scholarly journals Genome Skimming Reveals Widespread Hybridization in a Neotropical Flowering Plant Radiation

2021 ◽  
Vol 9 ◽  
Author(s):  
Oriane Loiseau ◽  
Talita Mota Machado ◽  
Margot Paris ◽  
Darina Koubínová ◽  
Kyle G. Dexter ◽  
...  
Keyword(s):  
Plant Diversity ◽  
Genomic Research ◽  
Flowering Plant ◽  
Tropical Plant ◽  
Tropical Diversity ◽  
Order Of Magnitude ◽  
Adaptive Radiations ◽  
Rapid Diversification ◽  
Genome Skimming ◽  
The Tropics

The tropics hold at least an order of magnitude greater plant diversity than the temperate zone, yet the reasons for this difference are still subject to debate. Much of tropical plant diversity is in highly speciose genera and understanding the drivers of such high species richness will help solve the tropical diversity enigma. Hybridization has recently been shown to underlie many adaptive radiations, but its role in the evolution of speciose tropical plant genera has received little attention. Here, we address this topic in the hyperdiverse Bromeliaceae genus Vriesea using genome skimming data covering the three genomic compartments. We find evidence for hybridization in ca. 11% of the species in our dataset, both within the genus and between Vriesea and other genera, which is commensurate with hybridization underlying the hyperdiversity of Vriesea, and potentially other genera in Tillandsioideae. While additional genomic research will be needed to further clarify the contribution of hybridization to the rapid diversification of Vriesea, our study provides an important first data point suggesting its importance to the evolution of tropical plant diversity.

Systematics and biogeography of the “Metacryphaeus group” Calmoniidae (Trilobita, Devonian), with comments on adaptive radiations and the geological history of the Malvinokaffric Realm

1993 ◽  
Vol 67 (4) ◽  
pp. 549-570 ◽  
Author(s):  
Bruce S. Lieberman
Keyword(s):  
New Species ◽  
South African ◽  
Evolutionary History ◽  
Geological History ◽  
Parsimony Analysis ◽  
Evolutionary Patterns ◽  
The Family ◽  
History Of ◽  
Adaptive Radiations ◽  
Rapid Diversification

Phylogenetic parsimony analysis was used to classify the Siegenian–Eifelian “Metacryphaeus group” of the family Calmoniidae. Thirty-eight exoskeletal characters for 16 taxa produced a shortest-length cladogram with a consistency index of 0.49. A classification based on retrieving the structure of this cladogram recognizes nine genera: Typhloniscus Salter, Plesioconvexa n. gen., Punillaspis Baldis and Longobucco, Eldredgeia n. gen., Clarkeaspis n. gen., Malvinocooperella n. gen., Wolfartaspis Cooper, Plesiomalvinella Lieberman, Edgecombe, and Eldredge (used to represent the malvinellid clade), and Metacryphaeus Reed. The malvinellid clade is most closely related to a revised monophyletic Metacryphaeus. Typhloniscus is the basal member of the “Metacryphaeus group,” and the monotypic Wolfartaspis is sister to the clade containing the malvinellids and Metacryphaeus. Six new species are diagnosed: Punillaspis n. sp. A, “Clarkeaspis” gouldi, Clarkeaspis padillaensis, Malvinocooperella pregiganteus, Metacryphaeus curvigena, and Metacryphaeus branisai. Primitively, this group has South African and Andean affinities, and its evolutionary history suggests rapid diversification. In addition, evolutionary patterns in this group, and the distribution of character reversals, call into question certain notions about the nature of adaptive radiations. The distributions of taxa may answer questions about the number of marine transgressive/regressive cycles in the Emsian–Eifelian of the Malvinokaffric Realm.

scholarly journals Polyploid Formation Shapes Flowering Plant Diversity

2014 ◽  
Vol 184 (4) ◽  
pp. 456-465 ◽  
Author(s):  
Samuel V. Scarpino ◽  
Donald A. Levin ◽  
Lauren Ancel Meyers
Keyword(s):  
Plant Diversity ◽  
Flowering Plant ◽  
Polyploid Formation

scholarly journals Past and future decline of tropical pelagic biodiversity

2020 ◽  
Vol 117 (23) ◽  
pp. 12891-12896 ◽  
Author(s):  
Moriaki Yasuhara ◽  
Chih-Lin Wei ◽  
Michal Kucera ◽  
Mark J. Costello ◽  
Derek P. Tittensor ◽  
...  
Keyword(s):  
Environmental Control ◽  
Research Question ◽  
Ocean Warming ◽  
Ice Age ◽  
Deep Time ◽  
Tropical Biodiversity ◽  
Diversity Gradient ◽  
Tropical Diversity ◽  
Distribution Shifts ◽  
The Tropics

A major research question concerning global pelagic biodiversity remains unanswered: when did the apparent tropical biodiversity depression (i.e., bimodality of latitudinal diversity gradient [LDG]) begin? The bimodal LDG may be a consequence of recent ocean warming or of deep-time evolutionary speciation and extinction processes. Using rich fossil datasets of planktonic foraminifers, we show here that a unimodal (or only weakly bimodal) diversity gradient, with a plateau in the tropics, occurred during the last ice age and has since then developed into a bimodal gradient through species distribution shifts driven by postglacial ocean warming. The bimodal LDG likely emerged before the Anthropocene and industrialization, and perhaps ∼15,000 y ago, indicating a strong environmental control of tropical diversity even before the start of anthropogenic warming. However, our model projections suggest that future anthropogenic warming further diminishes tropical pelagic diversity to a level not seen in millions of years.

Getting to the Roots of Flowering Plant Diversity

Science ◽  
1994 ◽  
Vol 264 (5165) ◽  
pp. 1549-1550 ◽  
Author(s):  
S. Nee ◽  
P. H. Harvey
Keyword(s):  
Plant Diversity ◽  
Flowering Plant

A more complete Rossby wave source

2020 ◽  
Author(s):  
Wolfgang Wicker ◽  
Richard Greatbatch
Keyword(s):  
Rossby Wave ◽  
Source Region ◽  
Absolute Vorticity ◽  
Wave Source ◽  
Upper Troposphere ◽  
Rossby Wave Source ◽  
Vorticity Advection ◽  
Order Of Magnitude ◽  
Wave Trains ◽  
The Tropics

<p>Tropical convection drives extratropical variability on subseasonal to interannual time-scales by exciting Rossby wave trains in the upper troposphere. Traditionally the relevant Rossby wave source is considered to be the sum of vortex stretching and vorticity advection by the divergent horizontal flow ( - ∇·<strong>u</strong><sub>χ</sub> (ζ+f) - <strong>u</strong><sub>χ</sub>·∇ (ζ+f)). Since absolute vorticity is very small at the equator, the equatorward flanks of the upper tropospheric jets have been regarded the source region of Rossby wave trains. In these considerations vertical momentum advection is neglected, although, it is an important source for westerly momentum at the equator. The curl of vertical momentum advection is the sum of vertical vorticity advection and vortex tilting ( -  ω ζ<sub>p</sub> - ω<sub>x</sub> v<sub>p</sub> + ω<sub>y</sub> u<sub>p</sub>). These contributions are smaller than the traditional Rossby wave source in midlatidues by about one order of magnitude but they are of similar size in the tropics.</p>

scholarly journals Assembly of tropical plant diversity on a local scale: Cyrtandra (Gesneriaceae) on Mount Kerinci, Sumatra

2004 ◽  
Vol 81 (1) ◽  
pp. 49-62 ◽  
Author(s):  
G. L. C. BRAMLEY ◽  
R. T. PENNINGTON ◽  
RADHIAH ZAKARIA ◽  
SRI SUDARMIYATI TJITROSOEDIRDJO ◽  
Q. C. B. CRONK
Keyword(s):  
Plant Diversity ◽  
Local Scale ◽  
Tropical Plant

scholarly journals The Value of Tropical Plant Diversity

EDIS ◽  
2019 ◽  
Vol 2019 (4) ◽  
pp. 5
Author(s):  
Cliff Martin ◽  
Zachary Brym
Keyword(s):  
Environmental Factors ◽  
Plant Diversity ◽  
Human Activities ◽  
Human Choice ◽  
Tropical Plant ◽  
Research And Education

This new 5-page document discusses plant diversity at the UF/IFAS Tropical Research and Education Center, environmental factors and human activities affecting these plants, assemblages of species based on levels of disturbance, human choice, and other factors, and the diverse needs these plants meet. Written by Cliff G. Martin and Zachary T. Brym, and published by the UF/IFAS Agronomy Department, June 2019. https://edis.ifas.ufl.edu/ag435

scholarly journals APPLES: Scalable Distance-based Phylogenetic Placement with or without Alignments

2018 ◽  
Author(s):  
Metin Balaban ◽  
Shahab Sarmashghi ◽  
Siavash Mirarab
Keyword(s):  
New Species ◽  
Maximum Likelihood ◽  
Metagenomic Data ◽  
Taxon Sampling ◽  
Phylogenetic Placement ◽  
Reference Set ◽  
Order Of Magnitude ◽  
Genome Skimming ◽  
A New Species ◽  
Memory Efficient

AbstractPlacing a new species on an existing phylogeny has increasing relevance to several applications. Placement can be used to update phylogenies in a scalable fashion and can help identify unknown query samples using (meta-)barcoding, skimming, or metagenomic data. Maximum likelihood (ML) methods of phylogenetic placement exist, but these methods are not scalable to reference trees with many thousands of leaves, limiting their ability to enjoy benefits of dense taxon sampling in modern reference libraries. They also rely on assembled sequences for the reference set and aligned sequences for the query. Thus, ML methods cannot analyze datasets where the reference consists of unassembled reads, a scenario relevant to emerging applications of genome-skimming for sample identification. We introduce APPLES, a distance-based method for phylogenetic placement. Compared to ML, APPLES is an order of magnitude faster and more memory efficient, and unlike ML, it is able to place on large backbone trees (tested for up to 200,000 leaves). We show that using dense references improves accuracy substantially so that APPLES on dense trees is more accurate than ML on sparser trees, where it can run. Finally, APPLES can accurately identify samples without assembled reference or aligned queries using kmer-based distances, a scenario that ML cannot handle. APPLES is available publically at github.com/balabanmetin/apples.

scholarly journals Genome skimming reveals novel plastid markers for the molecular identification of illegally logged African timber species

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0251655
Author(s):  
Maurizio Mascarello ◽  
Mario Amalfi ◽  
Pieter Asselman ◽  
Erik Smets ◽  
Olivier J. Hardy ◽  
...  
Keyword(s):  
Related Species ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Microscopic Analysis ◽  
Comparative Genomic ◽  
Timber Species ◽  
Illegal Logging ◽  
Closely Related Species ◽  
Genome Skimming ◽  
The Tropics

Tropical forests represent vast carbon stocks and continue to be key carbon sinks and buffer climate changes. The international policy constructed several mechanisms aiming at conservation and sustainable use of these forests. Illegal logging is an important threat of forests, especially in the tropics. Several laws and regulations have been set up to combat illegal timber trade. Despite significant enforcement efforts of these regulations, illegal logging continues to be a serious problem and impacts for the functioning of the forest ecosystem and global biodiversity in the tropics. Microscopic analysis of wood samples and the use of conventional plant DNA barcodes often do not allow to distinguish closely-related species. The use of novel molecular technologies could make an important contribution for the identification of tree species. In this study, we used high-throughput sequencing technologies and bioinformatics tools to obtain the complete de-novo chloroplast genome of 62 commercial African timber species using the genome skimming method. Then, we performed a comparative genomic analysis that revealed new candidate genetic regions for the discrimination of closely-related species. We concluded that genome skimming is a promising method for the development of plant genetic markers to combat illegal logging activities supporting CITES, FLEGT and the EU Timber Regulation.

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