Taxonomic review and phylogenetic inference elucidate the evolutionary history of Mesozoic Procercopidae, with new data from the Cretaceous Jehol Biota of NE China (Hemiptera, Cicadomorpha)

Many phylogenetic inference programs are available to infer evolutionary relationships among taxa using aligned sequences of characters, typically DNA or amino acids. These programs are often used to infer the evolutionary history of species. However, in most cases it is impossible to systematically verify the correctness of the tree returned by these programs, as the correct evolutionary history is generally unknown and unknowable. In addition, it is nearly impossible to verify whether any non-trivial tree is correct in accordance to the specification of the often complicated search and scoring algorithms. This difficulty is known as the oracle problem of software testing: there is no oracle that we can use to verify the correctness of the returned tree. This makes it very challenging to test the correctness of any phylogenetic inference programs. Here, we demonstrate how to apply a simple software testing technique, called Metamorphic Testing, to alleviate the oracle problem in testing phylogenetic inference programs. We have used both real and randomly generated test inputs to evaluate the effectiveness of metamorphic testing, and found that metamorphic testing can detect failures effectively in faulty phylogenetic inference programs with both types of test inputs.

Download Full-text

Hyperphalangy in a new sinemydid turtle from the Early Cretaceous Jehol Biota

PeerJ ◽

10.7717/peerj.5371 ◽

2018 ◽

Vol 6 ◽

pp. e5371 ◽

Cited By ~ 4

Author(s):

Shuai Shao ◽

Lan Li ◽

Yang Yang ◽

Chang-Fu Zhou

Keyword(s):

Early Cretaceous ◽

Evolutionary History ◽

Rare Condition ◽

Freshwater Turtle ◽

Aquatic Environments ◽

Jehol Biota ◽

The Family ◽

History Of ◽

Primitive Condition ◽

Phalangeal Formula

Hyperphalangy is a rare condition in extant aquatic turtles, and mainly limited to soft-shelled turtles. Here we report a new freshwater turtle,Jeholochelys lingyuanensisgen. et sp. nov. from the Early Cretaceous Jehol Biota of western Liaoning, China. This new turtle is characterized by a hyperphalangy condition with one additional phalanx in pedal digit V, rather than the primitive condition (phalangeal formula: 2-3-3-3-3) of crown turtles.J. lingyuanensisis recovered with other coexisting turtles in the family Sinemydidae in the phylogenetic analysis. This discovery further confirms that hyperphalangy occurred multiple times in the early evolutionary history of the crown turtles. Hyperphalangy is possibly a homoplasy inJeholochelysand the soft-shelled turtles to adapt to the aquatic environments.

Download Full-text

MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony

BMC Bioinformatics ◽

10.1186/s12859-020-03742-9 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Adam G. Diehl ◽

Alan P. Boyle

Keyword(s):

Evolutionary History ◽

Genomic Sequence ◽

Phylogenetic Inference ◽

Regulatory Sequence ◽

Ancestral Reconstruction ◽

Sequence Features ◽

Reconstruction Methods ◽

History Of ◽

Gain And Loss ◽

Species Specific

Abstract Background Comparative genomics studies are growing in number partly because of their unique ability to provide insight into shared and divergent biology between species. Of particular interest is the use of phylogenetic methods to infer the evolutionary history of cis-regulatory sequence features, which contribute strongly to phenotypic divergence and are frequently gained and lost in eutherian genomes. Understanding the mechanisms by which cis-regulatory element turnover generate emergent phenotypes is crucial to our understanding of adaptive evolution. Ancestral reconstruction methods can place species-specific cis-regulatory features in their evolutionary context, thus increasing our understanding of the process of regulatory sequence turnover. However, applying these methods to gain and loss of cis-regulatory features historically required complex workflows, preventing widespread adoption by the broad scientific community. Results MapGL simplifies phylogenetic inference of the evolutionary history of short genomic sequence features by combining the necessary steps into a single piece of software with a simple set of inputs and outputs. We show that MapGL can reliably disambiguate the mechanisms underlying differential regulatory sequence content across a broad range of phylogenetic topologies and evolutionary distances. Thus, MapGL provides the necessary context to evaluate how genomic sequence gain and loss contribute to species-specific divergence. Conclusions MapGL makes phylogenetic inference of species-specific sequence gain and loss easy for both expert and non-expert users, making it a powerful tool for gaining novel insights into genome evolution.

Download Full-text

A new phosphatized ophiuroid from the lower Triassic of Nevada and its position in the evolutionary history of the Ophiuroidea (Echinodermata)

Zootaxa ◽

10.11646/zootaxa.5071.3.4 ◽

2021 ◽

Vol 5071 (3) ◽

pp. 369-383

Author(s):

BEN THUY ◽

VIVIENNE MAXWELL ◽

SARA B. PRUSS

Keyword(s):

Fossil Record ◽

Evolutionary History ◽

Lower Triassic ◽

Phylogenetic Inference ◽

Phylogenetic Position ◽

Acid Extraction ◽

Early Triassic ◽

New Taxon ◽

History Of ◽

Bayesian Phylogenetic Inference

The Lower Triassic fossil record of brittle stars is relatively rich, yet most records published to date are based on poorly preserved or insufficiently known fossils. This hampers exhaustive morphological analyses, comparison with recent relatives or inclusion of Early Triassic ophiuroid taxa in phylogenetic estimates. Here, we describe a new ophiuroid from the Lower Triassic of Nevada, preserved as phosphatized skeletal parts and assigned to the new taxon Ophiosuperstes praeparvus gen. et sp. nov Maxwell, V. & Pruss. S.B. This unusual preservation of the fossils allowed for acid-extraction of an entire suite of dissociated skeletal parts, including lateral arm plates, ventral arm plates, vertebrae and various disk plates, thus unlocking sufficient morphological information to explore the phylogenetic position of the new taxon. Bayesian phylogenetic inference suggests a basalmost position of O. praeparvus within the Ophintegrida, sister to all other sampled members of that superorder. The existence of coeval but more derived ophiuroids suggests that O. praeparvus probably represents a member of a more ancient stem ophintegrid group persisting into the Early Triassic.

Download Full-text

The appearance and duration of the Jehol Biota: Constraint from SIMS U-Pb zircon dating for the Huajiying Formation in northern China

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1918272117 ◽

2020 ◽

Vol 117 (25) ◽

pp. 14299-14305 ◽

Cited By ~ 2

Author(s):

Saihong Yang ◽

Huaiyu He ◽

Fan Jin ◽

Fucheng Zhang ◽

Yuanbao Wu ◽

...

Keyword(s):

Evolutionary History ◽

Secondary Ion Mass Spectrometry ◽

Temporal Distribution ◽

Northern China ◽

Time Span ◽

Hebei Province ◽

Jehol Biota ◽

History Of ◽

Fossil Records ◽

Secondary Ion

The Lower Cretaceous Huajiying Formation of the Sichakou Basin in northern Hebei Province, northern China contains key vertebrate taxa of the early Jehol Biota, e.g.,Protopteryx fengningensis,Archaeornithura meemannae,Peipiaosteus fengningensis, andEoconfuciusornis zhengi. This formation arguably documents the second-oldest bird-bearing horizon, producing the oldest fossil records of the two major Mesozoic avian groups Enantiornithes and Ornithuromorpha. Hence, precisely determining the depositional ages of the Huajiying Formation would advance our understanding of the evolutionary history of the Jehol Biota. Here we present secondary ion mass spectrometry (SIMS) U-Pb zircon analysis results of eight interbedded tuff/tuffaceous sandstone samples from the Huajiying Formation. Our findings, combined with previous radiometric dates, suggest that the oldest enantiornithine and ornithuromorph birds in the Jehol Biota are ∼129−131 Ma, and that the Jehol Biota most likely first appeared at ∼135 Ma. This expands the biota’s temporal distribution from late Valanginian to middle Aptian with a time span of about 15 My.

Download Full-text

An unusual bird (Theropoda, Avialae) from the Early Cretaceous of Japan suggests complex evolutionary history of basal birds

Communications Biology ◽

10.1038/s42003-019-0639-4 ◽

2019 ◽

Vol 2 (1) ◽

Cited By ~ 2

Author(s):

Takuya Imai ◽

Yoichi Azuma ◽

Soichiro Kawabe ◽

Masateru Shibata ◽

Kazunori Miyata ◽

...

Keyword(s):

Early Cretaceous ◽

Evolutionary History ◽

Phylogenetic Analyses ◽

Eastern China ◽

First Record ◽

New Taxon ◽

Jehol Biota ◽

North Eastern ◽

History Of ◽

Complex Evolutionary History

AbstractThe Early Cretaceous basal birds were known largely from just two-dimensionally preserved specimens from north-eastern China (Jehol Biota), which has hindered our understanding of the early evolution of birds. Here, we present a three-dimensionally-preserved skeleton (FPDM-V-9769) of a basal bird from the Early Cretaceous of Fukui, central Japan. Unique features in the pygostyle and humerus allow the assignment of FPDM-V-9769 to a new taxon, Fukuipteryx prima. FPDM-V-9769 exhibits a set of features comparable to that of other basalmost birds including Archaeopteryx. Osteohistological analyses indicate that FPDM-V-9769 is subadult. Phylogenetic analyses resolve F. prima as a non-ornithothoracine avialan basal to Jeholornis and outgroup of the Pygostylia. This phylogenetic result may imply a complex evolutionary history of basal birds. To our knowledge, FPDM-V-9769 represents the first record of the Early Cretaceous non-ornithothoracine avialan outside of the Jehol Biota and increases our understanding of their diversity and distribution during the time.

Download Full-text

True hopper fossils (Fulgoromorpha and Cicadomorpha) in the Jurassic to Cretaceous of eastern Asia and their evolutionary implications

Geological Society London Special Publications ◽

10.1144/sp521-2021-18 ◽

2021 ◽

pp. SP521-2021-18

Author(s):

Jun Chen

Keyword(s):

Evolutionary History ◽

Systematic Position ◽

Eastern Asia ◽

Jehol Biota ◽

Late Mesozoic ◽

Early Diversification ◽

History Of ◽

Plant Feeders ◽

Fossil Data ◽

Very High

AbstractTrue hoppers, consisting of Fulgoromorpha and Cicadomorpha, are plant feeders with very high species-level diversity. A large amount of true hopper fossils have been reported from eastern Asia, especially from the Middle to Late Jurassic Yanliao Biota, the Early Cretaceous Jehol Biota and mid-Cretaceous Kachin amber in the last two decades. Herein, true hoppers from the Jurassic and Cretaceous of eastern Asia are reviewed, and combining palaeontological data from other regions of the world and recent advances of molecular studies, the evolutionary history of true hoppers in the mid-late Mesozoic is discussed. Permocicada beipiaoensis Wang, 1987 and Archijassus plurinervis Zhang, 1985 are here excluded from Prosboloidea and Archijassidae respectively. To the end of 2020, a total of 203 species with definite systematic position have been documented in the Jurassic and Cretaceous of eastern Asia (China, Myanmar, Siberia, Mongolia, Japan and Korea), and were attributed to 116 genera in 22 families and 7 superfamilies. Available fossil data suggest that true hopper components strongly changed in the Cretaceous: primitive groups reduced and went extinct successively, and the origin and/or early diversification of most lineages (family or subfamily level) occurred, likely owing to the displacement of host-plants in the angiosperm floristic revolution.

Download Full-text

Elaborating the role of reflection and individual differences in the study of folk-economic beliefs

Behavioral and Brain Sciences ◽

10.1017/s0140525x18000274 ◽

2018 ◽

Vol 41 ◽

Author(s):

Kevin Arceneaux

Keyword(s):

Decision Making ◽

Individual Differences ◽

Cognitive Processes ◽

Evolutionary History ◽

Behavioral Responses ◽

History Of ◽

Economic Beliefs

AbstractIntuitions guide decision-making, and looking to the evolutionary history of humans illuminates why some behavioral responses are more intuitive than others. Yet a place remains for cognitive processes to second-guess intuitive responses – that is, to be reflective – and individual differences abound in automatic, intuitive processing as well.

Download Full-text