Botanical 319 barraclough t 2010 evolving entities


The cosmopolitan moss Bryum argenteum in Antarctica: Since the onset of glaciation following the Oligocene 30—28 Ma , the prevalence of increasingly Two hypotheses, postglacial recruitment from extra-regional locations and in situ persistence, have been proposed to explain the biogeography of the contemporary species-poor terrestrial Antarctic biota. Bryophytes, which form a major group of the Antarctic flora, exhibit a strong, inherent ability to survive cold conditions but also have high long-distance dispersal capacities, which are compatible with both hypotheses. Here, we test these hypotheses by means of population genetic and phylogeographic analyses of the cosmopolitan moss Bryum argenteum. We find evidence for at least three independent colonisation events of the species in Antarctica. Ancestral area reconstruction coupled with molecular dating suggests colonisation times of the different Antarctic clades ranging from four million years for the oldest lineage to half a million years for the youngest lineage.

Multiple global radiations in tadpole shrimps challenge the concept of ‘living fossils’

PDF Abstract Reliable estimates on the ages of the major bee clades are needed to further understand the evolutionary history of bees and their close association with flowering plants. Divergence times have been estimated for a few groups of bees, but no study has yet provided estimates for all major bee lineages.

To date the origin of bees and their major clades, we first perform a phylogenetic analysis of bees including representatives from every extant family, subfamily and almost all tribes, using sequence data from seven genes. We then use this phylogeny to place 14 time calibration points based on information from the fossil record for an uncorrelated relaxed clock divergence time analysis taking into account uncertainties in phylogenetic relationships and the fossil record.

GALAPAGOS BIOGEOGRAPHY Hooker’s biogeographic observations – that direct ana- lysis of geographic patterns will provide historical information. In this radical departure from bio-.

The number of shared fragments between individuals for each pairwise comparison was determined manually in Microsoft Excel. We calculated the number of constraining nucleotides based on the number of nucleotides involved in restriction and selective PCR: These nucleotides constrain the results in that homologous fragments can be lost by a mutation at any one of the nucleotides involved in restriction or selective PCR; the greater the number of constraining nucleotides, the less likely a shared absence will be homologous.

Although Bayesian methods for AFLP markers have been developed, they are not computationally practical at this time. This large burn-in value was consistent with the observation that very divergent sequences take longer to converge. AFLP molecular clock We inferred the age of three nodes in our phylogeny based on estimates in the literature calibrated to the absolute age of fossils of centrarchid fishes Near and Benard, ; Near and Keck, Divergence times for each species pair were then extrapolated using the equation of the linear regression of AFLP distance on node age.

AFLP and mitochondrial distance analysis Cytochrome b cyt b sequences were obtained for 66 species from Genbank http: Microsoft Excel was also used to determine the correlation and statistical significance for each comparison. Percina, Ammocrypta and Etheostoma are monophyletic: However, Bayesian analysis Figure 2 yielded a polytomy between Percina, E. Figure 1 Neighbor-joining tree depicting hypothesized relationships among darters Etheostomatinae , based on AFLP characters.

Perca and Sander used as outgroups. Full size image Figure 2 Bayesian Tree showing relationships among darters Etheostomatinae.

Emeritus Professor Michael Crisp

Licence This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. The reanalysis of biogeography of the Asian tree frog, Rhacophorus Anura: Abstract Rapid uplifts of the Tibetan Plateau and climate change in Asia are thought to have profoundly modulated the diversification of most of the species distributed throughout Asia.

The ranoid tree frog genus Rhacophorus, the largest genus in the Rhacophoridae, is widely distributed in Asia and especially speciose in the areas south and east of the Tibetan Plateau. Here, we infer phylogenetic relationships among species and estimate divergence times, asking whether the spatiotemporal characteristics of diversification within Rhacophorus were related to rapid uplifts of the Tibetan Plateau and concomitant climate change. Phylogenetic analysis recovered distinct lineage structures in Rhacophorus, which indicated a clear distribution pattern from Southeast Asia toward East Asia and India.

Figure 2: Molecular dating analysis. The MCC chronogram of an Agaricomycetidae subset, with main focus on Boletales taxa, obtained from divergence time estimation using BEAST. The MCC chronogram of an Agaricomycetidae subset, with main focus on Boletales taxa, obtained from divergence time estimation using BEAST.

The rock layers that contain them are most often found atop layers that have non-flowering plant fossils, like gymnosperms. The abrupt appearance of flowering plants has long stood as evidence against evolution. It produced evolutionary dates that ran far afoul of those assigned to flower fossil strata. Yale professor of evolutionary biology Michael Donoghue and his fellow researchers conducted the study published in the Proceedings of the National Academy of Sciences.

Clashes between various molecular clock dates for the same organism, and between molecular clock and evolutionary fossil dates, are widespread, casting doubt on the whole methodology. In addition, discoveries made since molecular clock analyses began undermine the chief attribute of using clocks: Mutations and other causes of DNA base changes occur in different places on chromosomes at different times for different reasons.

These tree diagrams display possible evolutionary paths of various forms and sometimes include estimates of when each form evolved. If the evolutionary paradigm is correct, the dates determined by various molecular clock studies ought to coincide, and should also validate evolutionary dates attached to the fossils. Soltis found agreement on several points among plants, but six glaring unknowns were presented, including uncertainty over where and when to place most flowering plants in evolutionary history.

References The origin of angiosperms is still a mystery. Fact sheet from the University of Berkeley.

Researchers Date the Origins of Photosynthesis to 1.25 Billion Years Ago

Room , Valley Life Sciences Building University of California, Berkeley Berkeley, California, USA Coevolution between phytophagous insect antagonists and Carboniferous, Permian, and Triassic seed plant hosts at the level of their respective developmental tool kits with focus on selective forces that drive the logic of transcriptional regulation is proposed in the following essay to explain the origin and evolution of flowering plants and certain Holometabola.

I discuss potential coevolution of insect and seed plant helix-turn-helix proteins, specifically Engraled and Leafy enzymes that bind to cis-regulatory promoters controlling downstream expression of genes determining paedomorphic insect body patterns and plant cone and floral organ development. The picture of the rock slab on the left is of an indeterminate pentamerous fossil rosid flower Celastrales, Rosanae collected by Professor David L.

The image was captured in while the author was visiting Indiana University. Biologists have been encouraged to think ” The three essays on the succeeding web pages are written from this research perspective.

They indicate that the biogeographic history of Nothofagus is more complex than envisaged under opposing polarised views expressed in the ongoing controversy over the relevance of dispersal and vicariance for explaining plant biodiversity.

Preview PDF Abstract Statistical historical biogeographical methods rely on the use of models that assume various biogeographic processes. Until recently model selection remains an explored topic and the impacts of using different models on inferring biogeographic history are poorly understood. Focusing on the Neotropical weevils in the Exophthalmus genus complex Insecta: We also investigate the biogeographic events that have shaped patterns of distributions, diversification, and endemism in this group of weevils.

We sample representatives of 65 species of the Exophthalmus genus complex and 26 outgroup terminals from the Neotropics including Caribbean islands and mainland. We reconstruct a molecular phylogeny based on six genes and performed molecular dating using a relaxed clock with three fossil calibration points. Model selection strongly favors biogeographic models that include founder-event jump dispersal.

Without modeling jump dispersal, estimations based on the three biogeographic models are dramatically different, especially at early diverging nodes. When jump dispersal is modeled, however, the three biogeographic models perform similarly.

New Zealand

The first documented cases occurred in primates over 45 years ago, but the amount of virus genetic diversity detected within bat populations, which have recently been identified as potential reservoir hosts, suggests that the filoviruses are much older. Here, detailed Bayesian coalescent phylogenetic analyses are performed on 97 whole-genome sequences, 55 of which are newly reported, to comprehensively examine molecular evolutionary rates and estimate dates of common ancestry for viruses within the family Filoviridae.

Molecular evolutionary rates for viruses belonging to different species range from 0. Most recent common ancestry can be traced back only within the last 50 years for Reston ebolavirus and Zaire ebolavirus species and suggests that viruses within these species may have undergone recent genetic bottlenecks. Viruses within Marburg marburgvirus and Sudan ebolavirus species can be traced back further and share most recent common ancestors approximately and years before the present, respectively.

Examination of the whole family suggests that members of the Filoviridae, including the recently described Lloviu virus, shared a most recent common ancestor approximately 10, years ago.

Patterns of animal dispersal, vicariance and diversification in the Holarctic rived from morphological or molecular clock estimates, distribution of species diversity among infraregions, suggest a more complicated history. Nevertheless, events than the latter, but dating of the clades was.

This study aimed to investigate the origin of Malesian Begonia, the directionality of dispersal events within the Malesian archipelago and the impact of ancient water gaps on colonization patterns, and to identify drivers of diversification. Location Asia, Southeast Asia, Malesia. Methods Plastid DNA sequence data of representatives of all families of the Cucurbitales and Fagales matK, rbcL, trnL intron, trnL-F spacer, aligned positions, 92 taxa and a sample of all major Asian Begonia sections ndhA intron, ndhF-rpl32 spacer, rpl trnL spacer, aligned positions, taxa were analysed under an uncorrelated-rates relaxed molecular clock model to estimate the age of the Begonia crown group divergence and divergence ages within Asian Begonia.

Ancestral areas were reconstructed using a likelihood approach implementing a dispersal-extinction-cladogenesis model, and with a Bayesian approach to dispersal-vicariance analysis. Results The results indicated an initial diversification of Asian Begonia in continental Asia in the Miocene, and subsequent colonization of Malesia by multiple lineages. There was support for at least six independent dispersal events from continental Asia and western Malesia to Wallacea dating from the late Miocene to the Pleistocene.

Lineages within this section diversified rapidly since the Pliocene, coinciding with rapid orogenesis on Sulawesi and New Guinea. Main conclusions The predominant trend of Begonia dispersals between continental Asia and Malesia, and also within Malesia, has been from west to east. The water bodies separating the Sunda Shelf region from Wallacea have been porous barriers to dispersal in Begonia following the emergence of substantial land in eastern Malesia from the late Miocene onwards.

We hypothesize two major drivers of the diversification of Malesian Begonia:

Bayesian inference in phylogeny

This is an open access article distributed under the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Methods for estimating divergence times from molecular data have improved dramatically over the past decade, yet there are few studies examining alternative taxon sampling effects on node age estimates. Here, I investigate the effect of undersampling species diversity on node ages of the South American lizard clade Liolaemini using several alternative subsampling strategies for both time calibrations and taxa numbers.

Penalized likelihood PL and Bayesian molecular dating analyses were conducted on a densely sampled taxa mtDNA-based phylogenetic hypothesis of Iguanidae, including 92 Liolaemini species. Using all calibrations and penalized likelihood, clades with very low taxon sampling had node age estimates younger than clades with more complete taxon sampling. The effect of Bayesian and PL methods differed when either one or two calibrations only were used with dense taxon sampling.

engine of diversification in New World doves Kevin P. Johnson1* and Jason D. Weckstein2 land connection in generating diversity, through repeated rare dispersal events followed by isolation. Bayesian relaxed clock analysis of the molecular data.

Licence This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Morphological stasis, however, can potentially lead to diversification rates being underestimated. Recent phylogenetic reconstructions have shown a strong biogeographic signal, suggesting diversification due to continental breakup, and widespread cryptic speciation.

However, morphological conservatism makes it difficult to place fossil taxa in a phylogenetic context. Here we reveal for the first time the timing and tempo of tadpole shrimp diversification by inferring a robust multilocus phylogeny of Branchiopoda and applying Bayesian divergence dating techniques using reliable fossil calibrations external to Notostraca. The order has two extant genera, Triops and Lepidurus, in the family Triopsidae, with a yet undefined number of species.

Phylogenetic reconstructions of extant Notostraca show a strong biogeographic signal Mathers et al. In Triops, species complexes are largely restricted to single continents, while Lepidurus lineages show high levels of endemism Rogers, , patterns that suggest ancient radiation with diversification through continental break-up.

However, the extreme morphological conservatism of this order hampers both the taxonomy of extant species and the phylogenetic placement of fossil taxa, with little known about the timing and tempo of notostracan diversification. To address this difficulty we infer a robust phylogeny of all known notostracan species from both extant genera and seven branchiopod outgroups.

Staff Publications

I have a PhD from the University of Adelaide for studies on long-term change on arid zone vegetation in South Australia. Subsequently, at the Australian National Botanic Gardens, I developed a expertise in phylogenetics and classification of Australian plants, particularly the pea-flowered legumes, revising with collaborators the large genera Daviesia, Gastrolobium, Gompholobium and Jacksonia. More recently, my broad knowledge of the Australian flora has led me to address questions such as: How is biodiversity distributed in space and what factors limit distribution?

How have species and their traits diversified through time and what are the drivers?

Based on this, dating analyses were performed using a secondary calibration, and relaxed molecular clock models. The historical biogeography of Ochnaceae s.l. was reconstructed using Dispersal-Vicariance Analysis and Bayesian Binary MCMC.

PDF Abstract Knowing the geographical origin of economically important plants is important for genetic improvement and conservation, but has been slowed by uneven geographical sampling where relatives occur in remote areas of difficult access. Less biased species sampling can be achieved when herbarium collections are included as DNA sources. Here, we address the history of Cucurbitaceae, one of the most economically important families of plants, using a multigene phylogeny for of the genera and 25 per cent of the species.

Worldwide sampling was achieved by using specimens from 30 herbaria. Results reveal an Asian origin of Cucurbitaceae in the Late Cretaceous, followed by the repeated spread of lineages into the African, American and Australian continents via transoceanic long-distance dispersal LDD. North American cucurbits stem from at least seven range expansions of Central and South American lineages; Madagascar was colonized 13 times, always from Africa; Australia was reached 12 times, apparently always from Southeast Asia.

These and similar findings from other angiosperms stress the need for an increased tapping of museum collections to achieve extensive geographical sampling in plant phylogenetics.

Mary Berbee

Clades are colored as a function of the number of extant species within each order. Clades with unusual diversification rates are denoted with numbers, which indicate the order of which rate shifts were added by the stepwise AIC procedure. Yellow triangles indicate exceptional rates as compared to background rates.

Molecular clock-based divergence times for sister clades occurring on both sides of the Atlantic often implies Oligocene and Miocene over-water dispersal [53 x Clades, clocks, and continents: historical and biogeographical analysis of Myrtaceae, Vochysiaceae, and relatives in the southern hemisphere.

SHARE Although studying creativity is considered a legitimate scientific discipline nowadays, it is still a very young one. In the early s, a psychologist named J. Guilford was one of the first academic researchers who dared to conduct a study of creativity. He challenged research subjects to connect all nine dots using just four straight lines without lifting their pencils from the page.

Today many people are familiar with this puzzle and its solution. In the s, however, very few were even aware of its existence, even though it had been around for almost a century. If you have tried solving this puzzle, you can confirm that your first attempts usually involve sketching lines inside the imaginary square. The correct solution, however, requires you to draw lines that extend beyond the area defined by the dots. Only 20 percent managed to break out of the illusory confinement and continue their lines in the white space surrounding the dots.

The symmetry, the beautiful simplicity of the solution, and the fact that 80 percent of the participants were effectively blinded by the boundaries of the square led Guilford and the readers of his books to leap to the sweeping conclusion that creativity requires you to go outside the box. The idea went viral via s-era media and word of mouth, of course. Overnight, it seemed that creativity gurus everywhere were teaching managers how to think outside the box. Management consultants in the s and s even used this puzzle when making sales pitches to prospective clients.

Because the solution is, in hindsight, deceptively simple, clients tended to admit they should have thought of it themselves.

The Planet Strappers by Raymond Z. Gallun

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