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Article: The Neotropical endemic liverwort subfamily Micropterygioideae had circum-Antarctic links to the rest of the Lepidoziaceae during the early Cretaceous.

Rayos, Antonio L / Renner, Matthew A M / Ho, Simon Y W

2024 Volume 14, Issue 3, Page(s) e11066

Abstract: Lepidoziaceae are the third-largest family of liverworts, with about 860 species distributed on all continents. The evolutionary history of this family has not been satisfactorily resolved, with taxa such as Micropterygioideae yet to be included in ... ...

Abstract	Lepidoziaceae are the third-largest family of liverworts, with about 860 species distributed on all continents. The evolutionary history of this family has not been satisfactorily resolved, with taxa such as Micropterygioideae yet to be included in phylogenetic analyses. We inferred a dated phylogeny of Lepidoziaceae using a data set consisting of 13 genetic markers, sampled from 147 species. Based on our phylogenetic estimate, we used statistical dispersal-vicariance analysis to reconstruct the biogeographic history of the family. We inferred a crown age of 197 Ma (95% credible interval 157-240 Ma) for the family in the Australian region, with most major lineages also originating in the same region. Micropterygioideae are placed as the sister group to Lembidioideae, with these two lineages diverging from each other about 132 Ma in the South American-Australian region. With South America and Australia being connected through Antarctica at the time, our results suggest a circum-Antarctic link between Micropterygioideae and the rest of the family. Crown Micropterygioideae were inferred to have arisen 45 Ma in South America before the continent separated from Antarctica. Extinction from southern temperate regions might explain the present-day restriction of Micropterygioideae to the Neotropics. Our study reveals the influence of past geological events, such as continental drift, on the evolution and distribution of a widespread and diverse family of liverworts.
Language	English
Publishing date	2024-03-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2635675-2
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.11066
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Evaluating the Accuracy of Methods for Detecting Correlated Rates of Molecular and Morphological Evolution.

Asar, Yasmin / Sauquet, Hervé / Ho, Simon Y W

Systematic biology

2023 Volume 72, Issue 6, Page(s) 1337–1356

Abstract: Determining the link between genomic and phenotypic change is a fundamental goal in evolutionary biology. Insights into this link can be gained by using a phylogenetic approach to test for correlations between rates of molecular and morphological ... ...

Abstract	Determining the link between genomic and phenotypic change is a fundamental goal in evolutionary biology. Insights into this link can be gained by using a phylogenetic approach to test for correlations between rates of molecular and morphological evolution. However, there has been persistent uncertainty about the relationship between these rates, partly because conflicting results have been obtained using various methods that have not been examined in detail. We carried out a simulation study to evaluate the performance of 5 statistical methods for detecting correlated rates of evolution. Our simulations explored the evolution of molecular sequences and morphological characters under a range of conditions. Of the methods tested, Bayesian relaxed-clock estimation of branch rates was able to detect correlated rates of evolution correctly in the largest number of cases. This was followed by correlations of root-to-tip distances, Bayesian model selection, independent sister-pairs contrasts, and likelihood-based model selection. As expected, the power to detect correlated rates increased with the amount of data, both in terms of tree size and number of morphological characters. Likewise, greater among-lineage rate variation in the data led to improved performance of all 5 methods, particularly for Bayesian relaxed-clock analysis when the rate model was mismatched. We then applied these methods to a data set from flowering plants and did not find evidence of a correlation in evolutionary rates between genomic data and morphological characters. The results of our study have practical implications for phylogenetic analyses of combined molecular and morphological data sets, and highlight the conditions under which the links between genomic and phenotypic rates of evolution can be evaluated quantitatively.
MeSH term(s)	Phylogeny ; Bayes Theorem ; Likelihood Functions ; Computer Simulation ; Genomics ; Evolution, Molecular
Language	English
Publishing date	2023-09-11
Publishing country	England
Document type	Journal Article
ZDB-ID	1482572-7
ISSN	1076-836X ; 1063-5157
ISSN (online)	1076-836X
ISSN	1063-5157
DOI	10.1093/sysbio/syad055
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Article ; Online: Dating in the Dark: Elevated Substitution Rates in Cave Cockroaches (Blattodea: Nocticolidae) Have Negative Impacts on Molecular Date Estimates.

Kovacs, Toby G L / Walker, James / Hellemans, Simon / Bourguignon, Thomas / Tatarnic, Nikolai J / McRae, Jane M / Ho, Simon Y W / Lo, Nathan

Systematic biology

2024

Abstract: Rates of nucleotide substitution vary substantially across the Tree of Life, with potentially confounding effects on phylogenetic and evolutionary analyses. A large acceleration in mitochondrial substitution rate occurs in the cockroach family ... ...

Abstract	Rates of nucleotide substitution vary substantially across the Tree of Life, with potentially confounding effects on phylogenetic and evolutionary analyses. A large acceleration in mitochondrial substitution rate occurs in the cockroach family Nocticolidae, which predominantly inhabit subterranean environments. To evaluate the impacts of this among-lineage rate heterogeneity on estimates of phylogenetic relationships and evolutionary timescales, we analysed nuclear ultraconserved elements (UCEs) and mitochondrial genomes from nocticolids and other cockroaches. Substitution rates were substantially elevated in nocticolid lineages compared with other cockroaches, especially in mitochondrial protein-coding genes. This disparity in evolutionary rates is likely to have led to different evolutionary relationships being supported by phylogenetic analyses of mitochondrial genomes and UCE loci. Furthermore, Bayesian dating analyses using relaxed-clock models inferred much deeper divergence times compared with a flexible local clock. Our phylogenetic analysis of UCEs, which is the first genome-scale study to include all thirteen major cockroach families, unites Corydiidae and Nocticolidae and places Anaplectidae as the sister lineage to the rest of Blattoidea. We uncover an extraordinary level of genetic divergence in Nocticolidae, including two highly distinct clades that separated ~115 million years ago despite both containing representatives of the genus Nocticola. The results of our study highlight the potential impacts of high among-lineage rate variation on estimates of phylogenetic relationships and evolutionary timescales.
Language	English
Publishing date	2024-02-06
Publishing country	England
Document type	Journal Article
ZDB-ID	1482572-7
ISSN	1076-836X ; 1063-5157
ISSN (online)	1076-836X
ISSN	1063-5157
DOI	10.1093/sysbio/syae002
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Article ; Online: Dating the emergence of human pathogens.

Ho, Simon Y W / Duchêne, Sebastián

Science (New York, N.Y.)

2020 Volume 368, Issue 6497, Page(s) 1310–1311

MeSH term(s)	Animals ; Communicable Diseases, Emerging ; Humans ; Measles virus ; Rinderpest virus ; Time Factors
Keywords	covid19
Language	English
Publishing date	2020-06-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abc5746
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Article ; Online: Early diversifications of angiosperms and their insect pollinators: were they unlinked?

Asar, Yasmin / Ho, Simon Y W / Sauquet, Hervé

Trends in plant science

2022 Volume 27, Issue 9, Page(s) 858–869

Abstract: The present-day ubiquity of angiosperm-insect pollination has led to the hypothesis that these two groups coevolved early in their evolutionary history. However, recent fossil discoveries and fossil-calibrated molecular dating analyses challenge the ... ...

Abstract	The present-day ubiquity of angiosperm-insect pollination has led to the hypothesis that these two groups coevolved early in their evolutionary history. However, recent fossil discoveries and fossil-calibrated molecular dating analyses challenge the notion that early diversifications of angiosperms and insects were inextricably linked. In this article, we examine (i) the discrepancies between dates of emergence for angiosperms and major clades of insects; (ii) the long history of gymnosperm-insect pollination modes, which likely shaped early angiosperm-insect pollination mutualisms; and (iii) how the K-Pg (Cretaceous-Paleogene) mass extinction event was vital in propelling modern angiosperm-insect mutualisms. We posit that the early diversifications of angiosperms and their insect pollinators were largely decoupled until the end of the Cretaceous.
MeSH term(s)	Animals ; Biological Evolution ; Fossils ; Insecta ; Magnoliopsida/genetics ; Phylogeny ; Pollination
Language	English
Publishing date	2022-05-11
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	1305448-x
ISSN	1878-4372 ; 1360-1385
ISSN (online)	1878-4372
ISSN	1360-1385
DOI	10.1016/j.tplants.2022.04.004
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Article: Early diversifications of angiosperms and their insect pollinators: Were they unlinked?

Asar, Yasmin / Ho, Simon Y.W. / Sauquet, Hervé

Trends in plant science. 2022,

2022

Abstract	The present-day ubiquity of angiosperm-insect pollination has led to the hypothesis that these two groups coevolved early in their evolutionary history. However, recent fossil discoveries and fossil-calibrated molecular dating analyses challenge the notion that early diversifications of angiosperms and insects were inextricably linked. In this article we examine (i) the discrepancies between dates of emergence for angiosperms and major clades of insects; (ii) the long history of gymnosperm–insect pollination modes, which likely shaped early angiosperm–insect pollination mutualisms; and (iii) how the K–Pg mass extinction event was vital in propelling modern angiosperm-insect mutualisms. We posit that the early diversifications of angiosperms and their insect pollinators were largely decoupled until the end of the Cretaceous.
Keywords	Cretaceous period ; extinction ; fossils ; pollination
Language	English
Publishing place	Elsevier Ltd
Document type	Article
Note	Pre-press version
ZDB-ID	1305448-x
ISSN	1878-4372 ; 1360-1385
ISSN (online)	1878-4372
ISSN	1360-1385
DOI	10.1016/j.tplants.2022.04.004
Database	NAL-Catalogue (AGRICOLA)

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Article: Dating the emergence of human pathogens

Ho, Simon Y W / Duchêne, Sebastián

Science

Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #659376
Database	COVID19

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Article ; Online: ClockstaRX: Testing Molecular Clock Hypotheses With Genomic Data.

Duchêne, David A / Duchêne, Sebastián / Stiller, Josefin / Heller, Rasmus / Ho, Simon Y W

Genome biology and evolution

2023 Volume 16, Issue 4

Abstract: Phylogenomic data provide valuable opportunities for studying evolutionary rates and timescales. These analyses require theoretical and statistical tools based on molecular clocks. We present ClockstaRX, a flexible platform for exploring and testing ... ...

Abstract	Phylogenomic data provide valuable opportunities for studying evolutionary rates and timescales. These analyses require theoretical and statistical tools based on molecular clocks. We present ClockstaRX, a flexible platform for exploring and testing evolutionary rate signals in phylogenomic data. Here, information about evolutionary rates in branches across gene trees is placed in Euclidean space, allowing data transformation, visualization, and hypothesis testing. ClockstaRX implements formal tests for identifying groups of loci and branches that make a large contribution to patterns of rate variation. This information can then be used to test for drivers of genomic evolutionary rates or to inform models for molecular dating. Drawing on the results of a simulation study, we recommend forms of data exploration and filtering that might be useful prior to molecular-clock analyses.
MeSH term(s)	Evolution, Molecular ; Models, Genetic ; Genomics ; Genome ; Biological Evolution ; Phylogeny
Language	English
Publishing date	2023-05-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evae064
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Article ; Online: Novel typing scheme reveals emergence and genetic diversity of Chlamydia pecorum at the local management scale across two koala populations.

Fernandez, Cristina M / Krockenberger, Mark B / Ho, Simon Y W / Crowther, Mathew S / Mella, Valentina S A / Jelocnik, Martina / Wilmott, Lachlan / Higgins, Damien P

Veterinary microbiology

2024 Volume 293, Page(s) 110085

Abstract: To overcome shortcomings in discriminating Chlamydia pecorum strains infecting the koala (Phascolarctos cinereus) at the local level, we developed a novel genotyping scheme for this pathogen to inform koala management at a fine-scale subpopulation level. ...

Abstract	To overcome shortcomings in discriminating Chlamydia pecorum strains infecting the koala (Phascolarctos cinereus) at the local level, we developed a novel genotyping scheme for this pathogen to inform koala management at a fine-scale subpopulation level. We applied this scheme to two geographically distinct koala populations in New South Wales, Australia: the Liverpool Plains and the Southern Highlands to South-west Sydney (SHSWS). Our method provides greater resolution than traditional multi-locus sequence typing, and can be used to monitor strain emergence, movement, and divergence across a range of fragmented habitats. Within the Liverpool Plains population, suspected recent introduction of a novel strain was confirmed by an absence of genetic diversity at the earliest sampling events and limited diversity at recent sampling events. Across the partially fragmented agricultural landscape of the Liverpool Plains, diversity within a widespread sequence type suggests that this degree of fragmentation may hinder but not prevent spread. In the SHSWS population, our results suggest movement of a strain from the south, where diverse strains exist, into a previously Chlamydia-free area in the north, indicating the risk of expansion towards an adjacent Chlamydia-negative koala population in South-west Sydney. In the south of the SHSWS where koala subpopulations appear segregated, we found evidence of divergent strain evolution. Our tool can be used to infer the risks of strain introduction across fragmented habitats in population management, particularly through practices such as wildlife corridor constructions and translocations.
Language	English
Publishing date	2024-04-04
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	753154-0
ISSN	1873-2542 ; 0378-1135
ISSN (online)	1873-2542
ISSN	0378-1135
DOI	10.1016/j.vetmic.2024.110085
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Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Impacts of Taxon-Sampling Schemes on Bayesian Tip Dating Under the Fossilized Birth-Death Process.

Luo, Arong / Zhang, Chi / Zhou, Qing-Song / Ho, Simon Y W / Zhu, Chao-Dong

Systematic biology

2023 Volume 72, Issue 4, Page(s) 781–801

Abstract: Evolutionary timescales can be inferred by molecular-clock analyses of genetic data and fossil evidence. Bayesian phylogenetic methods such as tip dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors ... ...

Abstract	Evolutionary timescales can be inferred by molecular-clock analyses of genetic data and fossil evidence. Bayesian phylogenetic methods such as tip dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume that present-day taxa have been sampled randomly or exhaustively. In practice, taxon sampling is often carried out so as to include representatives of major lineages, such as orders or families. We examined the impacts of different densities of diversified sampling on Bayesian tip dating on unresolved fossilized birth-death (FBD) trees, in which fossil taxa are topologically constrained but their exact placements are averaged out. We used synthetic data generated by simulations of nucleotide sequence evolution, fossil occurrences, and diversified taxon sampling. Our analyses under the diversified-sampling FBD process show that increasing taxon-sampling density does not necessarily improve divergence-time estimates. However, when informative priors were specified for the root age or when tree topologies were fixed to those used for simulation, the performance of tip dating on unresolved FBD trees maintains its accuracy and precision or improves with taxon-sampling density. By exploring three situations in which models are mismatched, we find that including all relevant fossils, without pruning off those that are incompatible with the diversified-sampling FBD process, can lead to underestimation of divergence times. Our reanalysis of a eutherian mammal data set confirms some of the findings from our simulation study, and reveals the complexity of diversified taxon sampling in phylogenomic data sets. In highlighting the interplay of taxon-sampling density and other factors, the results of our study have practical implications for using Bayesian tip dating to infer evolutionary timescales across the Tree of Life. [Bayesian tip dating; eutherian mammals; fossilized birth-death process; phylogenomics; taxon sampling.].
MeSH term(s)	Humans ; Animals ; Phylogeny ; Bayes Theorem ; Time ; Fossils ; Computer Simulation ; Mammals
Language	English
Publishing date	2023-03-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1482572-7
ISSN	1076-836X ; 1063-5157
ISSN (online)	1076-836X
ISSN	1063-5157
DOI	10.1093/sysbio/syad011
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