A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer [PDF]
, 2005 We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition to branch lengths in the phylogeny. The likelihood for the changes in the size of a gene family across different organisms can be calculated in O(N+hM^2 ...
A.B. Simonson +43 more
arxiv +4 more sources
Unique Perfect Phylogeny Characterizations via Uniquely Representable Chordal Graphs [PDF]
arXiv, 2013 The perfect phylogeny problem is a classic problem in computational biology, where we seek an unrooted phylogeny that is compatible with a set of qualitative characters. Such a tree exists precisely when an intersection graph associated with the character set, called the partition intersection graph, can be triangulated using a restricted set of fill ...
Gysel, Rob
arxiv +2 more sources
Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts [PDF]
PeerJ, 2022 Shrimps of the family Alvinocarididae, endemic species to deep sea chemosynthetic ecosystems, harbor epibiotic microbes on gills which probably play important roles in the survival of the shrimps.
Min Hui +3 more
doaj +2 more sources
Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea [PDF]
PeerJ, 2022 Echinoids are an important component in benthic marine environments, which occur at all depths from the shallow-water hard substrates to abyssal depths.
Shao’e Sun, Ning Xiao, Zhongli Sha
doaj +2 more sources
A review of the common crab genus Macromedaeus Ward, 1942 (Brachyura, Xanthidae) from China Seas with description of a new species using integrative taxonomy methods [PDF]
PeerJ, 2022 Macromedaeus is one of the most common xanthid genera in shallow waters of the Indo-West Pacific. In this study, we describe a new species, Macromedaeus hainanensis sp. nov., and report on two newly recorded species, M. quinquedentatus (Krauss, 1843) and
Ziming Yuan, Wei Jiang, Zhongli Sha
doaj +2 more sources
Review of the genus Loimia Malmgren, 1866 (Annelida, Terebellidae) from China seas with recognition of two new species based on integrative taxonomy [PDF]
PeerJ, 2020 Specimens of the genus Loimia (Annelida, Terebellidae) deposited in the Marine Biological Museum of the Chinese Academy of Sciences (MBMCAS) together with materials newly collected from China seas were examined.
Weina Wang +3 more
doaj +2 more sources
Tabanids as possible pathogen vectors in Senegal (West Africa)
Parasites & Vectors, 2020 Background Species of the Tabanidae are potent vectors of human and animal diseases, but they have not been thoroughly investigated to date. In Senegal (West Africa), little information is available on these dipterans.
Mohamed Lamine Keita +4 more
doaj +1 more source
Diversity, 2022 The investigations of the molecular components of eye development and phototransduction in deep-sea species are important to elucidate the mechanism of their adaptation to dim light.
Min Hui +3 more
doaj +1 more source
Morphology and molecular phylogeny of three new deep-sea species of Chrysogorgia (Cnidaria, Octocorallia) from seamounts in the tropical Western Pacific Ocean [PDF]
PeerJ, 2020 Three new species of Chrysogorgia were discovered from seamounts in the tropical Western Pacific Ocean. Chrysogorgia dendritica sp. nov. and Chrysogorgia fragilis sp. nov. were collected from the Kocebu Guyot of the Magellan Seamount chain with the water
Yu Xu, Zifeng Zhan, Kuidong Xu
doaj +2 more sources
Scientific Reports, 2022 The deep sea (> 200 m) is considered as the largest and most remote biome, which characterized by low temperatures, low oxygen level, scarce food, constant darkness, and high hydrostatic pressure.
Shao’e Sun, Ning Xiao, Zhongli Sha
doaj +1 more source