UFBoot2: Improving the Ultrafast Bootstrap Approximation

Dictyochophyceae (silicoflagellates) are unicellular freshwater and marine algae (Heterokontophyta, stramenopiles). Despite their abundance in global oceans and potential ecological significance, discovered in recent years, neither nuclear nor organellar genomes of representatives of this group were sequenced until now. Here, we present the first complete plastid genome sequences of Dictyochophyceae, obtained from four species: Dictyocha speculum, Rhizochromulina marina, Florenciella parvula and Pseudopedinella elastica. Despite their comparable size and genetic content, these four plastid genomes exhibit variability in their organization: plastid genomes of F. parvula and P. elastica possess conventional quadripartite structure with a pair of inverted repeats, R. marina instead possesses two direct repeats with the same orientation and D. speculum possesses no repeats at all. We also observed a number of unusual traits in the plastid genome of D. speculum, including expansion of the intergenic regions, presence of an intron in the otherwise non‐intron‐bearing psaA gene, and an additional copy of the large subunit of RuBisCO gene (rbcL), the last of which has never been observed in any plastid genome. We conclude that despite noticeable gene content similarities between the plastid genomes of Dictyochophyceae and their relatives (pelagophytes, diatoms), the number of distinctive features observed in this lineage strongly suggests that additional taxa require further investigation.

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“…Branch support was calculated with 5,000 replications (‐bb option) using the ultrafast bootstrap approximation (Hoang et al. ).…”

Section: Methodsmentioning

confidence: 99%

Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization

Han

Maciszewski

Graf

et al. 2019

Journal of Phycology

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“…The substitution model for each partition was chosen by jModeltest2 (Darriba, Taboada, Doallo, & Posada, ) according to Akaike information criterion. Nodal support was assessed using 1,000 ultrafast bootstrap replicates (Hoang, Chernomor, von Haeseler, Minh, & Vinh, ). The choice of multiple outgroups comprising R. amplexicadatus and R. leschenaultii was made based on known polarity within the rousettine radiation (Almeida et al, ; Giannini & Simmons, ; Hassanin et al, ; Juste et al, ).…”

Section: Methodsmentioning

confidence: 99%

Pan African phylogeography and palaeodistribution of rousettine fruit bats: Ecogeographic correlation with Pleistocene climate vegetation cycles

Stribna

Romportl

Demjanovič

et al. 2019

Journal of Biogeography

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Aim The impact of Pleistocene climatic oscillations on tropical biomes is associated with changes in the extent of forest cover. Fruit bats have played a role in woodland dynamics via pollination and seed dispersal. We hypothesized that phylogeographic patterns of Rousettus on continental Africa and adjacent islands should show a signature of pluvial‐drought cycles, involving demographic expansions and contractions. Location Afrotropical, Malagasy and Saharo‐Arabian biogeographic realms. Taxon Genus Rousettus (Pteropodidae). Methods Phylogeographic and population genetic approaches using mitochondrial and microsatellite data were integrated with species distribution modelling of currently suitable habitats and those of the Last Glacial Maximum using climate simulations. Results Phylogenetic reconstruction yielded an Asian outgroup followed by pectinate branching of the Indian Ocean taxa and Rousettus aegyptiacus. While nuclear microsatellites were homogeneous across the African mainland, two mitochondrial haplogroups were found. Haplogroup I is widespread in regions with extensive tree cover, including tropical rain forests, and has close relationships to isolated lineages in the Middle East and islands in the Gulf of Guinea. Haplogroup II is sister to the rest of the R. aegyptiacus radiation and is found in eastern and southern Africa and the Sudanian savanna in habitats with semi‐open land cover. Main Conclusion Palaeodistributional modelling ascertained that the Indian Ocean islands provided more extensive areas of suitable habitat in the past relative to conditions today, suggesting stepping stone connectivity between Asia and Africa during Pleistocene interpluvial sea‐level lowstands. Inverse pluvial‐drought demography was detected in lineages ancestral to recent haplogroups, providing evidence of past forest refugia and complex ecogeographic scenarios of haplogroup origins involving allopatry and parapatry connected with the eastern Afromontane biodiversity hotspot, and subsequent admixture of nuclear gene pools. The Middle Eastern lineage probably originated during pluvial green Sahara periods, possibly in co‐evolution with ancestors of tree crop species domesticated later during the Neolithic revolution. The keystone role of rousettine bats for forest regeneration and their ability to pioneer dry and distant habitats emphasize their role in conservation biology and restoration ecology.

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“…Sequences were partitioned by codon position and the best substitution model for each partition was evaluated with modelfinder (Kalyaanamoorthy, Minh, Wong, Haeseler, & Jermiin, ), followed by maximum‐likelihood inference in iq‐tree 1.6.0 (Nguyen, Schmidt, Haeseler, & Minh, ), and 1,000 bootstrap replicates using the ultrafast bootstrap method UFBOOT2 (Hoang, Chernomor, Haeseler, Minh, & Vinh, ). Haplotype networks for major clades were inferred with popart 1.7 (Leigh & Bryant, ), using median joining networks (Bandelt, Forster, & Rohl, ).…”

Section: Methodsmentioning

confidence: 99%

Biogeography, habitat transitions and hybridization in a radiation of South American silverside fishes revealed by mitochondrial and genomic RAD data

et al. 2020

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Rivers and lake systems in the southern cone of South America have been widely influenced by historical glaciations, carrying important implications for the evolution of aquatic organisms, including prompting transitions between marine and freshwater habitats and by triggering hybridization among incipient species via waterway connectivity and stream capture events. Silverside fishes (Odontesthes) in the region comprise a radiation of 19 marine and freshwater species that have been hypothesized on the basis of morphological or mitochondrial DNA data to have either transitioned repeatedly into continental waters from the sea or colonized marine habitats following freshwater diversification. New double digest restriction‐site associated DNA data presented here provide a robust framework to investigate the biogeographical history of and habitat transitions in Odontesthes. We show that Odontesthes silversides originally diversified in the Pacific but independently colonized the Atlantic three times, producing three independent marine‐to‐freshwater transitions. Our results also indicate recent introgression of marine mitochondrial haplotypes into two freshwater clades, with more recurring instances of hybridization among Atlantic‐ versus Pacific‐slope species. In Pacific freshwater drainages, hybridization with a marine species appears to be geographically isolated and may be related to glaciation events. Substantial structural differences of estuarine gradients between these two geographical areas may have influenced the frequency, intensity and evolutionary effects of hybridization events.

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UFBoot2: Improving the Ultrafast Bootstrap Approximation

Cited by 619 publications

References 29 publications

Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization

Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization

Pan African phylogeography and palaeodistribution of rousettine fruit bats: Ecogeographic correlation with Pleistocene climate vegetation cycles

Biogeography, habitat transitions and hybridization in a radiation of South American silverside fishes revealed by mitochondrial and genomic RAD data

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