scholarly journals A molecular phylogeny of forktail damselflies (genus Ischnura) reveals a dynamic macroevolutionary history of female colour polymorphisms

2020 ◽  
Author(s):  
Rachel Blow ◽  
Beatriz Willink ◽  
Erik I. Svensson
Keyword(s):  
Molecular Phylogeny ◽  
Sexual Conflict ◽  
Evolutionary Dynamics ◽  
Molecular Data ◽  
Future Research ◽  
Ancestral State ◽  
Multispecies Coalescent ◽  
Geographic Range Size ◽  
Extant Species ◽  
History Of

AbstractColour polymorphisms are popular study systems among biologists interested in evolutionary dynamics, genomics, sexual selection and sexual conflict. In many damselflies, such as in the globally distributed genus Ischnura (forktails), female colour polymorphisms occur in some species. Female-polymorphic species contain two or three female morphs, one of which is malecoloured (androchrome or male mimic) and co-exists with sexually dimorphic (heterochrome) females. These female colour polymorphisms are considered to be maintained by frequencydependent sexual conflict, but their macroevolutionary histories are unknown, due to the lack of a robust molecular phylogeny. Here, we present the first time-calibrated phylogeny of Ischnura, using a multispecies coalescent approach (StarBEAST2), incorporating both molecular data and fossil information of 41 extant species (55% of the genus). We estimate the age of Ischnura to be between 13.8 and 23.4 millions of years, i.e. Miocene. We infer the ancestral state of this genus as female monomorphism with heterochrome females, with multiple gains and losses of polymorphisms, evidence of trans-species polymorphisms and a significant positive relationship between polymorphism incidence and current geographic range size. Our study provides a robust phylogenetic framework for future research on the dynamic macroevolutionary history of this clade with its extraordinary diversity of sex-limited female polymorphisms.

The unexpected, recent history of horsetails in Australia

2019 ◽  
Author(s):  
Andrew C. Rozefelds ◽  
Mary E. Dettmann ◽  
Anita K. Milroy ◽  
Andrew Hammond ◽  
H. Trevor Clifford ◽  
...  
Keyword(s):  
Spatial Arrangement ◽  
Molecular Data ◽  
Leaf Sheath ◽  
Late Eocene ◽  
Fossil Flora ◽  
Fossil Plants ◽  
Outer Cortex ◽  
Early Oligocene ◽  
Extant Species ◽  
History Of

A new fossil flora from central Queensland, of late Eocene or early Oligocene age, has yielded a diverse assemblage of flowering plants and ferns, including the first evidence of horsetails (Equisetum L.) from the Cenozoic of Australia. The fossils assigned to Equisetum are based on a stem fragment, 2–3mm in diameter, and spreading leaf sheath and diaphragm. The leaf sheath is interpreted to consist of ~24–30 leaves. The spatial arrangement of regularly arranged depressions in a section of the outer cortex is interpreted as evidence of the leaf vascular traces, and indicates a similar number of vascular traces. This specimen provides the youngest evidence of the genus from Australia and indicates that Equisetum survived for at least another 50 million years after it was thought to be extinct in Australia. Whereas molecular data for extant species of Equisetum collectively suggest a comparatively recent origin and radiation, the fossil record of the genus indicates a significantly longer and more complex history. Fossils, such as the new specimen from Makowata, Queensland, will, therefore, play a key role in understanding the history and past distribution of Equisetum in Australia. A key challenge is to assemble and characterise the morphological traits of these living and fossil plants to better understand the origins, history and radiation of this remarkable group of euphyllophytes.

A new species of Physaloptera (Nematoda: Spirurida) from Proechimys gardneri (Rodentia: Echimyidae) from the Amazon rainforest and molecular phylogenetic analyses of the genus

2019 ◽  
Vol 94 ◽  
Author(s):  
A. Maldonado ◽  
R.O. Simões ◽  
J. São Luiz ◽  
S.F. Costa-Neto ◽  
R.V. Vilela
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Amazon Rainforest ◽  
Ancestral State ◽  
Intermediate Hosts ◽  
The Status ◽  
Molecular Phylogenetic ◽  
History Of ◽  
A New Species

Abstract Nematodes of the genus Physaloptera are globally distributed and more than 100 species are known. Their life cycle involves insects, including beetles, cockroaches and crickets, as intermediate hosts. This study describes a new species of Physaloptera and reports molecular phylogenetic analyses to determine its relationships within the family Physalopteridae. Physaloptera amazonica n. sp. is described from the stomach of the caviomorph rodent Proechimys gardneri collected in the Amazon rainforest in the state of Acre, Brazil. The species is characterized by the male having the first and second pair of sessile papillae asymmetrically placed, lacking a median papilla-like protuberance between the third pairs of sessile papillae, differentiated by size and shape of the spicules, while females have four uterine branches. For both nuclear 18S rRNA and MT-CO1 gene-based phylogenies, we recovered Turgida sequences forming a clade nested within Physaloptera, thus making Physaloptera paraphyletic to the exclusion of Turgida, suggesting that the latter may have evolved from the former monodelphic ancestral state to a derived polydelphic state, or that some species of Physaloptera may belong to different genera. Relationships between most taxa within Physaloptera were poorly resolved in our phylogenies, producing multifurcations or a star phylogeny. The star-like pattern may be attributed to evolutionary processes where past simultaneous species diversification events took place. Physaloptera amazonica n. sp. formed an independent lineage, separately from the other species of Physaloptera, thus supporting the status of a new species. However, all molecular data suggested a closer relationship with other Neotropical species. In conclusion, we added a new species to this already largely diverse genus Physaloptera, bringing new insights to its phylogenetic relationships. Further analyses, adding more species and markers, should provide a better understanding of the evolutionary history of physalopterids.

scholarly journals Chloroplast phylogenomics and the dynamic evolution of Santalum (Santalaceae)

2021 ◽  
Author(s):  
Xiaojin Liu ◽  
Daping Xu ◽  
Zhou Hong ◽  
Ningnan Zhang ◽  
Zhiyi Cui
Keyword(s):  
Chloroplast Genome ◽  
Evolutionary Dynamics ◽  
Divergence Time ◽  
Major Type ◽  
Time Analysis ◽  
Chloroplast Genomes ◽  
Extant Species ◽  
History Of ◽  
Insight Into ◽  
Simple Sequence

Abstract Background Santalum (Santalaceae, sandalwood) is a hemiparasitic genus including approximately 15 extant species. It is known for its aromatic heartwood oil, which is used in incense and perfume. Demand for sandalwood-based products has led to drastic over-harvesting, and wild Santalum populations are now threatened. Knowledge of the phylogenetic relationships and genetic diversity will be critical for the conservation and proper management of this genus. Here, we sequenced the chloroplast genome of 11 Santalum species. The data were then used to investigate the chloroplast genome evolutionary dynamics and relationships and divergence time within Santalum and related species. Results The Santalum chloroplast genome contains the typical quadripartite structures, ranging from 143,291 to 144,263 bp. The chloroplast genome contains 124 genes. The whole set of ndh genes and the infA gene were found to lose their function. Between 17 and 31 SSRs were found in the Santalum chloroplast genome, and mononucleotide simple sequence repeats (SSRs) were the major type. The P-distance among the Santalum species was 0.0003 to 0.00828. Three mutation hotspot regions, 14 small inversions, and 460 indels events were discovered in the Santalum chloroplast genome. Our phylogenomic assessment provides improved resolution compared to past analyses. Our divergence time analysis shows that the crown age of Santalum was 8.46 Mya, the first divergence occurred around 6.97 Mya, and diversification was complete within approximately 1 Mya. Conclusions By sequencing the 12 chloroplast genomes of Santalum, we gain insight into the evolution of its chloroplast genomes. The chloroplast genome sequences had sufficient polymorphic information to elucidate the evolutionary history of Santalum.

scholarly journals The evolutionary history of Stomatopoda (Crustacea: Malacostraca) inferred from molecular data

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3844 ◽  
Author(s):  
Cara Van Der Wal ◽  
Shane T. Ahyong ◽  
Simon Y.W. Ho ◽  
Nathan Lo
Keyword(s):  
Phylogenetic Analyses ◽  
Sister Group ◽  
Molecular Data ◽  
Recent Common Ancestor ◽  
Ancestral State ◽  
Crown Group ◽  
Most Recent Common Ancestor ◽  
History Of ◽  
The Tropics ◽  
Age Constraints

The crustacean order Stomatopoda comprises seven superfamilies of mantis shrimps, found in coastal waters of the tropics and subtropics. These marine carnivores bear notable raptorial appendages for smashing or spearing prey. We investigated the evolutionary relationships among stomatopods using phylogenetic analyses of three mitochondrial and two nuclear markers. Our analyses recovered the superfamily Gonodactyloidea as polyphyletic, withHemisquillaas the sister group to all other extant stomatopods. A relaxed molecular clock, calibrated by seven fossil-based age constraints, was used to date the origin and major diversification events of stomatopods. Our estimates suggest that crown-group stomatopods (Unipeltata) diverged from their closest crustacean relatives about 340 Ma (95% CRI [401–313 Ma]). We found that the specialized smashing appendage arose after the spearing appendage ∼126 Ma (95% CRI [174–87 Ma]). Ancestral state reconstructions revealed that the most recent common ancestor of extant stomatopods had eyes with six midband rows of hexagonal ommatidia. Hexagonal ommatidia are interpreted as plesiomorphic in stomatopods, and this is consistent with the malacostracan ground-plan. Our study provides insight into the evolutionary timescale and systematics of Stomatopoda, although further work is required to resolve with confidence the phylogenetic relationships among its superfamilies.

scholarly journals RecPD: A Recombination-Aware Measure of Phylogenetic Diversity

2021 ◽  
Author(s):  
Cedoljub Bundalovic-Torma ◽  
Darrell Desveaux ◽  
David S Guttman
Keyword(s):  
Pseudomonas Syringae ◽  
Evolutionary History ◽  
Phylogenetic Diversity ◽  
Evolutionary Dynamics ◽  
Gene Families ◽  
Ancestral State ◽  
History Of ◽  
Preliminary Study ◽  
Potential Impact ◽  
Study Type

A critical step in studying biological features (e.g., genetic variants, gene families, metabolic capabilities, or taxa) underlying traits or outcomes of interest is assessing their diversity and distribution. Accurate assessments of these patterns are essential for linking features to traits or outcomes and understanding their functional impact. Consequently, it is of crucial importance that the metrics employed for quantifying feature diversity can perform robustly under any evolutionary scenario. However, the standard metrics used for quantifying and comparing the distribution of features, such as prevalence, phylogenetic diversity, and related approaches, either do not take into consideration evolutionary history, or assume strictly vertical patterns of inheritance. Consequently, these approaches cannot accurately assess diversity for features that have undergone recombination or horizontal transfer. To address this issue, we have devised RecPD, a novel recombination-aware phylogenetic-diversity metric for measuring the distribution and diversity of features under all evolutionary scenarios. RecPD utilizes ancestral-state reconstruction to map the presence / absence of features onto ancestral nodes in a species tree, and then identifies potential recombination events in the evolutionary history of the feature. We also derive a number of related metrics from RecPD that can be used to assess and quantify evolutionary dynamics and correlation of feature evolutionary histories. We used simulation studies to show that RecPD reliably identifies evolutionary histories under diverse recombination and loss scenarios. We then apply RecPD in a real-world scenario in a preliminary study type III effector protein families secreted by the plant pathogenic bacterium Pseudomonas syringae and demonstrate that prevalence is an inadequate metric that obscures the potential impact of recombination. We believe RecPD will have broad utility for revealing and quantifying complex evolutionary processes for features at any biological level.

scholarly journals Mesoamerica is a cradle and the Atlantic Forest is a museum of Neotropical butterfly diversity: insights from the evolution and biogeography of Brassolini (Lepidoptera: Nymphalidae)

2021 ◽  
Author(s):  
Pável Matos-Maraví ◽  
Niklas Wahlberg ◽  
André V L Freitas ◽  
Phil Devries ◽  
Alexandre Antonelli ◽  
...  
Keyword(s):  
Species Diversity ◽  
Environmental History ◽  
Atlantic Forest ◽  
Morphological Characters ◽  
Butterfly Species ◽  
Multispecies Coalescent ◽  
Extant Species ◽  
Speciation Rates ◽  
History Of ◽  
Stochastic Mapping

Abstract Regional species diversity is explained ultimately by speciation, extinction and dispersal. Here, we estimate dispersal and speciation rates of Neotropical butterflies to propose an explanation for the distribution and diversity of extant species. We focused on the tribe Brassolini (owl butterflies and allies), a Neotropical group that comprises 17 genera and 108 species, most of them endemic to rainforest biomes. We inferred a robust species tree using the multispecies coalescent framework and a dataset including molecular and morphological characters. This formed the basis for three changes in Brassolini classification: (1) Naropina syn. nov. is subsumed within Brassolina; (2) Aponarope syn. nov. is subsumed within Narope; and (3) Selenophanes orgetorix comb. nov. is reassigned from Catoblepia to Selenophanes. By applying biogeographical stochastic mapping, we found contrasting species diversification and dispersal dynamics across rainforest biomes, which might be explained, in part, by the geological and environmental history of each bioregion. Our results revealed a mosaic of biome-specific evolutionary histories within the Neotropics, where butterfly species have diversified rapidly (cradles: Mesoamerica), have accumulated gradually (museums: Atlantic Forest) or have diversified and accumulated alternately (Amazonia). Our study contributes evidence from a major butterfly lineage that the Neotropics are a museum and a cradle of species diversity.

scholarly journals Improvements in the fossil record may largely resolve the conflict between morphological and molecular estimates of mammal phylogeny

2018 ◽  
Author(s):  
Robin M. D. Beck ◽  
Charles Baillie
Keyword(s):  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Fossil Record ◽  
Morphological Character ◽  
Molecular Data ◽  
Morphological Data ◽  
Ancestral State ◽  
Case Scenario ◽  
State Reconstruction ◽  
Consensus View

AbstractMorphological phylogenies of mammals continue to show major conflicts with the robust molecular consensus view of their relationships. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships, particularly for fossil taxa for which, in most cases, molecular data is unlikely to ever become available. We tested this under a hypothetical “best case scenario” by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive molecular phylogeny of mammals, and then seeing what effect inclusion of these predicted ancestors had on unconstrained analyses of morphological data. We found that this resulted in topologies that are highly congruent with the molecular consensus, even when simulating the effect of incomplete fossilisation. Most strikingly, several analyses recovered monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record may be sufficient to largely reconcile morphological and molecular phylogenies of mammals, even with current morphological character sets.

The evolutionary history and molecular systematics of the Musteloidea

2018 ◽  
Author(s):  
Klaus-Peter Koepfli ◽  
Jerry W. Dragoo ◽  
Xiaoming Wang
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Molecular Data ◽  
Morphological Data ◽  
Species Boundaries ◽  
Extant Species ◽  
Taxonomic History ◽  
History Of ◽  
A New Species

This chapter provides a review of the evolutionary and taxonomic history of the Musteloidea, which is the most species-rich superfamily of the Carnivora, containing approximately 30% of the extant species in the order. An up-to-date summary of knowledge on the evolutionary and taxonomic history and phylogenetic relationships of the Mephitidae, Ailuridae, Procyonidae and Mustelidae is provided. Multilocus DNA sequences have made a large impact on the understanding of phylogenetic relationships among the Musteloidea. Molecular data have revealed distinct families (Ailuridae and Mephitidae) within the Musteloidea and have illuminated new relationships based on tempo and patterns of evolution within the Procyonidae. Morphological data in conjunction with molecular data have been used to elucidate species boundaries within certain musteloid genera and have led to the discovery of a new species. Research studies published during the last 30 years have enriched and transformed our understanding of the evolution of musteloid biodiversity.

Molecules, Morphology, Fossils and the Origination and Extinction Dynamics of Scleractinian Corals

2011 ◽  
Vol 17 ◽  
pp. 61-77
Author(s):  
Marcos S. Barbeitos
Keyword(s):  
Coral Reefs ◽  
Fossil Record ◽  
Molecular Phylogenetics ◽  
Evolutionary Dynamics ◽  
Scleractinian Corals ◽  
Future Research ◽  
Marine Biodiversity ◽  
Mass Extinctions ◽  
Extant Species ◽  
The Impact

The history of Scleractinian corals, richly documented by the fossil record, is one of complex dynamics linked to the dynamics of coral reefs themselves. In spite of all the waxing and waning of marine biodiversity throughout the post-Paleozoic, scleractinians have remained remarkably resilient as a lineage and have traversed two mass extinctions and repeated episodes of global change before becoming the chief builders of modern coral reefs. Understanding this history becomes all the more relevant in face of the current human driven coral reef biodiversity crisis. The advent of molecular phylogenetics has changed our perspective of those dynamics because it has uncovered pervasive morphological convergence in traditionally used taxonomic characters, revealing that the current classification is highly artificial. Taxonomy not only obscures important patterns, but also introduces artifacts into estimates of origination and extinction obtained directly from the fossil record. I present a brief review of the impact of molecular phylogenetics on the current understanding of coral evolution, with emphasis on the recently uncovered phyletic link between photosymbiotic, reef dwelling and azooxanthellate, deepwater coral biota. Then, I discuss the role of molecular-based techniques in a future research agenda of the evolutionary dynamics of the order. The greatest challenge for the future is the re-assessment of morphological characters from a cladistic perspective so that extinct and extant species are integrated in a unified phylogenetic framework, allowing rigorous testing of hypotheses on the fascinating biodiversity dynamics of the order.

scholarly journals Genetic analysis identifies the Ostrea stentina/aupouria/equestris oyster species complex in Hawai‘i, and resolves its lineage as the western Pacific O. equestris

2020 ◽  
Author(s):  
Jolene T. Sutton ◽  
Jared Nishimoto ◽  
Jeremy Schrader ◽  
Keinan Agonias ◽  
Nicole Antonio ◽  
...  
Keyword(s):  
Species Complex ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Western Pacific ◽  
Genetic Identification ◽  
Multiple Sources ◽  
Genomic Technologies ◽  
Extant Species ◽  
Commercial Species ◽  
History Of

AbstractBackgroundExtensive phenotypic plasticity in oysters makes them difficult to identify based on morphology alone, but their identities can be resolved by applying genetic and genomic technologies. In this study, we collected unknown oyster specimens from Hawaiian waters for genetic identification.MethodsWe sequenced two partial gene fragments, mitochondrial 16S ribosomal RNA (16S) and cytochrome c oxidase subunit I (COI), in 48 samples: 27 unidentified oyster specimens collected from two locations on O‘ahu, 13 known specimens from a hatchery in Hilo, Hawai‘i Island, and 8 known specimens from Hilo Bay, Hawai‘i Island.ResultsMolecular data identified approximately 85% of unknown samples as belonging to the Ostrea stentina/aupouria/equestris species complex, a globally distributed group with a history of uncertain and controversial taxonomic status. The remaining unknown samples were the native Dendostrea sandvichensis (G. B. Sowerby II, 1871), and nonnative Crassostrea gigas (Thunberg, 1793), the latter of which is a commercial species that was introduced to Hawai‘I from multiple sources during the 20th century. Phylogenetic analysis placed Hawai‘i Ostrea alongside samples from China, Japan, and New Zealand, grouping them within the recently classified western Pacific O. equestris. Until now, four extant species of true oyster have been documented in Hawai‘i. This study expands the known range of O. equestris by providing the first verification of its occurrence in Hawai‘i.

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