Reconstruction Of Phylogenetic Relationships Research Articles

MAGinator enables accurate profiling of de novo MAGs with strain-level phylogenies.

Metagenomic sequencing has provided great advantages in the characterisation of microbiomes, but currently available analysis tools lack the ability to combine subspecies-level taxonomic resolution and accurate abundance estimation with functional profiling of assembled genomes. To define the microbiome and its associations with human health, improved tools are needed to enable comprehensive understanding of the microbial composition and elucidation of the phylogenetic and functional relationships between the microbes. Here, we present MAGinator, a freely available tool, tailored for profiling of shotgun metagenomics datasets. MAGinator provides de novo identification of subspecies-level microbes and accurate abundance estimates of metagenome-assembled genomes (MAGs). MAGinator utilises the information from both gene- and contig-based methods yielding insight into both taxonomic profiles and the origin of genes and genetic content, used for inference of functional content of each sample by host organism. Additionally, MAGinator facilitates the reconstruction of phylogenetic relationships between the MAGs, providing a framework to identify clade-level differences.

The evolutionary pathways of <i>Oxytropis</i> species of the section <i>Verticillares</i> at the center of the section origin

Genetic diversity and phylogenetic relationships of Oxytropis species from the section Verticillares were studied based on nucleotide polymorphism of cpDNA intergenic spacers psbA-trnH, trnL-trnF, and trnS-trnG at the center of the section origin (Baikal Siberia and adjacent territories of South Siberia, Mongolia, and China). Moreover, at the first time the reconstruction of phylogenetic relationships of species from section Verticillares based on the analysis of ITS nrDNA has been performed. The paper summarizes new samples and new data for unstudied species and populations. 84.4% populations of 11 species are characterized by a high level of chloroplast haplotype diversity (h varies from 0.700 to 1.000). The majority of populations (71.9%) have high haplotype diversity with low nucleotide diversity. Three haplogroups revealed in the genealogical network of chlorotypes indicate that there are different evolutionary pathways of the species included in these groups: divergence of genetically isolated taxa in the zone of sympatry presumably on the base of ecological specialization; incomplete lineage sorting with preserving of ancestral polymorphism in combination with hybridization of weakly diversified taxa; allopatric divergence and polyploidization. Analysis of markers of chloroplast and nuclear genomes testify the rapid adaptive radiation of Oxytropis section Verticillares.

The evolutionary pathways of <i>Oxytropis</i> species of the section <i>Verticillares</i> at the center of the section origin

Genetic diversity and phylogenetic relationships of Oxytropis species from the section Verticillares were studied based on nucleotide polymorphism of cpDNA intergenic spacers psbA-trnH, trnL-trnF, and trnS-trnG at the center of the section origin (Baikal Siberia and adjacent territories of South Siberia, Mongolia, and China). Moreover, at the first time the reconstruction of phylogenetic relationships of species from section Verticillares based on the analysis of ITS nrDNA has been performed. The paper summarizes new samples and new data for unstudied species and populations. 84.4% populations of 11 species are characterized by a high level of chloroplast haplotype diversity (h varies from 0.700 to 1.000). The majority of populations (71.9%) have high haplotype diversity with low nucleotide diversity. Three haplogroups revealed in the genealogical network of chlorotypes indicate that there are different evolutionary pathways of the species included in these groups: divergence of genetically isolated taxa in the zone of sympatry presumably on the base of ecological specialization; incomplete lineage sorting with preserving of ancestral polymorphism in combination with hybridization of weakly diversified taxa; allopatric divergence and polyploidization. Analysis of markers of chloroplast and nuclear genomes testify the rapid adaptive radiation of Oxytropis section Verticillares.

Comparative Analysis of the Complete Mitochondrial Genomes of Three Sisoridae (Osteichthyes, Siluriformes) and the Phylogenetic Relationships of Sisoridae.

The family Sisoridae is one of the largest and most diverse Asiatic catfish families, with most species occurring in the water systems of the Qinhai-Tibetan Plateau and East Himalayas. At present, the phylogenetic relationship of the Sisoridae is relatively chaotic. In this study, the mitochondrial genomes (mitogenomes) of three species Creteuchiloglanis kamengensis, Glaridoglanis andersonii, and Exostoma sp. were systematically investigated, the phylogenetic relationships of the family were reconstructed and to determine the phylogenetic position of Exostoma sp. within Sisoridae. The lengths of the mitogenomes' sequences of C. kamengensis, G. andersonii, and Exostoma sp. were 16,589bp, 16,531bp, and 16,529bp, respectively. They all contained one identical control region (D-loop), two ribosomal RNAs (rRNAs), 13 protein-coding genes (PCGs) and 22 transfer RNA (tRNA) genes. We applied two approaches, Bayesian Inference (BI) and Maximum Likelihood (ML), to construct phylogenetic trees. Our findings revealed that the topological structure of both ML and BI trees exhibited significant congruence. Specifically, the phylogenetic tree strongly supports the monophyly of Sisorinae and Glyptosternoids and provides new molecular biological data to support the reconstruction of phylogenetic relationships with Sisoridae. This study is of great scientific value for phylogenetic and genetic variation studies of the Sisoridae.

Genomic insights into the evolution, pathogenicity, and extensively drug-resistance of emerging pathogens Kluyvera and Phytobacter.

Kluyvera is a Gram-negative, flagellated, motile bacillus within the Enterobacteriaceae. The case reports of clinical infections shed light on the importance of this organism as an emerging opportunistic pathogen. The genus Phytobacter, which often be misidentified with Kluyvera, is also an important clinically relevant member of the Enterobacteriaceae. However, the identification of Kluyvera and Phytobacter is problematic, and their phylogenetic relationship remains unclear. Here, 81 strains of Kluyvera and 16 strains of Phytobacter were collected. A series of comparative genomics approaches were applied to the phylogenetic relationship reconstruction, virulence related genes profiles description, and antibiotic resistance genes prediction. Using average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH), we offered reliable species designations of 97 strains, in which 40 (41.24%) strains were incorrectly labeled. A new Phytobacter genomospecies-1 were defined. Phytobacter and Kluyvera show great genome plasticity and inclusiveness, which may be related to their diverse ecological niches. An intergenomic distances threshold of 0.15875 was used for taxonomy reassignments at the phylogenomic-group level. Further principal coordinates analysis (PCoA) revealed 11 core genes of Kluyvera (pelX, mdtL, bglC, pcak-1, uhpB, ddpA-2, pdxY, oppD-1, cptA, yidZ, csbX) that could be served as potential identification targets. Meanwhile, the Phytobacter specific virulence genes clbS, csgA-C, fliS, hsiB1_vipA and hsiC1_vipB, were found to differentiate from Kluyvera. We concluded that the evolution rate of Kluyvera was 5.25E-6, approximately three times higher than that of Phytobacter. Additionally, the co-existence of ESBLs and carbapenem resistance genes were present in approximately 40% strains, suggesting the potential development of extensively drug-resistant or even fully drug-resistant strains. This work provided a better understanding of the differences between closely related species Kluyvera and Phytobacter. Their genomes exhibited great genome plasticity and inclusiveness. They not only possess a potential pathogenicity threat, but also a risk of multi-drug resistance. The emerging pathogens Kluyvera and Phytobacter warrant close attention.

Molecular identification, risk factor assessment, and phylogenetic analysis of tick-borne pathogens in symptomatic and asymptomatic cattle from South-Eastern Iran.

Tick-borne pathogens (TBPs) represent a substantial threat to cattle globally, exerting adverse impacts on production, health, and economic viability. This study delves into the prevalence and implications of TTBPs in cattle sourced from resource-limited smallholder livestock farms situated in southeastern Iran, proximate to Afghanistan and Pakistan. Blood and tick specimens were systematically collected from a cohort of 230 cattle, comprising 150 asymptomatic and 80 symptomatic individuals. Genomic DNA isolated from blood samples underwent rigorous examination for the presence of key TBPs, including Anaplasma marginale, A. phagocytophilum, A. bovis, A. centrale, Babesia bigemina, and Theileria annulata, utilizing multiple genetic markers. Nucleotide sequence analysis facilitated the reconstruction of phylogenetic relationships. The study also evaluated various potential risk factors, such as clinical status, gender, age, breed, tick infestation, and management practices, to elucidate their associations with TTBPs. Among the cattle cohort, a staggering 87.8% (202/230) tested positive for at least one pathogen. Prevalence statistics encompassed A. marginale (72.2%), T. annulata (68.3%), A. phagocytophilum/A. platys-like complex (66.1%), A. centrale (16.7%), B. bigemina (10.0%), and A. bovis (6.1%). Remarkably, mixed infections involving two, three, and four pathogens were detected in 23%, 52.1%, and 2.2% of animals, respectively. Notably, all asymptomatic cattle were positive for at least one TBP. Tick infestation was observed in 62.2% (143/230) of cattle, predominantly caused by Hyalomma anatolicum (82.5%), Rhipicephalus (Boophilus) annulatus (13.1%), and R. sanguineus sensu lato (4.4%). Risk factors linked to TBPs encompassed tick infestation, older age, and crossbred animals. Clinical presentations among symptomatic cattle encompassed fever, anemia, weight loss, anorexia, jaundice, and enlarged superficial lymph nodes. This study underscores the pivotal role of asymptomatic carriers in the propagation of TTBPs within endemic regions. Furthermore, it emphasizes the potential for the implementation of molecular diagnostics to unmask subclinical infections, thereby affording the opportunity for targeted interventions aimed at ameliorating the burden of TTBPs in resource-constrained smallholder dairy farms.

Differentiated genomic footprints suggest isolation and long-distance migration of Hmong-Mien populations

BackgroundThe underrepresentation of Hmong-Mien (HM) people in Asian genomic studies has hindered our comprehensive understanding of the full landscape of their evolutionary history and complex trait architecture. South China is a multi-ethnic region and indigenously settled by ethnolinguistically diverse HM, Austroasiatic (AA), Tai-Kadai (TK), Austronesian (AN), and Sino-Tibetan (ST) people, which is regarded as East Asia’s initial cradle of biodiversity. However, previous fragmented genetic studies have only presented a fraction of the landscape of genetic diversity in this region, especially the lack of haplotype-based genomic resources. The deep characterization of demographic history and natural-selection-relevant genetic architecture of HM people was necessary.ResultsWe reported one HM-specific genomic resource and comprehensively explored the fine-scale genetic structure and adaptative features inferred from the genome-wide SNP data of 440 HM individuals from 33 ethnolinguistic populations, including previously unreported She. We identified solid genetic differentiation between HM people and Han Chinese at 7.64‒15.86 years ago (kya) and split events between southern Chinese inland (Miao/Yao) and coastal (She) HM people in the middle Bronze Age period and the latter obtained more gene flow from Ancient Northern East Asians. Multiple admixture models further confirmed that extensive gene flow from surrounding ST, TK, and AN people entangled in forming the gene pool of Chinese coastal HM people. Genetic findings of isolated shared unique ancestral components based on the sharing alleles and haplotypes deconstructed that HM people from the Yungui Plateau carried the breadth of previously unknown genomic diversity. We identified a direct and recent genetic connection between Chinese inland and Southeast Asian HM people as they shared the most extended identity-by-descent fragments, supporting the long-distance migration hypothesis. Uniparental phylogenetic topology and network-based phylogenetic relationship reconstruction found ancient uniparental founding lineages in southwestern HM people. Finally, the population-specific biological adaptation study identified the shared and differentiated natural selection signatures among inland and coastal HM people associated with physical features and immune functions. The allele frequency spectrum of cancer susceptibility alleles and pharmacogenomic genes showed significant differences between HM and northern Chinese people.ConclusionsOur extensive genetic evidence combined with the historical documents supported the view that ancient HM people originated from the Yungui regions associated with ancient “Three-Miao tribes” descended from the ancient Daxi-Qujialing-Shijiahe people. Then, some have recently migrated rapidly to Southeast Asia, and some have migrated eastward and mixed respectively with Southeast Asian indigenes, Liangzhu-related coastal ancient populations, and incoming southward ST people. Generally, complex population migration, admixture, and adaptation history contributed to the complicated patterns of population structure of geographically diverse HM people.

Mitochondrial genomes provide new insights into the phylogeny and evolution of Anthomyiidae (Insecta: Diptera)

Anthomyiidae is a cosmopolitan and diverse family of Calyptratae, and is routinely considered to play key roles in both ecology and agriculture. The higher-level phylogenetic classification of Anthomyiidae has been highly controversial, necessitating further molecular data for precise reconstruction of phylogenetic relationships. In this study, we successfully acquired and annotated 18 new mitogenomes of anthomyiids. Moreover, the mitogenomes of the following genera Eustalomyia, Hyporites, Leucophora, Emmesomyia and Eutrichota are reported for the first time. The 18 mitogenomes are compared with confamilial species to assess genetic variation and to better understand evolutionary relationships within the family Anthomyiidae. In comparisons among 13 mitochondrial protein coding genes (PCG), the calculation of evolutionary rate exhibited nad1 as the fastest evolving gene in Anthomyiidae. Among the anthomyiids investigated, cox2 and nad4 had the lowest genetic distance across the 13 PCGs, suggesting a high degree of conservation for these two genes. Herein, we conducted phylogenetic analyses of the newly sequenced mitogenomes along with 11 known anthomyiids to investigate the interrelationships of Anthomyiidae. Our results indicate that Anthomyiidae is a monophyletic lineage and sister group to Scathophagidae, confirming prior findings based on morphological and molecular analyses. We recovered two subfamilies as monophyletic (Myopininae, Pegomyinae) while Anthomyiinae was polyphyletic. The great species diversity of anthomyiid flies limits the availability of mitogenomes for accurately resolving the phylogeny of Anthomyiidae. Nonetheless, our study provides novel insight into the molecular taxonomy, evolution, and phylogeny of the family Anthomyiidae.

The First Record of Ocypode sinensis (Decapoda: Ocypodidae) from the Korean Peninsula: How the Complete Mitochondrial Genome Elucidates the Divergence History of Ghost Crabs

Ghost crabs, as a species of the Ocypode within the subfamily Ocypodinae, are distributed in the upper intertidal zone worldwide and are ecologically remarkable. They play an important role in the energy circulation in the intertidal zone and are used as an ecological indicator to predict the impacts of environmental change or anthropogenic activities on the marine ecosystem. In this study, we provide the first evidence for the distribution of O. sinensis in Jeju Island and the southern coastal area on the Korean Peninsula. We generated a high-fidelity mitochondrial genome (mitogenome) for the species. The mitogenome was assembled into a circular chromosome of 15,589 bp, including 13 protein-coding genes, two ribosomal RNA genes, and twenty-two transfer RNA genes. High genetic variation compared with closely related species enabled the precise reconstruction of phylogenetic relationships and an estimation of the divergence times among the Ocypode species. The phylogenetic inference indicated that O. sinensis forms a monophyletic clade with O. cordimanus and diverged from ancestral species approximately 20.41 million years ago.

Genomic Characteristion of Opportunistic Pathogen Kluyvera Reveals a Novel CTX-M Subgroup.

A rising incidence of clinical infections has been caused by Kluyvera, a significant opportunistic pathogen. Meanwhile, Kluyvera acts as an important reservoir of blaCTX-Ms, which are the dominant genes of class A extended-spectrum β-lactamases (ESBLs). In this work, 60 strains of Kluyvera were subjected to phylogenetic relationship reconstruction, antimicrobial susceptibility testing, and antibiotic resistance genes prediction. All mature blaCTX-Ms were gathered to perform subgroup reclassification. The findings demonstrate that Kluyvera has a large gene pool with significant genetic flexibility. Notably, 25% of strains showed simultaneous detection of ESBLs and carbapenem resistance genes. The genotypes of fourteen novel blaCTX-Ms were identified. A new subgroup classification approach for blaCTX-Ms was defined by using 20 amino acid site variants, which could split blaCTX-Ms into 10 subgroups. The results of the subgroup division were consistent with the phylogenetic clustering. More significantly, we proposed a novel blaCTX-M subgroup, KLUS, that is chromosomally encoded in K. sichuanensis and the new species put forward in this study, showing amino acid differences from the currently known sequences. Cloning and transformation tests demonstrated that the recipient bacteria had a robust phenotype of cefotaxime resistance. Closely related Kluyvera species had blaCTX-Ms in the same subgroup. Our research lays the groundwork for a deeper comprehension of Kluyvera and emphasizes how important a blaCTX-M reservoir it is. We provide an update on blaCTX-M subgroups reclassification from the aspects of phylogenetic relationship, amino acid differences, and the new subgroup KLUS, which needs to be strengthen monitored due to its strong resistance phenotype to cefotaxime.

Collection of X-ray micro computed tomography images of shells of planktic foraminifera with curated taxonomy

Calcite shells of planktic foraminifera (Protista, Rhizaria) constitute a large portion of deep-sea sediments. The shells are constructed by sequential addition of partly overlapping chambers with diverse shapes, resulting in complex shell architectures, which are genetically fixed and diagnostic at the species level. The characterisation of the complete architecture requires three-dimensional imaging of the shell, including the partially or entirely covered juvenile chambers. Here we provide reconstructed x-ray micro computed tomography image stacks of 179 specimens of extant planktic foraminifera collected from plankton tows, sediment traps and surface sediments. The specimens have fully resolved and curated taxonomy and represent 43 of the currently recognised 48 holoplanktic species and subspecies. The image stacks form a basis for further applications, such as the characterisation of the architectural morphospace of the extant taxa, allowing studies of species functional ecology, calcification intensity and reconstructions of phylogenetic relationships.

Genomic evidence sheds new light on phylogeny of Rhabdophis nuchalis (sensu lato) complex (Serpentes: Natricidae)

Stable taxonomy and robust phylogeny are essential for the evolution and conservation of organisms. The Rhabdophis nuchalis (sensu lato) complex presently contains three species (R. nuchalis, R. chiwen, R. pentasupralabialis). Although several studies have explored the diversity and phylogeography of this group, certain issues related to systematics and taxonomy remain unresolved. Here, based on genome-wide data, including single nucleotide polymorphisms (SNPs) generated from ddRAD-seq and mitochondrial DNA (mtDNA), we re-evaluated the phylogenetic relationships and cryptic diversity of this species group. Our results are generally consistent with previous studies but provide some new insights. Phylogenetic relationship reconstruction based on SNPs and mtDNA revealed that three species in the R. nuchalis (sensu lato) complex did not form a monophyly but each species is well supported as monophyletic lineage in SNP-based analyses. Population structure analyses showed genetic admixture between several species pairs. Additionally, the population in eastern Yunnan, China, was identified as a potential cryptic species and thus described as a new species based on morphological data. From our results and previous studies, we redefined the distribution boundary for each species in the R. nuchalis (sensu lato) species complex.

First mitogenome phylogeny of the sun bear Helarctos malayanus reveals a deep split between Indochinese and Sundaic lineages.

The sun bear Helarctos malayanus is one of the most endangered ursids, and to date classification of sun bear populations has been based almost exclusively on geographic distribution and morphology. The very few molecular studies focussing on this species were limited in geographic scope. Using archival and non-invasively collected sample material, we have added a substantial number of complete or near-complete mitochondrial genome sequences from sun bears of several range countries of the species' distribution. We here report 32 new mitogenome sequences representing sun bears from Cambodia, Thailand, Peninsular Malaysia, Sumatra, and Borneo. Reconstruction of phylogenetic relationships revealed two matrilines that diverged ~295 thousand years ago: one restricted to portions of mainland Indochina (China, Cambodia, Thailand; "Mainland clade"), and one comprising bears from Borneo, Sumatra, Peninsular Malaysia but also Thailand ("Sunda clade"). Generally recent coalescence times in the mitochondrial phylogeny suggest that recent or historical demographic processes have resulted in a loss of mtDNA variation. Additionally, analysis of our data in conjunction with shorter mtDNA sequences revealed that the Bornean sun bear, classified as a distinct subspecies (H. m. euryspilus), does not harbor a distinctive matriline. Further molecular studies of H. malayanus are needed, which should ideally include data from nuclear loci.

Complete Mitogenome of the Triplophysa bombifrons: Comparative Analysis and Phylogenetic Relationships among the Members of Triplophysa.

In the last decade, the phylogenetic relationships within the genus Triplophysa have become controversial, due to a lack of molecular data. The mitochondrial genome plays a vital role in the reconstruction of phylogenetic relationships and in revealing the molecular evolution of bony fishes. Herein, we obtained the complete mitogenome of Triplophysa bombifrons via HiFi reads of the Pacbio Sequel II system and DNBSEQ short-reads. We compared all available mitogenomes of the Triplophysa genus and reconstructed the phylogeny of Nemacheilidae, based on the mitogenomes, using maximum likelihood (ML) methods. The results show that the complete mitogenome sequence of T. bombifrons was circular and 16,568 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), 2 ribosomal RNA (rRNA), and a typical control region (D-loop). The most common start codons were ATG, except for cox1, and TAA/TAG were the stop codons for all PCGs. In total, 677 SNPs and 9 INDELs have been found by comparing the sequence divergence between this study and previous reports. Purity selection was found in all PCGs. Phylogeny was inferred by analyzing the 13 PCGs and the concatenated nucleotide sequences of 30 mitogenomes. The phylogenetic analyses based on the nucleotides of the 13 PCGs supported the assumption that the Triplophysa genus can be divided into 4 main clades and demonstrated that T. bombifrons and T. tenuis are closely related species for the first time. This study laid the foundation for further study on the mitogenome and phylogeny of Nemacheilidae fishes.

Comparative analysis of the complete plastid genomes in Prunus subgenus Cerasus (Rosaceae): Molecular structures and phylogenetic relationships.

Prunus subgenus Cerasus (cherry) is an economically important group that distributed in temperate regions of the northern hemisphere. However, shared interspecific morphological traits and variability across taxa of Cerasus are among the impediments to taxonomic efforts to correctly delimit taxa. This is further complicated by a lack of genetic information on these taxa, with no focused genomic or phylogenetic studies being done on Cerasus. In this study, we conducted comparative analysis on the complete plastid genomes (plastomes) of 20 Cerasus species to gain a greater understanding of the attributes of the plastome of these taxa while helping resolve their phylogenetic placement in Prunus sensu lato and interspecific relationships within the subgenus. Our results displayed that (1) the plastomes of the 20 Cerasus species studied exhibited a typical quadripartite structure with conversed genome arrangement, structure, and moderate divergence. (2) The average size of complete plastomes for the Cerasus taxa studied was 157,861 bp, ranging from 157,458 to 158,024 bp. A total of 134 genes were annotated, including 86 protein-coding genes, 40 tRNAs, and 8 rRNAs across all species. In simple sequence repeat analysis, we found Cerasus had a comparable number of dispersed and tandem repeats to those identified in other angiosperm taxa, with only P. pseudocerasus found to contain trinucleotide repeats. Nucleotide diversity analysis revealed that the trnG-GCC gene and rpl32-trnL region had the highest Pi value showing potential as phylogenetic markers. (3) Two phylogenetic trees of the plastomes verified the monophyletic relationship of Cerasus and provided a more resolved species-level phylogeny. Our study provides detailed plastome information for exploring the phylogeny of subg. Cerasus taxa. We identified various types of repeats and nucleotide diversity hotspots, which can be a reference for species identification and reconstruction of phylogenetic relationships.

Phylogeography of ancient and modern brown bears from eastern Eurasia.

The brown bear (Ursus arctos) is an iconic carnivoran species of the Northern Hemisphere. Its population history has been studied extensively using mitochondrial markers, which demonstrated signatures of multiple waves of migration, arguably connected with glaciation periods. Among Eurasian brown bears, Siberian populations remain understudied. We have sequenced complete mitochondrial genomes of four ancient (~4.5-40 kya) bears from South Siberia and 19 modern bears from South Siberia and the Russian Far East. Reconstruction of phylogenetic relationships between haplotypes and evaluation of modern population structure have demonstrated that all the studied samples belong to the most widespread Eurasian clade 3. One of the ancient haplotypes takes a basal position relative to the whole of clade 3; the second is basal to the haplogroup 3a (the most common subclade), and two others belong to clades 3a1 and 3b. Modern Siberian bears retain at least some of this diversity; apart from the most common haplogroup 3a, we demonstrate the presence of clade 3b, which was previously found mainly in mainland Eurasia and Northern Japan. Our findings highlight the importance of South Siberia as a refugium for northern Eurasian brown bears and further corroborate the hypothesis of several waves of migration in the Pleistocene.

The complete plastomes of red fleshed pitaya (Selenicereus monacanthus) and three related Selenicereus species: insights into gene losses, inverted repeat expansions and phylogenomic implications.

The online version contains supplementary material available at 10.1007/s12298-021-01121-z.

Genomic patterns and the evolutionary origin of an invasive fungal pathogen (Hymenoscyphus fraxineus) in Europe

In the 1990s, a highly pathogenic and invasive lineage of the Asian ascomycete Hymenoscyphus fraxineus appeared in Europe. Spreading across the continent, the fungal lineage devastates common ash (Fraxinus excelsior) populations and is a threat to ash species worldwide.In contrast to highly diverse reference populations in Japan and East Russia, the expanding European population is characterized by the persistence of a mosaic of two ancestral haplotypes, and presumed constraints to recombination. Four hypotheses were proposed for the evolutionary origin of the European lineage. The first hypothesis H1 states that two, and only two, pathogenic founder individuals were transferred from Asia to Europe and successfully established. Alternatively, in addition to the fungus arriving in Europe, a change in function might have occurred and only then the lineage became invasive. The cause of such a change might have been H2: one to two mutations during meiosis; H3: the lateral transfer of a European cytoplasmatic element modifying the behavior of H. fraxineus; or H4: a hybridization event with a closely related European ascomycete.Only the hybridization hypothesis seems to explain all of the genome-wide characteristics observed for the nuclear genome. Existing reconstructions of phylogenetic relationships at different taxonomic levels provide the evolutionary context of the lineages potentially involved. Vital information was gained from three configurations of nucleotide diversity and population differentiation associated with the genomic mosaic of monomorphic tracts and diversity islands.This synthesis points to the importance of identifying the taxonomic and geographic origins of the conserved two genomic ancestries within the European lineage of H. fraxineus and of reconstructing the mosaic of ancestral parental haplotypes (ancestry blocks) across the genome. Only with this information at hand will it be possible, to reliably interpret population-genomic data in the search for the functional elements underlying this unbalanced host-pathogen system.

An examination of nectar production in 34 species of Dendrobium indicates that deceptive pollination in the orchids is not popular

AbstractNectar, the most common floral reward, is generally used to determine whether an orchid species involves deceptive pollination. Estimates of the deceptive pollination systems with nectarless flowers have ranged from one quarter to one third of the nearly 30 000 species of orchids. These estimates, however, are biased towards temperate‐zone, usually terrestrial, orchids. Here we investigated nectar production and property in 34 epiphytic orchid species of the Southeast Asian genus Dendrobium. Twenty‐one species were observed producing nectar. The amount and sugar concentration (in bagged flowers) of 12 species varied from 0.45 to 2.78 μL and from 8.1% to 31.1%. The nectar was sucrose‐dominant, typical of bee‐pollinated flowers. Reconstruction of phylogenetic relationship indicated that transition of nectar secretion occurred in the genus. Spur length was positively correlated with flower size but species with relatively long spurs tended to produce small volume of nectar. Nectar production was strikingly variable among and within individuals in some species, suggesting that a vital measurement of bagged and fresh flowers is needed. Given that the quantitative measurement of nectar or floral reward in orchid species remains scarce, an estimate of deceptive pollination systems awaits further survey in diverse genera.

Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits.

Both universal and family-specific targeted sequencing probe kits are becoming widely used for reconstruction of phylogenetic relationships in angiosperms. Within the pantropical Ochnaceae, we show that with careful data filtering, universal kits are equally as capable in resolving intergeneric relationships as custom probe kits. Furthermore, we show the strength in combining data from both kits to mitigate bias and provide a more robust result to resolve evolutionary relationships. We sampled 23 Ochnaceae genera and used targeted sequencing with two probe kits, the universal Angiosperms353 kit and a family-specific kit. We used maximum likelihood inference with a concatenated matrix of loci and multispecies-coalescence approaches to infer relationships in the family. We explored phylogenetic informativeness and the impact of missing data on resolution and tree support. For the Angiosperms353 data set, the concatenation approach provided results more congruent with those of the Ochnaceae-specific data set. Filtering missing data was most impactful on the Angiosperms353 data set, with a relaxed threshold being the optimum scenario. The Ochnaceae-specific data set resolved consistent topologies using both inference methods, and no major improvements were obtained after data filtering. Merging of data obtained with the two kits resulted in a well-supported phylogenetic tree. The Angiosperms353 data set improved upon data filtering, and missing data played an important role in phylogenetic reconstruction. The Angiosperms353 data set resolved the phylogenetic backbone of Ochnaceae as equally well as the family specific data set. All analyses indicated that both Sauvagesia L. and Campylospermum Tiegh. as currently circumscribed are polyphyletic and require revised delimitation.