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

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.

scholarly journals Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes

2021 ◽  
Vol 12 ◽  
Author(s):  
Jeffrey P. Rose ◽  
Ricardo Kriebel ◽  
Larissa Kahan ◽  
Alexa DiNicola ◽  
Jesús G. González-Gallegos ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Divergence Time ◽  
Time Estimation ◽  
Single Copy ◽  
Lineage Sorting ◽  
Divergence Time Estimation ◽  
Sequencing Technologies ◽  
Plastid Genomes ◽  
Gene Tree Discordance

Next-generation sequencing technologies have facilitated new phylogenomic approaches to help clarify previously intractable relationships while simultaneously highlighting the pervasive nature of incongruence within and among genomes that can complicate definitive taxonomic conclusions. Salvia L., with ∼1,000 species, makes up nearly 15% of the species diversity in the mint family and has attracted great interest from biologists across subdisciplines. Despite the great progress that has been achieved in discerning the placement of Salvia within Lamiaceae and in clarifying its infrageneric relationships through plastid, nuclear ribosomal, and nuclear single-copy genes, the incomplete resolution has left open major questions regarding the phylogenetic relationships among and within the subgenera, as well as to what extent the infrageneric relationships differ across genomes. We expanded a previously published anchored hybrid enrichment dataset of 35 exemplars of Salvia to 179 terminals. We also reconstructed nearly complete plastomes for these samples from off-target reads. We used these data to examine the concordance and discordance among the nuclear loci and between the nuclear and plastid genomes in detail, elucidating both broad-scale and species-level relationships within Salvia. We found that despite the widespread gene tree discordance, nuclear phylogenies reconstructed using concatenated, coalescent, and network-based approaches recover a common backbone topology. Moreover, all subgenera, except for Audibertia, are strongly supported as monophyletic in all analyses. The plastome genealogy is largely resolved and is congruent with the nuclear backbone. However, multiple analyses suggest that incomplete lineage sorting does not fully explain the gene tree discordance. Instead, horizontal gene flow has been important in both the deep and more recent history of Salvia. Our results provide a robust species tree of Salvia across phylogenetic scales and genomes. Future comparative analyses in the genus will need to account for the impacts of hybridization/introgression and incomplete lineage sorting in topology and divergence time estimation.

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

AoB Plants ◽  
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.

scholarly journals Phylogenetic Reconstruction and Divergence Time Estimation of Blumea DC. (Asteraceae: Inuleae) in China Based on nrDNA ITS and cpDNA trnL-F Sequences

Plants ◽  
2019 ◽  
Vol 8 (7) ◽  
pp. 210
Author(s):  
Ying-bo Zhang ◽  
Yuan Yuan ◽  
Yu-xin Pang ◽  
Fu-lai Yu ◽  
Chao Yuan ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Phylogenetic Reconstruction ◽  
Divergence Time ◽  
Herbal Medicines ◽  
Time Estimation ◽  
Nuclear Ribosomal Dna ◽  
Posterior Density ◽  
Divergence Time Estimation ◽  
Explosive Expansion ◽  
Highest Posterior Density

The genus Blumea is one of the most economically important genera of Inuleae (Asteraceae) in China. It is particularly diverse in South China, where 30 species are found, more than half of which are used as herbal medicines or in the chemical industry. However, little is known regarding the phylogenetic relationships and molecular evolution of this genus in China. We used nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) and chloroplast DNA (cpDNA) trnL-F sequences to reconstruct the phylogenetic relationship and estimate the divergence time of Blumea in China. The results indicated that the genus Blumea is monophyletic and it could be divided into two clades that differ with respect to the habitat, morphology, chromosome type, and chemical composition of their members. The divergence time of Blumea was estimated based on the two root times of Asteraceae. The results indicated that the root age of Asteraceae of 76–66 Ma may maintain relatively accurate divergence time estimation for Blumea, and Blumea might had diverged around 49.00–18.43 Ma. This common ancestor had an explosive expansion during the Oligocene and Miocene and two major clades were differentiated during these epochs 29.60 Ma (17.76–45.23 Ma 95% HPD (Highest Posterior Density). Evidence from paleogeography and paleoclimate studies has confirmed that Blumea experienced differentiation and an explosive expansion during the Oligocene and Miocene.

scholarly journals 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

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 260
Author(s):  
Tatiana E. Kramina ◽  
Maya V. Lysova ◽  
Tahir H. Samigullin ◽  
Ivan A. Schanzer ◽  
Mehmet U. Özbek ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Mediterranean Climate ◽  
Divergence Time ◽  
Time Estimation ◽  
Its2 Region ◽  
Divergence Time Estimation ◽  
Early Diversification ◽  
Plant Groups ◽  
History Of ◽  
Eastern Kazakhstan

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.

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

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.

scholarly journals Pattern and Timing of Diversification in the African Freshwater Fish Genus Distichodus (Characiformes: Distichodontidae)

2020 ◽  
Author(s):  
Jairo Arroyave ◽  
John S. S. Denton ◽  
Melanie L. J. Stiassny
Keyword(s):  
Freshwater Fish ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Time Estimation ◽  
Congo Basin ◽  
Similar Species ◽  
Divergence Time Estimation ◽  
Biogeographic History ◽  
History Of

Abstract Background: Distichodus is a clade of tropical freshwater fishes currently comprising 25 named species distributed continent-wide throughout the Nilo-Sudan and most Sub-Saharan drainages. This study investigates the phylogenetic relationships, timing of diversification, and biogeographic history of the genus from a taxonomically comprehensive mutilocus dataset analyzed using Maximum Likelihood and Bayesian methods of phylogenetic inference, coalescence-based species-tree estimation, divergence time estimation, and inference of geographic range evolution.Results: Analyses of comparative DNA sequence data in a phylogenetic context reveal the existence of two major clades of similar species-level diversity and provide support for the monophyletic status of most sampled species. Biogeographic reconstruction on a time-scaled phylogeny suggest that the origins of the genus date back to the late Oligocene and that current geographic distributions are the result of a Congo Basin origin followed by dispersal and range expansion into adjacent ichthyofaunal provinces at different times during the evolutionary history of the group.Conclusions: We present the most comprehensive phylogenetic, chronological, and biogeographic treatment yet conducted for the genus. The few instances of species paraphyly (D. teugelsi, D. fasciolatus) revealed by the resulting phylogenies are likely a consequence of post-divergence introgressive hybridization and/or incomplete lineage sorting due to recent speciation. Historical biogeographic findings are both in agreement and conflict with previous studies of other continent-wide African freshwater fish genera, suggesting a complex scenario for the assemblage of Africa’s continental ichthyofaunal communities.

scholarly journals Phylogenetic reconstruction and divergence time estimation of Blumea DC. (Asteraceae: Inuleae) in China based on nrDNA ITS and cpDNA trnL-F sequences

2018 ◽  
Author(s):  
Yingbo Zhang ◽  
Yuan Yuan ◽  
Yu-xin Pang ◽  
Fu-lai Yu ◽  
Dan Wang ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Phylogenetic Reconstruction ◽  
Divergence Time ◽  
Time Estimation ◽  
Nuclear Ribosomal Dna ◽  
Recent Common Ancestor ◽  
Chromosome Type ◽  
Divergence Time Estimation ◽  
Most Recent Common Ancestor ◽  
Explosive Expansion

The genus Blumea DC. is one of the economically most important genera of Inuleae (Asteraceae) in China. It is particularly diverse in south China, where 30 species occur, more than half of which are used as herbal medicine or in the chemical industry. However, little is known about the phylogenetic relationships and molecular evolution of this genus in China. We used nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) and chloroplast DNA (cpDNA) trnL-F sequences to reconstruct the phylogenetic relationship and estimate the divergence time of Blumea DC. in China. Results indicated the genus of Blumea DC. was monophyletic and could be divided into two clades, the two clades were resolved that differ with respect to habitat, morphology, chromosome type and chemical composition, of their members. Furthermore, based on the two root time of Asteraceae, the divergence time of Blumea DC. were compare estimated. Results indicated the most recent common ancestor of Asteraceae maybe originated from 76-66 Ma, and Blumea DC. maybe originated from 72.71-52.42 Ma, and had an explosive expansion during Oligocene and Miocene (30.09-11.44 Ma), two major clades were differentiated during the Palaeocene and Oligocene (66.29-46.72 Ma), also the evidence from paleogeography and paleoclimate also supported Blumea DC. had an differentiation and explosive expansion during Oligocene and Miocene.

scholarly journals Pattern and Timing of Diversification in the African Freshwater Fish Genus Distichodus (Characiformes: Distichodontidae)

2020 ◽  
Author(s):  
Jairo Arroyave ◽  
John S. S. Denton ◽  
Melanie L. J. Stiassny
Keyword(s):  
Freshwater Fish ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Time Estimation ◽  
Congo Basin ◽  
Similar Species ◽  
Divergence Time Estimation ◽  
Biogeographic History ◽  
History Of

Abstract Background : Distichodus is a clade of tropical freshwater fishes currently comprising 25 named species distributed continent-wide throughout the Nilo-Sudan and most Sub-Saharan drainages. This study investigates the phylogenetic relationships, timing of diversification, and biogeographic history of the genus from a taxonomically comprehensive mutilocus dataset analyzed using Maximum Likelihood and Bayesian methods of phylogenetic inference, coalescence-based species-tree estimation, divergence time estimation, and inference of geographic range evolution. Results: Analyses of comparative DNA sequence data in a phylogenetic context reveal the existence of two major clades of similar species-level diversity and provide support for the monophyletic status of most sampled species. Biogeographic reconstruction on a time-scaled phylogeny suggest that the origins of the genus date back to the late Oligocene and that current geographic distributions are the result of a Congo Basin origin followed by dispersal and range expansion into adjacent ichthyofaunal provinces at different times during the evolutionary history of the group. Conclusions : We present the most comprehensive phylogenetic, chronological, and biogeographic treatment yet conducted for the genus. The few instances of species paraphyly ( D. teugelsi, D. fasciolatus ) revealed by the resulting phylogenies are likely a consequence of post-divergence introgressive hybridization and/or incomplete lineage sorting due to recent speciation. Historical biogeographic findings are both in agreement and conflict with previous studies of other continent-wide African freshwater fish genera, suggesting a complex scenario for the assemblage of Africa’s continental ichthyofaunal communities.

scholarly journals Pattern and Timing of Diversification in the African Freshwater Fish Genus Distichodus (Characiformes: Distichodontidae)

2020 ◽  
Author(s):  
Jairo Arroyave ◽  
John S. S. Denton ◽  
Melanie L. J. Stiassny
Keyword(s):  
Freshwater Fish ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Time Estimation ◽  
Congo Basin ◽  
Similar Species ◽  
Divergence Time Estimation ◽  
Biogeographic History ◽  
History Of

Abstract Background : Distichodus is a clade of tropical freshwater fishes currently comprising 25 named species distributed continent-wide throughout the Nilo-Sudan and most Sub-Saharan drainages. This study investigates the phylogenetic relationships, timing of diversification, and biogeographic history of the genus from a taxonomically comprehensive mutilocus dataset analyzed using Maximum Likelihood and Bayesian methods of phylogenetic inference, coalescence-based species-tree estimation, divergence time estimation, and inference of geographic range evolution. Results: Analyses of comparative DNA sequence data in a phylogenetic context reveal the existence of two major clades of similar species-level diversity and provide support for the monophyletic status of most sampled species. Biogeographic reconstruction on a time-scaled phylogeny suggest that the origins of the genus date back to the late Oligocene and that current geographic distributions are the result of a Congo Basin origin followed by dispersal and range expansion into adjacent ichthyofaunal provinces at different times during the evolutionary history of the group. Conclusions : We present the most comprehensive phylogenetic, chronological, and biogeographic treatment yet conducted for the genus. The few instances of species paraphyly ( D. teugelsi, D. fasciolatus ) revealed by the resulting phylogenies are likely a consequence of post-divergence introgressive hybridization and/or incomplete lineage sorting due to recent speciation. Historical biogeographic findings are both in agreement and conflict with previous studies of other continent-wide African freshwater fish genera, suggesting a complex scenario for the assemblage of Africa’s continental ichthyofaunal communities.

Insights into the Evolutionary History of the Hawaiian Bidens (Asteraceae) Adaptive Radiation Revealed Through Phylogenomics

2020 ◽  
Vol 111 (1) ◽  
pp. 119-137 ◽  
Author(s):  
Matthew L Knope ◽  
M Renee Bellinger ◽  
Erin M Datlof ◽  
Timothy J Gallaher ◽  
Melissa A Johnson
Keyword(s):  
Adaptive Radiation ◽  
Incomplete Lineage Sorting ◽  
Divergence Time ◽  
Lineage Sorting ◽  
Crown Group ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Biogeographic History ◽  
History Of ◽  
Phylogenomic Analyses

Abstract Hawaiian plant radiations often result in lineages with exceptionally high species richness and extreme morphological and ecological differentiation. However, they typically display low levels of genetic variation, hindering the use of classic DNA markers to resolve their evolutionary histories. Here we utilize a phylogenomic approach to generate the first generally well-resolved phylogenetic hypothesis for the evolution of the Hawaiian Bidens (Asteraceae) adaptive radiation, including refined initial colonization and divergence time estimates. We sequenced the chloroplast genome (plastome) and nuclear ribosomal complex for 18 of the 19 endemic species of Hawaiian Bidens and 4 outgroup species. Phylogenomic analyses based on the concatenated dataset (plastome and nuclear) resulted in identical Bayesian and Maximum Likelihood trees with high statistical support at most nodes. Estimates from dating analyses were similar across datasets, with the crown group emerging ~1.76–1.82 Mya. Biogeographic analyses based on the nuclear and concatenated datasets indicated that colonization within the Hawaiian Islands generally followed the progression rule with 67–80% of colonization events from older to younger islands, while only 53% of events followed the progression rule in the plastome analysis. We find strong evidence for nuclear-plastome conflict indicating a potentially important role for hybridization in the evolution of the group. However, incomplete lineage sorting cannot be ruled out due to the small number of independent loci analyzed. This study contributes new insights into species relationships and the biogeographic history of the explosive Hawaiian Bidens adaptive radiation.

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