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PubMed Journal Database | Molecular phylogenetics and evolution RSS

08:14 EDT 26th May 2019 | BioPortfolio

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Showing PubMed Articles 1–25 of 449 from Molecular phylogenetics and evolution

Insights into the phylogeny of Hemiptera from increased mitogenomic taxon sampling.

Although reconstruction of the phylogeny of Hemiptera has progressed tremendously over the past two decades, some higher-level relationships remain poorly resolved. Here, we investigated the Hemiptera higher-level relationships using full mitochondrial genome data from 357 ingroup species, representing the most comprehensive sampling yet undertaken for reconstructing the phylogeny of this group. In this study, 92 mitochondrial genomes were newly determined. Various data treatment methods and substitution mo...

Phylogeny of the genus Hypophthalmus Cuvier, 1829 (Pimelodidae - Siluriformes), based on a multilocus analysis, indicates diversification and introgression in the Amazon basin.

The genus Hypophthalmus encompasses four valid South American freshwater catfish species: H. marginatus, H. edentatus, H. fimbriatus, and H. oremaculatus. More recently two new species were proposed Hypophthalmus n. sp. 1 and Hypophthalmus n. sp. 2. While Hypophthalmus species are a fundamentally important resource for the commercial fisheries that operate in the continental waters of the Amazon basin, their phylogenetic relationships and the true diversity of the genus have yet to be defined conclusively. ...

Using Nuclear Loci and Allelic Variation to Disentangle the Phylogeny of Phyllostachys (Poaceae, Bambusoideae).

With the development of sequencing technologies, the use of multiple genes has become conventional for resolving difficult phylogenies. However, this technique also presents challenges due to gene-tree discordance, as a result of incomplete lineage sorting (ILS) and reticulate evolution. Although alleles can show sequence variation within individuals, which contain information regarding the evolution of organisms, they continue to be ignored in almost all phylogenetic analyses using randomly phased genome s...

Low-copy nuclear sequence data confirm complex patterns of farina evolution in notholaenid ferns (Pteridaceae).

Notholaenids are an unusual group of ferns that have adapted to, and diversified within, the deserts of Mexico and the southwestern United States. With approximately 40 species, this group is noted for being desiccation-tolerant and having "farina"-powdery exudates of lipophilic flavonoid aglycones-that occur on both the gametophytic and sporophytic phases of their life cycle. The most recent circumscription of notholaenids based on plastid markers surprisingly suggests that several morphological characters...

The application of high-throughput sequencing for taxonomy: The case of Plantago subg. Plantago (Plantaginaceae).

Plantago is a cosmopolitan genus including over 250 species, concentrated in temperate and high-elevation tropical regions. The taxonomy of Plantago is very difficult, mainly because of its reduced morphology, which features relatively few characters for species classification. Consequently, the infrageneric classification of the genus remains controversial and inadequate. In this study we applied high-throughput plastid genome skimming to provide powerful phylogenetic resolution to clarify the relationship...

The Complete Organelle Genomes of Physochlaina orientalis: Insights into Short Sequence Repeats across Seed Plant Mitochondrial Genomes.

Short repeats (SR) play an important role in shaping seed plant mitochondrial genomes (mtDNAs). However, their origin, distribution, and relationships across the different plant lineages remain unresolved. We focus on the angiosperm family Solanaceae that shows a wide diversity in repeat content and extend the study to a wide diversity of seed plants. We determined the complete nucleotide sequences of the organellar genomes of the medicinal plant Physochlaina orientalis (Solanaceae), member of the tribe Hyo...

Cryptic speciation in the Chinese white pine (Pinus armandii): Implications for the high species diversity of conifers in the Hengduan Mountains, a global biodiversity hotspot.

Conifers are the largest and ecologically and economically most important component group of the gymnosperms. Despite their slow rate of molecular evolution, rapid and recent diversification was unexpectedly prevalent in this ancient group in the Hengduan Mountains, a world's biodiversity hotspot and gymnosperm diversity center in Southwest China. In this study, we investigated the underlying mechanisms and disentangled the interactions of geography and ecology in speciation and evolution in Pinus armandii,...

Tropical Asian Origin, Boreotropical Migration and Long-distance Dispersal in Nettles (Urticeae, Urticaceae).

The tribe Urticeae (Urticaceae), popularly known as Nettles, include 12 genera and ca. 200 species, constituting a diverse and cosmopolitan plant clade centered in tropical Asia, Africa, and South America. The global distribution of this clade makes it an excellent group to test hypotheses regarding the processes underlying tropical intercontinental disjunctions. More specifically, it allows us to test whether current distribution patterns resulted from recent transoceanic long-distance dispersal or ancient...

Miocene climate change as a driving force for multiple origins of annual species in Astragalus (Fabaceae, Papilionoideae).

Astragalus, a highly diverse genus of flowering plants with its highest center of diversity in West Asia, is a classic example of rapid species-level radiation and adaptation to a diversity of habitats throughout the world. We examined the historical biogeography of Astragalus using molecular dating and ancestral area reconstruction to understand how past climate changes, geographical patterns and transition in life history have provoked diversification of Astragalus. Our results suggest that Astragalus pro...

Molecular phylogeny of the Pectinoidea (Bivalvia) indicates Propeamussiidae to be a non-monophyletic family with one clade sister to the scallops (Pectinidae).

Scallops (Pectinidae) are one of the most diverse families of bivalves and have been a model system in evolutionary biology. However, in order to understand phenotypic evolution, the Pectinidae needs to be placed in a deeper phylogenetic framework within the superfamily Pectinoidea. We reconstructed a molecular phylogeny for 60 species from four of the five extant families within the Pectinoidea using a five gene dataset (12S, 16S, 18S, 28S rRNAs and histone H3). Our analyses give consistent support for the...

Historical biogeography of the fern genus Polystichum (Dryopteridaceae) in Austral South America.

A group of seven endemic Polystichum species inhabit Patagonia, the southern region of South America. To date, evolutionary relationships of these Austral South American Polystichum remain unknown. The biota of the Southern Andes appears to be more closely related to the temperate Australasian species than to northern South American ones. Differences morphological characters suggested that Austral South American Polystichum follow that biogeographical pattern, not being closely related to their congeners in...

Genetic data reveals a complex history of multiple admixture events in presently allopatric wild gingers (Asarum spp.) showing intertaxonomic clinal variation in calyx lobe length.

Clinal variation is a major pattern of observed phenotypic diversity and identifying underlying demographic processes is a necessary step to understand the establishment of clinal variation. The wild ginger series Sakawanum (genus Asarum) comprises four taxa, which exhibit intertaxonomic clinal variation in calyx lobe length across two continental islands isolated by a sea strait. To test alternative hypotheses of the evolutionary history and to determine the implications for the formation of clinal variati...

Phylogenomic analyses reveal an exceptionally high number of evolutionary shifts in a florally diverse clade of African legumes.

Detarioideae is well known for its high diversity of floral traits, including flower symmetry, number of organs, and petal size and morphology. This diversity has been characterized and studied at higher taxonomic levels, but limited analyses have been performed among closely related genera with contrasting floral traits due to the lack of fully resolved phylogenetic relationships. Here, we used four representative transcriptomes to develop an exome capture (target enrichment) bait for the entire subfamily ...

Nuclear and plastid DNA phylogeny of tribe Cardueae (Compositae) with Hyb-Seq data: A new subtribal classification and a temporal diversification framework.

Classification of tribe Cardueae in natural subtribes has always been a challenge due to the lack of support of some critical branches in previous phylogenies based on traditional Sanger markers. With the aim to propose a new subtribal delimitation, we applied a Hyb-Seq approach to a set of 76 Cardueae species representing all subtribes and informal groups defined in the tribe, targeting 1061 nuclear conserved orthology loci (COS) designed for Compositae and obtaining chloroplast coding regions as by-produc...

Biogeography of Mesalina (Reptilia: Lacertidae), with special emphasis on the Mesalina adramitana group from Arabia and the Socotra Archipelago.

The lacertid lizards of the genus Mesalina inhabit the arid regions of the Old World, from North Africa to NW India. Of the 19 recognized species within the genus, eleven occur in Arabia. In this study, we explore the genetic variability and phylogeographic patterns of the less studied M. adramitana group from southern Arabia and the Socotra Archipelago within the phylogenetic and biogeographic context of the entire genus. Our unprecedented sampling extends the distribution ranges of most Mesalina species a...

Morphological evolution and classification of the red algal order Ceramiales inferred using plastid phylogenomics.

The order Ceramiales contains about one third of red algal diversity and it was classically classified into four families according to morphology. The first phylogenies based on one or two molecular markers were poorly supported and failed to resolve these families as monophyletic. Nine families are currently recognized, but relationships within and among them are poorly understood. We produced a well-resolved phylogeny for the Ceramiales using plastid genomes for 80 (28 newly sequenced) representative spec...

Global phylogeography reveals the origin and the evolutionary history of the Gypsy moth (Lepidoptera, Erebidae).

We examined the global phylogeography of gypsy moth (Lymantria dispar L.) using molecular data based on mitochondrial and nuclear genes. Populations from all biogeographic regions of the native and introduced range of L. dispar, were sampled to fully document intraspecific and subspecies variation, identify potential cryptic species, and to clarify the relationships among major phylogeographic lineages. We recovered three major mtDNA lineages of L. dispar: Transcaucasia; East Asia+Japan; and Europe+Central ...

Flight over the Proto-Caribbean seaway: Phylogeny and macroevolution of Neotropical Anaeini leafwing butterflies.

Our understanding of the origin and evolution of the astonishing Neotropical biodiversity remains somewhat limited. In particular, decoupling the respective impacts of biotic and abiotic factors on the macroevolution of clades is paramount to understand biodiversity assemblage in this region. We present the first comprehensive molecular phylogeny for the Neotropical Anaeini leafwing butterflies (Nymphalidae, Charaxinae) and, applying likelihood-based methods, we test the impact of major abiotic (Andean orog...

Mechanisms of allopatric speciation in an Antillean damselfly genus (Odonata, Zygoptera): vicariance or long-distance dispersal?

We have examined divergence times of the Antillean damselfly genus Hypolestes, to elucidate which mechanism of allopatric speciation, vicariance or long-distance dispersal, could better explain the currently observed disjunct distributions of this genus. Samples of the three extant species of the genus, Hypolestes clara (Jamaica), H. hatuey (Hispaniola) and H. trinitatis (Cuba), were collected. Mitochondrial and nuclear DNA gene fragments were amplified to reconstruct phylogenetic relationships and estimate...

3RAD-based systematics of the transitional Nearctic-Neotropical lubber grasshopper genus Taeniopoda (Orthoptera: Romaleidae).

The genus Taeniopoda Stål (Romaleidae) is a group of Nearctic-Neotropical grasshoppers whose systematics has been largely neglected. A recent phylogenetic study based on morphology and mitochondrial and nuclear markers failed to resolve the species boundaries in this genus and showed a lack of reciprocal exclusivity between T. eques (Burmeister) and T. tamaulipensis Rehn. Here we assessed the species limits and phylogenetic relationships in Taeniopoda based on 3RAD data, and evaluated the presence of gene ...

Phylogenomics of the longitarsal Colossendeidae: The evolutionary history of an Antarctic sea spider radiation.

Sea spiders (Pycnogonida) constitute a group of marine benthic arthropods that has a particularly high species diversity in the Southern Ocean. The "longitarsal" group of the sea spider family Colossendeidae is especially abundant in this region. However, this group also includes some representatives from other oceans, which raises the question where the group originates from. Therefore, we here investigated the phylogeny of the group with a hybrid enrichment approach that yielded a dataset of 1607 genes an...

A brainstorm on the systematics of Turnera (Turneraceae, Malpighiales) caused by insights from molecular phylogenetics and morphological evolution.

With 145 species, Turnera is the largest genus of Turneraceae (Malpighiales). Despite several morphotaxonomic and cytogenetic studies, our knowledge about the phylogenetic relationships in Turnera remains mainly based on morphological data. Here, we reconstruct the most comprehensive phylogeny of Turnera with molecular data to understand the morphological evolution within this group and to assess its circumscription and infrageneric classification. We analyzed two nuclear and six plastid markers and 112 tax...

Phylogenomics clarifies biogeographic and evolutionary history, and conservation status of West Indian tremblers and thrashers (Aves: Mimidae).

The West Indian avifauna has provided fundamental insights into island biogeography, taxon cycles, and the evolution of avian behavior. Our interpretations, however, should rely on robust hypotheses of evolutionary relationships and consistent conclusions about taxonomic status in groups with many endemic island populations. Here we present a phylogenetic study of the West Indian thrashers, tremblers, and allies, an assemblage of at least 5 species found on 29 islands, including what is considered the Lesse...

Introgressive hybridisation between two widespread sharks in the east Pacific Region.

With just a handful of documented cases of hybridisation in cartilaginous fishes, shark hybridisation remains poorly investigated. Small amounts of admixture have been detected between Galapagos (Carcharhinus galapagensis) and dusky (Carcharhinus obscurus) sharks previously, generating a hypothesis of ongoing hybridisation. We sampled a large number of individuals from areas where the species co-occur (contact zones) across the Pacific Ocean and used both mitochondrial and nuclear-encoded SNPs to examine ge...

Dark offshoot: phylogenomic data sheds light on the evolutionary history of a new species of cave brittle star.

Caves are a useful system for testing evolutionary and biogeographic hypotheses, as they are isolated, and their environmental conditions have resulted in adaptive selection across different taxa. Although in recent years many more cave species have been discovered, cave-dwelling members of the class Ophiuroidea (brittle stars) remain scarce. Out of the more than two thousand species of brittle stars described to date, only two are regarded as true cave-dwellers. These occurrences represent rare colonising ...


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