Arthropod Origins: Integrating Paleontological and Molecular Evidence

2020 ◽  
Vol 51 (1) ◽  
pp. 1-25
Author(s):  
Gregory D. Edgecombe
Keyword(s):  
Nervous System ◽  
Fossil Record ◽  
Morphological Characters ◽  
Molecular Data ◽  
Trace Fossils ◽  
Total Evidence ◽  
Molecular Evidence ◽  
Stem Group ◽  
Clock Analysis ◽  
Coherent Picture

Phylogenomics underpins a stable and mostly well-resolved hypothesis for the interrelationships of extant arthropods. Exceptionally preserved fossils are integrated into this framework by coding their morphological characters, as exemplified by total-evidence dating approaches that treat fossils as dated tips in analyses numerically dominated by molecular data. Cambrian fossils inform on the sequence of character acquisition in the arthropod stem group and in the stems of its main extant clades. The arthropod head problem incorporates unique appendage combinations and remains of the nervous system in fossils into a scheme mostly based on neuroanatomy and Hox expression domains for extant forms. Molecular estimates of arthropod origins in the Cryogenian or Ediacaran predate a coherent picture from the arthropod fossil record, which commences as trace fossils in the earliest Cambrian. Probabilistic morphological clock analysis of trilobites, which exemplify the earliest arthropod body fossils, supports a Cambrian origin, without the need to posit an unfossilized Ediacaran history.

Molecular evidence for the hybrid origin of Rosa lichiangensis (Rosaceae)

Phytotaxa ◽  
2015 ◽  
Vol 222 (3) ◽  
pp. 221 ◽  
Author(s):  
Zhangming Zhu ◽  
Xinfen Gao
Keyword(s):  
Significant Role ◽  
Single Copy ◽  
Morphological Characters ◽  
Molecular Data ◽  
Natural Hybridization ◽  
Hybrid Origin ◽  
Molecular Evidence ◽  
Nuclear Marker

Natural hybridization was assumed to play a significant role in the diversification of Rosa. Rosa lichiangensis was suspected to be of hybrid origin based on its intermediate morphological characters between R. soulieana and R. multiflora var. cathayensis. In this study, four chloroplast regions (ndhC-trnV, ndhF-rpl32, ndhJ-trnF, and psbJ-petA) and a single copy nuclear marker (GAPDH) were used to test the hybrid origin of R. lichiangensis. The results from molecular data supported the hybrid origin of R. lichiangensis and further identified R. soulieana as its maternal progenitor and R. multiflora var. cathayensis as the paternal progenitor.

scholarly journals Early fossil record of Euarthropoda and the Cambrian Explosion

2018 ◽  
Vol 115 (21) ◽  
pp. 5323-5331 ◽  
Author(s):  
Allison C. Daley ◽  
Jonathan B. Antcliffe ◽  
Harriet B. Drage ◽  
Stephen Pates
Keyword(s):  
Fossil Record ◽  
Trace Fossils ◽  
Cambrian Explosion ◽  
Burgess Shale ◽  
Crown Group ◽  
Total Group ◽  
Stem Lineage ◽  
Coherent Picture ◽  
Insight Into ◽  
Phosphate Deposits

Euarthropoda is one of the best-preserved fossil animal groups and has been the most diverse animal phylum for over 500 million years. Fossil Konservat-Lagerstätten, such as Burgess Shale-type deposits (BSTs), show the evolution of the euarthropod stem lineage during the Cambrian from 518 million years ago (Ma). The stem lineage includes nonbiomineralized groups, such as Radiodonta (e.g., Anomalocaris) that provide insight into the step-by-step construction of euarthropod morphology, including the exoskeleton, biramous limbs, segmentation, and cephalic structures. Trilobites are crown group euarthropods that appear in the fossil record at 521 Ma, before the stem lineage fossils, implying a ghost lineage that needs to be constrained. These constraints come from the trace fossil record, which show the first evidence for total group Euarthropoda (e.g., Cruziana, Rusophycus) at around 537 Ma. A deep Precambrian root to the euarthropod evolutionary lineage is disproven by a comparison of Ediacaran and Cambrian lagerstätten. BSTs from the latest Ediacaran Period (e.g., Miaohe biota, 550 Ma) are abundantly fossiliferous with algae but completely lack animals, which are also missing from other Ediacaran windows, such as phosphate deposits (e.g., Doushantuo, 560 Ma). This constrains the appearance of the euarthropod stem lineage to no older than 550 Ma. While each of the major types of fossil evidence (BSTs, trace fossils, and biomineralized preservation) have their limitations and are incomplete in different ways, when taken together they allow a coherent picture to emerge of the origin and subsequent radiation of total group Euarthropoda during the Cambrian.

MOLECULAR SYSTEMATICS OF RHODODENDRON SUBGENUS TSUTSUSI (RHODOREAE, ERICOIDEAE, ERICACEAE)

2009 ◽  
Vol 66 (1) ◽  
pp. 81-95 ◽  
Author(s):  
K. A. Kron ◽  
E. A. Powell
Keyword(s):  
Molecular Systematics ◽  
Molecular Data ◽  
Total Evidence ◽  
Molecular Evidence ◽  
Northeastern Asia ◽  
Evergreen Species ◽  
The Third

Rhododendron subgenus Tsutsusi (Rhodoreae, Ericoideae, Ericaceae), commonly known as evergreen azaleas, includes approximately 117 deciduous and evergreen species from Japan, China and northeastern Asia. Subgenus Tsutsusi has been divided into two sections, Brachycalyx and Tsutsusi, based on characteristics of the leaves, young twigs and corolla. We obtained molecular data from three chloroplast (matK, ndhF and trnS-trnG) and two nuclear (nrITS and the third intron of rpb2) regions for 30 species of Rhododendron subgenus Tsutsusi and five species of Menziesia. Parsimony, Bayesian and likelihood analyses based on total evidence were used to assess the monophyly of the sections within Rhododendron subgenus Tsutsusi and relationships among the species sampled. In particular, the placement of the problematic Rhododendron tashiroi was addressed. Results support Rhododendron tashiroi as a member of the Rhododendron section Brachycalyx clade. Molecular evidence also supports a clade within Rhododendron section Tsutsusi containing R. indicum, R. tsusiophyllum, R. tschonoskii and R. serpyllifolium, species which were not previously considered closely related.

Total evidence phylogeny of the North American harvestman family Stygnopsidae (Opiliones : Laniatores : Grassatores) reveals hidden diversity

2017 ◽  
Vol 31 (3) ◽  
pp. 317 ◽  
Author(s):  
Jesús A. Cruz-López ◽  
Oscar F. Francke
Keyword(s):  
Bayesian Inference ◽  
Phylogenetic Analyses ◽  
Mitochondrial Protein ◽  
Morphological Characters ◽  
Molecular Data ◽  
Total Evidence ◽  
The North ◽  
Protein Encoding ◽  
The Status ◽  
Taxonomic Changes

Systematic relationships among Laniatores have received considerable attention during the past few years. Many significant taxonomic changes have been proposed, particularly in the superfamily Gonyleptoidea. As part of this superfamily, the basalmost Stygnopsidae is the least known family. In order to propose the first total evidence phylogeny of the family, we produced four datasets: three molecular markers – partial nuclear 28S, mitochondrial ribosomal 16S, mitochondrial protein-encoding cytochrome c oxidase subunit I; and 72 morphological characters. With these data, we performed three different phylogenetic analyses: (1) Bayesian Inference with molecular data, and (2) Bayesian Inference and (3) Maximum Likelihood using combined data. Our results are congruent: a monophyletic Stygnopsidae subdivided into two major clades: Stygnopsinae and Karosinae, subfam. nov. The following genera are redefined: Stygnopsis, Hoplobunus and Serrobunus stat. rev. The following taxa are described: Iztlina venefica, gen. nov., sp. nov. and Tonalteca, gen. nov. Additionally, the following changes are proposed: Serrobunus queretarius (Šilhavý, 1974), comb. nov., Stygnopsis apoalensis (Goodnight & Goodnight, 1973), comb. nov., Stygnopsis mexicana (Roewer, 1915), comb. nov., Stygnopsis oaxacensis (Goodnight & Goodnight, 1973), comb. nov., and Tonalteca spinooculorum (Goodnight & Goodnight, 1973), comb. nov. We also discuss the status of the genera Isaeus stat. rev. and Mexotroglinus. Finally, we discuss the evolution of male genitalia and convergence of selected homoplastic diagnostic characters.

Molecular phylogenetic analyses and morphological variation point to taxonomic problems among four genera of parasitoid doryctine wasps (Hymenoptera : Braconidae)

2015 ◽  
Vol 29 (6) ◽  
pp. 591 ◽  
Author(s):  
Marco Gebiola ◽  
Antonio P. Garonna ◽  
Umberto Bernardo ◽  
Sergey A. Belokobylskij
Keyword(s):  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Molecular Evidence ◽  
A Posteriori ◽  
Morphological Examination ◽  
Ongoing Effort ◽  
The Status ◽  
Molecular Phylogenetic

Doryctinae (Hymenoptera : Braconidae) is a large and diverse subfamily of parasitic wasps that has received much attention recently, with new species and genera described and phylogenies based on morphological and/or molecular data that have improved higher-level classification and species delimitation. However, the status of several genera is still unresolved, if not controversial. Here we focus on two related groups of such genera, Dendrosoter Wesmael–Caenopachys Foerster and Ecphylus Foerster–Sycosoter Picard & Lichtenstein. We integrated morphological and molecular (COI and 28S–D2 genes) evidence to highlight, by phylogenetic analyses (maximum likelihood and Bayesian) and a posteriori morphological examination, previously overlooked variation, which is here illustrated and discussed. Monophyly of Dendrosoter and Caenopachys and the presence of synapomorphic morphological characters support synonymy of Caenopachys under Dendrosoter. Low genetic differentiation and high variability for putatively diagnostic morphological characters found in both C. hartigii (Ratzeburg) and C. caenopachoides (Ruschka) supports synonymy of D. caenopachoides under D. hartigii, syn. nov. Morphological and molecular evidence together also indicate independent generic status for Sycosoter, stat. rev., which is here resurrected. This work represents a further advancement in the framework of the ongoing effort to improve systematics and classification of the subfamily Doryctinae.

scholarly journals Synonymization of the male-based ant genus Phaulomyrma (Hymenoptera, Formicidae) with Leptanilla based upon Bayesian total-evidence phylogenetic inference

2020 ◽  
Author(s):  
Zachary H. Griebenow
Keyword(s):  
Sequence Data ◽  
Phylogenetic Inference ◽  
Morphological Characters ◽  
Molecular Data ◽  
Total Evidence ◽  
Morphological Data ◽  
Systematic Revision ◽  
Dna Sequence Data ◽  
Evidence Framework ◽  
Nuclear Loci

Abstract.Although molecular data have proven indispensable in confidently resolving the phylogeny of many clades across the tree of life, these data may be inaccessible for certain taxa. The resolution of taxonomy in the ant subfamily Leptanillinae is made problematic by the absence of DNA sequence data for leptanilline taxa that are known only from male specimens, including the monotypic genus Phaulomyrma Wheeler & Wheeler. Focusing upon the considerable diversity of undescribed male leptanilline morphospecies, the phylogeny of 35 putative morphospecies sampled from across the Leptanillinae, plus an outgroup, is inferred from 11 nuclear loci and 41 discrete male morphological characters using a Bayesian total-evidence framework, with Phaulomyrma represented by morphological data only. Based upon the results of this analysis Phaulomyrma is synonymized with Leptanilla Emery, and male-based diagnoses for Leptanilla that are grounded in phylogeny are provided, under both broad and narrow circumscriptions of that genus. This demonstrates the potential utility of a total-evidence approach in inferring the phylogeny of rare extant taxa for which molecular data are unavailable and begins a long-overdue systematic revision of the Leptanillinae that is focused on male material.

scholarly journals Using more than the oldest fossils: Dating Osmundaceae by three Bayesian clock approaches

2014 ◽  
Author(s):  
Guido Grimm ◽  
Pashalia Kapli ◽  
Benjamin Bomfleur ◽  
Stephen McLoughlin ◽  
Susanne S Renner
Keyword(s):  
Dna Sequences ◽  
Fossil Record ◽  
Morphological Characters ◽  
Genetic Distances ◽  
Total Evidence ◽  
Extinction Rates ◽  
Sister Clade ◽  
Extant Species ◽  
Dating Methods ◽  
Divergence Dates

A major concern in molecular clock dating is how to use information from the fossil record to calibrate genetic distances from DNA sequences. Here we apply three Bayesian dating methods that differ in how calibration is achieved--"node dating" (ND) in BEAST, "total evidence" (TE) dating in MrBayes, and the "fossilized birth-death" (FBD) in FDPPDiv--to infer divergence times in the Osmundaceae or royal ferns. Osmundaceae have 13 species in four genera, two mainly in the Northern Hemisphere and two in South Africa and Australasia; they are the sister clade to the remaining leptosporangiate ferns. Their fossil record consists of at least 150 species in ~17 genera and three extinct families. For ND, we used the five oldest fossils, while for TE and FBD dating, which do not require forcing fossils to nodes and thus can use more fossils, we included up to 36 rhizome and frond compression/impression fossils, which for TE dating were scored for 33 morphological characters. We also subsampled 10%, 25%, and 50% of the 36 fossils to assess model sensitivity. FBD-derived divergence dates were generally greater than ages inferred from ND dating; two of seven TE-derived ages agreed with FBD-obtained ages, the others were much younger or much older than ND or FBD ages. We favour the FBD-derived ages because they best match the Osmundales fossil record (including Triassic fossils not used in our study). Under the preferred model, the clade encompassing extant Osmundaceae (and many fossils) dates to the latest Palaeozoic to Early Triassic; divergences of the extant species occurred during the Neogene. Under the assumption of constant speciation and extinction rates, FBD yielded 0.0299 (0.0099--0.0549) and 0.0240 (0.0039--0.0495) for these rates, whereas neontological data yielded 0.0314 and 0.0339. However, FBD estimates of speciation and extinction are sensitive to violations in the assumption of continuous fossil sampling, therefore these estimates should be treated with caution.

Taxonomy and phylogeny of Nitella (Charophyceae, Characeae) from Brazil with emphasis on the midwest and southeast regions

Phytotaxa ◽  
2018 ◽  
Vol 356 (3) ◽  
pp. 181
Author(s):  
FABIO RENATO BORGES ◽  
ORLANDO NECCHI JR
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Molecular Evidence ◽  
Type Specimens ◽  
Brazilian Studies ◽  
Two Populations ◽  
Section Level

The genus Nitella is the most species-rich within the Charales. Brazilian studies on the genus are relatively scarce and consist of floristic surveys, lacking modern and more precise information. This investigation applied scanning electron microscopy to analyze the oospore wall and molecular data associated with traditional morphological characters to analyze forty-two populations of Nitella from the midwest and southeast regions of Brazil. Forty-two new sequences of rbcL, twelve of ITS1 and twenty-three of ITS2 were generated for the five species recognized in this study: Nitella acuminata A. Braun ex Wallman, Nitella axillaris A. Braun, Nitella elegans B. P. Pal, Nitella flagellifera J. Groves & G. O. Allen and Nitella microcarpa A. Braun.. Phylogenetic analyses of sequences of these three markers were congruent in that they grouped our species with others from different countries to form five clades. Our results on ultrastrucure of the oospore wall were consistent with previous studies for the same species from other regions of the world. The data reinforced the conclusion that the use of ornamentation of oospore wall may be extremely useful for the construction of a natural system for Characeae at section level. Molecular evidence, reinforced by morphological data, for the Brazilian material analyzed suggests that Nitella subglomerata A. Braun and Nitella gollmeriana A. Braun could be synonymys of Nitella acuminata; and Nitella axilliformis K. Imahori appears to be the same as Nitella axillaris. However, no formal proposition was made considering that type specimens were not analyzed and these observations were based on a relatively small number of samples strictly from Brazil. We showed that even among geographically distant populations, such as from other continents, of some Nitella species, the degree of identity among DNA sequences was high.

Morphological characters and molecular data reveal a new species of Rhodonia (Polyporales, Basidiomycota) from China

Phytotaxa ◽  
2017 ◽  
Vol 328 (2) ◽  
pp. 175
Author(s):  
YUAN YUAN ◽  
LU-LU SHEN
Keyword(s):  
New Species ◽  
Rna Polymerase Ii ◽  
Dna Sequences ◽  
Large Subunit ◽  
Morphological Characteristics ◽  
Northwest China ◽  
Morphological Characters ◽  
Molecular Data ◽  
Molecular Evidence ◽  
A New Species

A new polypore, Rhodonia tianshanensis, collected from West Tianshan Nature Reserve in Xinjiang Autonomous Region (northwest China), is described and illustrated based on morphological characteristics and molecular evidence. It is characterized by having resupinate basidiomata with an oblique tube layer, fusoid cystidioles in the hymenium, and cylindrical basidiospores. Based on multiple loci DNA sequences including the internal transcribed spacer (ITS), the large subunit (nLSU), and the second subunit of RNA polymerase II (RPB2) regions, our phylogeny strongly supported R. tianshanensis as a new species belonging to the genus Rhodonia.

Heteroradulum yunnanensis sp. nov. (Auriculariales, Basidiomycota) evidenced by morphological characters and phylogenetic analyses in China

Phytotaxa ◽  
2020 ◽  
Vol 437 (2) ◽  
pp. 51-59
Author(s):  
QIAN-XIN GUAN ◽  
CHAO-MAO LIU ◽  
TANG-JIE ZHAO ◽  
CHANG-LIN ZHAO
Keyword(s):  
Growth Habit ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Morphological Characters ◽  
Molecular Data ◽  
Fungal Species ◽  
Molecular Evidence ◽  
Monophyletic Lineage ◽  
Thin Walled ◽  
Inference Methods

A new wood-inhabiting fungal species, Heteroradulum yunnanensis, is proposed based on a combination of morphological features and molecular evidence. The species is characterized by an annual growth habit, resupinate basidiomata with odontoid hymenial surface (50–100 µm long), more or less pronounced yellow stains in older basidiomata, a monomitic hyphal system with thin-walled, clamped generative hyphae and two to three-celled basidia and cylindrical, hyaline, thin-walled, smooth, IKI–, CB– basidiospores measuring as 17–24 ×5–8 µm. Sequences of ITS and LSU nrRNA gene regions of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and bayesian inference methods. The phylogenetic analyses based on molecular data of ITS+nLSU sequences showed that Heteroradulum yunnanensis formed a monophyletic lineage with a strong support (100% BS, 100% BP, 1.00 BPP) and then grouped with H. adnatum.

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