scholarly journals Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos

2020 ◽  
Author(s):  
Cen Guo ◽  
Peng-Fei Ma ◽  
Guo-Qian Yang ◽  
Xia-Ying Ye ◽  
Ying Guo ◽  
...  
Keyword(s):  
Evolutionary History ◽  
East Asian Monsoon ◽  
Nuclear Markers ◽  
Chloroplast Genomes ◽  
Analysis Workflow ◽  
History Of ◽  
Tree Estimation ◽  
Evolutionary Radiations ◽  
Genome Skimming ◽  
Parallel Sampling

Abstract Rapid evolutionary radiations are among the most challenging phylogenetic problems, wherein different types of data (e.g., morphology, molecular) or genetic markers (e.g., nuclear, organelle) often yield inconsistent results. The tribe Arundinarieae i.e., the temperate bamboos, is a clade of tetraploid originated 22 million years ago and subsequently radiated in East Asia. Previous studies of Arundinarieae have found conflicting relationships and/or low support. Here, we obtain nuclear markers from ddRAD data for 213 Arundinarieae taxa and parallel sampling of chloroplast genomes from genome-skimming for 147 taxa. We first assess the feasibility of using ddRAD-seq data for phylogenetic estimates of paleopolyploid and rapidly radiated lineages, optimize clustering thresholds and analysis workflow for orthology identification. Reference-based ddRAD data assembly approaches perform well and yield strongly supported relationships that are generally concordant with morphology-based taxonomy. We recover five major lineages, two of which are notable (the pachymorph and leptomorph lineages), in that they correspond with distinct rhizome morphologies. By contrast, the phylogeny from chloroplast genomes differed significantly. Based on multiple lines of evidence, the ddRAD tree is favored as the best species tree estimation for temperate bamboos. Using a time-calibrated ddRAD tree we find that Arundinarieae diversified rapidly around the mid-Miocene corresponding with intensification of the East Asian monsoon and the evolution of key innovations including the leptomorph rhizomes. Our results provide a highly resolved phylogeny of Arundinarieae, shed new light on the radiation and reticulate evolutionary history of this tribe, and provide an empirical example for the study of recalcitrant plant radiations.

scholarly journals Phylogenomic Reconstruction of the Neotropical Poison Frogs (Dendrobatidae) and Their Conservation

Diversity ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 126 ◽  
Author(s):  
Wilson X. Guillory ◽  
Morgan R. Muell ◽  
Kyle Summers ◽  
Jason L. Brown
Keyword(s):  
Bayesian Methods ◽  
Evolutionary History ◽  
Conservation Status ◽  
Nuclear Data ◽  
Nuclear Markers ◽  
Poison Frog ◽  
Sequence Capture ◽  
Genome Wide ◽  
Frog Species ◽  
History Of

The evolutionary history of the Dendrobatidae, the charismatic Neotropical poison frog family, remains in flux, even after a half-century of intensive research. Understanding the evolutionary relationships between dendrobatid genera and the larger-order groups within Dendrobatidae is critical for making accurate assessments of all aspects of their biology and evolution. In this study, we provide the first phylogenomic reconstruction of Dendrobatidae with genome-wide nuclear markers known as ultraconserved elements. We performed sequence capture on 61 samples representing 33 species across 13 of the 16 dendrobatid genera, aiming for a broadly representative taxon sample. We compare topologies generated using maximum likelihood and coalescent methods and estimate divergence times using Bayesian methods. We find most of our dendrobatid tree to be consistent with previously published results based on mitochondrial and low-count nuclear data, with notable exceptions regarding the placement of Hyloxalinae and certain genera within Dendrobatinae. We also characterize how the evolutionary history and geographic distributions of the 285 poison frog species impact their conservation status. We hope that our phylogeny will serve as a backbone for future evolutionary studies and that our characterizations of conservation status inform conservation practices while highlighting taxa in need of further study.

scholarly journals The convoluted evolutionary history of the capped-golden langur lineage (Cercopithecidae: Colobinae) – concatenation versus coalescent analyses

2018 ◽  
Author(s):  
Kunal Arekar ◽  
Abhijna Parigi ◽  
K. Praveen Karanth
Keyword(s):  
Evolutionary History ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Position ◽  
Lineage Sorting ◽  
Nuclear Markers ◽  
Mitochondrial Markers ◽  
Multispecies Coalescent ◽  
Nuclear Species ◽  
History Of ◽  
Golden Langur

AbstractEvolutionary studies have traditionally relied on concatenation based methods to reconstruct relationships from multiple markers. However, due to limitations of concatenation analyses, recent studies have proposed coalescent based methods to address evolutionary questions. Results from these methods tend to diverge from each other under situations where there is incomplete lineage sorting or hybridization. Here we used concatenation as well as multispecies coalescent (MSC) methods to understand the evolutionary origin of capped and golden langur (CG) lineage. Previous molecular studies have retrieved conflicting phylogenies, with mitochondrial tree grouping CG lineage with a largely Indian genus Semnopithecus, while nuclear markers support their affinities with a Southeast Asian genus, Trachypithecus. However, as pointed by others, the use of nuclear copies of mitochondrial DNA in the above studies might have generated the discordance. Because of this discordance, the phylogenetic position of CG lineage has been much debated in recent times. In this study, we have used nine nuclear and eight mitochondrial markers. Concatenated nuclear as well as the mitochondrial dataset recovered congruent relationships where CG lineage was sister to Trachypithecus. However nuclear species tree estimated using different MSC methods were incongruent with the above result, suggesting presence of incomplete lineage sorting (ILS)/hybridisation. Furthermore, CG lineage is morphologically intermediate between Semnopithecus and Trachypithecus. Based on this evidence, we argue that CG lineage evolved through hybridisation between Semnopithecus and Trachypithecus. Finally, we reason that both concatenation as well as coalescent methods should be used in conjunction for better understanding of various evolutionary hypotheses.

scholarly journals Phylogenetic reconciliation reveals extensive ancestral recombination in Sarbecoviruses and the SARS-CoV-2 lineage

2021 ◽  
Author(s):  
Sumaira Zaman ◽  
Samuel Sledzieski ◽  
Bonnie Berger ◽  
Yi-Chieh Wu ◽  
Mukul S. Bansal
Keyword(s):  
Evolutionary History ◽  
Viral Evolution ◽  
Emerging Pathogens ◽  
Phylogenetic Methods ◽  
History Of ◽  
Tree Estimation ◽  
Phylogenetic Reconciliation ◽  
Horseshoe Bat ◽  
Insight Into ◽  
Family Trees

An accurate understanding of the evolutionary history of rapidly-evolving viruses like SARS-CoV-2, responsible for the COVID-19 pandemic, is crucial to tracking and preventing the spread of emerging pathogens. However, viruses undergo frequent recombination, which makes it difficult to trace their evolutionary history using traditional phylogenetic methods. Here, we present a phylogenetic workflow, virDTL, for analyzing viral evolution in the presence of recombination. Our approach leverages reconciliation methods developed for inferring horizontal gene transfer in prokaryotes, and, compared to existing tools, is uniquely able to identify ancestral recombinations while accounting for several sources of inference uncertainty, including in the construction of a strain tree, estimation and rooting of gene family trees, and reconciliation itself. We apply this workflow to the Sarbecovirus subgenus and demonstrate how a principled analysis of predicted recombination gives insight into the evolution of SARS-CoV-2. In addition to providing confirming evidence for the horseshoe bat as its zoonotic origin, we identify several ancestral recombination events that merit further study.

scholarly journals Evolution and phylogeny of the deep-sea isopod families Desmosomatidae Sars, 1897 and Nannoniscidae Hansen, 1916  (Isopoda: Asellota)

2021 ◽  
Author(s):  
Saskia Brix ◽  
Christoph Held ◽  
Stefanie Kaiser ◽  
Robert M. Jennings ◽  
Amy Driskell ◽  
...  
Keyword(s):  
Deep Sea ◽  
Evolutionary History ◽  
Biogeographic Pattern ◽  
Phylogenetic Reconstructions ◽  
Molecular Tree ◽  
The Family ◽  
Close Relationship ◽  
History Of ◽  
Evolutionary Radiations ◽  
Relationship Of

AbstractIn the deep sea, the phylogeny and biogeography of only a few taxa have been well studied. Although more than 200 species in 32 genera have been described for the asellote isopod families Desmosomatidae Sars, 1897 and Nannoniscidae Hansen, 1916 from all ocean basins, their phylogenetic relationships are not completely understood. There is little doubt about the close relationship of these families, but the taxonomic position of a number of genera is so far unknown. Based on a combined morphological phylogeny using the Hennigian method with a dataset of 107 described species and a molecular phylogeny based on three markers (COI, 16S, and 18S) with 75 species (most new to science), we could separate Desmosomatidae and Nannoniscidae as separate families. However, we could not support the concept of the subfamilies Eugerdellatinae Hessler, 1970 and Desmosomatinae Hessler, 1970. Most genera of both families were well supported, but several genera appear as para- or even polyphyletic. Within both families, convergent evolution and analogies caused difficulty in defining apomorphies for phylogenetic reconstructions and this is reflected in the results of the concatenated molecular tree. There is no biogeographic pattern in the distribution as the genera occur over the entire Atlantic and Pacific Ocean, showing no specific phylogeographical pattern. Poor resolution at deep desmosomatid nodes may reflect the long evolutionary history of the family and rapid evolutionary radiations.

scholarly journals Mitochondrial Genome and Nuclear Markers Provide New Insight into the Evolutionary History of Macaques

PLoS ONE ◽  
2016 ◽  
Vol 11 (5) ◽  
pp. e0154665 ◽  
Author(s):  
Juan Jiang ◽  
Jianqiu Yu ◽  
Jing Li ◽  
Peng Li ◽  
Zhenxin Fan ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Evolutionary History ◽  
Nuclear Markers ◽  
History Of ◽  
Insight Into

Evolutionary history of mountain voles of the subgenus Aschizomys (Cricetidae, Rodentia), inferred from mitochondrial and nuclear markers

2020 ◽  
Vol 15 (3) ◽  
pp. 187-201
Author(s):  
Semen Yu. BODROV ◽  
Vera K. VASILJEVA ◽  
Innokentiy M. OKHLOPKOV ◽  
Nikolai V. MAMAYEV ◽  
Evgeniy S. ZAKHAROV ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Nuclear Markers ◽  
History Of ◽  
Mitochondrial And Nuclear Markers

scholarly journals Revealing the evolutionary history of a reticulate polyploid complex in the genus Isoëtes

2020 ◽  
Author(s):  
Jacob S. Suissa ◽  
Sylvia P. Kinosian ◽  
Peter W. Schafran ◽  
Jay F. Bolin ◽  
W. Carl Taylor ◽  
...  
Keyword(s):  
North American ◽  
Evolutionary History ◽  
Restriction Site ◽  
Reticulate Evolution ◽  
List Type ◽  
Reproductive Barriers ◽  
Nuclear Markers ◽  
History Of ◽  
High Level

SummaryPolyploidy and hybridization are important processes in the evolution of spore-dispersed plants. Few studies, however, focus these dynamics in heterosporous lycophytes, such as Isoëtes, where polyploid hybrids are common and thought to be important in the generation of their extant diversity. We investigate reticulate evolution in a complex of western North American quillworts (Isoëtes) and provide insights into the evolutionary history of hybrids, and the role of polyploidy in maintaining novel diversity.We utilize low copy nuclear markers, whole plastomes, restriction site-associated DNA sequencing, cytology, and reproductive status (fertile or sterile) to investigate the reticulate evolutionary history of western North American Isoëtes.We reconstruct the reticulate evolutionary history and directionality of hybridization events in this complex. The presence of high level polyploids, plus frequent homoploid and interploid hybridization suggests that there are low prezygotic reproductive barriers in this complex, hybridization is common and bidirectional between similar—but not divergent—cytotypes, and that allopolyploidization is important to restore fertility in some hybrid taxa.Our data provide five lines of evidence suggesting that hybridization and polyploidy can occur with frequency in the genus, and these evolutionary processes may be important in shaping extant Isoëtes diversity.

scholarly journals Different behaviour of mitochondrial and nuclear markers: introgression and the evolutionary history of Chrysocarabus (Coleoptera: Carabidae)

2006 ◽  
Vol 17 (3) ◽  
Author(s):  
Andreas Düring ◽  
Martina Brückner ◽  
Dietrich Mossakowski
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Gene Tree ◽  
Gene Trees ◽  
Nuclear Markers ◽  
Mitochondrial Haplotypes ◽  
History Of ◽  
Mitochondrial And Nuclear Markers

Phylogenetic analyses of Chrysocarabus taxa using different markers result in different phylogenetic trees. In particular, the mitochondrial gene tree contradicts the results of morphological and inbreeding studies. Two very different haplotypes of Carabus splendens Olivier, 1790 do not form a clade within this phylogenetic tree. We have earlier proposed that contradictory results are due to introgression. To verify our hypothesis, we analysed the internal transcribed spacer 2. No substitutions were observed in these nuclear sequences between the individuals of Carabus splendens, which contain the different mitochondrial haplotypes in question. The differences in the gene trees based on mitochondrial and nuclear sequences can be explained with at least two introgression events.

scholarly journals Genomic evidence of prevalent hybridization throughout the evolutionary history of the fig-wasp pollination mutualism

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Gang Wang ◽  
Xingtan Zhang ◽  
Edward Allen Herre ◽  
Doyle McKey ◽  
Carlos A. Machado ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Genomic Data ◽  
Host Switching ◽  
Fig Wasp ◽  
Chloroplast Genomes ◽  
Dominant Feature ◽  
Pollination Mutualism ◽  
History Of ◽  
Coevolutionary History

AbstractFicus (figs) and their agaonid wasp pollinators present an ecologically important mutualism that also provides a rich comparative system for studying functional co-diversification throughout its coevolutionary history (~75 million years). We obtained entire nuclear, mitochondrial, and chloroplast genomes for 15 species representing all major clades of Ficus. Multiple analyses of these genomic data suggest that hybridization events have occurred throughout Ficus evolutionary history. Furthermore, cophylogenetic reconciliation analyses detect significant incongruence among all nuclear, chloroplast, and mitochondrial-based phylogenies, none of which correspond with any published phylogenies of the associated pollinator wasps. These findings are most consistent with frequent host-switching by the pollinators, leading to fig hybridization, even between distantly related clades. Here, we suggest that these pollinator host-switches and fig hybridization events are a dominant feature of fig/wasp coevolutionary history, and by generating novel genomic combinations in the figs have likely contributed to the remarkable diversity exhibited by this mutualism.

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