Jaakko Hyvönen | University of Helsinki (original) (raw)

Papers by Jaakko Hyvönen

Research paper thumbnail of The diversity of the Polytrichopsida—a review

Bryophyte Diversity and Evolution, Jun 30, 2021

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Research paper thumbnail of Notoligotrichum synonymised with Atrichopsis (Polytrichaceae, Bryophyta), with two new species from South Africa

TAXON, 2021

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Research paper thumbnail of Genus Cladina and the section Unciales of the genus Cladonia(Cladoniaceae,lichenized Ascomycotina),a preliminary phylogenetic analysis

Journal of The Hattori Botanical Laboratory, 1995

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Research paper thumbnail of Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes

Frontiers in Genetics, 2020

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Research paper thumbnail of The plastid genome of Vanillon (Vanilla pompona, Orchidaceae)

Mitochondrial DNA Part B, 2017

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Research paper thumbnail of Sequencing the Plastid Genome of Giant Ragweed (Ambrosia trifida, Asteraceae) From a Herbarium Specimen

Frontiers in Plant Science, 2019

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Research paper thumbnail of The complete chloroplast genome sequence of the CAM epiphyte Spanish moss (Tillandsia usneoides, Bromeliaceae) and its comparative analysis

PLOS ONE, 2017

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Research paper thumbnail of The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae

PLOS ONE, 2018

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Research paper thumbnail of Global biogeographic patterns in bipolar moss species

Royal Society Open Science, 2017

A bipolar disjunction is an extreme, yet common, biogeographic pattern in non-vascular plants, ye... more A bipolar disjunction is an extreme, yet common, biogeographic pattern in non-vascular plants, yet its underlying mechanisms (vicariance or long-distance dispersal), origin and timing remain poorly understood. Here, combining a large-scale population dataset and multiple dating analyses, we examine the biogeography of four bipolar Polytrichales mosses, common to the Holarctic (temperate and polar Northern Hemisphere regions) and the Antarctic region (Antarctic, sub-Antarctic, southern South America) and other Southern Hemisphere (SH) regions. Our data reveal contrasting patterns, for three species were of Holarctic origin, with subsequent dispersal to the SH, while one, currently a particularly common species in the Holarctic ( Polytrichum juniperinum ), diversified in the Antarctic region and from here colonized both the Holarctic and other SH regions. Our findings suggest long-distance dispersal as the driver of bipolar disjunctions. We find such inter-hemispheric dispersals are r...

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Research paper thumbnail of The first Indian record of Pogonatum marginatum Mitt. (Polytrichaceae) from the Western Ghats

Bryophyte Diversity and Evolution, 2016

Pogonatum marginatum has been previously known from Sri Lanka and Vietnam. It was recently collec... more Pogonatum marginatum has been previously known from Sri Lanka and Vietnam. It was recently collected in the Agasthyamalai Biosphere Reserve in the Western Ghats (Kerala and Tamil Nadu), this being the first record of the plant in India. We provide a detailed description of the species with figures and a photographic plate, plus novel chloroplast gene sequences of the Indian plant, another specimen of the same species, and a close relative.

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Research paper thumbnail of Delongia gen. nov., a new genus of Polytrichaceae (Bryophyta) with two disjunct species in East Africa and the Himalaya

TAXON, 2015

Although the family Polytrichaceae contains the largest and structurally most complex of all moss... more Although the family Polytrichaceae contains the largest and structurally most complex of all mosses, a number of distantly related lineages share a relatively reduced gametophytic morphology and have historically been conflated under polyphyletic genera, most notably Oligotrichum s.l. Based on new and newly identified collections, phylogenetic analysis of nucleotide data, scanning electron microscopy and relaxed‐clock divergence time estimation, we recognise O. glaciale and O. cavallii under the new genus Delongia, which is more closely related to Psilopilum, Atrichum and Steereobryon than to Oligotrichum. The two species are mutually highly distinct in both morphological and molecular characters, with D. glacialis occurring across the Himalaya from Pakistan to Yunnan and D. cavallii found in the East African Rift Mountains and on the island of Réunion. Divergence time estimation suggests that the lineages represented by the extant species diverged from each other around the Oligoce...

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Research paper thumbnail of Phylogeny and taxonomy of the ‘manna lichens’

Mycological Progress, 2012

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Research paper thumbnail of Phylogeny of cetrarioid lichens (Parmeliaceae) inferred from ITS and b-tubulin sequences, morphology, anatomy and secondary chemistry

Mycological Progress, 2002

Phylogenetic relationships within the family Parmeliaceae (lichenized ascomycetes) with emphasis ... more Phylogenetic relationships within the family Parmeliaceae (lichenized ascomycetes) with emphasis on the heterogeneous group of cetrarioid lichens are reconstructed. The results are based on cladistic analyses of DNA-sequences, morphological and chemical data. Almost all currently recognized cetrarioid genera were included in the analyses together with parmelioid and alectorioid members of the presumably monophyletic family Parmeliaceae. We tried to sample taxonomic

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Research paper thumbnail of An annotated checklist of the mosses of Europe and Macaronesia

Journal of Bryology, 2006

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Research paper thumbnail of Multiple origins of symbioses between ascomycetes and bryophytes suggested by a five‐gene phylogeny

Cladistics, 2009

Numerous species of microscopic fungi inhabit mosses and hepatics. They are severely overlooked a... more Numerous species of microscopic fungi inhabit mosses and hepatics. They are severely overlooked and their identity and nutritional strategies are mostly unknown. Most of these bryosymbiotic fungi belong to the Ascomycota. Their fruit‐bodies are extremely small, often reduced and simply structured, which is why they cannot be reliably identified and classified by their morphological and anatomical characters. A phylogenetic hypothesis of bryosymbiotic ascomycetes is presented. New sequences of 78 samples, including 61 bryosymbionts, were produced, the total amount of terminals being 206. Of these, 202 are Ascomycetes. Sequences from the following five gene loci were used: rDNA SSU, rDNA LSU, RPB2, mitochondrial rDNA SSU, and rDNA 5.8S. The program TNT was used for tree search and support value estimation. We show that bryosymbiotic fungi occur in numerous lineages, one of which represents a newly discovered lineage among the Ascomycota and exhibits a tripartite association with cyano...

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Research paper thumbnail of Rooting morphologically divergent taxa – slow-evolving sequence data might help

When fossils are sparse and the lineages studied are very divergent morphologically, analyses bas... more When fossils are sparse and the lineages studied are very divergent morphologically, analyses based exclusively on morphology may lead to conflicting and unexpected hypotheses. Through integration of data from conservative genes/gene regions the terminals including these data can anchor or constrain the search, thereby practically circumscribing the search space of the combined analyses. In this study, we revisit the phylogeny of a highly divergent group of mosses, class Polytrichopsida. We supplemented the morphological matrix by adding sequence data of the nuclear gene 18S, chloroplast genesrbcL andrps4, plus the mitochondrial genenad5. For the phylogenetic analyses we used parsimony as the optimality criterion. Analyses that included all the terminals resulted in one most parsimonious tree with a clade comprised ofAlophosia azoricaand the fossilMeantoinea alophosioidesrepresenting the basal-most lineage. Analyses with different outgroup sampling produced the same topology for mos...

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Research paper thumbnail of Complete plastid genome sequence of African nightshade (Solanum scabrum) and comparative plastomics across Solanales

Solanaceae are a particularly interesting angiosperm family, not only because they include many m... more Solanaceae are a particularly interesting angiosperm family, not only because they include many major crop species such as potato, tomato, eggplant, pepper, tobacco and ornamentals like petunias, but also because numerous species are used as biological models. They have been widely used for understanding crop genetics and plant genome evolution in general. Sequencing efforts have been concentrated mostly to sequence genomes of important crop species of Solanaceae to understand the links between wild and cultivated members of the family. We present the complete plastome of African nightshade (Solanum scabrum Mill.) a hexaploid (2n = 6x = 72) species of the S. nigrum L. complex or Solanum sect. Solanum, a widely cultivated species across Africa. Recent studies highlight S. scabrum as a “super-vegetable” for its nutritional and environmental benefits with potential of global importance. The leaves and berries are the source of coloring plant extracts, inks and dyes, and they are rich in proteins, fibres, iron, vitamins and amino acids. Using 12,413,264 paired end reads deposited in the sequence read archive (SRA) we have assembled the plastid genome sequence of African nightshade with an estimated coverage of 123×. The plastid genome sequence had a total size of 155,522 bp, typical of Solanaceae with a large single copy (LSC) region of 85,896 bp and small single copy (SSC) region of 18,406 bp while the IRs comprised of 25,610 bp. We illustrate the role of Solanum scabrum and its comparative plastomics across Solanaceae and Convolvulaceae to understand the plastomics of Solanales.Peer reviewe

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Research paper thumbnail of From Finland to Japan to New Guinea to China : that is Timo Koponen, bryologist

From Finland to Japan to New Guinea to China :that is Timo Koponen, bryologist , From Finland to ... more From Finland to Japan to New Guinea to China :that is Timo Koponen, bryologist , From Finland to Japan to New Guinea to China :that is Timo Koponen, bryologist , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی

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Research paper thumbnail of Cladistic Analysis of the Hornworts (Anthocerotophyta)

Journal of The Hattori Botanical Laboratory, 1993

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Research paper thumbnail of On the bryogeography of Western Melanesia

Journal of The Hattori Botanical Laboratory, 1989

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Research paper thumbnail of The diversity of the Polytrichopsida—a review

Bryophyte Diversity and Evolution, Jun 30, 2021

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Research paper thumbnail of Notoligotrichum synonymised with Atrichopsis (Polytrichaceae, Bryophyta), with two new species from South Africa

TAXON, 2021

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Genus Cladina and the section Unciales of the genus Cladonia(Cladoniaceae,lichenized Ascomycotina),a preliminary phylogenetic analysis

Journal of The Hattori Botanical Laboratory, 1995

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes

Frontiers in Genetics, 2020

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Research paper thumbnail of The plastid genome of Vanillon (Vanilla pompona, Orchidaceae)

Mitochondrial DNA Part B, 2017

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Research paper thumbnail of Sequencing the Plastid Genome of Giant Ragweed (Ambrosia trifida, Asteraceae) From a Herbarium Specimen

Frontiers in Plant Science, 2019

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Research paper thumbnail of The complete chloroplast genome sequence of the CAM epiphyte Spanish moss (Tillandsia usneoides, Bromeliaceae) and its comparative analysis

PLOS ONE, 2017

Bookmarks Related papers MentionsView impact

Research paper thumbnail of The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae

PLOS ONE, 2018

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Global biogeographic patterns in bipolar moss species

Royal Society Open Science, 2017

A bipolar disjunction is an extreme, yet common, biogeographic pattern in non-vascular plants, ye... more A bipolar disjunction is an extreme, yet common, biogeographic pattern in non-vascular plants, yet its underlying mechanisms (vicariance or long-distance dispersal), origin and timing remain poorly understood. Here, combining a large-scale population dataset and multiple dating analyses, we examine the biogeography of four bipolar Polytrichales mosses, common to the Holarctic (temperate and polar Northern Hemisphere regions) and the Antarctic region (Antarctic, sub-Antarctic, southern South America) and other Southern Hemisphere (SH) regions. Our data reveal contrasting patterns, for three species were of Holarctic origin, with subsequent dispersal to the SH, while one, currently a particularly common species in the Holarctic ( Polytrichum juniperinum ), diversified in the Antarctic region and from here colonized both the Holarctic and other SH regions. Our findings suggest long-distance dispersal as the driver of bipolar disjunctions. We find such inter-hemispheric dispersals are r...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of The first Indian record of Pogonatum marginatum Mitt. (Polytrichaceae) from the Western Ghats

Bryophyte Diversity and Evolution, 2016

Pogonatum marginatum has been previously known from Sri Lanka and Vietnam. It was recently collec... more Pogonatum marginatum has been previously known from Sri Lanka and Vietnam. It was recently collected in the Agasthyamalai Biosphere Reserve in the Western Ghats (Kerala and Tamil Nadu), this being the first record of the plant in India. We provide a detailed description of the species with figures and a photographic plate, plus novel chloroplast gene sequences of the Indian plant, another specimen of the same species, and a close relative.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Delongia gen. nov., a new genus of Polytrichaceae (Bryophyta) with two disjunct species in East Africa and the Himalaya

TAXON, 2015

Although the family Polytrichaceae contains the largest and structurally most complex of all moss... more Although the family Polytrichaceae contains the largest and structurally most complex of all mosses, a number of distantly related lineages share a relatively reduced gametophytic morphology and have historically been conflated under polyphyletic genera, most notably Oligotrichum s.l. Based on new and newly identified collections, phylogenetic analysis of nucleotide data, scanning electron microscopy and relaxed‐clock divergence time estimation, we recognise O. glaciale and O. cavallii under the new genus Delongia, which is more closely related to Psilopilum, Atrichum and Steereobryon than to Oligotrichum. The two species are mutually highly distinct in both morphological and molecular characters, with D. glacialis occurring across the Himalaya from Pakistan to Yunnan and D. cavallii found in the East African Rift Mountains and on the island of Réunion. Divergence time estimation suggests that the lineages represented by the extant species diverged from each other around the Oligoce...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Phylogeny and taxonomy of the ‘manna lichens’

Mycological Progress, 2012

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Phylogeny of cetrarioid lichens (Parmeliaceae) inferred from ITS and b-tubulin sequences, morphology, anatomy and secondary chemistry

Mycological Progress, 2002

Phylogenetic relationships within the family Parmeliaceae (lichenized ascomycetes) with emphasis ... more Phylogenetic relationships within the family Parmeliaceae (lichenized ascomycetes) with emphasis on the heterogeneous group of cetrarioid lichens are reconstructed. The results are based on cladistic analyses of DNA-sequences, morphological and chemical data. Almost all currently recognized cetrarioid genera were included in the analyses together with parmelioid and alectorioid members of the presumably monophyletic family Parmeliaceae. We tried to sample taxonomic

Bookmarks Related papers MentionsView impact

Research paper thumbnail of An annotated checklist of the mosses of Europe and Macaronesia

Journal of Bryology, 2006

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Multiple origins of symbioses between ascomycetes and bryophytes suggested by a five‐gene phylogeny

Cladistics, 2009

Numerous species of microscopic fungi inhabit mosses and hepatics. They are severely overlooked a... more Numerous species of microscopic fungi inhabit mosses and hepatics. They are severely overlooked and their identity and nutritional strategies are mostly unknown. Most of these bryosymbiotic fungi belong to the Ascomycota. Their fruit‐bodies are extremely small, often reduced and simply structured, which is why they cannot be reliably identified and classified by their morphological and anatomical characters. A phylogenetic hypothesis of bryosymbiotic ascomycetes is presented. New sequences of 78 samples, including 61 bryosymbionts, were produced, the total amount of terminals being 206. Of these, 202 are Ascomycetes. Sequences from the following five gene loci were used: rDNA SSU, rDNA LSU, RPB2, mitochondrial rDNA SSU, and rDNA 5.8S. The program TNT was used for tree search and support value estimation. We show that bryosymbiotic fungi occur in numerous lineages, one of which represents a newly discovered lineage among the Ascomycota and exhibits a tripartite association with cyano...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Rooting morphologically divergent taxa – slow-evolving sequence data might help

When fossils are sparse and the lineages studied are very divergent morphologically, analyses bas... more When fossils are sparse and the lineages studied are very divergent morphologically, analyses based exclusively on morphology may lead to conflicting and unexpected hypotheses. Through integration of data from conservative genes/gene regions the terminals including these data can anchor or constrain the search, thereby practically circumscribing the search space of the combined analyses. In this study, we revisit the phylogeny of a highly divergent group of mosses, class Polytrichopsida. We supplemented the morphological matrix by adding sequence data of the nuclear gene 18S, chloroplast genesrbcL andrps4, plus the mitochondrial genenad5. For the phylogenetic analyses we used parsimony as the optimality criterion. Analyses that included all the terminals resulted in one most parsimonious tree with a clade comprised ofAlophosia azoricaand the fossilMeantoinea alophosioidesrepresenting the basal-most lineage. Analyses with different outgroup sampling produced the same topology for mos...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Complete plastid genome sequence of African nightshade (Solanum scabrum) and comparative plastomics across Solanales

Solanaceae are a particularly interesting angiosperm family, not only because they include many m... more Solanaceae are a particularly interesting angiosperm family, not only because they include many major crop species such as potato, tomato, eggplant, pepper, tobacco and ornamentals like petunias, but also because numerous species are used as biological models. They have been widely used for understanding crop genetics and plant genome evolution in general. Sequencing efforts have been concentrated mostly to sequence genomes of important crop species of Solanaceae to understand the links between wild and cultivated members of the family. We present the complete plastome of African nightshade (Solanum scabrum Mill.) a hexaploid (2n = 6x = 72) species of the S. nigrum L. complex or Solanum sect. Solanum, a widely cultivated species across Africa. Recent studies highlight S. scabrum as a “super-vegetable” for its nutritional and environmental benefits with potential of global importance. The leaves and berries are the source of coloring plant extracts, inks and dyes, and they are rich in proteins, fibres, iron, vitamins and amino acids. Using 12,413,264 paired end reads deposited in the sequence read archive (SRA) we have assembled the plastid genome sequence of African nightshade with an estimated coverage of 123×. The plastid genome sequence had a total size of 155,522 bp, typical of Solanaceae with a large single copy (LSC) region of 85,896 bp and small single copy (SSC) region of 18,406 bp while the IRs comprised of 25,610 bp. We illustrate the role of Solanum scabrum and its comparative plastomics across Solanaceae and Convolvulaceae to understand the plastomics of Solanales.Peer reviewe

Bookmarks Related papers MentionsView impact

Research paper thumbnail of From Finland to Japan to New Guinea to China : that is Timo Koponen, bryologist

From Finland to Japan to New Guinea to China :that is Timo Koponen, bryologist , From Finland to ... more From Finland to Japan to New Guinea to China :that is Timo Koponen, bryologist , From Finland to Japan to New Guinea to China :that is Timo Koponen, bryologist , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی

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Research paper thumbnail of Cladistic Analysis of the Hornworts (Anthocerotophyta)

Journal of The Hattori Botanical Laboratory, 1993

Bookmarks Related papers MentionsView impact

Research paper thumbnail of On the bryogeography of Western Melanesia

Journal of The Hattori Botanical Laboratory, 1989

Bookmarks Related papers MentionsView impact