Whole genome based insights into the phylogeny and evolution of the Juglandaceae

Abstract Background The walnut family (Juglandaceae) contains commercially important woody trees commonly called walnut, wingnut, pecan and hickory. Phylogenetic relationships and diversification within the Juglandaceae are classic and hot scientific topics that have been elucidated by recent fossil, morphological, molecular, and (paleo) environmental data. Further resolution of relationships among and within genera is still needed and can be achieved by analysis of the variation of chloroplast, mtDNA, and nuclear genomes. Results We reconstructed the backbone phylogenetic relationships of Juglandaceae using organelle and nuclear genome data from 27 species. The divergence time of Juglandaceae was estimated to be 78.7 Mya. The major lineages diversified in warm and dry habitats during the mid-Paleocene and early Eocene. The plastid, mitochondrial, and nuclear phylogenetic analyses all revealed three subfamilies, i.e., Juglandoideae, Engelhardioideae, Rhoipteleoideae. Five genera of Juglandoideae were strongly supported. Juglandaceae were estimated to have originated during the late Cretaceous, while Juglandoideae were estimated to have originated during the Paleocene, with evidence for rapid diversification events during several glacial and geological periods. The phylogenetic analyses of organelle sequences and nuclear genome yielded highly supported incongruence positions for J. cinerea, J. hopeiensis, and Platycarya strobilacea. Winged fruit were the ancestral condition in the Juglandoideae, but adaptation to novel dispersal and regeneration regimes after the Cretaceous-Paleogene boundary led to the independent evolution of zoochory among several genera of the Juglandaceae. Conclusions A fully resolved, strongly supported, time-calibrated phylogenetic tree of Juglandaceae can provide an important framework for studying classification, diversification, biogeography, and comparative genomics of plant lineages. Our addition of new, annotated whole chloroplast genomic sequences and identification of their variability informs the study of their evolution in walnuts (Juglandaceae).

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Whole Genome based Insights into the Phylogeny and Evolution of the Juglandaceae

10.21203/rs.3.rs-495294/v1 ◽

2021 ◽

Author(s):

Huijuan Zhou ◽

Yiheng Hu ◽

Aziz Ebrahimi ◽

Peiliang Liu ◽

Keith Woeste ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Divergence Time ◽

Nuclear Genome ◽

Early Eocene ◽

Genome Data ◽

Phylogenetic Resolution ◽

Rapid Diversification ◽

Commercially Important ◽

Phylogeny And Evolution

Abstract Background: The walnut family (Juglandaceae) contains commercially important woody trees commonly called walnut, wingnut, pecan and hickory. Phylogenetic relationships in the Juglandaceae are problematic, and their historical diversification has not been clarified, in part because of low phylogenetic resolution and/or insufficient marker variability. Results: We reconstructed the backbone phylogenetic relationships of Juglandaceae using organelle and nuclear genome data from 27 species. The divergence time of Juglandaceae was estimated to be 78.7 Mya. The major lineages diversified in warm and dry habitats during the mid-Paleocene and early Eocene. The plastid, mitochondrial, and nuclear phylogenetic analyses all revealed three subfamilies, i.e., Juglandoideae, Engelhardioideae, Rhoipteleoideae. Five genera of Juglandoideae were strongly supported. Juglandaceae were estimated to have originated during the late Cretaceous, while Juglandoideae were estimated to have originated during the Paleocene, with evidence for rapid diversification events during several glacial and geological periods. The phylogenetic analyses of organelle sequences and nuclear genome yielded highly supported incongruence positions for J. cinerea, J. hopeiensis, and Platycarya strobilacea. Winged fruit were the ancestral condition in the Juglandoideae, but adaptation to novel regeneration regimes after the Creaceous-Paleogene boundary led to the independent evolution of zoochory among several genera of the Juglandaceae. Conclusions: A fully resolved, strongly supported, time-calibrated phylogenetic tree of Juglandaceae can provide an important framework for studying classification, diversification, biogeography, and comparative genomics of plant lineages.

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An Exceptionally Preserved Specimen From the Green River Formation Elucidates Complex Phenotypic Evolution in Gruiformes and Charadriiformes

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2020.559929 ◽

2020 ◽

Vol 8 ◽

Author(s):

Grace Musser ◽

Julia A. Clarke

Keyword(s):

Fossil Record ◽

Phylogenetic Analyses ◽

Divergence Time ◽

Axial Skeleton ◽

Green River Formation ◽

New Taxon ◽

Early Eocene ◽

Phenotypic Evolution ◽

Green River ◽

Partial Skeleton

The stem lineage relationships and early phenotypic evolution of Charadriiformes (shorebirds) and Gruiformes (rails, cranes, and allies) remain unresolved. It is still debated whether these clades are sister-taxa. New phylogenetic analyses incorporating Paleogene fossils have the potential to reveal the evolutionary connections of these two speciose and evolutionarily critical neoavian subclades. Although Gruiformes have a rich Paleogene fossil record, most of these fossils have not been robustly placed. The Paleogene fossil record of Charadriiformes is scarce and largely consists of fragmentary single elements. Only one proposed Eocene charadriiform-like taxon, Scandiavis mikkelseni of Denmark, is represented by a partial skeleton. Here, we describe a new species from the early Eocene Green River Formation of North America comprising a partial skeleton and feather remains. Because the skeleton lacks the pectoral girdle and forelimbs as in S. mikkelseni, only features of the skull, axial skeleton, and hind limb are available to resolve the phylogenetic placement of this taxon. These anatomical subregions initially showed features seen in Charadriiformes and Gruiformes. To assess placement of this taxon, we use a matrix consisting of 693 morphological characters and 60 taxa, including S. mikkelseni and the oldest known charadriiform taxa represented by single elements. These more fragmentary records comprise two distal humeri from the earliest Eocene Naranbulag Formation of Mongolia and the early Eocene Nanjemoy Formation of Virginia. Our phylogenetic analyses recover the new taxon and S. mikkelseni alternatively as a charadriiform or as a stem-gruiform; placement is contingent upon enforced relationships for major neoavian subclades recovered by recent molecular-based phylogenies. Specifically, when constraint trees based on results that do not recover Charadriiformes and Gruiformes as sister-taxa are used, the new taxon and S. mikkelseni are recovered within stem Gruiformes. Both Paleogene fossil humeri are consistently recovered within crown Charadriiformes. If placement of these humeri or the new taxon as charadriiforms are correct, this may indicate that recent divergence time analyses have underestimated the crown age of another major crown avian subclade; however, more complete sampling of these taxa is necessary, especially of more complete specimens with pectoral elements.

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Notes, outline and divergence times of Basidiomycota

Fungal Diversity ◽

10.1007/s13225-019-00435-4 ◽

2019 ◽

Vol 99 (1) ◽

pp. 105-367 ◽

Cited By ~ 32

Author(s):

Mao-Qiang He ◽

Rui-Lin Zhao ◽

Kevin D. Hyde ◽

Dominik Begerow ◽

Martin Kemler ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Divergence Time ◽

Divergence Times ◽

Sequence Information ◽

Divergence Time Estimates ◽

Time Estimates ◽

The Family ◽

Life Mode ◽

Species Type ◽

Phylogeny And Evolution

AbstractThe Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.

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Molecular phylogeny and divergence time estimates in pennatulaceans (Cnidaria: Octocorallia: Pennatulacea)

Scientia Marina ◽

10.3989/scimar.05067.28a ◽

2020 ◽

Vol 84 (4) ◽

pp. 317-330

Author(s):

Francisco J. García-Cárdenas ◽

Mónica Núñez-Flores ◽

Pablo J. López-González

Keyword(s):

Dna Sequences ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Divergence Time ◽

Morphological Characters ◽

Nuclear Markers ◽

Divergence Time Estimates ◽

Time Estimates ◽

Soft Bottoms

Pennatulaceans are an important component of benthic marine communities usually related to soft bottoms. Despite their important ecological role, as yet little is known about their origin and divergence time. The first attempts to establish phylogenetic relationships among genera date from the early 20th century, when only morphological characters were available. In the last decade, phylogenetic analyses based on mitochondrial DNA sequences from a selected number of species have proposed a different hypothetical ancestor for this group, but their intergeneric relationships remain obscure. The present study is based on a combination of mitochondrial and nuclear markers (mtMutS, Cox1 and 28S rDNA), adding new molecular information about the phylogenetic relationships among the pennatulacean genera, including 38 new sequences belonging to 13 different species. Some of the phylogenetic relationships inferred in the present study question the current classification of sea pens based on morphology (at different taxonomic levels), clearly indicating that the two main groups Sessiliflorae and Subselliflorae, some of their main families (e.g. Pennatulidae, Umbellulidae, Virgulariidae) and some genera (e.g. Umbellula, Veretillum) are non-monophyletic. In addition, the veretillids, traditionally considered the most primitive pennatulaceans, are not shown as the earliest-diverging taxon. Moreover, an analysis of divergence time performed here suggested that the origin of the pennatulaceans dates from the Lower Cretaceous (Berriasian, ~144 Ma), in agreement with their sparsely known fossil record, while the initial divergence of most extant genera occurred in the Oligocene and Miocene times.

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Phylogenomic insights into biogeographic diversification and character evolution of the Sino-Japanese disjunctive Diabelia (Caprifoliaceae)

10.1101/2021.05.31.446416 ◽

2021 ◽

Author(s):

Xiurong Ke ◽

Diego F Morales-Briones ◽

Hongxin Wang ◽

Qinghui Sun ◽

Landis B Jacob ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

East Asian ◽

Divergence Time ◽

Time Estimation ◽

Distribution Patterns ◽

Ancestral Area ◽

Divergence Time Estimation ◽

Network Analyses ◽

Ancestral Area Reconstruction

Disjunctive distribution patterns and drivers of the Sino-Japanese flora in East Asia have attracted much attention in the past decades, which is also served as an important glacial sanctuary during the quaternary glacial period. However, few studies have focused on the phylogeography, diversification and evolution of morphological character at the genus level with both nuclear and plastid data. Diabelia (Caprifoliaceae) is an East Asian genus, with a disjunctive distribution across China, Japan and Korea, serving as an ideal group to explore the mechanism of East Asian flora speciation and diversification. However, the phylogenetic relationships among Diabelia remain elusive and species delimitation within the genus (three species or four species) are still controversial. In this study, we reconstructed the phylogenetic relationships among Diabelia based on nuclear and cpDNA by using target enrichment and genome skimming approaches, respectively. We found that the main clades within Diabelia were discordant between nuclear and plastid genome trees. Both nuclear and plastid phylogenetic analyses supported five main clades: D. serrata, D. tetrasepala, D. spathulata var. sanguinea, D. spathulata var. stenophylla and D. spathulata var. spathulata. Diabelia tetrasepala was inferred to be the result of a hybridization event from the species network analyses. The result of divergence time estimation and ancestral area reconstruction showed that Diabelia originated in Japan during the early Miocene, with subsequent gene flow between China, Japan and Korea. Overall, our results support the division of Diabelia into five main clades and this research provides new insights for the speciation process and taxonomy within Diabelia.

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Phylogenetic relationships of three families of the suborder Mononchina Kirjanova & Krall, 1969 inferred from 18S rDNA

Nematology ◽

10.1163/15685411-00002928 ◽

2015 ◽

Vol 17 (9) ◽

pp. 1113-1125 ◽

Cited By ~ 1

Author(s):

Mina Koohkan ◽

Ebrahim Shokoohi ◽

Peter Mullin

Keyword(s):

Maximum Likelihood ◽

Phylogenetic Relationships ◽

18S Rdna ◽

Phylogenetic Analyses ◽

Strong Support ◽

Nuclear Genome ◽

Sister Group ◽

Ssu Rdna ◽

Rdna Analysis

Mononchida is an order of predatory nematodes and includes the suborders Bathyodontina and Mononchina. In this survey, sequences of the 18S rDNA were amplified and used to reconstruct the phylogeny of the Mononchina. Phylogenetic analyses using Neighbour Joining (NJ) and Maximum Likelihood (ML) were employed with five outgroup taxa and 65 mononch sequences including 14 new sequences from Iran. Both analyses indicated that the Anatonchus is monophyletic. Actus was placed as the sister group of Mylonchulus with weak and strong support, respectively, from the ML and NJ analyses. In both phylogenetic analyses, trees obtained from SSU rDNA alignments were subdivided into five highly- or moderately-supported clades, designated Clade I: Mylonchulus spp., Clade II: Actus salvadoricus, Clade III: Anatonchus spp., a group comprising the genera Clarkus, Coomansus, Miconchus and Prionchulus, Clade IV: Mononchus spp., and Clade V: Granonchulus sp. The 18S rDNA analysis demonstrated that this region of the nuclear genome can be used to resolve the relationships of members of this suborder.

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The origin of Rhinocerotoidea and phylogeny of Ceratomorpha (Mammalia, Perissodactyla)

Communications Biology ◽

10.1038/s42003-020-01205-8 ◽

2020 ◽

Vol 3 (1) ◽

Author(s):

Bin Bai ◽

Jin Meng ◽

Chi Zhang ◽

Yan-Xin Gong ◽

Yuan-Qing Wang

Keyword(s):

New Species ◽

Bayesian Inference ◽

Phylogenetic Relationships ◽

Inner Mongolia ◽

Middle Eocene ◽

Phylogenetic Analyses ◽

Early Eocene ◽

New Materials ◽

Inference Methods ◽

Erlian Basin

AbstractRhinoceroses have been considered to have originated from tapiroids in the middle Eocene; however, the transition remains controversial, and the first unequivocal rhinocerotoids appeared about 4 Ma later than the earliest tapiroids of the Early Eocene. Here we describe 5 genera and 6 new species of rhinoceroses recently discovered from the early Eocene to the early middle Eocene deposits of the Erlian Basin of Inner Mongolia, China. These new materials represent the earliest members of rhinocerotoids, forstercooperiids, and/or hyrachyids, and bridge the evolutionary gap between the early Eocene ceratomorphs and middle Eocene rhinocerotoids. The phylogenetic analyses using parsimony and Bayesian inference methods support their affinities with rhinocerotoids, and also illuminate the phylogenetic relationships and biogeography of Ceratomorpha, although some discrepancies are present between the two criteria. The nearly contemporary occurrence of various rhinocerotoids indicates that the divergence of different rhinocerotoid groups occurred no later than the late early Eocene, which is soon after the split between the rhinocerotoids and the tapiroids in the early early Eocene. However, the Bayesian tip-dating estimate suggests that the divergence of different ceratomorph groups occurred in the middle Paleocene.

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High-Throughput Genomic Data Reveal Complex Phylogenetic Relationships in Stylosanthes Sw (Leguminosae)

Frontiers in Genetics ◽

10.3389/fgene.2021.727314 ◽

2021 ◽

Vol 12 ◽

Author(s):

Maria Alice Silva Oliveira ◽

Tomáz Nunes ◽

Maria Aparecida Dos Santos ◽

Danyelle Ferreira Gomes ◽

Iara Costa ◽

...

Keyword(s):

Comparative Analysis ◽

High Throughput ◽

Phylogenetic Relationships ◽

High Throughput Sequencing ◽

De Novo ◽

Species Recognition ◽

Phylogenetic Analyses ◽

Nuclear Genome ◽

Proximal Region ◽

Legume Crop

Allopolyploidy is widely present across plant lineages. Though estimating the correct phylogenetic relationships and origin of allopolyploids may sometimes become a hard task. In the genus Stylosanthes Sw. (Leguminosae), an important legume crop, allopolyploidy is a key speciation force. This makes difficult adequate species recognition and breeding efforts on the genus. Based on comparative analysis of nine high-throughput sequencing (HTS) samples, including three allopolyploids (S. capitata Vogel cv. “Campo Grande,” S. capitata “RS024” and S. scabra Vogel) and six diploids (S. hamata Taub, S. viscosa (L.) Sw., S. macrocephala M. B. Ferreira and Sousa Costa, S. guianensis (Aubl.) Sw., S. pilosa M. B. Ferreira and Sousa Costa and S. seabrana B. L. Maass & 't Mannetje) we provide a working pipeline to identify organelle and nuclear genome signatures that allowed us to trace the origin and parental genome recognition of allopolyploids. First, organelle genomes were de novo assembled and used to identify maternal genome donors by alignment-based phylogenies and synteny analysis. Second, nuclear-derived reads were subjected to repetitive DNA identification with RepeatExplorer2. Identified repeats were compared based on abundance and presence on diploids in relation to allopolyploids by comparative repeat analysis. Third, reads were extracted and grouped based on the following groups: chloroplast, mitochondrial, satellite DNA, ribosomal DNA, repeat clustered- and total genomic reads. These sets of reads were then subjected to alignment and assembly free phylogenetic analyses and were compared to classical alignment-based phylogenetic methods. Comparative analysis of shared and unique satellite repeats also allowed the tracing of allopolyploid origin in Stylosanthes, especially those with high abundance such as the StyloSat1 in the Scabra complex. This satellite was in situ mapped in the proximal region of the chromosomes and made it possible to identify its previously proposed parents. Hence, with simple genome skimming data we were able to provide evidence for the recognition of parental genomes and understand genome evolution of two Stylosanthes allopolyploids.

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Genome-wide identification of sucrose nonfermenting-1-related protein kinase (SnRK) genes in barley and RNA-seq analyses of their expression in response to abscisic acid treatment

BMC Genomics ◽

10.1186/s12864-021-07601-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Zhiwei Chen ◽

Longhua Zhou ◽

Panpan Jiang ◽

Ruiju Lu ◽

Nigel G. Halford ◽

...

Keyword(s):

Abscisic Acid ◽

Gene Family ◽

Stress Responses ◽

Phylogenetic Analyses ◽

Regulatory Elements ◽

Gene Promoters ◽

Related Protein ◽

Rna Seq ◽

Response Elements ◽

Genome Data

Abstract Background Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signalling, in some cases involving the stress hormone, abscisic acid (ABA). The burgeoning and divergence of the plant gene family has led to the evolution of three subfamilies, SnRK1, SnRK2 and SnRK3, of which SnRK2 and SnRK3 are unique to plants. Therefore, the study of SnRKs in crops may lead to the development of strategies for breeding crop varieties that are more resilient under stress conditions. In the present study, we describe the SnRK gene family of barley (Hordeum vulgare), the widespread cultivation of which can be attributed to its good adaptation to different environments. Results The barley HvSnRK gene family was elucidated in its entirety from publicly-available genome data and found to comprise 50 genes. Phylogenetic analyses assigned six of the genes to the HvSnRK1 subfamily, 10 to HvSnRK2 and 34 to HvSnRK3. The search was validated by applying it to Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genome data, identifying 50 SnRK genes in rice (four OsSnRK1, 11 OsSnRK2 and 35 OsSnRK3) and 39 in Arabidopsis (three AtSnRK1, 10 AtSnRK2 and 26 AtSnRK3). Specific motifs were identified in the encoded barley proteins, and multiple putative regulatory elements were found in the gene promoters, with light-regulated elements (LRE), ABA response elements (ABRE) and methyl jasmonate response elements (MeJa) the most common. RNA-seq analysis showed that many of the HvSnRK genes responded to ABA, some positively, some negatively and some with complex time-dependent responses. Conclusions The barley HvSnRK gene family is large, comprising 50 members, subdivided into HvSnRK1 (6 members), HvSnRK2 (10 members) and HvSnRK3 (34 members), showing differential positive and negative responses to ABA.

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Unexpected larger distribution of paleogene stem-rollers (AVES, CORACII): new evidence from the Eocene of Patagonia, Argentina

Scientific Reports ◽

10.1038/s41598-020-80479-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Federico J. Degrange ◽

Diego Pol ◽

Pablo Puerta ◽

Peter Wilf

Keyword(s):

Hind Limb ◽

Divergence Time ◽

First Record ◽

Morphological Data ◽

New Taxon ◽

Early Eocene ◽

Important Data ◽

New Material ◽

Holarctic Region ◽

New Evidence

AbstractHere we present the first record of a stem-Coracii outside the Holarctic region, found in the early Eocene of Patagonia at the Laguna del Hunco locality. Ueekenkcoracias tambussiae gen. et sp. nov. consists of an incomplete right hind limb that presents the following combination of characters, characteristic of Coracii: relatively short and stout tibiotarsus, poorly developed crista cnemialis cranialis, short and wide tarsometatarsus, with the tuberositas m. tibialis cranialis located medially on the shaft, and curved and stout ungual phalanges. Although the presence of a rounded and conspicuous foramen vasculare distale and the trochlea metatarsi II strongly deflected medially resemble Primobucconidae, a fossil group only found in the Eocene of Europe and North America, our phylogenetic analysis indicates the new taxon is the basalmost known Coracii. The unexpected presence of a stem-Coracii in the Eocene of South America indicates that this clade had a more widespread distribution than previously hypothesized, already extending into the Southern Hemisphere by the early Eocene. Ueekenkcoracias tambussiae represents new evidence of the increasing diversity of stem lineages of birds in the Eocene. The new material provides novel morphological data for understanding the evolutionary origin and radiation of rollers and important data for estimates of the divergence time of the group.

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