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opencc-zeroJun 2022View details →

The evolution of multi-gene families and metabolic pathways in the evening primroses (Oenothera: Onagraceae): a comparative transcriptomics approach

The plant genus Oenothera has played an important role in the study of genome evolution and plant defense and reproduction. Here, we built on the 1kp transcriptomic dataset and developed a molecular resource of 63 transcriptomes and present a large-scale comparative study across 29 Oenothera species. We produced 2.3 million transcripts and 25.4 Mb of total length assembly per individual. We used this transcriptome resource to examine genome-wide evolutionary patterns and functional diversification by searching for orthologous genes and performed gene family evolution analysis. We found wide heterogeneity in gene family evolution across the genus, with section Oenothera exhibiting the most pronounced evolutionary changes. Overall, more significant expansions occurred than contractions. We also analyzed the molecular evolution of phenolic metabolism by retrieving proteins annotated for phenolic enzymatic complexes. We identified 1,568 phenolic genes arranged into 83 multigene families that varied widely across the genus. All taxa experienced rapid phenolic evolution involving 33 gene families, which exhibited large expansions, gaining about 2-fold more genes than they lost. Upstream enzymes phenylalanine ammonia-lyase (PAL) and 4-coumaroyl: CoA ligase (4CL) accounted for most of the significant expansions and contractions. Our results suggest that adaptive responses to environmental stress coupled with non-adaptive evolutionary forces have contributed to Oenothera diversification and rapid gene family evolution.

opencc-zeroJan 2023View details →

Multi-gene phylogeny of North American clear-winged moths (Lepidoptera: Sesiidae): A foundation for future evolutionary study of a speciose mimicry complex

Sesiids are a diverse group of predominantly diurnal moths, many of which are Batesian mimics of Hymenoptera. However, their diversity and relationships are poorly understood. A multi-gene phylogenetic analysis of 48 North American sesiid species confirmed the traditional taxonomic tribal ranks, demonstrated the paraphyly of Carmenta and Synanthedon with respect to several other genera, and ultimately provided minimal phylogenetic resolution within and between North American and European groups. Character support from each gene suggested inconsistency between the phylogenetic signal of the CAD gene and that of the other four genes. However, removal of CAD from subsequent phylogenetic analyses did not substantially change the initial phylogenetic results or return Carmenta and Synanthedon as reciprocally monophyletic, suggesting it was not impacting the overall phylogenetic signal. The lack of resolution using genes that are typically informative at the species level for other lepidopterans suggests a surprisingly rapid radiation of species in Carmenta/Synanthedon. This group also exhibits a wide range of mimicry strategies and hostplant usage, which could be fertile ground for future study.

publicJan 2023View details →

Multi-gene phylogeny of North American clear-winged moths (Lepidoptera: Sesiidae): A foundation for future evolutionary study of a speciose mimicry complex

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publicJun 2022View details →

The evolution of multi-gene families and metabolic pathways in the evening primroses (Oenothera: Onagraceae): a comparative transcriptomics approach

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Supplementary material 7 from: Wiemers M, Chazot N, Wheat CW, Schweiger O, Wahlberg N (2020) A complete time-calibrated multi-gene phylogeny of the European butterflies. ZooKeys 938: 97-124. https://doi.org/10.3897/zookeys.938.50878

Figure S5. Time-calibrated tree of European butterflies Section IV: Nymphalidae Part II: Subfamilies Libytheinae, Danainae & Satyrinae

Supplementary material 4 from: Wiemers M, Chazot N, Wheat CW, Schweiger O, Wahlberg N (2020) A complete time-calibrated multi-gene phylogeny of the European butterflies. ZooKeys 938: 97-124. https://doi.org/10.3897/zookeys.938.50878

Figure S2. Time-calibrated tree of European butterflies Section I: Papilionidae, Hesperiidae & Pieridae

Supplementary material 6 from: Wiemers M, Chazot N, Wheat CW, Schweiger O, Wahlberg N (2020) A complete time-calibrated multi-gene phylogeny of the European butterflies. ZooKeys 938: 97-124. https://doi.org/10.3897/zookeys.938.50878

Figure S4. Time-calibrated tree of European butterflies Section III: Nymphalidae Part I: Subfamilies Limenitidinae, Heliconiinae, Apaturinae & Nymphalinae

Supplementary material 1 from: Wiemers M, Chazot N, Wheat CW, Schweiger O, Wahlberg N (2020) A complete time-calibrated multi-gene phylogeny of the European butterflies. ZooKeys 938: 97-124. https://doi.org/10.3897/zookeys.938.50878

Table listing of European butterfly species with higher taxonomy, voucher codes and accession numbers for the sequences used to build the phylogeny.

opencc-zeroDec 2017View details →

dryad32/100

Data from: Bryozoan genera Fenestrulina and Microporella no longer confamilial; multi-gene phylogeny supports separation

Bryozoans are a moderately diverse, mostly marine phylum with a fossil record extending to the early Ordovician. Compared to other phyla, little is known about their phylogenetic relationships at both lower and higher taxonomic levels. Hence, an effort is being made to elucidate the phylogenetic relationships among bryozoans. Here, we present newly sequenced nuclear and mitochondrial genes for 21 cheilostome bryozoans and compile these with existing orthologous molecular data. Using these data, we focus on reconstructing the phylogenetic relationships of Fenestrulina and Microporella, two species-rich genera. They are currently placed in a globally distributed family, Microporellidae, defined by having a semicircular primary orifice and a proximal ascopore, although there are indirect inferences in the morphological literature that suggest they might not be confamilial. Our six-gene phylogenetic analysis reveals that the genera Fenestrulina and Microporella are each monophyletic, with the sister clade to Microporella comprising non-microporellids. These genera thus have a polyphyletic relationship and should not be placed in the same family. Our result supports the reinstatement of the family Fenestrulinidae Jullien, 1888 for Fenestrulina and genera with comparable frontal shield and ooecial morphologies. Our well-supported phylogeny based on independent molecular data lends credit to existing phylogenetic hypotheses based on morphological observations but does not conform to the current classification of these particular bryozoans. This illustrates the general need for a rethink of bryozoan higher-level systematics, ideally based on both morphological and molecular data.

FIGURE 3 in Morphology and multi-gene phylogeny reveal a new fungal genus and species from Hevea brasiliensis latex in Yunnan, China

FIGURE 3. Heveicola xishuangbannaensis (KUMCC 21-0086, ex-type) on PDA. A. Germinated conidium. B, C. Upper and lower view of cultures on PDA. D–F, K. Synnemata on PDA medium. G–I. Conidia growing from mycelia. L. Conidiophores with conidia. J, M. Conidia. Scale bars: A, G = 50 μm, F = 500 μm, H = 100 μm, I = 40 μm, J, L, M = 30 μm, K = 150 μm.

FIGURE 2 in Morphology and multi-gene phylogeny reveal a new fungal genus and species from Hevea brasiliensis latex in Yunnan, China

FIGURE 2. Heveicola xishuangbannaensis (HKAS 115759, holotype). A–C.Appearance of colonies on the substrate. D, E. Conidiophores with conidia. F–O. Conidia. Scale bars: D–F = 50 μm, G–I, K, L = 10 μm, J, M–O = 30 μm.

FIGURE 1 in Morphology and multi-gene phylogeny reveal a new fungal genus and species from Hevea brasiliensis latex in Yunnan, China

FIGURE 1. RAxML tree based on a combined dataset of LSU, SSU, rpb2 and tef1-α partial sequences. Bootstrap support values for maximum likelihood (ML) equal to or higher than 60% and Bayesian probability (BYPP) equal to or higher than 0.90 are given above/ below the branches. Newly generated sequences are shown in red.

FIGURE 4 in Morphology and multi-gene phylogeny reveal a new fungal genus and species from Hevea brasiliensis latex in Yunnan, China

FIGURE 4. Split graph showing results of PHI test of Heveicola xishuangbannaensis and closely related taxa using LogDet transformation and splits decomposition. PHI test results Φw ≤ 0.05 indicate that there is significant recombination within the dataset. The new taxon is in red font.

opencc-zeroFeb 2022View details →

dryad32/100

Sergestidae shrimp family single- and multi-gene alignments and tree files

Deep-sea shrimp belonging to the family Sergestidae provide a unique system for studying the evolution of bioluminescence. Most species within the family possess autogenic bioluminescent photophores in one of three distinct forms: lensed photophores, non-lensed photophores, or internal organs of Pesta. This morphological diversity across Sergestidae has resulted in recent major taxonomic revisions, dividing the two major genera (Sergia and Sergestes) into 15. Here, we capitalize on molecular data to construct an updated genus-level phylogeny of sergestid shrimp. DNA was successfully extracted from approximately 87 individuals belonging to 13 of the 15 newly proposed genera. We implemented a "genome skimming" approach, allowing us to capture mitochondrial genomic data across 19 Sergestidae species. Additional individuals have been incorporated into the phylogeny through Sanger sequencing of both nuclear (H3, NAK) and mitochondrial (16S and COI) genes. The resulting molecular phylogeny is compared with previous morphological trees with specific attention to genus-level relationships. The -sergestes group was rendered non-monophyletic, and the -sergia group was recovered as monophyletic. Ancestral state reconstructions of light organ type indicate the organs of Pesta is the ancestral state for the family. Non-lensed photophores evolved once across the -sergia group, but were later lost in the deepest living genus, Sergia. Lensed photophores also evolved once within the genera Prehensilosergia, Lucensosersgia, and Challengerosergia. Our findings identify preliminary patterns across light organ type and species' depth distributions, however future research that incorporates finer-scale depth data and more species is needed to confirm our findings.

FIGURES 17–22 in Review of Australian Scirtes Illiger, Ora Clark and Exochomoscirtes Pic (Coleoptera: Scirtidae) including descriptions of new species, new groups and a multi-gene molecular phylogeny of Australian and non-Australian species

FIGURES 17–22. Tegmen and penis of: 17) Scirtes auratus; 18) S. serratus; 19) S. interstinctus; 20) S. lynnae; 21) S. albamaculatus. 22) Penis of S. pinjarraensis.

FIGURES 23–28. 23 in Review of Australian Scirtes Illiger, Ora Clark and Exochomoscirtes Pic (Coleoptera: Scirtidae) including descriptions of new species, new groups and a multi-gene molecular phylogeny of Australian and non-Australian species

FIGURES 23–28. 23) Male terminalia of Scirtes zwicki: a) tergite 8, b) tergite 9, c) sternite 9, d) trigonium, e) tegmen. 24) Habitus photograph of Scirtes zwicki; 25) ditto, ♀ S. albamaculatus. 26) Clypeolabrum of last instar larva of S. lynnae; 27) ditto, S. serratus; 28) ditto, S. triangularis.

FIGURES 11–16 in Review of Australian Scirtes Illiger, Ora Clark and Exochomoscirtes Pic (Coleoptera: Scirtidae) including descriptions of new species, new groups and a multi-gene molecular phylogeny of Australian and non-Australian species

FIGURES 11–16. Prehensors and bursal sclerites of: 11) Scirtes helmsi; 12) S. brisbanensis; 13) S. peniculus; 14) S. pinjarraensis; 15) S. storeyi; 16) S. triangularis.

FIGURE 1 in Review of Australian Scirtes Illiger, Ora Clark and Exochomoscirtes Pic (Coleoptera: Scirtidae) including descriptions of new species, new groups and a multi-gene molecular phylogeny of Australian and non-Australian species

FIGURE 1. Phylogenetic tree of Australian Scirtes, Ora, Exochomoscirtes and some related Asian species, based on Bayesian inference (BI) analysis of concatenated sequence data of COI, EF1-a and TOP1. A tree with identical topology was obtained using ML analyses of the same data set and a concatenated dataset comprising only COI and TOP1. Numbers on branches give posterior probabilities (left) from BI analyses and bootstrap proportions (right) as a percentage of 500 pseudoreplicates from a ML analysis.

FIGURES 6–10 in Review of Australian Scirtes Illiger, Ora Clark and Exochomoscirtes Pic (Coleoptera: Scirtidae) including descriptions of new species, new groups and a multi-gene molecular phylogeny of Australian and non-Australian species

FIGURES 6–10. Prehensor and bursal sclerite of: 6) Scirtes albamaculatus; 7) S. exoletus; 8) S. nigerpalpus; 9) S. orientalis; 10) S. zwicki.