Journal: Molecular Phylogenetics and Evolution

Abbreviation

Mol. Phylogenet. Evol.

Publisher

Elsevier

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ISSN

1055-7903
1095-9513

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Publications1 - 10 of 21
  • A recent evolutionary origin of a bacterial small RNA that controls multicellular fruiting body development
    Item type: Journal Article
    Chen, I. Chen Kimberly; Griesenauer, Brad; Yu, Yuen-Tsu Nicco; et al. (2014)
    Molecular Phylogenetics and Evolution
    In animals and plants, non-coding small RNAs regulate the expression of many genes at the post-transcriptional level. Recently, many non-coding small RNAs (sRNAs) have also been found to regulate a variety of important biological processes in bacteria, including social traits, but little is known about the phylogenetic or mechanistic origins of such bacterial sRNAs. Here we propose a phylogenetic origin of the myxobacterial sRNA Pxr, which negatively regulates the initiation of fruiting body development in Myxococcus xanthus as a function of nutrient level, and also examine its diversification within the Myxococcocales order. Homologs of pxr were found throughout the Cystobacterineae suborder (with a few possible losses) but not outside this clade, suggesting a single origin of the Pxr regulatory system in the basal Cystobacterineae lineage. Rates of pxr sequence evolution varied greatly across Cystobacterineae sub-clades in a manner not predicted by overall genome divergence. A single copy of pxr was found in most species with 17% of nucleotide positions being polymorphic among them. However three tandem paralogs were present within the genus Cystobacter and these alleles together exhibited an elevated rate of divergence. There appears to have been strong selection for maintenance of a predicted stem-loop structure, as polymorphisms accumulated preferentially at loop or bulge regions or as complementary substitutions within predicted stems. All detected pxr homologs are located in the intergenic region between the σ54-dependent response regulator nla19 and a predicted NADH dehydrogenase gene, but other neighboring gene content has diversified.
  • Diversification of the cold-adapted butterfly genus Oeneis related to Holarctic biogeography and climatic niche shifts
    Item type: Journal Article
    Kleckova, I.; Cesanek, M.; Fric, Z.; et al. (2015)
    Molecular Phylogenetics and Evolution
  • Inclusivity is key to progressing coral biodiversity research: Reply to comment by Bonito et al. (2021)
    Item type: Other Journal Item
    Wepfer, Patricia; Nakajima, Yuichi; Sutthacheep, Makamas; et al. (2021)
    Molecular Phylogenetics and Evolution
  • Evolutionary history of synthesis pathway genes for phloroglucinol and cyanide antimicrobials in plant-associated fluorescent pseudomonads
    Item type: Journal Article
    Frapolli, Michele; Pothier, Joël F.; Défago, Geneviève; et al. (2012)
    Molecular Phylogenetics and Evolution
  • Molecular phylogenetics of Hypoxidaceae
    Item type: Journal Article
    Kocyan, Alexander; Snijman, Deirdre A.; Forest, Félix; et al. (2011)
    Molecular Phylogenetics and Evolution
  • Inter- and intra-archipelago dynamics of population structure and gene flow in a Polynesian bird
    Item type: Journal Article
    Mapel, Xena M.; Gyllenhaal, Ethan F.; Modak, Tejashree H.; et al. (2021)
    Molecular Phylogenetics and Evolution
    Islands are separated by natural barriers that prevent gene flow between terrestrial populations and promote allopatric diversification. Birds in the South Pacific are an excellent model to explore the interplay between isolation and gene flow due to the region's numerous archipelagos and well-characterized avian communities. The wattled honeyeater complex (Foulehaio spp.) comprises three allopatric species that are widespread and common across Fiji, Tonga, Samoa, and Wallis and Futuna. Here, we explored patterns of diversification within and among these lineages using genomic and morphometric data. We found support for three clades of Foulehaio corresponding to three recognized species. Within F. carunculatus, population genetic analyses identified nine major lineages, most of which were composed of sub-lineages that aligned nearly perfectly to individual island populations. Despite genetic structure and great geographic distance between populations, we found low levels of gene flow between populations in adjacent archipelagos. Additionally, body size of F. carunculatus varied randomly with respect to evolutionary history (as Ernst Mayr predicted), but correlated negatively with island size, consistent with the island rule. Our findings support a hypothesis that widespread taxa can show population structure between immediately adjacent islands, and likely represent many independent lineages loosely connected by gene flow. © 2020 Elsevier Inc.
  • Slow and steady wins the race: Diversification rate is independent from body size and lifestyle in Malagasy skinks (Squamata: Scincidae: Scincinae)
    Item type: Journal Article
    Belluardo, Francesco; Muñoz-Pajares, A. Jesús; Miralles, Aurélien; et al. (2023)
    Molecular Phylogenetics and Evolution
    Most of the unique and diverse vertebrate fauna that inhabits Madagascar derives from in situ diversification from colonisers that reached this continental island through overseas dispersal. The endemic Malagasy Scincinae lizards are amongst the most species-rich squamate groups on the island. They colonised all bioclimatic zones and display many ecomorphological adaptations to a fossorial (burrowing) lifestyle. Here we propose a new phylogenetic hypothesis for their diversification based on the largest taxon sampling so far compiled for this group. We estimated divergence times and investigated several aspects of their diversification (diversification rate, body size and fossorial lifestyle evolution, and biogeography). We found that diversification rate was constant throughout most of the evolutionary history of the group, but decreased over the last 6–4 million years and independently from body size and fossorial lifestyle evolution. Fossoriality has evolved from fully quadrupedal ancestors at least five times independently, which demonstrates that even complex morphological syndromes – in this case involving traits such as limb regression, body elongation, modification of cephalic scalation, depigmentation, and eyes and ear-opening regression – can evolve repeatedly and independently given enough time and eco-evolutionary advantages. Initial diversification of the group likely occurred in forests, and the divergence of sand-swimmer genera around 20 Ma appears linked to a period of aridification. Our results show that the large phenotypic variability of Malagasy Scincinae has not influenced diversification rate and that their rich species diversity results from a constant accumulation of lineages through time. By compiling large geographic and trait-related datasets together with the computation of a new time tree for the group, our study contributes important insights on the diversification of Malagasy vertebrates.
  • Diversification and repeated morphological transitions in endoparasitic cnidarians (Myxozoa: Malacosporea)
    Item type: Journal Article
    Hartikainen, Hanna; Gruhl, Alexander; Okamura, Beth (2014)
    Molecular Phylogenetics and Evolution
  • Introgression is widespread in the radiation of carnivorous Nepenthes pitcher plants
    Item type: Journal Article
    Scharmann, Mathias; Wistuba, Andreas; Widmer, Alex (2021)
    Molecular Phylogenetics and Evolution
  • Cardinal characters on a slippery slope - A re-evaluation of phylogeny, character evolution, and evolutionary rates in the jelly lichens (Collemataceae s. str.)
    Item type: Journal Article
    Garcia Otalora, Monica Andrea; Martinez, Isabel; Aragón, Gregorio; et al. (2013)
    Molecular Phylogenetics and Evolution
Publications1 - 10 of 21