Taxonomic Sections Research Articles

Seasonal development rhythm of representatives of the genus <i>Spiraea</i> L. during introduction in the European North-East of Russia (Komi Republic)

Shrubs of the genus Spiraea L. are distinguished by a great variety of ornamental features, but are still underused in ornamental horticulture in the northern territories. The issues of passing the seasonal cycle of plants under new harsh climatic conditions remain fragmentarily studied. The research was aimed at examining the features and identifying patterns of the seasonal rhythm of introduced species of the genus Spiraea L. The research was carried out on the basis of the collection of the Botanical Garden of the Institute of Biology, located in the middle taiga subzone of Komi Republic. Plants to be observed included nine species of three taxonomic sections of the genus Spiraea L. The long-term averages of phenological phases and periods of seasonal rhythm of species, as well as variability of features based on the results of phenological observations for six years in the period 2013-2018 were determined. The vegetation period of plants under new conditions lasts up to 145 days and corresponds to the vegetation period of the introduction station. Shoot growth lasts from 65 to 80 days in different species. The sequence of flowering, differences in the dates of onset and duration of flowering in different Spiraea species of three sections were noted. The duration of the prefloral period ranges from 18 to 41 %, the flowering period – from 8 to 31 % of the total vegetation period of plants. The total duration of flowering of the studied species accounts for almost 100 days. The least variability is specific for the period of vegetation of species (variability index up to 5.9 %), the greatest variability – for the period of flowering of plants (variability – up to 26.7 %). The taxonomic factor (85-91 %) was revealed to influence the passage of the generative phases of the seasonal cycle. The correlation interaction was determined between the main phenophases and the early leaf fall phase. The seasonal type of growth and phenological development of Spiraea plants is characterized by an early beginning and end of vegetation, a relatively short period of growth of shoots, and the consistency of average phenological dates. This phenorhythm of the studied species of the genus Spiraea demonstrates their potential for ornamental gardening in the northern region.

A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE – ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES

Verbesina L. is a genus of the tribe Heliantheae, subtribe Verbesininae (Asteraceae), with distribution in the Americas, where Mexico and the Andes harbour the richest concentration of species. The approximately 325 species in the genus are shrubs, subshrubs, trees and rarely herbs. Despite its high species diversity and biogeographical importance, the only available phylogenetic hypothesis for Verbesina was based on chloroplast DNA restriction site data. In the present study, nuclear ITS and ETS DNA sequence data were used with an expanded taxon sampling, particularly among the South American Verbesina species, to improve phylogenetic resolution and support, clarify infrageneric relationships, and resolve biogeographical questions in the genus. The results of our new analysis corroborate the monophyly of Verbesina, but its current classification into 12 taxonomic sections, based on morphological characters such as phyllotaxis, head size, corolla colour, and presence of ray flowers, is not congruent with the molecular phylogeny, in which most sections are polyphyletic. We also show that Verbesina diverged in the late Miocene of North America, about 8 Ma. At least two independent Pleistocene dispersals into South America across the Isthmus of Panama and along the Southern Andes are evident, beginning around 3.23 Ma (1.27–3.23 Ma) in the Middle Pliocene, and resulting in an extra-Amazonian distribution of the genus inSouth America. Diversification in South America began around 2.83 Ma with occupation of the Andes. Colonisation of Brazil is estimated to have occurred around 2.15 Ma, from Andean lineages.

Evolution of Cherries (Prunus Subgenus Cerasus) Based on Chloroplast Genomes

Cherries (Prunus Subgenus Cerasus) have economic value and ecological significance, yet their phylogeny, geographic origin, timing, and dispersal patterns remain challenging to understand. To fill this gap, we conducted a comprehensive analysis of the complete chloroplast genomes of 54 subg. Cerasus individuals, along with 36 additional genomes from the NCBI database, resulting in a total of 90 genomes for comparative analysis. The chloroplast genomes of subg. Cerasus exhibited varying sizes and consisted of 129 genes, including protein-coding, transfer RNA, and ribosomIal RNA genes. Genomic variation was investigated through InDels and SNPs, showcasing distribution patterns and impact levels. A comparative analysis of chloroplast genome boundaries highlighted variations in inverted repeat (IR) regions among Cerasus and other Prunus species. Phylogeny based on whole-chloroplast genome sequences supported the division of Prunus into three subgenera, I subg. Padus, II subg. Prunus and III subg. Cerasus. The subg. Cerasus was subdivided into seven lineages (IIIa to IIIg), which matched roughly to taxonomic sections. The subg. Padus first diverged 51.42 Mya, followed by the separation of subg. Cerasus from subg. Prunus 39.27 Mya. The subg. Cerasus started diversification at 15.01 Mya, coinciding with geological and climatic changes, including the uplift of the Qinghai–Tibet Plateau and global cooling. The Himalayans were the refuge of cherries, from which a few species reached Europe through westward migration and another species reached North America through northeastward migration. The mainstage of cherry evolution was on the Qing–Tibet Plateau and later East China and Japan as well. These findings strengthen our understanding of the evolution of cherry and provide valuable insights into the conservation and sustainable utilization of cherry’s genetic resources.

Allele mining of eukaryotic translation initiation factor genes in Prunus for the identification of new sources of resistance to sharka

Members of the eukaryotic translation initiation complex are co-opted in viral infection, leading to susceptibility in many crop species, including stone fruit trees (Prunus spp.). Therefore, modification of one of those eukaryotic translation initiation factors or changes in their gene expression may result in resistance. We searched the crop and wild Prunus germplasm from the Armeniaca and Amygdalus taxonomic sections for allelic variants in the eIF4E and eIFiso4E genes, to identify alleles potentially linked to resistance to Plum pox virus (PPV). Over one thousand stone fruit accessions (1397) were screened for variation in eIF4E and eIFiso4E transcript sequences which are in single copy within the diploid Prunus genome. We identified new alleles for both genes differing from haplotypes associated with PPV susceptible accessions. Overall, analyses showed that eIFiso4E is genetically more constrained since it displayed less polymorphism than eIF4E. We also demonstrated more variations at both loci in the related wild species than in crop species. As the eIFiso4E translation initiation factor was identified as indispensable for PPV infection, a selection of ten different eIFiso4E haplotypes along 13 accessions were tested by infection with PPV and eight of them displayed a range of reduced susceptibility to resistance, indicating new potential sources of resistance to sharka.

Arachis species: High‐quality forage crops—nutritional properties and breeding strategies to expand their utilization and feeding value

AbstractPlants of the genus Arachis originated from South America and are cultivated worldwide. The genus Arachis contains 83 species and nine intrageneric taxonomic sections. The cultivated peanut (Arachis hypogaea L.) belongs to the Arachis section, the forage peanut (Arachis pintoi Krapov. & W. C. Greg.) belongs to the Caulorrhizae section, and the perennial peanut (Arachis glabrata Benth.) belongs to the Rhizomatosae section. These three peanut species have been developed for use as fodder crops. This review summarizes the forage value of Arachis species. Forage and perennial peanuts can be intercropped with forage species to feed livestock. The cultivated peanut vines and peanut by‐products, such as peanut skins and peanut meal, are also high‐quality fodder used to feed sheep, cattle, and poultry. A major limiting factor in terms of adopting forage and perennial peanuts as forage crops is their limited resistance to frosts, resulting from their low winter hardiness. Therefore, the feeding value of cultivated peanuts is higher compared to forage and perennial peanuts. This review suggests that Arachis is a suitable forage crop, focusing on their nutritional properties and breeding to increase their performance under cultivation and feeding value.

Repeated evolution of pollination syndromes in a highly diverse bromeliad lineage is correlated with shifts in life form and habitat

AbstractMutualistic plant-pollinator interactions play a critical role in the diversification of flowering plants. The spatiotemporal correlates of such interactions can be understood in a phylogenetic context. Here, we generate ddRAD-seq data for the highly diverse Vriesea-Stigmatodon lineage to test for correlated trait evolution among pollination syndromes and life form, habitat type, and altitude. Our results show that pollination syndromes are correlated with changes in life form and habitat type. The ancestor of the Vriesea-Stigmatodon lineage was likely bat pollinated, rock dwelling and inhabited open, mid-elevation forests. Transitions from bat to hummingbird pollination are correlated with transitions to the epiphytic life form in shaded habitats, whereas bat pollination is correlated with the rock-dwelling life form and open habitats. Our dated phylogenetic tree reveals independent origins of hummingbird pollination, occurring twice in Vriesea at c. 5.8 and 5.4 Mya. The timing for the shifts in pollination syndrome coincides with geological and environmental transformations across the Serra do Mar Mountain Chain, which increased habitat heterogeneity where Vriesea and their mutualists diversified. The phylogenetic tree reinforces the non-monophyly of taxonomic sections within the genus Vriesea previously defined by flower morphology, indicating that some lineages should be treated as species complexes. This study identifies synergetic drivers of speciation in a tropical biodiversity hotspot.

Detection and quantification of the histone code in the fungal genus Aspergillus

In eukaryotes, the combination of different histone post-translational modifications (PTMs) – the histone code – impacts the chromatin organization as compact and transcriptionally silent heterochromatin or accessible and transcriptionally active euchromatin. Although specific histone PTMs have been studied in fungi, an overview of histone PTMs and their relative abundance is still lacking. Here, we used mass spectrometry to detect and quantify histone PTMs in three fungal species belonging to three distinct taxonomic sections of the genus Aspergillus (Aspergillus niger, Aspergillus nidulans (two strains), and Aspergillus fumigatus). We overall detected 23 different histone PTMs, including a majority of lysine methylations and acetylations, and 23 co-occurrence patterns of multiple histone PTMs. Among those, we report for the first time the detection of H3K79me1, H3K79me2, and H4K31ac in Aspergilli. Although all three species harbour the same PTMs, we found significant differences in the relative abundance of H3K9me1/2/3, H3K14ac, H3K36me1 and H3K79me1, as well as the co-occurrence of acetylation on both K18 and K23 of histone H3 in a strain-specific manner. Our results provide novel insights about the underexplored complexity of the histone code in filamentous fungi, and its functional implications on genome architecture and gene regulation.

Clinical Treatments of Various Diseases with The Root of Astragalus Membranaceus

Astragalus L., is one of the largest genuses of flowering plants in the Leguminosae family. As annual or perennial herbs, sub shrubs, or shrubs, the plants of Astragalus L. are widely distributed throughout the temperate and arid regions. So far, the genus has been estimated to contain 2000–3000 species and more than 250 taxonomic sections in the world. Astragalus can significantly improve motor and memory impairment following D-galactose induced senescence in mice, which suggests anti-aging effects and possibly a delay in senility of middle-aged mice. The root of A. membranceus (Fisch.) Bge. var. mongholicus (Bge.) Hsiao (Radix Astragali) is a precious medicine in TCM, which has the properties of intensifying phagocytosis of reticuloendothelial systems, stimulating pituitary-adrenal cortical activity, and restoring depleted red blood cell formation in bone marrow. Clinically, it is used to treat chronic phlegmatic disorders and general gastrointestinal disturbances including stomach ulcers and diarrhea. It has been used in traditional Chinese medicine (TCM) in the treatment of various renal diseases for over 2000 years and was recorded in Shen Nong’s Materia Medica, which was written in the Han dynasty. Also, it is famed for its antimicrobial, antiperspirant, anti-inflammatory, diuretic and tonic effects. Some plants in the Astragalus genus are well known for their pharmacological properties, particularly hepatoprotective, immunostimulant, and antiviral activities. While, the most common use of this genus is as forage for livestock and wild animals, some plants in this genus have been recognized as being used in foods, medicines, cosmetics, as substitutes for tea or coffee, or as sources of vegetable gums. Saponins, flavonoids, and polysaccharides are believed to be the principle active constituents of Astragalus. This herb possesses tonic, hepatoprotective, diuretic, and expectorant properties and has been shown to exhibit immunomodulating, antihyperglycemic, and antiviral activities, among others. Traditionally, it was used to treat weakness, wounds, anemia, fever, multiple allergies, chronic fatigue, and loss of appetite, uterine bleeding, and uterine prolapse. The plants have also been used for treatment of diabetes, nephritis, leukemia, stomach ulcers, hypertension and chronic bronchitis.

Genetic relationships of Arachis (Fabaceae) accessions based on microsatellite markers

The genus Arachis is endemic to South America and contains 83 described species assembled into nine taxonomical sections. The section Arachis is of particular interest because it includes the cultivated peanut (A. hypogaea) and its closely related wild species. In this study, we used 26 microsatellite markers to analyze the genetic variability and relationships of some recently collected germplasm accessions of species in the Arachis section, with emphasis on the B genome species. The knowledge of the genetic relationships among species and accessions is necessary for a more efficient management of germplasm collections and use of wild species for crop improvement. This is especially important for the B genome species, as only one accession of A. ipaënsis, the B genome donor to the allotetraploid A. hypogaea (AABB), is available in germplasm collections worldwide. The results shed more light on the genetic relationships between accessions of A. ipaënsis, A. gregoryi, A. magna, A. valida and A. williamsii, what expands the number of accessions for incorporation of useful genes from the species associated with the peanut B genome. The analyses also showed a generally high level of intraspecific genetic variability, but usually grouped the accessions according to their genome types and species. However, accessions of some species did not group as expected, and these results suggest the need of further taxonomic revision of a few taxa, especially some accessions of A. gregoryi, A. magna and A. kuhlmannii and the circumscriptions of sections Erectoides and Procumbentes.

Biogeography of the Sunda Shelf revisited: Insights from Macaranga section Pruinosae (Euphorbiaceae)

The Southeast Asian region of Sundaland is among the world’s major biodiversity hotspots. The region’s biodiversity coupled with its complex and dynamic geographic and climatic histories makes it an ideal region to study the various factors that determine the diversification and distribution patterns of tropical biota. Here we investigate the biogeographic patterns in the partly myrmecophyticMacarangasectionPruinosaeto reveal some of the factors that play a role in determining the distribution of biota in Sundaland. We used single nucleotide polymorphisms (SNP) data derived from GBS, a next generation sequencing technique, in maximum likelihood and cluster analyses to determine phylogenetic relationships and population structures within this taxonomic section. Bayesian inference based on secondary calibration points and ancestral area reconstruction analyses were performed to infer spatial–temporal origins of the major lineages in the section. The results from these analyses were further substantiated using nuclear microsatellite data obtained from a broader sample set of two widely distributed species within the section:Macaranga giganteaandMacaranga pruinosa. Phylogenetic and cluster analyses reveal four well-defined, discrete species groups within sectionPruinosae, all of which but one originated in Borneo with the crown node dated at 3.58 mya. Biogeographic patterns within the species reveal a biogeographic barrier between east and west Sundaland besides bringing to light the role played by various geological factors, especially the Crocker Range, on Borneo. Patterns also reveal a biogeographic barrier between the Bangka/Belitung islands and Sumatra for ant-free, swamp-adapted species. This study provides evidence that geographic barriers, edaphic conditions, and ecological adaptations are tightly linked and that their mutual interaction determines the diversification and distribution of species.

Chlorophyll Pigment and Leaf Macronutrient Trait Variation of Four Salix Species in Elevated CO2, under Soil Moisture Stress and Fertilization Treatments

Leaf chlorophyll pigment and macronutrient concentrations were quantified for four willow species (Salix cordata (COR), S. discolor (DIS), S. eriocephala (ERI) and S. interior (INT)) while growing under 2 × 2 factorial of ambient and elevated CO2 and well-watered and drought-stressed soil moisture treatments (Expt. 1). After the first year, we saw no difference in stem biomass between CO2 treatments. In the following year, a second experiment was conducted on a subset of well-watered willows as a 2 × 2 factorial of atmospheric CO2 and soil fertilization (FERT). For both years of Expt. 1, chlorophyll a, b, a + b (TCC) and carotenoids (CAR) significantly downregulated in response to elevated CO2 (eCO2) and upregulated in response to drought (DRT). In Expt. 2, FERT mitigated CO2 downregulation of TCC and CAR, and upregulated TCC and CAR. Across species, ERI had the greatest pigment concentrations followed by either COR or DIS. Except for one case, INT had the lowest pigment concentrations. A significant species x FERT interaction was due to magnitude effects. The CHLa:b ratio was not affected by CO2 or DRT but did increase in response to FERT. INT had the greatest CHLa:b ratio followed by DIS, then either ERI or COR. In the second year, TCC:CAR ratio decreased in response to eCO2 and increased in response to DRT and FERT. In Expt. 1, leaf N was the only nutrient to significantly downregulate in response to eCO2; whereas all other nutrient levels remained unchanged. In response to DRT, leaf N and Mg upregulated; whereas leaf P, K, and Ca were downregulated. In response to eCO2 in Expt. 2, again only leaf N downregulated; whereas all other nutrients remained unchanged. All leaf nutrients upregulated in response to FERT. Of the four species, INT had the greatest leaf N and K, and the lowest Ca. Species variation was important, but so to was clonal variation in response to change. Indeed, INT leaf chlorophyll and macronutrients are significantly different or segregated from the other three willow species and this may be related to the evolutionary origins of INT, and other species of the taxonomic section Longifoliae, in the arid southwest USA and Mexico. Furthermore, under low nutrient conditions, it may be necessary to fertilize the plants to see a biomass response to eCO2.

Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi.

The fungal genus Aspergillus contains a diversity of species divided into taxonomic sections of closely related species. Section Flavi contains 33 species, many of industrial, agricultural, or medical relevance. Here, we analyze the mitochondrial genomes (mitogenomes) of 20 Flavi species-including 18 newly assembled mitogenomes-and compare their evolutionary history and codon usage bias patterns to their nuclear counterparts. Codon usage bias refers to variable frequencies of synonymous codons in coding DNA and is shaped by a balance of neutral processes and natural selection. All mitogenomes were circular DNA molecules with highly conserved gene content and order. As expected, genomic content, including GC content, and genome size differed greatly between mitochondrial and nuclear genomes. Phylogenetic analysis based on 14 concatenated mitochondrial genes predicted evolutionary relationships largely consistent with those predicted by a phylogeny constructed from 2,422 nuclear genes. Comparing similarities in interspecies patterns of codon usage bias between mitochondrial and nuclear genomes showed that species grouped differently by patterns of codon usage bias depending on whether analyses were performed using mitochondrial or nuclear relative synonymous usage values. We found that patterns of codon usage bias at gene level are more similar between mitogenomes of different species than the mitogenome and nuclear genome of the same species. Finally, we inferred that, although most genes-both nuclear and mitochondrial-deviated from the neutral expectation for codon usage, mitogenomes were not under translational selection while nuclear genomes were under moderate translational selection. These results contribute to the study of mitochondrial genome evolution in filamentous fungi.

Morphometric analysis and genetic diversity in Hypericum L. using sequence related amplified polymorphism

There are about 484 species of Hypericum in the Guttiferae family, which includes Hypericoideae. In Iran, species of this genus are mainly found in the north, northwest, and center of the country, and they are key contributors to the floral elements of the Hyrcanian mountains, Irano-Turanian, and Mediterranean regions (such as the Zagros). Medicinal, commercial, and horticultural values are associated with these plants.The genetic diversity was assessed through Sequence-related amplified polymorphism. To uncover genetic diversity and species characteristics in Hypericum species, were studied through a combination of morphological and molecular data. Eighty-five individuals related to 7 Hypericum were collected in 6 provinces. A total of 76 (Number of total loci) (NTL) DNA bands were produced through polymerase chain reaction amplifications (PCR) amplification of seven Hypericum species. These bands were produced with the combinations of 5 selective primers. The total number of amplified fragments ranged from 10 to 20. According to the SRAP (Sequence-related amplified polymorphism) markers analysis, H. perforatum and H. asperulum had the lowest similarity. This study also detected a significant signature of isolation by distance (Mantel test results). Present results showed that sequence-related amplified polymorphism have the potential to identify and decipher genetic affinity in Hypericum species. Current results have implications in biodiversity and conservation programs. Besides this, present results could pave the way for selecting suitable ecotypes for forage and pasture purposes in Iran. Genus Hypericum (Guttiferae, Hypericoideae) is perennial, belonging to the Hypericaceae family, having 484 species in forms of trees, shrubs, and herbs, distributed in 36 taxonomic sections. The genetic diversity was assessed through Sequence-related amplified polymorphism. To uncover genetic diversity and species characteristics in Hypericum species, were studied through a combination of morphological and molecular data. Eighty-five individuals related to 7 Hypericum were collected in 6 provinces. A total of 76 (Number of total loci) (NTL) DNA bands were produced through polymerase chain reaction amplifications (PCR) amplification of seven Hypericum species. These bands were produced with the combinations of 5 selective primers. The total number of amplified fragments ranged from 10 to 20. According to the SRAP (Sequence-related amplified polymorphism) markers analysis, H. perforatum and H. asperulum had the lowest similarity. This study also detected a significant signature of isolation by distance (Mantel test results). Present results showed that sequence-related amplified polymorphism have the potential to identify and decipher genetic affinity in Hypericum species. Current results have implications in biodiversity and conservation programs. Besides this, present results could pave the way for selecting suitable ecotypes for forage and pasture purposes in Iran.

Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species.

Opposing changes in the abundance of satellite DNA and long terminal repeat (LTR) retroelements are the main contributors to the variation in genome size and heterochromatin amount in Arachis diploids. The South American genus Arachis (Fabaceae) comprises 83 species organized in nine taxonomic sections. Among them, section Arachis is characterized by species with a wide genome and karyotype diversity. Such diversity is determined mainly by the amount and composition of repetitive DNA. Here we performed computational analysis on low coverage genome sequencing to infer the dynamics of changes in major repeat families that led to the differentiation of genomes in diploid species (x = 10) of genus Arachis, focusing on section Arachis. Estimated repeat content ranged from 62.50 to 71.68% of the genomes. Species with different genome composition tended to have different landscapes of repeated sequences. Athila family retrotransposons were the most abundant and variable lineage among Arachis repeatomes, with peaks of transpositional activity inferred at different times in the evolution of the species. Satellite DNAs (satDNAs) were less abundant, but differentially represented among species. High rates of evolution of an AT-rich superfamily of satDNAs led to the differential accumulation of heterochromatin in Arachis genomes. The relationship between genome size variation and the repetitive content is complex. However, largest genomes presented a higher accumulation of LTR elements and lower contents of satDNAs. In contrast, species with lowest genome sizes tended to accumulate satDNAs in detriment of LTR elements. Phylogenetic analysis based on repetitive DNA supported the genome arrangement of section Arachis. Altogether, our results provide the most comprehensive picture on the repeatome dynamics that led to the genome differentiation of Arachis species.

Morphological and Molecular Evidence Support Elevating Erythroxylum macrophyllum var. savannarum (Erythroxylaceae) to Specific Status

Abstract— Erythroxylum macrophyllum is a morphologically variable and widely distributed species complex in Central and South America with several sub-specific taxa and numerous species included in its synonymy. A single variety grows in the Colombo-Venezuelan savanna region which can be distinguished from the rest of the E. macrophyllum complex by the size of leaves, cataphyll and stipule characteristics, and shape of calyx lobes. A molecular phylogeny reconstructed from 519 nuclear genes also reveals that the savanna variety is more closely related to E. acuminatum and E. pauciflorum than E. macrophyllum. This phylogenomic evidence also suggests Erythroxylum sect. Macrocalyx, to which E. macrophyllum belongs, is a polyphyletic taxonomic section. We thus propose elevating this variety to specific status, as Erythroxylum savannarum. We provide an updated taxonomic description, information about its habitat and distribution, and justify its informal IUCN categorization of Near Threatened (NT).

Молекулярно-филогенетическое исследование рода Hypericum L. во флоре Азербайджана

Hypericum is one of the 100 largest flowering plant genera forming the family Hypericaceae Juss., which belongs to the clusioid clade of the Malpighiales. Hypericum is represented in Azerbaijan flora by 19 native species and 1 subspecies belonging to 7 taxonomic sections. The chloroplast DNA of 8 species from the genus was studied by PCR-RFLP analysis. Total genomic DNA was extracted from leaf tissue using the DNeasyPlantMini kit. (Qiagen Inc.; Valencia, CA, USA) following the supplied protocol and quanti field using a Nanodrop (Nanodrop Technologies; Wilmington, DE, USA) spectrophotometer. The article is part of an experimental study that comprises molecular-phylogenetic research of this genus in the flora of Azerbaijan.

Challenges of applying monophyly in the phylogenetic shallows: taxonomic reappraisal of the Dactylorhiza maculata group

SummaryThe first study of the taxonomically critical European orchid genus Dactylorhiza to use next-generation DNA sequencing generated the statistically best-supported reconstruction of its phylogeny to date. However, the two competing topologies obtained within the monophyletic Section Maculatae differed radically in the placement of the D. maculata s.s.–D. foliosa clade. Both topologies showed D. foliosa to be nested deeply within D. maculata s.s., and suggested that D. saccifera s.l. is paraphyletic, D. saccifera s.s. from south-eastern Europe and Asia Minor diverging before D. gervasiana from south-central Europe (a taxon typically viewed as a subspecies of D. saccifera or, more often, ignored completely). The poorly-sampled but character-rich morphometric comparison presented here suggests that D. saccifera s.s. and D. gervasiana cannot be distinguished with confidence using morphological characters and that, if D. gervasiana is accepted as a species, it is effectively cryptic. The diploid D. foliosa is accepted as an island endemic species, despite rendering paraphyletic the autotetraploid D. maculata s.s.; all other named taxa within the D. maculata s.s. clade are considered infraspecific. Dactylorhiza fuchsii is indisputably a bona fide species rather than a subspecies but it does not merit becoming the basis of a taxonomic section separate from D. maculata s.s. The strongly contrasting degrees of molecular vs morphological disparity reported here are representative of a more general trend evident in groups that have experienced comparatively recent speciation, as is the need to recognise occasional paraphyletic species when circumscribing species by integrating genotypic and phenotypic data categories. Explicit taxonomic criteria combined with a comparative, monographic approach are needed to achieve consistency of ranking. Disproving hypotheses of species status is judged a criminally underrated activity, actually being as important to outcomes as much-vaunted species "discovery".

Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization.

BackgroundHawthorn species (Crataegus L.; Rosaceae tribe Maleae) form a well-defined clade comprising five subgeneric groups readily distinguished using either molecular or morphological data. While multiple subsidiary groups (taxonomic sections, series) are recognized within some subgenera, the number of and relationships among species in these groups are subject to disagreement. Gametophytic apomixis and polyploidy are prevalent in the genus, and disagreement concerns whether and how apomictic genotypes should be recognized taxonomically. Recent studies suggest that many polyploids arise from hybridization between members of different infrageneric groups.MethodsWe used target capture and high throughput sequencing to obtain nucleotide sequences for 257 nuclear loci and nearly complete chloroplast genomes from a sample of hawthorns representing all five currently recognized subgenera. Our sample is structured to include two examples of intersubgeneric hybrids and their putative diploid and tetraploid parents. We queried the alignment of nuclear loci directly for evidence of hybridization, and compared individual gene trees with each other, and with both the maximum likelihood plastome tree and the nuclear concatenated and multilocus coalescent-based trees. Tree comparisons provided a promising, if challenging (because of the number of comparisons involved) method for visualizing variation in tree topology. We found it useful to deploy comparisons based not only on tree-tree distances but also on a metric of tree-tree concordance that uses extrinsic information about the relatedness of the terminals in comparing tree topologies.ResultsWe obtained well-supported phylogenies from plastome sequences and from a minimum of 244 low copy-number nuclear loci. These are consistent with a previous morphology-based subgeneric classification of the genus. Despite the high heterogeneity of individual gene trees, we corroborate earlier evidence for the importance of hybridization in the evolution of Crataegus. Hybridization between subgenus Americanae and subgenus Sanguineae was documented for the origin of Sanguineae tetraploids, but not for a tetraploid Americanae species. This is also the first application of target capture probes designed with apple genome sequence. We successfully assembled 95% of 257 loci in Crataegus, indicating their potential utility across the genera of the apple tribe.

Niche Shifts, Hybridization, Polyploidy and Geographic Parthenogenesis in Western North American Hawthorns (Crataegus subg. Sanguineae, Rosaceae)

We compare biogeographic and morphological parameters of two agamic complexes of western North American hawthorns so as to evaluate possible explanations of the differences in range between sexually reproducing taxa and their apomictic sister taxa. We have documented range, breeding system, morphology, leaf vascular architecture, and niche breadth in these hawthorns, for which phylogenetic relationships and ploidy levels are known. Species distribution data from herbarium specimens and online databases were analyzed in order to compare ranges and climate niches described by bioclimatic variables. Flow cytometry documented ploidy level and breeding system. Voucher specimens provided morphometric data that were analyzed using uni- and multivariate methods. Members of two black-fruited taxonomic sections of Crataegus subg. Sanguineae (sections Douglasianae, Salignae) have previously been identified as hybrids. They are presumptively self-fertile polyploids with pseudogamous gametophytic apomixis. Their morphologies, geographic ranges, and niche characteristics resemble those of their diploid, sexual parent or are intermediate between them and those of their other parent, one or both of two partially sympatric tetraploid apomicts in red-fruited C. subg. Americanae with much wider distributions. Comparing sections Douglasianae and Salignae suggests that geographic parthenogenesis (larger range sizes in apomicts, compared to sexually reproducing taxa) may have less to do with adaptation than it does with reproductive assurance in the pseudogamously apomictic and self-compatible hybrids. Greater climate niche breadth in allopolyploids compared to diploids similarly may be more due to parental traits than to effects of genome duplication per se.

On the availability of the recently proposed nomen Leptodactylus avivoca (Anura, Leptodactylidae)

In a recent contribution to the systematics of Leptodactylus Fitzinger, 1826 frogs endemic to the Brazilian campo rupestre (Carvalho et al. 2021), we revealed a genetically divergent lineage as an unnamed species distributed in the northern portion of the Espinhaço Mountain Range (EMR). The species was named and described as Leptodactylus avivoca in the taxonomic account section of the same paper, where a definition and diagnosis were provided to satisfy the provisions regarding the availability and validity of new nomina (see Chapters 4 and 6 of the International Code of Zoological Nomenclature, hereinafter the Code; Anonymous 1999). On that occasion, because of space limits imposed by the journal, we had to transfer most of the new species description into an Appendix, keeping in the main publication only the minimum requirements that would satisfy the rules and recommendations governed by the Code, thereby ensuring the availability and validity of the proposed new name. As a result of the transference from the main text to the Appendix, we ended up not taking notice that the species’ holotype had not been fixed in the main publication and appeared only as part of Appendix S1. Additionally, this Appendix was made available only as Online Supporting Material (Carvalho et al. 2021: Appendix S1) and not published alongside the main publication in the printed version. That rendered the proposition of Leptodactylus avivoca as originally published an atelonym (sensu Dubois 2011), i.e. an unavailable nomen (sensu Dubois 2000) as a consequence of the lack of explicit fixation of a holotype and statement of the collection where it was deposited in the main publication (Article 16.4 of the Code). In this paper, we intend to correct this nomenclatural oversight by proposing a new (homographic) nomen for the new Leptodactylus species, which corresponds to a genetic lineage endemic to the northern portion of the EMR, and also provide a definition and differential diagnosis in its own clade (L. plaumanni clade; sensu Carvalho et al. 2021).