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

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12418
Author(s):  
Aaron Liston ◽  
Kevin A. Weitemier ◽  
Lucas Letelier ◽  
János Podani ◽  
Yu Zong ◽  
...  

Background Hawthorn 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. Methods We 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. Results We 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.

Forests ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 265
Author(s):  
Mihnea Cățeanu ◽  
Arcadie Ciubotaru

Laser scanning via LiDAR is a powerful technique for collecting data necessary for Digital Terrain Model (DTM) generation, even in densely forested areas. LiDAR observations located at the ground level can be separated from the initial point cloud and used as input for the generation of a Digital Terrain Model (DTM) via interpolation. This paper proposes a quantitative analysis of the accuracy of DTMs (and derived slope maps) obtained from LiDAR data and is focused on conditions common to most forestry activities (rough, steep terrain with forest cover). Three interpolation algorithms were tested: Inverse Distance Weighted (IDW), Natural Neighbour (NN) and Thin-Plate Spline (TPS). Research was mainly focused on the issue of point data density. To analyze its impact on the quality of ground surface modelling, the density of the filtered data set was artificially lowered (from 0.89 to 0.09 points/m2) by randomly removing point observations in 10% increments. This provides a comprehensive method of evaluating the impact of LiDAR ground point density on DTM accuracy. While the reduction of point density leads to a less accurate DTM in all cases (as expected), the exact pattern varies by algorithm. The accuracy of the LiDAR-derived DTMs is relatively good even when LiDAR sampling density is reduced to 0.40–0.50 points/m2 (50–60 % of the initial point density), as long as a suitable interpolation algorithm is used (as IDW proved to be less resilient to density reductions below approximately 0.60 points/m2). In the case of slope estimation, the pattern is relatively similar, except the difference in accuracy between IDW and the other two algorithms is even more pronounced than in the case of DTM accuracy. Based on this research, we conclude that LiDAR is an adequate method for collecting morphological data necessary for modelling the ground surface, even when the sampling density is significantly reduced.


BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yiheng Wang ◽  
Sheng Wang ◽  
Yanlei Liu ◽  
Qingjun Yuan ◽  
Jiahui Sun ◽  
...  

Abstract Background Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing. Results The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT(GGU), and trnT(UGU)-trnL, and a total of 42–47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus. Conclusions Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.


2020 ◽  
Vol 35 (3) ◽  
pp. 457-463
Author(s):  
Huixia Lan ◽  
Xiangzhi Wang ◽  
Shixin Qi ◽  
Da Yang ◽  
Hao Zhang

AbstractUsing the acclimated activated sludge from the pulping middle-stage effluent, the effect of pH shock on the micro-oxygen activated sludge system with a nano-magnetic powder/graphene oxide composite was studied. The results showed that the removal rates of chemical oxygen demand (CODCr) and ultraviolet adsorption at 254 nm (UV254) decreased. Also, the sludge settling performance was poor due to the impact of pH, but the impact resistance of nano-magnetic powder/graphene oxide group (MGO group) was higher and the recovery was faster. Results of high throughput sequencing indicated that the diversity of microbial community was reduced by the impact of pH, but it was significantly higher in MGO group than in the blank group. The dominant bacteria after pH shock or recovery in both of the system had a large difference. The percentage of the dominant bacteria in the MGO group was higher than that in the blank group. The MGO group had higher electron transfer system (ETS) activity which made the system having a strong pH impact resistance.


Polar Biology ◽  
2021 ◽  
Author(s):  
Eleanor E. Jackson ◽  
Ian Hawes ◽  
Anne D. Jungblut

AbstractThe undulating ice of the McMurdo Ice Shelf, Southern Victoria Land, supports one of the largest networks of ice-based, multiyear meltwater pond habitats in Antarctica, where microbial mats are abundant and contribute most of the biomass and biodiversity. We used 16S rRNA and 18S rRNA gene high-throughput sequencing to compare variance of the community structure in microbial mats within and between ponds with different salinities and pH. Proteobacteria and Cyanobacteria were the most abundant phyla, and composition at OTU level was highly specific for the meltwater ponds with strong community sorting along the salinity gradient. Our study provides the first detailed evaluation of eukaryote communities for the McMurdo Ice Shelf using the 18S rRNA gene. They were dominated by Ochrophyta, Chlorophyta and Ciliophora, consistent with previous microscopic analyses, but many OTUs belonging to less well-described heterotrophic protists from Antarctic ice shelves were also identified including Amoebozoa, Rhizaria and Labyrinthulea. Comparison of 16S and 18S rRNA gene communities showed that the Eukaryotes had lower richness and greater similarity between ponds in comparison with Bacteria and Archaea communities on the McMurdo Ice shelf. While there was a weak correlation between community dissimilarity and geographic distance, the congruity of microbial assemblages within ponds, especially for Bacteria and Archaea, implies strong habitat filtering in ice shelf meltwater pond ecosystems, especially due to salinity. These findings help to understand processes that are important in sustaining biodiversity and the impact of climate change on ice-based aquatic habitats in Antarctica.


2021 ◽  
Vol 7 (7) ◽  
pp. 565
Author(s):  
Anindita Lahiri ◽  
Brian R. Murphy ◽  
Trevor R. Hodkinson

Fraxinus excelsior populations are in decline due to the ash dieback disease Hymenoscyphus fraxineus. It is important to understand genotypic and environmental effects on its fungal microbiome to develop disease management strategies. To do this, we used culture dependent and culture independent approaches to characterize endophyte material from contrasting ash provenances, environments, and tissues (leaves, roots, seeds). Endophytes were isolated and identified using nrITS, LSU, or tef DNA loci in the culture dependent assessments, which were mostly Ascomycota and assigned to 37 families. Few taxa were shared between roots and leaves. The culture independent approach used high throughput sequencing (HTS) of nrITS amplicons directly from plant DNA and detected 35 families. Large differences were found in OTU diversity and community composition estimated by the contrasting approaches and these data need to be combined for estimations of the core endophyte communities. Species richness and Shannon index values were highest for the leaf material and the French population. Few species were shared between seed and leaf tissue. PCoA and NMDS of the HTS data showed that seed and leaf microbiome communities were highly distinct and that there was a strong influence of Fraxinus species identity on their fungal community composition. The results will facilitate a better understanding of ash fungal ecology and are a step toward identifying microbial biocontrol systems to minimize the impact of the disease.


2021 ◽  
Author(s):  
Pablo Poulain ◽  
Anne Le Friant ◽  
Rodrigo Pedreros ◽  
Anne Mangeney ◽  
Andrea Filippini ◽  
...  

<p>Since May 2018, Mayotte island has experienced an important seismic activity linked to the on-going sismo-volcanic crisis. The epicenters of the seismic swarms are located between 5 and 15 km east of Petite Terre for the main swarm, and 25 km east of Petite Terre for the secondary swarm. Although variations in the number of earthquakes and their distribution have been observed since the start of the eruption in early July 2018 [Lemoine A.(2020), Cesca et al.(2020)], a continuous seismicity persists and could generate several earthquakes of magnitudes close to M4 widely felt by the population. This recurrent seismicity could weaken the steep submarine slopes of Mayotte, as highlighted by the high resolution bathymetry data collected during the MAYOBS cruise in May 2019 (Feuillet et al.,submitted) and trigger submarine landslides with associated tsunamis.</p><p>To address the hazards associated with such events, we analyzed morphological data to define 8 scenarios of potential submarine slides with volumes ranging from 11,25.10<sup>6</sup> to 800.10<sup>6</sup> m<sup>3</sup> and we simulate the landslide dynamics and generated waves. We use two complementary numerical models: (i) the code HYSEA to simulate the dynamic of the submarine granular flows and the water wave generation, and (ii) the Boussinesq FUNWAVE- TVD model simulate the waves propagation and the inundation on Mayotte. The effect of the time at which the models are coupled is investigated.</p><p>The most impacting submarine slide scenarios are located close to Petite Terre at a shallow depth. They can locally generate a sea surface elevation more than a meter in local areas especially at Petite Terre. The various simulations show that parts of the island are particularly sensitive to the risk of tsunamis. Indeed, some scenarios that does not cause significant coastal flooding still seems to cause significant hazards in these exposed areas. The barrier reef around Mayotte has a prominent role in controlling the wave propagation towards the island and therefore reducing the impact on land. It should be noted that the arrival of tsunamis on the coastline is not necessarily preceded by a retreat from the sea and the waves can reach the coasts of Mayotte very quicky (few minutes).</p><p> </p><p>Cesca, S., Letort, J., Razafindrakoto, H.N.T. et al. Drainage of a deep magma reservoir near Mayotte inferred from seismicity and deformation. Nat. Geosci. <strong>13, </strong>87–93 (2020). https://doi.org/10.1038/s41561-019-0505-5</p><p>Feuillet, N, Jorry, S. J., Crawford, W, Deplus, C. Thinon, I, Jacques, E. Saurel, J.M., Lemoine, A., Paquet, F., Daniel, R., Gaillot, A., Satriano, C., Peltier, A., Aiken, C., Foix, O., Kowalski, P., Laurent, A., Beauducel, F., Grandin, R., Ballu, V., Bernard, P., Donval, J.P., Geli, L., Gomez, J. Guyader, V., Pelleau, P., Rinnert, E., Bertil, D., Lemarchand, A., Van der Woerd, J.et al. (in rev). Birth of a large volcano offshore Mayotte through lithosphere-scale rifting, Nature.</p><p>Anne Lemoine, Pierre Briole, Didier Bertil, Agathe Roullé, Michael Foumelis, Isabelle Thinon, Daniel Raucoules, Marcello de Michele, Pierre Valty, Roser Hoste Colomer, The 2018–2019 seismo-volcanic crisis east of Mayotte, Comoros islands: seismicity and ground deformation markers of an exceptional submarine eruption, Geophysical Journal International, Volume 223, Issue 1, October 2020, Pages 22–44, https://doi.org/10.1093/gji/ggaa273</p>


2012 ◽  
Vol 10 (1) ◽  
pp. 19-44 ◽  
Author(s):  
Alfy Morales-Cazan ◽  
James S. Albert

The systematics and taxonomy of poeciliid fishes (guppies and allies) remain poorly understood despite the relative importance of these species as model systems in the biological sciences. This study focuses on testing the monophyly of the nominal poeciliine tribe Heterandriini and the genus Heterandria, through examination of the morphological characters on which the current classification is based. These characters include aspects of body shape (morphometrics), scale and fin-ray counts (meristics), pigmentation, the cephalic laterosensory system, and osteological features of the neurocranium, oral jaws and suspensorium, branchial basket, pectoral girdle, and the gonopodium and its supports. A Maximum Parsimony analysis was conducted of 150 characters coded for 56 poeciliid and outgroup species, including 22 of 45 heterandriin species (from the accounted in Parenti & Rauchenberger, 1989), or seven of nine heterandriin species (from the accounted in Lucinda & Reis, 2005). Multistate characters were analyzed as both unordered and ordered, and iterative a posteriori weighting was used to improve tree resolution. Tree topologies obtained from these analyses support the monophyly of the Middle American species of "Heterandria," which based on available phylogenetic information, are herein reassigned to the genus Pseudoxiphophorus. None of the characters used in previous studies to characterize the nominal taxon Heterandriini are found to be unambiguously diagnostic. Some of these characters are shared with species in other poeciliid tribes, and others are reversed within the Heterandriini. These results support the hypothesis that Pseudoxiphophorus is monophyletic, and that this clade is not the closest relative of H. formosa (the type species) from southeastern North America. Available morphological data are not sufficient to assess the phylogenetic relationships of H. formosa with respect to other members of the Heterandriini. The results further suggest that most tribe-level taxa of the Poeciliinae are not monophyletic, and that further work remains to resolve the evolutionary relationships of this group.


2018 ◽  
Vol 19 (12) ◽  
pp. 3780 ◽  
Author(s):  
Dingxuan He ◽  
Andrew Gichira ◽  
Zhizhong Li ◽  
John Nzei ◽  
Youhao Guo ◽  
...  

The order Nymphaeales, consisting of three families with a record of eight genera, has gained significant interest from botanists, probably due to its position as a basal angiosperm. The phylogenetic relationships within the order have been well studied; however, a few controversial nodes still remain in the Nymphaeaceae. The position of the Nuphar genus and the monophyly of the Nymphaeaceae family remain uncertain. This study adds to the increasing number of the completely sequenced plastid genomes of the Nymphaeales and applies a large chloroplast gene data set in reconstructing the intergeneric relationships within the Nymphaeaceae. Five complete chloroplast genomes were newly generated, including a first for the monotypic Euryale genus. Using a set of 66 protein-coding genes from the chloroplast genomes of 17 taxa, the phylogenetic position of Nuphar was determined and a monophyletic Nymphaeaceae family was obtained with convincing statistical support from both partitioned and unpartitioned data schemes. Although genomic comparative analyses revealed a high degree of synteny among the chloroplast genomes of the ancient angiosperms, key minor variations were evident, particularly in the contraction/expansion of the inverted-repeat regions and in RNA-editing events. Genome structure, and gene content and arrangement were highly conserved among the chloroplast genomes. The intergeneric relationships defined in this study are congruent with those inferred using morphological data.


PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5382 ◽  
Author(s):  
Fernanda Cornejo-Granados ◽  
Luigui Gallardo-Becerra ◽  
Miriam Leonardo-Reza ◽  
Juan Pablo Ochoa-Romo ◽  
Adrian Ochoa-Leyva

The shrimp or prawn is the most valuable traded marine product in the world market today and its microbiota plays an essential role in its development, physiology, and health. The technological advances and dropping costs of high-throughput sequencing have increased the number of studies characterizing the shrimp microbiota. However, the application of different experimental and bioinformatics protocols makes it difficult to compare different studies to reach general conclusions about shrimp microbiota. To meet this necessity, we report the first meta-analysis of the microbiota from freshwater and marine shrimps using all publically available sequences of the 16S ribosomal gene (16S rRNA gene). We obtained data for 199 samples, in which 63.3% were from marine (Alvinocaris longirostris, Litopenaeus vannamei and Penaeus monodon), and 36.7% were from freshwater (Macrobrachium asperulum, Macrobrachium nipponense, Macrobranchium rosenbergii, Neocaridina denticulata) shrimps. Technical variations among studies, such as selected primers, hypervariable region, and sequencing platform showed a significant impact on the microbiota structure. Additionally, the ANOSIM and PERMANOVA analyses revealed that the most important biological factor in structuring the shrimp microbiota was the marine and freshwater environment (ANOSIM R = 0.54, P = 0.001; PERMANOVA pseudo-F = 21.8, P = 0.001), where freshwater showed higher bacterial diversity than marine shrimps. Then, for marine shrimps, the most relevant biological factors impacting the microbiota composition were lifestyle (ANOSIM R = 0.341, P = 0.001; PERMANOVA pseudo-F = 8.50, P = 0.0001), organ (ANOSIM R = 0.279, P = 0.001; PERMANOVA pseudo-F = 6.68, P = 0.001) and developmental stage (ANOSIM R = 0.240, P = 0.001; PERMANOVA pseudo-F = 5.05, P = 0.001). According to the lifestyle, organ, developmental stage, diet, and health status, the highest diversity were for wild-type, intestine, adult, wild-type diet, and healthy samples, respectively. Additionally, we used PICRUSt to predict the potential functions of the microbiota, and we found that the organ had more differentially enriched functions (93), followed by developmental stage (12) and lifestyle (9). Our analysis demonstrated that despite the impact of technical and bioinformatics factors, the biological factors were also statistically significant in shaping the microbiota. These results show that cross-study comparisons are a valuable resource for the improvement of the shrimp microbiota and microbiome fields. Thus, it is important that future studies make public their sequencing data, allowing other researchers to reach more powerful conclusions about the microbiota in this non-model organism. To our knowledge, this is the first meta-analysis that aims to define the shrimp microbiota.


The Auk ◽  
2007 ◽  
Vol 124 (1) ◽  
pp. 71-84 ◽  
Author(s):  
W. Andrew Cox ◽  
Rebecca T. Kimball ◽  
Edward L. Braun

Abstract The evolutionary relationship between the New World quail (Odontophoridae) and other groups of Galliformes has been an area of debate. In particular, the relationship between the New World quail and guineafowl (Numidinae) has been difficult to resolve. We analyzed >8 kb of DNA sequence data from 16 taxa that represent all major lineages of Galliformes to resolve the phylogenetic position of New World quail. A combined data set of eight nuclear loci and three mitochondrial regions analyzed with maximum parsimony, maximum likelihood, and Bayesian methods provide congruent and strong support for New World quail being basal members of a phasianid clade that excludes guineafowl. By contrast, the three mitochondrial regions exhibit modest incongruence with each other. This is reflected in the combined mitochondrial analyses that weakly support the Sibley-Ahlquist topology that placed the New World quail basal in relation to guineafowl and led to the placement of New World quail in its own family, sister to the Phasianidae. However, simulation-based topology tests using the mitochondrial data were unable to reject the topology suggested by our combined (mitochondrial and nuclear) data set. By contrast, similar tests using our most likely topology and our combined nuclear and mitochondrial data allow us to strongly reject the Sibley-Ahlquist topology and a topology based on morphological data that unites Old and New World quail. Posición Filogenética de las Codornices del Nuevo Mundo (Odontophoridae): Ocho Loci Nucleares y Tres Regiones Mitocondriales Contradicen la Morfología y la Filogenia de Sibley y Ahlquist


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