Phylogenetic Placement and Phylogeography of Large-Flowered Lotus Species (Leguminosae) Formerly Classified in Dorycnium: Evidence of Pre-Pleistocene Differentiation of Western and Eastern Intraspecific Groups

The Mediterranean region is a center of species and genetic diversity of many plant groups, which served as a source of recolonization of temperate regions of Eurasia in Holocene. We investigate the evolutionary history of species currently classified in Lotus sect. Bonjeanea in the context of the evolution of the genus Lotus as a whole, using phylogenetic, phylogeographic and dating analyses. Of three species of the section, L. rectus and L. hirsutus have wide Mediterranean distribution while L. strictus has a disjunctive range in Bulgaria, Turkey, Armenia, Eastern Kazakhstan, and adjacent parts of Russia and China. We used entire nuclear ribosomal ITS1-5.8S-ITS2 region (nrITS) and a plastid dataset (rps16 and trnL-F) to reconstruct phylogenetic relationships within Lotus with an extended representation of Bonjeanea group. We analyzed the phylogeographic patterns within each species based on the plastid dataset. For divergence time estimation, the nrITS dataset was analyzed. Our results confirmed the non-monophyletic nature of the section Bonjeanea. They indicate that Lotus is likely to have diverged about 15.87 (9.99–19.81) million years ago (Ma), which is much older than an earlier estimate of ca. 5.54 Ma. Estimated divergence ages within L. strictus, L. rectus, and L. hisrutus (6.1, 4.94, and 4.16 Ma, respectively) well predate the onset of the current type of Mediterranean climate. Our data suggest that relatively ancient geological events and/or climatic changes apparently played roles in early diversification of Lotus and its major clades, as well as in formation of phylogeographic patterns, in at least some species.

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Out of the Qinghai-Tibetan Plateau (QTP) and rapid radiation across Eurasia for Allium section Daghestanica (Amaryllidaceae)

AoB Plants ◽

10.1093/aobpla/plab017 ◽

2021 ◽

Author(s):

Min-Jie Li ◽

Huan-Xi Yu ◽

Xian-Lin Guo ◽

Xing-Jin He

Keyword(s):

Evolutionary History ◽

Divergence Time ◽

Time Estimation ◽

Adjacent Region ◽

Rapid Radiation ◽

Divergence Time Estimation ◽

Species Diversification ◽

The Third ◽

Evolutionary Line ◽

History Of

Abstract The disjunctive distribution (Europe-Caucasus-Asia) and species diversification across Eurasia for the genus Allium sect. Daghestanica has fascinating attractions for researchers aiming to understanding the development and history of the modern Eurasia flora. However, no any studies have been carried out to address the evolutionary history of this section. Based on the nrITS and cpDNA fragments (trnL-trnF and rpl32-trnL), the evolutionary history of the third evolutionary line (EL3) of the genus Allium was reconstructed and we further elucidate the evolutionary line of sect. Daghestanica under this background. Our molecular phylogeny recovered two highly supported clades in sect. Daghestanica: the Clade I includes Caucasian-European species and Asian A. maowenense, A. xinlongense and A. carolinianum collected in Qinghai; the Clade II comprises Asian yellowish tepal species, A. chrysanthum, A. chrysocephalum, A. herderianum, A. rude and A. xichuanense. The divergence time estimation and biogeography inference indicated that Asian ancestor located in the QTP and the adjacent region could have migrated to Caucasus and Europe distributions around the Late Miocene and resulted in further divergence and speciation; Asian ancestor underwent the rapid radiation in the QTP and the adjacent region most likely due to the heterogeneous ecology of the QTP resulted from the orogeneses around 4–3 Mya. Our study provides a picture to understand the origin and species diversification across Eurasia for sect. Daghestanica.

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The diversification of termites: inferences from a complete species-level phylogeny

10.1101/2020.12.07.414342 ◽

2020 ◽

Author(s):

Marcio R. Pie ◽

Tiago F. Carrijo ◽

Fernanda S. Caron

Keyword(s):

Divergence Time ◽

Soil Formation ◽

Time Estimation ◽

Species Level ◽

The Other ◽

Ecological Processes ◽

Divergence Time Estimation ◽

Speciation Rates ◽

History Of ◽

Worker Castes

AbstractTermites play a major role in a variety of ecological processes in tropical and subtropical biomes worldwide, such as decomposition, soil formation and aeration, and nutrient cycling. These important ecosystem services were achieved through their highly complex societies and remarkable adaptations, including the evolution of sterile worker castes, the acquisition of endosymbionts, and the capacity for extensive environmental engineering, yet the causes and consequences of their ecological success are still poorly understood. The goals of our study were (1) to provide the first complete, species-level phylogeny of all currently recognized termite species by integrating the available genetic and taxonomic data, as well as methods of phylogenetic imputation and divergence time estimation; and (2) to explore variation in speciation rates among termite lineages. We provide the inferred relationships as a set of 1,000 pseudo-posterior trees, which can be used in future comparative analyses. We demonstrate that speciation rates have been relatively constant throughout the history of termites, with two positive shifts in speciation rates: one at their origin of Euisoptera and the other concordant with evolution of Termitidae. On the other hand, there was no obvious trend towards deceleration in speciation rates for termites as a whole, nor within the most species-rich families. The provided trees might represent a valuable resource for termite comparative studies by summarizing the available phylogenetic information, while accounting for uncertainty in the inferred topologies.

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A ‘living fossil’ eel (Anguilliformes: Protanguillidae, fam. nov.) from an undersea cave in Palau

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2011.1289 ◽

2011 ◽

Vol 279 (1730) ◽

pp. 934-943 ◽

Cited By ~ 40

Author(s):

G. David Johnson ◽

Hitoshi Ida ◽

Jiro Sakaue ◽

Tetsuya Sado ◽

Takashi Asahida ◽

...

Keyword(s):

Evolutionary History ◽

Divergence Time ◽

Time Estimation ◽

Sister Group ◽

Morphological Characters ◽

Morphological Evidence ◽

Living Fossil ◽

Divergence Time Estimation ◽

New Family ◽

Republic Of Palau

We report the discovery of an enigmatic, small eel-like fish from a 35 m-deep fringing-reef cave in the western Pacific Ocean Republic of Palau that exhibits an unusual suite of morphological characters. Many of these uniquely characterize the Recent members of the 19 families comprising the elopomorph order Anguilliformes, the true eels. Others are found among anguilliforms only in the Cretaceous fossils, and still others are primitive with respect to both Recent and fossil eels. Thus, morphological evidence explicitly places it as the most basal lineage (i.e. the sister group of extant anguilliforms). Phylogenetic analysis and divergence time estimation based on whole mitogenome sequences from various actinopterygians, including representatives of all eel families, demonstrate that this fish represents one of the most basal, independent lineages of the true eels, with a long evolutionary history comparable to that of the entire Anguilliformes (approx. 200 Myr). Such a long, independent evolutionary history dating back to the early Mesozoic and a retention of primitive morphological features (e.g. the presence of a premaxilla, metapterygoid, free symplectic, gill rakers, pseudobranch and distinct caudal fin rays) warrant recognition of this species as a ‘living fossil’ of the true eels, herein described as Protanguilla palau genus et species nov. in the new family Protanguillidae.

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Mahonia vs. Berberis Unloaded: Generic Delimitation and Infrafamilial Classification of Berberidaceae Based on Plastid Phylogenomics

Frontiers in Plant Science ◽

10.3389/fpls.2021.720171 ◽

2022 ◽

Vol 12 ◽

Author(s):

Chia-Lun Hsieh ◽

Chih-Chieh Yu ◽

Yu-Lan Huang ◽

Kuo-Fang Chung

Keyword(s):

Incomplete Lineage Sorting ◽

Divergence Time ◽

Time Estimation ◽

Nuclear Ribosomal Dna ◽

Length Variation ◽

Lineage Sorting ◽

Divergence Time Estimation ◽

Generic Delimitation ◽

History Of

The early-diverging eudicot family Berberidaceae is composed of a morphologically diverse assemblage of disjunctly distributed genera long praised for their great horticultural and medicinal values. However, despite century-long studies, generic delimitation of Berberidaceae remains controversial and its tribal classification has never been formally proposed under a rigorous phylogenetic context. Currently, the number of accepted genera in Berberidaceae ranges consecutively from 13 to 19, depending on whether to define Berberis, Jeffersonia, and Podophyllum broadly, or to segregate these three genera further and recognize Alloberberis, Mahonia, and Moranothamnus, Plagiorhegma, and Dysosma, Diphylleia, and Sinopodophyllum, respectively. To resolve Berberidaceae’s taxonomic disputes, we newly assembled 23 plastomes and, together with 85 plastomes from the GenBank, completed the generic sampling of the family. With 4 problematic and 14 redundant plastome sequences excluded, robust phylogenomic relationships were reconstructed based on 93 plastomes representing all 19 genera of Berberidaceae and three outgroups. Maximum likelihood phylogenomic relationships corroborated with divergence time estimation support the recognition of three subfamilies Berberidoideae, Nandinoideae, and Podophylloideae, with tribes Berberideae and Ranzanieae, Leonticeae and Nandineae, and Podophylleae, Achlydeae, Bongardieae tr. nov., Epimedieae, and Jeffersonieae tr. nov. in the former three subfamilies, respectively. By applying specifically stated criteria, our phylogenomic data also support the classification of 19 genera, recognizing Alloberberis, Mahonia, and Moranothamnus, Plagiorhegma, and Diphylleia, Dysosma, and Sinopodophyllum that are morphologically and evolutionarily distinct from Berberis, Jeffersonia, and Podophyllum, respectively. Comparison of plastome structures across Berberidaceae confirms inverted repeat expansion in the tribe Berberideae and reveals substantial length variation in accD gene caused by repeated sequences in Berberidoideae. Comparison of plastome tree with previous studies and nuclear ribosomal DNA (nrDNA) phylogeny also reveals considerable conflicts at different phylogenetic levels, suggesting that incomplete lineage sorting and/or hybridization had occurred throughout the evolutionary history of Berberidaceae and that Alloberberis and Moranothamnus could have resulted from reciprocal hybridization between Berberis and Mahonia in ancient times prior to the radiations of the latter two genera.

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Phylogeny and divergence time estimation of Coreoleuciscus splendidus populations (Teleostei: Cypriniformes) endemic to Korea based on complete mitogenome sequences

Genes & Genomics ◽

10.1007/s13258-011-0098-x ◽

2012 ◽

Vol 34 (2) ◽

pp. 149-156 ◽

Cited By ~ 1

Author(s):

Keun-Yong Kim ◽

Yoon Kwon Nam ◽

In-Chul Bang

Keyword(s):

Divergence Time ◽

Time Estimation ◽

Divergence Time Estimation ◽

Complete Mitogenome

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Phylogeny and divergence time estimation of the genus Didymodon (Pottiaceae) based on nuclear and chloroplast markers

Journal of Systematics and Evolution ◽

10.1111/jse.12831 ◽

2022 ◽

Author(s):

Guo‐Li Zhang ◽

Chao Feng ◽

Jin Kou ◽

Yu Han ◽

Yu Zhang ◽

...

Keyword(s):

Divergence Time ◽

Time Estimation ◽

Divergence Time Estimation ◽

Chloroplast Markers

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A new endemic family of New Zealand passerine birds: adding heat to a biodiversity hotspot

Australian Journal of Zoology ◽

10.1071/zo07007 ◽

2007 ◽

Vol 55 (2) ◽

pp. 73 ◽

Cited By ~ 33

Author(s):

Amy Driskell ◽

Les Christidis ◽

B. J. Gill ◽

Walter E. Boles ◽

F. Keith Barker ◽

...

Keyword(s):

New Zealand ◽

Evolutionary History ◽

Divergence Time ◽

Biodiversity Hotspot ◽

Passerine Birds ◽

New Family ◽

Close Relationship ◽

History Of ◽

Anthornis Melanura ◽

Notiomystis Cincta

The results of phylogenetic analysis of two molecular datasets sampling all three endemic New Zealand ‘honeyeaters’ (Prosthemadera novaeseelandiae, Anthornis melanura and Notiomystis cincta) are reported. The undisputed relatedness of the first two species to other honeyeaters (Meliphagidae), and a close relationship between them, are demonstrated. However, our results confirm that Notiomystis is not a honeyeater, but is instead most closely related to the Callaeidae (New Zealand wattlebirds) represented by Philesturnus carunculatus in our study. An estimated divergence time for Notiomystis and Philesturnus of 33.8 mya (Oligocene) suggests a very long evolutionary history of this clade in New Zealand. As a taxonomic interpretation of these data we place Notiomystis in a new family of its own which takes the name Notiomystidae. We expect this new phylogenetic and taxonomic information to assist policy decisions for the conservation of this rare bird.

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