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Article ; Online: Embracing uncertainty: The way forward in plant fossil phylogenetics.

Coiro, Mario

2024 Volume 111, Issue 2, Page(s) e16282

Abstract: Although molecular phylogenetics remains the most widely used method of inferring the evolutionary history of living groups, the last decade has seen a renewed interest in morphological phylogenetics, mostly driven by the promises that integrating the ... ...

Abstract	Although molecular phylogenetics remains the most widely used method of inferring the evolutionary history of living groups, the last decade has seen a renewed interest in morphological phylogenetics, mostly driven by the promises that integrating the fossil record in phylogenetic trees offers to our understanding of macroevolutionary processes and dynamics and the possibility that the inclusion of fossil taxa could lead to more accurate phylogenetic hypotheses. The plant fossil record presents some challenges to its integration in a phylogenetic framework. Phylogenies including plant fossils often retrieve uncertain relationships with low support, or lack of resolution. This low support is due to the pervasiveness of morphological convergence among plant organs and the fragmentary nature of many plant fossils, and it is often perceived as a fundamental weakness reducing the utility of plant fossils in phylogenetics. Here I discuss the importance of uncertainty in morphological phylogenetics and how we can identify important information from different patterns and types of uncertainty. I also review a set of methodologies that can allow us to understand the causes underpinning uncertainty and how these practices can help us to further our knowledge of plant fossils. I also propose that a new visual language, including the use of networks instead of trees, represents an improvement on the old visualization based on consensus trees and more adequately serves phylogeneticists working with plant fossils. This set of methods and visualization tools represents an important way forward in a fundamental field for our understanding of the evolutionary history of plants.
MeSH term(s)	Phylogeny ; Fossils ; Uncertainty ; Biological Evolution ; Plants/genetics
Language	English
Publishing date	2024-02-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2935-x
ISSN	1537-2197 ; 0002-9122
ISSN (online)	1537-2197
ISSN	0002-9122
DOI	10.1002/ajb2.16282
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Article ; Online: Disparity of cycad leaves dispels the living fossil metaphor.

Coiro, Mario / Seyfullah, Leyla Jean

Communications biology

2024 Volume 7, Issue 1, Page(s) 328

Abstract: The living fossil metaphor is tightly linked with the cycads. This group of gymnosperms is supposed to be characterised by long-term morphological stasis, particularly after their peak of diversity and disparity in the Jurassic. However, no formal test ... ...

Abstract	The living fossil metaphor is tightly linked with the cycads. This group of gymnosperms is supposed to be characterised by long-term morphological stasis, particularly after their peak of diversity and disparity in the Jurassic. However, no formal test of this hypothesis exists. Here, we use a recent phylogenetic framework and an improved character matrix to reconstruct the Disparity Through Time for cycad leaves using a Principal Coordinate Analysis and employing Pre-Ordination Ancestral State Reconstruction to test the impact of sampling on the results. Our analysis shows that the cycad leaf morsphospace expanded up to the present, with numerous shifts in its general positioning, independently of sampling biases. Moreover, they also show that Zamiaceae expanded rapidly in the Early Cretaceous and continued to expand up to the present, while now-extinct clades experienced a slow contraction from their peak in the Triassic. We also show that rates of evolution were constantly high up to the Early Cretaceous, and then experienced a slight decrease in the Paleogene, followed by a Neogene acceleration. These results show a much more dynamic history for cycads, and suggest that the 'living fossil' metaphor is actually a hindrance to our understanding of their macroevolution.
MeSH term(s)	Cycadopsida ; Phylogeny ; Plant Leaves
Language	English
Publishing date	2024-03-14
Publishing country	England
Document type	Journal Article
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-024-06024-9
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Article ; Online: Parallel evolution of angiosperm-like venation in Peltaspermales: a reinvestigation of Furcula.

Coiro, Mario / McLoughlin, Stephen / Steinthorsdottir, Margret / Vajda, Vivi / Fabrikant, Dolev / Seyfullah, Leyla J

The New phytologist

2024

Abstract: Leaf venation is a pivotal trait in the success of vascular plants. Whereas gymnosperms have single or sparsely branched parallel veins, angiosperms developed a hierarchical structure of veins that form a complex reticulum. Its physiological consequences ...

Abstract	Leaf venation is a pivotal trait in the success of vascular plants. Whereas gymnosperms have single or sparsely branched parallel veins, angiosperms developed a hierarchical structure of veins that form a complex reticulum. Its physiological consequences are considered to have enabled angiosperms to dominate terrestrial ecosystems in the Late Cretaceous and Cenozoic. Although a hierarchical-reticulate venation also occurs in some groups of extinct seed plants, it is unclear whether these are stem relatives of angiosperms or have evolved these traits in parallel. Here, we re-examine the morphology of the enigmatic foliage taxon Furcula, a potential early Mesozoic angiosperm relative, and argue that its hierarchical vein network represents convergent evolution (in the Late Triassic) with flowering plants (which developed in the Early Cretaceous) based on details of vein architecture and the absence of angiosperm-like stomata and guard cells. We suggest that its nearest relatives are Peltaspermales similar to Scytophyllum and Vittaephyllum, the latter being a genus that originated during the Late Triassic (Carnian) and shares a hierarchical vein system with Furcula. We further suggest that the evolution of hierarchical venation systems in the early Permian, the Late Triassic, and the Early Cretaceous represent 'natural experiments' that might help resolve the selective pressures enabling this trait to evolve.
Language	English
Publishing date	2024-04-16
Publishing country	England
Document type	Journal Article
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.19726
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Article: Pliocene Lythrum (loosestrife, Lythraceae) pollen from Portugal and the Neogene establishment of European lineages

Vieira, Manuel / Zetter, Reinhard / Coiro, Mario / Grímsson, Friðgeir

Review of palaeobotany and palynology. 2022 Jan., v. 296

2022

Abstract: The fossil record of Lythrum is scarce and every new find brings an extra piece of the puzzle to the obscure phytogeographic history of this genus. Lythrum pollen is unique and has the potential to be recognized in palynological assemblages. Therefore, ... ...

Abstract	The fossil record of Lythrum is scarce and every new find brings an extra piece of the puzzle to the obscure phytogeographic history of this genus. Lythrum pollen is unique and has the potential to be recognized in palynological assemblages. Therefore, the few pre-Holocene fossil records are all pollen described from North America, Russia, and Europe. The European records are both most numerous and geologically younger than those from other parts of the Northern Hemisphere. Earliest European Lythrum pollen records are of late Miocene age and parallel to starting crown group radiation in the Eurasian clade of Lythrum. European Miocene to Pliocene Lythrum pollen morphology is comparable to that of extant species. Interestingly, the late Miocene expansion of Lythrum into Europe coincides with the decline of Decodon, and Lythrum appears to replace Decodon in late Neogene fossil palynological assemblages.
Keywords	Decodon ; Lythrum ; Miocene epoch ; Pliocene epoch ; Russia ; fossils ; paleobotany ; palynology ; phytogeography ; pollen ; pollen morphology ; North America ; Portugal
Language	English
Dates of publication	2022-01
Publishing place	Elsevier B.V.
Document type	Article
ISSN	0034-6667
DOI	10.1016/j.revpalbo.2021.104548
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Reconciling fossils with phylogenies reveals the origin and macroevolutionary processes explaining the global cycad biodiversity

Coiro, Mario / Allio, Rémi / Mazet, Nathan / Seyfullah, Leyla J. / Condamine, Fabien L.

New Phytologist. 2023 Nov., v. 240, no. 4 p.1616-1635

2023

Abstract: The determinants of biodiversity patterns can be understood using macroevolutionary analyses. The integration of fossils into phylogenies offers a deeper understanding of processes underlying biodiversity patterns in deep time. Cycadales are considered a ...

Abstract	The determinants of biodiversity patterns can be understood using macroevolutionary analyses. The integration of fossils into phylogenies offers a deeper understanding of processes underlying biodiversity patterns in deep time. Cycadales are considered a relict of a once more diverse and globally distributed group but are restricted to low latitudes today. We still know little about their origin and geographic range evolution. Combining molecular data for extant species and leaf morphological data for extant and fossil species, we study the origin of cycad global biodiversity patterns through Bayesian total‐evidence dating analyses. We assess the ancestral geographic origin and trace the historical biogeography of cycads with a time‐stratified process‐based model. Cycads originated in the Carboniferous on the Laurasian landmass and expanded in Gondwana in the Jurassic. Through now‐vanished continental connections, Antarctica and Greenland were crucial biogeographic crossroads for cycad biogeography. Vicariance is an essential speciation mode in the deep and recent past. Their latitudinal span increased in the Jurassic and restrained toward subtropical latitudes in the Neogene in line with biogeographic inferences of high‐latitude extirpations. We show the benefits of integrating fossils into phylogenies to estimate ancestral areas of origin and to study evolutionary processes explaining the global distribution of present‐day relict groups.
Keywords	Bayesian theory ; Carboniferous period ; Cycadales ; Jurassic period ; Neogene period ; biodiversity ; fossils ; geographical distribution ; latitude ; models ; phylogeny ; provenance ; Antarctica ; Greenland
Language	English
Dates of publication	2023-11
Size	p. 1616-1635.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.19010
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Stomatal development in the cycad family Zamiaceae.

Coiro, Mario / Barone Lumaga, Maria Rosaria / Rudall, Paula J

Annals of botany

2021 Volume 128, Issue 5, Page(s) 577–588

Abstract: Background and aims: The gymnosperm order Cycadales is pivotal to our understanding of seed-plant phylogeny because of its phylogenetic placement close to the root node of extant spermatophytes and its combination of both derived and plesiomorphic ... ...

Abstract	Background and aims: The gymnosperm order Cycadales is pivotal to our understanding of seed-plant phylogeny because of its phylogenetic placement close to the root node of extant spermatophytes and its combination of both derived and plesiomorphic character states. Although widely considered a 'living fossil' group, extant cycads display a high degree of morphological and anatomical variation. We investigate stomatal development in Zamiaceae to evaluate variation within the order and homologies between cycads and other seed plants. Methods: Leaflets of seven species across five genera representing all major clades of Zamiaceae were examined at various stages of development using light microscopy and confocal microscopy. Key results: All genera examined have lateral subsidiary cells of perigenous origin that differ from other pavement cells in mature leaflets and could have a role in stomatal physiology. Early epidermal patterning in a 'quartet' arrangement occurs in Ceratozamia, Zamia and Stangeria. Distal encircling cells, which are sclerified at maturity, are present in all genera except Bowenia, which shows relatively rapid elongation and differentiation of the pavement cells during leaflet development. Conclusions: Stomatal structure and development in Zamiaceae highlights some traits that are plesiomorphic in seed plants, including the presence of perigenous encircling subsidiary cells, and reveals a clear difference between the developmental trajectories of cycads and Bennettitales. Our study also shows an unexpected degree of variation among subclades in the family, potentially linked to differences in leaflet development and suggesting convergent evolution in cycads.
MeSH term(s)	Cycadopsida ; Fossils ; Phylogeny ; Seeds ; Zamiaceae
Language	English
Publishing date	2021-07-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1461328-1
ISSN	1095-8290 ; 0305-7364
ISSN (online)	1095-8290
ISSN	0305-7364
DOI	10.1093/aob/mcab095
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Article ; Online: Reconciling fossils with phylogenies reveals the origin and macroevolutionary processes explaining the global cycad biodiversity.

Coiro, Mario / Allio, Rémi / Mazet, Nathan / Seyfullah, Leyla J / Condamine, Fabien L

The New phytologist

2023 Volume 240, Issue 4, Page(s) 1616–1635

Abstract	The determinants of biodiversity patterns can be understood using macroevolutionary analyses. The integration of fossils into phylogenies offers a deeper understanding of processes underlying biodiversity patterns in deep time. Cycadales are considered a relict of a once more diverse and globally distributed group but are restricted to low latitudes today. We still know little about their origin and geographic range evolution. Combining molecular data for extant species and leaf morphological data for extant and fossil species, we study the origin of cycad global biodiversity patterns through Bayesian total-evidence dating analyses. We assess the ancestral geographic origin and trace the historical biogeography of cycads with a time-stratified process-based model. Cycads originated in the Carboniferous on the Laurasian landmass and expanded in Gondwana in the Jurassic. Through now-vanished continental connections, Antarctica and Greenland were crucial biogeographic crossroads for cycad biogeography. Vicariance is an essential speciation mode in the deep and recent past. Their latitudinal span increased in the Jurassic and restrained toward subtropical latitudes in the Neogene in line with biogeographic inferences of high-latitude extirpations. We show the benefits of integrating fossils into phylogenies to estimate ancestral areas of origin and to study evolutionary processes explaining the global distribution of present-day relict groups.
MeSH term(s)	Phylogeny ; Fossils ; Bayes Theorem ; Cycadopsida/anatomy & histology ; Biodiversity
Language	English
Publishing date	2023-06-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.19010
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Cenozoic migration of a desert plant lineage across the North Atlantic

Denk, Thomas / Bouchal, Johannes M. / Güner, H. Tuncay / Coiro, Mario / Butzmann, Rainer / Pigg, Kathleen B. / Tiffney, Bruce H.

New Phytologist. 2023 June, v. 238, no. 6 p.2668-2684

2023

Abstract: Previous paleobotanical work concluded that Paleogene elements of the sclerophyllous subhumid vegetation of western Eurasia and western North America were endemic to these disjunct regions, suggesting that the southern areas of the Holarctic flora were ... ...

Abstract	Previous paleobotanical work concluded that Paleogene elements of the sclerophyllous subhumid vegetation of western Eurasia and western North America were endemic to these disjunct regions, suggesting that the southern areas of the Holarctic flora were isolated at that time. Consequently, molecular studies invoked either parallel adaptation to dry climates from related ancestors, or long‐distance dispersal in explaining disjunctions between the two regions, dismissing the contemporaneous migration of dry‐adapted lineages via land bridges as unlikely. We report Vauquelinia (Rosaceae), currently endemic to western North America, in Cenozoic strata of western Eurasia. Revision of North American fossils previously assigned to Vauquelinia confirmed a single fossil‐species of Vauquelinia and one of its close relative Kageneckia. We established taxonomic relationships of fossil‐taxa using diagnostic character combinations shared with modern species and constructed a time‐calibrated phylogeny. The fossil record suggests that Vauquelinia, currently endemic to arid and subdesert environments, originated under seasonally arid climates in the Eocene of western North America and subsequently crossed the Paleogene North Atlantic land bridge (NALB) to Europe. This pattern is replicated by other sclerophyllous, dry‐adapted and warmth‐loving plants, suggesting that several of these taxa potentially crossed the North Atlantic via the NALB during Eocene times.
Keywords	Eocene epoch ; Vauquelinia ; flora ; fossils ; paleobotany ; phylogeny ; subhumid zones ; vegetation ; xerophytes ; Eurasia ; Europe ; North America
Language	English
Dates of publication	2023-06
Size	p. 2668-2684.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.18743
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Eobowenia gen. nov. from the Early Cretaceous of Patagonia: indication for an early divergence of Bowenia?

Coiro, Mario / Pott, Christian

BMC evolutionary biology

2017 Volume 17, Issue 1, Page(s) 97

Abstract: Background: Even if they are considered the quintessential "living fossils", the fossil record of the extant genera of the Cycadales is quite poor, and only extends as far back as the Cenozoic. This lack of data represents a huge hindrance for the ... ...

Abstract	Background: Even if they are considered the quintessential "living fossils", the fossil record of the extant genera of the Cycadales is quite poor, and only extends as far back as the Cenozoic. This lack of data represents a huge hindrance for the reconstruction of the recent history of this important group. Among extant genera, Bowenia (or cuticles resembling those of extant Bowenia) has been recorded in sediments from the Late Cretaceous and the Eocene of Australia, but its phylogenetic placement and the inference from molecular dating still imply a long ghost lineage for this genus. Results: We re-examine the fossil foliage Almargemia incrassata from the Lower Cretaceous Anfiteatro de Ticó Formation in Patagonia, Argentina, in the light of a comparative cuticular analysis of extant Zamiaceae. We identify important differences with the other member of the genus, viz. A. dentata, and bring to light some interesting characters shared exclusively between A. incrassata and extant Bowenia. We interpret our results to necessitate the erection of the new genus Eobowenia to accommodate the fossil leaf earlier assigned as Almargemia incrassata. We then perfom phylogenetic analyses, including the first combined morphological and molecular analysis of the Cycadales, that indicate that the newly erected genus could be related to extant Bowenia. Conclusion: Eobowenia incrassata could represent an important clue for the understanding of evolution and biogeography of the extant genus Bowenia, as the presence of Eobowenia in Patagonia is yet another piece of the biogeographic puzzle that links southern South America with Australasia.
MeSH term(s)	Argentina ; Australia ; Biological Evolution ; Cycadopsida ; Fossils ; Genetic Speciation ; Phylogeny ; Plant Leaves/anatomy & histology ; South America
Language	English
Publishing date	2017-04-07
Publishing country	England
Document type	Journal Article
ISSN	1471-2148
ISSN (online)	1471-2148
DOI	10.1186/s12862-017-0943-x
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Article ; Online: Xylem Characterization Using Improved Pseudo-Schiff Propidium Iodide Staining of Whole Mount Samples and Confocal Laser-Scanning Microscopy.

Coiro, Mario / Truernit, Elisabeth

Methods in molecular biology (Clifton, N.J.)

2017 Volume 1544, Page(s) 127–132

Abstract: An improved pseudo-Schiff propidium iodide staining technique well suited for, but not limited to, the visualization of xylem cell walls in whole mount samples is presented. The pseudo-Schiff reaction results in covalent binding of the fluorescent dye ... ...

Abstract	An improved pseudo-Schiff propidium iodide staining technique well suited for, but not limited to, the visualization of xylem cell walls in whole mount samples is presented. The pseudo-Schiff reaction results in covalent binding of the fluorescent dye propidium iodide to cell walls. This stable linkage permits the use of clearing agents after staining, which is itself improved following pretreatment of the plant tissue. A subsequent acid alcohol washing step eliminates unbound propidium iodide to reduce background fluorescence. The method can be used for characterizing xylem cell structure in different organs and species without the need for tissue sectioning.
Language	English
Publishing date	2017
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-6722-3_11
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