Neighbor-Net Network Research Articles

DNA barcoding and morphological identification of Astragalus in Iran: Advantages to molecular approach

Astragalus is a crucial forage plant in the rangelands of northeastern Iran. However, identifying different species of Astragalus can be challenging due to their overlapping morphological features. In this study, we aimed to determine the relationships between 12 Astragalus species using both morphological and molecular traits. We also evaluated the effectiveness of DNA barcoding as a tool for identifying rangeland species of Astragalus in Northeast Iran. We examined five DNA barcodes, including three cpDNA regions (trnH-psbA, rpl32-trnL(UAG), and matK) and two nuclear sequences (ITS and ETS). We found that the plastid markers (rpl32-trnL(UAG, matK) were the most effective in differentiating between species. We also found that morphological data, as represented by the Neighbor-Net network and UPGMA dendrogram, had the potential to separate Astragalus species. We identified matK as the best and most accurate marker for barcoding, as trnH-psbA had some defects due to sequence size and alignment issues. Our study highlights the importance of using barcoding for quick and accurate recognition of plant species and shows the plastid markers were the most effective in differentiating between species.

2180. Pseudomonas aeruginosa epidemic high-risk clones and their association with multidrug-resistant

Abstract Background Pseudomonas aeruginosa (PAE) is an opportunistic pathogen associated with a variety of hospital infections. Treatment of infections caused by PAE is challenging due to the emergence of multidrug-resistant (MDR), which is associated with increased morbidity, mortality, and healthcare costs. Clonal spread and the presence of resistance genes probably explain the successful propagation of MDR. In Ecuador, data on the molecular epidemiology, as well as circulating clones, are limited. Therefore, the objective of this study is to know the population structure of PAE by identifying clones in clinical samples in Quito-Ecuador. Methods A significant set (45) of randomly selected clinical PAE isolates, including multidrug and non-multidrug resistant isolates, were assigned to sequence types (STs) and compared them with their antibiotic susceptibility profile. The genetic diversity was assessed by applying the multilocus sequence typing (MLST) scheme (Figure 1) and the genetic relationships between different STs were corroborated by the phylogenetic neighbor-net network (Figure 2).Figure 1.Analysis of the allelic profiles using eBURST algorithm.Figure 2.Splits Tree showing the distribution of all the sequence types obtained for the clinical Pseudomonas aeruginosa isolates studied. The Splits Tree was based on the analysis of the allelic profiles of the acsA, aroE, guaA, mutL, nuoD, ppsA and trpE genes. Asterisk mark (*) indicates the MDR isolates Results The analysis of seven loci, acsA, aroE, guaA, mutL, nuoD, ppsA and trpE, identified 24 different ST and the most prevalent STs were ST-3750 and ST-253. A SplitsTree was constructed with all the isolates analyzed. The majority of the MDR isolates were included in ST-3750 and ST-253, also 3 singleton ST was identified in to MDR isolates. The 20 different ST was found to non-MDR isolates, and only 3 ST were found in more the one isolates. Conclusion The population structure of clinical PAE presents in these isolates indicate a significant association between MDR isolates and the clonal types: all ST-3750 and ST-253 isolates were MDR. ST-3750 is closely related strains to the ST111 (CC111), and ST-253 and ST111 are a group of successful high-risk clones and widely distributed worldwide. The multiresistant-isolates studied are grouped in the most prevalent sequence types found, and the susceptible isolates correspond mainly to singleton sequence types. Therefore, these high-risk clones and their association with multidrug resistance phenotypes are contributing to the spread of MDR in Quito-Ecuador. Disclosures Jeannete Zurita, n/a, Pfizer: Grant/Research Support

Phylogenetic and Evolutionary Analysis of Plant Small RNA 2'-O-Methyltransferase (HEN1) Protein Family.

HUA ENHANCER 1 (HEN1) is a pivotal mediator in protecting sRNAs from 3'-end uridylation and 3' to 5' exonuclease-mediated degradation in plants. Here, we investigated the pattern of the HEN1 protein family evolutionary history and possible relationships in the plant lineages using protein sequence analyses and conserved motifs composition, functional domain identification, architecture, and phylogenetic tree reconstruction and evolutionary history inference. According to our results, HEN1 protein sequences bear several highly conserved motifs in plant species retained during the evolution from their ancestor. However, several motifs are present only in Gymnosperms and Angiosperms. A similar trend showed for their domain architecture. At the same time, phylogenetic analysis revealed the grouping of the HEN1 proteins in the three main super clads. In addition, the Neighbor-net network analysis result provides some nodes have multiple parents indicating a few conflicting signals in the data, which is not the consequence of sampling error, the effect of the selected model, or the estimation method. By reconciling the protein and species tree, we considered the gene duplications in several given species and found 170 duplication events in the evolution of HEN1 in the plant lineages. According to our analysis, the main HEN1 superclass mostly showed orthologous sequences that illustrate the vertically transmitting of HEN1 to the main lines. However, in both orthologous and paralogs, we predicted insignificant structural deviations. Our analysis implies that small local structural changes that occur continuously during the folds can moderate the changes created in the sequence. According to our results, we proposed a hypothetical model and evolutionary trajectory for the HEN1 protein family in the plant kingdom.

Genome-Wide SNP Analysis Reveals the Genetic Diversity and Population Structure of the Domestic Reindeer Population (Rangifer tarandus) Inhabiting the Indigenous Tofalar Lands of Southern Siberia

Operating under the assumption that decline in population size increases the threat of loss of genetic diversity, herein, our first aim was to monitor and document the genetic diversity and population structure of the endemic Tuva–Tofalar reindeer, the number of which has seen a dramatic decrease. Second, we were interested in understanding of Tuva reindeer genetic relationship with four officially recognized reindeer breeds, whose wild populations inhabit the Far North of Russia, as well as with the domestic reindeer making up the Mongolian population. Our results, based on the genome-wide SNP genotypes generated by the BovineHD BeadChip, revealed a low level of genetic variability of Tuva population in terms of the values of both allelic and genetic diversity. The ADMIXTURE analysis, the PCA plot, and the Neighbor Net network results, showed that Tuva population shared genetic background with reindeer inhabiting Mongolia, an implication of their common origin. Moreover, all statistic approaches used in our study showed a distinctive shared genetic structure revealed in independent clusters found in the composition of: an admixed cluster of Tuvan and Mongolian populations, a cluster of domestic reindeer breeds, and a cluster of the wild populations—all of which indirectly points to the possibility of the independent origins (with regard to the domestication) of the reindeer groups studied herein. We believe that our findings will contribute to the formation of a rational basis for solving problems related to the conservation of domestic Tuva-Tofalar reindeer in order to increase the number of this substantial reindeer population which will contribute to the sustainable functioning of ecosystems and the lives and culture of indigenous peoples inhabiting the southern sections of Eastern Siberia.

Cultural macroevolution in the middle to late Holocene Arctic of east Siberia and north America

A fundamental debate in evolutionary theory concerns the scale of evolutionary process. For cultural evolution, it is well understood that cultural elements on the scales of basic units of information (i.e. how to manufacture a lithic tool) change over time. We also recognize change in more complexly integrated cultural traditions spanning composite technologies to the fundamentals of social and political systems. The question remains as to whether change in the latter entities is a byproduct of evolution on lower scales leading to blended higher level entities or if evolutionary process actually unfolds on higher integrated scales. This study poses a test of the opposing hypotheses that evolution acts on the highest (species-like) scale versus the lowest (ephemeral traits) scales using data from the Middle to late Holocene Siberian and American Arctic. Results of modelling using Bayesian phylogenetic and Neighbornet Network procedures suggest that two distinct Arctic cultures, termed Paleo-Inuit and Neo-Inuit, evolved as species-like entities. Once established each evolved further on lower scales leading to blended within-group outcomes. We argue that cultural evolution is best understood as a process that can simultaneously act on multiple scales.

Integrative taxonomy clarifies species limits in the hitherto monotypic passion‐vine butterfly genera Agraulis and Dryas (Lepidoptera, Nymphalidae, Heliconiinae)

AbstractThe Heliconiini genera Agraulis and Dryas are widely distributed throughout the Neotropics and into adjacent temperate regions, and although they are currently treated as monotypic, both show significant geographic phenotypic variation. In this work, we employ six genetic markers (4199 bp), two mitochondrial and four nuclear, to perform coalescent species delimitation analyses in Bayesian Phylogenetics and Phylogeography (BPP) and in integrated BPP (iBPP), the latter also includes linear measurements and wings landmarks. We also analyze cytochrome c oxidase I (COI) barcode sequences for each genus using genetic distances, haplotype networks and a character‐based approach. Based on the model testing results, complemented with data from previous studies, we performed morphometric analyses to compare fore and hindwing size, aspect ratio and shape among the new species. In addition, we compared the forewing spot pattern of hypothesizes species using the r package patternize and, for Dryas, compared the colour patterns of mature larvae. Model testing of the molecular species delimitation outputs favoured a seven species hypothesis for Agraulis and a four species hypothesis for Dryas. Average distances among COI barcode sequences of these groups were from 1.09 to 5.81% in Agraulis and from 1.09 to 3.44% in Dryas. Within‐group distances ranged from 0 to 1.11% and between 0 and 2.43%, respectively. NeighborNet haplotype networks showed that all but one of the species are monophyletic, and the character‐based approach found exclusive diagnostic positions for most species, while the rest can be recognized by unique combinations of the 44 informative nucleotide positions analysed. Morphometric analysis supported all species of Agraulis and Dryas based on wing shape, and also in several cases on wing sizes and aspect ratio (hindwing length–forewing length), including A. v. galapagensis, which was absent from the molecular study. The analysis of the forewing spot pattern also revealed differences among most species hypothesis. The colour pattern of the last instar larva is also diagnostic for each Dryas species hypothesis. Locality data for species in both genera show that most of them are allopatric albeit a few have contact zones being parapatric at some locations. Based on the observed genetic differences, which covary with morphology and geographical distribution, we recommend the recognition of eight species of Agraulis: A. incarnata, A. vanillae, A. forbesi new status, A. insularis reinstated status, A. maculosa new status, A. lucina reinstated status, A. galapagensis new status and one undescribed species, and four species of Dryas: D. iulia, D. dominicana revised status, D. lucia revised status and D. alcionea reinstated status. Further work is needed to investigate, which selective forces have led to the current configurations of venation and wing shape, the probable gene flow among species with a focus on Agraulis and gather more data on species ecology.LSIDurn: lsid: zoobank.org: pub: 9E8C9F6E‐91C3‐4FB2‐804D‐1A9C4BD2EABB.

'Candidatus Mycoplasma haematohydrochoerus', a novel hemoplasma species in capybaras (Hydrochoerus hydrochaeris) from Brazil.

Three different species of hemoplasmas have been described in rodents, Mycoplasma coccoides, 'Candidatus Mycoplasma haemomuris' and 'Candidatus Mycoplasma haemosphiggurus'. Additionally, potentially novel hemoplasma species have been detected in wild rodents from Brazil, including capybaras (Hydrochoerus hydrochaeris). Capybaras are the largest rodent in the world and are well adapted to live within close proximity to humans, which increases the risk to spread of zoonotic pathogens. Herein, we investigate the occurrence and genetic diversity of hemoplasmas infecting free-ranging capybaras from southern Brazil. Blood samples and ticks from 17 capybaras were collected. Packed cell volume and total plasma protein were measured, DNA was extracted, and further screened by species-specific and pan-hemoplasma PCR assays targeting the 16S rRNA gene of hemoplasmas. Sixteen out of 17 (94.12%; 95% CI: 73.02-98.95%) were anemic. Only one young female was hypoproteinemic. All capybaras were infested by adults and nymphs of Amblyomma dubitatum ticks. Using the PCR assay targeting the 16S rRNA gene of M. coccoides, 13/17 (76.47%; 95% CI: 52.74-90.44%) capybaras were positive for hemoplasmas. When DNA samples were tested by the pan-hemoplasma PCR, 16/17 (94.12%; 95% CI: 73.02-98.95%) animals were positive. One out of 11 (9.09%) adult ticks salivary glands tested positive for hemoplasma by the pan-hemoplasma PCR assay. Sequencing and phylogenetic analysis of the 16S and 23S rRNA gene fragments confirmed that animals were infected by a novel hemotropic Mycoplasma sp. previously reported in capybaras from Brazil. Additionally, sequencing and phylogenetic analysis of the 23S rRNA gene from three hemoplasma-positive capybaras samples from a previous study performed in midwestern Brazil also confirm our findings. Based on phylogenetic and Neighbor-Net network analysis of the 16S rRNA and 23S rRNA genes, the name 'Candidatus Mycoplasma haematohydrochoerus' is proposed for this novel organism.

A Microsatellite Genotyping-Based Genetic Study of Interspecific Hybridization between the Red and Sika Deer in the Western Czech Republic.

Simple SummaryThe sika deer is a very flexible invasive species, capable of living dynamically in both large forests and mixed environment characterized by a prevalence of agricultural land. The Japanese sika deer was introduced to the Czech Republic at the end of the 19th century. The success of an introduced alien species may consist in their hybridizing with closely related taxa. Where few barriers to gene flow exist, rapid introgression of genetic traits from one species into another frequently occurs. The current Czech sika populations embody the most abundant and expanding group in continental Europe. In western Bohemia, we confirmed the interspecific hybridization with the native red deer. In this context, the red deer gene pool is endangered. The animals proliferate steadily in all directions and will most probably spread all over the Czech Republic if no major, timely changes in game management are adopted.Although inter-species hybrids between the red and sika deer can be phenotypically determined only exceptionally, there is the eventuality of identification via molecular genetic analysis. We used bi-parentally inherited microsatellite markers and a Bayesian statistical framework to re-examine the proportion of hybrids in the Czech red and sika deer populations. In total, 123 samples were collected, and the nuclear dataset consisted of 2668 allelic values. The number of alleles per locus ranged from 10 (BM1818) to 22 (BM888 and T193), yielding the mean of 16 alleles per locus across the deer. The mean allelic diversity of the red deer markedly exceeded that of the Japanese sika deer. Interspecific hybrids were detected, enabling us to confirm the genetic introgression of the sika deer into the red deer populations and vice versa in western Bohemia. The mean hybrid score equaled 10.6%, with 14.3% of the hybrids being among red deer–like individuals and 6.7% among sika-like ones. At two western Bohemian locations, namely, Doupovské hory and Slavkovský les, the total percentages of hybrid animals equaled 18.8 and 8.9, respectively. No red deer alleles were detected in the sika populations of the subregions of Kladská, Žlutice, and Lány. The NeighborNet network clearly separated the seven red and sika deer sampling populations according to the geography. The knowledge gained from the evaluated data is applicable in hunting management to reduce hybridization with the European deer.

The gut microbiome of the Sunda pangolin (Manis javanica) reveals its adaptation to specialized myrmecophagy.

BackgroundThe gut microbiomes of mammals are closely related to the diets of their hosts. The Sunda pangolin (Manis javanica) is a specialized myrmecophage, but its gut microbiome has rarely been studied.MethodsUsing high-throughput Illumina barcoded 16S rRNA amplicons of nine fecal samples from nine captive Sunda pangolins, we investigated their gut microbiomes.ResultsThe detected bacteria were classified into 14 phyla, 24 classes, 48 orders, 97 families, and 271 genera. The main bacterial phyla were Firmicutes (73.71%), Proteobacteria (18.42%), Actinobacteria (3.44%), and Bacteroidetes (0.51%). In the PCoA and neighbor-net network (PERMANOVA: pangolins vs. other diets, weighted UniFrac distance p < 0.01, unweighted UniFrac distance p < 0.001), the gut microbiomes of the Sunda pangolins were distinct from those of mammals with different diets, but were much closer to other myrmecophages, and to carnivores, while distant from herbivores. We identified some gut microbiomes related to the digestion of chitin, including Lactococcus, Bacteroides, Bacillus, and Staphylococcus species, which confirms that the gut microbiome of pangolins may help them to digest chitin.SignificanceThe results will aid studies of extreme dietary adaption and the mechanisms of diet differentiation in mammals, as well as metagenomic studies, captive breeding, and ex situ conservation of pangolins.

Phylogeny and biogeography of the genus Hesperis (Brassicaceae, tribe Hesperideae) inferred from nuclear ribosomal DNA sequence data

Despite its complicated taxonomy, the genus Hesperis has not yet been subjected to any detailed molecular phylogenetic study and little is known about its monophyly, origin and biogeographical history, as well as the evolution of morphological characters. Here, we present for the first time comprehensive molecular analyses (nuclear ribosomal ITS sequences) of approximately 40 Hesperis species which represent the full range of morphological variation and the entire geographic distribution area of the genus. Based on our results, monophyly of the genus Hesperis has been proved. Moreover, our phylogenetic analysis shows that almost all traditionally defined sections are not monophyletic. NeighborNet network analysis was performed in order to visualize conflicting phylogenetic signals. The split-graph corresponds to the major clades represented in the consensus tree and revealed a hybridization signal in the evolutionary history of only a single Hesperis species. Divergence time estimations indicate that the origin of Hesperis (7.66–19.9 Mya) coincides with the expansion of grasslands and the closure of the proto-Mediterranean Sea in the middle Miocene. Therefore, diversification within Hesperis was affected by global climate changes, substantial tectonic rearrangements and the expansion of open vegetation systems in the Miocene, all of which had a great impact on the speciation history of the Irano-Turanian flora and fauna. Furthermore, two new species from West of Iran are described and illustrated here. They are readily distinguished from their closely related species by morphological characters such as stem height, leaf shape, pedicel, sepal and fruit indumentum, petal size, stigma shape and seed characters.

Do We Need to Identify Adaptive Genetic Variation When Prioritizing Populations for Conservation?

When prioritizing populations for conservation of a given species, it is unclear whether the distribution of standing genetic variation can be used as a suitable proxy for the distribution of useful adaptive genetic variation. We tested whether using genome-wide and putatively adaptive genetic variation give similar prioritization results. We identified adaptive loci via their association with either environmental factors or phenotypic traits using two genomic data sets: yellow warblers (Setophaga petechia) across North America and lodgepole pines (Pinus contorta) in western Canada. We measured pairwise differentiation among populations using a principal components analysis and used a phylogenetic approach (NeighborNet networks) coupled with a measure of evolutionary distinctiveness (Shapley value) to attribute a priority rank to each population. Overall, we found that prioritization rankings using adaptive variation alone were not significantly divergent from rankings based on genome-wide genetic variation. Our testing framework might be of immediate use to conservation practitioners collecting next-generation sequencing data, and we call for further investigation in other species. Our results suggest that we may not need to pursue the contingent step of identifying adaptive variation in species of concern before prioritizing populations, i.e. a naive approach of using genome-wide genetic variation might be a suitable proxy for identifying local adaptation.

Molecular and morphological investigation in Hymenocrater: species delimitation, relationship, divergence time and DNA barcoding

Hymenocrater comprises of 11 species throught the world. The genus is an Irano-Turanian elements, which has several usages in traditional medicine. Northeast of Iran is the main geographical region of Hymenocrater species. The aims of the peresent study was to delimit 11 species of Hymenocrater to determine the species relationships based on morphological and molecular data (cp-DNA sequence), to produce divergence time and to construct barcode gap using the internal transcribed sequence because of adulteration of this genus in local markets. According to the results, Neighbor-Net network and UPGMA dendrogram of morphological data can delimit Hymenocrater species. Meanwhile, analyses of Chloroplast sequences (psbA-trnH) revealed that the species relationship and delimitation are difficult and complicated due to gene flow, hybridization, gene duplication, reticulation and chloroplast capture. Divergence time of Hymenocrater species estimated from Bayesian Evolutionary Sampling Trees date were seven million years ago. The center origin of Hymenocrater in Iran is Razavi Khorasan. Genetic fingerprinting of correctly identified medicinal species provides standard for comparing plant specimens sold in the market with true to type medicinal plant. Therefore, ITS sequences are important for barcoding this medicinally significant plant. It is correctly identified medicinal species, which will be used as standard for evaluating market sold plants.

Genomic Characterization of the Istrian Shorthaired Hound.

Simple SummaryIstrian shorthaired hound is an old indigenous Croatian dog breed. However, there is no data available about its genetic diversity, population structure, and inbreeding level, which would be needed for advanced management and conservation of this breed. We studied the population structure using 220K SNP array and compared the genomic data with the genealogical records. This allowed us to place Istrian shorthaired hound on the map of the world dog populations. The Istrian shorthaired hound has a relatively high effective population size and low level of inbreeding. Its genome contains a higher number of short runs of homozygosity compared to other analysed breeds, thus confirming the old origin of the breed and balanced use of breeding animals. The breed was placed in the same clade with Italian hunting breeds suggesting that the Istrian shorthaired hound was probably used for the development of some of these breeds. The genomic analysis importantly contributes to the development of future breeding strategies and supports the conservation of the Istrian shorthaired hound.Istrian shorthaired hound is an old indigenous Croatian dog breed with historical traces of its origin, which date back to the 14th century. Due to its intelligence and great hunting abilities, it is considered an excellent hunting dog. Despite its ancient origin, there is no data on genetic diversity, population structure, and degree of inbreeding that could be used for advanced management and conservation of this breed. Our study aimed to provide a high-resolution population structure of the Istrian shorthaired hound using a 220K HD SNP array, to compare the obtained data with the genealogical records and to place the breed in a broader context of world dog populations. Relatively high population size and low inbreeding coefficient estimated from genealogical data indicate a preserved genetic diversity in this breed. The principle component analysis, the NeighborNet network, and TreeMix were used to determine the genetic relationship between the Istrian shorthaired hound and other breeds. The Istrian shorthaired hound was found to be genetically related to Italian hunting dogs sharing the same branch with the Segugio Italiano a Pelo Raso and Segugio Italiano a Pelo Forte. The ADMIXTURE analysis indicated that the Istrian shorthaired hound could be involved in the development of some other hunting dog breeds. The estimated effective population size (Ne) based on SNP data was similar to Ne calculated from genealogical data indicating the absence of bottlenecks and well-balanced use of breeding animals. The low genomic inbreeding coefficient, together with the higher number of short runs of homozygosity, observed in the Istrian shorthaired hound, confirms the ancient origin of the breed based on historical documents. The analysis of selective sweeps identified genomic regions with the strongest selection signals in the vicinity of the genes associated with cognitive performance and behavior. Genome analysis proved to be a useful tool for estimating population parameters and can be implemented in the conservation plan for this indigenous breed.

The molecular taxonomy of three endemic Central Asian species of Ranunculus(Ranunculaceae)

Worldwide, the genus Ranunculus includes approximately 600 species and is highly genetically diverse. Recent taxonomic reports suggest that the genus has a monophyletic origin, divided into two subgenera, and consists of 17 sections. The Central Asian country of Kazakhstan has 62 species of the genus that have primarily been collected in the central part of the country. The latest collection trips in southern parts of the country have led to the description of a wider distribution area for Ranunculus and the identification of a new species Ranunculus talassicus Schegol. et A.L. Ebel from Western Tien Shan. Therefore, in this study, attempts were made to assess the molecular taxonomic positions of R. talassicus and two other species endemic to the Central Asian region R. karkaralensis Schegol. and R. pskemensis V.N. Pavlov in relation to other species of the genus, using internal transcribed spacer (ITS) molecular genetic markers. The ITS-aligned sequences of 22 local Central Asian accessions and 43 accession sequences available in the National Center for Biotechnology Information (NCBI) database allowed the construction of a maximum parsimony phylogenetic tree and a Neighbor-Net network. The results indicated that R. talassicus and R. pskemensis could be assigned to section Ranunculastrum. Additionally, an assessment of the network suggested that R. pskemensis was the rooting taxon for the group of species containing R. talassicus, and that R. illyricus L. and R. pedatus Waldst. & Kit. were founders of a prime rooting node for the Ranunculastrum section of the genus. The ITS-aligned sequences showed that R. karkaralensis was indifferent with respect to three other species in the Ranunculus section of the genus, i.e., R. acris L., R. grandifolius C.A. Mey., and R. subborealis Tzvelev. The study indicated that the assessments of ITS-based phylogenetic tree and Neighbor-Net network provided new insights into the taxonomic positions of three endemic species from Central Asia.

Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides.

Plesiomonas shigelloides is an emerging pathogen that has been shown to be involved in gastrointestinal diseases and extraintestinal infections in humans. However, the taxonomic position, evolutionary dynamics, and pathogenesis of P. shigelloides remain unclear. We reported the draft genome sequences of 12 P. shigelloides strains representing different serogroups. We were able to determine a clear distinction between P. shigelloides and other members of Enterobacterales via core genome phylogeny, Neighbor-Net network, and average genome identity analysis. The pan-genome analysis of P. shigelloides revealed extensive genetic diversity and presented large flexible gene repertoires, while the core genome phylogeny exhibited a low level of clonality. The discordance between the core genome phylogeny and the pan-genome phylogeny indicated that flexible accessory genomes account for an important proportion of the evolution of P. shigelloides, which was subsequently characterized by determinations of hundreds of horizontally transferred genes (horizontal genes), massive gene expansions and contractions, and diverse mobile genetic elements (MGEs). The apparently high levels of horizontal gene transfer (HGT) in P. shigelloides were conferred from bacteria with novel properties from other taxa (mainly Vibrionaceae and Aeromonadaceae), which caused the historical taxonomic confusion and shaped the virulence gene pools. Furthermore, P. shigelloides genomes contain many macromolecular secretion system genes, virulence factor genes, and resistance genes, indicating its potential to cause intestinal and invasive infections. Collectively, our work provides insights into the phylogenetic position, evolutionary dynamic, and pathogenesis of P. shigelloides at the genomic level, which could facilitate the observation and research of this important pathogen.IMPORTANCE The taxonomic position of P. shigelloides has been the subject of debate for a long time, and until now, the evolutionary dynamics and pathogenesis of P. shigelloides were unclear. In this study, pan-genome analysis indicated extensive genetic diversity and the presence of large and variable gene repertoires. Our results revealed that horizontal gene transfer was the focal driving force for the genetic diversity of the P. shigelloides pan-genome and might have contributed to the emergence of novel properties. Vibrionaceae and Aeromonadaceae were found to be the predominant donor taxa for horizontal genes, which might have caused the taxonomic confusion historically. Comparative genomic analysis revealed the potential of P. shigelloides to cause intestinal and invasive diseases. Our results could advance the understanding of the evolution and pathogenesis of P. shigelloides, particularly in elucidating the role of horizontal gene transfer and investigating virulence-related elements.

Taming the Red Bastards: Hybridisation and species delimitation in the Rhodanthemum arundanum-group (Compositae, Anthemideae)

Delineating species boundaries in a group of recently diverged lineages is challenging due to minor morphological differences, low genetic differentiation and the occurrence of gene flow among taxa. Here, we employ traditional Sanger sequencing and restriction-site associated DNA (RAD) sequencing, to investigate species delimitation in the close-knit Moroccan daisy group around Rhodanthemum arundanum B.H.Wilcox & al. that diverged recently during the Quaternary. After evaluation of genotyping errors and parameter optimisation in the course of de-novo assembly of RADseq reads in Ipyrad, we assess hybridisation patterns in the study group based on different data assemblies and methods (Neighbor-Net networks, FastStructure and ABBA-BABA tests). RADseq data and Sanger sequences are subsequently used for delimitation of species, using both, multi-species coalescent methods (Stacey and Snapp) and a novel approach based on consensus k-means clustering. In addition to the unveiling of two novel subspecies in the R. arundanum-group, our study provides insights into the performance of different species delimitation methods in the presence of hybridisation and varying quantities of data.

Possible transmission of Sarcoptes scabiei between herbivorous Japanese serows and omnivorous Caniformia in Japan: a cryptic transmission and persistence?

BackgroundTwo transmission patterns of Sarcoptes scabiei in host mammal communities have been reported based on microsatellite-level genetic studies in the last two decades. While one involves restrictions among different host taxa, the other is associated with predator–prey interactions between different host taxa. In contrast to these observations, the present study reports a possible irregular case of transmission of S. scabiei between herbivorous Japanese serow and omnivorous Caniformia mammals in Japan, though under very weak predator–prey relationships.MethodsDNA from 93 Sarcoptes mites isolated from omnivorous Caniformia (such as the domestic dog, raccoon dog, raccoon and Japanese marten), omnivorous Cetartiodactyla (wild boar) and herbivorous Cetartiodactyla (Japanese serow) in Japan were analyzed by amplifying nine microsatellite markers. Principal components analyses (PCA), Bayesian clustering analyses using STRUCTURE software, and phylogenetic analyses by constructing a NeighborNet network were applied to determine the genetic relationships among mites associated with host populations.ResultsIn all the analyses, the genetic differentiation of Sarcoptes mites from wild boars and Japanese serows was observed. Conversely, considerably close genetic relationships were detected between Caniformia-derived and Japanese serow-derived mites. Because the predator–prey interactions between the omnivorous Caniformia and herbivorous Japanese serow are quite limited and epidemiological history shows at least a 10-year lag between the emergence of sarcoptic mange in Japanese serow and that in Caniformia, the transmission of S. scabiei from Caniformia to Japanese serow is highly suspected.ConclusionsThe close genetic relationships among mites beyond Host–taxon relationships and without obvious predator–prey interactions in Caniformia and Japanese serow deviate from previously reported S. scabiei transmission patterns. This type of cryptic relationship of S. scabiei populations may exist in local mammalian communities worldwide and become a risk factor for the conservation of the remnant and fragmented populations of wild mammals.

Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from east African, north African, and Asian conspecifics.

Indigenous goats make significant contributions to Cameroon’s national and local economy, but little effort has been devoted to identifying the populations. Here, we assessed the genetic diversity and demographic dynamics of Cameroon goat populations using mitochondrial DNA (two populations) and autosomal markers (four populations) generated with the Caprine 50K SNP chip. To infer genetic relationships at continental and global level, genotype data on six goat populations from Ethiopia and one population each from Egypt, Morocco, Iran, and China were included in the analysis. The mtDNA analysis revealed 83 haplotypes, all belonging to haplogroup A, in Cameroon goats. Four haplotypes were shared between goats found in Cameroon, Mozambique, Namibia, Zimbabwe, Kenya, and Ethiopia. Analysis of autosomal SNPs in Cameroon goats revealed the lowest HO (0.335±0.13) and HE (0.352±0.15) in the North-west Highland and Central Highland populations, respectively. Overall, the highest HO (0.401±0.12) and HE (0.422±0.12) were found for Barki and Iranian goats, respectively. Barki goats had the highest average MAF, while Central Highland Cameroon goats had the lowest. Overall, Cameroon goats demonstrated high FIS. AMOVA revealed that 13.29% of the variation was explained by genetic differences between the six population groups. Low average FST (0.01) suggests intermixing among Cameroon goats. All measures indicated that Cameroon goats are closer to Moroccan goats than to other goat populations. PCA and STRUCTURE analyses poorly differentiated the Cameroon goats, as did genetic distance, Neighbor-Net network, and neighbor-joining tree analyses. The haplotype analysis of mtDNA showed the initial dispersion of goats to Cameroon and central Africa from north-east Africa following the Nile Delta. Whereas, the approximate Bayesian computation indicated Cameroon goats were separated from Moroccan goats after 506 generations in later times (~1518 YA), as supported by the phylogenetic net-work and admixture outputs. Overall, indigenous goats in Cameroon show weak phylogenetic structure, suggesting either extensive intermixing.

High genetic diversity and differentiation of an extremely narrowly distributed and critically endangered decaploid rose (Rosa praelucens): implications for its conservation

Rosa praelucens is a critically endangered decaploid alpine rose with an extremely narrow geographic distribution in Northwestern Yunnan, China. We sampled almost all the extant individuals (527 individuals in 31 natural locations and 56 individuals preserved in three local living collections) to assess the genetic variation and to probe the genetic connectivity among the individuals and populations based on three cpDNA intergenic spacers and six fluorescent amplified fragment length polymorphism (AFLP) markers. The morphological traits from seven populations were also measured. R. praelucens exhibited high levels of morphological variation, genetic diversity, and differentiation. The extant individuals were clustered into eight groups in neighbor-net networks, and subsequent Bayesian analysis assigned them into three larger gene pools, both in accordance with their morphological traits, especially flower color. The living collections embraced two private cpDNA haplotypes and included three out of the species’ total eight AFLP genotypes. Rhizome clonal growth, decaploid, and mixed breeding system may largely contribute to high genetic diversity and differentiation in R. praelucens. We concluded that the endangered status of R. praelucens may mainly be due to habitat fragmentation and loss and inherent reproductive difficulties, rather than low genetic diversity. The populations contributing higher cpDNA genetic diversity, representing more AFLP genotypes, and encompassing private cpDNA haplotypes should be given conservation priority by creating plant-micro reserves. The living collections should also be targeted for further ex situ conservation, population recovery, and reintroduction of R. praelucens plants.

Genetic structure and demographic history of Lymantria dispar (Linnaeus, 1758) (Lepidoptera: Erebidae) in its area of origin and adjacent areas.

We analyzed the population genetic structure and demographic history of 20 Lymantria dispar populations from Far East Asia using microsatellite loci and mitochondrial genes. In the microsatellite analysis, the genetic distances based on pairwise F ST values ranged from 0.0087 to 0.1171. A NeighborNet network based on pairwise F ST genetic distances showed that the 20 regional populations were divided into five groups. Bayesian clustering analysis (K = 3) demonstrated the same groupings. The populations in the Korean Peninsula and adjacent regions, in particular, showed a mixed genetic pattern. In the mitochondrial genetic analysis based on 98 haplotypes, the median‐joining network exhibited a star shape that was focused on three high‐frequency haplotypes (Haplotype 1: central Korea and adjacent regions, Group 1; Haplotype 37: southern Korea, Group 2; and Haplotype 90: Hokkaido area, Group 3) connected by low‐frequency haplotypes. The mismatch distribution dividing the three groups was unimodal. In the neutral test, Tajima's D and Fu's FS tests were negative. We can thus infer that the Far East Asian populations of L. dispar underwent a sudden population expansion. Based on the age expansion parameter, the expansion time was inferred to be approximately 53,652 years before present (ybp) for Group 1, approximately 65,043 ybp for Group 2, and approximately 76,086 ybp for Group 3. We propose that the mixed genetic pattern of the inland populations of Far East Asia is due to these expansions and that the inland populations of the region should be treated as valid subspecies that are distinguishable from other subspecies by genetic traits.