Age estimation for the genus Cymbidium (Orchidaceae: Epidendroideae) with implementation of fossil data calibration using molecular markers (ITS2 & matK) and phylogeographic inference from ancestral area reconstruction

2016 ◽  
Vol 14 (06) ◽  
pp. 1660001 ◽  
Author(s):  
Ruchishree Konhar ◽  
Manish Debnath ◽  
Jean Valrie Marbaniang ◽  
Devendra Kumar Biswal ◽  
Pramod Tandon
Keyword(s):  
Life Forms ◽  
Ancestral Area ◽  
Tropical Regions ◽  
Ancestral Area Reconstruction ◽  
History Of ◽  
Public Repositories ◽  
Bayesian Relaxed Clock ◽  
The Tropics ◽  
Fossil Data ◽  
Relaxed Clock

Intercontinental dislocations between tropical regions harboring two-thirds of the flowering plants have always drawn attention from taxonomists and biogeographers. One such family belonging to angiosperms is Orchidaceae with an herbaceous habit and high species diversity in the tropics. Here, we investigate the evolutionary and biogeographical history of the genus Cymbidium, which represents a monophyletic subfamily (Epidendroideae) of the orchids and comprises 50 odd species that are distinctly distributed in tropical to temperate regions. Much is not known about correlations among the level of CAM activity (one of the photosynthetic pathways often regarded as an adaptation to water stress in land plants), habitat, life forms, and phylogenetic relationships of orchids from an evolutionary perspective. A relatively well-resolved and highly supported phylogeny for Cymbidium orchids is reconstructed based on sequence analysis of ITS2 and matK regions from the chloroplast DNA available in public repositories viz. GenBank at NCBI. This study examines a genus level analysis by integrating different molecular matrices to existing fossil data on orchids in a molecular Bayesian relaxed clock employed in BEAST and assessed divergence times for the genus Cymbidium with a focus on evolutionary history of photosynthetic characters. Our study has enabled age estimations (45Ma) as well as ancestral area reconstruction for the genus Cymbidium using BEAST by addition of previously analyzed two internal calibration points.

scholarly journals Age estimation for Asian Cymbidium (Orchidaceae: Epidendroideae) with implementation of fossil data calibration using molecular markers (ITS2 & matK) implying phylogeographic inference

2013 ◽  
Author(s):  
Devendra K Biswal ◽  
Jean V Marbaniang ◽  
Pramod Tandon
Keyword(s):  
Land Plants ◽  
Tropical Regions ◽  
The Public ◽  
Plant Group ◽  
History Of ◽  
Bayesian Relaxed Clock ◽  
The Tropics ◽  
Fossil Data ◽  
Relationship Of ◽  
First Time

Abstract: Intercontinental dislocations between tropical regions harboring two-thirds of the flowering plants have always drawn attention from taxonomists and bio-geographers. The focus had always been on woody land plants rather than on herbs. Orchidaceae is one such family belonging to angiosperms, with an herbaceous habit and high species diversity in the tropics. Here, we investigate the evolutionary and bio-geographical history of the genus Cymbidium, which represents a monophyletic subfamily (Epidendroideae) of the orchids and comprises 50 odd species that are disjunctly distributed in tropical to temperate regions. A relatively well-resolved and highly supported phylogeny of Cymbidiums was reconstructed based on sequence analyses of internal transcribed spacer (ITS2) regions and maturaseK (matK) from the chloroplast region available on the public domain in GenBank at NCBI. Crassulacean acid metabolism (CAM) is one of the photosynthetic pathways regarded as adaptation to water stress in land plants. Hardly any information exists on correlations among the level of CAM activity, habitat, life form, and phylogenetic relationship of a plant group from an evolutionary perspective. This study examines a genus level analyses by integrating ITS and matK data to all fossil data available on orchids in a molecular Bayesian relaxed clock employed in BEAST and assessed divergence times for the genus Cymbidium with a focus on evolutionary plasticity of photosynthetic characters. Our study has enabled age estimations for the genus Cymbidum (12Ma) for the first time using BEAST by addition of previously analyzed two internal calibration points.

scholarly journals Age estimation for Asian Cymbidium (Orchidaceae: Epidendroideae) with implementation of fossil data calibration using molecular markers (ITS2 & matK) implying phylogeographic inference

2013 ◽  
Author(s):  
Devendra K Biswal ◽  
Jean V Marbaniang ◽  
Pramod Tandon
Keyword(s):  
Land Plants ◽  
Tropical Regions ◽  
The Public ◽  
Plant Group ◽  
History Of ◽  
Bayesian Relaxed Clock ◽  
The Tropics ◽  
Fossil Data ◽  
Relationship Of ◽  
First Time

Abstract: Intercontinental dislocations between tropical regions harboring two-thirds of the flowering plants have always drawn attention from taxonomists and bio-geographers. The focus had always been on woody land plants rather than on herbs. Orchidaceae is one such family belonging to angiosperms, with an herbaceous habit and high species diversity in the tropics. Here, we investigate the evolutionary and bio-geographical history of the genus Cymbidium, which represents a monophyletic subfamily (Epidendroideae) of the orchids and comprises 50 odd species that are disjunctly distributed in tropical to temperate regions. A relatively well-resolved and highly supported phylogeny of Cymbidiums was reconstructed based on sequence analyses of internal transcribed spacer (ITS2) regions and maturaseK (matK) from the chloroplast region available on the public domain in GenBank at NCBI. Crassulacean acid metabolism (CAM) is one of the photosynthetic pathways regarded as adaptation to water stress in land plants. Hardly any information exists on correlations among the level of CAM activity, habitat, life form, and phylogenetic relationship of a plant group from an evolutionary perspective. This study examines a genus level analyses by integrating ITS and matK data to all fossil data available on orchids in a molecular Bayesian relaxed clock employed in BEAST and assessed divergence times for the genus Cymbidium with a focus on evolutionary plasticity of photosynthetic characters. Our study has enabled age estimations for the genus Cymbidum (12Ma) for the first time using BEAST by addition of previously analyzed two internal calibration points.

Species Delimitation and evolutionary history of tree frogs in the Hyla chinensis-group (Hylidae, Amphibian)

2019 ◽  
Author(s):  
Tao Pan ◽  
Guiyou Wu ◽  
Xing Kang ◽  
Peng Yan ◽  
Izaz Ali ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Divergence Time ◽  
Distinct Species ◽  
Species Group ◽  
Early Miocene ◽  
Evolutionary Divergence ◽  
Dabie Mountains ◽  
Ancestral Area ◽  
Ancestral Area Reconstruction ◽  
History Of

Abstract Background Species are the cornerstone in many domains of biology research, which made the accurate species delimitation became critically important. In this study, the systematics and biogeography of the Hyla chinensis -group were analyzed based on phylogeny, species delimitation and ancestral area reconstruction methods.Results The phylogenetic results showed six specific clusters existed in the H. chinensis- group. BPP analysis indicated that six distinct species exist due to the high probability values (>0.95), which were also supported by the BF analysis. The divergence time of the H. chinensis -group is estimated to date back to 18.84 Mya in the early Miocene. Combining the results of ancestral area reconstruction, the H. chinensis -group might have originated from Guangxi-Hainan, then spread eastwardly and reached Nanling mountains, Wuyi mountains, Huangshan mountains and Taiwan. In rightabout colonization, it is gradually extended to the Yunnan-Guizhou Plateau, Sichuan basin, Qinling mountains and Dabie mountains. Considering the geological movement from early Miocene to Pliocene, the colonization pattern of the H. chinensis -group maybe closely related to the progressive uplift of Qinghai-Tibetan Plateau (QTP) and historical climate change.Conclusions Our study provides evidence for species delimitation and speciation process within the H. chinensis -group. Our study supports the hypothesis that the evolutionary divergence in this species group was a consequence of the progressive uplift of QTP and environmental change.

scholarly journals A Laurasian origin for a pantropical bird radiation is supported by genomic and fossil data (Aves: Coraciiformes)

2019 ◽  
Vol 286 (1910) ◽  
pp. 20190122 ◽  
Author(s):  
Jenna M. McCullough ◽  
Robert G. Moyle ◽  
Brian T. Smith ◽  
Michael J. Andersen
Keyword(s):  
Evolutionary Dynamics ◽  
Species Tree ◽  
Old World ◽  
Avian Order ◽  
History Of ◽  
The Tropics ◽  
Fossil Data ◽  
Old World Tropics ◽  
New Framework

The evolution of pantropically distributed clades has puzzled palaeo- and neontologists for decades regarding the different hypotheses about where they originated. In this study, we explored how a pantropical distribution arose in a diverse clade with a rich fossil history: the avian order Coraciiformes. This group has played a central role in the debate of the biogeographical history of Neoaves. However, the order lacked a coherent species tree to inform study of its evolutionary dynamics. Here, we present the first complete species tree of Coraciiformes, produced with 4858 ultraconserved elements, which supports two clades: (1) Old World-restricted bee-eaters, rollers and ground-rollers; and (2) New World todies and motmots, and cosmopolitan kingfishers. Our results indicated two pulses of diversification: (1) major lineages of Coraciiformes arose in Laurasia approximately 57 Ma, followed by independent dispersals into equatorial regions, possibly due to tracking tropical habitat into the lower latitudes—the Coracii (Coraciidae + Brachypteraciidae) into the Afrotropics, bee-eaters throughout the Old World tropics, and kingfishers into the Australasian tropics; and (2) diversification of genera in the tropics during the Miocene and Pliocene. Our study supports the important role of Laurasia as the geographical origin of a major pantropical lineage and provides a new framework for comparative analyses in this charismatic bird radiation.

From the desert it came: evolution of the Australian paper daisy genus Leucochrysum (Asteraceae, Gnaphalieae)

2016 ◽  
Vol 29 (3) ◽  
pp. 176 ◽  
Author(s):  
Alexander N. Schmidt-Lebuhn ◽  
Kiarrah J. Smith
Keyword(s):  
Arid Zone ◽  
Nuclear Gene ◽  
Amplicon Sequencing ◽  
Success Rates ◽  
Ancestral Area ◽  
Biogeographic History ◽  
Molecular Phylogenetic ◽  
Ancestral Area Reconstruction ◽  
History Of ◽  
Australian Flora

Present patterns of diversity in the Australian flora have been shaped by increasing seasonality since the Eocene, and by pronounced aridification in the past 3 million years. Arid-zone plants are commonly hypothesised to be the products of radiations of ancestrally temperate or coastal lineages, as in the case of the everlasting paper daisy tribe Gnaphalieae (Asteraceae). However, these inferences are often based on higher-level phylogenies, whereas evolutionary processes in the Australian Gnaphalieae have rarely been studied at the species level. Here, we reconstructed the phylogeny and biogeographic history of the small, but ecologically diverse, paper daisy genus Leucochrysum, to examine recent habitat shifts and character changes, at the same time exploring the feasibility of using amplicon sequencing of low-copy nuclear gene regions to resolve phylogenetic relationships in Australian Gnaphalieae. On the balance of evidence, outgroup comparison and ancestral-area reconstruction support an ancestral range in the arid zone with subsequent diversification towards the south-east, demonstrating a complex evolutionary history with a re-colonisation of temperate areas. Low amplification success rates suggest that methods other than amplicon sequencing of currently available primers will be more promising for molecular phylogenetic work at a larger scale.

scholarly journals Leaf evolution in Southern Hemisphere conifers tracks the angiosperm ecological radiation

2011 ◽  
Vol 279 (1727) ◽  
pp. 341-348 ◽  
Author(s):  
Ed Biffin ◽  
Timothy J. Brodribb ◽  
Robert S. Hill ◽  
Philip Thomas ◽  
Andrew J. Lowe
Keyword(s):  
Leaf Morphology ◽  
Terrestrial Ecosystems ◽  
Time Constraints ◽  
Ecological Radiation ◽  
Leaf Evolution ◽  
Climatic Range ◽  
Bayesian Relaxed Clock ◽  
The Tropics ◽  
Relaxed Clock ◽  
Lineage Diversification

The angiosperm radiation has been linked to sharp declines in gymnosperm diversity and the virtual elimination of conifers from the tropics. The conifer family Podocarpaceae stands as an exception with highest species diversity in wet equatorial forests. It has been hypothesized that efficient light harvesting by the highly flattened leaves of several podocarp genera facilitates persistence with canopy-forming angiosperms, and the angiosperm ecological radiation may have preferentially favoured the diversification of these lineages. To test these ideas, we develop a molecular phylogeny for Podocarpaceae using Bayesian-relaxed clock methods incorporating fossil time constraints. We find several independent origins of flattened foliage types, and that these lineages have diversified predominantly through the Cenozoic and therefore among canopy-forming angiosperms. The onset of sustained foliage flattening podocarp diversification is coincident with a declining diversification rate of scale/needle-leaved lineages and also with ecological and climatic transformations linked to angiosperm foliar evolution. We demonstrate that climatic range evolution is contingent on the underlying state for leaf morphology. Taken together, our findings imply that as angiosperms came to dominate most terrestrial ecosystems, competitive interactions at the foliar level have profoundly shaped podocarp geography and as a consequence, rates of lineage diversification.

scholarly journals Phylogeography of Nasutitermes ephratae (Termitidae: Nasutitermitinae) in Neotropical region

2022 ◽  
Author(s):  
Amanda de Faria Santos ◽  
Eliana Marques Cancello ◽  
Adriana Coletto Morales
Keyword(s):  
Genetic Structure ◽  
Central America ◽  
Divergence Time ◽  
Haplotype Network ◽  
Neotropical Region ◽  
Ancestral Area ◽  
Genetic Patterns ◽  
Dispersal Route ◽  
Ancestral Area Reconstruction ◽  
History Of

Abstract The neotropical region ranks third in the number of termites with five different families. Of these, Termitidae is the most diverse and includes the species Nasutitermes ephratae and is common in the neotropics. To date, only one study has been published about phylogeographic issues in neotropical termites (N. corniger). Here, we aimed to investigate and analyze the population genetic patterns of N. ephratae and then evaluated the phylogeographical processes involved in the evolutionary history of the species. We used the mitochondrial genes 16S rRNA and COII as molecular markers: These were sequenced for 128 samples of N. ephratae. We estimated the genetic diversity and divergence time as well as the demographic and genetic structure analyses. We also produced ancestral area reconstruction and a haplotype network. The results showed high genetic variability, recent demographic expansion, and strong genetic structure. We also inferred a dispersal route for the species that occurred in both directions between South and Central America. The results emphasize a temporary separation between the South and Central America population that affected the origin of the current Central America populations. These were formed form different phylogeographic histories.

scholarly journals The historical biogeography of Mammalia

2011 ◽  
Vol 366 (1577) ◽  
pp. 2478-2502 ◽  
Author(s):  
Mark S. Springer ◽  
Robert W. Meredith ◽  
Jan E. Janecka ◽  
William J. Murphy
Keyword(s):  
South America ◽  
Ancestral Reconstruction ◽  
Ancestral Area ◽  
Mammal Fauna ◽  
Reconstruction Methods ◽  
Binary Coding ◽  
Single Character ◽  
Extant Species ◽  
Ancestral Area Reconstruction ◽  
History Of

Palaeobiogeographic reconstructions are underpinned by phylogenies, divergence times and ancestral area reconstructions, which together yield ancestral area chronograms that provide a basis for proposing and testing hypotheses of dispersal and vicariance. Methods for area coding include multi-state coding with a single character, binary coding with multiple characters and string coding. Ancestral reconstruction methods are divided into parsimony versus Bayesian/likelihood approaches. We compared nine methods for reconstructing ancestral areas for placental mammals. Ambiguous reconstructions were a problem for all methods. Important differences resulted from coding areas based on the geographical ranges of extant species versus the geographical provenance of the oldest fossil for each lineage. Africa and South America were reconstructed as the ancestral areas for Afrotheria and Xenarthra, respectively. Most methods reconstructed Eurasia as the ancestral area for Boreoeutheria, Euarchontoglires and Laurasiatheria. The coincidence of molecular dates for the separation of Afrotheria and Xenarthra at approximately 100 Ma with the plate tectonic sundering of Africa and South America hints at the importance of vicariance in the early history of Placentalia. Dispersal has also been important including the origins of Madagascar's endemic mammal fauna. Further studies will benefit from increased taxon sampling and the application of new ancestral area reconstruction methods.

scholarly journals Dipole patterns in tropical precipitation were pervasive across landmasses throughout Marine Isotope Stage 5

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Katrina Nilsson-Kerr ◽  
Pallavi Anand ◽  
Philip B. Holden ◽  
Steven C. Clemens ◽  
Melanie J. Leng
Keyword(s):  
Large Scale ◽  
Marine Isotope Stage ◽  
Convergence Zone ◽  
Inter Tropical Convergence Zone ◽  
Tropical Regions ◽  
Tropical Precipitation ◽  
Rainfall Patterns ◽  
Marine Isotope Stage 5 ◽  
Climate Cooling ◽  
The Tropics

AbstractMost of Earth’s rain falls in the tropics, often in highly seasonal monsoon rains, which are thought to be coupled to the inter-hemispheric migrations of the Inter-Tropical Convergence Zone in response to the seasonal cycle of insolation. Yet characterization of tropical rainfall behaviour in the geologic past is poor. Here we combine new and existing hydroclimate records from six large-scale tropical regions with fully independent model-based rainfall reconstructions across the last interval of sustained warmth and ensuing climate cooling between 130 to 70 thousand years ago (Marine Isotope Stage 5). Our data-model approach reveals large-scale heterogeneous rainfall patterns in response to changes in climate. We note pervasive dipole-like tropical precipitation patterns, as well as different loci of precipitation throughout Marine Isotope Stage 5 than recorded in the Holocene. These rainfall patterns cannot be solely attributed to meridional shifts in the Inter-Tropical Convergence Zone.

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