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A molecular phylogeny of the stingless bee genus Melipona (Hymenoptera: Apidae)

RAMIREZ, Santiago R.; NIEH, James C.; QUENTAL, Tiago B.; ROUBIK, David W.; IMPERATRIZ-FONSECA, Vera L.; PIERCE, Naomi E.
Fonte: ACADEMIC PRESS INC ELSEVIER SCIENCE Publicador: ACADEMIC PRESS INC ELSEVIER SCIENCE
Tipo: Artigo de Revista Científica
ENG
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56.12%
Stingless bees (Meliponini) constitute a diverse group of highly eusocial insects that occur throughout tropical regions around the world. The meliponine genus Melipona is restricted to the New World tropics and has over 50 described species. Melipona, like Apis, possesses the remarkable ability to use representational communication to indicate the location of foraging patches. Although Melipona has been the subject of numerous behavioral, ecological, and genetic studies, the evolutionary history of this genus remains largely unexplored. Here, we implement a multigene phylogenetic approach based on nuclear, mitochondrial, and ribosomal loci, coupled with molecular clock methods, to elucidate the phylogenetic relationships and antiquity of subgenera and species of Melipona. Our phylogenetic analysis resolves the relationship among subgenera and tends to agree with morphology-based classification hypotheses. Our molecular clock analysis indicates that the genus Melipona shared a most recent common ancestor at least similar to 14-17 million years (My) ago. These results provide the groundwork for future comparative analyses aimed at understanding the evolution of complex communication mechanisms in eusocial Apidae. (C) 2010 Elsevier Inc. All rights reserved.; ORBS (Opportunities for Research in the Behavioral Sciences Program); ORBS (Opportunities for Research in the Behavioral Sciences Program); National Science Foundation (NSF)[DEB 0608409]; U.S. National Science Foundation (NSF); U.S. National Science Foundation (NSF); National Science Foundation (NSF)[NSF-IBN 0316697]; National Science Foundation (NSF)[NSF DEB 0447242]; U.S. National Science Foundation (NSF); U.S. National Science Foundation (NSF); National Science Foundation (NSF)[NSF-IBN 0545856]; Putnam Expedition Fund; Putnam Expedition Fund

The timing of Neotropical speciation dynamics: A reconstruction of Myiopagis flycatcher diversification using phylogenetic and paleogeographic data

RHEINDT, Frank E.; CHRISTIDIS, Les; CABANNE, Gustavo S.; MIYAKI, Cristina; NORMAN, Janette A.
Fonte: ACADEMIC PRESS INC ELSEVIER SCIENCE Publicador: ACADEMIC PRESS INC ELSEVIER SCIENCE
Tipo: Artigo de Revista Científica
ENG
Relevância na Pesquisa
46.3%
Neotropical forests have brought forth a large proportion of the world`s terrestrial biodiversity, but the underlying evolutionary mechanisms and their timing require further elucidation. Despite insights gained from phylogenetic studies, uncertainties about molecular clock rates have hindered efforts to determine the timing of diversification processes. Moreover, most molecular research has been detached from the extensive body of data on Neotropical geology and paleogeography. We here examine phylogenetic relationships and the timing of speciation events in a Neotropical flycatcher genus (Myiopagis) by using calibrations from modern geologic data in conjunction with a number of recently developed DNA sequence dating algorithms and by comparing these estimates with those based on a range of previously proposed molecular clock rates. We present a well-supported hypothesis of systematic relationships within the genus. Our age estimates of Myiopagis speciation events based on paleogeographic data are in close agreement with nodal ages derived from a ""traditional"" avian mitochondrial 2%/My clock, while contradicting other clock rates. Our comparative approach corroborates the consistency of the traditional avian mitochondrial clock rate of 2%/My for tyrant-flycatchers. Nevertheless...

Filogenia molecular de Liolaemus arambarensis Verrastro, Veronese, Bujes & Dias Fialho, 2003 (Iguana: Liolaemidae)

Pisetta, Nádia Franco
Fonte: Universidade Federal do Rio Grande do Sul Publicador: Universidade Federal do Rio Grande do Sul
Tipo: Trabalho de Conclusão de Curso Formato: application/pdf
POR
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56.03%
A análise filogenética é empregada para inferir a história evolutiva das espécies, sugerindo possíveis eventos que afetaram sua diversificação. Liolaemus arambarensis, descrito recentemente, é um lagarto pequeno endêmico das restingas da margem oeste da Laguna dos Patos, no estado do Rio Grande do Sul. Nesse estudo, foi utilizado um conjunto de dados de quatro locos genéticos independentes (dois genes mitocondriais (mtDNA) analisados em conjunto, e três locos autossômicos independentes) foi usado para inferir a relação filogenética entre essa e outras espécies proximamente relacionadas pertencentes ao subgrupo “wiegmannii”: L. lutzae, L. occipitalis, L. salinicola, L. scapularis, L. multimaculatus e L. wiegmannii. Uma árvore de gene foi estimada para cada marcador independente através das abordagens Bayesiana e de máxima verossimilhança, enquanto a árvore de espécies foi feita usando dados concatenados ou baseada em uma abordagem Bayesiana de coalescência, permitindo lidar explicitamente com as discrepâncias entre as árvores de gene. Para calibrar o relógio molecular foi utilizada uma taxa de substituição para o gene CytB descrita na literatura e definido um prior na raiz da árvore usando resultados da literatura tendo L. darwinii como grupo externo. As análises realizadas neste estudo suportam a relação irmã entre L. arambarensise L. lutzae...

Nuclear rDNA-based molecular clock of the evolution of triatominae (Hemiptera: Reduviidae), vectors of Chagas disease

Bargues,MD; Marcilla,A; Ramsey,JM; Dujardin,JP; Schofield,CJ; Mas-Coma,S
Fonte: Instituto Oswaldo Cruz, Ministério da Saúde Publicador: Instituto Oswaldo Cruz, Ministério da Saúde
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/08/2000 EN
Relevância na Pesquisa
66.18%
The evolutionary history and times of divergence of triatomine bug lineages are estimated from molecular clocks inferred from nucleotide sequences of the small subunit SSU (18S) and the second internal transcribed spacer (ITS-2) of the nuclear ribosomal DNA of these reduviids. The 18S rDNA molecular clock rate in Triatominae, and Prosorrhynchan Hemiptera in general, appears to be of 1.8% per 100 million years (my). The ITS-2 molecular clock rate in Triatominae is estimated to be around 0.4-1% per 1 my, indicating that ITS-2 evolves 23-55 times faster than 18S rDNA. Inferred chronological data about the evolution of Triatominae fit well with current hypotheses on their evolutionary histories, but suggest reconsideration of the current taxonomy of North American species complexes.

Age at first reproduction explains rate variation in the strepsirrhine molecular clock

Tsantes, C.; Steiper, M. E.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46.26%
Although the molecular clock hypothesis posits that the rate of molecular change is constant over time, there is evidence that rates vary among lineages. Some of the strongest evidence for variable molecular rates comes from the primates; e.g., the “hominoid slowdown.” These rate differences are hypothesized to correlate with certain species attributes, such as generation time and body size. Here, we examine rates of molecular change in the strepsirrhine suborder of primates and test whether body size or age at first reproduction (a proxy for generation time) explains patterns of rate variation better than a null model where the molecular clock is independent of these factors. To examine these models, we analyzed DNA sequences from four pairs of recently diverged strepsirrhine sister taxa to estimate molecular rates by using sign tests, likelihood ratio tests, and regression analyses. Our analysis does not support a model where body weight or age at first reproduction strongly influences rates of molecular evolution across mitochondrial and nuclear sites. Instead, our analysis supports a model where age at first reproduction influences neutral evolution in the nuclear genome. This study supports the generation time hypothesis for rate variation in the nuclear molecular clock. Molecular clock variation due to generation time may help to resolve the discordance between molecular and paleontological estimates for divergence date estimates in primate evolution.

The cardiomyocyte molecular clock, regulation of Scn5a, and arrhythmia susceptibility

Schroder, Elizabeth A.; Lefta, Mellani; Zhang, Xiping; Bartos, Daniel; Feng, Han-Zhong; Zhao, Yihua; Patwardhan, Abhijit; Jin, Jian-Ping; Esser, Karyn A.; Delisle, Brian P.
Fonte: American Physiological Society Publicador: American Physiological Society
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46.28%
The molecular clock mechanism underlies circadian rhythms and is defined by a transcription-translation feedback loop. Bmal1 encodes a core molecular clock transcription factor. Germline Bmal1 knockout mice show a loss of circadian variation in heart rate and blood pressure, and they develop dilated cardiomyopathy. We tested the role of the molecular clock in adult cardiomyocytes by generating mice that allow for the inducible cardiomyocyte-specific deletion of Bmal1 (iCSΔBmal1). ECG telemetry showed that cardiomyocyte-specific deletion of Bmal1 (iCSΔBmal1−/−) in adult mice slowed heart rate, prolonged RR and QRS intervals, and increased episodes of arrhythmia. Moreover, isolated iCSΔBmal1−/− hearts were more susceptible to arrhythmia during electromechanical stimulation. Examination of candidate cardiac ion channel genes showed that Scn5a, which encodes the principle cardiac voltage-gated Na+ channel (NaV1.5), was circadianly expressed in control mouse and rat hearts but not in iCSΔBmal1−/− hearts. In vitro studies confirmed circadian expression of a human Scn5a promoter-luciferase reporter construct and determined that overexpression of clock factors transactivated the Scn5a promoter. Loss of Scn5a circadian expression in iCSΔBmal1−/− hearts was associated with decreased levels of NaV1.5 and Na+ current in ventricular myocytes. We conclude that disruption of the molecular clock in the adult heart slows heart rate...

Circadian Rhythms, the Molecular Clock, and Skeletal Muscle

Harfmann, Brianna D.; Schroder, Elizabeth A.; Esser, Karyn A.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46.29%
Circadian rhythms are the approximate 24-h biological cycles that function to prepare an organism for daily environmental changes. They are driven by the molecular clock, a transcriptional:translational feedback mechanism that in mammals involves the core clock genes Bmal1, Clock, Per1/2, and Cry1/2. The molecular clock is present in virtually all cells of an organism. The central clock in the suprachiasmatic nucleus (SCN) has been well studied, but the clocks in the peripheral tissues, such as heart and skeletal muscle, have just begun to be investigated. Skeletal muscle is one of the largest organs in the body, comprising approximately 45% of total body mass. More than 2300 genes in skeletal muscle are expressed in a circadian pattern, and these genes participate in a wide range of functions, including myogenesis, transcription, and metabolism. The circadian rhythms of skeletal muscle can be entrained both indirectly through light input to the SCN and directly through time of feeding and activity. It is critical for the skeletal muscle molecular clock not only to be entrained to the environment but also to be in synchrony with rhythms of other tissues. When circadian rhythms are disrupted, the observed effects on skeletal muscle include fiber-type shifts...

Circadian Rhythms, the Molecular Clock, and Skeletal Muscle

Lefta, Mellani; Wolff, Gretchen; Esser, Karyn A.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em //2011 EN
Relevância na Pesquisa
46.34%
Almost all organisms ranging from single cell bacteria to humans exhibit a variety of behavioral, physiological, and biochemical rhythms. In mammals, circadian rhythms control the timing of many physiological processes over a 24-h period, including sleep-wake cycles, body temperature, feeding, and hormone production. This body of research has led to defined characteristics of circadian rhythms based on period length, phase, and amplitude. Underlying circadian behaviors is a molecular clock mechanism found in most, if not all, cell types including skeletal muscle. The mammalian molecular clock is a complex of multiple oscillating networks that are regulated through transcriptional mechanisms, timed protein turnover, and input from small molecules. At this time, very little is known about circadian aspects of skeletal muscle function/metabolism but some progress has been made on understanding the molecular clock in skeletal muscle. The goal of this chapter is to provide the basic terminology and concepts of circadian rhythms with a more detailed review of the current state of knowledge of the molecular clock, with reference to what is known in skeletal muscle. Research has demonstrated that the molecular clock is active in skeletal muscles and that the muscle-specific transcription factor...

Casein Kinase 1 Proteomics Reveal Prohibitin 2 Function in Molecular Clock

Kategaya, Lorna S.; Hilliard, Aisha; Zhang, Louying; Ptáček, Louis J.; Fu, Ying-Hui; Asara, John M
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
EN_US
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56.18%
Throughout the day, clock proteins synchronize changes in animal physiology (e.g., wakefulness and appetite) with external cues (e.g., daylight and food). In vertebrates, both casein kinase 1 delta and epsilon (CK1(delta) and CK1(epsilon)) regulate these circadian changes by phosphorylating other core clock proteins. In addition, CK1 can regulate circadian-dependent transcription in a non-catalytic manner, however, the mechanism is unknown. Furthermore, the extent of functional redundancy between these closely related kinases is debated. To further advance knowledge about CK1(delta) and CK1(epsilon) mechanisms of action in the biological clock, we first carried out proteomic analysis of both kinases in human cells. Next, we tested interesting candidates in a cell-based circadian readout which resulted in the discovery of PROHIBITIN 2 (PHB2) as a modulator of period length. Decreasing the expression of PHB2 increases circadian-driven transcription, thus revealing PHB2 acts as an inhibitor in the molecular clock. While stable binding of PHB2 to either kinase was not detected, knocking down CK1(epsilon) expression increases PHB2 protein levels and, unexpectedly, knocking down CK1(delta) decreases PHB2 transcript levels. Thus, isolating CK1 protein complexes led to the identification of PHB2 as an inhibitor of circadian transcription. Furthermore...

Sociality and the rate of molecular evolution

Bromham, Lindell; Leijs, Remko
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Publicado em //2005 EN
Relevância na Pesquisa
56.06%
The molecular clock does not tick at a uniform rate in all taxa but may be influenced by species characteristics. Eusocial species (those with reproductive division of labor) have been predicted to have faster rates of molecular evolution than their nonsocial relatives because of greatly reduced effective population size; if most individuals in a population are nonreproductive and only one or few queens produce all the offspring, then eusocial animals could have much lower effective population sizes than their solitary relatives, which should increase the rate of substitution of "nearly neutral" mutations. An earlier study reported faster rates in eusocial honeybees and vespid wasps but failed to correct for phylogenetic nonindependence or to distinguish between potential causes of rate variation. Because sociality has evolved independently in many different lineages, it is possible to conduct a more wide-ranging study to test the generality of the relationship. We have conducted a comparative analysis of 25 phylogenetically independent pairs of social lineages and their nonsocial relatives, including bees, wasps, ants, termites, shrimps, and mole rats, using a range of available DNA sequences (mitochondrial and nuclear DNA coding for proteins and RNAs...

Time-dependent rates of molecular evolution

Ho, S.; Lanfear, R.; Bromham, L.; Phillips, M.; Soubrier, J.; Rodrigo, A.; Cooper, A.
Fonte: Blackwell Publishing Ltd Publicador: Blackwell Publishing Ltd
Tipo: Artigo de Revista Científica
Publicado em //2011 EN
Relevância na Pesquisa
56.03%
For over half a century, it has been known that the rate of morphological evolution appears to vary with the time frame of measurement. Rates of microevolutionary change, measured between successive generations, were found to be far higher than rates of macroevolutionary change inferred from the fossil record. More recently, it has been suggested that rates of molecular evolution are also time dependent, with the estimated rate depending on the timescale of measurement. This followed surprising observations that estimates of mutation rates, obtained in studies of pedigrees and laboratory mutation-accumulation lines, exceeded long-term substitution rates by an order of magnitude or more. Although a range of studies have provided evidence for such a pattern, the hypothesis remains relatively contentious. Furthermore, there is ongoing discussion about the factors that can cause molecular rate estimates to be dependent on time. Here we present an overview of our current understanding of time-dependent rates. We provide a summary of the evidence for time-dependent rates in animals, bacteria and viruses. We review the various biological and methodological factors that can cause rates to be time dependent, including the effects of natural selection...

Linking the embryonic clock with temporal collinearity of Hox gene activation

Fernandes, Catarina Sofia Rodrigues
Fonte: Faculdade de Ciências e Tecnologia Publicador: Faculdade de Ciências e Tecnologia
Tipo: Dissertação de Mestrado
Publicado em //2010 ENG
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56.14%
Dissertação apresentada para a obtenção do Grau de Mestre em Genética Molecular e Biomedicina, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia; Somitogenesis is a crucial process in vertebrate embryo development, whereby mesodermal-derived structures, called somites, are repeatedly formed along the anteriorposterior(AP) body axis. A molecular clock, first evidenced by cyclic expression of the hairy1 gene, sets the pace of somite formation. Although somites are morphologically identical, they are actually molecularly different. The identity of each embryonic segment is determined by combinatorial expression of hox genes. Previous studies showed that Hairy1 protein interacts with the mesodermal identity protein Brachyury, which is also required for hox gene activation. To assess if the embryonic clock is timing hox gene activation, hairy1 and brachyury were cloned into an expression vector containing a fluorescent reporter gene. The resulting plasmids were subsequently electroporated in chick embryos at stage 3HH-4HH and the embryos incubated for further development. Phenotype analysis of electroporated embryos suggests that over-expression of either hairy1 or Brachyury genes delays or even prevents somite formation...

What (molecular) time is it? : using ancient DNA to date evolutionary events.

Soubrier, Julien Benoit Adrien
Fonte: Universidade de Adelaide Publicador: Universidade de Adelaide
Tipo: Tese de Doutorado
Publicado em //2012
Relevância na Pesquisa
56.03%
This work aims to explore the use of genetic sequences sampled serially through time (heterochronous data), to infer the timescale of past evolutionary events. Such data can be generated from preserved sub-fossil or fossil organismal remains (like mummified tissues, fossilized bones or coprolites), and then used to observe genetic modifications in real-time. Most importantly, the dates of the samples provide firm temporal tie points for their genetic sequences, and can be used to calibrate phylogenetic reconstructions. This thesis presents several case studies where ancient DNA was used to re-calibrate evolutionary timescales. In every situation, the use of heterochronous data led to elevated molecular rate estimates, resulting in the reconstruction of younger timescales, as compared to estimates based on fossil calibrations. These observations are in agreement with the recent demonstration that molecular rates vary according to the time period over which they are calculated. This work shows that, ancient DNA offers crucial temporal information to reliably estimate the timescale of recent population evolution, and is generally the only source of direct calibration available for this specific timeframe. Along with the results specific to each organism studied (hyena...

There is no universal molecular clock for invertebrates, but rate variation does not scale with body size

Thomas, Jessica A.; Welch, John J.; Woolfit, Megan; Bromham, Lindell
Fonte: National Academy of Sciences (USA) Publicador: National Academy of Sciences (USA)
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
66.08%
The existence of a universal molecular clock has been called into question by observations that substitution rates vary widely between lineages. However, increasing empirical evidence for the systematic effects of different life history traits on the rate

The Modern Molecular Clock

Bromham, Lindell; Penny, David
Fonte: Nature Publishing Group Publicador: Nature Publishing Group
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
66.14%
The discovery of the molecular clock - a relatively constant rate of molecular evolution-provided an insight into the mechanisms of molecular evolution, and created one of the most useful new tools in biology. The unexpected constancy of rate was explaine

Metabolic rate does not calibrate the molecular clock

Lanfear, Robert; Thomas, Jessica; Welch, John J.; Brey, Thomas; Bromham, Lindell
Fonte: National Academy of Sciences (USA) Publicador: National Academy of Sciences (USA)
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
56.04%
Rates of molecular evolution vary widely among lineages, but the causes of this variation remain poorly understood. It has been suggested that mass-specific metabolic rate may be one of the key factors determining the rate of molecular evolution, and that

Sociality and the Rate of Molecular Evolution

Bromham, Lindell; Leys, Remko
Fonte: Society for Molecular Biology Evolution Publicador: Society for Molecular Biology Evolution
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
66.14%
The molecular clock does not tick at a uniform rate in all taxa but may be influenced by species characteristics. Eusocial species (those with reproductive division of labor) have been predicted to have faster rates of molecular evolution than their nonso

An explicit Poisson-Kolmogorov-Smirnov test for the molecular clock in phylogenies

Marcon, Fernando; Antoneli, Fernando; Briones, Marcelo R. S.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 21/05/2015
Relevância na Pesquisa
46.27%
Divergence dates estimates are central to understand evolutionary processes and depend, in the case of molecular phylogenies, on tests for the molecular clock. Testing for global and local clocks generally compare a clock-constrained tree versus a non-clock tree (e.g. the likelihood ratio test). These tests verify the evolutionary rate homogeneity among taxa and usually employ the chi-square test for rejection/acceptance of the "clock-like" phylogeny. The paradox is that the molecular clock hypothesis, as proposed, is a Poisson process, and therefore, non-homogeneous. Here we propose a method for testing the molecular clock in phylogenies that is built upon the assumption of Poisson stochastic process that accommodates rate heterogeneity and is based on ensembles of trees inferred by the Bayesian method. The observed distribution of branch lengths (number of substitutions) is obtained from the ensemble of post burn-in Bayesian search. The parameter $\lambda$ of the expected Poisson distribution is given by the average branch length of this ensemble. The goodness-of-fit test is performed using a modified Kolmogorov-Smirnov test for Poisson distributions. The method here introduced uses a large number of statistically equivalent phylogenies to obtain the observed distribution. This circumvents problems of small sample size (lack of power and lack of information)...

Molecular Clock on a Neutral Network

Raval, Alpan
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 28/05/2007
Relevância na Pesquisa
56.1%
The number of fixed mutations accumulated in an evolving population often displays a variance that is significantly larger than the mean (the overdispersed molecular clock). By examining a generic evolutionary process on a neutral network of high-fitness genotypes, we establish a formalism for computing all cumulants of the full probability distribution of accumulated mutations in terms of graph properties of the neutral network, and use the formalism to prove overdispersion of the molecular clock. We further show that significant overdispersion arises naturally in evolution when the neutral network is highly sparse, exhibits large global fluctuations in neutrality, and small local fluctuations in neutrality. The results are also relevant for elucidating the topological structure of a neutral network from empirical measurements of the substitution process.; Comment: 10 pages

A molecular clock for coccolithophores and implications for selectivity of phytoplankton extinctions across the K/T boundary

Medlin, L. K.; Sáez, Alberto G.; Young, Jeremy R.
Fonte: Elsevier Publicador: Elsevier
Tipo: Artículo Formato: 43048 bytes; application/pdf
ENG
Relevância na Pesquisa
66.1%
18 pages, 3 figures.-- Supplementary information (Suppl. Fig. 1: Phylogram of tufA tree, all outgroups collapsed to one triangle, Suppl. Fig. 2: Phylgoram of 18S rRNA tree) available within the article.; Available online Sep 10, 2007.-- Full-text article version available at: http://publicationslist.org/asaez; A molecular clock has been constructed for the haptophyte algae using the 18S rDNA gene and calibrated using the fossil record of the coccolithophorid algae, which have the best fossil record of any microalgal group. There is high consistency between the molecular genetic estimates of relative timing of divergence and palaeontological estimates of divergence times, so ages can be inferred for undated nodes in the tree with a reasonable degree of confidence. The placement of the K/T boundary across the tree strongly supports the palaeontological model that extant coccolithophorid algae diversified after this event and are the survivors of a few lineages that survived this major extinction. In contrast, the non-calcifying haptophytes are diverse before and after the extinction, with no evidence of bottlenecking associated with the event. This result is surprising, because it has been assumed that ability to produce resting stages was a key determinant of phytoplankton survival across the K/T boundary...