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31,286 result(s) for "molecular phylogenetics"
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An updated phylogeny and classification of Lamiaceae subfamily Lamioideae
Lamioideae comprise the second-largest subfamily in Lamiaceae. Although considerable progress has recently been made in Lamioideae phylogenetics, the subfamily remains one of the most poorly investigated subfamilies in Lamiaceae. Here we present a taxonomic update of the subfamily based on earlier published data as well as 71 new DNA extracts from relevant in-and outgroup taxa, and DNA sequence data from four chloroplast regions (matK, rpsl6, trnL intron and trnL-F spacer). The phylogenetic positions of 10 out of 13 previously unplaced small or monotypic Asian lamioid genera and 37 additional lamioid species have been identified, and the classification is updated accordingly. Results from parsimony and Bayesian phylogenetic methods corroborate earlier results, but phylogenetic resolution as well as overall branch support are improved. All newly added genera are assigned to earlier established tribes or the new tribe Paraphlomideae Bendiksby, which includes Ajugoides, Matsumurella and Paraphlomis. Acanthoprasium is resurrected as a genus. Transfer of species is proposed to accommodate the monophyly of two genera (Lamium, Otostegia), whereas ten genera remain non-monophyletic (Ballota s. str., Lagopsis, Leonotis, Leonurus, Leucas, Microtoena, Phlomoides, Sideritis, Stachys, Thuspeinanta). Eriophyton and Stachyopsis have been included in Lamieae, Hypogomphia in Stachydeae, and Loxocalyx in Leonureae. Betonica, Colquhounia, Galeopsis, and Roylea remain unclassified at the tribal level. Lamium chinense and three East Asian Galeobdolon species are transferred to Matsumurella. Sulaimania and four Otostegia species are transferred to Moluccella. Alajja and three Lamium species are transferred to Eriophyton. In total, 14 new combinations are made, one at the rank of subgenus and 13 at the rank of species.
The comparative approach in evolutionary anthropology and biology
Comparison is fundamental to evolutionary anthropology. When scientists study chimpanzee cognition, for example, they compare chimp performance on cognitive tasks to the performance of human children on the same tasks. And when new fossils are found, such as those of the tiny humans of Flores, scientists compare these remains to other fossils and contemporary humans. Comparison provides a way to draw general inferences about the evolution of traits and therefore has long been the cornerstone of efforts to understand biological and cultural diversity. Individual studies of fossilized remains, living species, or human populations are the essential units of analysis in a comparative study; bringing these elements into a broader comparative framework allows the puzzle pieces to fall into place, creating a means of testing adaptive hypotheses and generating new ones. With this book, Charles L. Nunn intends to ensure that evolutionary anthropologists and organismal biologists have the tools to realize the potential of comparative research. Nunn provides a wide-ranging investigation of the comparative foundations of evolutionary anthropology in past and present research, including studies of animal behavior, biodiversity, linguistic evolution, allometry, and cross-cultural variation. He also points the way to the future, exploring the new phylogeny-based comparative approaches and offering a how-to manual for scientists who wish to incorporate these new methods into their research.
A new species of the genus Boulenophrys (Anura, Megophryidae) from Southwest China
The Asian horned toad subfamily Megophryinae (Bonaparte, 1850) currently comprises more than 140 species and is widely distributed in southern China, as well as in Tropical Asia from India and Bhutan to the Philippines. During amphibian surveys conducted at Mt.Daxue Nature Reserve on June 28-30, 2023, we collected specimens of within the genus Boulenophrys . Based on molecular phylogenetic analyses and morphological comparisons, we describe this taxon as a new species from southwestern China. Molecular phylogenetic analyses based on mitochondrial DNA strongly support the new species as a sister species of B. jiangi . The uncorrected genetic distances between the 16S rRNA and COI genes between the new species and its closest congener were 9.3% and 8.1%, respectively. The new species could be distinguished from its congeners by a combination of the following characters: (1) adult males have a moderate body size (SVL 37.1–40.6 mm), differing from B. jiangi in having longer hindlimbs when adpressed anteriorly—the tibiotarsal articulation reaches the mid-level of the eye when extended (vs. only reaching the area between the tympanum and the eye in B. jiangi ); (2) vomerine ridge present and vomerine teeth absent; (3) tongue not notched behind; (4) a small horn-like tubercle at the edge of each upper eyelid; (5) tympanum distinctly visible, rounded; (6) toes lacking lateral fringes and webbing; (7) Distinct relative finger lengths: II < I < V < III in the new species (vs. I < II < V < III in B. jiangi ); (8) heels overlapping when thighs are positioned at right angles to the body; (9) tibiotarsal articulation reaching the level of the middle of the eye when leg is stretched forward; (10) an internal single subgular vocal sac in male; (11) dense nuptial spines on dorsal bases of fingers I and II in breeding adult males;(12) Eye diameter (ED) significantly smaller than that of B. jiangi (ED: 4.00±0.28 in the new species vs. 5.00±0.38 in B. jiangi , P < 0.05).
Generic delimitation and historical biogeography in the early-divergent 'ambavioid' lineage of Annonaceae: Cananga, Cyathocalyx and Drepananthus
Generic delimitation of Cyathocalyx and Drepananthus has been controversial, with some authors recognizing them as distinct genera, and others recognizing a more broadly defined Cyathocalyx, inclusive of Drepananthus. Some doubt also exists regarding the relationships between these taxa and Cananga. Molecular phylogenetic analyses are presented based on combined psbA-trnH spacer, trnL-F, matK and rbcL sequences. Results indicate that Cananga, Cyathocalyx s.str. and Drep ananthus form three generally well-supported clades, although with inadequate resolution of relationships among the three clades. Morphological variation is re-evaluated, and the narrower delimitation of Cyathocalyx proposed, necessitating 21 new nomenclatural combinations following the recognition of Drepananthus as a distinct genus. Divergence times are estimated using an uncorrelated lognormal distributed (UCLD) relaxed molecular clock. Historical biogeographical analysis suggests that the ambavioid lineage originated in Africa, with subsequent dispersal into Asia. Alternative hypotheses for this dispersal, involving rafting on the Indian tectonic plate versus migration via the extensive boreotropical forests associated with the Eocene thermal maximum, are evaluated, and the latter route identified as the most consistent with the divergence age estimates and the geological and palaeoclimatic data.
Stolonicaulon: A Section-Puzzle within Marsupella (Gymnomitriaceae, Marchantiophyta)
Marsupella sect. Stolonicaulon is not speciose and is a commonly neglected section within the genus, which currently includes three species with somewhat similar morphologies (wiry shoots with distanced leaves) and distributions in the mountains of tropical and subtropical regions (SE (Southeast) Asia, the Venezuelan Andes, and the high mountains of SE Brazil). After studying materials that were found to be dissimilar to the “traditional” Marsupella that were collected in the last decade by the authors of this article, it was found that these plants belong to three new-for-science species, and all of these species should be included in Marsupella sect. Stolonicaulon. The newly described species have expanded the boundaries of morphological variability, not only for the section itself, but also for the genus based on two findings: (1) the leaves of Marsupella sect. Stolonicaulon can be either appressed and entire or spaced and deeply divided (thus, the plants could occasionally be similar to Cephaloziella or Anastrophyllum); (2) some species of the section possess regular underleaf production. The first discovery of regular underleaves in Marsupella, as noted in two of the three newly described taxa, is the main morphological novelty described in this paper. The development of regular underleaves is a presumable relict character that brings Marsupella closer to Nardia, which was recently transferred to the Gymnomitriaceae and occupies an isolated position within its own subfamily, Nardioideae.
Systematics and character evolution of Tabernaemontaneae (Apocynaceae, Rauvolfioideae) based on molecular and morphological evidence
Tabernaemontaneae (Rauvolfioideae, Apocynaceae) are small trees with mainly animal-dispersed fleshy fruits and arillate seeds represented in the tropics of Africa, Asia, the Pacific and America. The tribe is characterized by complex indole alkaloids, thus its species play a prominent role in traditional medicine. Taxonomically, the Tabernaemontaneae have a convoluted history fraught with contention as to tribal, subtribal, generic and sectional delimitation, with some authors recognizing Ambelanieae and Macoubeeae as separate tribes and others including them in an expanded Tabernaemontaneae s.l. In the species-rich pantropical genus Tabernaemontana, seven sections and up to 30 segregate genera have been described during the past 100 years, giving it the dubious distinction of being the most disputed genus in Apocynaceae s.str. Here 420 new chloroplast DNA sequences from 104 species, including representatives of all satellite genera ever recognized in the Tabernaemontaneae, were analyzed phylogenetically to evaluate previous circumscriptions of Tabernaemontaneae and test the sectional treatment of Tabernaemontana. The Tabernaemontaneae s.l. as currently circumscribed was shown to be monophyletic. Of the 19 genera recognized in the most recent classification, 15 are maintained. The genera Bonafousia, Stemmadenia, Stenosolen and Woytokowskia are nested within Tabernaemontana. Of the seven current sections of Tabernaemontana, the four that included taxa from more than one continent were found to be para- or polyphyletic. All natural groups recovered within Tabernaemontana were found to correspond to geographic areas. Mapping of 29 selected morphological characters onto the molecular tree recovered recurrent suites of co-occurring character states and identified three synapomorphies characterizing the Tabernaemontaneae s.l.: (1) specialized anthers with massive lignified guide-rails; and a differentiated style-head with (2) a five-lobed upper crest and (3) a thickened basal flange. A new combination for the subtribe Ambelaniinae and the necessary new combinations resulting from merging Stemmadenia into Tabernaemontana are made.
Molecular phylogeny and taxonomy of the genus Lamium L. (Lamiaceae): Disentangling origins of presumed allotetraploids
This is the first comprehensive molecular investigation of the genus Lamium L. We have addressed phylogenetic relationships and presumed allopolyploid speciation by use of nuclear (NRPA2, 5S-NTS) and chloroplast (matK, psbA-trnH, rps16, trnL, trnL-F, trnS-G) DNA sequence data. Nuclear and chloroplast data were incongruent, and nuclear data showed better correlation with morphology. Bayesian and parsimony phylogenetic results show that (1) Lamium galeobdolon is sister to all remaining Lamium species; (2) Wiedemannia is nested within Lamium; (3) L. amplexicaule is polyphyletic; (4) most tetraploids are of hybrid origin; (5) L. amplexicaule var. orientale is allotetraploid; and (6) Mennema's (1989) infrageneric classification is not corroborated by molecular data. Based on the molecular results, and taking morphology into account, we suggest resurrection of two species: L. aleppicum and L. paczoskianum.
Molecular phylogenetics of the Mesoamerican bamboo Olmeca (Poaceae, Bambuseae): Implications for taxonomy
Phylogenetic analyses based on five DNA plastid sequences from representative taxa of the Neotropical woody bamboo subtribe Guaduinae were performed to determine the generic limits of Olmeca and the relationships among its species. The phylogenetic position of a putative new taxon from Mexico was also determined. It appeared that, additional to the two species recognized in Olmeca, two Mesoamerican species of Aulonemia—A. clarkiae and A. fulgor—should be transferred to Olmeca. This transfer is supported by morphology. Individuals of an undescribed taxon from the Isthmus of Tehuantepec, Mexico, were also retrieved embedded in the Olmeca group and are newly described as O. zapotecorum. The distribution range of the redefined genus Olmeca, currently composed of five species, now extends from southern Mexico to Honduras.
Parasitic angiosperms
Angiosperms that morphologically and physiologically attach to other flowering plants by means of a haustorium have evolved 12 times independently resulting in 292 genera and ca. 4750 species. Although hemiparasites predominate, holoparasitism has evolved in all but two clades, Cassytha (Lauraceae) and Krameria (Krameriaceae). Santalales contains the largest number of genera (179) and species (2428) among the 12 parasitic plant lineageswhereas Orobanchaceae is the largest single family with 102 genera and over 2100 species. This review presents the current state of knowledge on the molecular phylogenetic relationships among all clades of parasitic angiosperms. These methods have been particularly important in revealing the closest non-parasitic relatives of holoparasites, plants that exhibit reduced morphologies, increased substitution rates, and frequent horizontal gene transfers, all of which confound phylogenetics. Although comprehensive molecular phylogenies are still lacking for many of the large genera, nearly complete generic level sampling exists, thus allowing unprecedented understanding of the evolutionary relationships within and among these fascinating plants.
Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans
Xenarthra (armadillos, sloths, and anteaters) constitutes one of the four major clades of placental mammals. Despite their phylogenetic distinctiveness in mammals, a reference phylogeny is still lacking for the 31 described species. Here we used Illumina shotgun sequencing to assemble 33 new complete mitochondrial genomes, establishing Xenarthra as the first major placental clade to be fully sequenced at the species level for mitogenomes. The resulting data set allowed the reconstruction of a robust phylogenetic framework and timescale that are consistent with previous studies conducted at the genus level using nuclear genes. Incorporating the full species diversity of extant xenarthrans points to a number of inconsistencies in xenarthran systematics and species definition. We propose to split armadillos into two distinct families Dasypodidae (dasypodines) and Chlamyphoridae (euphractines, chlamyphorines, and tolypeutines) to better reflect their ancient divergence, estimated around 42 Ma. Species delimitation within long-nosed armadillos (genus Dasypus) appeared more complex than anticipated, with the discovery of a divergent lineage in French Guiana. Diversification analyses showed Xenarthra to be an ancient clade with a constant diversification rate through time with a species turnover driven by high but constant extinction. We also detected a significant negative correlation between speciation rate and past temperature fluctuations with an increase in speciation rate corresponding to the general cooling observed during the last 15 My. Biogeographic reconstructions identified the tropical rainforest biome of Amazonia and the Guiana Shield as the cradle of xenarthran evolutionary history with subsequent dispersions into more open and dry habitats.