51
|
Liu L, Hao ZZ, Liu YY, Wei XX, Cun YZ, Wang XQ. Phylogeography of Pinus armandii and its relatives: heterogeneous contributions of geography and climate changes to the genetic differentiation and diversification of Chinese white pines. PLoS One 2014; 9:e85920. [PMID: 24465789 PMCID: PMC3897548 DOI: 10.1371/journal.pone.0085920] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 12/09/2013] [Indexed: 11/19/2022] Open
Abstract
Geographic barriers and Quaternary climate changes are two major forces driving the evolution, speciation, and genetic structuring of extant organisms. In this study, we used Pinus armandii and eleven other Asian white pines (subsection Strobus, subgenus Pinus) to explore the influences of geographic factors and Pleistocene climatic oscillations on species in South China, a region known to be centers of plant endemism and biodiversity hotspots. Range-wide patterns of genetic variation were investigated using chloroplast and mitochondrial DNA markers, with extensive sampling throughout the entire range of P. armandii. Both cpDNA and mtDNA revealed that P. armandii exhibits high levels of genetic diversity and significant population differentiation. Three geographically distinct subdivisions corresponding to the Qinling-Daba Mountains (QDM), Himalaya-Hengduan Mountains (HHM) and Yungui Plateau (YGP) were revealed in mainland China by cpDNA. Their break zone was located in the southeastern margin of the Qinghai-Tibetan Plateau (QTP). A series of massive mountains, induced by the QTP uplift, imposed significant geographic barriers to genetic exchange. The disjunct distribution patterns of ancestral haplotypes suggest that a large continuous population of the white pines may have existed from southwest to subtropical China. Repeated range shifts in response to the Pleistocene glaciations led to the isolation and diversification of the subtropical species. The two Taiwanese white pines share a common ancestor with the species in mainland China and obtain their chloroplasts via long-distance pollen dispersal from North Asian pines. Distinct genetic patterns were detected in populations from the Qinling-Daba Mountains, Yungui Plateau, Himalaya-Hengduan Mountains, and subtropical China, indicating significant contributions of geographic factors to the genetic differentiation in white pines. Our study depicts a clear picture of the evolutionary history of Chinese white pines and highlights the heterogeneous contributions of geography and Pleistocene climatic fluctuations to the extremely high plant species diversity and endemism in South China.
Collapse
Affiliation(s)
- Liu Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Zhen-Zhen Hao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Yan-Yan Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Xiao-Xin Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | | | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
52
|
Layeghifard M, Peres-Neto PR, Makarenkov V. Inferring explicit weighted consensus networks to represent alternative evolutionary histories. BMC Evol Biol 2013; 13:274. [PMID: 24359207 PMCID: PMC3898054 DOI: 10.1186/1471-2148-13-274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 12/16/2013] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The advent of molecular biology techniques and constant increase in availability of genetic material have triggered the development of many phylogenetic tree inference methods. However, several reticulate evolution processes, such as horizontal gene transfer and hybridization, have been shown to blur the species evolutionary history by causing discordance among phylogenies inferred from different genes. METHODS To tackle this problem, we hereby describe a new method for inferring and representing alternative (reticulate) evolutionary histories of species as an explicit weighted consensus network which can be constructed from a collection of gene trees with or without prior knowledge of the species phylogeny. RESULTS We provide a way of building a weighted phylogenetic network for each of the following reticulation mechanisms: diploid hybridization, intragenic recombination and complete or partial horizontal gene transfer. We successfully tested our method on some synthetic and real datasets to infer the above-mentioned evolutionary events which may have influenced the evolution of many species. CONCLUSIONS Our weighted consensus network inference method allows one to infer, visualize and validate statistically major conflicting signals induced by the mechanisms of reticulate evolution. The results provided by the new method can be used to represent the inferred conflicting signals by means of explicit and easy-to-interpret phylogenetic networks.
Collapse
Affiliation(s)
- Mehdi Layeghifard
- Département des Sciences biologiques, Université du Québec à Montréal (UQÀM), CP 8888, Succ. Centre Ville, Montréal, QC H3C 3P8, Canada
- Département d’Informatique, Université du Québec à Montréal (UQÀM), CP 8888, Succ. Centre Ville, Montréal, QC H3C 3P8, Canada
| | - Pedro R Peres-Neto
- Département des Sciences biologiques, Université du Québec à Montréal (UQÀM), CP 8888, Succ. Centre Ville, Montréal, QC H3C 3P8, Canada
| | - Vladimir Makarenkov
- Département d’Informatique, Université du Québec à Montréal (UQÀM), CP 8888, Succ. Centre Ville, Montréal, QC H3C 3P8, Canada
| |
Collapse
|
53
|
Niche divergence versus neutral processes: combined environmental and genetic analyses identify contrasting patterns of differentiation in recently diverged pine species. PLoS One 2013; 8:e78228. [PMID: 24205167 PMCID: PMC3812143 DOI: 10.1371/journal.pone.0078228] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 09/10/2013] [Indexed: 11/19/2022] Open
Abstract
Background and Aims Solving relationships of recently diverged taxa, poses a challenge due to shared polymorphism and weak reproductive barriers. Multiple lines of evidence are needed to identify independently evolving lineages. This is especially true of long-lived species with large effective population sizes, and slow rates of lineage sorting. North American pines are an interesting group to test this multiple approach. Our aim is to combine cytoplasmic genetic markers with environmental information to clarify species boundaries and relationships of the species complex of Pinus flexilis, Pinus ayacahuite, and Pinus strobiformis. Methods Mitochondrial and chloroplast sequences were combined with previously obtained microsatellite data and contrasted with environmental information to reconstruct phylogenetic relationships of the species complex. Ecological niche models were compared to test if ecological divergence is significant among species. Key Results and Conclusion Separately, both genetic and ecological evidence support a clear differentiation of all three species but with different topology, but also reveal an ancestral contact zone between P. strobiformis and P. ayacahuite. The marked ecological differentiation of P. flexilis suggests that ecological speciation has occurred in this lineage, but this is not reflected in neutral markers. The inclusion of environmental traits in phylogenetic reconstruction improved the resolution of internal branches. We suggest that combining environmental and genetic information would be useful for species delimitation and phylogenetic studies in other recently diverged species complexes.
Collapse
|
54
|
Eckert AJ, Bower AD, Jermstad KD, Wegrzyn JL, Knaus BJ, Syring JV, Neale DB. Multilocus analyses reveal little evidence for lineage-wide adaptive evolution within major clades of soft pines (Pinus subgenus Strobus). Mol Ecol 2013; 22:5635-50. [PMID: 24134614 DOI: 10.1111/mec.12514] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 08/27/2013] [Accepted: 08/29/2013] [Indexed: 12/26/2022]
Abstract
Estimates from molecular data for the fraction of new nonsynonymous mutations that are adaptive vary strongly across plant species. Much of this variation is due to differences in life history strategies as they influence the effective population size (Ne ). Ample variation for these estimates, however, remains even when comparisons are made across species with similar values of Ne . An open question thus remains as to why the large disparity for estimates of adaptive evolution exists among plant species. Here, we have estimated the distribution of deleterious fitness effects (DFE) and the fraction of adaptive nonsynonymous substitutions (α) for 11 species of soft pines (subgenus Strobus) using DNA sequence data from 167 orthologous nuclear gene fragments. Most newly arising nonsynonymous mutations were inferred to be so strongly deleterious that they would rarely become fixed. Little evidence for long-term adaptive evolution was detected, as all 11 estimates for α were not significantly different from zero. Nucleotide diversity at synonymous sites, moreover, was strongly correlated with attributes of the DFE across species, thus illustrating a strong consistency with the expectations from the Nearly Neutral Theory of molecular evolution. Application of these patterns to genome-wide expectations for these species, however, was difficult as the loci chosen for the analysis were a biased set of conserved loci, which greatly influenced the estimates of the DFE and α. This implies that genome-wide parameter estimates will need truly genome-wide data, so that many of the existing patterns documented previously for forest trees (e.g. little evidence for signature of selection) may need revision.
Collapse
Affiliation(s)
- Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | | | | | | | | | | | | |
Collapse
|
55
|
The evolutionary genetics of the genes underlying phenotypic associations for loblolly pine (Pinus taeda, Pinaceae). Genetics 2013; 195:1353-72. [PMID: 24121773 DOI: 10.1534/genetics.113.157198] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
A primary goal of evolutionary genetics is to discover and explain the genetic basis of fitness-related traits and how this genetic basis evolves within natural populations. Unprecedented technological advances have fueled the discovery of genetic variants associated with ecologically relevant phenotypes in many different life forms, as well as the ability to scan genomes for deviations from selectively neutral models of evolution. Theoretically, the degree of overlap between lists of genomic regions identified using each approach is related to the genetic architecture of fitness-related traits and the strength and type of natural selection molding variation at these traits within natural populations. Here we address for the first time in a plant the degree of overlap between these lists, using patterns of nucleotide diversity and divergence for >7000 unique amplicons described from the extensive expressed sequence tag libraries generated for loblolly pine (Pinus taeda L.) in combination with the >1000 published genetic associations. We show that loci associated with phenotypic traits are distinct with regard to neutral expectations. Phenotypes measured at the whole plant level (e.g., disease resistance) exhibit an approximately twofold increase in the proportion of adaptive nonsynonymous substitutions over the genome-wide average. As expected for polygenic traits, these signals were apparent only when loci were considered at the level of functional sets. The ramifications of this result are discussed in light of the continued efforts to dissect the genetic basis of quantitative traits.
Collapse
|
56
|
Hernández-León S, Gernandt DS, Pérez de la Rosa JA, Jardón-Barbolla L. Phylogenetic relationships and species delimitation in pinus section trifoliae inferrred from plastid DNA. PLoS One 2013; 8:e70501. [PMID: 23936218 PMCID: PMC3728320 DOI: 10.1371/journal.pone.0070501] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Accepted: 06/21/2013] [Indexed: 11/23/2022] Open
Abstract
Recent diversification followed by secondary contact and hybridization may explain complex patterns of intra- and interspecific morphological and genetic variation in the North American hard pines (Pinus section Trifoliae), a group of approximately 49 tree species distributed in North and Central America and the Caribbean islands. We concatenated five plastid DNA markers for an average of 3.9 individuals per putative species and assessed the suitability of the five regions as DNA bar codes for species identification, species delimitation, and phylogenetic reconstruction. The ycf1 gene accounted for the greatest proportion of the alignment (46.9%), the greatest proportion of variable sites (74.9%), and the most unique sequences (75 haplotypes). Phylogenetic analysis recovered clades corresponding to subsections Australes, Contortae, and Ponderosae. Sequences for 23 of the 49 species were monophyletic and sequences for another 9 species were paraphyletic. Morphologically similar species within subsections usually grouped together, but there were exceptions consistent with incomplete lineage sorting or introgression. Bayesian relaxed molecular clock analyses indicated that all three subsections diversified relatively recently during the Miocene. The general mixed Yule-coalescent method gave a mixed model estimate of only 22 or 23 evolutionary entities for the plastid sequences, which corresponds to less than half the 49 species recognized based on morphological species assignments. Including more unique haplotypes per species may result in higher estimates, but low mutation rates, recent diversification, and large effective population sizes may limit the effectiveness of this method to detect evolutionary entities.
Collapse
Affiliation(s)
- Sergio Hernández-León
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, México City, Mexico
| | - David S. Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, México City, Mexico
| | | | - Lev Jardón-Barbolla
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, México City, Mexico
| |
Collapse
|
57
|
Ramadugu C, Pfeil BE, Keremane ML, Lee RF, Maureira-Butler IJ, Roose ML. A six nuclear gene phylogeny of Citrus (Rutaceae) taking into account hybridization and lineage sorting. PLoS One 2013; 8:e68410. [PMID: 23874615 PMCID: PMC3713030 DOI: 10.1371/journal.pone.0068410] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 05/29/2013] [Indexed: 12/14/2022] Open
Abstract
Background Genus Citrus (Rutaceae) comprises many important cultivated species that generally hybridize easily. Phylogenetic study of a group showing extensive hybridization is challenging. Since the genus Citrus has diverged recently (4–12 Ma), incomplete lineage sorting of ancestral polymorphisms is also likely to cause discrepancies among genes in phylogenetic inferences. Incongruence of gene trees is observed and it is essential to unravel the processes that cause inconsistencies in order to understand the phylogenetic relationships among the species. Methodology and Principal Findings (1) We generated phylogenetic trees using haplotype sequences of six low copy nuclear genes. (2) Published simple sequence repeat data were re-analyzed to study population structure and the results were compared with the phylogenetic trees constructed using sequence data and coalescence simulations. (3) To distinguish between hybridization and incomplete lineage sorting, we developed and utilized a coalescence simulation approach. In other studies, species trees have been inferred despite the possibility of hybridization having occurred and used to generate null distributions of the effect of lineage sorting alone (by coalescent simulation). Since this is problematic, we instead generate these distributions directly from observed gene trees. Of the six trees generated, we used the most resolved three to detect hybrids. We found that 11 of 33 samples appear to be affected by historical hybridization. Analysis of the remaining three genes supported the conclusions from the hybrid detection test. Conclusions We have identified or confirmed probable hybrid origins for several Citrus cultivars using three different approaches–gene phylogenies, population structure analysis and coalescence simulation. Hybridization and incomplete lineage sorting were identified primarily based on differences among gene phylogenies with reference to null expectations via coalescence simulations. We conclude that identifying hybridization as a frequent cause of incongruence among gene trees is critical to correctly infer the phylogeny among species of Citrus.
Collapse
Affiliation(s)
- Chandrika Ramadugu
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, California, United States of America
| | - Bernard E. Pfeil
- Commonwealth Scientific and Industrial Research Organisation Plant Industry, Canberra, Australian Capital Territory, Australia
- DBES, Gothenburg University, Gothenburg, Sweden
- * E-mail:
| | - Manjunath L. Keremane
- United States Department of Agriculture–Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California, United States of America
| | - Richard F. Lee
- United States Department of Agriculture–Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California, United States of America
| | - Ivan J. Maureira-Butler
- Agriaquaculture Nutritional Genomic Center, Centro de Genómica Nutricional Agroacuícola, Genomics and Bioinformatics Unit, Temuco, Chile
| | - Mikeal L. Roose
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, California, United States of America
| |
Collapse
|
58
|
Flores-Rentería L, Wegier A, Ortega Del Vecchyo D, Ortíz-Medrano A, Piñero D, Whipple AV, Molina-Freaner F, Domínguez CA. Genetic, morphological, geographical and ecological approaches reveal phylogenetic relationships in complex groups, an example of recently diverged pinyon pine species (Subsection Cembroides). Mol Phylogenet Evol 2013; 69:940-9. [PMID: 23831459 DOI: 10.1016/j.ympev.2013.06.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 04/29/2013] [Accepted: 06/18/2013] [Indexed: 11/24/2022]
Abstract
Elucidating phylogenetic relationships and species boundaries within complex taxonomic groups is challenging for intrinsic and extrinsic (i.e., technical) reasons. Mexican pinyon pines are a complex group whose phylogenetic relationships and species boundaries have been widely studied but poorly resolved, partly due to intrinsic ecological and evolutionary features such as low morphological and genetic differentiation caused by recent divergence, hybridization and introgression. Extrinsic factors such as limited sampling and difficulty in selecting informative molecular markers have also impeded progress. Some of the Mexican pinyon pines are of conservation concern but others may remain unprotected because the species boundaries have not been established. In this study we combined approaches to resolve the phylogenetic relationships in this complex group and to establish species boundaries in four recently diverged taxa: P. discolor, P. johannis, P. culminicola and P. cembroides. We performed phylogenetic analyses using the chloroplast markers matK and psbA-trnH as well as complete and partial chloroplast genomes of species of Subsection Cembroides. Additionally, we performed a phylogeographic analysis combining genetic data (18 chloroplast markers), morphological data and geographical data to define species boundaries in four recently diverged taxa. Ecological divergence was supported by differences in climate among localities for distinct genetic lineages. Whereas the phylogenetic analysis inferred with matK and psbA-trnH was unable to resolve the relationships in this complex group, we obtained a resolved phylogeny with the use of the chloroplast genomes. The resolved phylogeny was concordant with a haplotype network obtained using chloroplast markers. In species with potential for recent divergence, hybridization or introgression, nonhierarchical network-based approaches are probably more appropriate to protect against misclassification due to incomplete lineage sorting. The boundaries among genetic lineages were delimited by the inclusion of morphological, geographical and ecological data in the haplotype network. These multiple lines of evidence help to assign species boundaries in this complex group. P. johannis, P. discolor, P. culminicola and P. cembroides are different species based on their genetic, morphological and ecological niche differences. We suggest a reevaluation of the conservation status of these species considering the information generated in this study.
Collapse
Affiliation(s)
- Lluvia Flores-Rentería
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Coyoacán, DF 04510, Mexico; Department of Biological Sciences and Merriam-Powell Center for Environmental Research, Northern Arizona University, Flagstaff, AZ 86011, USA.
| | | | | | | | | | | | | | | |
Collapse
|
59
|
Moncada B, Lücking R, Suárez A. Molecular phylogeny of the genus Sticta (lichenized Ascomycota: Lobariaceae) in Colombia. FUNGAL DIVERS 2013. [DOI: 10.1007/s13225-013-0230-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
60
|
Bornholdt R, Helgen K, Koepfli KP, Oliveira L, Lucherini M, Eizirik E. Taxonomic revision of the genusGalictis(Carnivora: Mustelidae): species delimitation, morphological diagnosis, and refined mapping of geographical distribution. Zool J Linn Soc 2013. [DOI: 10.1111/j.1096-3642.2012.00859.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
61
|
Domrachev DV, Karpova EV, Goroshkevich SN, Tkachev AV. Comparative analysis of volatiles from needles of five-needle pines of northern and eastern Eurasia. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2012. [DOI: 10.1134/s1068162012070059] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
62
|
Phylogenetic analysis of Primula section Primula reveals rampant non-monophyly among morphologically distinct species. Mol Phylogenet Evol 2012; 65:23-34. [DOI: 10.1016/j.ympev.2012.05.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 05/11/2012] [Accepted: 05/16/2012] [Indexed: 11/21/2022]
|
63
|
Lovo J, Winkworth RC, Mello-Silva R. New insights into Trimezieae (Iridaceae) phylogeny: what do molecular data tell us? ANNALS OF BOTANY 2012; 110:689-702. [PMID: 22711695 PMCID: PMC3400455 DOI: 10.1093/aob/mcs127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 04/24/2012] [Indexed: 06/01/2023]
Abstract
BACKGROUND AND AIMS The Neotropical tribe Trimezieae are taxonomically difficult. They are generally characterized by the absence of the features used to delimit their sister group Tigridieae. Delimiting the four genera that make up Trimezieae is also problematic. Previous family-level phylogenetic analyses have not examined the monophyly of the tribe or relationships within it. Reconstructing the phylogeny of Trimezieae will allow us to evaluate the status of the tribe and genera and to examine the suitability of characters traditionally used in their taxonomy. METHODS Maximum parsimony and Bayesian phylogenetic analyses are presented for 37 species representing all four genera of Trimezieae. Analyses were based on nrITS sequences and a combined plastid dataset. Ancestral character state reconstructions were used to investigate the evolution of ten morphological characters previously considered taxonomically useful. KEY RESULTS Analyses of nrITS and plastid datasets strongly support the monophyly of Trimezieae and recover four principal clades with varying levels of support; these clades do not correspond to the currently recognized genera. Relationships within the four clades are not consistently resolved, although the conflicting resolutions are not strongly supported in individual analyses. Ancestral character state reconstructions suggest considerable homoplasy, especially in the floral characters used to delimit Pseudotrimezia. CONCLUSIONS The results strongly support recognition of Trimezieae as a tribe but suggest that both generic- and species-level taxonomy need revision. Further molecular analyses, with increased sampling of taxa and markers, are needed to support any revision. Such analyses will help determine the causes of discordance between the plastid and nuclear data and provide a framework for identifying potential morphological synapomorphies for infra-tribal groups. The results also suggest Trimezieae provide a promising model for evolutionary research.
Collapse
Affiliation(s)
- Juliana Lovo
- Universidade de São Paulo, Instituto de Biociências, Departamento de Botânica, Rua do Matão, 277, 05508-090 São Paulo, SP, Brazil.
| | | | | |
Collapse
|
64
|
Himmelreich S, Breitwieser I, Oberprieler C. Phylogeny, biogeography, and evolution of sex expression in the southern hemisphere genus Leptinella (Compositae, Anthemideae). Mol Phylogenet Evol 2012; 65:464-81. [PMID: 22776547 DOI: 10.1016/j.ympev.2012.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 06/25/2012] [Accepted: 07/01/2012] [Indexed: 10/28/2022]
Abstract
Leptinella is exceptional in the Anthemideae (Compositae) in its evolution of dimorphic sex expression. A molecular phylogeny including 40 of its 42 described taxa based on nucleotide sequences from two plastid regions (psbA-trnH and trnC-petN spacers) and one nuclear marker (nrDNA ITS) is presented. Phylogenetic reconstruction was hampered by inadequate phylogenetic signal indicating recent radiation of species during the last 5 Ma and high level of reticulate evolution presumably caused by hybridisation and polyploidisation. Nevertheless, Leptinella is nested within a paraphyletic genus Cotula that also engulfs the South American genus Soliva. Within Leptinella, the highly polyploid and sexually polymorphic subgenus Leptinella is monophyletic, while subgenus Oligoleima as well as subgenus Radiata are polyphyletic. We found a basal split between a lineage of Australian and New Guinean taxa and one of largely New Zealand taxa. At least five long-distance dispersal events have to be assumed in order to explain the distribution pattern in Leptinella. Among those, one is from New Zealand to Australia, while the others are dispersals to South America and to several subantarctic islands. The phylogeny presented here indicates that the ancestral sex expression in Leptinella is monoecy and that dioecy and paradioecy are derived conditions. High ploidy is especially common in the dioica-group, where dioecy is also common. However, the occurrence of a dioecious sex expression in tetraploid representatives of this group and of polyploidy in other clades that only exhibit monoecious or paradioecious conditions indicate that there is no consistent correlation between these two characters.
Collapse
Affiliation(s)
- Sven Himmelreich
- Institute of Botany, University of Regensburg, Regensburg, Germany.
| | | | | |
Collapse
|
65
|
Chemisquy MA, Morrone O. Molecular phylogeny of Gavilea (Chloraeinae: Orchidaceae) using plastid and nuclear markers. Mol Phylogenet Evol 2012; 62:889-97. [DOI: 10.1016/j.ympev.2011.11.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 11/25/2011] [Accepted: 11/26/2011] [Indexed: 11/16/2022]
|
66
|
Wirtz N, Printzen C, Lumbsch HT. Using haplotype networks, estimation of gene flow and phenotypic characters to understand species delimitation in fungi of a predominantly Antarctic Usnea group (Ascomycota, Parmeliaceae). ORG DIVERS EVOL 2011. [DOI: 10.1007/s13127-011-0066-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
67
|
Li Z, Zou J, Mao K, Lin K, Li H, Liu J, Källman T, Lascoux M. POPULATION GENETIC EVIDENCE FOR COMPLEX EVOLUTIONARY HISTORIES OF FOUR HIGH ALTITUDE JUNIPER SPECIES IN THE QINGHAI-TIBETAN PLATEAU. Evolution 2011; 66:831-845. [DOI: 10.1111/j.1558-5646.2011.01466.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
68
|
Gangloff B, Shirihai H, Watling D, Cruaud C, Couloux A, Tillier A, Pasquet E, Bretagnolle V. The complete phylogeny of Pseudobulweria, the most endangered seabird genus: systematics, species status and conservation implications. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0261-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
69
|
Wachowiak W, Palmé AE, Savolainen O. Speciation history of three closely related pines Pinus mugo (T.), P. uliginosa (N.) and P. sylvestris (L.). Mol Ecol 2011; 20:1729-43. [PMID: 21375633 DOI: 10.1111/j.1365-294x.2011.05037.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nucleotide polymorphisms at genomic regions including 17 nuclear loci, two chloroplast and one mitochondrial DNA fragments were used to study the speciation history of three pine species: dwarf mountain pine (Pinus mugo), peat-bog pine (P. uliginosa) and Scots pine (P. sylvestris). We set out to investigate three specific speciation scenarios: (I) P. uliginosa is a homoploid hybrid between the other two, (II) the species have evolved without gene flow after divergence and (III) there has been substantial gene flow between the species since their divergence. Overall, the genetic data suggest that P. mugo and P. uliginosa share the same gene pool (average net divergence of 0.0001) and that the phenotypic differences (e.g. growth form) are most likely due to very limited areas of the genome. P. mugo and P. uliginosa are more diverged from P. sylvestris than from each other (average net divergence of 0.0027 and 0.0026, respectively). The nucleotide patterns can best be explained by the divergence with migration speciation scenario, although the hybrid speciation scenario with small genomic contribution from P. sylvestris cannot be completely ruled out. We suggest that the large amount of shared polymorphisms between the pine taxa and the lack of monophyly at all loci studied between P. sylvestris and P. mugo-P. uliginosa can largely be explained by relatively recent speciation history and large effective population sizes but also by interspecific gene flow. These closely related pine taxa form an excellent system for searching for loci involved in adaptive variation as they are differentiated in phenotype and ecology but have very similar genetic background.
Collapse
Affiliation(s)
- Witold Wachowiak
- Department of Biology, University of Oulu, 90014, Oulu, Finland.
| | | | | |
Collapse
|
70
|
Eckert AJ, van Heerwaarden J, Wegrzyn JL, Nelson CD, Ross-Ibarra J, González-Martínez SC, Neale DB. Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae). Genetics 2010; 185:969-82. [PMID: 20439779 PMCID: PMC2907212 DOI: 10.1534/genetics.110.115543] [Citation(s) in RCA: 242] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 04/20/2010] [Indexed: 12/21/2022] Open
Abstract
Natural populations of forest trees exhibit striking phenotypic adaptations to diverse environmental gradients, thereby making them appealing subjects for the study of genes underlying ecologically relevant phenotypes. Here, we use a genome-wide data set of single nucleotide polymorphisms genotyped across 3059 functional genes to study patterns of population structure and identify loci associated with aridity across the natural range of loblolly pine (Pinus taeda L.). Overall patterns of population structure, as inferred using principal components and Bayesian cluster analyses, were consistent with three genetic clusters likely resulting from expansions out of Pleistocene refugia located in Mexico and Florida. A novel application of association analysis, which removes the confounding effects of shared ancestry on correlations between genetic and environmental variation, identified five loci correlated with aridity. These loci were primarily involved with abiotic stress response to temperature and drought. A unique set of 24 loci was identified as F(ST) outliers on the basis of the genetic clusters identified previously and after accounting for expansions out of Pleistocene refugia. These loci were involved with a diversity of physiological processes. Identification of nonoverlapping sets of loci highlights the fundamental differences implicit in the use of either method and suggests a pluralistic, yet complementary, approach to the identification of genes underlying ecologically relevant phenotypes.
Collapse
Affiliation(s)
- Andrew J. Eckert
- Section of Evolution and Ecology, Center for Population Biology, and Department of Plant Sciences, University of California, Davis, California 95616, Southern Institute of Forest Genetics, U. S. Department of Agriculture Forest Service, Saucier, Mississippi 39574, Department of Forest Systems and Resources, Forest Research Institute, Center of Forest Research, Institito Nacional de Investigacion y Tecnologia Agraria y Alimentaria, 28040 Madrid, Spain, and Institute of Forest Genetics, Pacific Southwest Research Station, U. S. Department of Agriculture, Davis, California 95616
| | - Joost van Heerwaarden
- Section of Evolution and Ecology, Center for Population Biology, and Department of Plant Sciences, University of California, Davis, California 95616, Southern Institute of Forest Genetics, U. S. Department of Agriculture Forest Service, Saucier, Mississippi 39574, Department of Forest Systems and Resources, Forest Research Institute, Center of Forest Research, Institito Nacional de Investigacion y Tecnologia Agraria y Alimentaria, 28040 Madrid, Spain, and Institute of Forest Genetics, Pacific Southwest Research Station, U. S. Department of Agriculture, Davis, California 95616
| | - Jill L. Wegrzyn
- Section of Evolution and Ecology, Center for Population Biology, and Department of Plant Sciences, University of California, Davis, California 95616, Southern Institute of Forest Genetics, U. S. Department of Agriculture Forest Service, Saucier, Mississippi 39574, Department of Forest Systems and Resources, Forest Research Institute, Center of Forest Research, Institito Nacional de Investigacion y Tecnologia Agraria y Alimentaria, 28040 Madrid, Spain, and Institute of Forest Genetics, Pacific Southwest Research Station, U. S. Department of Agriculture, Davis, California 95616
| | - C. Dana Nelson
- Section of Evolution and Ecology, Center for Population Biology, and Department of Plant Sciences, University of California, Davis, California 95616, Southern Institute of Forest Genetics, U. S. Department of Agriculture Forest Service, Saucier, Mississippi 39574, Department of Forest Systems and Resources, Forest Research Institute, Center of Forest Research, Institito Nacional de Investigacion y Tecnologia Agraria y Alimentaria, 28040 Madrid, Spain, and Institute of Forest Genetics, Pacific Southwest Research Station, U. S. Department of Agriculture, Davis, California 95616
| | - Jeffrey Ross-Ibarra
- Section of Evolution and Ecology, Center for Population Biology, and Department of Plant Sciences, University of California, Davis, California 95616, Southern Institute of Forest Genetics, U. S. Department of Agriculture Forest Service, Saucier, Mississippi 39574, Department of Forest Systems and Resources, Forest Research Institute, Center of Forest Research, Institito Nacional de Investigacion y Tecnologia Agraria y Alimentaria, 28040 Madrid, Spain, and Institute of Forest Genetics, Pacific Southwest Research Station, U. S. Department of Agriculture, Davis, California 95616
| | - Santíago C. González-Martínez
- Section of Evolution and Ecology, Center for Population Biology, and Department of Plant Sciences, University of California, Davis, California 95616, Southern Institute of Forest Genetics, U. S. Department of Agriculture Forest Service, Saucier, Mississippi 39574, Department of Forest Systems and Resources, Forest Research Institute, Center of Forest Research, Institito Nacional de Investigacion y Tecnologia Agraria y Alimentaria, 28040 Madrid, Spain, and Institute of Forest Genetics, Pacific Southwest Research Station, U. S. Department of Agriculture, Davis, California 95616
| | - David. B. Neale
- Section of Evolution and Ecology, Center for Population Biology, and Department of Plant Sciences, University of California, Davis, California 95616, Southern Institute of Forest Genetics, U. S. Department of Agriculture Forest Service, Saucier, Mississippi 39574, Department of Forest Systems and Resources, Forest Research Institute, Center of Forest Research, Institito Nacional de Investigacion y Tecnologia Agraria y Alimentaria, 28040 Madrid, Spain, and Institute of Forest Genetics, Pacific Southwest Research Station, U. S. Department of Agriculture, Davis, California 95616
| |
Collapse
|
71
|
Whittall JB, Syring J, Parks M, Buenrostro J, Dick C, Liston A, Cronn R. Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines. Mol Ecol 2010; 19 Suppl 1:100-14. [PMID: 20331774 DOI: 10.1111/j.1365-294x.2009.04474.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Critical to conservation efforts and other investigations at low taxonomic levels, DNA sequence data offer important insights into the distinctiveness, biogeographic partitioning and evolutionary histories of species. The resolving power of DNA sequences is often limited by insufficient variability at the intraspecific level. This is particularly true of studies involving plant organelles, as the conservative mutation rate of chloroplasts and mitochondria makes it difficult to detect polymorphisms necessary to track genealogical relationships among individuals, populations and closely related taxa, through space and time. Massively parallel sequencing (MPS) makes it possible to acquire entire organelle genome sequences to identify cryptic variation that would be difficult to detect otherwise. We are using MPS to evaluate intraspecific chloroplast-level divergence across biogeographic boundaries in narrowly endemic and widespread species of Pinus. We focus on one of the world's rarest pines - Torrey pine (Pinus torreyana) - due to its conservation interest and because it provides a marked contrast to more widespread pine species. Detailed analysis of nearly 90% ( approximately 105 000 bp each) of these chloroplast genomes shows that mainland and island populations of Torrey pine differ at five sites in their plastome, with the differences fixed between populations. This is an exceptionally low level of divergence (1 polymorphism/ approximately 21 kb), yet it is comparable to intraspecific divergence present in widespread pine species and species complexes. Population-level organelle genome sequencing offers new vistas into the timing and magnitude of divergence within species, and is certain to provide greater insight into pollen dispersal, migration patterns and evolutionary dynamics in plants.
Collapse
Affiliation(s)
- J B Whittall
- Department of Biology, Santa Clara University, CA 95053, USA
| | | | | | | | | | | | | |
Collapse
|
72
|
Li Y, Stocks M, Hemmilä S, Källman T, Zhu H, Zhou Y, Chen J, Liu J, Lascoux M. Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci. Mol Biol Evol 2009; 27:1001-14. [PMID: 20031927 DOI: 10.1093/molbev/msp301] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nucleotide variation at 12-16 nuclear loci was studied in three spruce species from the Qinghai-Tibetan Plateau (QTP), Picea likiangensis, P. wilsonii, and P. purpurea, and one species from the Tian Shan mountain range, P. schrenkiana. Silent nucleotide diversity was limited in P. schrenkiana and high in the three species from the QTP, with values higher than in boreal spruce species, despite their much more restricted distributions compared with that of the boreal species. In contrast to European boreal species that have experienced severe bottlenecks in the past, coalescent-based analysis suggests that DNA polymorphism in the species from the QTP and adjacent areas is compatible with the standard neutral model (P. likiangensis, P. wilsonii, and P. schrenkiana) or with population growth (P. purpurea). In order to test if P. purpurea is a diploid hybrid of P. likiangensis and P. wilsonii, we used a combination of approaches, including model-based inference of population structure, isolation-with-migration models, and recent theoretical results on the effect of introgression on the geographic distribution of diversity. In contrast to the three other species, each of which was predominantly assigned to a single cluster in the Structure analysis, P. purpurea individuals were scattered over the three main clusters and not, as we had expected, confined to the P. likiangensis and P. wilsonii clusters. Furthermore, the contribution of P. schrenkiana was by far the largest one. In agreement with this, the divergence between P. purpurea and P. schrenkiana was lower than the divergence of either P. likiangensis or P. wilsonii from P. schrenkiana. These results, together with previous ones showing that P. purpurea and P. wilsonii share the same haplotypes at both chloroplast and mitochondrial markers, suggest that P. purpurea has a complex origin, possibly involving additional species.
Collapse
Affiliation(s)
- Yuan Li
- Institute of Molecular Ecology, The MOE Key Laboratory of Arid and Grassland Ecology, College of Life Science, Lanzhou University, Lanzhou, Gansu, China
| | | | | | | | | | | | | | | | | |
Collapse
|
73
|
Parks M, Cronn R, Liston A. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol 2009; 7:84. [PMID: 19954512 PMCID: PMC2793254 DOI: 10.1186/1741-7007-7-84] [Citation(s) in RCA: 358] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 12/02/2009] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Molecular evolutionary studies share the common goal of elucidating historical relationships, and the common challenge of adequately sampling taxa and characters. Particularly at low taxonomic levels, recent divergence, rapid radiations, and conservative genome evolution yield limited sequence variation, and dense taxon sampling is often desirable. Recent advances in massively parallel sequencing make it possible to rapidly obtain large amounts of sequence data, and multiplexing makes extensive sampling of megabase sequences feasible. Is it possible to efficiently apply massively parallel sequencing to increase phylogenetic resolution at low taxonomic levels? RESULTS We reconstruct the infrageneric phylogeny of Pinus from 37 nearly-complete chloroplast genomes (average 109 kilobases each of an approximately 120 kilobase genome) generated using multiplexed massively parallel sequencing. 30/33 ingroup nodes resolved with > or = 95% bootstrap support; this is a substantial improvement relative to prior studies, and shows massively parallel sequencing-based strategies can produce sufficient high quality sequence to reach support levels originally proposed for the phylogenetic bootstrap. Resampling simulations show that at least the entire plastome is necessary to fully resolve Pinus, particularly in rapidly radiating clades. Meta-analysis of 99 published infrageneric phylogenies shows that whole plastome analysis should provide similar gains across a range of plant genera. A disproportionate amount of phylogenetic information resides in two loci (ycf1, ycf2), highlighting their unusual evolutionary properties. CONCLUSION Plastome sequencing is now an efficient option for increasing phylogenetic resolution at lower taxonomic levels in plant phylogenetic and population genetic analyses. With continuing improvements in sequencing capacity, the strategies herein should revolutionize efforts requiring dense taxon and character sampling, such as phylogeographic analyses and species-level DNA barcoding.
Collapse
Affiliation(s)
- Matthew Parks
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Richard Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, 97331, USA
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| |
Collapse
|
74
|
Fulton TL, Strobeck C. Multiple markers and multiple individuals refine true seal phylogeny and bring molecules and morphology back in line. Proc Biol Sci 2009; 277:1065-70. [PMID: 19939841 DOI: 10.1098/rspb.2009.1783] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Despite decades of study, some aspects of Phocidae (Pinnipedia, Carnivora) phylogeny still remain unresolved. Using the largest novel dataset to date, including all extant phocids and comprising 15 nuclear and 13 mitochondrial genes, we illustrate the utility of including multiple individuals per species in resolving rapid radiations, and provide new insight into phocid phylogeny. In line with longstanding morphological views, Pusa is recovered as monophyletic for the first time with genetic data. The data are also used to explore the relationship between genetic distance and taxonomic rank. Intraspecific sampling also highlights the discrepancy between molecular and morphological rates of evolution within Phocidae.
Collapse
Affiliation(s)
- Tara Lynn Fulton
- Department of Biology, University of Alberta, Edmonton, Alberta, Canada.
| | | |
Collapse
|
75
|
Jakob SS, Blattner FR. Two extinct diploid progenitors were involved in allopolyploid formation in the Hordeum murinum (Poaceae: Triticeae) taxon complex. Mol Phylogenet Evol 2009; 55:650-9. [PMID: 19850141 DOI: 10.1016/j.ympev.2009.10.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Revised: 10/12/2009] [Accepted: 10/13/2009] [Indexed: 10/20/2022]
Abstract
Wall barley (Hordeum murinum) occurs with three subspecies, naturally distributed from southern Central Asia through the Mediterranean region to northwestern Europe, but now is an invasive weed in many parts of the world. Subspecies glaucum is diploid, while subspp. murinum and leporinum are tetraploids, the latter also occurring with a hexaploid cytotype. Earlier analyses were inconclusive regarding auto- or allopolyploid origins of subspp. murinum and leporinum. We analyzed the phylogeny of the taxon group using amplified fragment length polymorphisms (AFLP), sequences of cloned PCR products of the nuclear ribosomal DNA internal transcribed spacer region (ITS), a part of the nuclear single-copy gene topoisomerase 6 (Topo6) spanning two introns, and sequences of the chloroplast trnL-F region together with length variation at six chloroplast microsatellite loci, including multiple individuals of each subspecies and cytotype, covering the entire natural distribution area of the species. Phylogenetic analyses with all used markers differentiate diploid and polyploids. Sequences of both nuclear regions indicated that diploid subsp. glaucum was involved in tetraploid formation together with a now extinct species belonging to the same Hordeum genome group (Xu). Furthermore, AFLP and ITS analyses suggest that a third, though closely related extinct taxon contributed to hexaploid formation. No method was able to discern tetraploid subspp. murinum and leporinum, which we attribute to the young age of subsp. murinum. None of the used molecular markers revealed a strong geographic pattern of genetic variation that would allow comprehensive phylogeographic analysis, most probably due to the very effective seed dispersal of the taxa.
Collapse
Affiliation(s)
- Sabine S Jakob
- Leibniz Institute of Plant Genetics and Crop Research (IPK), D-06466 Gatersleben, Germany
| | | |
Collapse
|
76
|
Dragon JA, Barrington DS. Systematics of the Carex aquatilis and C. lenticularis lineages: Geographically and ecologically divergent sister clades of Carex section Phacocystis (Cyperaceae). AMERICAN JOURNAL OF BOTANY 2009; 96:1896-1906. [PMID: 21622311 DOI: 10.3732/ajb.0800404] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Carex aquatilis is a highly diverse and geographically widespread member of one of the largest genera of flowering plants, Carex, and is ideally suited for the study of the role of hybridization and niche partitioning in ecological speciation. Phylogenetic analyses of nuclear ITS and ETS 1f and chloroplast psbA-trnH DNA sequences support the monophyly of a broadly defined Carex aquatilis-Carex lenticularis lineage, which includes C. aquatilis and C. lenticularis and their allies within section Phacocystis. However, neither taxon is monophyletic as currently circumscribed. The C. aquatilis lineage includes C. aquatilis and four morphologically and molecularly distinct salt-tolerant maritime taxa with which C. aquatilis s.s. is reported to form stabilized homoploid hybrids. The C. lenticularis lineage includes a paraphyletic C. lenticularis and seven allied species from both the New and Old World. The data provided here allow recognition of four species within the North American endemic C. lenticularis and suggest a neotropical origin for the C. lenticularis lineage with subsequent radiation and divergence through northwestern North America to Asia and via northeastern North America to Europe and southern South America. Evolutionary rate analyses indicate an origin for the C. aquatilis-C. lenticularis group around 1.89 million years ago during the early Pleistocene.
Collapse
Affiliation(s)
- Julie A Dragon
- Plant Biology Department, 109 Carrigan Drive, University of Vermont, Burlington, Vermont 05405 USA
| | | |
Collapse
|
77
|
Tsutsui K, Suwa A, Sawada K, Kato T, Ohsawa TA, Watano Y. Incongruence among mitochondrial, chloroplast and nuclear gene trees in Pinus subgenus Strobus (Pinaceae). JOURNAL OF PLANT RESEARCH 2009; 122:509-21. [PMID: 19529882 DOI: 10.1007/s10265-009-0246-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Accepted: 05/05/2009] [Indexed: 05/21/2023]
Abstract
Introgression has been considered to be one of main factors leading to phylogenetic incongruence among different datasets at lower taxonomic levels. In the plants of Pinaceae, the mtDNA, cpDNA, and nuclear DNA (nrDNA) may have different evolutionary histories through introgression because they are inherited maternally, paternally and biparentally, respectively. We compared mtDNA, cpDNA, and two low-copy nrDNA phylogenetic trees in the genus Pinus subgenus Strobus, in order to detect unknown past introgression events in this group. nrDNA trees were mostly congruent with the cpDNA tree, and supported the recent sectional and subsectional classification system. In contrast, mtDNA trees split the members of sect. Quinquefoliae into two groups that were not observed in the other gene trees. The factors constituting incongruence may be divided into the following two categories: the different splits within subsect. Strobus, and the non-monophyly of subsect. Gerardianae. The former was hypothesized to have been caused by the past introgression of cpDNA, mtDNA or both between Eurasian and North American species through Beringia. The latter was likely caused by the chimeric structure of the mtDNA sequence of P. bungeana, which might have originated through past hybridization, or through a horizontal transfer event and subsequent recombination.
Collapse
Affiliation(s)
- Kiyomi Tsutsui
- Department of Biology, Faculty of Science, Chiba University, Yayoi, Inage, Chiba 263-8522, Japan
| | | | | | | | | | | |
Collapse
|
78
|
Willyard A, Cronn R, Liston A. Reticulate evolution and incomplete lineage sorting among the ponderosa pines. Mol Phylogenet Evol 2009; 52:498-511. [DOI: 10.1016/j.ympev.2009.02.011] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Revised: 02/10/2009] [Accepted: 02/13/2009] [Indexed: 10/21/2022]
|
79
|
Degnan JH, Rosenberg NA. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol 2009; 24:332-40. [PMID: 19307040 DOI: 10.1016/j.tree.2009.01.009] [Citation(s) in RCA: 1094] [Impact Index Per Article: 72.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Revised: 12/17/2008] [Accepted: 01/05/2009] [Indexed: 01/29/2023]
Affiliation(s)
- James H Degnan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
| | | |
Collapse
|
80
|
Okuyama Y, Kato M. Unveiling cryptic species diversity of flowering plants: successful biological species identification of Asian Mitella using nuclear ribosomal DNA sequences. BMC Evol Biol 2009; 9:105. [PMID: 19445708 PMCID: PMC2695457 DOI: 10.1186/1471-2148-9-105] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2009] [Accepted: 05/16/2009] [Indexed: 11/18/2022] Open
Abstract
Background Although DNA sequence analysis is becoming a powerful tool for identifying species, it is not easy to assess whether the observed genetic disparity corresponds to reproductive isolation. Here, we compared the efficiency of biological species identification between nuclear ribosomal and chloroplast DNA sequences, focusing on an Asian endemic perennial lineage of Mitella (Asimitellaria; Saxifragaceae). We performed artificial cross experiments for 43 pairs of ten taxonomic species, and examined their F1 hybrid pollen fertility in vitro as a quantitative measure of postzygotic reproductive isolation. Results A nonlinear, multiple regression analysis indicated that the nuclear ribosomal DNA distances are sufficient to explain the observed pattern of F1 hybrid pollen fertility, and supplementation with chloroplast DNA distance data does not improve the explanatory power. Overall, with the exception of a recently diverged species complex with more than three biological species, nuclear ribosomal DNA sequences successfully circumscribed ten distinct biological species, of which two have not been described (and an additional one has not been regarded as a distinct taxonomic species) to date. Conclusion We propose that nuclear ribosomal DNA sequences contribute to reliable identification of reproductively isolated and cryptic species of Mitella. More comparable studies for other plant groups are needed to generalize our findings to flowering plants.
Collapse
Affiliation(s)
- Yudai Okuyama
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
| | | |
Collapse
|
81
|
Altaba CR. Universal artifacts affect the branching of phylogenetic trees, not universal scaling laws. PLoS One 2009; 4:e4611. [PMID: 19242549 PMCID: PMC2644784 DOI: 10.1371/journal.pone.0004611] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Accepted: 01/21/2009] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The superficial resemblance of phylogenetic trees to other branching structures allows searching for macroevolutionary patterns. However, such trees are just statistical inferences of particular historical events. Recent meta-analyses report finding regularities in the branching pattern of phylogenetic trees. But is this supported by evidence, or are such regularities just methodological artifacts? If so, is there any signal in a phylogeny? METHODOLOGY In order to evaluate the impact of polytomies and imbalance on tree shape, the distribution of all binary and polytomic trees of up to 7 taxa was assessed in tree-shape space. The relationship between the proportion of outgroups and the amount of imbalance introduced with them was assessed applying four different tree-building methods to 100 combinations from a set of 10 ingroup and 9 outgroup species, and performing covariance analyses. The relevance of this analysis was explored taking 61 published phylogenies, based on nucleic acid sequences and involving various taxa, taxonomic levels, and tree-building methods. PRINCIPAL FINDINGS All methods of phylogenetic inference are quite sensitive to the artifacts introduced by outgroups. However, published phylogenies appear to be subject to a rather effective, albeit rather intuitive control against such artifacts. The data and methods used to build phylogenetic trees are varied, so any meta-analysis is subject to pitfalls due to their uneven intrinsic merits, which translate into artifacts in tree shape. The binary branching pattern is an imposition of methods, and seldom reflects true relationships in intraspecific analyses, yielding artifactual polytomies in short trees. Above the species level, the departure of real trees from simplistic random models is caused at least by two natural factors--uneven speciation and extinction rates; and artifacts such as choice of taxa included in the analysis, and imbalance introduced by outgroups and basal paraphyletic taxa. This artifactual imbalance accounts for tree shape convergence of large trees. SIGNIFICANCE There is no evidence for any universal scaling in the tree of life. Instead, there is a need for improved methods of tree analysis that can be used to discriminate the noise due to outgroups from the phylogenetic signal within the taxon of interest, and to evaluate realistic models of evolution, correcting the retrospective perspective and explicitly recognizing extinction as a driving force. Artifacts are pervasive, and can only be overcome through understanding the structure and biological meaning of phylogenetic trees. Catalan Abstract in Translation S1.
Collapse
Affiliation(s)
- Cristian R Altaba
- Laboratory of Human Systematics, University of the Balearic Islands, Balearic Islands, Spain.
| |
Collapse
|
82
|
Seberg O, Petersen G. How many loci does it take to DNA barcode a crocus? PLoS One 2009; 4:e4598. [PMID: 19240801 PMCID: PMC2643479 DOI: 10.1371/journal.pone.0004598] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Accepted: 01/12/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND DNA barcoding promises to revolutionize the way taxonomists work, facilitating species identification by using small, standardized portions of the genome as substitutes for morphology. The concept has gained considerable momentum in many animal groups, but the higher plant world has been largely recalcitrant to the effort. In plants, efforts are concentrated on various regions of the plastid genome, but no agreement exists as to what kinds of regions are ideal, though most researchers agree that more than one region is necessary. One reason for this discrepancy is differences in the tests that are used to evaluate the performance of the proposed regions. Most tests have been made in a floristic setting, where the genetic distance and therefore the level of variation of the regions between taxa is large, or in a limited set of congeneric species. METHODOLOGY AND PRINCIPAL FINDINGS Here we present the first in-depth coverage of a large taxonomic group, all 86 known species (except two doubtful ones) of crocus. Even six average-sized barcode regions do not identify all crocus species. This is currently an unrealistic burden in a barcode context. Whereas most proposed regions work well in a floristic context, the majority will--as is the case in crocus--undoubtedly be less efficient in a taxonomic setting. However, a reasonable but less than perfect level of identification may be reached--even in a taxonomic context. CONCLUSIONS/SIGNIFICANCE The time is ripe for selecting barcode regions in plants, and for prudent examination of their utility. Thus, there is no reason for the plant community to hold back the barcoding effort by continued search for the Holy Grail. We must acknowledge that an emerging system will be far from perfect, fraught with problems and work best in a floristic setting.
Collapse
Affiliation(s)
- Ole Seberg
- Laboratory of Molecular Systematics, Natural History Museum of Denmark, Copenhagen, Denmark.
| | | |
Collapse
|
83
|
KING MATTHEWG, ROALSON ERICH. Discordance between phylogenetics and coalescent-based divergence modelling: exploring phylogeographic patterns of speciation in theCarex macrocephalaspecies complex. Mol Ecol 2009; 18:468-82. [DOI: 10.1111/j.1365-294x.2008.04033.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
84
|
SCHLAEPFER DANIELR, EDWARDS PETERJ, WIDMER ALEX, BILLETER REGULA. Phylogeography of native ploidy levels and invasive tetraploids ofSolidago gigantea. Mol Ecol 2008; 17:5245-56. [DOI: 10.1111/j.1365-294x.2008.03980.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
85
|
EDWARDS CE, SOLTIS DE, SOLTIS PS. Using patterns of genetic structure based on microsatellite loci to test hypotheses of current hybridization, ancient hybridization and incomplete lineage sorting inConradina(Lamiaceae). Mol Ecol 2008; 17:5157-74. [DOI: 10.1111/j.1365-294x.2008.03985.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
86
|
Pettengill JB, Neel MC. Phylogenetic patterns and conservation among North American members of the genus Agalinis (Orobanchaceae). BMC Evol Biol 2008; 8:264. [PMID: 18822144 PMCID: PMC2564944 DOI: 10.1186/1471-2148-8-264] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Accepted: 09/26/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND North American Agalinis Raf. species represent a taxonomically challenging group and there have been extensive historical revisions at the species, section, and subsection levels of classification. The genus contains many rare species, including the federally listed endangered species Agalinis acuta. In addition to evaluating the degree to which historical classifications at the section and subsection levels are supported by molecular data sampled from 79 individuals representing 29 Agalinis species, we assessed the monophyly of 27 species by sampling multiple individuals representing different populations of those species. Twenty-one of these species are of conservation concern in at least some part of their range. RESULTS Phylogenetic relationships estimated using maximum likelihood analyses of seven chloroplast DNA loci (aligned length = 11,076 base pairs (bp) and the nuclear ribosomal DNA ITS (internal transcribed spacer) locus (733 bp); indicated no support for the historically recognized sections except for Section Erectae. Our results suggest that North American members of the genus comprise six major lineages, however we were not able to resolve branching order among many of these lineages. Monophyly of 24 of the 29 sampled species was supported based on significant branch lengths of and high bootstrap support for subtending branches. However, there was no statistical support for the monophyly of A. acuta with respect to Agalinis tenella and Agalinis decemloba. Although most species were supported, deeper relationships among many species remain ambiguous. CONCLUSION The North American Agalinis species sampled form a well supported, monophyletic group within the family Orobanchaceae relative to the outgroups sampled. Most hypotheses regarding section- and subsection-level relationships based on morphology were not supported and taxonomic revisions are warranted. Lack of support for monophyly of Agalinis acuta leaves the important question regarding its taxonomic status unanswered. Lack of resolution is potentially due to incomplete lineage sorting of ancestral polymorphisms among recently diverged species; however the gene regions examined did distinguish among almost all other species in the genus. Due to the important policy implications of this finding we are further evaluating the evolutionary distinctiveness of A. acuta using morphological data and loci with higher mutation rates.
Collapse
Affiliation(s)
- James B Pettengill
- Behavior, Ecology, Evolution, and Systematics Graduate Program, University of Maryland College Park, College Park, MD 20742 USA
| | - Maile C Neel
- Behavior, Ecology, Evolution, and Systematics Graduate Program, University of Maryland College Park, College Park, MD 20742 USA
- Department of Plant Science and Landscape Architecture and Department of Entomology, University of Maryland College Park, College Park, MD 20742 USA
| |
Collapse
|
87
|
Maureira-Butler IJ, Pfeil BE, Muangprom A, Osborn TC, Doyle JJ. The Reticulate History of Medicago (Fabaceae). Syst Biol 2008; 57:466-82. [DOI: 10.1080/10635150802172168] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Iván J. Maureira-Butler
- Department of Plant Biology, Cornell University Ithaca, NY 14853, USA; E-mail: (J.J.D.)
- Agro aquaculture Nutritional Genomic Center (CGNA) Plant Biotechnology Unit INIA-Carillanca P.O. Box 58-D, Temuco, Chile
| | - Bernard E. Pfeil
- Department of Plant Biology, Cornell University Ithaca, NY 14853, USA; E-mail: (J.J.D.)
- CSIRO Plant Industry GPO Box 1600, Canberra, ACT 2601, Australia I.J.M.-B. and B.E.P. contributed equally to this work
| | - Amorntip Muangprom
- National Center for Genetic Engineering and Biotechnology Klong Luang, Pathumthani 12120, Thailand
| | - Thomas C. Osborn
- Seminis Vegetable seeds (A Division of Monsanto) State Highway 16, Woodland, CA 95695, USA
| | - Jeff J. Doyle
- Department of Plant Biology, Cornell University Ithaca, NY 14853, USA; E-mail: (J.J.D.)
| |
Collapse
|
88
|
Liston A, Parker-Defeniks M, Syring JV, Willyard A, Cronn R. Interspecific phylogenetic analysis enhances intraspecific phylogeographical inference: a case study in Pinus lambertiana. Mol Ecol 2007; 16:3926-37. [PMID: 17850554 DOI: 10.1111/j.1365-294x.2007.03461.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Pinus lambertiana (sugar pine) is an economically and ecologically important conifer with a 1600-km latitudinal range extending from Oregon, USA, to northern Baja California, Mexico. Like all North American white pines (subsect. Strobus), sugar pine is highly susceptible to white pine blister rust, a disease caused by the fungus Cronartium ribicola. We conducted a chloroplast DNA (cpDNA) survey of Pinus subsect. Strobus with comprehensive geographical sampling of P. lambertiana. Sequence analysis of 12 sugar pine individuals revealed strong geographical differentiation for two chloroplast haplotypes. A diagnostic restriction site survey of an additional 72 individuals demarcated a narrow 150-km contact zone in northeastern California. In the contact zone, maternal (megagametophtye) and paternal (embryo) haplotypes were identified in 31 single seeds, demonstrating bidirectional pollen flow extending beyond the range of maternal haplotypes. The frequencies of the Cr1 allele for white pine blister rust major gene resistance, previously determined for 41 seed zones, differ significantly among seed zones that are fixed for the alternate haplotypes, or contain a mixture of both haplotypes. Interspecific phylogenetic analysis reveals that the northern sugar pine haplotype belongs to a clade that includes Pinus albicaulis (whitebark pine) and all of the East Asian white pines. Furthermore, there is little cpDNA divergence between northern sugar pine and whitebark pine (dS = 0.00058). These results are consistent with a Pleistocene migration of whitebark pine into North America and subsequent chloroplast introgression from whitebark pine to sugar pine. This study demonstrates the importance of placing phylogeographical results in a broader phylogenetic context.
Collapse
Affiliation(s)
- Aaron Liston
- Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State University, Corvallis, Oregon 97331, USA.
| | | | | | | | | |
Collapse
|
89
|
Willyard A, Ann W, Syring J, Gernandt DS, Liston A, Cronn R. Fossil Calibration of Molecular Divergence Infers a Moderate Mutation Rate and Recent Radiations for Pinus. Mol Biol Evol 2006; 24:90-101. [PMID: 16997907 DOI: 10.1093/molbev/msl131] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Silent mutation rate estimates for Pinus vary 50-fold, ranging from angiosperm-like to among the slowest reported for plants. These differences either reflect extraordinary genomic processes or inconsistent fossil calibration, and they have important consequences for population and biogeographical inferences. Here we estimate mutation rates from 4 Pinus species that represent the major lineages using 11 nuclear and 4 chloroplast loci. Calibration was tested at the divergence of Pinus subgenera with the oldest leaf fossil from subg. Strobus (Eocene; 45 MYA) or a recently published subg. Strobus wood fossil (Cretaceous; 85 MYA). These calibrations place the origin of Pinus 190-102 MYA and give absolute silent rate estimates of 0.70-1.31x10(-9) and 0.22-0.42x10(-9).site-1.year-1 for the nuclear and chloroplast genomes, respectively. These rates are approximately 4- to 20-fold slower than angiosperms, but unlike many previous estimates, they are more consistent with the high per-generation deleterious mutation rates observed in pines. Chronograms from nuclear and chloroplast genomes show that the divergence of subgenera accounts for about half of the time since Pinus diverged from Picea, with subsequent radiations occurring more recently. By extending the sampling to encompass the phylogenetic diversity of Pinus, we predict that most extant subsections diverged during the Miocene. Moreover, subsect. Australes, Ponderosae, and Contortae, containing over 50 extant species, radiated within a 5 Myr time span starting as recently as 18 MYA. An Eocene divergence of pine subgenera (using leaf fossils) does not conflict with fossil-based estimates of the Pinus-Picea split, but a Cretaceous divergence using wood fossils accommodates Oligocene fossils that may represent modern subsections. Because homoplasy and polarity of character states have not been tested for fossil pine assignments, the choice of fossil and calibration node represents a significant source of uncertainty. Based on several lines of evidence (including agreement with ages inferred using calibrations outside of Pinus), we conclude that the 85 MYA calibration at the divergence of pine subgenera provides a reasonable lower bound and that further refinements in age and mutation rate estimates will require a synthetic examination of pine fossil history.
Collapse
Affiliation(s)
- Ann Willyard
- Department of Botany and Plant Pathology, Oregon State University, USA
| | | | | | | | | | | |
Collapse
|