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Huang Y, Jin XJ, Zhang CY, Li P, Meng HH, Zhang YH. Plastome evolution of Engelhardia facilitates phylogeny of Juglandaceae. BMC PLANT BIOLOGY 2024; 24:634. [PMID: 38971744 PMCID: PMC11227234 DOI: 10.1186/s12870-024-05293-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/12/2024] [Indexed: 07/08/2024]
Abstract
BACKGROUND Engelhardia (Juglandaceae) is a genus of significant ecological and economic importance, prevalent in the tropics and subtropics of East Asia. Although previous efforts based on multiple molecular markers providing profound insights into species delimitation and phylogeography of Engelhardia, the maternal genome evolution and phylogeny of Engelhardia in Juglandaceae still need to be comprehensively evaluated. In this study, we sequenced plastomes from 14 samples of eight Engelhardia species and the outgroup Rhoiptelea chiliantha, and incorporated published data from 36 Juglandaceae and six outgroup species to test phylogenetic resolution. Moreover, comparative analyses of the plastomes were conducted to investigate the plastomes evolution of Engelhardia and the whole Juglandaceae family. RESULTS The 13 Engelhardia plastomes were highly similar in genome size, gene content, and order. They exhibited a typical quadripartite structure, with lengths from 161,069 bp to 162,336 bp. Three mutation hotspot regions (TrnK-rps16, ndhF-rpl32, and ycf1) could be used as effective molecular markers for further phylogenetic analyses and species identification. Insertion and deletion (InDels) may be an important driving factor for the evolution of plastomes in Juglandoideae and Engelhardioideae. A total of ten codons were identified as the optimal codons in Juglandaceae. The mutation pressure mostly contributed to shaping codon usage. Seventy-eight protein-coding genes in Juglandaceae experienced relaxed purifying selection, only rpl22 and psaI genes showed positive selection (Ka/Ks > 1). Phylogenetic results fully supported Engelhardia as a monophyletic group including two sects and the division of Juglandaceae into three subfamilies. The Engelhardia originated in the Late Cretaceous and diversified in the Late Eocene, and Juglandaceae originated in the Early Cretaceous and differentiated in Middle Cretaceous. The phylogeny and divergence times didn't support rapid radiation occurred in the evolution history of Engelhardia. CONCLUSION Our study fully supported the taxonomic treatment of at the section for Engelhardia species and three subfamilies for Juglandaceae and confirmed the power of phylogenetic resolution using plastome sequences. Moreover, our results also laid the foundation for further studying the course, tempo and mode of plastome evolution of Engelhardia and the whole Juglandaceae family.
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Affiliation(s)
- Yue Huang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Xin-Jie Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China
| | - Can-Yu Zhang
- Yunnan Normal University, Kunming, 650500, Yunnan, China
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hong-Hu Meng
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation & Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China.
| | - Yong-Hua Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China.
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China.
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Zhang R, Drummond AJ, Mendes FK. Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters. Syst Biol 2024; 73:102-124. [PMID: 38085256 PMCID: PMC11129596 DOI: 10.1093/sysbio/syad067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/23/2023] [Accepted: 11/07/2023] [Indexed: 05/28/2024] Open
Abstract
Time-scaled phylogenetic trees are an ultimate goal of evolutionary biology and a necessary ingredient in comparative studies. The accumulation of genomic data has resolved the tree of life to a great extent, yet timing evolutionary events remain challenging if not impossible without external information such as fossil ages and morphological characters. Methods for incorporating morphology in tree estimation have lagged behind their molecular counterparts, especially in the case of continuous characters. Despite recent advances, such tools are still direly needed as we approach the limits of what molecules can teach us. Here, we implement a suite of state-of-the-art methods for leveraging continuous morphology in phylogenetics, and by conducting extensive simulation studies we thoroughly validate and explore our methods' properties. While retaining model generality and scalability, we make it possible to estimate absolute and relative divergence times from multiple continuous characters while accounting for uncertainty. We compile and analyze one of the most data-type diverse data sets to date, comprised of contemporaneous and ancient molecular sequences, and discrete and continuous morphological characters from living and extinct Carnivora taxa. We conclude by synthesizing lessons about our method's behavior, and suggest future research venues.
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Affiliation(s)
- Rong Zhang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School 169857, Singapore
| | - Alexei J Drummond
- Centre for Computational Evolution, The University of Auckland, Auckland 1010, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Fábio K Mendes
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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Zhou H, Zhang X, Liu H, Ma J, Hao F, Ye H, Wang Y, Zhang S, Yue M, Zhao P. Chromosome-level genome assembly of Platycarya strobilacea. Sci Data 2024; 11:269. [PMID: 38443357 PMCID: PMC10914804 DOI: 10.1038/s41597-024-03107-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 02/29/2024] [Indexed: 03/07/2024] Open
Abstract
Platycarya strobilacea belongs to the walnut family (Juglandaceae), is commonly known as species endemic to East Asia, and is an ecologically important, wind pollinated, woody deciduous tree. To facilitate this ancient tree for the ecological value and conservation of this ancient tree, we report a new high-quality genome assembly of P. strobilacea. The genome size was 677.30 Mb, with a scaffold N50 size of 45,791,698 bp, and 98.43% of the assembly was anchored to 15 chromosomes. We annotated 32,246 protein-coding genes in the genome, of which 96.30% were functionally annotated in six databases. This new high-quality assembly of P. strobilacea provide valuable resource for the phylogenetic and evolutionary analysis of the walnut family and angiosperm.
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Affiliation(s)
- Huijuan Zhou
- Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Shaanxi Academy of Science, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Xuedong Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Jiayu Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Fan Hao
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Yaling Wang
- Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Shaanxi Academy of Science, Xi'an, Shaanxi, 710061, China
| | - Shuoxin Zhang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ming Yue
- Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Shaanxi Academy of Science, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China.
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Groh JS, Vik DC, Stevens KA, Brown PJ, Langley CH, Coop G. Distinct ancient structural polymorphisms control heterodichogamy in walnuts and hickories. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.23.573205. [PMID: 38187547 PMCID: PMC10769452 DOI: 10.1101/2023.12.23.573205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The maintenance of stable mating type polymorphisms is a classic example of balancing selection, underlying the nearly ubiquitous 50/50 sex ratio in species with separate sexes. One lesser known but intriguing example of a balanced mating polymorphism in angiosperms is heterodichogamy - polymorphism for opposing directions of dichogamy (temporal separation of male and female function in hermaphrodites) within a flowering season. This mating system is common throughout Juglandaceae, the family that includes globally important and iconic nut and timber crops - walnuts (Juglans), as well as pecan and other hickories (Carya). In both genera, heterodichogamy is controlled by a single dominant allele. We fine-map the locus in each genus, and find two ancient (>50 Mya) structural variants involving different genes that both segregate as genus-wide trans-species polymorphisms. The Juglans locus maps to a ca. 20 kb structural variant adjacent to a probable trehalose phosphate phosphatase (TPPD-1), homologs of which regulate floral development in model systems. TPPD-1 is differentially expressed between morphs in developing male flowers, with increased allele-specific expression of the dominant haplotype copy. Across species, the dominant haplotype contains a tandem array of duplicated sequence motifs, part of which is an inverted copy of the TPPD-1 3' UTR. These repeats generate various distinct small RNAs matching sequences within the 3' UTR and further downstream. In contrast to the single-gene Juglans locus, the Carya heterodichogamy locus maps to a ca. 200-450 kb cluster of tightly linked polymorphisms across 20 genes, some of which have known roles in flowering and are differentially expressed between morphs in developing flowers. The dominant haplotype in pecan, which is nearly always heterozygous and appears to rarely recombine, shows markedly reduced genetic diversity and is over twice as long as its recessive counterpart due to accumulation of various types of transposable elements. We did not detect either genetic system in other heterodichogamous genera within Juglandaceae, suggesting that additional genetic systems for heterodichogamy may yet remain undiscovered.
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Affiliation(s)
- Jeffrey S Groh
- Department of Evolution and Ecology, University of California, Davis
- Center for Population Biology, University of California, Davis
| | - Diane C Vik
- Department of Evolution and Ecology, University of California, Davis
| | - Kristian A Stevens
- Department of Evolution and Ecology, University of California, Davis
- Department of Computer Science, University of California, Davis
| | - Patrick J Brown
- Department of Plant Sciences, University of California, Davis
| | - Charles H Langley
- Department of Evolution and Ecology, University of California, Davis
- Center for Population Biology, University of California, Davis
| | - Graham Coop
- Department of Evolution and Ecology, University of California, Davis
- Center for Population Biology, University of California, Davis
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Hand SJ, Maugoust J, Beck RMD, Orliac MJ. A 50-million-year-old, three-dimensionally preserved bat skull supports an early origin for modern echolocation. Curr Biol 2023; 33:4624-4640.e21. [PMID: 37858341 DOI: 10.1016/j.cub.2023.09.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 07/24/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023]
Abstract
Bats are among the most recognizable, numerous, and widespread of all mammals. But much of their fossil record is missing, and bat origins remain poorly understood, as do the relationships of early to modern bats. Here, we describe a new early Eocene bat that helps bridge the gap between archaic stem bats and the hyperdiverse modern bat radiation of more than 1,460 living species. Recovered from ∼50 million-year-old cave sediments in the Quercy Phosphorites of southwestern France, Vielasia sigei's remains include a near-complete, three-dimensionally preserved skull-the oldest uncrushed bat cranium yet found. Phylogenetic analyses of a 2,665 craniodental character matrix, with and without 36.8 kb of DNA sequence data, place Vielasia outside modern bats, with total evidence tip-dating placing it sister to the crown clade. Vielasia retains the archaic dentition and skeletal features typical of early Eocene bats, but its inner ear shows specializations found in modern echolocating bats. These features, which include a petrosal only loosely attached to the basicranium, an expanded cochlea representing ∼25% basicranial width, and a long basilar membrane, collectively suggest that the kind of laryngeal echolocation used by most modern bats predates the crown radiation. At least 23 individuals of V. sigei are preserved together in a limestone cave deposit, indicating that cave roosting behavior had evolved in bats by the end of the early Eocene; this period saw the beginning of significant global climate cooling that may have been an evolutionary driver for bats to first congregate in caves.
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Affiliation(s)
- Suzanne J Hand
- ESSRC, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jacob Maugoust
- Institut des Sciences de l'Evolution, UMR 5554 CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Robin M D Beck
- School of Science, Engineering and Environment, University of Salford, Manchester M5 4WT, UK.
| | - Maeva J Orliac
- Institut des Sciences de l'Evolution, UMR 5554 CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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López-Martínez AM, Schönenberger J, von Balthazar M, González-Martínez CA, Ramírez-Barahona S, Sauquet H, Magallón S. Integrating Fossil Flowers into the Angiosperm Phylogeny Using Molecular and Morphological Evidence. Syst Biol 2023; 72:837-855. [PMID: 36995161 DOI: 10.1093/sysbio/syad017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 03/31/2023] Open
Abstract
Fossils are essential to infer past evolutionary processes. The assignment of fossils to extant clades has traditionally relied on morphological similarity and on apomorphies shared with extant taxa. The use of explicit phylogenetic analyses to establish fossil affinities has so far remained limited. In this study, we built a comprehensive framework to investigate the phylogenetic placement of 24 exceptionally preserved fossil flowers. For this, we assembled a new species-level data set of 30 floral traits for 1201 extant species that were sampled to capture the stem and crown nodes of all angiosperm families. We explored multiple analytical approaches to integrate the fossils into the phylogeny, including different phylogenetic estimation methods, topological-constrained analyses, and combining molecular and morphological data of extant and fossil species. Our results were widely consistent across approaches and showed minor differences in the support of fossils at different phylogenetic positions. The placement of some fossils agrees with previously suggested relationships, but for others, a new placement is inferred. We also identified fossils that are well supported within particular extant families, whereas others showed high phylogenetic uncertainty. Finally, we present recommendations for future analyses combining molecular and morphological evidence, regarding the selection of fossils and appropriate methodologies, and provide some perspectives on how to integrate fossils into the investigation of divergence times and the temporal evolution of morphological traits. [Angiosperms; fossil flowers; phylogenetic uncertainty; RoguePlots.].
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Affiliation(s)
- Andrea M López-Martínez
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico
| | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna 1030, Austria
| | - Maria von Balthazar
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna 1030, Austria
| | - César A González-Martínez
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico
| | - Santiago Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico
| | - Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW 2000, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico
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Song H, Huang L, Xiang H, Quan C, Jin J. First reliable Miocene fossil winged fruits record of Engelhardia in Asia through anatomical investigation. iScience 2023; 26:106867. [PMID: 37260748 PMCID: PMC10227380 DOI: 10.1016/j.isci.2023.106867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/01/2023] [Accepted: 05/09/2023] [Indexed: 06/02/2023] Open
Abstract
Fossil genera with similar features to the winged fruits of the living Engelhardia Lesch. ex Blume (e.g., Palaeocarya G. Saporta) have been widely reported in Cenozoic fossil floras of the Northern Hemisphere. However, fossil winged fruits of Engelhardia with detailed anatomical structures have only been found in the upper Eocene of North America. This study reports the first Engelhardia fossil winged fruits with detailed anatomical structures in East Asia from the Miocene Erzitang Formation of Guangxi, South China. The anatomical and morphological features of the new fossils, including the unique structure of secondary septa, clearly distinguish them from other fossil genera and show unambiguously their attribution to the genus Engelhardia. This discovery suggests that Engelhardia had reached its modern distribution during the Miocene and the climate of the Guiping Basin in Guangxi during the Miocene was similar to that of present-day tropical and subtropical regions in Asia.
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Affiliation(s)
- Hanzhang Song
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Luliang Huang
- School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Helanlin Xiang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Cheng Quan
- School of Earth Science & Resources, Chang'an University, Xi'an 710061, China
| | - Jianhua Jin
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
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Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes. Nat Commun 2023; 14:617. [PMID: 36739280 PMCID: PMC9899254 DOI: 10.1038/s41467-023-36247-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 01/20/2023] [Indexed: 02/06/2023] Open
Abstract
In lineages of allopolyploid origin, sets of homoeologous chromosomes may coexist that differ in gene content and syntenic structure. Presence or absence of genes and microsynteny along chromosomal blocks can serve to differentiate subgenomes and to infer phylogenies. We here apply genome-structural data to infer relationships in an ancient allopolyploid lineage, the walnut family (Juglandaceae), by using seven chromosome-level genomes, two of them newly assembled. Microsynteny and gene-content analyses yield identical topologies that place Platycarya with Engelhardia as did a 1980s morphological-cladistic study. DNA-alignment-based topologies here and in numerous earlier studies instead group Platycarya with Carya and Juglans, perhaps misled by past hybridization. All available data support a hybrid origin of Juglandaceae from extinct or unsampled progenitors nested within, or sister to, Myricaceae. Rhoiptelea chiliantha, sister to all other Juglandaceae, contains proportionally more DNA repair genes and appears to evolve at a rate 2.6- to 3.5-times slower than the remaining species.
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Beck RMD, de Vries D, Janiak MC, Goodhead IB, Boubli JP. Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches. J Hum Evol 2023; 174:103293. [PMID: 36493598 DOI: 10.1016/j.jhevol.2022.103293] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 12/12/2022]
Abstract
There have been multiple published phylogenetic analyses of platyrrhine primates (New World monkeys) using both morphological and molecular data, but relatively few that have integrated both types of data into a total evidence approach. Here, we present phylogenetic analyses of recent and fossil platyrrhines, based on a total evidence data set of 418 morphological characters and 10.2 kilobases of DNA sequence data from 17 nuclear genes taken from previous studies, using undated and tip-dating approaches in a Bayesian framework. We compare the results of these analyses with molecular scaffold analyses using maximum parsimony and Bayesian approaches, and we use a formal information theoretic approach to identify unstable taxa. After a posteriori pruning of unstable taxa, the undated and tip-dating topologies appear congruent with recent molecular analyses and support largely similar relationships, with strong support for Stirtonia as a stem alouattine, Neosaimiri as a stem saimirine, Cebupithecia as a stem pitheciine, and Lagonimico as a stem callitrichid. Both analyses find three Greater Antillean subfossil platyrrhines (Xenothrix, Antillothrix, and Paralouatta) to form a clade that is related to Callicebus, congruent with a single dispersal event by the ancestor of this clade to the Greater Antilles. They also suggest that the fossil Proteropithecia may not be closely related to pitheciines, and that all known platyrrhines older than the Middle Miocene are stem taxa. Notably, the undated analysis found the Early Miocene Panamacebus (currently recognized as the oldest known cebid) to be unstable, and the tip-dating analysis placed it outside crown Platyrrhini. Our tip-dating analysis supports a late Oligocene or earliest Miocene (20.8-27.0 Ma) age for crown Platyrrhini, congruent with recent molecular clock analyses.
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Affiliation(s)
- Robin M D Beck
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK.
| | - Dorien de Vries
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Mareike C Janiak
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Ian B Goodhead
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Jean P Boubli
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
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10
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Schoonderwoerd KM, Friedman WE. Interspecific morphological variation in Juglandoideae resting bud organization: a winter's tale? ANNALS OF BOTANY 2022; 129:679-696. [PMID: 35390122 PMCID: PMC9113150 DOI: 10.1093/aob/mcac050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/02/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS Dormant resting buds are frequently regarded as static units, with protective cataphylls on the outside and embryonic foliage leaves on the inside. How the presence of cataphylls influences the dynamic, cyclical, annually repeating sequence of leaf forms that a resting bud gives rise to has rarely been interrogated. To examine the connection between dormant structure and growing-season development, we compare the complete seasonal heteroblastic sequence of leaf forms of six species of temperate Juglandaceae with distinctly different vegetative resting bud structures. These include buds with cataphylls; buds without cataphylls; and buds with caducous cataphylls that are lost before the onset of winter. METHODS In a common garden setting over a 7-month growing season, the dimensions of 2249 individual vegetative metamers were tracked from first exposure to abscission along the shoots of saplings and mature trees. The timing of metamer initiation within terminal buds was investigated using micro-CT scanning. Character state transitions of resting bud types were estimated using a phylogenetic tree of Juglandaceae. KEY RESULTS The presence of cataphylls within a heteroblastic sequence is associated with a single cohort of foliage leaves that flush and abscise synchronously. This growing pattern is highly determinate, with next year's terminal-bud cataphylls already initiated before spring leaf out. In contrast, in sequences without cataphylls, shorter-lived foliage leaves appear and abscise in a staggered fashion. Despite these differences in leaf demography, all examined heteroblastic sequences produce a series of small, caducous leaf forms that precede terminal bud set. CONCLUSIONS The ubiquity of caducous leaf forms in Juglandoideae may point to the importance of shoot tip protection far beyond the dormant season. In addition, the presence or absence of cataphylls in resting buds is indicative of distinct shoot ontogenetic patterns, and functional strategies, in summer.
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Affiliation(s)
- Kristel M Schoonderwoerd
- Harvard University, Organismic and Evolutionary Biology, 26 Oxford Street, Cambridge, MA 02138, USA
- The Arnold Arboretum of Harvard University, 1300 Centre Street, Boston, MA 02131, USA
| | - William E Friedman
- Harvard University, Organismic and Evolutionary Biology, 26 Oxford Street, Cambridge, MA 02138, USA
- The Arnold Arboretum of Harvard University, 1300 Centre Street, Boston, MA 02131, USA
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11
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Tang KK, Smith SY, Atkinson BA. Extending beyond Gondwana: Cretaceous Cunoniaceae from western North America. THE NEW PHYTOLOGIST 2022; 234:704-718. [PMID: 35043416 DOI: 10.1111/nph.17976] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Cunoniaceae are important elements of rainforests across the Southern Hemisphere. Many of these flowering plants are considered Paleo-Antarctic Rainforest Lineages that had a Gondwanan distribution since the Paleocene. Fossils of several modern genera within the family, such as Ceratopetalum, have indicated biogeographical connections between South America and Australia in the Cenozoic. Here, we report a dramatic geographical range extension for Ceratopetalum, and Cunoniaceae as a whole, based on two exceptionally preserved fossil winged fruits from Campanian (c. 82-80 Ma old) deposits on Sucia Island, Washington, USA. The fossils were studied using physical sectioning, light microscopy, micro-computed tomography scanning and multiple phylogenetic analyses. The fossil fruits share diagnostic characters with Ceratopetalum such as the presence of four to five persistent calyx lobes, a prominent nectary disk, persistent stamens, a semi-inferior ovary and two persistent styles. Based on morphological comparisons with fruits of extant species and support from phylogenetic analyses, the fossils are assigned to a new species Ceratopetalum suciensis. These fossils are the first unequivocal evidence of crown Cunoniaceae from the Cretaceous of North America, indicating a more complicated biogeographical history for this important Gondwanan family.
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Affiliation(s)
- Keana K Tang
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
- Biodiversity Institute, University of Kansas, Lawrence, KS, 66045, USA
| | - Selena Y Smith
- Earth and Environmental Sciences and Museum of Paleontology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Brian A Atkinson
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
- Biodiversity Institute, University of Kansas, Lawrence, KS, 66045, USA
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Opening a door to the spatiotemporal history of plants from the tropical Indochina Peninsula to subtropical China. Mol Phylogenet Evol 2022; 171:107458. [DOI: 10.1016/j.ympev.2022.107458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 12/11/2022]
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13
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Xi J, Lv S, Zhang W, Zhang J, Wang K, Guo H, Hu J, Yang Y, Wang J, Xia G, Fan G, Wang X, Xiao L. Comparative plastomes of Carya species provide new insights into the plastomes evolution and maternal phylogeny of the genus. FRONTIERS IN PLANT SCIENCE 2022; 13:990064. [PMID: 36407576 PMCID: PMC9667483 DOI: 10.3389/fpls.2022.990064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/21/2022] [Indexed: 05/03/2023]
Abstract
Carya, in the Juglandiodeae subfamily, is to a typical temperate-subtropical forest-tree genus for studying the phylogenetic evolution and intercontinental disjunction between eastern Asia (EA) and North America (NA). Species of the genus have high economic values worldwide for their high-quality wood and the rich healthy factors of their nuts. Although previous efforts based on multiple molecular markers or genome-wide SNPs supported the monophyly of Carya and its two EA and NA major subclades, the maternal phylogeny of Carya still need to be comprehensively evaluated. The variation of Carya plastome has never been thoroughly characterized. Here, we novelly present 19 newly generated plastomes of congeneric Carya species, including the recently rediscovered critically endangered C. poilanei. The overall assessment of plastomes revealed highly conservative in the general structures. Our results indicated that remarkable differences in several plastome features are highly consistent with the EA-NA disjunction and showed the relatively diverse matrilineal sources among EA Carya compared to NA Carya. The maternal phylogenies were conducted with different plastome regions and full-length plastome datasets from 30 plastomes, representing 26 species in six genera of Juglandoideae and Myrica rubra (as root). Six out of seven phylogenetic topologies strongly supported the previously reported relationships among genera of Juglandoideae and the two subclades of EA and NA Carya, but displayed significant incongruencies between species within the EA and NA subclades. The phylogenetic tree generated from full-length plastomes demonstrated the optimal topology and revealed significant geographical maternal relationships among Carya species, especially for EA Carya within overlapping distribution areas. The full-length plastome-based phylogenetic topology also strongly supported the taxonomic status of five controversial species as separate species of Carya. Historical and recent introgressive hybridization and plastid captures might contribute to plastome geographic patterns and inconsistencies between topologies built from different datasets, while incomplete lineage sorting could account for the discordance between maternal topology and the previous nuclear genome data-based phylogeny. Our findings highlight full-length plastomes as an ideal tool for exploring maternal relationships among the subclades of Carya, and potentially in other outcrossing perennial woody plants, for resolving plastome phylogenetic relationships.
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Affiliation(s)
- Jianwei Xi
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Saibin Lv
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Weiping Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Jingbo Zhang
- Department of Biological Sciences, St. John’s University - Queens, NY, United States
- *Correspondence: Lihong Xiao, ; Jingbo Zhang,
| | - Ketao Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Haobing Guo
- The Beijing Genomics Institute (BGI) -Qingdao, The Beijing Genomics Institute (BGI)-Shenzhen, Qingdao, China
| | - Jie Hu
- The Beijing Genomics Institute (BGI) -Qingdao, The Beijing Genomics Institute (BGI)-Shenzhen, Qingdao, China
| | - Yang Yang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Jianhua Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Guohua Xia
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Guangyi Fan
- The Beijing Genomics Institute (BGI) -Qingdao, The Beijing Genomics Institute (BGI)-Shenzhen, Qingdao, China
| | - Xinwang Wang
- Pecan Breeding and Genetics, Southern Plains Agricultural Research Center, USDA-ARS, College Station, TX, United States
| | - Lihong Xiao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- *Correspondence: Lihong Xiao, ; Jingbo Zhang,
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Luo J, Chen J, Guo W, Yang Z, Lim KJ, Wang Z. Reassessment of Annamocarya sinesis ( Carya sinensis) Taxonomy through Concatenation and Coalescence Phylogenetic Analysis. PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010052. [PMID: 35009055 PMCID: PMC8747223 DOI: 10.3390/plants11010052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 05/20/2023]
Abstract
Due to its peculiar morphological characteristics, there is dispute as to whether the genus of Annamocarya sinensis, a species of Juglandaceae, is Annamocarya or Carya. Most morphologists believe it should be distinguished from the Carya genus while genomicists suggest that A. sinensis belongs to the Carya genus. To explore the taxonomic status of A. sinensis using chloroplast genes, we collected chloroplast genomes of 16 plant species and assembled chloroplast genomes of 10 unpublished Carya species. We analyzed all 26 species' chloroplast genomes through two analytical approaches (concatenation and coalescence), using the entire and unique chloroplast coding sequence (CDS) and entire and protein sequences. Our results indicate that the analysis of the CDS and protein sequences or unique CDS and unique protein sequence of chloroplast genomes shows that A. sinensis indeed belongs to the Carya genus. In addition, our analysis shows that, compared to single chloroplast genes, the phylogeny trees constructed using numerous genes showed higher consistency. Moreover, the phylogenetic analysis calculated with the coalescence method and unique gene sequences was more robust than that done with the concatenation method, particularly for analyzing phylogenetically controversial species. Through the analysis, our results concluded that A. sinensis should be called C. sinensis.
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Affiliation(s)
- Jie Luo
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (J.L.); (J.C.); (W.G.); (Z.Y.)
| | - Junhao Chen
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (J.L.); (J.C.); (W.G.); (Z.Y.)
- Department of Biology, Saint Louis University, St. Louis, MO 63104, USA
| | - Wenlei Guo
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (J.L.); (J.C.); (W.G.); (Z.Y.)
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhengfu Yang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (J.L.); (J.C.); (W.G.); (Z.Y.)
| | - Kean-Jin Lim
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (J.L.); (J.C.); (W.G.); (Z.Y.)
- Correspondence: (K.-J.L.); (Z.W.)
| | - Zhengjia Wang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (J.L.); (J.C.); (W.G.); (Z.Y.)
- Correspondence: (K.-J.L.); (Z.W.)
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Zhang Q, Ree RH, Salamin N, Xing Y, Silvestro D. Fossil-Informed Models Reveal a Boreotropical Origin and Divergent Evolutionary Trajectories in the Walnut Family (Juglandaceae). Syst Biol 2021; 71:242-258. [PMID: 33964165 PMCID: PMC8677545 DOI: 10.1093/sysbio/syab030] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 05/03/2021] [Accepted: 05/03/2021] [Indexed: 12/12/2022] Open
Abstract
Temperate woody plants in the Northern Hemisphere have long been known to exhibit high species richness in East Asia and North America and significantly lower diversity in Europe, but the causes of this pattern remain debated. Here, we quantify the roles of dispersal, niche evolution, and extinction in shaping the geographic diversity of the temperate woody plant family Juglandaceae (walnuts and their relatives). Integrating evidence from molecular, morphological, fossil, and (paleo)environmental data, we find strong support for a Boreotropical origin of the family with contrasting evolutionary trajectories between the temperate subfamily Juglandoideae and the tropical subfamily Engelhardioideae. Juglandoideae rapidly evolved frost tolerance when the global climate shifted to ice-house conditions from the Oligocene, with diversification at high latitudes especially in Europe and Asia during the Miocene. Subsequent range contraction at high latitudes and high levels of extinction in Europe driven by global cooling led to the current regional disparity in species diversity. Engelhardioideae showed temperature conservatism while adapting to increased humidity, tracking tropical climates to low latitudes since the middle Eocene with comparatively little diversification, perhaps due to high competition in the tropical zone. The biogeographic history of Juglandaceae shows that the North Atlantic land bridge and Europe played more critical roles than previously thought in linking the floras of East Asia and North America, and showcases the complex interplay among climate change, niche evolution, dispersal, and extinction that shaped the modern disjunct pattern of species richness in temperate woody plants. [Boreotropical origin; climatic niche evolution; disjunct distribution; dispersal; diversity anomaly; extinction; Juglandaceae.].
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Affiliation(s)
- Qiuyue Zhang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303 Mengla, China
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- College of Resources and Environment, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Richard H Ree
- Life Sciences Section, Negaunee Integrative Research Center, Field Museum, Chicago, IL, 60605, USA
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Yaowu Xing
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303 Mengla, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, 666303 Mengla, China
| | - Daniele Silvestro
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
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16
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Zhou H, Hu Y, Ebrahimi A, Liu P, Woeste K, Zhao P, Zhang S. Whole genome based insights into the phylogeny and evolution of the Juglandaceae. BMC Ecol Evol 2021; 21:191. [PMID: 34674641 PMCID: PMC8529855 DOI: 10.1186/s12862-021-01917-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/22/2021] [Indexed: 11/10/2022] Open
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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Affiliation(s)
- Huijuan Zhou
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Yiheng Hu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Aziz Ebrahimi
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, 47907, Indiana, USA
| | - Peiliang Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Keith Woeste
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, 47907, Indiana, USA
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China.
| | - Shuoxin Zhang
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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17
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Zhou H, Hu Y, Ebrahimi A, Liu P, Woeste K, Zhao P, Zhang S. Whole genome based insights into the phylogeny and evolution of the Juglandaceae. BMC Ecol Evol 2021. [PMID: 34674641 DOI: 10.21203/rs.3.rs-495294/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
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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Affiliation(s)
- Huijuan Zhou
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Yiheng Hu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Aziz Ebrahimi
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, 47907, Indiana, USA
| | - Peiliang Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Keith Woeste
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, 47907, Indiana, USA
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China.
| | - Shuoxin Zhang
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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18
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Yang YY, Qu XJ, Zhang R, Stull GW, Yi TS. Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture. Mol Phylogenet Evol 2021; 163:107232. [PMID: 34129935 DOI: 10.1016/j.ympev.2021.107232] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/21/2021] [Accepted: 06/10/2021] [Indexed: 11/17/2022]
Abstract
Plastid phylogenomic analyses have shed light on many recalcitrant relationships across the angiosperm Tree of Life and continue to play an important role in plant phylogenetics alongside nuclear data sets given the utility of plastomes for revealing ancient and recent introgression. Here we conduct a plastid phylogenomic study of Fagales, aimed at exploring contentious relationships (e.g., the placement of Myricaceae and some intergeneric relationships in Betulaceae, Juglandaceae, and Fagaceae) and dissecting conflicting phylogenetic signals across the plastome. Combining 102 newly sequenced samples with publically available plastomes, we analyzed a dataset including 256 species and 32 of the 34 total genera of Fagales, representing the largest plastome-based study of the order to date. We find strong support for a sister relationship between Myricaceae and Juglandaceae, as well as strongly supported conflicting signal for alternative generic relationships in Betulaceae and Juglandaceae. These conflicts highlight the sensitivity of plastid phylogenomic analyses to genic composition, perhaps due to the prevalence of uninformative loci and heterogeneity in signal across different regions of the plastome. Phylogenetic relationships were geographically structured in subfamily Quercoideae, with Quercus being non-monophyletic and its sections forming clades with co-distributed Old World or New World genera of Quercoideae. Compared against studies based on nuclear genes, these results suggest extensive introgression and chloroplast capture in the early diversification of Quercus and Quercoideae. This study provides a critical plastome perspective on Fagales phylogeny, setting the stage for future studies employing more extensive data from the nuclear genome.
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Affiliation(s)
- Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, Shangdong 250014, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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Corrales A, Xu H, Garibay-Orijel R, Alfonso-Corrado C, Williams-Linera G, Chu C, Truong C, Jusino MA, Clark-Tapia R, Dalling JW, Liu Y, Smith ME. Fungal communities associated with roots of two closely related Juglandaceae species with a disjunct distribution in the tropics. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2020.101023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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20
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Schönenberger J, von Balthazar M, López Martínez A, Albert B, Prieu C, Magallón S, Sauquet H. Phylogenetic analysis of fossil flowers using an angiosperm-wide data set: proof-of-concept and challenges ahead. AMERICAN JOURNAL OF BOTANY 2020; 107:1433-1448. [PMID: 33026116 PMCID: PMC7702048 DOI: 10.1002/ajb2.1538] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/08/2020] [Indexed: 05/29/2023]
Abstract
PREMISE Significant paleobotanical discoveries in recent decades have considerably improved our understanding of the early evolution of angiosperms and their flowers. However, our ability to test the systematic placement of fossil flowers on the basis of phylogenetic analyses has remained limited, mainly due to the lack of an adequate, angiosperm-wide morphological data set for extant taxa. Earlier attempts to place fossil flowers phylogenetically were, therefore, forced to make prior qualitative assessments of the potential systematic position of fossils and to restrict phylogenetic analyses to selected angiosperm subgroups. METHODS We conduct angiosperm-wide molecular backbone analyses of 10 fossil flower taxa selected from the Cretaceous record. Our analyses make use of a floral trait data set built within the framework of the eFLOWER initiative. We provide an updated version of this data set containing data for 28 floral and two pollen traits for 792 extant species representing 372 angiosperm families. RESULTS We find that some fossils are placed congruently with earlier hypotheses while others are found in positions that had not been suggested previously. A few take up equivocal positions, including the stem branches of large clades. CONCLUSIONS Our study provides an objective approach to test for the phylogenetic position of fossil flowers across angiosperms. Such analyses may provide a complementary tool for paleobotanical studies, allowing for a more comprehensive understanding of fossil phylogenetic relationships in angiosperms. Ongoing work focused on extending the sampling of extant taxa and the number of floral traits will further improve the applicability and accuracy of our approach.
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Affiliation(s)
- Jürg Schönenberger
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14ViennaA‐1030Austria
| | - Maria von Balthazar
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14ViennaA‐1030Austria
| | - Andrea López Martínez
- Instituto de BiologíaUniversidad Nacional Autónoma de MéxicoCircuito Exterior, Ciudad Universitaria, CoyoacánMéxico City04510Mexico
| | - Béatrice Albert
- Ecologie Systématique EvolutionUniv. Paris‐SudCNRSAgroParisTechUniversité Paris‐SaclayOrsay91400France
| | - Charlotte Prieu
- Ecologie Systématique EvolutionUniv. Paris‐SudCNRSAgroParisTechUniversité Paris‐SaclayOrsay91400France
| | - Susana Magallón
- Instituto de BiologíaUniversidad Nacional Autónoma de MéxicoCircuito Exterior, Ciudad Universitaria, CoyoacánMéxico City04510Mexico
| | - Hervé Sauquet
- Ecologie Systématique EvolutionUniv. Paris‐SudCNRSAgroParisTechUniversité Paris‐SaclayOrsay91400France
- National Herbarium of New South Wales (NSW)Royal Botanic Gardens and Domain TrustSydneyNSW2000Australia
- Evolution and Ecology Research CentreSchool of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyAustralia
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Zhang CY, Ling Low S, Song YG, Nurainas, Kozlowski G, Li L, Zhou SS, Tan YH, Cao GL, Zhou Z, Meng HH, Li J. Shining a light on species delimitation in the tree genus Engelhardia Leschenault ex Blume (Juglandaceae). Mol Phylogenet Evol 2020; 152:106918. [PMID: 32738292 DOI: 10.1016/j.ympev.2020.106918] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 10/23/2022]
Abstract
Enhanced efficacy in species delimitation is critically important in biology given the pending biodiversity crisis under global warming and anthropogenic activity. In particular, delineation of traditional classifications in view of the complexity of species requires an integrative approach to effectively define species boundaries, and this is a major focus of systematic biology. Here, we explored species delimitation of Engelhardia in tropical and subtropical Asia. In total, 716 individuals in 71 populations were genotyped using five chloroplast regions, one nuclear DNA region (nrITS), and 11 nuclear simple sequence repeats (nSSR). Phylogenetic trees were constructed and relationships among species were assessed. Molecular analyses were then combined with 14 morphological characteristics of 720 specimens to further explore the species boundaries of Engelhardia. Integrating phylogenetic and morphological clusters provided well-resolved relationships to delineate seven species. The results suggested that: first, that E. fenzelii, E. roxburghiana, E. hainanensis, E. apoensis, and E. serrata are distinct species; second, E. spicata var. spicata, E. spicata var. aceriflora, E. spicata var. colebrookeana, and E. rigida should be combined under E. spicata and treated as a species complex; third, E. serrata var. cambodica should be raised to species level and named E. villosa. We illuminated that bias thresholds determining the cluster number for delimiting species boundaries were substantially reduced when morphological data were incorporated. Our results urge caution when using the concepts of subspecies and varieties in order to prevent confusion, particularly with respect to species delimitation for tropical and subtropical species. In some cases, re-ranking or combining subspecies and/or varieties may enable more accurate species delimitation.
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Affiliation(s)
- Can-Yu Zhang
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shook Ling Low
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Yi-Gang Song
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai 201602, China; Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Nurainas
- Department of Biology, Faculty of Math. & Nat. Sci. Andalas University, Padang 25163, West Sumatra, Indonesia
| | - Gregor Kozlowski
- Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Lang Li
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650023, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla 666303, China
| | - Shi-Shun Zhou
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar
| | - Yun-Hong Tan
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla 666303, China
| | - Guan-Long Cao
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hong-Hu Meng
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650023, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar.
| | - Jie Li
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650023, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla 666303, China.
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Mu XY, Tong L, Sun M, Zhu YX, Wen J, Lin QW, Liu B. Phylogeny and divergence time estimation of the walnut family (Juglandaceae) based on nuclear RAD-Seq and chloroplast genome data. Mol Phylogenet Evol 2020; 147:106802. [DOI: 10.1016/j.ympev.2020.106802] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 03/18/2020] [Accepted: 03/18/2020] [Indexed: 11/25/2022]
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Guo W, Chen J, Li J, Huang J, Wang Z, Lim KJ. Portal of Juglandaceae: A comprehensive platform for Juglandaceae study. HORTICULTURE RESEARCH 2020; 7:35. [PMID: 32194971 PMCID: PMC7072074 DOI: 10.1038/s41438-020-0256-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/25/2019] [Accepted: 01/15/2020] [Indexed: 05/22/2023]
Abstract
Juglandaceae species are plants of great economic value and have been cultivated, domesticated, and utilized by human society for a long time. Their edible, nutrient-rich nuts and tough, durable wood have attracted the attention of botanists and breeders. With the advent of the genomics era, genome sequencing of the Juglandaceae family has been greatly accelerated, and a large amount of data has been generated. In this paper, we introduce the Portal of Juglandaceae (PJU), a tool to bring all these data together. The PJU contains genomes, gene-coding sequences, protein sequences, various types of annotation information, expression data, and miRNA data, which are configured with BLAST, JBrowse, and our self-developed synteny analysis tool. The PJU has a user-friendly and straightforward interface that performs a variety of query tasks with a few simple operations. In the future, we hope that the PJU will serve as a hub for the study of the Juglandaceae family.
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Affiliation(s)
- Wenlei Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an District, 311300 Hangzhou, Zhejiang China
| | - Junhao Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an District, 311300 Hangzhou, Zhejiang China
| | - Jian Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an District, 311300 Hangzhou, Zhejiang China
| | - Jianqin Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an District, 311300 Hangzhou, Zhejiang China
| | - Zhengjia Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an District, 311300 Hangzhou, Zhejiang China
| | - Kean-Jin Lim
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an District, 311300 Hangzhou, Zhejiang China
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Evaluating the Performance of Multiple Imputation Methods for Handling Missing Values in Time Series Data: A Study Focused on East Africa, Soil-Carbonate-Stable Isotope Data. STATS 2019. [DOI: 10.3390/stats2040032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In all fields of quantitative research, analysing data with missing values is an excruciating challenge. It should be no surprise that given the fragmentary nature of fossil records, the presence of missing values in geographical databases is unavoidable. As in such studies ignoring missing values may result in biased estimations or invalid conclusions, adopting a reliable imputation method should be regarded as an essential consideration. In this study, the performance of singular spectrum analysis (SSA) based on L 1 norm was evaluated on the compiled δ 13 C data from East Africa soil carbonates, which is a world targeted historical geology data set. Results were compared with ten traditionally well-known imputation methods showing L 1 -SSA performs well in keeping the variability of the time series and providing estimations which are less affected by extreme values, suggesting the method introduced here deserves further consideration in practice.
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25
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Morris AB, Shaw J. Markers in time and space: A review of the last decade of plant phylogeographic approaches. Mol Ecol 2019; 27:2317-2333. [PMID: 29675939 DOI: 10.1111/mec.14695] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 03/22/2018] [Accepted: 03/26/2018] [Indexed: 01/28/2023]
Abstract
Plant studies comprise a relatively small proportion of the phylogeographic literature, likely as a consequence of the fundamental challenges posed by the complex genomic structures and life history strategies of these organisms. Comparative plastomics (i.e., comparisons of mutation rates within and among regions of the chloroplast genome) across plant lineages has led to an increased understanding of which markers are likely to provide the most information at low taxonomic levels. However, the extent to which the results of such work have influenced the literature has not been fully assessed, nor has the extent to which plant phylogeographers explicitly analyse markers in time and space, both of which are integral components of the field. Here, we reviewed more than 400 publications from the last decade of plant phylogeography to specifically address the following questions: (i) What is the phylogenetic breadth of studies to date? (ii) What molecular markers have been used, and why were they chosen? (iii) What kinds of markers are most frequently used and in what combinations? (iv) How frequently are divergence time estimation and ecological niche modelling used in plant phylogeography? Our results indicate that chloroplast DNA sequence data remain the primary tool of choice, followed distantly by nuclear DNA sequences and microsatellites. Less than half (42%) of all studies use divergence time estimation, while even fewer use ecological niche modelling (14%). We discuss the implications of our findings, as well as the need for community standards on data reporting.
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Affiliation(s)
- Ashley B Morris
- Department of Biology and Center for Molecular Biosciences, Middle Tennessee State University, Murfreesboro, Tennessee
| | - Joey Shaw
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, Tennessee
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26
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Voglmayr H, Jaklitsch WM, Mohammadi H, Kazemzadeh Chakusary M. The genus Juglanconis ( Diaporthales) on Pterocarya. Mycol Prog 2019; 18:425-437. [PMID: 30906242 PMCID: PMC6399749 DOI: 10.1007/s11557-018-01464-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/05/2018] [Accepted: 12/12/2018] [Indexed: 10/27/2022]
Abstract
Based on molecular phylogenetic analyses of a multigene matrix of partial nuSSU-ITS-LSU rDNA, cal, his, ms204, rpb1, rpb2, tef1 and tub2 sequences, recent European and Iranian collections of Melanconium pterocaryae from the type host, Pterocarya fraxinifolia, are shown to be distinct from the Japanese Melanconis pterocaryae from Pterocarya rhoifolia, and both are confirmed as closely related members of the recently described genus Juglanconis. Therefore, the new name Juglanconis japonica is proposed for Melanconis pterocaryae. As no type collection could be traced, Melanconium pterocaryae (syn. J. pterocaryae) is neotypified, described and illustrated, and it is recorded for Europe for the first time. During field surveys in natural stands of P. fraxinifolia in Guilan province (Iran), Juglanconis pterocaryae was consistently isolated from tissues affected by branch and trunk cankers, twig dieback and wood necrosis, indicating that it is the causal agent of these diseases. The external and internal symptoms associated with these trunk diseases are described and illustrated.
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Affiliation(s)
- Hermann Voglmayr
- 1Division of Systematic and Evolutionary Botany, Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Wien, Austria
| | - Walter M Jaklitsch
- 1Division of Systematic and Evolutionary Botany, Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Wien, Austria.,2Department of Forest and Soil Sciences, BOKU-University of Natural Resources and Life Sciences, Institute of Forest Entomology, Forest Pathology and Forest Protection, Franz Schwackhöfer Haus, Peter-Jordan-Straße 82/I, 1190 Vienna, Austria
| | - Hamid Mohammadi
- 3Department of Plant Protection, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 7616914111 Iran
| | - Mohammad Kazemzadeh Chakusary
- 3Department of Plant Protection, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 7616914111 Iran
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27
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Zhu T, Wang L, You FM, Rodriguez JC, Deal KR, Chen L, Li J, Chakraborty S, Balan B, Jiang CZ, Brown PJ, Leslie CA, Aradhya MK, Dandekar AM, McGuire PE, Kluepfel D, Dvorak J, Luo MC. Sequencing a Juglans regia × J. microcarpa hybrid yields high-quality genome assemblies of parental species. HORTICULTURE RESEARCH 2019; 6:55. [PMID: 30937174 PMCID: PMC6431679 DOI: 10.1038/s41438-019-0139-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/09/2019] [Accepted: 03/10/2019] [Indexed: 05/22/2023]
Abstract
Members of the genus Juglans are monecious wind-pollinated trees in the family Juglandaceae with highly heterozygous genomes, which greatly complicates genome sequence assembly. The genomes of interspecific hybrids are usually comprised of haploid genomes of parental species. We exploited this attribute of interspecific hybrids to avoid heterozygosity and sequenced an interspecific hybrid Juglans microcarpa × J. regia using a novel combination of single-molecule sequencing and optical genome mapping technologies. The resulting assemblies of both genomes were remarkably complete including chromosome termini and centromere regions. Chromosome termini consisted of arrays of telomeric repeats about 8 kb long and heterochromatic subtelomeric regions about 10 kb long. The centromeres consisted of arrays of a centromere-specific Gypsy retrotransposon and most contained genes, many of them transcribed. Juglans genomes evolved by a whole-genome-duplication dating back to the Cretaceous-Paleogene boundary and consist of two subgenomes, which were fractionated by numerous short gene deletions evenly distributed along the length of the chromosomes. Fractionation was shown to be asymmetric with one subgenome exhibiting greater gene loss than the other. The asymmetry of the process is ongoing and mirrors an asymmetry in gene expression between the subgenomes. Given the importance of J. microcarpa × J. regia hybrids as potential walnut rootstocks, we catalogued disease resistance genes in the parental genomes and studied their chromosomal distribution. We also estimated the molecular clock rates for woody perennials and deployed them in estimating divergence times of Juglans genomes and those of other woody perennials.
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Affiliation(s)
- Tingting Zhu
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Le Wang
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6 Canada
| | - Juan C. Rodriguez
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Karin R. Deal
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Limin Chen
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Jie Li
- Genome Center, University of California, Davis, CA 95616 USA
| | | | - Bipin Balan
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Cai-Zhong Jiang
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
- Crops Pathology and Genetics Research Unit, USDA-ARS, Davis, CA 95616 USA
| | - Patrick J. Brown
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Charles A. Leslie
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | | | - Abhaya M. Dandekar
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Patrick E. McGuire
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Daniel Kluepfel
- Crops Pathology and Genetics Research Unit, USDA-ARS, Davis, CA 95616 USA
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
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28
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Zhang Q, Onstein RE, Little SA, Sauquet H. Estimating divergence times and ancestral breeding systems in Ficus and Moraceae. ANNALS OF BOTANY 2019; 123:191-204. [PMID: 30202847 PMCID: PMC6344110 DOI: 10.1093/aob/mcy159] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 08/06/2018] [Indexed: 05/30/2023]
Abstract
Background and Aims Although dioecy, which characterizes only 6 % of angiosperm species, has been considered an evolutionary dead end, recent studies have demonstrated that this is not necessarily the case. Moraceae (40 genera, 1100 spp., including Ficus, 750 spp.) are particularly diverse in breeding systems (including monoecy, gynodioecy, androdioecy and dioecy) and thus represent a model clade to study macroevolution of dioecy. Methods Ancestral breeding systems of Ficus and Moraceae were inferred. To do so, a new dated phylogenetic tree of Ficus and Moraceae was first reconstructed by combining a revised 12-fossil calibration set and a densely sampled molecular data set of eight markers and 320 species. Breeding system evolution was then reconstructed using both parsimony and model-based (maximum likelihood and Bayesian) approaches with this new time scale. Key Results The crown group ages of Ficus and Moraceae were estimated in the Eocene (40.6-55.9 Ma) and Late Cretaceous (73.2-84.7 Ma), respectively. Strong support was found for ancestral dioecy in Moraceae. Although the ancestral state of Ficus remained particularly sensitive to model selection, the results show that monoecy and gynodioecy evolved from dioecy in Moraceae, and suggest that gynodioecy probably evolved from monoecy in Ficus. Conclusions Dioecy was found not to be an evolutionary dead end in Moraceae. This study provides a new time scale for the phylogeny and a new framework of breeding system evolution in Ficus and Moraceae.
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Affiliation(s)
- Qian Zhang
- Laboratoire Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Renske E Onstein
- Laboratoire Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
- German Centre for Integrative Biodiversity Research (iDiv), Halle‐Jena‐Leipzig, Leipzig, Germany
| | - Stefan A Little
- Laboratoire Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Hervé Sauquet
- Laboratoire Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, Australia
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Corrales A, Henkel TW, Smith ME. Ectomycorrhizal associations in the tropics - biogeography, diversity patterns and ecosystem roles. THE NEW PHYTOLOGIST 2018; 220:1076-1091. [PMID: 29689121 DOI: 10.1111/nph.15151] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/20/2018] [Indexed: 06/08/2023]
Abstract
Contents Summary 1076 I. Introduction 1076 II. Historical overview 1077 III. Identities and distributions of tropical ectomycorrhizal plants 1077 IV. Dominance of tropical forests by ECM trees 1078 V. Biogeography of tropical ECM fungi 1081 VI. Beta diversity patterns in tropical ECM fungal communities 1082 VII. Conclusions and future research 1086 Acknowledgements 1087 References 1087 SUMMARY: Ectomycorrhizal (ECM) associations were historically considered rare or absent from tropical ecosystems. Although most tropical forests are dominated by arbuscular mycorrhizal (AM) trees, ECM associations are widespread and found in all tropical regions. Here, we highlight emerging patterns of ECM biogeography, diversity and ecosystem functions, identify knowledge gaps, and offer direction for future research. At the continental and regional scales, tropical ECM systems are highly diverse and vary widely in ECM plant and fungal abundance, diversity, composition and phylogenetic affinities. We found strong regional differences among the dominant host plant families, suggesting that biogeographical factors strongly influence tropical ECM symbioses. Both ECM plants and fungi also exhibit strong turnover along altitudinal and soil fertility gradients, suggesting niche differentiation among taxa. Ectomycorrhizal fungi are often more abundant and diverse in sites with nutrient-poor soils, suggesting that ECM associations can optimize plant nutrition and may contribute to the maintenance of tropical monodominant forests. More research is needed to elucidate the diversity patterns of ECM fungi and plants in the tropics and to clarify the role of this symbiosis in nutrient and carbon cycling.
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Affiliation(s)
- Adriana Corrales
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Terry W Henkel
- Department of Biological Sciences, Humboldt State University, Arcata, CA, 95521, USA
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
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Hsu Y, Cocroft RB, Snyder RL, Lin C. You stay, but I Hop: Host shifting near and far co-dominated the evolution of Enchenopa treehoppers. Ecol Evol 2018; 8:1954-1965. [PMID: 29468015 PMCID: PMC5817127 DOI: 10.1002/ece3.3815] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 11/24/2017] [Accepted: 12/06/2017] [Indexed: 12/11/2022] Open
Abstract
The importance and prevalence of phylogenetic tracking between hosts and dependent organisms caused by co-evolution and shifting between closely related host species have been debated for decades. Most studies of phylogenetic tracking among phytophagous insects and their host plants have been limited to insects feeding on a narrow range of host species. However, narrow host ranges can confound phylogenetic tracking (phylogenetic tracking hypothesis) with host shifting between hosts of intermediate relationship (intermediate hypothesis). Here, we investigated the evolutionary history of the Enchenopa binotata complex of treehoppers. Each species in this complex has high host fidelity, but the entire complex uses hosts across eight plant orders. The phylogenies of E. binotata were reconstructed to evaluate whether (1) tracking host phylogeny; or (2) shifting between intermediately related host plants better explains the evolutionary history of E. binotata. Our results suggest that E. binotata primarily shifted between both distant and intermediate host plants regardless of host phylogeny and less frequently tracked the phylogeny of their hosts. These findings indicate that phytophagous insects with high host fidelity, such as E. binotata, are capable of adaptation not only to closely related host plants but also to novel hosts, likely with diverse phenology and defense mechanisms.
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Affiliation(s)
- Yu‐Hsun Hsu
- Department of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | | | - Robert L. Snyder
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
- Present address:
Department of BiologyState University of New York College at PotsdamPotsdamNYUSA
| | - Chung‐Ping Lin
- Department of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
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31
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Abstract
The great bulk of the angiosperm fossil record consists of isolated fossil leaves that preserve abundant shape and venation (leaf architectural) information but are difficult to identify because they are not attached to other plant organs. Thus, poor taxonomic knowledge has tempered the tremendous potential of fossil leaves for constructing finely resolved records of biodiversity through time, extinction and recovery, past climate change and biotic response, paleoecology, and plant-animal associations. Moreover, paleoecological and paleoclimatic interpretations of fossil leaves are in great need of new approaches. Recent work is rapidly increasing the scientific value of fossil angiosperm leaves through advances in traditional paleobotanical reconstruction, phylogenetic understanding of both leaf architecture and the response of leaf shape to climate, quantitative plant ecology using measurable, correlatable leaf traits, and improved understanding of insect leaf-feeding damage. These emerging areas offer many novel opportunities to link paleoecology and neoecology. Increased collaboration across traditionally separate research areas is critical to continued success.
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Bomfleur B, Grimm GW, McLoughlin S. The fossil Osmundales (Royal Ferns)-a phylogenetic network analysis, revised taxonomy, and evolutionary classification of anatomically preserved trunks and rhizomes. PeerJ 2017; 5:e3433. [PMID: 28713650 PMCID: PMC5508817 DOI: 10.7717/peerj.3433] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 05/17/2017] [Indexed: 12/03/2022] Open
Abstract
The Osmundales (Royal Fern order) originated in the late Paleozoic and is the most ancient surviving lineage of leptosporangiate ferns. In contrast to its low diversity today (less than 20 species in six genera), it has the richest fossil record of any extant group of ferns. The structurally preserved trunks and rhizomes alone are referable to more than 100 fossil species that are classified in up to 20 genera, four subfamilies, and two families. This diverse fossil record constitutes an exceptional source of information on the evolutionary history of the group from the Permian to the present. However, inconsistent terminology, varying formats of description, and the general lack of a uniform taxonomic concept renders this wealth of information poorly accessible. To this end, we provide a comprehensive review of the diversity of structural features of osmundalean axes under a standardized, descriptive terminology. A novel morphological character matrix with 45 anatomical characters scored for 15 extant species and for 114 fossil operational units (species or specimens) is analysed using networks in order to establish systematic relationships among fossil and extant Osmundales rooted in axis anatomy. The results lead us to propose an evolutionary classification for fossil Osmundales and a revised, standardized taxonomy for all taxa down to the rank of (sub)genus. We introduce several nomenclatural novelties: (1) a new subfamily Itopsidemoideae (Guaireaceae) is established to contain Itopsidema, Donwelliacaulis, and Tiania; (2) the thamnopteroid genera Zalesskya, Iegosigopteris, and Petcheropteris are all considered synonymous with Thamnopteris; (3) 12 species of Millerocaulis and Ashicaulis are assigned to modern genera (tribe Osmundeae); (4) the hitherto enigmatic Aurealcaulis is identified as an extinct subgenus of Plenasium; and (5) the poorly known Osmundites tuhajkulensis is assigned to Millerocaulis. In addition, we consider Millerocaulis stipabonettiorum a possible member of Palaeosmunda and Millerocaulis estipularis as probably constituting the earliest representative of the (Todea-)Leptopteris lineage (subtribe Todeinae) of modern Osmundoideae.
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Affiliation(s)
- Benjamin Bomfleur
- Institut für Geologie und Paläontologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
- Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Guido W. Grimm
- Department für Paläontologie, Universität Wien, Wien, Austria
- Orléans, France
| | - Stephen McLoughlin
- Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden
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Ware JL, Barden P. Incorporating fossils into hypotheses of insect phylogeny. CURRENT OPINION IN INSECT SCIENCE 2016; 18:69-76. [PMID: 27939713 DOI: 10.1016/j.cois.2016.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/12/2016] [Indexed: 06/06/2023]
Abstract
Fossils represent stem and crown lineages, and their inclusion in phylogenetic reconstruction influences branch lengths, topology, and divergence time estimation. In addition, paleontological data may inform trends in morphological evolution as well as biogeographic history. Here we review the incorporation of fossils in studies of insect evolution, from morphological analyses to combined 'total evidence' node dating analyses. We discuss challenges associated with fossil based phylogenetics, and suggest best practices for use in tree reconstruction.
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Affiliation(s)
- Jessica L Ware
- Rutgers University, 195 University Ave, Newark, NJ 07102, United States.
| | - Phillip Barden
- Rutgers University, 195 University Ave, Newark, NJ 07102, United States
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Larson-Johnson K. Phylogenetic investigation of the complex evolutionary history of dispersal mode and diversification rates across living and fossil Fagales. THE NEW PHYTOLOGIST 2016; 209:418-435. [PMID: 26204796 DOI: 10.1111/nph.13570] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 06/20/2015] [Indexed: 05/26/2023]
Abstract
As a primary determinant of spatial structure in angiosperm populations, fruit dispersal may impact large-scale ecological and evolutionary processes. Essential to understanding these mechanisms is an accurate reconstruction of dispersal mode over the entire history of an angiosperm lineage. A total-evidence phylogeny is presented for most fossil fruit and all extant genera in Fagales over its c. 95 million yr history. This phylogeny - the largest of its kind to include plant fossils - was used to reconstruct an evolutionary history directly informed by fossil morphologies and to assess relationships among dispersal mode, biogeographic range size, and diversification rate. Reconstructions indicate four transitions to wind dispersal and seven to biotic dispersal, with the phylogenetic integration of fossils crucial to understanding these patterns. Complexity further increased when more specialized behaviors were considered, with fluttering, gliding, autorotating, and scatter-hoarding evolving multiple times across the order. Preliminary biogeographic analyses suggest larger range sizes in biotically dispersed lineages, especially when pollination mode was held constant. Biotically dispersed lineages had significantly higher diversification rates than abiotically dispersed lineages, although transitions in dispersal mode alone cannot explain all detected diversification rate shifts across Fagales.
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Affiliation(s)
- Kathryn Larson-Johnson
- Department of the Geophysical Sciences, The University of Chicago, 5734 South Ellis Avenue, Chicago, IL, 60637, USA
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Guillerme T, Cooper N. Effects of missing data on topological inference using a Total Evidence approach. Mol Phylogenet Evol 2015; 94:146-58. [PMID: 26335040 DOI: 10.1016/j.ympev.2015.08.023] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 08/24/2015] [Accepted: 08/26/2015] [Indexed: 11/25/2022]
Abstract
To fully understand macroevolutionary patterns and processes, we need to include both extant and extinct species in our models. This requires phylogenetic trees with both living and fossil taxa at the tips. One way to infer such phylogenies is the Total Evidence approach which uses molecular data from living taxa and morphological data from living and fossil taxa. Although the Total Evidence approach is very promising, it requires a great deal of data that can be hard to collect. Therefore this method is likely to suffer from missing data issues that may affect its ability to infer correct phylogenies. Here we use simulations to assess the effects of missing data on tree topologies inferred from Total Evidence matrices. We investigate three major factors that directly affect the completeness and the size of the morphological part of the matrix: the proportion of living taxa with no morphological data, the amount of missing data in the fossil record, and the overall number of morphological characters in the matrix. We infer phylogenies from complete matrices and from matrices with various amounts of missing data, and then compare missing data topologies to the "best" tree topology inferred using the complete matrix. We find that the number of living taxa with morphological characters and the overall number of morphological characters in the matrix, are more important than the amount of missing data in the fossil record for recovering the "best" tree topology. Therefore, we suggest that sampling effort should be focused on morphological data collection for living species to increase the accuracy of topological inference in a Total Evidence framework. Additionally, we find that Bayesian methods consistently outperform other tree inference methods. We therefore recommend using Bayesian consensus trees to fix the tree topology prior to further analyses.
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Affiliation(s)
- Thomas Guillerme
- School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland; Trinity Centre for Biodiversity Research, Trinity College Dublin, Dublin 2, Ireland.
| | - Natalie Cooper
- School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland; Trinity Centre for Biodiversity Research, Trinity College Dublin, Dublin 2, Ireland; Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
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Manos PS, Meireles JE. Biogeographic analysis of the woody plants of the Southern Appalachians: Implications for the origins of a regional flora. AMERICAN JOURNAL OF BOTANY 2015; 102:780-804. [PMID: 26022491 DOI: 10.3732/ajb.1400530] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 04/21/2015] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY We investigated the origins of 252 Southern Appalachian woody species representing 158 clades to analyze larger patterns of biogeographic connectivity around the northern hemisphere. We tested biogeographic hypotheses regarding the timing of species disjunctions to eastern Asia and among areas of North America. METHODS We delimited species into biogeographically informative clades, compiled sister-area data, and generated graphic representations of area connections across clades. We calculated taxon diversity within clades and plotted divergence times. KEY RESULTS Of the total taxon diversity, 45% were distributed among 25 North American endemic clades. Sister taxa within eastern North America and eastern Asia were proportionally equal in frequency, accounting for over 50% of the sister-area connections. At increasing phylogenetic depth, connections to the Old World dominated. Divergence times for 65 clades with intercontinental disjunctions were continuous, whereas 11 intracontinental disjunctions to western North America and nine to eastern Mexico were temporally congruent. CONCLUSIONS Over one third of the clades have likely undergone speciation within the region of eastern North America. The biogeographic pattern for the region is asymmetric, consisting of mostly mixed-aged, low-diversity clades connecting to the Old World, and a minority of New World clades. Divergence time data suggest that climate change in the Late Miocene to Early Pliocene generated disjunct patterns within North America. Continuous splitting times during the last 45 million years support the hypothesis that widespread distributions formed repeatedly during favorable periods, with serial cooling trends producing pseudocongruent area disjunctions between eastern North America and eastern Asia.
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Affiliation(s)
- Paul S Manos
- Department of Biology, Box 90338 Duke University, Durham, North Carolina 27708-0338 USA
| | - José Eduardo Meireles
- Department of Biology, Box 90338 Duke University, Durham, North Carolina 27708-0338 USA
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Martínez C, Carvalho MR, Madriñán S, Jaramillo CA. A Late Cretaceous Piper (Piperaceae) from Colombia and diversification patterns for the genus. AMERICAN JOURNAL OF BOTANY 2015; 102:273-289. [PMID: 25667080 DOI: 10.3732/ajb.1400427] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY Documented fossil floras in the neotropics are sparse, yet their records provide evidence on the spatial and temporal occurrence of taxa, allowing for testing of biogeographical and diversification scenarios on individual lineages. A new fossil Piper from the Late Cretaceous of Colombia is described here, and its importance for assessing diversification patterns in the genus is addressed. METHODS Leaf architecture of 32 fossil leaf compressions from the Guaduas Formation was compared with that of 294 extant angiosperm species. The phylogenetic position of the fossil named Piper margaritae sp. nov. was established based on leaf traits and a molecular scaffold of Piper. The age of the fossil was independently used as a calibration point for divergence time estimations. KEY RESULTS Natural affinities of P. margaritae to the Schilleria clade of Piper indicate that the genus occurred in tropical America by the Late Cretaceous. Estimates of age divergence and lineage accumulation reveal that most of the extant diversity of the genus accrued during the last ∼30 Myr. CONCLUSIONS The recent radiation of Piper is coeval with both the Andean uplift and the emergence of Central America, which have been proposed as important drivers of diversity. This pattern could exemplify a recurrent theme among many neotropical plant lineages.
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Affiliation(s)
- Camila Martínez
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panamá
| | - Mónica R Carvalho
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panamá L. H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, New York 14850 USA
| | - Santiago Madriñán
- Laboratorio de Botánica y Sistemática, Universidad de los Andes, Apartado Aéreo 4976, Bogotá, Colombia
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Extant diversity of bryophytes emerged from successive post-Mesozoic diversification bursts. Nat Commun 2014; 5:5134. [PMID: 25346115 DOI: 10.1038/ncomms6134] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 09/03/2014] [Indexed: 02/06/2023] Open
Abstract
Unraveling the macroevolutionary history of bryophytes, which arose soon after the origin of land plants but exhibit substantially lower species richness than the more recently derived angiosperms, has been challenged by the scarce fossil record. Here we demonstrate that overall estimates of net species diversification are approximately half those reported in ferns and ∼30% those described for angiosperms. Nevertheless, statistical rate analyses on time-calibrated large-scale phylogenies reveal that mosses and liverworts underwent bursts of diversification since the mid-Mesozoic. The diversification rates further increase in specific lineages towards the Cenozoic to reach, in the most recently derived lineages, values that are comparable to those reported in angiosperms. This suggests that low diversification rates do not fully account for current patterns of bryophyte species richness, and we hypothesize that, as in gymnosperms, the low extant bryophyte species richness also results from massive extinctions.
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Xing Y, Onstein RE, Carter RJ, Stadler T, Peter Linder H. FOSSILS AND A LARGE MOLECULAR PHYLOGENY SHOW THAT THE EVOLUTION OF SPECIES RICHNESS, GENERIC DIVERSITY, AND TURNOVER RATES ARE DISCONNECTED. Evolution 2014; 68:2821-32. [DOI: 10.1111/evo.12489] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 06/15/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Yaowu Xing
- Institut für Systematische Botanik; Universität Zürich; Zollikerstrasse107 8008 Zürich Switzerland
| | - Renske E. Onstein
- Institut für Systematische Botanik; Universität Zürich; Zollikerstrasse107 8008 Zürich Switzerland
| | - Richard J. Carter
- Institut für Systematische Botanik; Universität Zürich; Zollikerstrasse107 8008 Zürich Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering; Eidgenössische Technische Hochschule Zürich; 4058 Basel Switzerland
| | - H. Peter Linder
- Institut für Systematische Botanik; Universität Zürich; Zollikerstrasse107 8008 Zürich Switzerland
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Dávalos LM, Velazco PM, Warsi OM, Smits PD, Simmons NB. Integrating Incomplete Fossils by Isolating Conflicting Signal in Saturated and Non-Independent Morphological Characters. Syst Biol 2014; 63:582-600. [DOI: 10.1093/sysbio/syu022] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Fukuhara T, Tokumaru SI. Inflorescence dimorphism, heterodichogamy and thrips pollination in Platycarya strobilacea (Juglandaceae). ANNALS OF BOTANY 2014; 113:467-476. [PMID: 24305967 PMCID: PMC3906971 DOI: 10.1093/aob/mct278] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 10/14/2013] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS Unlike other taxa in Juglandaceae or in closely related families, which are anemophilous, Platycarya strobilacea has been suggested to be entomophilous. In Juglandaceae, Juglans and Carya show heterodichogamy, a reproductive strategy in which two morphs coexist in a population and undergo synchronous reciprocal sex changes. However, there has been no study focusing on heterodichogamy in the other six or seven genera, including Platycarya. METHODS Inflorescence architecture, sexual expression and pollination biology were examined in a P. strobilacea population in Japan. Flowering phenology was monitored daily for 24 trees in 2008 and 27 in 2009. Flower visitors and inhabitants were recorded or collected from different sexes and stages. KEY RESULTS The population of P. strobilacea showed heterodichogamous phenology with protogynous and duodichogamous-protandrous morphs. This dimorphism in dichogamy was associated with distinct inflorescence morphologies. Thrips pollination was suggested by the frequent presence of thrips with attached pollen grains, the scarcity of other insect visitors, the synchronicity of thrips number in male spikes with the maturation of female flowers, and morphological characters shared with previously reported thrips-pollinated plants. Male spikes went through two consecutive stages: bright yellow and strong-scented M1 stage, and brownish and little-scented M2 stage. The latter contained more thrips, synchronized better with the receptive stage of female flowers of the reciprocal morph and is probably the main period of pollen export. CONCLUSIONS Platycarya strobilacea is heterodichogamous and thrips-pollinated, both of which are relatively rare conditions in angiosperms. In male spikes of P. strobilacea, there is probably a temporal decoupling of pollinator attraction and pollen export.
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Zhang JB, Li RQ, Xiang XG, Manchester SR, Lin L, Wang W, Wen J, Chen ZD. Integrated fossil and molecular data reveal the biogeographic diversification of the eastern Asian-eastern North American disjunct hickory genus (Carya Nutt.). PLoS One 2013; 8:e70449. [PMID: 23875028 PMCID: PMC3713062 DOI: 10.1371/journal.pone.0070449] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 06/18/2013] [Indexed: 12/01/2022] Open
Abstract
The hickory genus (Carya) contains ca. 17 species distributed in subtropical and tropical regions of eastern Asia and subtropical to temperate regions of eastern North America. Previously, the phylogenetic relationships between eastern Asian and eastern North American species of Carya were not fully confirmed even with an extensive sampling, biogeographic and diversification patterns had thus never been investigated in a phylogenetic context. We sampled 17 species of Carya and 15 species representing all other genera of the Juglandaceae as outgroups, with eight nuclear and plastid loci to reconstruct the phylogeny of Carya. The phylogenetic positions of seven extinct genera of the Juglandaceae were inferred using morphological characters and the molecular phylogeny as a backbone constraint. Divergence times within Carya were estimated with relaxed Bayesian dating. Biogeographic analyses were performed in DIVA and LAGRANGE. Diversification rates were inferred by LASER and APE packages. Our results support two major clades within Carya, corresponding to the lineages of eastern Asia and eastern North America. The split between the two disjunct clades is estimated to be 21.58 (95% HPD 11.07-35.51) Ma. Genus-level DIVA and LAGRANGE analyses incorporating both extant and extinct genera of the Juglandaceae suggested that Carya originated in North America, and migrated to Eurasia during the early Tertiary via the North Atlantic land bridge. Fragmentation of the distribution caused by global cooling in the late Tertiary resulted in the current disjunction. The diversification rate of hickories in eastern North America appeared to be higher than that in eastern Asia, which is ascribed to greater ecological opportunities, key morphological innovations, and polyploidy.
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Affiliation(s)
- Jing-Bo Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Rui-Qi Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Guo Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Steven R. Manchester
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
| | - Li Lin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
- * E-mail: (ZDC); (JW)
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- * E-mail: (ZDC); (JW)
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Bonito G, Smith ME, Nowak M, Healy RA, Guevara G, Cázares E, Kinoshita A, Nouhra ER, Domínguez LS, Tedersoo L, Murat C, Wang Y, Moreno BA, Pfister DH, Nara K, Zambonelli A, Trappe JM, Vilgalys R. Historical biogeography and diversification of truffles in the Tuberaceae and their newly identified southern hemisphere sister lineage. PLoS One 2013; 8:e52765. [PMID: 23300990 PMCID: PMC3534693 DOI: 10.1371/journal.pone.0052765] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 11/22/2012] [Indexed: 11/18/2022] Open
Abstract
Truffles have evolved from epigeous (aboveground) ancestors in nearly every major lineage of fleshy fungi. Because accelerated rates of morphological evolution accompany the transition to the truffle form, closely related epigeous ancestors remain unknown for most truffle lineages. This is the case for the quintessential truffle genus Tuber, which includes species with socio-economic importance and esteemed culinary attributes. Ecologically, Tuber spp. form obligate mycorrhizal symbioses with diverse species of plant hosts including pines, oaks, poplars, orchids, and commercially important trees such as hazelnut and pecan. Unfortunately, limited geographic sampling and inconclusive phylogenetic relationships have obscured our understanding of their origin, biogeography, and diversification. To address this problem, we present a global sampling of Tuberaceae based on DNA sequence data from four loci for phylogenetic inference and molecular dating. Our well-resolved Tuberaceae phylogeny shows high levels of regional and continental endemism. We also identify a previously unknown epigeous member of the Tuberaceae--the South American cup-fungus Nothojafnea thaxteri (E.K. Cash) Gamundí. Phylogenetic resolution was further improved through the inclusion of a previously unrecognized Southern hemisphere sister group of the Tuberaceae. This morphologically diverse assemblage of species includes truffle (e.g. Gymnohydnotrya spp.) and non-truffle forms that are endemic to Australia and South America. Southern hemisphere taxa appear to have diverged more recently than the Northern hemisphere lineages. Our analysis of the Tuberaceae suggests that Tuber evolved from an epigeous ancestor. Molecular dating estimates Tuberaceae divergence in the late Jurassic (~156 million years ago), with subsequent radiations in the Cretaceous and Paleogene. Intra-continental diversification, limited long-distance dispersal, and ecological adaptations help to explain patterns of truffle evolution and biodiversity.
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Affiliation(s)
- Gregory Bonito
- Deparment of Biology, Duke University, Durham, North Carolina, United States of America.
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Ronquist F, Klopfstein S, Vilhelmsen L, Schulmeister S, Murray DL, Rasnitsyn AP. A total-evidence approach to dating with fossils, applied to the early radiation of the hymenoptera. Syst Biol 2012; 61:973-99. [PMID: 22723471 PMCID: PMC3478566 DOI: 10.1093/sysbio/sys058] [Citation(s) in RCA: 446] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 10/19/2011] [Accepted: 06/07/2012] [Indexed: 12/04/2022] Open
Abstract
Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically, we compare node dating using nine calibration points derived from the fossil record with total-evidence dating based on 343 morphological characters scored for 45 fossil (4--20 complete) and 68 extant taxa. In both cases we use molecular data from seven markers (∼5 kb) for the extant taxa. Because it is difficult to model speciation, extinction, sampling, and fossil preservation realistically, we develop a simple uniform prior for clock trees with fossils, and we use relaxed clock models to accommodate rate variation across the tree. Despite considerable uncertainty in the placement of most fossils, we find that they contribute significantly to the estimation of divergence times in the total-evidence analysis. In particular, the posterior distributions on divergence times are less sensitive to prior assumptions and tend to be more precise than in node dating. The total-evidence analysis also shows that four of the seven Hymenoptera calibration points used in node dating are likely to be based on erroneous or doubtful assumptions about the fossil placement. With respect to the early radiation of Hymenoptera, our results suggest that the crown group dates back to the Carboniferous, ∼309 Ma (95% interval: 291--347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic. [Bayesian inference; fossil dating; morphological evolution; relaxed clock; statistical phylogenetics.].
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Affiliation(s)
- Fredrik Ronquist
- Department of Biodiversity Informatics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden.
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Nauheimer L, Metzler D, Renner SS. Global history of the ancient monocot family Araceae inferred with models accounting for past continental positions and previous ranges based on fossils. THE NEW PHYTOLOGIST 2012; 195:938-950. [PMID: 22765273 DOI: 10.1111/j.1469-8137.2012.04220.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The family Araceae (3790 species, 117 genera) has one of the oldest fossil records among angiosperms. Ecologically, members of this family range from free-floating aquatics (Pistia and Lemna) to tropical epiphytes. Here, we infer some of the macroevolutionary processes that have led to the worldwide range of this family and test how the inclusion of fossil (formerly occupied) geographical ranges affects biogeographical reconstructions. Using a complete genus-level phylogeny from plastid sequences and outgroups representing the 13 other Alismatales families, we estimate divergence times by applying different clock models and reconstruct range shifts under different models of past continental connectivity, with or without the incorporation of fossil locations. Araceae began to diversify in the Early Cretaceous (when the breakup of Pangea was in its final stages), and all eight subfamilies existed before the K/T boundary. Early lineages persist in Laurasia, with several relatively recent entries into Africa, South America, South-East Asia and Australia. Water-associated habitats appear to be ancestral in the family, and DNA substitution rates are especially high in free-floating Araceae. Past distributions inferred when fossils are included differ in nontrivial ways from those without fossils. Our complete genus-level time-scale for the Araceae may prove to be useful for ecological and physiological studies.
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Affiliation(s)
- Lars Nauheimer
- Systematic Botany and Biology, Department of Biology, University of Munich (LMU), Menzinger-Str. 67, 80638 Munich, Germany
- Present address: Molecular Evolution and Systematics of Plants, Institute of Biology, University Leipzig, Johannisallee 21-23, 04103 Leipzig, Germany
| | - Dirk Metzler
- Evolutionary Biology, Department of Biology, University of Munich (LMU), Grosshaderner-Str. 2, 82152 Planegg-Martinsried, Germany
| | - Susanne S Renner
- Systematic Botany and Biology, Department of Biology, University of Munich (LMU), Menzinger-Str. 67, 80638 Munich, Germany
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Wiens JJ, Tiu J. Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling. PLoS One 2012; 7:e42925. [PMID: 22900065 PMCID: PMC3416753 DOI: 10.1371/journal.pone.0042925] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 07/16/2012] [Indexed: 11/18/2022] Open
Abstract
Background Phylogenies are essential to many areas of biology, but phylogenetic methods may give incorrect estimates under some conditions. A potentially common scenario of this type is when few taxa are sampled and terminal branches for the sampled taxa are relatively long. However, the best solution in such cases (i.e., sampling more taxa versus more characters) has been highly controversial. A widespread assumption in this debate is that added taxa must be complete (no missing data) in order to save analyses from the negative impacts of limited taxon sampling. Here, we evaluate whether incomplete taxa can also rescue analyses under these conditions (empirically testing predictions from an earlier simulation study). Methodology/Principal Findings We utilize DNA sequence data from 16 vertebrate species with well-established phylogenetic relationships. In each replicate, we randomly sample 4 species, estimate their phylogeny (using Bayesian, likelihood, and parsimony methods), and then evaluate whether adding in the remaining 12 species (which have 50, 75, or 90% of their data replaced with missing data cells) can improve phylogenetic accuracy relative to analyzing the 4 complete taxa alone. We find that in those cases where sampling few taxa yields an incorrect estimate, adding taxa with 50% or 75% missing data can frequently (>75% of relevant replicates) rescue Bayesian and likelihood analyses, recovering accurate phylogenies for the original 4 taxa. Even taxa with 90% missing data can sometimes be beneficial. Conclusions We show that adding taxa that are highly incomplete can improve phylogenetic accuracy in cases where analyses are misled by limited taxon sampling. These surprising empirical results confirm those from simulations, and show that the benefits of adding taxa may be obtained with unexpectedly small amounts of data. These findings have important implications for the debate on sampling taxa versus characters, and for studies attempting to resolve difficult phylogenetic problems.
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Affiliation(s)
- John J Wiens
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America.
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Fritsch PW, Cruz BC. Phylogeny of Cercis based on DNA sequences of nuclear ITS and four plastid regions: Implications for transatlantic historical biogeography. Mol Phylogenet Evol 2012; 62:816-25. [DOI: 10.1016/j.ympev.2011.11.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 11/02/2011] [Accepted: 11/17/2011] [Indexed: 10/15/2022]
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Sauquet H, Ho SYW, Gandolfo MA, Jordan GJ, Wilf P, Cantrill DJ, Bayly MJ, Bromham L, Brown GK, Carpenter RJ, Lee DM, Murphy DJ, Sniderman JMK, Udovicic F. Testing the Impact of Calibration on Molecular Divergence Times Using a Fossil-Rich Group: The Case of Nothofagus (Fagales). Syst Biol 2011; 61:289-313. [DOI: 10.1093/sysbio/syr116] [Citation(s) in RCA: 296] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Hervé Sauquet
- Laboratoire Écologie, Systématique, Évolution, Université Paris-Sud, CNRS UMR 8079, 91405 Orsay, France
| | - Simon Y. W. Ho
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
- School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Maria A. Gandolfo
- L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Gregory J. Jordan
- School of Plant Science, University of Tasmania, Private bag 55, Hobart, TAS 7001, Australia
| | - Peter Wilf
- Department of Geosciences, Pennsylvania State University, University Park, PA 16802, USA
| | - David J. Cantrill
- National Herbarium of Victoria, Royal Botanic Gardens Melbourne, Private Bag 2000, South Yarra, VIC 3141, Australia
| | - Michael J. Bayly
- School of Botany, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Lindell Bromham
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
| | - Gillian K. Brown
- National Herbarium of Victoria, Royal Botanic Gardens Melbourne, Private Bag 2000, South Yarra, VIC 3141, Australia
- School of Botany, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Raymond J. Carpenter
- Department of Ecology and Environmental Biology, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Daphne M. Lee
- Department of Geology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Daniel J. Murphy
- National Herbarium of Victoria, Royal Botanic Gardens Melbourne, Private Bag 2000, South Yarra, VIC 3141, Australia
| | - J. M. Kale Sniderman
- School of Geography and Environmental Science, Monash University, Melbourne, VIC 3800, Australia
| | - Frank Udovicic
- National Herbarium of Victoria, Royal Botanic Gardens Melbourne, Private Bag 2000, South Yarra, VIC 3141, Australia
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Herrera F, Manchester SR, Hoot SB, Wefferling KM, Carvalho MR, Jaramillo C. Phytogeographic implications of fossil endocarps of Menispermaceae from the Paleocene of Colombia. AMERICAN JOURNAL OF BOTANY 2011; 98:2004-2017. [PMID: 22114219 DOI: 10.3732/ajb.1000461] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY Fossil leaves of Menispermaceae were previously described from the Paleocene of Colombia. Because of strong homoplasy of leaf characters, the fossils could not be placed more specifically within recognized clades, and additional data were needed to specify intrafamilial and paleogeographic relationships during the Paleocene. METHODS Fossil endocarps of Menispermaceae were collected from the Cerrejón Formation, the recently discovered Bogotá flora, and Wyoming (∼60 Ma). We surveyed the endocarp morphology of almost all extant genera, conducted character optimization, a molecular scaffold analysis, and critically reviewed the related fossil genera. KEY RESULTS Parallel syndromes of fruit characters have appeared in unrelated clades of the family according to current phylogenetic reconstructions. However, mapping selected endocarp characters across those clades that contain horseshoe-shaped endocarps facilitates identification and phylogenetic assessment of the fossils. Three fossil species are recognized. One of them belongs to the extant genus Stephania, which today grows only in Africa and Australasia. Palaeoluna gen. nov. is placed within the pantropical clade composed of extant Stephania, Cissampelos, and Cyclea; this morphogenus is also recognized from the Paleocene of Wyoming. Menispina gen. nov. shows similarity with several unrelated clades. CONCLUSIONS The new fossils from Colombia reveal a complex paleobiogeographic history of the recognized clades within Menispermaceae, suggesting a more active exchange among neotropical, paleotropical, North American, and European paleoforests than previously recognized. In addition, the new fossils indicate that neotropical forests were an important biome for the radiation and dispersal of derived lineages in Menispermaceae after the Cretaceous-Paleogene boundary.
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Affiliation(s)
- Fabiany Herrera
- Department of Biology-Florida Museum of Natural History, University of Florida, Gainesville, 32611, USA.
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