scholarly journals Reconstruction of the spatio-temporal diversification and ecological niche evolution of Helianthemum (Cistaceae) in the Canary Islands using genotyping-by-sequencing data

2020 ◽  
Author(s):  
Rafael G Albaladejo ◽  
Sara Martín-Hernanz ◽  
J Alfredo Reyes-Betancort ◽  
Arnoldo Santos-Guerra ◽  
María Olangua-Corral ◽  
...  
Keyword(s):  
Canary Islands ◽  
Ecological Niche ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Genotyping By Sequencing ◽  
Niche Conservatism ◽  
Sequencing Data ◽  
History Of ◽  
Spatio Temporal ◽  
Dispersal Events

Abstract Background and Aims Several biogeographical models have been proposed to explain the colonization and diversification patterns of Macaronesian lineages. In this study, we calculated the diversification rates and explored what model best explains the current distribution of the 15 species endemic to the Canary Islands belonging to Helianthemum sect. Helianthemum (Cistaceae). Methods We performed robust phylogenetic reconstructions based on genotyping-by-sequencing data and analysed the timing, biogeographical history and ecological niche conservatism of this endemic Canarian clade. Key Results Our phylogenetic analyses provided strong support for the monophyly of this clade, and retrieved five lineages not currently restricted to a single island. The pristine colonization event took place in the Pleistocene (~1.82 Ma) via dispersal to Tenerife by a Mediterranean ancestor. Conclusions The rapid and abundant diversification (0.75–1.85 species per million years) undergone by this Canarian clade seems the result of complex inter-island dispersal events followed by allopatric speciation driven mostly by niche conservatism, i.e. inter-island dispersal towards niches featuring similar environmental conditions. Nevertheless, significant instances of ecological niche shifts have also been observed in some lineages, making an important contribution to the overall diversification history of this clade.

scholarly journals Mastering the difficulties presented by the peculiarities of island life. A commentary on: ‘Reconstruction of the spatio-temporal diversification and ecological niche evolution ofHelianthemum(Cistaceae) in the Canary Islands using genotyping-by-sequence data’

2021 ◽  
Vol 127 (5) ◽  
pp. iii-iv
Author(s):  
Mark Carine
Keyword(s):  
Canary Islands ◽  
Ecological Niche ◽  
Sequence Data ◽  
Genotyping By Sequencing ◽  
Sequencing Data ◽  
Niche Evolution ◽  
Spatio Temporal

This article comments on:Rafael G. Albaladejo, Sara Martín-Hernanz, J. Alfredo Reyes-Betancort, Arnoldo Santos-Guerra, María Olangua-Corral and Abelardo Aparicio Reconstruction of the spatio-temporal diversification and ecological niche evolution of Helianthemum (Cistaceae) in the Canary Islands using genotyping-by-sequencing data, Annals of Botany, Volume 127, Issue 5, 16 April 2021, Pages 597–611, https://doi.org/10.1093/aob/mcaa090

Colonization history of the Canary Islands endemic Lavatera acerifolia, (Malvaceae) unveiled with genotyping‐by‐sequencing data and niche modelling

2020 ◽  
Vol 47 (4) ◽  
pp. 993-1005 ◽  
Author(s):  
Irene Villa‐Machío ◽  
Alejandro G. Fernández de Castro ◽  
Javier Fuertes‐Aguilar ◽  
Gonzalo Nieto Feliner
Keyword(s):  
Canary Islands ◽  
Genotyping By Sequencing ◽  
Sequencing Data ◽  
Niche Modelling ◽  
Colonization History ◽  
History Of

scholarly journals RAD sequencing data reveal a radiation of willow species (Salix L., Salicaceae) in the Hengduan Mountains and adjacent areas

2020 ◽  
Author(s):  
Li He ◽  
Natascha Dorothea Wagner ◽  
Elvira Hörandl
Keyword(s):  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Ecological Factors ◽  
Glacial Refugia ◽  
Hengduan Mountains ◽  
Sequencing Data ◽  
Niche Modelling ◽  
Altitudinal Distribution ◽  
Mountain System ◽  
Spatio Temporal

AbstractThe Hengduan Mountains (HDM) in South West China are an important hotspot of plant diversity and endemism and considered to be a secondary diversification center for the woody plant genus Salix (Salicaceae). This study aimed to reconstruct the spatio-temporal evolution of the Salix Chamaetia-Vetrix clade in the HDM and to test for the occurrence of a radiation. We inferred phylogenetic relationships based on more than 34,000 RAD loci of 27 species. Phylogenetic analyses recovered a well-resolved tree topology with two major clades, the Eurasian and the HDM clade and a divergence time of c. 23.9 Ma. The HDM clade comprises two subclades. The species of the HDM clade originated in north HDM and adjacent areas and then dispersed into the south HDM, westwards to the Himalayas and eastwards to the Qinling Mountains. Niche modelling analyses revealed that during the last glacial maximum, range contractions were observed in the northern areas, while southward expansions resulted in range overlaps. The reconstruction of putative adaptive character evolution of plant height, inflorescence and flower morphology indicate that adaptations to altitudinal distribution contributed to the diversification of the HDM willows. Our data indicate that a radiation occurred in HDM within the Salix Chamaetia-Vetrix clade. Dispersal within the mountain system and to adjacent regions as well as survival in glacial refugia have shaped the biogeographical history of the clade. Differentiation along altitudinal zonation concomitant to morphological adaptations to colder climates may be important ecological factors for the high species diversity of Salix in this area.

scholarly journals New distributional opportunities with niche innovation in Eurasian snowfinches

2021 ◽  
Author(s):  
Marlon E. Cobos ◽  
Yalin Cheng ◽  
Gang Song ◽  
Fumin Lei ◽  
A. Townsend Peterson
Keyword(s):  
Range Expansion ◽  
Ecological Niche ◽  
Evolutionary History ◽  
Niche Conservatism ◽  
Niche Evolution ◽  
Temperature And Precipitation ◽  
Precipitation Characteristics ◽  
History Of ◽  
Analytical Approaches ◽  
Distributional Potential

This study explores the evolutionary history of ecological niche characters in the Eurasian snowfinch lineage. Specifically, we use new analytical approaches to reconstruct ecological niche evolution, taking uncertainty in knowledge of the ecological niche limits into account. We found an overall pattern of niche conservatism in relation to both temperature and precipitation characteristics of niches, but for one dramatic niche evolution event, in Montifringilla nivalis. Interestingly, this species is also that which has by far the broadest geographic distribution among snowfinches. We conclude that an evolutionary change in niche characteristics perhaps within M. nivalis (i.e., present in some and not all of its populations) made possible the broad, westward range expansion of that species, thus changing the distributional potential of the snowfinch lineage dramatically.

scholarly journals Iroki: automatic customization and visualization of phylogenetic trees

2017 ◽  
Author(s):  
Ryan M. Moore ◽  
Amelia O. Harrison ◽  
Sean M. McAllister ◽  
Shawn W. Polson ◽  
K. Eric Wommack
Keyword(s):  
Web Application ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Community Diversity ◽  
Sequencing Data ◽  
Link Type ◽  
Large Trees ◽  
History Of ◽  
Microbial Groups

ABSTRACTPhylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki’s utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal (http://virome.dbi.udel.edu). Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.

Phylogeny and Biogeography of Acaena (Rosaceae) and its Relatives: Evidence of Multiple Long-Distance Dispersal Events Across the Globe

2021 ◽  
Vol 46 (4) ◽  
pp. 998-1010
Author(s):  
Javier Jauregui-Lazo ◽  
Daniel Potter
Keyword(s):  
South Africa ◽  
New Zealand ◽  
Southern Hemisphere ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Disjunct Distribution ◽  
Long Distance Dispersal ◽  
Long Distance ◽  
Biogeographic Patterns ◽  
Dispersal Events

Abstract— Acaena (Rosaceae) is the most complex and ecologically variable genus in Sanguisorbinae. Although it has been the subject of several taxonomic treatments, the largest phylogenetic analysis to date only sampled a small fraction of the total global diversity (five to seven out of 45 to 50 species). This study included most of the species to elucidate the phylogenetic relationships of Acaena and biogeographic patterns in Sanguisorbinae. Phylogenetic analyses of non-coding nuclear (ITS region) and chloroplast (trnL-F) DNA sequence markers using maximum likelihood and Bayesian analyses suggested that Acaena is a paraphyletic group with species of Margyricarpus and Tetraglochin nested within it. We identified strong support for eight subclades that are geographically or taxonomically structured. Nevertheless, the species-level relationships within subclades are still uncertain, which may be due to rapid diversification and lack of informative characters in the markers used. Sanguisorbinae, a primarily Southern Hemisphere clade, exhibits a classic Gondwana disjunct distribution. This current distribution is explained primarily by eight long-distance dispersal events. Our results suggested that Sanguisorbinae split into Cliffortia and Acaena around 13.6 mya. While Cliffortia diversified in southern South Africa, Acaena experienced several migration events in the Southern Hemisphere. Our estimation of the ancestral range suggested that Acaena likely originated in South Africa, followed by migration and subsequent diversification into southern South America. From there, the genus migrated to New Zealand, throughout the Andes, and to tropical areas in Central America, reaching as far north as California. Chile and New Zealand are the main sources of propagules for dispersal as well as the greatest diversity for the genus. The evolutionary relationships of species in Acaena combine a history of rapid diversifications, long-distance dispersals, and genetic variation within some taxa. Further research should be undertaken to clarify the infraspecific classification of A. magellanica.

scholarly journals Molecular Systematics and Biogeography of Antillean Thrashers, Tremblers, and Mockingbirds (Aves: Mimidae)

The Auk ◽  
2001 ◽  
Vol 118 (1) ◽  
pp. 35-55 ◽  
Author(s):  
Jeffrey S. Hunt ◽  
Eldredge Bermingham ◽  
Robert E. Ricklefs
Keyword(s):  
Mitochondrial Dna ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Sequence Divergence ◽  
The West ◽  
Island Populations ◽  
Mimus Polyglottos ◽  
History Of ◽  
Dumetella Carolinensis ◽  
Phylogenetic Hypotheses

Abstract We constructed phylogenetic hypotheses for Greater and Lesser Antillean Mimidae, including five endemic species of tremblers and thrashers that represent the best plausible example of an avian radiation within the Lesser Antilles. Phylogenetic relationships were inferred from analysis of 3,491 base pairs (bp) of mitochondrial DNA (mtDNA) and roughly 780 bp of the nuclear-encoded myoglobin gene. We used a subset of mtDNA gene sequences and pcrRFLP analysis to evaluate the phylogeographic relationships among individuals representing island populations of the Brown and Gray tremblers (Cinclocerthia ruficauda and C. gutturalis), Pearly-eyed Thrasher (Margarops fuscatus), Scaly-breasted Thrasher (Margarops fuscus), and Antillean and continental populations of the Tropical (Mimus gilvus) and Northern mockingbirds (Mimus polyglottos). Phylogeographic analysis distinguished three strongly differentiated mtDNA clades among tremblers, as well as distinct southern (St. Lucia and Martinique) and northern (Dominica to Montserrat) mtDNA lineages of the Scaly-breasted Thrasher. Minor geographic subdivision was also observed between continental and Antillean populations of the Tropical Mockingbird. Phylogenetic analyses of species-level Mimidae relationships that are based on mtDNA and nuclear sequences provide strong support for the monophyly and Antillean origin of a clade that consists of the tremblers, Pearly-eyed Thrasher, and Scaly-breasted Thrasher, but reject the monophyly of the genus Margarops. Phylogenetic analysis cannot confirm the monophyly of all endemic Antillean mimids because of the apparently contemporaneous diversification of the Antillean White-breasted Thrasher (Ramphocinclus brachyurus) with the continental Gray Catbird (Dumetella carolinensis) and Black Catbird (Melanoptila glabrirostris). However, an insertion and a deletion in the myoglobin intron 2 sequence support grouping the West Indian thrashers and tremblers, from which we infer that the endemic Lesser Antillean mimids are an indigenous radiation. Assuming a constant mtDNA clock for the Mimidae, the splitting of the Northern and Tropical mockingbird lineages is roughly contemporaneous with the separation of the three trembler clades, as well as the two Scaly-breasted Thrasher clades. Application of a mitochondrial DNA clock ticking at 2% sequence divergence per million years (Ma), suggests that the history of the endemic thrasher and trembler lineage in the West Indies extends back about 4 Ma, and the three distinct clades of tremblers split about 2 Ma ago.

scholarly journals Iroki: automatic customization and visualization of phylogenetic trees

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8584 ◽  
Author(s):  
Ryan M. Moore ◽  
Amelia O. Harrison ◽  
Sean M. McAllister ◽  
Shawn W. Polson ◽  
K. Eric Wommack
Keyword(s):  
Web Application ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Community Diversity ◽  
Sequencing Data ◽  
Link Type ◽  
Large Trees ◽  
History Of ◽  
Microbial Groups

Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki’s utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal http://virome.dbi.udel.edu. Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.

scholarly journals Traveler, a New DD35E Family of Tc1/Mariner Transposons, Invaded Vertebrates Very Recently

2020 ◽  
Vol 12 (3) ◽  
pp. 66-76 ◽  
Author(s):  
Wencheng Zong ◽  
Bo Gao ◽  
Mohamed Diaby ◽  
Dan Shen ◽  
Saisai Wang ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Evolutionary Dynamics ◽  
Phylogenetic Analyses ◽  
Nuclear Localization Sequence ◽  
Sequencing Data ◽  
Vertebrate Lineage ◽  
New Members ◽  
Reading Frame ◽  
Localization Sequence ◽  
History Of

Abstract The discovery of new members of the Tc1/mariner superfamily of transposons is expected based on the increasing availability of genome sequencing data. Here, we identified a new DD35E family termed Traveler (TR). Phylogenetic analyses of its DDE domain and full-length transposase showed that, although TR formed a monophyletic clade, it exhibited the highest sequence identity and closest phylogenetic relationship with DD34E/Tc1. This family displayed a very restricted taxonomic distribution in the animal kingdom and was only detected in ray-finned fish, anura, and squamata, including 91 vertebrate species. The structural organization of TRs was highly conserved across different classes of animals. Most intact TR transposons had a length of ∼1.5 kb (range 1,072–2,191 bp) and harbored a single open reading frame encoding a transposase of ∼340 aa (range 304–350 aa) flanked by two short-terminal inverted repeats (13–68 bp). Several conserved motifs, including two helix-turn-helix motifs, a GRPR motif, a nuclear localization sequence, and a DDE domain, were also identified in TR transposases. This study also demonstrated the presence of horizontal transfer events of TRs in vertebrates, whereas the average sequence identities and the evolutionary dynamics of TR elements across species and clusters strongly indicated that the TR family invaded the vertebrate lineage very recently and that some of these elements may be currently active, combining the intact TR copies in multiple lineages of vertebrates. These data will contribute to the understanding of the evolutionary history of Tc1/mariner transposons and that of their hosts.

scholarly journals The phylogeographic history of Krascheninnikovia reflects the development of dry steppes and semi-deserts in Eurasia

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Anna Seidl ◽  
Karin Tremetsberger ◽  
Simon Pfanzelt ◽  
Frank R. Blattner ◽  
Barbara Neuffer ◽  
...  
Keyword(s):  
North America ◽  
Central Asia ◽  
Genotyping By Sequencing ◽  
Climatic Conditions ◽  
Sequencing Data ◽  
The Caspian Sea ◽  
Dry Steppe ◽  
Steppe Belt ◽  
History Of ◽  
Suitable Habitats

AbstractConstituting one of Earth’s major biomes, steppes are characterised by naturally treeless extra-tropical vegetation. The formation of the Eurasian steppe belt, the largest steppe region in the world, began in Central Asia during the Neogene. In the glacial stages of the Pleistocene, steppe displaced forest vegetation, which in turn recolonised the area during the warmer interglacial periods, thus affecting the distribution of plants adapted to these habitats. Krascheninnikovia ceratoides (Chenopodiaceae) is a plant characteristic of dry steppe and semi-desert formations. Earlier studies showed that the ancestor of this autochthonous steppe element originated in Central Asia during the Miocene/Pliocene, i.e., in the same region and at the same time as the first appearance of steppe vegetation. However, as the extant lineages of Krascheninnikovia ceratoides diversified only 2.2 ± 0.9 Mya, it may represent a modern element of current dry steppe and semi-desert formations, rather than a component of the first steppe precursors of the Miocene. As such, it may have capitalised on the climatic conditions of the cold stages of the Quaternary to expand its range and colonise suitable habitats outside of its area of origin. To test this hypothesis, phylogeographic methods were applied to high-resolution genotyping-by-sequencing data. Our results indicate that Krascheninnikovia originated in western Central Asia and the Russian Altai, then spread to Europe in the West, and reached North America in the East. The populations of eastern Central Asia and North America belong to the same clade and are genetically clearly distinct from the Euro-Siberian populations. Among the populations west of the Altai Mountains, the European populations are genetically distinct from all others, which could be the result of the separation of populations east and west of the Urals caused by the Pleistocene transgressions of the Caspian Sea.

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