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Mammals from ‘down under’: a multi-gene species-level phylogeny of marsupial mammals (Mammalia, Metatheria)
PeerJ - Tập 3 - Trang e805
Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. The expanding crowd of scientists and clinicians wanting to make use of sequencing datasets can choose among a range of multipurpose software platforms, the use of which can be intimidating for non-expert users. Among available pipeline options for high-throughput 16S rRNA gene analysis, the R programming language and software environment for statistical computing stands out for its power and increased flexibility, and the possibility to adhere to most recent best practices and to adjust to individual project needs. Here we present the Rhea pipeline, a set of R scripts that encode a series of well-documented choices for the downstream analysis of Operational Taxonomic Units (OTUs) tables, including normalization steps,alpha - andbeta -diversity analysis, taxonomic composition, statistical comparisons, and calculation of correlations. Rhea is primarily a straightforward starting point for beginners, but can also be a framework for advanced users who can modify and expand the tool. As the community standards evolve, Rhea will adapt to always represent the current state-of-the-art in microbial profiles analysis in the clear and comprehensive way allowed by the R language. Rhea scripts and documentation are freely available athttps://lagkouvardos.github.io/Rhea .
PeerJ - Tập 5 - Trang e2836
A proposed terminology for the dentition of gomphodont cynodonts and dental morphology in Diademodontidae and Trirachodontidae Gomphodont cynodonts were close relatives of mammals and one of the Mesozoic lineages of cynodont therapsids that became extinct at the end of the Triassic. Gomphodonts were omnivorous to herbivorous animals characterized by labiolingually expanded postcanines, which allowed tooth-to-tooth occlusion. The morphology of the upper and lower postcanines presents important means of distinguishing among major lineages within Gomphodontia, that is, Diademodontidae, Trirachodontidae, and Traversodontidae, but the dentition of most Diademodontidae and Trirachodontidae remain poorly documented. Here, we present a comprehensive description of the dentition of each diademodontid and trirachodontid species, as well as detailed illustrations of each dental unit, after firsthand examination of material and 3D reconstructions of postcanine teeth. Based on dental morphology,Trirachodon berryi and “Trirachodon kannemeyeri ,” considered as separate taxa by some authors are here interpreted as representing different ontogenetic stages of the same species. Likewise,Sinognathus andBeishanodon , thought to belong to non-cynognathian cynodonts and traversodontids by some authors, are referred to Trirachodontidae and Gomphodontia based on dental characters, respectively. Finally, we propose a standardized list of terms and abbreviations for incisors, canines, and postcanines anatomical entities, with the goal of facilitating future descriptions and communication between researchers studying the gomphodont dentition.
PeerJ - Tập 7 - Trang e6752
East palearctic treefrog past and present habitat suitability using ecological niche models Ecological niche modeling is a tool used to determine current potential species’ distribution or habitat suitability models which can then be used to project suitable areas in time. Projections of suitability into past climates can identify locations of climate refugia, or areas with high climatic stability likely to contain the highest levels of genetic diversity and stable populations when climatic conditions are less suitable in other parts of the range. Modeling habitat suitability for closely related species in recent past can also reveal potential periods and regions of contact and possible admixture. In the east palearctic, there are fiveDryophytes (Hylid treefrog) clades belonging to two groups:Dryophytes japonicus group: Clades A and B; andDryophytes immaculatus group:Dryophytes immaculatus ,Dryophytes flaviventris , andDryophytes suweonensis . We used maximum entropy modeling to determine the suitable ranges of these five clades during the present and projected to the Last Glacial Maximum (LGM) and Last Interglacial (LIG) periods. We also calculated climatic stability for each clade to identify possible areas of climate refugia. Our models indicated suitable range expansion during the LGM for four clades with the exclusion ofD. immaculatus . High climatic stability in our models corresponded to areas with the highest numbers of recorded occurrences in the present. The models produced here can additionally serve as baselines for models of suitability under climate change scenarios and indicate species ecological requirements.
PeerJ - Tập 10 - Trang e12999
Phylogeography of the rare and endangered lycophyte<i>Isoetes yunguiensis</i> Background Isoetes yunguiensis Q. F. Wang & W. C. Taylor is a lycophyte of an ancient genus, and it is endemic to China. It is a first-class protected plant in China. This living fossil is used in paleoecology and studies on the evolution of Lycophytes in the Yunnan-Guizhou Plateau. In recent years, human activities have caused the disappearance of several wild populations, and the number of plants in the existing populations is low. Study of the genetic structure, distribution pattern, and historical dynamics ofI .yunguiensis in all areas of its distribution is of guiding significance for its rational and effective protection.Methods Expressed sequence tag-simple sequence repeat (EST-SSR) markers were used to study the genetic diversity and structure ofI .yunguiensis , and noncoding chloroplast DNA (cpDNA) sequences were used to study the pedigree, population dynamics history, and glacial shelter ofI. yunguiensis . A maximum entropy model was used to predict the past, present, and future distribution patterns ofI. yunguiensis . Results Analysis with EST-SSR markers revealed thatI. yunguiensis showed high genetic diversity and that genetic variation was significantly higher within populations than between populations. Based on cpDNA data, it was concluded that there was no significant geographic pedigree in the whole area ofI. yunguiensis distribution (NST = 0.344 > GST = 0.183,p > 0.05); 21 haplotypes were detected using DnaSP v5. Neutral test and LAMARC simulation showed thatI. yunguiensis has experienced rapid expansion in recent years. The maximum entropy model predicted that the potential distribution area ofI. yunguiensis in the last glacial maximum period has increased significantly compared with the present distribution area, but the future distribution area did not show substantial changes.
PeerJ - Tập 8 - Trang e8270
Does polyandry really pay off? The effects of multiple mating and number of fathers on morphological traits and survival in clutches of nesting green turtles at Tortuguero
PeerJ - Tập 3 - Trang e880
Sequence and structure analyses of lytic polysaccharide monooxygenases mined from metagenomic DNA of humus samples around white-rot fungi in Cuc Phuong tropical forest, Vietnam
PeerJ - Tập 12 - Trang e17553 - 2024
#Chitin-active and cellulose-active LPMOs; Metagenomics; Fungal-bacterialrelationships; Protein spatial conformation prediction
ToxGen: an improved reference database for the identification of type B-trichothecene genotypes in<i>Fusarium</i> Type B trichothecenes, which pose a serious hazard to consumer health, occur worldwide in grains. These mycotoxins are produced mainly by three different trichothecene genotypes/chemotypes: 3ADON (3-acetyldeoxynivalenol), 15ADON (15-acetyldeoxynivalenol) and NIV (nivalenol), named after these three major mycotoxin compounds. Correct identification of these genotypes is elementary for all studies relating to population surveys, fungal ecology and mycotoxicology. Trichothecene producers exhibit enormous strain-dependent chemical diversity, which may result in variation in levels of the genotype’s determining toxin and in the production of low to high amounts of atypical compounds. New high-throughput DNA-sequencing technologies promise to boost the diagnostics of mycotoxin genotypes. However, this requires a reference database containing a satisfactory taxonomic sampling of sequences showing high correlation to actually produced chemotypes. We believe that one of the most pressing current challenges of such a database is the linking of molecular identification with chemical diversity of the strains, as well as other metadata. In this study, we use the Tri12 gene involved in mycotoxin biosynthesis for identification of Tri genotypes through sequence comparison. Tri12 sequences from a range of geographically diverse fungal strains comprising 22Fusarium species were stored in the ToxGen database, which covers descriptive and up-to-date annotations such as indication on Tri genotype and chemotype of the strains, chemical diversity, information on trichothecene-inducing host, substrate or media, geographical locality, and most recent taxonomic affiliations. The present initiative bridges the gap between the demands of comprehensive studies on trichothecene producers and the existing nucleotide sequence databases, which lack toxicological and other auxiliary data. We invite researchers working in the fields of fungal taxonomy, epidemiology and mycotoxicology to join the freely available annotation effort.
PeerJ - Tập 5 - Trang e2992
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