scholarly journals Towards a global perspective for Salvia L: Phylogeny, diversification, and floral evolution

2021 ◽  
Author(s):  
Fatemeh Moein ◽  
Ziba Jamzad ◽  
Mohammadreza Rahiminejad ◽  
Jacob Brian Landis ◽  
Mansour Mirtadzadini ◽  
...  
Keyword(s):  
Divergence Time ◽  
Global Perspective ◽  
Ancestral State ◽  
Pollination System ◽  
Divergence Time Estimates ◽  
Corolla Length ◽  
Asian Species ◽  
Show Evidence ◽  
Phylogenetic Resolution ◽  
Lever Mechanism

Premise of this study: Salvia is the most species-rich genus in Lamiaceae, encompassing approximately 1000 species distributed all over the world. We sought a new evolutionary perspective for Salvia by employing macroevolutionary analyses to address the tempo and mode of diversification. To study the association of floral traits with speciation and extinction, we modeled and explored the evolution of corolla length and the lever-mechanism pollination system across our Salvia phylogeny. Methods: We reconstructed a multigene phylogeny for 366 species of Salvia in the broad sense including all major recognized lineages and numerous species from Iran, a region previously overlooked in studies of the genus. Our phylogenetic data in combination with divergence time estimates were used to examine the evolution of corolla length, woody vs. herbaceous habit, and presence vs. absence of a lever mechanism. We investigated the timing and dependence of Salvia diversification related to corolla length evolution through a disparity test and BAMM analysis. A HiSSE model was used to evaluate the dependency of diversification on the lever-mechanism pollination system in Salvia. Key Results: Based on recent investigations and classifications, Salvia is monophyletic and comprises ~1000 species. Our inclusion, for the first time, of a comprehensive sampling for Iranian species of Salvia provides higher phylogenetic resolution for southwestern Asian species than obtained in previous studies. A medium corolla length (15-18mm) was reconstructed as the ancestral state for Salvia with multiple shifts to shorter and longer corollas. Macroevolutionary model analyses indicate that corolla length disparity is high throughout Salvia evolution, significantly different from expectations under a Brownian motion model during the last 28 million years of evolution. Our analyses show evidence of a higher diversification rate of corolla length for some Andean species of Salvia compared to other members of the genus. Based on our tests of diversification models, we reject the hypothesis of a direct effect of the lever mechanism on Salvia diversification. Conclusions: Using a broader species sampling than previous studies, we obtained a well-resolved phylogeny for southwest Asian species of Salvia. Corolla length is an adaptive trait throughout the Salvia phylogeny with a higher rate of diversification in the South American clade. Our results suggest caution in considering the lever-mechanism pollination system as one of the main drivers of speciation in Salvia.

scholarly journals Shortcomings of Phylogenetic Studies on Recent Radiated Insular Groups: A Meta-Analysis Using Cabo Verde Biodiversity

2019 ◽  
Vol 20 (11) ◽  
pp. 2782 ◽  
Author(s):  
Maria M. Romeiras ◽  
Ana Rita Pena ◽  
Tiago Menezes ◽  
Raquel Vasconcelos ◽  
Filipa Monteiro ◽  
...  
Keyword(s):  
Phylogenetic Signal ◽  
Meta Analysis ◽  
Divergence Time ◽  
Oceanic Islands ◽  
Published Data ◽  
Cabo Verde ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Macaronesian Islands ◽  
Phylogenetic Resolution

Over the previous decades, numerous studies focused on how oceanic islands have contributed to determine the phylogenetic relationships and times of origin and diversification of different endemic lineages. The Macaronesian Islands (i.e., Azores, Madeira, Selvagens, Canaries, and Cabo Verde), harbour biotas with exceptionally high levels of endemism. Within the region, the vascular plants and reptiles constitute two of the most important radiations. In this study we compare relevant published phylogenetic data and diversification rates retrieved within Cabo Verde endemic lineages and discuss the importance of choosing appropriate phylogeny-based methods to investigate diversification dynamics on islands. From this selective literature-based review, we summarize the software packages used in Macaronesian studies and discuss their adequacy considering the published data to obtain well-supported phylogenies in the target groups. We further debate the importance of Next Generation Sequencing (NGS), to investigate the evolutionary processes of diversification in the Macaronesian Islands. Analysis of genomic data provides phylogenetic resolution for rapidly evolving species radiations, suggesting a great potential to improve the phylogenetic signal and divergence time estimates in insular lineages. The most important Macaronesian reptile radiations provide good case-studies to compare classical phylogenetic methods with new tools, such as phylogenomics, revealing a high value for research on this hotspot area.

scholarly journals Mitogenomic phylogeny of Callithrix with special focus on human transferred taxa

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Joanna Malukiewicz ◽  
Reed A. Cartwright ◽  
Nelson H. A. Curi ◽  
Jorge A. Dergam ◽  
Claudia S. Igayara ◽  
...  
Keyword(s):  
Atlantic Forest ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Complete Sequence ◽  
Special Focus ◽  
Brazilian Atlantic Forest ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Mtdna Haplotypes ◽  
Show Evidence

Abstract Background Callithrix marmosets are a relatively young primate radiation, whose phylogeny is not yet fully resolved. These primates are naturally para- and allopatric, but three species with highly invasive potential have been introduced into the southeastern Brazilian Atlantic Forest by the pet trade. There, these species hybridize with each other and endangered, native congeners. We aimed here to reconstruct a robust Callithrix phylogeny and divergence time estimates, and identify the biogeographic origins of autochthonous and allochthonous Callithrix mitogenome lineages. We sequenced 49 mitogenomes from four species (C. aurita, C. geoffroyi, C. jacchus, C. penicillata) and anthropogenic hybrids (C. aurita x Callithrix sp., C. penicillata x C. jacchus, Callithrix sp. x Callithrix sp., C. penicillata x C. geoffroyi) via Sanger and whole genome sequencing. We combined these data with previously published Callithrix mitogenomes to analyze five Callithrix species in total. Results We report the complete sequence and organization of the C. aurita mitogenome. Phylogenetic analyses showed that C. aurita was the first to diverge within Callithrix 3.54 million years ago (Ma), while C. jacchus and C. penicillata lineages diverged most recently 0.5 Ma as sister clades. MtDNA clades of C. aurita, C. geoffroyi, and C. penicillata show intraspecific geographic structure, but C. penicillata clades appear polyphyletic. Hybrids, which were identified by phenotype, possessed mainly C. penicillata or C. jacchus mtDNA haplotypes. The biogeographic origins of mtDNA haplotypes from hybrid and allochthonous Callithrix were broadly distributed across natural Callithrix ranges. Our phylogenetic results also evidence introgression of C. jacchus mtDNA into C. aurita. Conclusion Our robust Callithrix mitogenome phylogeny shows C. aurita lineages as basal and C. jacchus lineages among the most recent within Callithrix. We provide the first evidence that parental mtDNA lineages of anthropogenic hybrid and allochthonous marmosets are broadly distributed inside and outside of the Atlantic Forest. We also show evidence of cryptic hybridization between allochthonous Callithrix and autochthonous C. aurita. Our results encouragingly show that further development of genomic resources will allow to more clearly elucidate Callithrix evolutionary relationships and understand the dynamics of Callithrix anthropogenic introductions into the Brazilian Atlantic Forest.

scholarly journals Taxonomy, Phylogeny, Molecular Dating and Ancestral State Reconstruction of Xylariomycetidae (Sordariomycetes)

2021 ◽  
Author(s):  
Milan C. Samarakoon ◽  
Kevin D Hyde ◽  
Sajeewa S. N. Maharachchikumbura ◽  
Marc Stadler ◽  
E. B. Gareth Jones ◽  
...  
Keyword(s):  
Divergence Time ◽  
Molecular Dating ◽  
Character State ◽  
Ancestral State ◽  
New Host ◽  
State Reconstruction ◽  
Divergence Time Estimates ◽  
New Family ◽  
Ancestral Character State ◽  
Time Estimates

Abstract Xylariomycetidae ( Ascomycota ) is a highly diversified group with variable stromatic characters. Our research focused on inconspicuous stromatic xylarialean taxa from China, Italy, Russia, Thailand and the United Kingdom. Detailed morphological descriptions, illustrations and combined ITS-LSU- rpb 2- tub 2- tef 1 phylogenies revealed 38 taxa from our collections belonging to Amphisphaeriales and Xylariales . A new family ( Appendicosporaceae ), five new genera ( Magnostiolata , Melanostictus , Neoamphisphaeria , Nigropunctata and Paravamsapriya ), 27 new species ( Acrocordiella photiniicola , Allocryptovalsa sichuanensis , Amphisphaeria parvispora , Anthostomella lamiacearum , Apiospora guiyangensis , Ap. sichuanensis , Biscogniauxia magna , Eutypa camelliae , Helicogermslita clypeata , Hypocopra zeae , Magnostiolata mucida , Melanostictus longiostiolatus , Me. thailandicus , Nemania longipedicellata , Ne. delonicis , Ne. paraphysata , Ne. thailandensis , Neoamphisphaeria hyalinospora , Neoanthostomella bambusicola , Nigropunctata bambusicola , Ni. nigrocircularis , Ni. thailandica , Occultitheca rosae , Paravamsapriya ostiolata , Peroneutypa leucaenae , Seiridium italicum and Vamsapriya mucosa ) and seven new host/geographical records are introduced and reported. Divergence time estimates indicate that Delonicicolales diverged from Amphisphaeriales + Xylariales at 161 (123–197) MYA. Amphisphaeriales and Xylariales diverged 154 (117–190) MYA with a crown age of 127 (92–165) MYA and 147 (111–184) MYA, respectively. Appendicosporaceae ( Amphisphaeriales ) has a stem age of 89 (65–117) MYA. Ancestral character state reconstruction indicates that astromatic, clypeate ascomata with aseptate, hyaline ascospores that lack germ slits may probably be ancestral Xylariomycetidae having plant-fungal endophytic associations. The Amphisphaeriales remained mostly astromatic with common septate, hyaline ascospores. Stromatic variations may have developed mostly during the Cretaceous period. Brown ascospores are common in Xylariales , but they first appeared in Amphisphaeriaceae , Melogrammataceae and Sporocadaceae during the early Cretaceous. The ascospore germ slits appeared only in Xylariales during the Cretaceous after the divergence of Lopadostomataceae . Hyaline, filiform and apiospores may have appeared as separate lineages providing the basis to Xylariaceae , which may have diverged independently. The future classification of polyphyletic xylarialean taxa will not be based on stromatic variations, but the type of ring, the colour of the ascospores, and the presence or absence of the type of germ slit.

scholarly journals Asterid Phylogenomics/Phylotranscriptomics Uncover Morphological Evolutionary Histories and Support Phylogenetic Placement for Numerous Whole-Genome Duplications

2020 ◽  
Vol 37 (11) ◽  
pp. 3188-3210 ◽  
Author(s):  
Caifei Zhang ◽  
Taikui Zhang ◽  
Federico Luebert ◽  
Yezi Xiang ◽  
Chien-Hsun Huang ◽  
...  
Keyword(s):  
Morphological Evolution ◽  
Divergence Time ◽  
Morphological Diversity ◽  
Data Sets ◽  
Whole Genome ◽  
Ancestral State ◽  
Divergence Time Estimates ◽  
Whole Genome Duplications ◽  
Time Estimates ◽  
Genome Duplications

Abstract Asterids are one of the most successful angiosperm lineages, exhibiting extensive morphological diversity and including a number of important crops. Despite their biological prominence and value to humans, the deep asterid phylogeny has not been fully resolved, and the evolutionary landscape underlying their radiation remains unknown. To resolve the asterid phylogeny, we sequenced 213 transcriptomes/genomes and combined them with other data sets, representing all accepted orders and nearly all families of asterids. We show fully supported monophyly of asterids, Berberidopsidales as sister to asterids, monophyly of all orders except Icacinales, Aquifoliales, and Bruniales, and monophyly of all families except Icacinaceae and Ehretiaceae. Novel taxon placements benefited from the expanded sampling with living collections from botanical gardens, resolving hitherto uncertain relationships. The remaining ambiguous placements here are likely due to limited sampling and could be addressed in the future with relevant additional taxa. Using our well-resolved phylogeny as reference, divergence time estimates support an Aptian (Early Cretaceous) origin of asterids and the origin of all orders before the Cretaceous–Paleogene boundary. Ancestral state reconstruction at the family level suggests that the asterid ancestor was a woody terrestrial plant with simple leaves, bisexual, and actinomorphic flowers with free petals and free anthers, a superior ovary with a style, and drupaceous fruits. Whole-genome duplication (WGD) analyses provide strong evidence for 33 WGDs in asterids and one in Berberidopsidales, including four suprafamilial and seven familial/subfamilial WGDs. Our results advance the understanding of asterid phylogeny and provide numerous novel evolutionary insights into their diversification and morphological evolution.

scholarly journals Mitogenomic Phylogeny of Callithrix with Special Focus on Human Transferred Taxa

2020 ◽  
Author(s):  
Joanna Malukiewicz ◽  
Reed A. Cartwright ◽  
Nelson H.A. Curi ◽  
Jorge A. Dergam ◽  
Claudia S. Igayara ◽  
...  
Keyword(s):  
Atlantic Forest ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Complete Sequence ◽  
Special Focus ◽  
Brazilian Atlantic Forest ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Mtdna Haplotypes ◽  
Show Evidence

AbstractBackgroundCallithrix marmosets are a relatively young non-human primate radiation, whose phylogeny is not yet full resolved. These primates are naturally para- and allopatric, but three species with highly invasive potential have been introduced into the southeastern Brazilian Atlantic Forest by the pet trade. There, these species hybridize with each other and endangered, native congeners. We aimed in this study to reconstruct a robust Callithrix phylogeny and divergence time estimates, as well as identify autochthonous and allochthonous Callithrix mitogenome lineages across Brazil. We sequenced 49 mitogenomes from four species (C. aurita, C. geoffroyi, C. jacchus, C. penicillata) and anthropogenic hybrids (C. aurita x Callithrix sp., C. penicillata x C. jacchus, Callithrix sp. x Callithrix sp., C. penicillata x C. geoffroyi) via Sanger and whole genome sequencing. We combined these data with previously published Callithrix mtDNA genomes to analyze five Callithrix species in total.ResultsWe report the complete sequence and organization of the C. aurita mtDNA genome. Phylogenetic analyses showed that C. aurita was the first to diverge within Callithrix 3.54 million years ago (MYA), while C. jacchus and C. penicillata lineages diverged most recently 0.5 MYA as sister clades. MtDNA clades of C. aurita, C. geoffroyi, and C. penicillata show intraspecific geographic structure, but C. penicillata clades appear polyphyletic. Hybrids, which were identified by phenotype, possessed mainly C. penicillata or C. jacchus mtDNA haplotypes. The geographic origins of mtDNA haplotypes from hybrid and allochthonous Callithrix were broadly distributed across natural Callithrix ranges. Our phylogenetic results also evidence introgression of C. jacchus mtDNA into C. aurita.ConclusionOur robust Callithrix mitogenome phylogeny shows C. aurita lineages as basal and C. jacchus lineages among the most recent within Callithrix. We provide the first evidence that parental mtDNA lineages of anthropogenic hybrid and allochtonous marmosets are broadly distributed inside and outside of the Atlantic Forest. We also show evidence of cryptic hybridization between allochthonous Callithrix and autochthonous C. aurita. Our results encouragingly show that further development of genomic resources will allow to more clearly elucidate Callithrix evolutionary relationships and understand the dynamics of Callithrix anthropogenic introductions into the Brazilian Atlantic Forest.

Molecular phylogeny and divergence time estimates of Penaeid Shrimp Lineages (Decapoda: Penaeidae)

Zootaxa ◽  
2009 ◽  
Vol 2107 (1) ◽  
pp. 41-52 ◽  
Author(s):  
CAROLINA M VOLOCH ◽  
PABLO R FREIRE ◽  
CLAUDIA A M RUSSO
Keyword(s):  
Fossil Record ◽  
Divergence Time ◽  
Penaeid Shrimp ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Global Clock ◽  
Late Tertiary ◽  
The Family ◽  
Molecular Studies ◽  
Triassic Period

Fossil record of penaeids indicates that the family exists since the Triassic period, but extant genera appeared only recently in Tertiary strata. Molecular based divergence time estimates on the matter of penaeid radiation were never properly addressed, due to shortcomings of the global molecular clock assumptions. Here, we studied the diversification patterns of the family, uncovering, more specifically, a correlation between fossil and extant Penaeid fauna. For this, we have used a Bayesian framework that does not assume a global clock. Our results suggest that Penaeid genera originated between 20 million years ago and 43 million years ago, much earlier than expected by previous molecular studies. Altogether, these results promptly discard late Tertiary or even Quaternary hypotheses that presumed a major glaciations influence on the diversification patterns of the family.

scholarly journals Out of the Neotropics: Late Cretaceous colonization of Australasia by American arthropods

2012 ◽  
Vol 279 (1742) ◽  
pp. 3501-3509 ◽  
Author(s):  
Prashant P. Sharma ◽  
Gonzalo Giribet
Keyword(s):  
Late Cretaceous ◽  
Divergence Time ◽  
Disjunct Distribution ◽  
Continental Margins ◽  
Divergence Time Estimates ◽  
Evolutionary Origins ◽  
Source Regions ◽  
Time Estimates ◽  
Fiji Islands ◽  
The Pacific

The origins of tropical southwest Pacific diversity are traditionally attributed to southeast Asia or Australia. Oceanic and fragment islands are typically colonized by lineages from adjacent continental margins, resulting in attrition of diversity with distance from the mainland. Here, we show that an exceptional tropical family of harvestmen with a trans-Pacific disjunct distribution has its origin in the Neotropics. We found in a multi-locus phylogenetic analysis that the opilionid family Zalmoxidae, which is distributed in tropical forests on both sides of the Pacific, is a monophyletic entity with basal lineages endemic to Amazonia and Mesoamerica. Indo-Pacific Zalmoxidae constitute a nested clade, indicating a single colonization event. Lineages endemic to putative source regions, including Australia and New Guinea, constitute derived groups. Divergence time estimates and probabilistic ancestral area reconstructions support a Neotropical origin of the group, and a Late Cretaceous ( ca 82 Ma) colonization of Australasia out of the Fiji Islands and/or Borneo, which are consistent with a transoceanic dispersal event. Our results suggest that the endemic diversity within traditionally defined zoogeographic boundaries might have more complex evolutionary origins than previously envisioned.

scholarly journals Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated

2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i884-i894
Author(s):  
Jose Barba-Montoya ◽  
Qiqing Tao ◽  
Sudhir Kumar
Keyword(s):  
Divergence Time ◽  
Sequence Divergence ◽  
Molecular Dating ◽  
Divergence Times ◽  
Time Reversibility ◽  
Sequence Alignments ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Substitution Process ◽  
The Impact

Abstract Motivation As the number and diversity of species and genes grow in contemporary datasets, two common assumptions made in all molecular dating methods, namely the time-reversibility and stationarity of the substitution process, become untenable. No software tools for molecular dating allow researchers to relax these two assumptions in their data analyses. Frequently the same General Time Reversible (GTR) model across lineages along with a gamma (+Γ) distributed rates across sites is used in relaxed clock analyses, which assumes time-reversibility and stationarity of the substitution process. Many reports have quantified the impact of violations of these underlying assumptions on molecular phylogeny, but none have systematically analyzed their impact on divergence time estimates. Results We quantified the bias on time estimates that resulted from using the GTR + Γ model for the analysis of computer-simulated nucleotide sequence alignments that were evolved with non-stationary (NS) and non-reversible (NR) substitution models. We tested Bayesian and RelTime approaches that do not require a molecular clock for estimating divergence times. Divergence times obtained using a GTR + Γ model differed only slightly (∼3% on average) from the expected times for NR datasets, but the difference was larger for NS datasets (∼10% on average). The use of only a few calibrations reduced these biases considerably (∼5%). Confidence and credibility intervals from GTR + Γ analysis usually contained correct times. Therefore, the bias introduced by the use of the GTR + Γ model to analyze datasets, in which the time-reversibility and stationarity assumptions are violated, is likely not large and can be reduced by applying multiple calibrations. Availability and implementation All datasets are deposited in Figshare: https://doi.org/10.6084/m9.figshare.12594638.

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