Phylogenomics supports a Cenozoic rediversification of the “living fossil” Isoetes

AbstractThe fossil record provides an invaluable insight into the temporal origins of extant lineages of organisms. However, establishing the relationships between fossils and extant lineages can be difficult in groups with low rates of morphological change over time. Molecular dating can potentially circumvent this issue by allowing distant fossils to act as calibration points, but rate variation across large evolutionary scales can bias such analyses. In this study, we apply multiple dating methods to genome-wide datasets to infer the origin of extant species of Isoetes, a group of mostly aquatic and semi-aquatic isoetalean lycopsids, which closely resemble fossil forms dating back to the Triassic. Rate variation observed in chloroplast genomes hampers accurate dating, but genome-wide nuclear markers place the origin of extant diversity within this group in the mid-Paleogene, 45-60 million years ago. Our genomic analyses coupled with a careful evaluation of the fossil record indicate that despite resembling forms from the Triassic, extant Isoetes species do not represent the remnants of an ancient and widespread group, but instead have spread around the globe in the relatively recent past.

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Highly Resolved Phylogenetic Relationships within Order Acipenseriformes According to Novel Nuclear Markers

Genes ◽

10.3390/genes10010038 ◽

2019 ◽

Vol 10 (1) ◽

pp. 38 ◽

Cited By ~ 4

Author(s):

Dehuai Luo ◽

Yanping Li ◽

Qingyuan Zhao ◽

Lianpeng Zhao ◽

Arne Ludwig ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Single Copy ◽

Species Trees ◽

Degenerate Primers ◽

Nuclear Markers ◽

Gene Markers ◽

Fossil Species ◽

Living Fossil ◽

Molecular Clock Model ◽

Extant Species

Order Acipenseriformes contains 27 extant species distributed across the northern hemisphere, including so-called “living fossil” species of garfish and sturgeons. Previous studies have focused on their mitochondrial genetics and have rarely used nuclear genetic data, leaving questions as to their phylogenetic relationships. This study aimed to utilize a bioinformatics approach to screen for candidate single-copy nuclear genes, using transcriptomic data from sturgeon species and genomic data from the spotted gar, Lepisosteus oculatus. We utilized nested polymerase chain reaction (PCR) and degenerate primers to identify nuclear protein-coding (NPC) gene markers to determine phylogenetic relationships among the Acipenseriformes. We identified 193 nuclear single-copy genes, selected from 1850 candidate genes with at least one exon larger than 700 bp. Forty-three of these genes were used for primer design and development of 30 NPC markers, which were sequenced for at least 14 Acipenseriformes species. Twenty-seven NPC markers were found completely in 16 species. Gene trees according to Bayesian inference (BI) and maximum likelihood (ML) were calculated based on the 30 NPC markers (20,946 bp total). Both gene and species trees produced very similar topologies. A molecular clock model estimated the divergence time between sturgeon and paddlefish at 204.1 Mya, approximately 10% later than previous estimates based on cytochrome b data (184.4 Mya). The successful development and application of NPC markers provides a new perspective and insight for the phylogenetic relationships of Acipenseriformes. Furthermore, the newly developed nuclear markers may be useful in further studies on the conservation, evolution, and genomic biology of this group.

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Evolution of seahorses' upright posture was linked to Oligocene expansion of seagrass habitats

Biology Letters ◽

10.1098/rsbl.2009.0152 ◽

2009 ◽

Vol 5 (4) ◽

pp. 521-523 ◽

Cited By ~ 32

Author(s):

Peter R. Teske ◽

Luciano B. Beheregaray

Keyword(s):

Fossil Record ◽

Sequence Data ◽

Morphological Evolution ◽

Molecular Techniques ◽

Molecular Dating ◽

Upright Posture ◽

Tectonic Events ◽

Extant Species ◽

The Family ◽

Transitional Forms

Seahorses (Syngnathidae: Hippocampus ) are iconic marine teleosts that are readily identifiable by their upright posture. The fossil record is inadequate to shed light on the evolution of this trait because it lacks transitional forms. There are, however, extant syngnathid species (the pygmy pipehorses) that look like horizontally swimming seahorses and that might represent a surviving evolutionary link between the benthic seahorses and other, free-swimming members of the family Syngnathidae. Using sequence data from five nuclear loci, we confirm the sister taxon relationship between seahorses and pygmy pipehorses. Molecular dating indicates that the two taxa diverged during the Late Oligocene. During this time, tectonic events in the Indo-West Pacific resulted in the formation of vast amounts of new shallow-water areas and associated expansion of seagrass habitats that would have favoured the seahorses’ upright posture by improving their camouflage while not affecting their manoeuvrability negatively. The molecular techniques employed here provide new insights into the evolution of a taxon whose fossil record is incomplete, but whose evolutionary history is so recent that the major stages of morphological evolution are still represented in extant species.

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Investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary

10.1101/2021.06.27.450013 ◽

2021 ◽

Author(s):

Andrew M Ritchie ◽

Xia Hua ◽

Lindell Bromham

Keyword(s):

Dna Sequences ◽

Empirical Studies ◽

Divergence Time ◽

Molecular Dating ◽

Rate Variation ◽

Substitution Rates ◽

Molecular Change ◽

Dna Evidence ◽

Dating Methods ◽

Speciation Rates

Background An accurate timescale of evolutionary history is essential to testing hypotheses about the influence of historical events and processes, and the timescale for evolution is increasingly derived from analysis of DNA sequences. But variation in the rate of molecular evolution complicates the inference of time from DNA. Evidence is growing for numerous factors, such as life history and habitat, that are linked both to the molecular processes of mutation and fixation and to rates of macroevolutionary diversification. However, the most widely used models of molecular rate variation, such as the uncorrelated and autocorrelated lognormal clocks, rely on idealised models of rate variation and molecular dating methods are rarely tested against complex models of rate change. One relationship that is not accounted for in molecular dating is the potential for interaction between molecular substitution rates and speciation, a relationship that has been supported by empirical studies in a growing number of taxa. If these relationships are as widespread as evidence indicates, they may have a significant influence on molecular dates. Results We simulate phylogenies and molecular sequences under three different realistic rate variation models - one in which speciation rates and substitution rates both vary but are unlinked, one in which they covary continuously and one punctuated model in which molecular change is concentrated in speciation events, using empirical case studies to parameterise realistic simulations. We test two commonly used "relaxed clock" molecular dating methods against these realistic simulations to explore the degree of error in molecular dates under each model. We find average divergence time inference errors ranging from 12% of node age for the unlinked model when reconstructed under an uncorrelated rate prior, to up to 93% when punctuated simulations are reconstructed under an autocorrelated prior. Conclusions We demonstrate the potential for substantial errors in molecular dates when both speciation rates and substitution rates vary between lineages. This study highlights the need for tests of molecular dating methods against realistic models of rate variation generated from empirical parameters and known relationships.

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Chloroplast phylogenomics and the dynamic evolution of Santalum (Santalaceae)

10.21203/rs.3.rs-154608/v1 ◽

2021 ◽

Author(s):

Xiaojin Liu ◽

Daping Xu ◽

Zhou Hong ◽

Ningnan Zhang ◽

Zhiyi Cui

Keyword(s):

Chloroplast Genome ◽

Evolutionary Dynamics ◽

Divergence Time ◽

Major Type ◽

Time Analysis ◽

Chloroplast Genomes ◽

Extant Species ◽

History Of ◽

Insight Into ◽

Simple Sequence

Abstract Background Santalum (Santalaceae, sandalwood) is a hemiparasitic genus including approximately 15 extant species. It is known for its aromatic heartwood oil, which is used in incense and perfume. Demand for sandalwood-based products has led to drastic over-harvesting, and wild Santalum populations are now threatened. Knowledge of the phylogenetic relationships and genetic diversity will be critical for the conservation and proper management of this genus. Here, we sequenced the chloroplast genome of 11 Santalum species. The data were then used to investigate the chloroplast genome evolutionary dynamics and relationships and divergence time within Santalum and related species. Results The Santalum chloroplast genome contains the typical quadripartite structures, ranging from 143,291 to 144,263 bp. The chloroplast genome contains 124 genes. The whole set of ndh genes and the infA gene were found to lose their function. Between 17 and 31 SSRs were found in the Santalum chloroplast genome, and mononucleotide simple sequence repeats (SSRs) were the major type. The P-distance among the Santalum species was 0.0003 to 0.00828. Three mutation hotspot regions, 14 small inversions, and 460 indels events were discovered in the Santalum chloroplast genome. Our phylogenomic assessment provides improved resolution compared to past analyses. Our divergence time analysis shows that the crown age of Santalum was 8.46 Mya, the first divergence occurred around 6.97 Mya, and diversification was complete within approximately 1 Mya. Conclusions By sequencing the 12 chloroplast genomes of Santalum, we gain insight into the evolution of its chloroplast genomes. The chloroplast genome sequences had sufficient polymorphic information to elucidate the evolutionary history of Santalum.

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Using more than the oldest fossils: Dating Osmundaceae by three Bayesian clock approaches

10.1101/010496 ◽

2014 ◽

Author(s):

Guido Grimm ◽

Pashalia Kapli ◽

Benjamin Bomfleur ◽

Stephen McLoughlin ◽

Susanne S Renner

Keyword(s):

Dna Sequences ◽

Fossil Record ◽

Morphological Characters ◽

Genetic Distances ◽

Total Evidence ◽

Extinction Rates ◽

Sister Clade ◽

Extant Species ◽

Dating Methods ◽

Divergence Dates

A major concern in molecular clock dating is how to use information from the fossil record to calibrate genetic distances from DNA sequences. Here we apply three Bayesian dating methods that differ in how calibration is achieved--"node dating" (ND) in BEAST, "total evidence" (TE) dating in MrBayes, and the "fossilized birth-death" (FBD) in FDPPDiv--to infer divergence times in the Osmundaceae or royal ferns. Osmundaceae have 13 species in four genera, two mainly in the Northern Hemisphere and two in South Africa and Australasia; they are the sister clade to the remaining leptosporangiate ferns. Their fossil record consists of at least 150 species in ~17 genera and three extinct families. For ND, we used the five oldest fossils, while for TE and FBD dating, which do not require forcing fossils to nodes and thus can use more fossils, we included up to 36 rhizome and frond compression/impression fossils, which for TE dating were scored for 33 morphological characters. We also subsampled 10%, 25%, and 50% of the 36 fossils to assess model sensitivity. FBD-derived divergence dates were generally greater than ages inferred from ND dating; two of seven TE-derived ages agreed with FBD-obtained ages, the others were much younger or much older than ND or FBD ages. We favour the FBD-derived ages because they best match the Osmundales fossil record (including Triassic fossils not used in our study). Under the preferred model, the clade encompassing extant Osmundaceae (and many fossils) dates to the latest Palaeozoic to Early Triassic; divergences of the extant species occurred during the Neogene. Under the assumption of constant speciation and extinction rates, FBD yielded 0.0299 (0.0099--0.0549) and 0.0240 (0.0039--0.0495) for these rates, whereas neontological data yielded 0.0314 and 0.0339. However, FBD estimates of speciation and extinction are sensitive to violations in the assumption of continuous fossil sampling, therefore these estimates should be treated with caution.

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Fossil wood of Syzygium from the Miocene of Guangxi, South China: the earliest fossil evidence of the genus in eastern Asia

IAWA Journal ◽

10.1163/22941932-bja10069 ◽

2021 ◽

pp. 1-7

Author(s):

Yifan Li ◽

Luliang Huang ◽

Cheng Quan ◽

Jianhua Jin ◽

Alexei A. Oskolski

Keyword(s):

New Species ◽

South China ◽

Fossil Record ◽

Fossil Wood ◽

Molecular Dating ◽

Eastern Asia ◽

Fossil Evidence ◽

Extant Species ◽

Asian Lineage ◽

A New Species

Abstract A new species, Syzygium guipingensis sp. nov. (Myrtaceae), is described based on mummified fossil wood from the Miocene Erzitang Formation of Guiping Basin, Guangxi, South China. This species represents the most ancient reliable fossil record of the genus Syzygium in eastern Asia, showing the greatest similarity to the extant species S. buxifolium Hook. et Arnott. Its occurrence in the Miocene is consistent with the diversification age of the Asian lineage within Syzygium as estimated by molecular dating (11.4 Ma). The fossil record of Syzygium suggests that this genus migrated from Australia to eastern Asia in the Miocene, coincidently with the formation of island chains between these continents.

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The soft explosive model of placental mammal evolution

10.1101/251520 ◽

2018 ◽

Author(s):

Matthew J Phillips ◽

Carmelo Fruciano

Keyword(s):

Life History ◽

Molecular Dating ◽

Rate Variation ◽

Recent Criticism ◽

Model Errors ◽

Statistical Confidence ◽

Dating Methods ◽

Bird Evolution ◽

Adaptive Radiations ◽

Mammal Faunas

AbstractRecent molecular dating estimates for placental mammals echo fossil inferences for an explosive interordinal diversification, but typically place this event some 10-20 million years earlier than the Paleocene fossils, among apparently more “primitive” mammal faunas. However, current models of molecular evolution do not adequately account for parallel rate changes, and result in dramatic divergence underestimates for large, long-lived mammals such as whales and hominids. Calibrating among these taxa shifts the rate model errors deeper in the tree, inflating interordinal divergence estimates. We employ simulations based on empirical rate variation, which show that this “error-shift inflation” can explain previous molecular dating overestimates relative to fossil inferences. Molecular dating accuracy is substantially improved in the simulations by focusing on calibrations for taxa that retain plesiomorphic life-history characteristics. Applying this strategy to the empirical data favours the soft explosive model of placental evolution, in line with traditional palaeontological interpretations – a few Cretaceous placental lineages give rise to a rapid interordinal diversification following the 66 Ma Cretaceous-Paleogene boundary mass extinction. Our soft explosive model for the diversification of placental mammals brings into agreement previously incongruous molecular, fossil, and ancestral life history estimates, and closely aligns with a growing consensus for a similar model for bird evolution. We show that recent criticism of the soft explosive model relies on ignoring both experimental controls and statistical confidence, as well as misrepresentation, and inconsistent interpretations of morphological phylogeny. More generally, we suggest that the evolutionary properties of adaptive radiations may leave current molecular dating methods susceptible to overestimating the timing of major diversification events.

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Genome-wide correlation analysis to identify amplitude regulators of circadian transcriptome output

Scientific Reports ◽

10.1038/s41598-020-78851-9 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Evan S. Littleton ◽

Madison L. Childress ◽

Michaela L. Gosting ◽

Ayana N. Jackson ◽

Shihoko Kojima

Keyword(s):

Clock Genes ◽

Circadian System ◽

Average Level ◽

Relative Amplitude ◽

Critical Component ◽

Period 2 ◽

Genome Wide ◽

Mouse Tissues ◽

Rhythmic Gene ◽

Insight Into

AbstractCell-autonomous circadian system, consisting of core clock genes, generates near 24-h rhythms and regulates the downstream rhythmic gene expression. While it has become clear that the percentage of rhythmic genes varies among mouse tissues, it remains unclear how this variation can be generated, particularly when the clock machinery is nearly identical in all tissues. In this study, we sought to characterize circadian transcriptome datasets that are publicly available and identify the critical component(s) involved in creating this variation. We found that the relative amplitude of 13 genes and the average level of 197 genes correlated with the percentage of cycling genes. Of those, the correlation of Rorc in both relative amplitude and the average level was one of the strongest. In addition, the level of Per2AS, a novel non-coding transcript that is expressed at the Period 2 locus, was also linearly correlated, although with a much lesser degree compared to Rorc. Overall, our study provides insight into how the variation in the percentage of clock-controlled genes can be generated in mouse tissues and suggests that Rorc and potentially Per2AS are involved in regulating the amplitude of circadian transcriptome output.

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Genome-wide identification of chitinase genes in Thalassiosira pseudonana and analysis of their expression under abiotic stresses

BMC Plant Biology ◽

10.1186/s12870-021-02849-2 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Haomiao Cheng ◽

Zhanru Shao ◽

Chang Lu ◽

Delin Duan

Keyword(s):

Abiotic Stresses ◽

Chitinase Activity ◽

Thalassiosira Pseudonana ◽

Centric Diatom ◽

Carbon And Nitrogen ◽

Genome Wide ◽

Duplication Events ◽

The Many ◽

Chitinase Genes ◽

Insight Into

Abstract Background The nitrogen-containing polysaccharide chitin is the second most abundant biopolymer on earth and is found in the cell walls of diatoms, where it serves as a scaffold for biosilica deposition. Diatom chitin is an important source of carbon and nitrogen in the marine environment, but surprisingly little is known about basic chitinase metabolism in diatoms. Results Here, we identify and fully characterize 24 chitinase genes from the model centric diatom Thalassiosira pseudonana. We demonstrate that their expression is broadly upregulated under abiotic stresses, despite the fact that chitinase activity itself remains unchanged, and we discuss several explanations for this result. We also examine the potential transcriptional complexity of the intron-rich T. pseudonana chitinase genes and provide evidence for two separate tandem duplication events during their evolution. Conclusions Given the many applications of chitin and chitin derivatives in suture production, wound healing, drug delivery, and other processes, new insight into diatom chitin metabolism has both theoretical and practical value.

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