Uncertainties surrounding the evolutionary origin of the epipelagic fish family Scombridae (tunas and mackerels) are symptomatic of the difficulties in resolving suprafamilial relationships within Percomorpha, a hyperdiverse teleost radiation that contains approximately 17,000 species placed in 13 ill-defined orders and 269 families. Here we find that scombrids share a common ancestry with 14 families based on (i) bioinformatic analyses using partial mitochondrial and nuclear gene sequences from all percomorphs deposited in GenBank (10,733 sequences) and...

Background: Tribe Orchideae dominates the orchid flora of the temperate Northern Hemisphere but its representatives in East Asia had been subject to less intensive phylogenetic study than those in Eurasia and North America. Although this situation was improved recently by the molecular phylogenetic study of Jin et al., comparatively few species were analyzed from the species-rich and taxonomically controversial East Asian Amitostigma alliance. Here, we present a framework nrITS tree of 235 accessions of Orchideae...

Floristic surveys are crucial to the conservation of biodiversity, but the vast majority of such surveys are limited to listing species names, and few take into account the evolutionary history of species. Here, we combine classical taxonomic and molecular phylogenetic (DNA barcoding) approaches to catalog the biodiversity of pteridophytes (ferns and lycophytes) of the Nectandra Cloud Forest Reserve, Costa Rica. Surveys were carried out over three field seasons (2008, 2011, and 2013), resulting in 176...

Molecular evolutionary rates vary among lineages and influence the evolutionary process. Here, we report elevated genome-wide mutation rates in Podostemaceae, a family of aquatic plants with a unique body plan that allows members to live on submerged rocks in fast-flowing rivers. Molecular evolutionary analyses using 1,640 orthologous gene groups revealed two historical increases in evolutionary rates: the first at the emergence of the family and the second at the emergence of Podostemoideae, which is the...

Traditional Chinese medicine (TCM) prescriptions have multiple bioactive properties. “Gui Zhi–Shao Yao” herb pair is widely used to treat chronic pain (CP), as well as anxiety and depression. However, its related targets and underlying mechanisms have not been deciphered. In this study, the network pharmacology method was used to explore the bioactive components and targets of “Gui Zhi–Shao Yao” herb pair and further elucidate its potential biological mechanisms of action in the treatment of CP...

Islands are a challenging habitat for organisms with weak dispersal power. We aimed to elucidate how geological history, geography, accidental dispersal events and species ecology affected different colonisation and genetic divergence patterns on continental and oceanic islands among species of a cicada group, which are poor dispersers. Location: Japanese Archipelago, Ogasawara Islands, Ryukyu Archipelago. Taxon: Cicadas of the genus Meimuna (Hemiptera: Cicadidae). We performed phylogenetic analysis, divergence time estimation, and ancestral area reconstruction using two...

Additional file 1: Figure S1. Physical maps of nucleomorph chromosome 1 for three Cryptomonas species (5 strains in total). Genes on the left indicate transcription from bottom to top, and genes on the right indicate transcription from top to bottom. Colors of the CDS blocks correspond to predicted functional categories, and re-arranged genes are highlighted in yellow. Gene losses between the photosynthetic species C. curvata and the non-photosynthetic species C. paramecium and Cryptomonas sp. CCAC1634B...

Additional file 3: Table S2. KEGG and GO annotation clustering of regulated genes in LINP1-depleted cells

Additional file 4: Table S3. List of proteins specifically associating with LINP1 identified by RNA pulldown followed by HPLC-MS

Background: Antarctic notothenioids are an impressive adaptive radiation. While they share recent common ancestry with several species-depauperate lineages that exhibit a relictual distribution in areas peripheral to the Southern Ocean, an understanding of their evolutionary origins and biogeographic history is limited as the sister lineage of notothenioids remains unidentified. The phylogenetic placement of notothenioids among major lineages of perciform fishes, which include sculpins, rockfishes, sticklebacks, eelpouts, scorpionfishes, perches, groupers and soapfishes, remains unresolved. We investigate...

Additional file 2: Table S1. Gene content of eight cryptophyte nucleomorph genomes. Table S2. Sequence similarities of hypothetical ORFs across eight cryptophyte nucleomorph genomes. Table S3. Conserved hypothetical ORFs (nORFs) in eight cryptophyte nucleomorph genomes.

Temporal and spatial changes of ten conifer genera that are endemic to East Asia were analyzed based on fossil data from humid temperate forests in the Japanese Islands and Korean Peninsula to elucidate the phytogeographic history, and to understand differences between those genera eliminated from the Japanese Islands and those remained extant. All these genera, except for Thujopsis, have existed in the area since the Paleogene and remained in the Japanese islands after initial separation...

A major challenge in evolutionary developmental biology is to understand how genetic mutations underlie phenotypic changes. In principle, selective pressures on the phenotype screen the gene pool of the population. Teeth are an excellent model for understanding evolutionary changes in the genotype-phenotype relationship since they exist throughout vertebrates. Genetically modified mice (mutants) with abnormalities in teeth have been used to explore tooth development. The relationship between signaling pathways and molar shape, however, remains elusive due...

Variation in mitochondrial genome composition across intraspecific, interspecific, and higher taxonomic scales has been little studied in lichen obligate symbioses. Cladonia is one of the most diverse and ecologically important lichen genera, with over 500 species representing an array of unique morphologies and chemical profiles. Here, we assess mitochondrial genome diversity and variation in this flagship genus, with focused sampling of two clades of the “true” reindeer lichens, Cladonia subgenus Cladina, and additional genomes from...

Additional file 5: Table S4. KEGG annotation clustering of regulated proteins specifically associating with LINP1 identified by RNA pulldown followed by HPLC-MS

Additional file 2: Table S1. Differentially expressed genes in response to LINP1 depletion

A new polyconitid rudist, Magallanesia canaliculata gen. et sp. nov., of probably late Albian age, is described from the Pulangbato area, central Cebu Island, the Philippines in the western Central Pacific and Takuyo Daini Seamount, now located in the Northwest Pacific. It is similar to Praecaprotina Yabe and Nagao, 1926, a Japanese – Central Pacific endemic genus of late Aptian – early Albian age, but differs in having canals that developed by partitioning of the...

Additional file 5: Table S4. KEGG annotation clustering of regulated proteins specifically associating with LINP1 identified by RNA pulldown followed by HPLC-MS

Additional file 6: Table S5. Oligonucleotides used for qRT-PCR, knockout, knockdown and ISH detection

Aim: Vicariance events have been proposed as a major source of lineage divergence on continental islands, whereas dispersal events followed by isolation have been proposed as the major cause on oceanic islands. However, organisms on continental islands may include taxa with characteristics similar to those on oceanic islands. Lineage divergence unassociated with the geological events that separated islands may also have occurred. This study addresses these possibilities through morphological and molecular phylogeographic analyses of land...

Although sunlight is essential for plant growth and development, the relative importance of each spectral region in shaping functional traits is poorly understood, particularly in dynamic light environments such as forest ecosystems. We examined responses of 25 functional traits from groups of 11 shade-intolerant and 12 understorey shade-tolerant forb species grown outdoors under five filter treatments differing in spectral transmittance: (1) transmitting c 95% of solar radiation; (2) attenuating ultraviolet-B (UV-B); (3) attenuating all UV;...

The segmented trapdoor spiders (Liphistiidae) are the sole surviving family of the suborder Mesothelae, which forms the sister lineage to all other living spiders. Liphistiids have retained a number of plesiomorphic traits and their present-day distribution is limited to East and Southeast Asia. Studying this group has the potential to shed light on the deep evolutionary history of spiders, but the phylogeny and divergence times of the family have not been resolved with confidence. We...

Traditional Chinese medicine (TCM) prescriptions have multiple bioactive properties. “Gui Zhi–Shao Yao” herb pair is widely used to treat chronic pain (CP), as well as anxiety and depression. However, its related targets and underlying mechanisms have not been deciphered. In this study, the network pharmacology method was used to explore the bioactive components and targets of “Gui Zhi–Shao Yao” herb pair and further elucidate its potential biological mechanisms of action in the treatment of CP...

Genital morphology reveals rapid diversification among species, and species-specific divergence in genital morphology may result in reproductive isolation and promote speciation. Natural selection against maladaptive hybridization may cause species-specific genital divergence. In this context, divergence in mating traits is expected to be greater between sympatric populations than between allopatric populations in a pair of species, known as reproductive character displacement (RCD). However, there are few examples of RCD in the genital morphology of closely related...

Identifying the phylogenomic underpinnings of specialized phenotypes that fueled evolutionary transitions into new adaptive zones is central to evolutionary biology. The order Eulipotyphla (e.g., moles, shrews, and hedgehogs) is ideally suited to address this question as semi-fossorial, fossorial, and semi-aquatic forms have repeatedly arisen from terrestrial forbearers. However, our understanding of the ecomorphological pathways leading to these diverse lifestyles has been confounded by a fragmentary fossil record and potential morphological convergence. The net surface charge...