed under the Mozilla Public License and available at: http://www.kofler.or.at/bioinformatics/PanGEA
Project description:High-throughput DNA sequencing can identify organisms and describe population structures in many environmental and clinical samples. Current technologies generate millions of reads in a single run, requiring extensive computational strategies to organize, analyze and interpret those sequences. A series of bioinformatics tools for high-throughput sequencing analysis, including pre-processing, clustering, database matching and classification, have been compiled into a pipeline called PANGEA. The PANGEA pipeline was written in Perl and can be run on Mac OSX, Windows or Linux. With PANGEA, sequences obtained directly from the sequencer can be processed quickly to provide the files needed for sequence identification by BLAST and for comparison of microbial communities. Two different sets of bacterial 16S rRNA sequences were used to show the efficiency of this workflow. The first set of 16S rRNA sequences is derived from various soils from Hawaii Volcanoes National Park. The second set is derived from stool samples collected from diabetes-resistant and diabetes-prone rats. The workflow described here allows the investigator to quickly assess libraries of sequences on personal computers with customized databases. PANGEA is provided for users as individual scripts for each step in the process or as a single script where all processes, except the chi(2) step, are joined into one program called the 'backbone'.
Project description:Madagascar's rain forests are characterized by extreme and uneven patterns of species richness and endemicity, the biogeographic and evolutionary origins of which are poorly understood.Here we use a time-calibrated phylogeny of a dominant group of trees in Madagascar's eastern rain forests, Canarium, and related Burseraceae (Canarieae), to test biogeographic hypotheses regarding the origin and radiation of the flora of this unique biome.Our findings strongly support the monophyly of Malagasy Canarium, suggesting that this clade represents a previously undocumented in situ radiation. Contrary to expectations of dispersal from Africa during the Oligocene, concurrent with the formation of Madagascar's rain forest biome, our analyses support a late Miocene origin for Malagasy Canarium, probably by long distance dispersal from Southeast Asia.Our study illustrates the importance of considering long distance dispersal as a viable explanation for clades with pantropical distributions diversifying subsequent to the Oligocene, and it highlights the formation of the Indo-Australian Archipelago and associated fast-moving equatorial surface currents, suggesting an under-appreciated evolutionary link among tropical centers of endemism.We postulate that the relatively recent establishment and radiation of Canarium in Madagascar may have been facilitated by the highly stochastic climates associated with these forest ecosystems.
Project description:Oceanic dispersal has emerged as an important factor contributing to biogeographic patterns in numerous taxa. Chameleons are a clear example of this, as they are primarily found in Africa and Madagascar, but the age of the family is post-Gondwanan break-up. A Malagasy origin for the family has been suggested, yet this hypothesis has not been tested using modern biogeographic methods with a dated phylogeny. To examine competing hypotheses of African and Malagasy origins, we generated a dated phylogeny using between six and 13 genetic markers, for up to 174 taxa representing greater than 90 per cent of all named species. Using three different ancestral-state reconstruction methods (Bayesian and likelihood approaches), we show that the family most probably originated in Africa, with two separate oceanic dispersals to Madagascar during the Palaeocene and the Oligocene, when prevailing oceanic currents would have favoured eastward dispersal. Diversification of genus-level clades took place in the Eocene, and species-level diversification occurred primarily in the Oligocene. Plio-Pleistocene speciation is rare, resulting in a phylogeny dominated by palaeo-endemic species. We suggest that contraction and fragmentation of the Pan-African forest coupled to an increase in open habitats (savannah, grassland, heathland), since the Oligocene played a key role in diversification of this group through vicariance.