Molecular Phylogenetic Research Articles

A new odorous frog species of Odorrana (Amphibia, Anura, Ranidae) from Guizhou Province, China.

The frog genus Odorrana is distributed across east and southeastern Asia. Based on morphological differences and molecular phylogenetics, a new species of the genus occurring from Leigong Mountain in Guizhou Province, China is described. Phylogenetic analyses based on DNA sequences of the mitochondrial 12S rRNA, 16S rRNA, and ND2 genes supported the new species as an independent lineage. The uncorrected genetic distances between the 12S rRNA, 16S rRNA, and ND2 genes between the new species and its closest congener were 5.0%, 4.9%, and 16.3%, respectively. The new species is distinguished from its congeners by a combination of the following characters: body size moderate (SVL 39.1-49.4 mm in males, 49.7 mm in female); head width larger than head length; tympanum distinctly visible; small rounded granules scattered all over dorsal body and limbs; dorsolateral folds absent; heels overlapping when thighs are positioned at right angles to the body; tibiotarsal articulation reaching the level between eye to nostril when leg stretched forward; vocal sacs absent in male and nuptial pads present on the base of finger I.

Plastid genome of Passiflora tripartita var. mollissima (poro-poro) from Huánuco, Peru.

Passiflora tripartita var. mollissima, known locally as poro-poro, is an important native fruit used in traditional Peruvian medicine with relevant agro-industrial and pharmaceutical potential for its antioxidant capacity for human health. However, to date, only a few genetic data are available, which limits exploring its genetic diversity and developing new genetic studies for its improvement. We report the poro-poro plastid genome to expand the knowledge of its molecular markers, evolutionary studies, molecular pathways, and conservation genetics. The complete chloroplast (cp) genome is 163,451 bp in length with a typical quadripartite structure, containing a large single-copy region of 85,525 bp and a small single-copy region of 13,518 bp, separated by a pair of inverted repeat regions (IR) of 32,204 bp, and the overall GC content was 36.87%. This cp genome contains 128 genes (110 genes were unique and 18 genes were found duplicated in each IR region), including 84 protein-coding genes, 36 transfer RNA-coding genes, eight ribosomal RNA-coding genes, and 13 genes with introns (11 genes with one intron and two genes with two introns). The inverted repeat region boundaries among species were similar in organization, gene order, and content, with a few revisions. The phylogenetic tree reconstructed based on single-copy orthologous genes and maximum likelihood analysis demonstrates poro-poro is most closely related to Passiflora menispermifolia and Passiflora oerstedii. In summary, our study constitutes a valuable resource for studying molecular evolution, phylogenetics, and domestication. It also provides a powerful foundation for conservation genetics research and plant breeding programs. To our knowledge, this is the first report on the plastid genome of Passiflora tripartita var. mollissima from Peru.

Molecular phylogeny and ethology of the Family Plagiostomidae (Platyhelminthes, Prolecithophora), with integrative description of a new species, Plagiostomum robusta A. Wang, sp. nov.

The taxon Prolecithophora, which is closely related to the well-known clade Tricladida, is rarely studied, particularly in terms of molecular phylogeny and behavioral characteristics. In this study, we employed an integrative analysis of molecular phylogeny, histology, and ethology to describe a new marine species, Plagiostomum robusta A.Wang, sp. nov. of the order Prolecithophora. Additionally, we obtained its nearly complete mitogenome sequence with annotations of 12 protein-coding genes, two rRNA genes and 22 tRNA genes. P. robusta is characterized by several features, including a pair of short tentacles, a terminal mouth and a terminal gonopore, a large variable pharynx, two extended front ends of the intestine, paired testes located behind the ovaries and outside the vitellaria, a muscular and movable distal sac, and a long tubular penis surrounded by a sheath. The phylogenetic analysis, based on 18S rDNA and 28S rDNA, revealed that the new species formed a clade with six Plagiostomum flatworms, indicating a close kinship with Plagiostomum. Despite contradictions between the traditional morphological classification system and the results of molecular phylogenetics, we chose to assign the new species to Plagiostomum based on comprehensive considerations. Moreover, our study has provided more insights into the behavioral features of Plagiostomidae species, as we found that P. robusta fed on other flatworms and engaged in cannibalism, and unexpectedly it mated via hypodermic inpregnation. This study represents the first comprehensive description of the reproductive behavior of Plagiostomidae species, contributing to the more in-depth understanding of the biological characteristics of this group.

Calanthe yingjiangensis (Epidendroideae; Orchidaceae), a new species from China: evidence from morphological and molecular data

A new species of Orchidaceae, Calanthe yingjiangensis, is described from Yingjiang (Yunnan, China) based on morphology and molecular phylogenetics. This new species is like C. puberula, but it differs from the latter in its midlob of lip with an elliptic yellow spot near the base of the column and four purple veins, triangular lateral lip lobs that is much smaller than middle lobe and twisted lateral sepals. Molecular phylogenetic analyses based on three plastid DNA makers (rbcL, matK and trnL-trnF) and nuclear ribosomal ITS support C. yingjiangensis as sister to C. puberula in Calanthe section Vernae.

Identifying global conservation priorities for terrestrial vertebrates based on multiple dimensions of biodiversity.

The Kunming-Montreal Global Biodiversity Framework of the Convention on Biological Diversity calls for an expansion of the current protected areas (PAs) to cover at least 30% of global land and water areas by 2030 (i.e., the 30×30 target). Efficient spatial planning for PA expansion is an urgent need for global conservation practice. A spatial prioritization framework considering multiple dimensions of biodiversity is critical for improving the efficiency of the spatial planning of PAs, yet it remains a challenge. We developed an index for the identification of priority areas based on functionally rare, evolutionarily distinct, and globally endangered species (FREDGE) and applied it to 21,536 terrestrial vertebrates. We determined species distributions, conservation status (global endangerment), molecular phylogenies (evolutionary distinctiveness), and life-history traits (functional rarity). Madagascar, Central America, and the Andes were of high priority for the conservation of multiple dimensions of terrestrial vertebrate biodiversity. However, 68.8% of grid cells in these priority areas had <17% of their area covered by PAs, and these priority areas were under intense anthropogenic and climate change threats. These results highlight the difficulties of conserving multiple dimensions of biodiversity. Our global analyses of the geographical patterns of multiple dimensions of terrestrial vertebrate biodiversity demonstrate the insufficiency of the conservation of different biodiversity dimensions, and our index, based on multiple dimensions of biodiversity, provides a useful tool for guiding future spatial prioritization of PA expansion to achieve the 30×30 target under serious pressures.

The global genetic diversity of planktonic foraminifera reveals the structure of cryptic speciation in plankton.

The nature and extent of diversity in the plankton has fascinated scientists for over a century. Initially, the discovery of many new species in the remarkably uniform and unstructured pelagic environment appeared to challenge the concept of ecological niches. Later, it became obvious that only a fraction of plankton diversity had been formally described, because plankton assemblages are dominated by understudied eukaryotic lineages with small size that lack clearly distinguishable morphological features. The high diversity of the plankton has been confirmed by comprehensive metabarcoding surveys, but interpretation of the underlying molecular taxonomies is hindered by insufficient integration of genetic diversity with morphological taxonomy and ecological observations. Here we use planktonic foraminifera as a study model and reveal the full extent of their genetic diversity and investigate geographical and ecological patterns in their distribution. To this end, we assembled a global data set of ~7600 ribosomal DNA sequences obtained from morphologically characterised individual foraminifera, established a robust molecular taxonomic framework for the observed diversity, and used it to query a global metabarcoding data set covering ~1700 samples with ~2.48 billion reads. This allowed us to extract and assign 1 million reads, enabling characterisation of the structure of the genetic diversity of the group across ~1100 oceanic stations worldwide. Our sampling revealed the existence of, at most, 94 distinct molecular operational taxonomic units (MOTUs) at a level of divergence indicative of biological species. The genetic diversity only doubles the number of formally described species identified by morphological features. Furthermore, we observed that the allocation of genetic diversity to morphospecies is uneven. Only 16 morphospecies disguise evolutionarily significant genetic diversity, and the proportion of morphospecies that show genetic diversity increases poleward. Finally, we observe that MOTUs have a narrower geographic distribution than morphospecies and that in some cases the MOTUs belonging to the same morphospecies (cryptic species) have different environmental preferences. Overall, our analysis reveals that even in the light of global genetic sampling, planktonic foraminifera diversity is modest and finite. However, the extent and structure of the cryptic diversity reveals that genetic diversification is decoupled from morphological diversification, hinting at different mechanisms acting at different levels of divergence.

Bidirectional biotic interchange between Taiwan Island and Mainland China via land bridges—A case study of Obeidia Walker (Geometridae, Lepidoptera)

AbstractBiotic exchanges between Taiwan and Mainland China have shaped the biodiversity and ecosystems of both regions. Exchanges from Mainland China to Taiwan have received more attention, mainly studied in terrestrial vertebrates, while the reverse direction and invertebrates have largely been overlooked. Here, we explore the dispersal events between these two regions based on the moths of three species groups of Obeidia, including Taiwan taxa and its relatives from mainland. We conducted mixed methods and analysis, including reconstructing a phylogenetic tree, estimating associated divergence times and inferring ancestral areas and source regions, to explore the phylogeographical structure and genetic pattern of three groups based on eight genes. Our results revealed a structure of three clades and every clade included at least one Taiwanese taxa and its closest relatives of mainland of China, and also served Taiwan as an important source region of two mainland taxa. Our study revealed various origin pattern and dispersal models on the basis of three species groups of Obeidia. Bi‐directional biotic exchange via a land bridge were found: four Taiwanese taxa originated from mainland, and two of them migrated back to mainland. Both eastern Himalayas and south China are important origin areas for Taiwan biota, and the dominant source region may need multiple insect cases to confirm. Our study also provided evidences for disjunct distribution from the perspective of insecta molecular phylogeny.

Molecular and metabolites characterisation of Inonotus rickii: a medicinal mushroom from Western Ghats of India and its biological activities

ABSTRACT Mushrooms are a rich source of biologically active compounds. Meanwhile, Inonotus species reported abundant bioactive chemicals. Therefore, the current study aims to evaluate the antibacterial, antioxidant, and anticancer potential of Inonotus rickii (Pat.), a less-studied mushroom with an unverified identity, collected from the Western Ghats of Maharashtra, and its metabolic profiling. The morphological traits and spores were examined through a compound microscope and scanning electron microscope (SEM) to confirm the species. Further, the ITS-5.8S region of the sample DNA was amplified using PCR, and species I. rickii was confirmed through molecular phylogeny. The I. rickii sample extracts demonstrated biological activity against Propionibacterium acnes, Vibrio cholera, and Bacillus subtilis. However, tested antioxidant capacity revealed an increase in activity with an increase in extract concentration. Moreover, the extract showed anticancer potential against Human Breast Cancer Cell Lines MCF-7 with IC50 greater than 80 µg/mL. The FTIR analysis and HRLCMS based metabolic profiling of I. rickii reported various chemical groups and bioactive metabolites, respectively. It might, however, be used as a nutraceutical and in the healthcare industry.

Molecular Phylogenetics and Light Microscopy Reveal “True” and “False” Calacarines and Novel Genital Structures in Gall Mites (Acariformes, Eriophyoidea)

Gall mites (Eriophyoidea) are cosmopolitan microscopic phytoparasites that often transmit viruses and induce gallogenesis. The tribe Calacarini is diagnosed by a set of plesiomorphic and homoplastic traits, including elimination of setae sc shared with other lineages of Eriophyoidea. We reviewed data on the generic diversity of calacarines, revised the concept of the type genus Calacarus Keifer 1940, and proposed three zones (MZ, SMZ, LZ) in the prodorsal shields of calacarines to simplify descriptions of their shield patterns. We describe three new calacarine species (Calacarus baviensisn. sp., C. burchelliaen. sp., and Viginticus searsiaen. sp.) from indigenous dicotyledonous trees from South Africa and Vietnam and report on new findings of Paracalacarus podocarpi Keifer in Brazil, Jiangsuacarus sp. in the USA, and Calacarus pusillus Pye in Latvia and Russia. The latter represents the new most northern locality of Calacarini. Reinvestigating the type species of Jaranasia Chandrapatya &amp; Boczek 2000 revealed that absence of setae l’’ II is the only character separating it from Jiangsuacarus Xue 2009. We proposed two new combinations: Jiangsuacarus sesleriae (Skoracka 2004) n. comb. (transferred from Jaranasia) and Procalacarus mussaendae (Keifer 1977) n. comb. (transferred from Calacarus). Partial sequences of Cox1 and 28S genes were obtained for six calacarines, some of them originating from old ethanol material kept at room temperature. Molecular phylogenetics revealed a stable cluster of “true” calacarine sequences comprising Calacarus, Jaranasia, Latitudo, and Viginticus and a polyphyletic group of erroneous sequences assigned to Calacarini in GenBank. All investigated females of calacarines have a pair of genital tubules associated with the vestibulum and hypothesized to participate in fertilization. This finding may contribute to resolving the question on how the fusion of gametes happens in gall mites.

A Taxonomic Review of South African Indigenous Meliaceae Using Molecular Systematics and Anatomical Data

The Meliaceae are broadly distributed worldwide, with about 50 genera and over 1400 species. There are 11 genera in South Africa, with 13 indigenous and three naturalized species. Considering the diversity of the indigenous species of this family in South Africa and the lack of recent studies encompassing these species, a taxonomic revision of the South African indigenous species of Meliaceae is presented here. Phylogenetic analysis, anatomical data, herbarium collections, and online data sources were used in this study. The results confirm the monophyly of Melioideae and Swietenioideae. The incongruence of Turraea previously reported was resolved in this study. Most representative genera of South African Meliaceae were recovered monophyletic with strong support. However, multiple samplings of species and including more markers could provide a better understanding of the relationships among South African species of Meliaceae. The review of the taxonomy of the South African Meliaceae, and especially the study of diagnostic characters and hitherto recorded natural distributions, have value in providing an up-to-date inventory of the indigenous genera and species and an easy means of identifying the taxa. Anatomical characters may be of systematic value to explore higher-level relationships in the family. This study is a contribution to tropical botany and to a more comprehensive database for the Meliaceae.

Integrative description of a new species of Dugesia (Platyhelminthes, Tricladida, Dugesiidae) from Shennongjia, Central China.

A new species of the genus Dugesia (Platyhelminthes, Tricladida, Dugesiidae) from Xiangxi River, Shennongjia Forestry District, Hubei Province, China, is described on the basis of an integrative approach, involving morphology, and molecular systematics. The new species Dugesia saccaria A-T. Wang & Sluys, sp. nov. is characterized by the following features: a dumb-bell-shaped, muscularized hump located just anterior to the knee-shaped bend in the bursal canal; a ventrally displaced ejaculatory duct, which, however, opens terminally through the dorsal portion of the blunt tip of the penis papilla; a ventrally located seminal vesicle, giving rise to a vertically running duct that eventually curves downwards to communicate with the ejaculatory duct via a small diaphragm; oviducts opening asymmetrically into the dorsal portion of the common atrium and at the knee-shaped part of the bursal canal. The phylogenetic position of the new species was determined using four molecular markers (18S rDNA; ITS-1; 28S rDNA; COI), which suggested that it groups with other species of Dugesia from the Australasian and Oriental biogeographical regions.

Molecular phylogeny of Enkianthus Lour. (Ericaceae) based on chloroplast and nuclear DNA sequences with an emphasis on the origin of polyploid species

Enkianthus is a small genus of Ericaceae mostly in east Asia, most constituent species with important ornamental and ecological values. Due to limited sampling of Chinese species and neglect of the origin of polyploid species in previous studies, phylogenetic relationships within this genus remain elusive. Using six chloroplast DNA fragments (psbA-trnH, rpl32-trnL, trnL-trnF, rps16-trnQ, psbJ-petA and matK), nuclear ribosomal internal transcribed spacer (nrITS) and one single-copy nuclear gene (OG9899), we reconstructed the phylogenetic relationships of most Enkianthus species, with a special attempt to decipher the origin of polyploids within the genus. The phylogenetic trees excluding polyploid species indicated that the sections of Meisteria, Andromedina and Enkianthus were all monophyletic groups, with sect. Enkianthus first branching out. The position of E. tubulatus was in conflict between cpDNA and nuclear gene trees, indicating that this species could be of hybrid origin. After the inclusion of polyploid species, we found that members of sect. Enkiantella clustered either with sect. Meisteria or with sect. Andromedina in nuclear gene trees, suggesting this section might be derived from allopolyploidy. The close affinity of sect. Enkiantella with sect. Meisteria in cpDNA tree implies that the members of sect. Meisteria might be the maternal progenitor of sect. Enkiantella. In addition, the octoploid species E. campanulatus might be either an autopolyploid or an allopolyploid with one of its progenitors originating from sect. Meisteria. Our findings provide a robust phylogenetic framework for the evolutionary study and the utility of germplasm resources of Enkianthus. The results of this study will also be helpful for the breeding of Enkianthus cultivars.

DNA taxonomy reveals high species diversity among the stygobiont genus Metastenasellus (Crustacea, Isopoda) in African groundwater

This study aimed to explore the species diversity within the isopod genus Metastenasellus in Benin and Cameroon. Compared to other parts of the world, the described diversity of stygobiotic crustaceans in Africa is low due to a dearth of studies and taxonomic expertise. However, recent research activities in Benin and Cameroon suggest higher groundwater diversity than previously envisioned. Recent sampling campaigns in these countries have shown that Metastenasellus is a major group in the underground aquatic environment. The accumulation of biological material provided an opportunity to explore species diversity within the genus using a DNA taxonomy approach based on the cytochrome c oxidase subunit I (COI) gene fragment. Despite the limitations of using a single-locus approach for species delimitation, an overview of the diversity within the genus Metastenasellus was obtained, revealing the presence of 23 distinct lineages. Several elements suggest that most, if not all, of these lineages represent valid species. These include high genetic distances between lineages, morphologically distinct species separated by genetic distances of the same order of magnitude as between other described lineages, and the coexistence of different lineages at the same stations. Despite a limited sampling effort, these first results indicate a high level of species diversity and endemism within Metastenasellus in the studied regions. The narrow geographic distribution of the lineages suggests strong isolation and limited dispersal abilities. This study highlights the potential for discovering a significant number of new species within this genus and emphasizes the need for further research to uncover the extent of diversity in African stygobiotic isopods.

Revision of Eupyrochroa Blair, 1914 (Coleoptera: Pyrochroidae) based on morphological comparison and molecular phylogenetics.

Eupyrochroa Blair, 1914 is a small genus of fire-colored beetles (Coleoptera: Pyrochroidae) with two putative species recorded from limited historical distributions in China. The two species, E. insignita (Fairmaire, 1894) and E. limbaticollis (Pic, 1909), have been distinguished on the basis of color differences in the pronotum and scutellum, characters now known to exhibit significant variability. In the present study, adult morphology of the two species was compared, and partial fragments of cytochrome c oxidase subunit I (COI) from 36 samples representing 14 pyrochroid species were obtained by extraction and a GenBank search. Nucleotide composition, genetic distance, and phylogeny were analyzed. The results of morphological and molecular analyses indicate consistency, suggesting that the two species are indistinguishable by any significant measure. Therefore, Eupyrochroa limbaticollis (Pic, 1909) is proposed as a junior synonym of E. insignita (Fairmaire, 1894). The species is also redescribed and illustrated, including both adults and larvae.

To and fro in the archipelago: Repeated inter-island dispersal and New Guinea’s orogeny affect diversification of Delias, the world’s largest butterfly genus

The world’s largest butterfly genus Delias, commonly known as Jezebels, comprises ca. 251 species found throughout Asia, Australia, and Melanesia. Most species are endemic to islands in the Indo-Australian Archipelago or to New Guinea and nearby islands in Melanesia, and many species are restricted to montane habitats over 1200 m. We inferred an extensively sampled and well-supported molecular phylogeny of the group to better understand the spatial and temporal dimensions of its diversification. The remarkable diversity of Delias evolved in just ca. 15–16 Myr (crown age). The most recent common ancestor of a clade with most of the species dispersed out of New Guinea ca. 14 Mya, but at least six subsequently diverging lineages dispersed back to the island. Diversification was associated with frequent dispersal of lineages among the islands of the Indo-Australian Archipelago, and the divergence of sister taxa on a single landmass was rare and occurred only on the largest islands, most notably on New Guinea. We conclude that frequent inter-island dispersal during the Neogene—likely facilitated by frequent sea level change—sparked much diversification during that period. Many extant New Guinea lineages started diversifying 5 Mya, suggesting that orogeny facilitated their diversification. Our results largely agree with the most recently proposed species group classification system, and we use our large taxon sample to extend this system to all described species. Finally, we summarize recent insights to speculate how wing pattern evolution, mimicry, and sexual selection might also contribute to these butterflies’ rapid speciation and diversification.

Isolation and characterisation of 17 microsatellite DNA loci from RAD reduced-representation genomes for Asian warty newts, genus Paramesotriton (Caudata: Salamandridae).

Asian warty newts, genus Paramesotriton, are endemic to southern China and northern Vietnam. Despite the achievements in biodiversity, molecular systematics and biogeography of species in this genus, population genetic diversity studies are lacking due to the lack of economical and available genetic markers. In this study, we developed 17 highly polymorphic microsatellite loci from RAD simplified genomic data for the Asian warty newts, genus Paramesotriton and successfully completed cross-species amplification tests on 20 samples of four species of Paramesotriton. These microsatellite markers can be used as important tools to study population genetic structure, levels of gene flow, population differentiation, mating systems and landscape genetics within the genus Paramesotriton and, thus, to make scientific conservation decisions and actions for the conservation of these rare and endangered amphibians.

DNA Barcoding Analysis of Trinidad Haemagogus Mosquitoes Reveals Evidence for Putative New Species.

Background: Haemagogus janthinomys is a primary sylvan vector of yellow fever virus and the emerging Mayaro virus. However, despite its medical importance, there is a dearth of data on the molecular taxonomy of this mosquito species. Methods: In this study, DNA barcoding analysis was performed on 64 adult female mosquitoes from Trinidad morphologically identified as Hg. janthinomys. The mitochondrial cytochrome c oxidase I (COI) gene and ribosomal DNA internal transcribed spacer 2 (ITS2) region of the mosquitoes were PCR amplified and sequenced, and molecular phylogenies inferred. Results: The BLASTN analysis showed that only 20% (n = 13/66) of COI sequences had high similarity (>99% identity) to Hg. janthinomys and the remaining sequences had low similarity (<90% identity) to reference GenBank sequences. Phylogenetic analysis of COI sequences revealed the presence of four strongly supported groups, with one distinct clade that did not align with any reference sequences. Corresponding ITS2 sequences for samples in this distinct COI group clustered into three clades. Conclusions: These molecular findings suggest the existence of a putative new Haemagogus mosquito species and underscore the need for further, more in-depth investigations into the taxonomy and classification of the Haemagogus genus.

Speciation in the Iranian plateau: Molecular phylogeny and evolutionary history of the Persian long‐tailed desert lizard

AbstractMesalina watsonana is a well‐known species of small lacertid lizards with an extensive species distribution that exhibits high genetic diversity. The species has a wide distribution range in Iran, some parts of Turkmenistan, Afghanistan, Pakistan, and northwest India. This study aims to generate phylogenetic and phylogeographic evidence to derive taxonomic recommendations supporting. Furthermore, this species can be used as a model for examining Iranian Platuea's historical biogeography. We conducted a very detailed sampling of its distribution and used genetic approaches. Phylogenetic analyses were done implementing two mitochondrial (Cytb and 16S) and one nuclear (C‐mos) gene fragments. Combination of these results indicated that seven well‐supported distinct clades exist within this species complex, i.e. Kerman clade, Esfarayen clade, Halil clade, Ardestan clade, M. watsonana clade, Bardaskan Clade, and Khuzestan Clade in Iran. Also, our results revealed that several distinct clades diverged due to geologic events when the Dasht‐e‐Kavir and the Zagros Mountains were formed. It seems that the ancestor of M. watsonana spread to Iranian Plateau before the formation of the Zagros Mountains. Orogenic activities of the Zagros Mountains and the formation of deserts have influenced the separation of these lineages from the Late Miocene by allopatric speciation. Generally, our findings suggest that each of the seven clades corresponding to distinct geographic regions deserves to be elevated to the species level.

First Report of Polygonatum cyrtonema Hua Root Rot Caused by Trichoderma virens in China.

Polygonatum cyrtonema Hua is a traditional Chinese medicine, which has anti-oxidant, anti-inflammatory, immunomodulatory, and other pharmacological effects (Lu et al. 2023). In June 2022, A disease of root rot was observed on P. cyrtonema plants in Tonggu County (28°63'89″N, 114°48'07″E), Jiangxi Province, China. The disease incidence was approximately 30% in a surveyed area of 3 hectares, which contained approximately 20,000 plants. Initially, the above-ground parts of the plants did not show any obvious symptoms. However, the underground roots exhibited red-brown spots that gradually expanded and sunken areas appeared, and the diseased plants presented leaf chlorosis and red-brown discoloration of the tubers, eventually leading to plant death. To identify the pathogen, symptomatic root tissues (0.5×0.5×0.5cm) from the lesion margin surface were sterilized with 75% ethanol for 30s, 3% NaClO for 3 min followed by rinsing three times with sterile water. The sterile root pieces were placed on potato dextrose agar (PDA) and incubated at 25℃. Thirteen pure fungal isolates with the same morphological characteristics were obtained by monosporic isolation from 20 pieces of roots, and the representative isolates, HJGF1-1, HJGF1-2 were used for morphological studies and phylogenetic analyses. Initially, the two colonies on PDA appeared white with cotton-shaped aerial hyphae, which later turned light green to green and formed concentric rings. At the end of the conidiophores, 3 to 6 pear-shaped branches are irregularly gathered, and the angles between the branches are acute. The conidia were mostly solitary ellipsoid or obovate with the size of (3.7-5.9) × (3.6-4.5) μm (n=100). These morphological characteristics are consistent with the description of a Trichoderma spp. (Kamala et al. 2015). For molecular identification, the internal transcribed spacer (ITS), translation elongation factor 1-alpha (TEF-1α) and RNA polymerase II second largest subunit (RPB2) sequences were PCR amplified using primer pairs of ITS1/ITS4 (White et al. 1990), EF1-728F/EF1-986R (Carbone et al. 1999), and RPB2-5F2/RPB2-7cR (O'Donnell et al. 2022), respectively. BLAST analysis showed that the ITS, TEF-1α and RPB2 sequences of isolates HJGF1-1 (GenBank accession nos. OR229621, OR290791, OR334600) and HJGF1-2 (GenBank accession nos. OR229622, OR290792, OR334600) showed 99%-100% identity with multiple GenBank sequences of Trichoderma virens. A phylogenetic tree based on concatenated sequences of ITS, TEF-1α and RPB2 using maximum-likelihood analyses revealed that the two isolates HJGF1-1 and HJGF1-2 were in the same clade with T. virens strains. The two isolates were identified as T. virens based on the morphological characteristics and molecular phylogeny. To test pathogenicity, ten healthy P. cyrtonema plants (one tuber each, 5 tubers per isolate, n=10) in the field were pin-pricked with a sterile needle and pour-inoculated with 5 mL spore suspension per tuber (1× 107 conidia/ mL) with a temperature of about 28℃. Another five tubers were were pin-pricked with a sterile needle, inoculated with sterile water and served as controls. The resulting symptoms were similar to those on the original infected plants in the field, and control tubers remained symptomless fourteen days after inoculation. T. virens was reisolated from the diseased tubers, nevertheless no pathogenic fungus was isolated from the control tubers. T. virens has been reported causing disease on tulip bulb (Lou et al. 2003) but has not previously been reported causing disease on P. cyrtonema. Although several species of Trichoderma are known to be beneficial microorganisms, the beneficial fungus may have had an evolutionary period of interaction with plants in which it behaved as a plant pathogen (Poveda et al. 2022). To our knowledge, this is the first report of T. virens infecting P. cyrtonema in China. This result may expanded the etiological study of T. virens and the control strategy of P. cyrtonema root rot.

Abstract IA015: Phylomedicine of cancers and tumors: A molecular phylogenetic approach to oncology

Abstract Genetic mutations arising from germline and somatic cell divisions cause cellular diversification and form the need for integrating an evolutionary perspective in oncology. Such mutations can lead to the emergence of aberrant cell types, driving the progression of tumorigenic and metastatic cancer subclones. Advances in single-cell and bulk sequencing technologies now routinely reveal a trove of genetic alterations in cancer cells, tissues, and genes. These data enable the reconstruction of detailed cellular phylogenies and the evolutionary trajectories of genes implicated in cancer. This presentation will introduce our approaches for reconstructing cellular phylogenies and their downstream applications in genomic medicine. They include novel approaches for inferring cellular phylogenies by correcting for inaccuracies in single-cell genomic data and separating mixed subclone signals in bulk sequencing data through molecular evolutionary principles. Incorporating accurate phylogenetic relationships, we have developed many computational methods, including diagnosing functional outcomes of nonsynonymous mutations, tracking metastatic pathways retrospectively, and predicting the risk of hematological malignancies. This presentation will briefly introduce these approaches and suggest that integrating molecular phylogenetics with genomic science—Phylomedicine—holds promise for enhancing the fundamental understanding of cancers and advancing approaches to predicting, diagnosing, and treating cancers. Citation Format: Sudhir Kumar. Phylomedicine of cancers and tumors: A molecular phylogenetic approach to oncology [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr IA015.