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

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.

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The age of flowering plants is unknown

10.32942/osf.io/n4v6b ◽

2021 ◽

Author(s):

Hervé Sauquet ◽

Santiago Ramírez-Barahona ◽

Susana Magallón

Keyword(s):

Molecular Data ◽

Flowering Plants ◽

Molecular Dating ◽

Flowering Plant ◽

Recent Common Ancestor ◽

Crown Group ◽

Most Recent Common Ancestor ◽

Research Fields ◽

History Of ◽

Future Work

The origin of flowering plants (angiosperms) was one of the most transformative events in the history of our planet. Despite considerable interest from multiple research fields, numerous questions remain, including the age of the group as a whole. Recent studies have reported a perplexing range of estimates for the crown-group age of angiosperms, from ca. 140 Ma (Early Cretaceous) to 270 Ma (Permian). Both ends of the spectrum are now supported by both quantitative analyses of the fossil record and fossil-calibrated molecular dating analyses. Here, we first clarify and distinguish among the three ages of angiosperms: the age of their divergence with acrogymnosperms (stem age), the age(s) of emergence of their unique, distinctive features including flowers (morphological age), and the age of the most recent common ancestor of all their living species (crown age). We then demonstrate, based on recent studies, that fossil-calibrated molecular dating estimates of the crown-group age of angiosperms have little to do with either the amount of molecular data or the number of internal fossil calibrations included. Instead, we argue that this age is almost entirely conditioned by its own prior. Lastly, we discuss which future discoveries or novel types of analyses are most likely to bring more definitive answers. In the meantime, we propose that the age of angiosperms is best described as unknown (140–270 Ma) and that future work that depends on the time scale of flowering plant diversification be designed to integrate over this vexing uncertainty.

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Chromosomal dynamics in space and time: evolutionary history of Mycetophylax ants across past climatic changes in the Brazilian Atlantic coast

Scientific Reports ◽

10.1038/s41598-019-55135-5 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 3

Author(s):

Ricardo Micolino ◽

Maykon Passos Cristiano ◽

Natália Martins Travenzoli ◽

Denilce Meneses Lopes ◽

Danon Clemes Cardoso

Keyword(s):

Evolutionary History ◽

Chromosomal Rearrangements ◽

Atlantic Coast ◽

Ecological Impact ◽

Divergence Time ◽

Molecular Data ◽

Recent Common Ancestor ◽

Integrative Approach ◽

Most Recent Common Ancestor ◽

History Of

AbstractFungus-farming ants of the genus Mycetophylax exhibit intra and interspecific chromosome variability, which makes them suitable for testing hypotheses about possible chromosomal rearrangements that endure lineage diversification. We combined cytogenetic and molecular data from Mycetophylax populations from coastal environments to trace the evolutionary history of the clade in light of chromosomal changes under a historical and geographic context. Our cytogenetic analyses revealed chromosomal differences within and among species. M. morschi exhibited three distinct karyotypes and considerable variability in the localization of 45S rDNA clusters. The molecular phylogeny was congruent with our cytogenetic findings. Biogeographical and divergence time dating analyses estimated that the most recent common ancestor of Mycetophylax would have originated at about 30 Ma in an area including the Amazon and Southern Grasslands, and several dispersion and vicariance events may have occurred before the colonization of the Brazilian Atlantic coast. Diversification of the psammophilous Mycetophylax first took place in the Middle Miocene (ca. 18–10 Ma) in the South Atlantic coast, while “M. morschi” lineages diversified during the Pliocene-Pleistocene transition (ca. 3–2 Ma) through founder-event dispersal for the Northern coastal regions. Psammophilous Mycetophylax diversification fits into the major global climatic events that have had a direct impact on the changes in sea level as well as deep ecological impact throughout South America. We assume therefore that putative chromosomal rearrangements correlated with increased ecological stress during the past climatic transitions could have intensified and/or accompanied the divergence of the psammophilous Mycetophylax. We further reiterate that “M. morschi” comprises a complex of at least three well-defined lineages, and we emphasize the role of this integrative approach for the identification and delimitation of evolutionary lineages.

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

Journal of Helminthology ◽

10.1017/s0022149x19000610 ◽

2019 ◽

Vol 94 ◽

Cited By ~ 1

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.

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Early-diverging bumblebees from across the roof of the world: the high-mountain subgenus Mendacibombus revised from species’ gene coalescents and morphology (Hymenoptera, Apidae)

Zootaxa ◽

10.11646/zootaxa.4204.1.1 ◽

2016 ◽

Vol 4204 (1) ◽

pp. 1 ◽

Cited By ~ 14

Author(s):

PAUL H. WILLIAMS ◽

JIAXING HUANG ◽

PIERRE RASMONT ◽

JIANDONG AN

Keyword(s):

Incomplete Lineage Sorting ◽

Sister Group ◽

Process Models ◽

Coi Gene ◽

Colour Pattern ◽

Recent Common Ancestor ◽

High Mountain ◽

Crown Group ◽

Most Recent Common Ancestor ◽

Colour Patterns

The bumblebees of the subgenus Mendacibombus of the genus Bombus are the sister group to all other extant bumblebees and are unusual among bees for specialising in some of the highest elevation habitats with entomophilous plants on Earth. Most named taxa in this group (24 available names, from a total of 49 published names) were described originally from small differences in the colour pattern of the hair, many as parts (e.g. subspecies) of just one species. Subsequent taxonomic treatments recognised multiple species, but have described very few morphological characters, most of which are in the male genitalia. We examined 4413 specimens representing all of the named taxa from throughout the group’s global range to describe variation in DNA, in skeletal morphology, and in the colour patterns of the hair. Using Bayesian inference of the phylogeny from an evolutionary model for the fast-evolving COI gene, and fitting either general mixed Yule/coalescent models or Poisson tree process models, we identify COI gene coalescents, which are expected to characterise species as evolutionarily independent lineages. None of the conditions most likely to compromise this interpretation (biased sampling, paralogy, introgression, heteroplasmy, incomplete lineage sorting) appears to be a substantial problem in this case. In an integrative analysis, we show that colour patterns are often variable within these groups and do not diagnose the same groups as we recognise from genes; in contrast, the groups recognised from gene coalescents can also be diagnosed from differences we identify in morphology. We infer that the 12 groups with coalescents in the COI gene that are corroborated by morphology constitute species, whereas many of these species are polymorphic in colour pattern. Lectotypes are designated for 15 taxa in order to reduce uncertainty in the identity and application of the names. We provide new morphological keys and distribution maps for the species. Then we use four genes (fast-evolving mitochondrial COI and 16S; and slower nuclear PEPCK and opsin) to obtain an absolute chronogram of phylogenetic relationships among the species. From published estimates that the most recent common ancestor of the subgenus Mendacibombus diverged from the other bumblebees at the beginning of the Oligocene, our results support the crown group of Mendacibombus as having diversified in the late Miocene, events that both appear to have been associated with periods of climate cooling. Relative conservatism in the alpine/subalpine climate niche of Mendacibombus, as compared with the much more diversified climate niches in the sister group of all other bumblebees, may have contributed to constraining the number of Mendacibombus species to just one twentieth of the total number of extant bumblebee species.

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Phylogenetic relationships, origin and historical biogeography of the genus Sprattus (Clupeiformes: Clupeidae)

PeerJ ◽

10.7717/peerj.11737 ◽

2021 ◽

Vol 9 ◽

pp. e11737

Author(s):

Cristian B. Canales-Aguirre ◽

Peter A. Ritchie ◽

Sebastián Hernández ◽

Victoria Herrera-Yañez ◽

Sandra Ferrada Fuentes ◽

...

Keyword(s):

Southern Hemisphere ◽

Northern Hemisphere ◽

Dna Sequences ◽

Phylogenetic Analyses ◽

Historical Biogeography ◽

Ancestral Population ◽

Recent Common Ancestor ◽

Most Recent Common Ancestor ◽

The Tropics ◽

Two Populations

The genus Sprattus comprises five species of marine pelagic fishes distributed worldwide in antitropical, temperate waters. Their distribution suggests an ancient origin during a cold period of the earth’s history. In this study, we evaluated this hypothesis and corroborated the non-monophyly of the genus Sprattus, using a phylogenetic approach based on DNA sequences of five mitochondrial genome regions. Sprattus sprattus is more closely related to members of the genus Clupea than to other Sprattus species. We also investigated the historical biogeography of the genus, with the phylogenetic tree showing two well-supported clades corresponding to the species distribution in each hemisphere. Time-calibrated phylogenetic analyses showed that an ancient divergence between Northern and Southern Hemispheres occurred at 55.8 MYBP, followed by a diversification in the Oligocene epoch in the Northern Hemisphere clade (33.8 MYBP) and a more recent diversification in the Southern Hemisphere clade (34.2 MYBP). Historical biogeography analyses indicated that the most recent common ancestor (MRCA) likely inhabited the Atlantic Ocean in the Southern Hemisphere. These results suggest that the ancestral population of the MRCA diverged in two populations, one was dispersed to the Northern Hemisphere and the other across the Southern Hemisphere. Given that the Eocene was the warmest epoch since the Paleogene, the ancestral populations would have crossed the tropics through deeper cooler waters, as proposed by the isothermal submergence hypothesis. The non-monophyly confirmed for the genus Sprattus indicates that its systematics should be re-evaluated.

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Paleogenomics illuminates the evolutionary history of the extinct Holocene “horned” crocodile of Madagascar, Voay robustus

Communications Biology ◽

10.1038/s42003-021-02017-0 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

E. Hekkala ◽

J. Gatesy ◽

A. Narechania ◽

R. Meredith ◽

M. Russello ◽

...

Keyword(s):

Ancient Dna ◽

Evolutionary History ◽

Phylogenetic Analyses ◽

Sister Group ◽

Molecular Data ◽

Sister Group Relationship ◽

Molecular Fossil ◽

Close Relationship ◽

History Of ◽

Competing Hypotheses

AbstractAncient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions. In particular, molecular data from extinct Holocene island faunas have revealed surprising biogeographic scenarios. Here, we recovered partial mitochondrial (mt) genomes for 1300–1400 year old specimens (n = 2) of the extinct “horned” crocodile, Voay robustus, collected from Holocene deposits in southwestern Madagascar. Phylogenetic analyses of partial mt genomes and tip-dated timetrees based on molecular, fossil, and stratigraphic data favor a sister group relationship between Voay and Crocodylus (true crocodiles). These well supported trees conflict with recent morphological systematic work that has consistently placed Voay within Osteolaeminae (dwarf crocodiles and kin) and provide evidence for likely homoplasy in crocodylian cranial anatomy and snout shape. The close relationship between Voay and Crocodylus lends additional context for understanding the biogeographic origins of these genera and refines competing hypotheses for the recent extinction of Voay from Madagascar.

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Corrigendum to: Phylogeny and biogeography of the ant subfamily Myrmeciinae (Hymenoptera : Formicidae)

Invertebrate Systematics ◽

10.1071/is02046_co ◽

2003 ◽

Vol 17 (4) ◽

pp. 605 ◽

Cited By ~ 1

Author(s):

Philip S. Ward ◽

Seán G. Brady

Keyword(s):

Sequence Data ◽

Strong Support ◽

Sister Group ◽

Molecular Data ◽

Morphological Data ◽

Recent Common Ancestor ◽

Bootstrap Support ◽

Data Set ◽

Molecular Sequence Data ◽

Most Recent Common Ancestor

We investigated phylogenetic relationships among the 'primitive' Australian ant genera Myrmecia and Nothomyrmecia (stat. rev.) and the Baltic amber fossil genus Prionomyrmex, using a combination of morphological and molecular data. Outgroups for the analysis included representatives from a variety of potential sister-groups, including five extant subfamilies of ants and one extinct group (Sphecomyrminae). Parsimony analysis of the morphological data provides strong support (~95% bootstrap proportions) for the monophyly of (1) genus Myrmecia, (2) genus Prionomyrmex, and (3) a clade containing those two genera plus Nothomyrmecia. A group comprising Nothomyrmecia and Prionomyrmex is also upheld (85% bootstrap support). Molecular sequence data (~2200 base pairs from the 18S and 28S ribosomal RNA genes) corroborate these findings for extant taxa, with Myrmecia and Nothomyrmecia appearing as sister-groups with ~100% bootstrap support under parsimony, neighbour-joining and maximum-likelihood analyses. Neither the molecular nor the morphological data set allows us to identify unambiguously the sister-group of (Myrmecia + (Nothomyrmecia + Prionomyrmex)). Rather, Myrmecia and relatives are part of an unresolved polytomy that encompasses most of the ant subfamilies. Taken as a whole, our results support the contention that many of the major lineages of ants – including a clade that later came to contain Myrmecia, Nothomyrmecia and Prionomyrmex – arose at around the same time during a bout of diversification in the middle or late Cretaceous. On the basis of Bayesian dating analysis, the estimated age of the most recent common ancestor of Myrmecia and Nothomyrmecia is 74 million years (95% confidence limits, 53–101�million years), a result consistent with the origin of the myrmeciine stem lineage in the Cretaceous. The ant subfamily Myrmeciinae is redefined to contain two tribes, Myrmeciini (genus Myrmecia) and Prionomyrmecini (Nothomyrmecia and Prionomyrmex). Phylogenetic analysis of the enigmatic Argentine fossils Ameghinoia and Polanskiella demonstrates that they are also members of the Myrmeciinae, probably more closely related to Prionomyrmecini than to Myrmeciini. Thus, the myrmeciine ants appear to be a formerly widespread group that retained many ancestral formicid characteristics and that became extinct everywhere except in the Australian region.

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Discovery of a glowing millipede in California and the gradual evolution of bioluminescence in Diplopoda

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1500014112 ◽

2015 ◽

Vol 112 (20) ◽

pp. 6419-6424 ◽

Cited By ~ 14

Author(s):

Paul E. Marek ◽

Wendy Moore

Keyword(s):

Molecular Phylogenetics ◽

Light Emission ◽

Sister Group ◽

High Elevation ◽

Recent Common Ancestor ◽

Crown Group ◽

Most Recent Common Ancestor ◽

Gradual Evolution ◽

Directional Change ◽

Repeated Evolution

The rediscovery of the Californian millipede Xystocheir bistipita surprisingly reveals that the species is bioluminescent. Using molecular phylogenetics, we show that X. bistipita is the evolutionary sister group of Motyxia, the only genus of New World bioluminescent millipedes. We demonstrate that bioluminescence originated in the group’s most recent common ancestor and evolved by gradual, directional change through diversification. Because bioluminescence in Motyxia has been experimentally demonstrated to be aposematic, forewarning of the animal’s cyanide-based toxins, these results are contrary to aposematic theory and empirical evidence that a warning pattern cannot evolve gradually in unpalatable prey. However, gradual evolution of a warning pattern is plausible if faint light emission served another function and was co-opted as an aposematic signal later in the diversification of the genus. Luminescence in Motyxia stem-group taxa may have initially evolved to cope with reactive oxygen stress triggered by a hot, dry environment and was repurposed for aposematism by high-elevation crown-group taxa colonizing new habitats with varying levels of predation. The discovery of bioluminescence in X. bistipita and its pivotal phylogenetic location provides insight into the independent and repeated evolution of bioluminescence across the tree of life.

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Origin and evolution of papillomavirus (onco)genes and genomes

10.1101/428912 ◽

2018 ◽

Cited By ~ 1

Author(s):

Anouk Willemsen ◽

Ignacio G. Bravo

Keyword(s):

Common Ancestor ◽

Current Knowledge ◽

Phylogenetic Analyses ◽

Genotypic Diversity ◽

Recent Common Ancestor ◽

Origin And Evolution ◽

Most Recent Common Ancestor ◽

History Of ◽

E6 And E7 ◽

E7 Proteins

ABSTRACTPapillomaviruses (PVs) are ancient viruses infecting vertebrates, from fish to mammals. Although the genomes of PVs are small and show conserved synteny, PVs display large genotypic diversity and ample variation in the phenotypic presentation of the infection. Most PVs genomes contain two small early genes E6 and E7. In a bunch of closely related human PVs, the E6 and E7 proteins provide the viruses with oncogenic potential.The recent discoveries of PVs without E6 and E7 in different fish species place a new root on the PV tree, and suggest that the ancestral PV consisted of the minimal PV backbone E1-E2-L2-L1.Bayesian phylogenetic analyses date the most recent common ancestor of the PV backbone to 424 million years ago (Ma). Common ancestry tests on extant E6 and E7 genes indicate that they share respectively a common ancestor dating back to at least 184 Ma. In AlphaPVs infecting primates, the appearance of the E5 oncogene 53-58 Ma concurred with i) a significant increase in substitution rate, ii) a basal radiation, and iii) key gain of functions in E6 and E7. This series of events was instrumental to build the extant phenotype of oncogenic human PVs.Our results assemble the current knowledge on PV diversity and present an ancient evolutionary timeline punctuated by evolutionary innovations in the history of this successful viral family.

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Phylogeny and biogeography of the ant subfamily Myrmeciinae (Hymenoptera : Formicidae)

Invertebrate Systematics ◽

10.1071/is02046 ◽

2003 ◽

Vol 17 (3) ◽

pp. 361 ◽

Cited By ~ 47

Author(s):

Philip S. Ward ◽

Seán G. Brady

Keyword(s):

Sequence Data ◽

Strong Support ◽

Sister Group ◽

Molecular Data ◽

Morphological Data ◽

Recent Common Ancestor ◽

Bootstrap Support ◽

Data Set ◽

Molecular Sequence Data ◽

Most Recent Common Ancestor

We investigated phylogenetic relationships among the 'primitive' Australian ant genera Myrmecia and Nothomyrmecia (stat. rev.) and the Baltic amber fossil genus Prionomyrmex, using a combination of morphological and molecular data. Outgroups for the analysis included representatives from a variety of potential sister-groups, including five extant subfamilies of ants and one extinct group (Sphecomyrminae). Parsimony analysis of the morphological data provides strong support (~95% bootstrap proportions) for the monophyly of (1) genus Myrmecia, (2) genus Prionomyrmex, and (3) a clade containing those two genera plus Nothomyrmecia. A group comprising Nothomyrmecia and Prionomyrmex is also upheld (85% bootstrap support). Molecular sequence data (~2200 base pairs from the 18S and 28S ribosomal RNA genes) corroborate these findings for extant taxa, with Myrmecia and Nothomyrmecia appearing as sister-groups with ~100% bootstrap support under parsimony, neighbour-joining and maximum-likelihood analyses. Neither the molecular nor the morphological data set allows us to identify unambiguously the sister-group of (Myrmecia + (Nothomyrmecia + Prionomyrmex)). Rather, Myrmecia and relatives are part of an unresolved polytomy that encompasses most of the ant subfamilies. Taken as a whole, our results support the contention that many of the major lineages of ants – including a clade that later came to contain Myrmecia, Nothomyrmecia and Prionomyrmex – arose at around the same time during a bout of diversification in the middle or late Cretaceous. On the basis of Bayesian dating analysis, the estimated age of the most recent common ancestor of Myrmecia and Nothomyrmecia is 74 million years (95% confidence limits, 53–101million years), a result consistent with the origin of the myrmeciine stem lineage in the Cretaceous. The ant subfamily Myrmeciinae is redefined to contain two tribes, Myrmeciini (genus Myrmecia) and Prionomyrmecini (Nothomyrmecia and Prionomyrmex). Phylogenetic analysis of the enigmatic Argentine fossils Ameghinoia and Polanskiella demonstrates that they are also members of the Myrmeciinae, probably more closely related to Prionomyrmecini than to Myrmeciini. Thus, the myrmeciine ants appear to be a formerly widespread group that retained many ancestral formicid characteristics and that became extinct everywhere except in the Australian region.

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