Towards the next generation of species delimitation methods: an overview of Machine Learning applications DOI Creative Commons
Matheus Salles, Fabrícius M. C. B. Domingos

Опубликована: Дек. 7, 2023

Species delimitation is the process of distinguishing between populations same species and distinct a particular group organisms. Various methods exist for inferring limits, with most them being rooted in Coalescent Theory. Their primary goal to identify independently evolving lineages that should represent separate species. models have improved by enabling explicit testing hypotheses regarding evolutionary independence among lineages. However, they some limitations, especially complex scenarios, large datasets, varying genetic data types. In this context, machine learning (ML) can be considered as promising analytical tool, clearly provides an effective way explore dataset structures when species-level divergences are hypothesised. review, we examine use ML provide overview critical appraisal existing workflows. We also simple explanations on how main types approaches operate, which help researchers students interested field. While current designed infer limits analytically powerful, present specific limitations not definitive alternatives traditional coalescent delimitation. For instance, there clear utilisation simulated data, supervised deep approaches, type representation used each approach. then discuss strengths weaknesses pipelines, propose best practices delimitation, offer insights into potential future applications. Generative adversarial networks domain adaptation techniques, could partially address misspecification issue related simulating data. Besides, integrating hypothesis process, alongside available coalescent-based methods, enable more comprehensive exploration parameters, improving accuracy biological interpretability analyses. Additionally, suggest guidelines enhancing accessibility, effectiveness, objectivity processes, aiming transformative perspective subject.

Язык: Английский

Advancing Pyrus phylogeny: Deep genome skimming‐based inference coupled with paralogy analysis yields a robust phylogenetic backbone and an updated infrageneric classification of the pear genus (Maleae, Rosaceae) DOI
Ze‐Tao Jin, Dai‐Kun Ma, Guang‐Ning Liu

и другие.

Taxon, Год журнала: 2024, Номер 73(3), С. 784 - 799

Опубликована: Март 28, 2024

Abstract The lack of a robust phylogenetic backbone has posed significant challenges to proposing an infrageneric taxonomic classification the pear genus, Pyrus , widely distributed Eurasian lineage Rosaceae. This issue been exacerbated by limited informative loci and inaccessible taxon sampling. To address these limitations, we conducted extensive sampling, encompassing 78 ingroup individuals representing 32 species, along with 4 outgroup species. comprehensive sampling strategy covers wide range morphological geographical variations. enable accurate phylogenomic inference, assembled 801 single‐copy nuclear genes 72 plastid coding sequences from deep genome skimming (DGS) data. Additionally, employed tree‐based method for orthology which led generation three orthologous datasets: one‐to‐one orthologs (1to1), monophyletic outgroups (MO), rooted ingroups (RT). results yielded both analyses consistently support monophyly two well‐supported clades, Occidental Oriental were recovered in nine trees. Integrating evidence morphology phylogenomics, propose updated consists subgenera: P. subg. Pashia stat. nov. revised provides more framework understanding evolutionary relationships within genus.

Язык: Английский

Процитировано

12
Nuclear phylogenomics of angiosperms and insights into their relationships and evolution DOI Creative Commons
Guojin Zhang, Hong Mā

Journal of Integrative Plant Biology, Год журнала: 2024, Номер 66(3), С. 546 - 578

Опубликована: Янв. 30, 2024

Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of angiosperms in fossil record was referred to Darwin as "abominable mystery," hence contributing heightened interest angiosperm evolution. display wide ranges morphological, physiological, and ecological characters, some which have probably influenced their species richness. evolutionary analyses these characteristics help address questions diversification require well resolved phylogeny. Following great successes phylogenetic using plastid sequences, dozens thousands nuclear genes from next-generation sequencing been used phylogenomic analyses, providing phylogenies new insights into evolution angiosperms. In this review we focus on recent large clades, orders, families, subdivisions families provide a summarized Nuclear Phylogenetic Tree Angiosperm Families. newly established relationships highlighted compared previous results. sequenced genomes Amborella, Nymphaea, Chloranthus, Ceratophyllum, monocots, Magnoliids, basal eudicots, facilitated phylogenomics among five major clades. All but one 64 orders were included except placements several orders. Most robust highly supported placements, especially for within important families. Additionally, examine divergence time estimation biogeographic basis frameworks discuss differences analyses. Furthermore, implications ancestral reconstruction characters groups, limitations current studies, taxa that future attention.

Язык: Английский

Процитировано

8
Unraveling the Web of Life: Incomplete lineage sorting and hybridization as primary mechanisms over polyploidization in the evolutionary dynamics of pear species DOI Creative Commons
Ze‐Tao Jin, Xiao-Hua Lin, Dai‐Kun Ma

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 30, 2024

Abstract In contrast to the traditional Tree of Life (ToL) paradigm, Web (WoL) model provides a more nuanced and precise depiction organismal phylogeny, particularly considering prevalent incongruence observed among gene/species trees. The lack generalized pipeline for teasing apart potential evolutionary mechanisms—such as Incomplete Lineage Sorting (ILS), hybridization, introgression, polyploidization, Whole-Genome Duplication—poses significant challenges delineation WoL. pear genus Pyrus , characterized by extensive hybridization events, serves an excellent investigating This study introduces novel Step-by-Step Exclusion (SSE) approach deciphering complexities inherent in Our findings indicate: 1) ILS, rather than is identified primary driver behind origin from arid regions Himalayas-Central Asia; 2) two subgenera have independent trajectories, facilitated geographical barriers that arose via uplift Tibetan Plateau increased aridity Central 3) ILS diversification Oriental pears, while alone has driven reticulate evolution Occidental pears; 4) establishment Silk Road during Han Dynasty acted conduit genetic exchange between pears. SSE universally applicable framework mechanisms defining WoL paradigm.

Язык: Английский

Процитировано

4
Glycyrrhiza, a commonly used medicinal herb: Review of species classification, pharmacology, active ingredient biosynthesis, and synthetic biology DOI Creative Commons
Liwei Wu, Tingyu Ma,

Chenxi Zang

и другие.

Journal of Advanced Research, Год журнала: 2024, Номер unknown

Опубликована: Ноя. 1, 2024

Язык: Английский

Процитировано

4
Integrated metabolomic and transcriptomic analysis provides insights into the flavonoid formation in different Glycyrrhiza species DOI
Yuping Li, Ziyan Xie, Yun Huang

и другие.

Industrial Crops and Products, Год журнала: 2023, Номер 208, С. 117796 - 117796

Опубликована: Ноя. 24, 2023

Язык: Английский

Процитировано

9
Species delimitation and phylogenetic relationships of the Prionospio complex (Annelida, Spionidae) in the Northeast Atlantic DOI Creative Commons
Martin Hektoen, Torkild Bakken, Torbjørn Ekrem

и другие.

Zoologica Scripta, Год журнала: 2024, Номер 53(3), С. 358 - 375

Опубликована: Фев. 5, 2024

Abstract The Prionospio complex comprises the most diverse and group within polychaete family Spionidae. phylogenetic relationships are still poorly understood, generic breakdown is unstable. In this study, we assessed diversity, relationships, distribution of species occurring in Norwegian waters. We analysed mitochondrial genomes nuclear ribosomal DNA assembled via whole‐genome shotgun sequencing, Sanger sequenced fragments COI 16S rDNA. sequencing proved challenging group, where was only amplified successfully 14% specimens. By molecular delimitation algorithms, our study revealed presence four well‐supported but currently undescribed observed a novel pattern polychaetes coastal waters, certain demonstrated ranges spanning over 7000 km. Such wide parallels patterns deep‐sea species, suggesting that factors beyond recent anthropogenic translocations involved. Our analysis 38 enabled us to hypothesise on 14 . suggested two characters previously used designate genera: beginning branchiae from chaetiger 3 pinnules branchiae, might have evolved more than one time complex. return Aurospio banyulensis genus according diagnosis resulting tree nested among species. findings provide new insights into diversity contribute better understanding marine benthic biodiversity importance taxonomic accuracy conservation management practices.

Язык: Английский

Процитировано

3
Comparative genomics and phylogenomics of the genus Glycyrrhiza (Fabaceae) based on chloroplast genomes DOI Creative Commons
Liwei Wu,

Panhui Fan,

Jiaying Cai

и другие.

Frontiers in Pharmacology, Год журнала: 2024, Номер 15

Опубликована: Март 7, 2024

Glycyrrhiza (Fabaceae) species are rich in metabolites and widely used medicine. Research on the chloroplast genome of is important for understanding its phylogenetics, biogeography, genetic diversity, identification, medicinal properties. In this study, comparative genomics phylogenomics were analyzed based genome. The genomes six obtained using various assembly annotation tools. final assembled sizes ranged from 126,380 bp to 129,115 bp, with a total 109–110 genes annotated. Comparative results showed that typically lacking inverted repeat regions, length, structure, GC content, codon usage, gene distribution highly similar. Bioinformatics analysis revealed presence 69–96 simple sequence repeats 61–138 long genomes. Combining mVISTA nucleotide four variable regions screened identification relationship studies. Selection pressure indicated overall purifying selection , few positively selected potentially linked environmental adaptation. Phylogenetic analyses involving all tribes Fabaceae published elucidated evolutionary relationships, divergence time estimation estimated chronological order differentiations within family. phylogenetic subfamilies formed distinct clusters, consistent classification scheme subfamilies. addition, repeat-lacking clade subfamily Papilionoideae clustered together, it was last differentiate. Co-linear confirmed conserved nature genomes, instances rearrangements inversions observed Papilionoideae.

Язык: Английский

Процитировано

3
Integrated Metabolomic and Transcriptomic Analysis Reveals the Pharmacological Effects and Differential Mechanisms of Isoflavone Biosynthesis in Four Species of Glycyrrhiza DOI Open Access
Yinhua Lü, Zhen Ding, Daoyuan Zhang

и другие.

International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(6), С. 2539 - 2539

Опубликована: Март 12, 2025

Licorice (Glycyrrhiza L.) is a globally popular medicinal and edible plant, with nearly 30 species distributed across all continents. The usable part primarily the root. To understand metabolic differences among different Glycyrrhiza species, we selected four performed comprehensive analyses of their roots. Metabolomic profiling was conducted using UPLC-MS/MS GC-MS, while transcriptomic analysis carried out RNA-sequencing. A total 2716 metabolites were identified, including flavonoids (527 types) terpenoids (251 types), various other components. Subsequently, network pharmacology employed to explore value potential pharmacological ingredients these metabolites. Joint metabolomic data revealed significant in differentially accumulated (DAMs) expressed genes (DEGs) pairwise comparisons species. These enriched isoflavone pathway. Further investigation into regulatory mechanisms biosynthesis identified key involved biosynthesis. Finally, made reasonable predictions suitable habitats for aiming provide new insights development utilization licorice resources. results this study can serve as basis in-depth research on regulation licorice.

Язык: Английский

Процитировано

0
Contributions of interspecific hybrids to genetic variability in Glycyrrhiza uralensis and G. glabra DOI Creative Commons
Jungeun Kim, Jeonghoon Lee, Jong‐Soo Kang

и другие.

Scientific Reports, Год журнала: 2025, Номер 15(1)

Опубликована: Март 13, 2025

Licorice (Glycyrrhiza L.), a medicinally and economically significant genus in the Fabaceae, is known for synthesizing glycyrrhizin. Here, we present newly assembled genome of Glycyrrhiza uralensis, key species distributed across Central East Asia. Using Oxford Nanopore, Hi-C, Illumina sequencing, 415 Mbp with an N50 47 Mbp. While structure was similar to previously reported assemblies, structural variations were observed all eight chromosomes. Re-sequencing data from 29 individuals, including G. glabra, their hybrids, revealed genetic diversity, population structure, hybridization events. Phylogenomic analyses using nuclear plastid genomes demonstrated phylogenetic incongruence, supporting between uralensis glabra. Our network gene flow test identified hybrid groups (Ggu1, Ggu2, Gug) acting as bridges species. Demographic history inferred via PSMC showed thrived during Middle Pleistocene, size fluctuations hybrids. Current low heterozygosity high differentiation suggest long-term geographic ecological isolation, reducing flow. findings advance understanding evolutionary help conservation molecular breeding these

Язык: Английский

Процитировано

0
Pathogen Management in Glycyrrhiza glabra: Microbial Interactions and Phylogenetic Insights DOI

Khabib Kushiev,

R Kuralova,

Tokhir Husanov

и другие.

Journal of Phytopathology, Год журнала: 2025, Номер 173(2)

Опубликована: Март 1, 2025

ABSTRACT The plant‐associated microbial communities are crucial for understanding their roles in enhancing plant health and productivity. This research aimed to isolate characterize bacterial strains from the roots of Glycyrrhiza glabra L. using 16S rRNA gene sequencing explore phylogenetic relationships functional potential. Root samples were collected Gulistan phytogeographic region, isolated through serial dilution cultured on nutrient agar. Genomic DNA was extracted, performed identify isolates, followed by analysis MEGA X software. results revealed three dominant Bacillus species: licheniformis , subtilis halotolerans . exhibited significant enzyme activities, including protease, amylase cellulase production, suggesting organic matter degradation cycling. Furthermore, greenhouse trials demonstrated enhanced growth parameters such as root length, height biomass, reflecting potential growth‐promoting rhizobacteria (PGPR). Antibiotic production assays indicated capacity biocontrol against pathogens, reinforcing role disease suppression. study emphasizes ecological significance spp. sustainable agriculture application biofertilizers agents. Future should focus field metabolomic elucidate molecular mechanisms underlying beneficial interactions, further optimizing use crop improvement strategies.

Язык: Английский

Процитировано

0