PeerJ Preprints: Taxonomyhttps://peerj.com/preprints/index.atom?journal=peerj&subject=2700Taxonomy articles published in PeerJ PreprintsComparative studies of Echinometra mathaei species complex (Echinoidea: Camarodonta: Echinometridae) from two sites in Western Visayas, Philippines (Taklong Island, Guimaras and Nabas, Aklan)https://peerj.com/preprints/279862019-10-282019-10-28Joseph Ricky TamayoMaria Celia D Malay
Echinometra mathaei is a species complex with its constituent reproductively-isolated species informally called A, B, C and D based on studies done in Okinawa and the Red Sea. Little research has been done on this genus, and to our knowledge no studies have been done on the E. mathaei complex in the Philippines. To help clarify species delineations in the E. mathaei complex, a comparative study was done between two localities in Western Visayas, Philippines: the Taklong Island National Marine Reserve, in Nueva Valencia, Guimaras and Barangay Unidos in Nabas, Aklan. Morphological characteristics (spine color, milled rings, and skin around the peristome) and tubefeet and gonad spicules were observed. Two or possibly three species of Echinometra were found in the two sites based on their morphology and spicules, namely: Echinometra sp. A, Echinometra sp. C, and Echinometra affinity C, which resembles sp. C but differs in the milled rings and gonad spicules. Echinometra sp. C and E. affinity C cannot be distinguished on the basis of field-visible characters, thus the two morphs are referred to as Echinometra VC for the purpose of field surveys. Echinometra VC and Echinometra sp. A exhibited differences in abundance (VC was much more common) and microhabitat (VC was restricted to rocky shores and never observed in coral communities). To study the abundance and distribution of Echinometra VC, 50 m by 2 m belt transects were surveyed along the rocky shores of both sites: two parallel transects (at 0 m and at 0.9 m) and a perpendicular transect (only in Nabas), each with three replicates. The transect data showed that the mean densities for 0 m and 0.9 m in Nabas are significantly higher in Taklong yielding p-values of 0.001 and 0.002, respectively, when analyzed using t-test.Of the two sites, only Nabas showed a significant difference between the mean densities at 0 m and 0.9 m, with the mean density at 0.9 m significantly higher than that of 0 m yielding a p-value of 0.02 when analyzed using two-sample t-test. A Poisson regression on the perpendicular transect data from Nabas showed a trend of increasing Echinometra density with increasing distance from the shore. In the future, DNA barcoding and cross-fertilization studies should be performed in order to confirm the species of Echinometra observed. Many factors can affect the density and distribution of Echinometra, so further studies must be conducted to explain observed differences in their distribution and abundance.
Echinometra mathaei is a species complex with its constituent reproductively-isolated species informally called A, B, C and D based on studies done in Okinawa and the Red Sea. Little research has been done on this genus, and to our knowledge no studies have been done on the E. mathaei complex in the Philippines. To help clarify species delineations in the E. mathaei complex, a comparative study was done between two localities in Western Visayas, Philippines: the Taklong Island National Marine Reserve, in Nueva Valencia, Guimaras and Barangay Unidos in Nabas, Aklan. Morphological characteristics (spine color, milled rings, and skin around the peristome) and tubefeet and gonad spicules were observed. Two or possibly three species of Echinometra were found in the two sites based on their morphology and spicules, namely: Echinometra sp. A, Echinometra sp. C, and Echinometra affinity C, which resembles sp. C but differs in the milled rings and gonad spicules. Echinometra sp. C and E. affinity C cannot be distinguished on the basis of field-visible characters, thus the two morphs are referred to as Echinometra VC for the purpose of field surveys. Echinometra VC and Echinometra sp. A exhibited differences in abundance (VC was much more common) and microhabitat (VC was restricted to rocky shores and never observed in coral communities). To study the abundance and distribution of Echinometra VC, 50 m by 2 m belt transects were surveyed along the rocky shores of both sites: two parallel transects (at 0 m and at 0.9 m) and a perpendicular transect (only in Nabas), each with three replicates. The transect data showed that the mean densities for 0 m and 0.9 m in Nabas are significantly higher in Taklong yielding p-values of 0.001 and 0.002, respectively, when analyzed using t-test.Of the two sites, only Nabas showed a significant difference between the mean densities at 0 m and 0.9 m, with the mean density at 0.9 m significantly higher than that of 0 m yielding a p-value of 0.02 when analyzed using two-sample t-test. A Poisson regression on the perpendicular transect data from Nabas showed a trend of increasing Echinometra density with increasing distance from the shore. In the future, DNA barcoding and cross-fertilization studies should be performed in order to confirm the species of Echinometra observed. Many factors can affect the density and distribution of Echinometra, so further studies must be conducted to explain observed differences in their distribution and abundance.Phylogeny of Libellulidae: are there relationships between molecular phylogenetics and morphological analysis of wing shape of dragonflies?https://peerj.com/preprints/279582019-09-122019-09-12Shu T HuangHai R WangWan Q YangYa C SiYu T WangMeng L SunXin QiYi Bai
Background: Establishing the species limits and resolving phylogenetic relationships are primary goals of taxonomists and evolutionary biologists. At present, a controversial question is about interspecific phylogenetic information in morphological features. Are the interspecific relationships established based on genetic information consistent with the traditional classification system? To address these problems, this study analyzed the wing shape structure of 10 species of Libellulidae, explored the relationship between wing shape and dragonfly behavior and living habits, and established an interspecific morphological relationship tree based on wing shape data. By analyzing the sequences of mitochondrial COI gene and the nuclear genes 18S, 28S rRNA and ITS in 10 species of dragonflies, the interspecific relationship was established. Method: The wing shape information of the male forewings and hindwings was obtained by the geometric morphometrics method. The inter-species wing shape relationship was obtained by principal component analysis (PCA) in MorphoJ1.06 software. The inter-species wing shape relationship tree was obtained by cluster analysis (UPGMA) using Mesquite3.2 software. The COI, 18S, ITS and 28S genes of 10 species dragonfly were blasted and processed by BioEdit v6 software. The maximum parsimony (MP) tree was established by Puap4.0 software. The Bayes inference (BI) tree was established by MrBayes 3.2.6 in Geneious software. Results: The main difference in forewings among the 10 species of dragonfly was the apical, radial and discoidal regions dominated by the wing nodus. In contrast, the main difference among the hindwings was the apical and anal regions dominated by the wing nodus. The change in wing shape was closely related to the ability of dragonfly to migrate. The interspecific relationship based on molecular data showed that the species of Orthetrum genus branched independently of the other species. Compared to the molecular tree of 10 species, the wing shape clustering showed some phylogenetic information on the forewing shape (with large differences in the forewing shape tree vs. molecular tree), and there was no interspecific phylogenetic information of the hindwing shape tree vs. molecular tree. Conclusion: The dragonfly wing shape characteristics are closely related to its migration ability. Species with strong ability to migrate have the forewing shape that is longer and narrower, and have larger anal region, whereas the species that prefer short-distance hovering or standing still for a long time have forewing that are wider and shorter, and the anal region is smaller. Integrating morphological and molecular data to evaluate the relationship among dragonfly species shows there is some interspecific phylogenetic information in the forewing shape and none in the hindwing shape. The various regions of the forewing and hindwing are inconsistent, which may be due to their different functions.
Background: Establishing the species limits and resolving phylogenetic relationships are primary goals of taxonomists and evolutionary biologists. At present, a controversial question is about interspecific phylogenetic information in morphological features. Are the interspecific relationships established based on genetic information consistent with the traditional classification system? To address these problems, this study analyzed the wing shape structure of 10 species of Libellulidae, explored the relationship between wing shape and dragonfly behavior and living habits, and established an interspecific morphological relationship tree based on wing shape data. By analyzing the sequences of mitochondrial COI gene and the nuclear genes 18S, 28SrRNA and ITS in 10 species of dragonflies, the interspecific relationship was established. Method: The wing shape information of the male forewings and hindwings was obtained by the geometric morphometrics method. The inter-species wing shape relationship was obtained by principal component analysis (PCA) in MorphoJ1.06 software. The inter-species wing shape relationship tree was obtained by cluster analysis (UPGMA) using Mesquite3.2 software. The COI, 18S, ITS and 28S genes of 10 species dragonfly were blasted and processed by BioEdit v6 software. The maximum parsimony (MP) tree was established by Puap4.0 software. The Bayes inference (BI) tree was established by MrBayes 3.2.6 in Geneious software. Results: The main difference in forewings among the 10 species of dragonfly was the apical, radial and discoidal regions dominated by the wing nodus. In contrast, the main difference among the hindwings was the apical and anal regions dominated by the wing nodus. The change in wing shape was closely related to the ability of dragonfly to migrate. The interspecific relationship based on molecular data showed that the species of Orthetrum genus branched independently of the other species. Compared to the molecular tree of 10 species, the wing shape clustering showed some phylogenetic information on the forewing shape (with large differences in the forewing shape tree vs. molecular tree), and there was no interspecific phylogenetic information of the hindwing shape tree vs. molecular tree. Conclusion: The dragonfly wing shape characteristics are closely related to its migration ability. Species with strong ability to migrate have the forewing shape that is longer and narrower, and have larger anal region, whereas the species that prefer short-distance hovering or standing still for a long time have forewing that are wider and shorter, and the anal region is smaller. Integrating morphological and molecular data to evaluate the relationship among dragonfly species shows there is some interspecific phylogenetic information in the forewing shape and none in the hindwing shape. The various regions of the forewing and hindwing are inconsistent, which may be due to their different functions.Late Toarcian marine gastropods from the Cleveland Basin, UK: systematics, palaeobiogeography and contribution to biotic recovery from the early Toarcian extinction eventhttps://peerj.com/preprints/279472019-09-092019-09-09Mariel FerrariCrispin TS LittleJed W Atkinson
As part of a study to evaluate the recovery from the early Toarcian extinction event in the Cleveland Basin, 477 new gastropod specimens were collected from mid-late Toarcian rocks of the Ravenscar section, North Yorkshire, UK. The gastropods were preserved in two modes: 1) specimens preserved with recrystallized shells, mainly in the Whitby Mudstone Formation, but also some in the Blea Wyke Sandstone Formation; 2) specimens preserved as external moulds in mineralized patches of shells in the Yellow Sandstone Member. The fossil assemblage comprised fifteen species, of which three are new: Katosira? bicarinata sp. nov., Turritelloidea stepheni sp. nov. and Striactaenonina elegans sp. nov. Four species are described in open nomenclature, as Tricarilda? sp. Jurilda sp., Cylindrobullina sp. and Cossmannina sp. The other species have previously been described: Coelodiscus minutus (Schübler in Zieten), Procerithium quadrilineatum (Römer), Pseudokatosira undulata (Benz in von Zieten), Palaeorissoina aff. acuminata (Gründel), Pietteia unicarinata (Hudleston), Globularia cf. canina (Hudleston), Striactaeonina cf. richterorum Schulbert & Nützel, Striactaenonina aff. tenuistriata (Hudleston) and Sulcoactaeon sedgvici (Phillips). Most of these species are the earliest records of their respective genera and show palaeobiogeographical connections with contemporary gastropod associations from other regions of Europe and South America. The taxonomic composition of the late Toarcian Cleveland Basin gastropod assemblage differs substantially from the faunas of the late Pliensbachian and early Toarcian Tenuicostatum Zone, showing the strong effect of the early Toarcian mass extinction event on the marine gastropod communities in the basin. Only a few gastropod species are shared between the late Toarcian faunas and the much more diverse Aalenian gastropod faunas in the Cleveland Basin, suggesting there was a facies control on gastropod occurrences at that time. This is also a potential explanation for the taxonomic differences between the late Toarcian gastropod faunas in the Cleveland Basin and those in France, and Northern and Southern Germany.
As part of a study to evaluate the recovery from the early Toarcian extinction event in the Cleveland Basin, 477 new gastropod specimens were collected from mid-late Toarcian rocks of the Ravenscar section, North Yorkshire, UK. The gastropods were preserved in two modes: 1) specimens preserved with recrystallized shells, mainly in the Whitby Mudstone Formation, but also some in the Blea Wyke Sandstone Formation; 2) specimens preserved as external moulds in mineralized patches of shells in the Yellow Sandstone Member. The fossil assemblage comprised fifteen species, of which three are new: Katosira? bicarinata sp. nov., Turritelloideastepheni sp. nov. and Striactaenoninaelegans sp. nov. Four species are described in open nomenclature, as Tricarilda? sp. Jurilda sp., Cylindrobullina sp. and Cossmannina sp. The other species have previously been described: Coelodiscus minutus (Schübler in Zieten), Procerithium quadrilineatum (Römer), Pseudokatosira undulata (Benz in von Zieten), Palaeorissoina aff. acuminata (Gründel), Pietteia unicarinata (Hudleston), Globularia cf. canina (Hudleston), Striactaeonina cf. richterorum Schulbert & Nützel, Striactaenonina aff. tenuistriata (Hudleston) and Sulcoactaeon sedgvici (Phillips). Most of these species are the earliest records of their respective genera and show palaeobiogeographical connections with contemporary gastropod associations from other regions of Europe and South America. The taxonomic composition of the late Toarcian Cleveland Basin gastropod assemblage differs substantially from the faunas of the late Pliensbachian and early Toarcian Tenuicostatum Zone, showing the strong effect of the early Toarcian mass extinction event on the marine gastropod communities in the basin. Only a few gastropod species are shared between the late Toarcian faunas and the much more diverse Aalenian gastropod faunas in the Cleveland Basin, suggesting there was a facies control on gastropod occurrences at that time. This is also a potential explanation for the taxonomic differences between the late Toarcian gastropod faunas in the Cleveland Basin and those in France, and Northern and Southern Germany.Pharaoh’s Dance: the oak genomic mosaichttps://peerj.com/preprints/274052019-06-042019-06-04Andrew L Hipp
When we look at an oak, we see one organism, despite the fact that each of the estimated 25,808 genes in the oak genome has a unique history. Here I review why the evolutionary history of oaks comprises a variety of phylogenetic histories that trace disparate histories of introgression, stochastic allele extinction, and population divergence. I describe recent phylogenomic work that dissects the multiple phylogenetic histories constituting the history of white oak movements between the Americas and Eurasia. Finally, I argue that the patterns and causes of genomic mosaicism should be a central focus of inquiry for oak phylogenetic work in the coming decade.
When we look at an oak, we see one organism, despite the fact that each of the estimated 25,808 genes in the oak genome has a unique history. Here I review why the evolutionary history of oaks comprises a variety of phylogenetic histories that trace disparate histories of introgression, stochastic allele extinction, and population divergence. I describe recent phylogenomic work that dissects the multiple phylogenetic histories constituting the history of white oak movements between the Americas and Eurasia. Finally, I argue that the patterns and causes of genomic mosaicism should be a central focus of inquiry for oak phylogenetic work in the coming decade.Angiosperm phylogeny poster (APP) – Flowering plant systematics, 2019https://peerj.com/preprints/23202019-05-292019-05-29Theodor C H ColeHartmut H HilgerPeter Stevens
The Angiosperm Phylogeny Poster – Flowering Plant Systematics is an educational poster presenting an overview of the evolutionary relationships among flowering plants, based on APG IV/APweb and in this update chiefly following the topology of PPA ("Plastid Phylogenomic Angiosperm" see Li HT et al. 2019). The phylogenetic tree depicts the 64 orders and the majority of the 416 families, listing the main apo- and plesiomorphies as well as diagnostic and nondiagnostic anatomical, morphological, and phytochemical features for orders and higher ranks within the tree along with the number of families, genera, and species for each order. The intuitive color-coding facilitates memorization and teaching. The poster is now available in 25 languages (all downloadable from ResearchGate).
The Angiosperm Phylogeny Poster – Flowering Plant Systematics is an educational poster presenting an overview of the evolutionary relationships among flowering plants, based on APG IV/APweb and in this update chiefly following the topology of PPA ("Plastid Phylogenomic Angiosperm" see Li HT et al. 2019). The phylogenetic tree depicts the 64 orders and the majority of the 416 families, listing the main apo- and plesiomorphies as well as diagnostic and nondiagnostic anatomical, morphological, and phytochemical features for orders and higher ranks within the tree along with the number of families, genera, and species for each order. The intuitive color-coding facilitates memorization and teaching. The poster is now available in 25 languages (all downloadable from ResearchGate).Understanding the chemical basis for the preferential ionization of specific biomolecules in mass spectrometry analysis of microbial cellshttps://peerj.com/preprints/277592019-05-262019-05-26Wenfa Ng
Mass spectrometry-enabled microbial identification has successfully demonstrated the feasibility of using profiled biomolecules for identifying microorganisms based on a chemometric or proteome database search approach. However, mechanisms driving the preferential ionization and detection of particular biomolecules in various types of mass spectrometry remain poorly understood. Specifically, mass spectra obtained from different microbial species remain poorly annotated with respect to the specific types of biomolecules accounting for the peaks. For example, while ribosomal proteins are known to be a significant class of biomolecules that could partially account for the profiled mass peaks in mass spectra of microorganisms, other classes of proteins and biomolecules remain poorly annotated. This raises the important question of how different mass spectrometry approaches ionize different types of biomolecules from a cellular matrix. Specifically, mass spectra of microorganisms reveal that only a couple of mass peaks could capture the phylogeny of a species. However, the proteome of a cell is much larger and more complicated, and yet is not fully profiled by different types of mass spectrometry methods. For example, electrospray ionization mass spectrometry (ESI-MS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) could only provide a small snapshot of the entire bacterial proteome. It could be argued that different mass spectrometry methods provide complementary views of a particular proteome. However, the question remains, how do proteins and biomolecules interact with the different sample preparation and mass spectrometry analysis methods for generating an ion cloud for separation in a mass spectrometer? Thus, efforts could be directed towards understanding how different types of proteins could be preferentially ionized by MALDI-TOF MS. Specifically, different reagents could be used to perform chemical pretreatment on the proteome, which would subsequently be analyzed by mass spectrometry. Thus, a correlative map between types of chemical pretreatment used and the corresponding mass spectra could be obtained. Collectively, knowledge gleaned from the research would illuminate the chemical basis by which specific biomolecules are preferentially ionized under particular conditions, which would inform the development of strategies for increasing the subset of biomolecules ionized from a cellular proteome. Such chemical rules would also aid in the interpretation of mass spectra obtained, particularly in understanding the biological context of the experiment. Overall, the key goal of this research is to help answer the question: what is the biological basis and context of the mass spectrum obtained from cells?
Mass spectrometry-enabled microbial identification has successfully demonstrated the feasibility of using profiled biomolecules for identifying microorganisms based on a chemometric or proteome database search approach. However, mechanisms driving the preferential ionization and detection of particular biomolecules in various types of mass spectrometry remain poorly understood. Specifically, mass spectra obtained from different microbial species remain poorly annotated with respect to the specific types of biomolecules accounting for the peaks. For example, while ribosomal proteins are known to be a significant class of biomolecules that could partially account for the profiled mass peaks in mass spectra of microorganisms, other classes of proteins and biomolecules remain poorly annotated. This raises the important question of how different mass spectrometry approaches ionize different types of biomolecules from a cellular matrix. Specifically, mass spectra of microorganisms reveal that only a couple of mass peaks could capture the phylogeny of a species. However, the proteome of a cell is much larger and more complicated, and yet is not fully profiled by different types of mass spectrometry methods. For example, electrospray ionization mass spectrometry (ESI-MS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) could only provide a small snapshot of the entire bacterial proteome. It could be argued that different mass spectrometry methods provide complementary views of a particular proteome. However, the question remains, how do proteins and biomolecules interact with the different sample preparation and mass spectrometry analysis methods for generating an ion cloud for separation in a mass spectrometer? Thus, efforts could be directed towards understanding how different types of proteins could be preferentially ionized by MALDI-TOF MS. Specifically, different reagents could be used to perform chemical pretreatment on the proteome, which would subsequently be analyzed by mass spectrometry. Thus, a correlative map between types of chemical pretreatment used and the corresponding mass spectra could be obtained. Collectively, knowledge gleaned from the research would illuminate the chemical basis by which specific biomolecules are preferentially ionized under particular conditions, which would inform the development of strategies for increasing the subset of biomolecules ionized from a cellular proteome. Such chemical rules would also aid in the interpretation of mass spectra obtained, particularly in understanding the biological context of the experiment. Overall, the key goal of this research is to help answer the question: what is the biological basis and context of the mass spectrum obtained from cells?CAM: An alignment-free method to recover phylogenies using codon aversion motifshttps://peerj.com/preprints/277562019-05-242019-05-24Justin B MillerLauren M McKinnonMichael F WhitingPerry G Ridge
Background. Common phylogenomic approaches for recovering phylogenies are often time-consuming and require annotations for orthologous gene relationships that are not always available. In contrast, alignment-free phylogenomic approaches typically use structure and oligomer frequencies to calculate pairwise distances between species. We have developed an algorithm to quickly calculate distances between species based on codon aversion.
Methods. Utilizing a novel alignment-free character state, we present CAM, an alignment-free approach to recover phylogenies by comparing differences in codon aversion motifs (i.e., the set of unused codons within each gene) across all genes within a species. Synonymous codon usage is non-random and differs between organisms, between genes, and even within a single gene, where many genes do not use all possible codons. We report a comprehensive analysis of codon aversion within 229 742 339 genes from 23 428 species across all kingdoms of life, and we provide an alignment-free framework for its use in a phylogenetic construct. For each species, we first construct a set of codon aversion motifs spanning all genes within that species. We define the pairwise distance between two species, A and B, as one minus the number of shared codon aversion motifs divided by the total codon aversion motifs of the species, A or B, containing the fewest motifs. This approach allows us to calculate pairwise distances even when substantial differences in the number of genes or a high rate of divergence between species exists. Finally, we use neighbor-joining to recover phylogenies.
Results. Using the Open Tree of Life and NCBI Taxonomy Database as expected phylogenies, our approach compares well, recovering phylogenies that largely match expected trees and are comparable to trees recovered using maximum likelihood and other alignment-free approaches. Our technique is much faster than maximum likelihood and similar in accuracy to other alignment-free approaches. Therefore, we propose that codon aversion be considered a phylogenetically conserved character that may be used in future phylogenomic studies.
Availability. CAM, documentation, and test files are freely available on GitHub at https://github.com/ridgelab/cam
Background. Common phylogenomic approaches for recovering phylogenies are often time-consuming and require annotations for orthologous gene relationships that are not always available. In contrast, alignment-free phylogenomic approaches typically use structure and oligomer frequencies to calculate pairwise distances between species. We have developed an algorithm to quickly calculate distances between species based on codon aversion.Methods. Utilizing a novel alignment-free character state, we present CAM, an alignment-free approach to recover phylogenies by comparing differences in codon aversion motifs (i.e., the set of unused codons within each gene) across all genes within a species. Synonymous codon usage is non-random and differs between organisms, between genes, and even within a single gene, where many genes do not use all possible codons. We report a comprehensive analysis of codon aversion within 229 742 339 genes from 23 428 species across all kingdoms of life, and we provide an alignment-free framework for its use in a phylogenetic construct. For each species, we first construct a set of codon aversion motifs spanning all genes within that species. We define the pairwise distance between two species, A and B, as one minus the number of shared codon aversion motifs divided by the total codon aversion motifs of the species, A or B, containing the fewest motifs. This approach allows us to calculate pairwise distances even when substantial differences in the number of genes or a high rate of divergence between species exists. Finally, we use neighbor-joining to recover phylogenies.Results. Using the Open Tree of Life and NCBI Taxonomy Database as expected phylogenies, our approach compares well, recovering phylogenies that largely match expected trees and are comparable to trees recovered using maximum likelihood and other alignment-free approaches. Our technique is much faster than maximum likelihood and similar in accuracy to other alignment-free approaches. Therefore, we propose that codon aversion be considered a phylogenetically conserved character that may be used in future phylogenomic studies.Availability. CAM, documentation, and test files are freely available on GitHub at https://github.com/ridgelab/camBryophyte Phylogeny Poster (BPP)https://peerj.com/preprints/275712019-05-242019-05-24Theodor C H ColeHartmut H HilgerBernard Goffinet
Bryophyte Phylogeny Poster
This educational poster presents an overview of the evolutionary relationships among nonvascular land plants based on data published up to spring 2019. The phylogenetic tree depicts the divisions, subclasses, orders, and families of "bryophytes", listing the main apomorphies and plesiomorphies as well as diagnostic and nondiagnostic anatomical, morphological, and phytochemical features also for the higher ranks within the tree. The intuitive color-coding facilitates memorization and teaching. Translations are now available in 16 languages (all freely accessible via ResearchGate and other platforms). This is part of a series of educational posters on the phylogeny of land plants
Bryophyte Phylogeny PosterThis educational poster presents an overview of the evolutionary relationships among nonvascular land plants based on data published up to spring 2019. The phylogenetic tree depicts the divisions, subclasses, orders, and families of "bryophytes", listing the main apomorphies and plesiomorphies as well as diagnostic and nondiagnostic anatomical, morphological, and phytochemical features also for the higher ranks within the tree. The intuitive color-coding facilitates memorization and teaching. Translations are now available in 16 languages (all freely accessible via ResearchGate and other platforms). This is part of a series of educational posters on the phylogeny of land plantsEarly Agenian rhinocerotids from Wischberg (Canton Bern, Switzerland) and clarification of the systematics of the genus Diaceratheriumhttps://peerj.com/preprints/277352019-05-162019-05-16Claire JameJérémy TissierOlivier MaridetDamien Becker
Background. Wischberg is a Swiss locality in Bern Canton which has yielded numerous vertebrates remains from the earliest Miocene (= MN1). It has a very rich faunal diversity, one of the richest in Switzerland for this age. Among all the mammals reported in the original faunal list 70 years ago, three rhinocerotid species were identified. The material consists of two fragmentary skulls, cranial fragments, several mandibles, teeth and postcranial bones, in a rather good state of preservation.
Results. After reexamination of the material from this locality (curated in three different Swiss museums), and comparison with holotype specimens, we show that all rhinocerotid specimens from Wischberg can be referred to just two species. Most of the material can be attributed to the large size teleoceratine Diaceratherium lemanense, while only a few specimens, including a skull and mandible, belong to the much smaller sized Pleuroceros pleuroceros. We describe and illustrate for the first time most of these fossil remains. However, the systematics of the genus Diaceratherium is currently controversial, and we attempt to elucidate it based on our new observations, though a large-scale phylogenetic study should be done in the future to resolve it. The rhinocerotid association found in Wischberg is nonetheless typical of the MN1 biozone, which results from a faunal renewal occurring just before the end of the Oligocene.
Background. Wischberg is a Swiss locality in Bern Canton which has yielded numerous vertebrates remains from the earliest Miocene (= MN1). It has a very rich faunal diversity, one of the richest in Switzerland for this age. Among all the mammals reported in the original faunal list 70 years ago, three rhinocerotid species were identified. The material consists of two fragmentary skulls, cranial fragments, several mandibles, teeth and postcranial bones, in a rather good state of preservation.Results. After reexamination of the material from this locality (curated in three different Swiss museums), and comparison with holotype specimens, we show that all rhinocerotid specimens from Wischberg can be referred to just two species. Most of the material can be attributed to the large size teleoceratine Diaceratherium lemanense, while only a few specimens, including a skull and mandible, belong to the much smaller sized Pleuroceros pleuroceros. We describe and illustrate for the first time most of these fossil remains. However, the systematics of the genus Diaceratherium is currently controversial, and we attempt to elucidate it based on our new observations, though a large-scale phylogenetic study should be done in the future to resolve it. The rhinocerotid association found in Wischberg is nonetheless typical of the MN1 biozone, which results from a faunal renewal occurring just before the end of the Oligocene.Development of genomic simple sequence repeat markers for Glycyrrhiza lepidota and cross-amplification of other Glycyrrhiza specieshttps://peerj.com/preprints/276902019-04-292019-04-29Jun Hyoung BangChi Eun HongSebastin RaveendarKyong Hwan BangKyung Ho MaSoon Wook KwonHojin RyuIck Hyun JoJong Wook Chung
Background. Licorice (Glycyrrhiza spp. L.) is used as a natural sweetener and medicinal herb. Molecular studies have been conducted to find differences between wild and cultivated species because most wild species are highly resistant to abiotic and biotic stresses compared with their cultivated counterparts. However, few molecular markers have been developed for studying the genetic diversity and population structure of licorice species and to identify differences between cultivars. Thus, the present study aimed to develop a set of genomic simple sequence repeat (SSR) markers for molecular studies of these species.
Methods. We designed 100 SSR markers based on the whole-genome sequence data of wild Glycyrrhiza lepidota and selected 62 SSR markers.
Results. The genetic diversity analysis using these markers identified 2–23 alleles, and the major allele frequency, observed heterozygosity, genetic diversity, and polymorphism information content were 0.11–0.91, 0–0.90, 0.17–0.94, and 0.15–0.93, respectively. Interspecies transferability values were 93.5%, 91.6%, and 91.1% for G. echinata, G. glabra, and G. uralensis, respectively. Phylogenetic analysis clustered cultivated (group 1) and wild (group 2) species into three and two subgroups, respectively. The SSR markers developed here can be applied to genetic diversity, population structure, and cultivar differentiation studies, as well as to breeding of licorice varieties.
Background. Licorice (Glycyrrhiza spp. L.) is used as a natural sweetener and medicinal herb. Molecular studies have been conducted to find differences between wild and cultivated species because most wild species are highly resistant to abiotic and biotic stresses compared with their cultivated counterparts. However, few molecular markers have been developed for studying the genetic diversity and population structure of licorice species and to identify differences between cultivars. Thus, the present study aimed to develop a set of genomic simple sequence repeat (SSR) markers for molecular studies of these species.Methods. We designed 100 SSR markers based on the whole-genome sequence data of wild Glycyrrhiza lepidota and selected 62 SSR markers.Results. The genetic diversity analysis using these markers identified 2–23 alleles, and the major allele frequency, observed heterozygosity, genetic diversity, and polymorphism information content were 0.11–0.91, 0–0.90, 0.17–0.94, and 0.15–0.93, respectively. Interspecies transferability values were 93.5%, 91.6%, and 91.1% for G. echinata, G. glabra, and G. uralensis, respectively. Phylogenetic analysis clustered cultivated (group 1) and wild (group 2) species into three and two subgroups, respectively. The SSR markers developed here can be applied to genetic diversity, population structure, and cultivar differentiation studies, as well as to breeding of licorice varieties.