Firefly bioluminescence outshines aerial predators

Bioluminescence is found across life and has many functions. Yet we understand very little about its timing and origins, particularly as a predator avoidance strategy. Understanding the timing between bioluminescence and predator origins has yet to be examined and can help elucidate the evolution of the ecologically important signal aposematism. Using the most prevalent bioluminescent group, fireflies, where bioluminescence primarily functions as aposematic and sexual signals, the timing for the origins of both potential predators of fireflies and bioluminescence is explored. Divergence time estimations were performed using a genomic-scale phylogenetic reconstruction Lampyridae, and multiple fossil calibration points, allowing for a robust estimate for the origin of beetle bioluminescence as both a terrestrial and aerial signal. Our results recover the origins of terrestrial beetle bioluminescence at 141 mya and aerial bioluminescence at 133 mya. These ages predate the origins of all known extant aerial predators (i.e., bats and birds) and support the much older terrestrial predators (frogs, ground beetles, lizards, snakes, and hunting spiders) as the most likely drivers of bioluminescence in beetles.

Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes)

Shorebirds (Charadriiformes) are a globally distributed clade of modern birds and, due to their ecological and morphological disparity, a frequent subject of comparative studies. While molecular phylogenies have been instrumental to resolving the suprafamilial backbone of the charadriiform tree, several higher-level relationships, including the monophyly of plovers (Charadriidae) and the phylogenetic positions of several monotypic families, have remained unclear. The timescale of shorebird evolution also remains uncertain as a result of extensive disagreements among the published divergence dating studies, stemming largely from different choices of fossil calibrations. Here, we present the most comprehensive non-supertree phylogeny of shorebirds to date, based on a total-evidence dataset comprising 336 ingroup taxa (89\% of all extant species), 24 loci (15 mitochondrial and 9 nuclear), and 69 morphological characters. Using this phylogeny, we clarify the charadriiform evolutionary timeline by conducting a node-dating analysis based on a subset of 8 loci tested to be clock-like and 16 carefully selected, updated, and vetted fossil calibrations. Our concatenated, species-tree, and total-evidence analyses consistently support plover monophyly and are generally congruent with the topologies of previous studies, suggesting that the higher-level relationships among shorebirds are largely settled. However, several localized conflicts highlight areas of persistent uncertainty within the gulls (Laridae), true auks (Alcinae), and sandpipers (Scolopacidae). At shallower levels, our phylogenies reveal instances of genus-level nonmonophyly that suggest changes to currently accepted taxonomies. Our node-dating analyses consistently support a mid-Paleocene origin for the Charadriiformes and an early diversification for most major subclades. However, age estimates for more recent divergences vary between different relaxed clock models, and we demonstrate that this variation can affect phylogeny-based macroevolutionary studies. Our findings demonstrate the impact of fossil calibration choice on the resulting divergence time estimates, and the sensitivity of diversification rate analyses to the modeling assumptions made in time tree inference.

Geologically calibrated mammalian tree and the corresponding global events, including birth of human

The robust timetree could be constructed using a calibration function of BEAST v1. X released in 2018 simply by applying times of the most recent (= the latest) common ancestors (tMRCAs) for specific monophyletic species groups (clades). The present research is probably the first trial to fully use the calibration function in BEAST X. The specific node age (child tMRCA) in BEAST X = “minimum age” in conventional MCMCTree, but the “maximum age” in MCMCTree can be equivalent to, e.g., the parent node age (parent tMRCA) in BEAST X. We applied 19 mammalian fossil calibration ages considering Benton et al. (2015; solely their minimum ages), including those of fossil Gorilla and Pan + one geologic event calibration age for otters (= Quaternary isolation time of the Ryukyu islands and start of vicariant speciation), and we estimated our targeted splitting age of Homo and Pan at 5.69 Ma (calibration dates by Benton et al., 2015 were incorrect). After the initial rifting at 120 Ma, the Atlantic Ocean spread over 500 km on Chron 34 (84 Ma), and Afrotheria (Africa) and Xenarthra (South America) started vicariant speciation at this time (~ 70 Ma), reflecting the progressed continental isolation. Ordinal-level differentiations started just after the K-Pg boundary (66.0 Ma), and this timing reconfirmed that mammalian radiation occurred by rapidly filling the niches left vacant by the non-avian dinosaurs. In addition, we made a base substitution rate vs age diagram using the BEAST X function and showed that the rate exponentially increased and accelerated toward the Holocene, other than having the 55 Ma mild peak reflecting the post K-Pg mammalian explosion. The increased rate might have consequently increased the biodiversity, and extensive adaptive radiation might have ultimately birthed Homo sapiens. The basic factor of radiation might be the generation and spreading of C4 grasses since 20 Ma, which has been linked to increasing carbon fixation, decreasing atmospheric CO2 concentrations, cooling Earth, and triggering the Quaternary (2.58 Ma ~) glacier-inter glacier cycle and severe climatic change. Note that Perissodactyla and Cetartiodactyla (Laurasiatheria) feed on C4 grasses (savanna), and Carnivora (also Laurasiatheria) is the predator, also suggesting coevolutions since 20 Ma.

Large-scale phylogenomic analyses reveal the monophyly of bryophytes and Neoproterozoic origin of land plants

The relationships among the four major embryophyte lineages (mosses, liverworts, hornworts, vascular plants) and the timing of the origin of land plants are enigmatic problems in plant evolution. Here, we resolve the monophyly of bryophytes by improving taxon sampling of hornworts and eliminating the effect of synonymous substitutions. We then estimate the divergence time of crown embryophytes based on three fossil calibration strategies, and reveal that maximum calibration constraints have a major effect on estimating the time of origin of land plants. Moreover, comparison of priors and posteriors provides a guide for evaluating the optimal calibration strategy. By considering the reliability of fossil calibrations and the influences of molecular data, we estimate that land plants originated in the Precambrian (980 − 682 Ma), much older than widely recognized. Our study highlights the important contribution of molecular data when faced with contentious fossil evidence, and that fossil calibrations used in estimating the timescale of plant evolution require critical scrutiny.

Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes

The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversification of members of the order are still a matter of debate. Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora. We assembled 51 new mitogenomes from 13 families, and aligned them with available mitogenomes by selecting only those showing more than 1% of nucleotide divergence and excluding those suspected to be of low-quality or from misidentified taxa. Our final alignment included 220 taxa representing 2,442 mitogenomes. Our analyses led to a robust resolution of suprafamilial and intrafamilial relationships. We identified 21 fossil calibration points to estimate a molecular timescale for carnivorans. According to our divergence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloidea/Pinnipedia) diverged from each other during the Eocene, while all major groups of Feliformia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial divergences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene.

Post-Triassic Spermatophyta Timetree Adding the Quaternary Radiated Asarum Wild Gingers

BackgroundAngiospermae radiation was known as the mid-Cretaceous event, but adaptive radiation of Asarum is also expected in the Quaternary. In order to know such the Angiospermae evolutionary history through the time, we constructed a whole Spermatophyta timetree employing BEAST v1. X associated with robust fossil calibration function.ResultsWe successfully and precisely dated the Spermatophyta phylogeny, and the Angiospermae topology was concordant to the APG system. Using another function of BEAST, we discovered the exponential increase in base substitution rate in recent geologic time, and another rise of rate at the mid-Cretaceous time. These increasing events correspond to the Quaternary and mid-Cretaceous Angiospermae radiations.ConclusionsA probable cause of the recently increasing rate and the consequent radiation was ultimately generation of C4 grasses, reduction of atomospheric CO2, and the start of the Quaternary glacial period. Mid-Cretaceous event was explained by co-radiation with insect beetles as the food plant.

Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes

The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversifications are still a matter of debate.Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora. We assembled 51 new mitogenomes from 13 families, and aligned them with available mitogenomes by selecting only those showing more than 1% of nucleotide divergence and excluding those suspected to be of low-quality or from misidentified taxa. Our final alignment included 220 taxa representing 2,442 mitogenomes. Our analyses led to a robust resolution of suprafamilial and intrafamilial relationships. We identified 22 fossil calibration points to estimate a molecular timescale for carnivorans. According to our divergence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloidea/Pinnipedia) diverged from each other during the Eocene, while all major groups of Feliformia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial divergences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene.

Aenigmachannidae, a new family of snakehead fishes (Teleostei: Channoidei) from subterranean waters of South India

Pronounced organism-wide morphological stasis in evolution has resulted in taxa with unusually high numbers of primitive characters. These ‘living fossils’ hold a prominent role for our understanding of the diversification of the group in question. Here we provide the first detailed osteological analysis of Aenigmachanna gollum based on high-resolution nano-CT scans and one cleared and stained specimen of this recently described snakehead fish from subterranean waters of Kerala in South India. In addition to a number of derived and unique features, Aenigmachanna has several characters that exhibit putatively primitive conditions not encountered in the family Channidae. Our morphological analysis provides evidence for the phylogenetic position of Aenigmachanna as the sister group to Channidae. Molecular analyses further emphasize the uniqueness of Aenigmachanna and indicate that it is a separate lineage of snakeheads, estimated to have split from its sister group at least 34 or 109 million years ago depending on the fossil calibration employed. This may indicate that Aenigmachanna is a Gondwanan lineage, which has survived break-up of the supercontinent, with India separating from Africa at around 120 mya. The surprising morphological disparity of Aenigmachanna from members of the Channidae lead us to erect a new family of snakehead fishes, Aenigmachannidae, sister group to Channidae, to accommodate these unique snakehead fishes.

The Biogeography of Dromiciops in Southern South America: middle Miocene transgressions, speciation and associations with Nothofagus

AimSeveral geological events affecting Southern South America during the middle Miocene climatic optimum acted as important drivers of diversification to the biota. This is the case of Microbiotheria, for which Dromiciops is considered the sole surviving lineage, the sister group of Eomarsupialia (Australian marsupials). Three main Dromiciops genetic lineages are known, whose divergence was initially attributed to recent Pleistocene glaciations. Using fossil-calibrated dating on nuclear and mitochondrial genes, here we reevaluate this hypothesis and report an older (Miocenic) biogeographic history for the genus.LocationSouthern South America.MethodsPhylogenetic reconstruction using sequences from two mitochondrial DNA and four nuclear DNA genes in 159 specimens, from 31 sites across Chile and Argentina. Divergence time estimation using fossil calibration.ResultsOur phylogenetic analysis resolved four well supported clades with discrete geographic distributions. The oldest and most differentiated clade corresponds to that of the northern distribution (35.2°S to 39.3°S), which would be a different species (D. bozinovici, sensu D’elia et al. 2016). According to our estimations, this species shared a common ancestor with D. gliroides (southern clades) about 13 million years ago (95% CI: 6.4-25.3). The southern clades (39.6°S to 42.0°S), showed a divergence time ranging from 9.57 to 6.5 Mya. Strong genetic structure was detected from north to south but not across the Andes, or between Chiloé island/ mainland. Demographic equilibrium is inferred to the northern clade, and recent demographic expansions was detected in the central and southern clades.Main conclusionsThe whole diversification of Dromiciops occurred within the Miocene, being the Middle Miocene transgression (MMT), the massive marine flooding that covered several lowlands of the western face of los Andes between 38-48° S, the most likely diversifying force. This was the result of an increase in global sea levels due to the Miocene climatic optimum, which shaped the biogeographic origin of several species, including Nothofagus forests, the habitat main of Dromiciops.

Phylogenomics of Piranhas and Pacus (Serrasalmidae) Uncovers How Dietary Convergence and Parallelism Obfuscate Traditional Morphological Taxonomy

The Amazon and neighboring South American river basins harbor the world’s most diverse assemblages of freshwater fishes. One of the most prominent South American fish families is the Serrasalmidae (pacus and piranhas), found in nearly every continental basin. Serrasalmids are keystone ecological taxa, being some of the top riverine predators as well as the primary seed dispersers in the flooded forest. Despite their widespread occurrence and notable ecologies, serrasalmid evolutionary history and systematics are controversial. For example, the sister taxon to serrasalmids is contentious, the relationships of major clades within the family are inconsistent across different methodologies, and half of the extant serrasalmid genera are suggested to be non-monophyletic. We analyzed exon capture to reexamine the evolutionary relationships among 63 (of 99) species across all 16 serrasalmid genera and their nearest outgroups, including multiple individuals per species to account for cryptic lineages. To reconstruct the timeline of serrasalmid diversification, we time-calibrated this phylogeny using two different fossil-calibration schemes to account for uncertainty in taxonomy with respect to fossil teeth. Finally, we analyzed diet evolution across the family and comment on associated changes in dentition, highlighting the ecomorphological diversity within serrasalmids. We document widespread non-monophyly of genera within Myleinae, as well as between Serrasalmus and Pristobrycon, and propose that reliance on traits like teeth to distinguish among genera is confounded by ecological homoplasy, especially among herbivorous and omnivorous taxa. We clarify the relationships among all serrasalmid genera, propose new subfamily affiliations, and support hemiodontids as the sister taxon to Serrasalmidae. [Characiformes; exon capture; ichthyochory; molecular time-calibration; piscivory.]