Complex Evolutionary History Research Articles

Evolutionary and functional analyses of LRP5 in archaic and extant modern humans

BackgroundThe human lineage has undergone a postcranial skeleton gracilization (i.e. lower bone mass and strength relative to body size) compared to other primates and archaic populations such as the Neanderthals. This gracilization has been traditionally explained by differences in the mechanical load that our ancestors exercised. However, there is growing evidence that gracilization could also be genetically influenced.ResultsWe have analyzed the LRP5 gene, which is known to be associated with high bone mineral density conditions, from an evolutionary and functional point of view. Taking advantage of the published genomes of archaic Homo populations, our results suggest that this gene has a complex evolutionary history both between archaic and living humans and within living human populations. In particular, we identified the presence of different selective pressures in archaics and extant modern humans, as well as evidence of positive selection in the African and South East Asian populations from the 1000 Genomes Project. Furthermore, we observed a very limited evidence of archaic introgression in this gene (only at three haplotypes of East Asian ancestry out of the 1000 Genomes), compatible with a general erasing of the fingerprint of archaic introgression due to functional differences in archaics compared to extant modern humans. In agreement with this hypothesis, we observed private mutations in the archaic genomes that we experimentally validated as putatively increasing bone mineral density. In particular, four of five archaic missense mutations affecting the first β-propeller of LRP5 displayed enhanced Wnt pathway activation, of which two also displayed reduced negative regulation.ConclusionsIn summary, these data suggest a genetic component contributing to the understanding of skeletal differences between extant modern humans and archaic Homo populations.

Copy number and sequence variation in rDNA of Daphnia pulex from natural populations: insights from whole-genome sequencing.

Ribosomal DNA (rDNA) has a vital role in ribosome biogenesis as it contains the genes that encode ribosomal RNA (rRNA) separated by intergenic spacers (IGSs). The rRNA genes occur in hundreds to tens of thousands of copies per haploid genome in eukaryotes and are generally highly conserved with low variation within species. Due to the repetitive nature and large size of rDNA arrays, detecting intraindividual variation can be difficult. In this study, we use whole-genome sequences of 169 Daphnia pulex individuals from 10 natural populations to measure the copy number and sequence variation in rDNA. This revealed that variation in rDNA copy number between individuals spans an order of magnitude. We further observed a substantial level of sequence variation within individual genomes. As expected, single-nucleotide polymorphisms occurred in regions of lower functional constraint such as the IGS and expansion segments of the rRNA genes. The presence of strong linkage disequilibrium among variants facilitated identification of haplotypes within each population. Although there was evidence of recombination among haplotypes from different populations, it is insufficient to eliminate linkage disequilibrium within populations. Estimating copy number and haplotype diversity within individuals revealed that the level of intraindividual sequence variation is not strongly correlated with copy number. The observed patterns of variation highlight a complex evolutionary history of rDNA in D. pulex. Future research should explore the functional implications of rDNA copy number and sequence variation on organismal phenotypes.

Camelus knoblochi genome reveals the complex evolutionary history of Old World camels

Extant Old World camels (genus Camelus) contributed to the economic and cultural exchanges between the East and West for thousands of years.1,2 Although many remains have been unearthed,3,4,5 we know neither whether the prevalent hybridization observed between extant Camelus species2,6,7 also occurred between extinct lineages and the ancestors of extant Camelus species nor why some populations became extinct while others survived. To investigate these questions, we generated paleogenomic and stable isotope data from an extinct two-humped camel species, Camelus knoblochi. We find that in the mitochondrial phylogeny, all C.knoblochi form a paraphyletic group that nests within the diversity of modern, wild two-humped camels (Camelus ferus). In contrast, they are clearly distinguished from both wild and domesticated (Camelus bactrianus) two-humped camels on the nuclear level. Moreover, the divergence pattern of the three camel species approximates a trifurcation, because the most common topology is only slightly more frequent than the two other possible topologies. This mito-nuclear phylogenetic discordance likely arose due to interspecific gene flow between all three species, suggesting that interspecific hybridization is not exclusive to modern camels but a recurrent phenomenon throughout the evolutionary history of the genus Camelus. These results suggest that the genomic complexity of Old World camels' evolutionary history is underestimated when considering data from only modern species. Finally, we find that C.knoblochi populations began declining prior to the last glacial maximum and, by integrating palaeoecological evidence and stable isotope data, suggest that this was likely due to failure to adapt to a changing environment.

UCE-derived mitochondrial phylogeny reveals pervasive mito-nuclear discordances in serotine bats (genus Eptesicus) and complex evolutionary history in Eptesicus (Histiotus)

Studies of evolution and biodiversity require solid understanding of species systematics revealed by molecular phylogeny using multilocus genomic data. Multilocus analyses, nevertheless, remain difficult in non-model taxa due to limited access to samples and molecular resources. To help overcome this limitation, ultra-conserved elements (UCEs) have been developed to generate large nuclear datasets and build more robust species phylogenies. Recently, MitoFinder pipeline was developed to further extract mitochondrial genes from the off-target sequences in UCE libraries to allow mito-nuclear comparison and increase the mitochondrial genomic database. Here we applied MitoFinder to published UCE datasets of serotine bats (genus Eptesicus) and focused on E. (Histiotus) whose evolutionary history is poorly understood. Our results showed extensive mito-nuclear discordances in the divergence of major clades in Eptesicus and within E. (Histiotus), indicating potential incomplete lineage sorting and historical mitochondrial introgression within and across subgenera. Moreover, we collected several new samples of E. (Histiotus), including the first molecular data of the recently described E. (H) diaphanopterus, and combined available published sequences to generate the most taxa-complete mitochondrial phylogeny of E. (Histiotus) bats. Results supported the early divergence of E. (H.) magellanicus and the species status of E. (H.) diaphanopterus. In addition, we found strong evidence of cryptic diversity, with potentially new taxa in Peru, Uruguay, and Brazil, which needs to be evaluated in future studies using complementary data. Our study enriched the sequence database of serotine bats and shed light on the hidden diversity and complex evolutionary history of E. (Histiotus).

Skull of a new periptychid mammal from the lower Paleocene Denver Formation of Colorado (Corral Bluffs, El Paso County)

The Periptychidae, an extinct group of archaic ungulates (‘condylarths’), were the most speciose eutherian mammals in the earliest Paleocene of North America, epitomizing mammalian ascendency after the Cretaceous–Paleogene (K–Pg) mass extinction. Although periptychids are mostly known from fragmentary gnathic remains, the Corral Bluffs area within the Denver Basin, Colorado, has yielded numerous exceptionally well-preserved mammalian fossils, including periptychids, from the earliest Paleocene. Here we describe a partial cranium and articulated dentaries plus an additional unassociated dentary fragment of a small-bodied (~273–455 g) periptychid from ca. 610 thousand years after the K–Pg mass extinction (Puercan 2 North American Land Mammal ‘age’) at Corral Bluffs. Based on these new fossils we erect Militocodon lydae gen. et sp. nov. The dentition of M. lydae exhibits synapomorphies that diagnose the Conacodontinae, but it is plesiomorphic relative to Oxyacodon, resembling putatively basal periptychids like Mimatuta and Maiorana in several dental traits. As such, we interpret M. lydae as a basal conacodontine. Its skull anatomy does not reveal clear periptychid synapomorphies and instead resembles that of arctocyonids and other primitive eutherians. M. lydae falls along a dental morphocline from basal periptychids to derived conacodontines, which we hypothesize reflects a progressive, novel modification of the hypocone to enhance orthal shearing and crushing rather than grinding mastication. The discovery and thorough descriptions and comparisons of the partial M. lydae skull represent an important step toward unraveling the complex evolutionary history of periptychid mammals.

Unravelling the effects of magmatic fractionation, fluid phase separation and dilution on the composition of magmatic-hydrothermal fluids of the Cornubian Batholith (SW England)

The compositional evolution of magmatic-hydrothermal fluids from the SnW mineralized Cornubian batholith was investigated via in situ fluid inclusion LA-ICP-MS microanalysis and reveals a large degree of variation between intrusive stages and at the sample scale, with complexities due to superposition of several mechanisms affecting fluids chemistry during the protracted evolution of the batholith. Despite large ranges of salinities (from <1 wt% to 48 wt% NaCleq.), the effects of individual processes such as magmatic differentiation, fluid saturation and boiling, fluid mixing and dilution can all be discerned on the basis of fluid inclusion trace element geochemistry combined with detailed petrography and microthermometry.In all samples, different fluid types (aqueous liquid-rich, vapor-rich and brine inclusions) were identified in variable proportions and microthermometry revealed complex temporal trends. Granite-related samples from the G5 intrusive stage are characterized by intermediate density fluids undergoing magmatic fractionation under pressure conditions above 1.5 kbar, indicated by successively decreasing fluid salinities with concomitant increases in Li, B, Rb and Cs concentrations. The latter two elements later strongly partitioned in the brine phase upon boiling, together with most of the other Cl-complexing elements (e.g., Fe, Mn, Pb, Zn). Those brines subsequently underwent progressive dilution with meteoric waters that caused a decrease in the concentration of all elements (besides B) and homogenization temperatures. In G3 granite from Dartmoor, on the other hand, brine inclusions represent the earliest fluid type while intermediate density fluids are absent, and a large salinity range in the fluid inclusion record associated with a decrease in homogenization temperatures represents their progressive dilution with meteoric fluid. The lack of intermediate density fluids at Dartmoor indicates fluid exsolution at relatively low pressures resulting in immediate phase separation into brine and vapor.All studied samples associated with ore mineralization display only the trend of dilution of high-salinity magmatic fluids. Their transition metal contents (e.g. Fe, Mn, Pb and Zn) show the expected positive correlation with salinity of the fluids. Conversely, the compositional trends observed for Sn and particularly W are more enigmatic, as they do not appear to significantly fractionate during most of the physicochemical processes outlined above and appear to be unrelated to fluid salinity, opposite of what would be expected for Sn as it is dominantly transported in Cl-complexes.This study highlights the key advantages of high-resolution geochemical fluid inclusion studies in discerning a variety of magmatic and post-magmatic processes in fluids in comparison to bulk fluid inclusion techniques or more simplistic fluid inclusions studies which might overlook important aspects of the typically complex history of fluids evolution in magmatic-hydrothermal systems.

Haplotype-resolved genomes of octoploid species in Phyllanthaceae family reveal a critical role for polyploidization and hybridization in speciation.

The Phyllanthaceae family comprises a diverse range of plants with medicinal, edible, and ornamental value, extensively cultivated worldwide. Polyploid species commonly occur in Phyllanthaceae. Due to the rather complex genomes and evolutionary histories, their speciation process has been still lacking in research. In this study, we generated chromosome-scale haplotype-resolved genomes of two octoploid species (Phyllanthus emblica and Sauropus spatulifolius) in Phyllanthaceae family. Combined with our previously reported one tetraploid (Sauropus androgynus) and one diploid species (Phyllanthus cochinchinensis) from the same family, we explored their speciation history. The three polyploid species were all identified as allopolyploids with subgenome A/B. Each of their two distinct subgenome groups from various species was uncovered to independently share a common diploid ancestor (Ancestor-AA and Ancestor-BB). Via different evolutionary routes, comprising various scenarios of bifurcating divergence, allopolyploidization (hybrid polyploidization), and autopolyploidization, they finally evolved to the current tetraploid S. androgynus, and octoploid S. spatulifolius and P. emblica, respectively. We further discuss the variations in copy number of alleles and the potential impacts within the two octoploids. In addition, we also investigated the fluctuation of metabolites with medical values and identified the key factor in its biosynthesis process in octoploids species. Our study reconstructed the evolutionary history of these Phyllanthaceae species, highlighting the critical roles of polyploidization and hybridization in their speciation processes. The high-quality genomes of the two octoploid species provide valuable genomic resources for further research of evolution and functional genomics.

The influence of the land-to-sea macroevolutionary transition on vertebral column disparification in Pinnipedia.

The repeated returns of vertebrates to the marine ecosystems since the Triassic serve as an evolutionary model to understand macroevolutionary change. Here we investigate the effects of the land-to-sea transition on disparity and constraint of the vertebral column in aquatic carnivorans (Carnivora; Pinnipedia) to assess how their functional diversity and evolutionary innovations influenced major radiations of crown pinnipeds. We use three-dimensional geometric morphometrics and multivariate analysis for high-dimensional data under a phylogenetic framework to quantify vertebral size and shape in living and extinct pinnipeds. Our analysis demonstrates an important shift in vertebral column evolution by 10-12 million years ago, from an unconstrained to a constrained evolutionary scenario, a point of time that coincides with the major radiation of crown pinnipeds. Moreover, we also demonstrate that the axial skeleton of phocids and otariids followed a different path of morphological evolution that was probably driven by their specialized locomotor strategies. Despite this, we found a significant effect of habitat preference (coastal versus pelagic) on vertebral morphology of crown taxa regardless of the family they belong. In summary, our analysis provides insights into how the land-to-sea transition influenced the complex evolutionary history of pinniped vertebral morphology.

Museum Genomics Reveals the Hybrid Origin of an Extinct Crater Lake Endemic.

Crater lake fishes are common evolutionary model systems, with recent studies suggesting a key role for gene flow in promoting rapid adaptation and speciation. However, the study of these young lakes can be complicated by human-mediated extinctions. Museum genomics approaches integrating genetic data from recently extinct species are, therefore, critical to understanding the complex evolutionary histories of these fragile systems. Here, we examine the evolutionary history of an extinct Southern Hemisphere crater lake endemic, the rainbowfish Melanotaenia eachamensis. We undertook a comprehensive sampling of extant rainbowfish populations of the Atherton Tablelands of Australia alongside historical museum material to understand the evolutionary origins of the extinct crater lake population and the dynamics of gene flow across the ecoregion. The extinct crater lake species is genetically distinct from all other nearby populations due to historic introgression between 2 proximate riverine lineages, similar to other prominent crater lake speciation systems, but this historic gene flow has not been sufficient to induce a species flock. Our results suggest that museum genomics approaches can be successfully combined with extant sampling to unravel complex speciation dynamics involving recently extinct species.

Variability in genome size of Trigonella foenum-graecum, Trigonella corniculata and Trigonella caerulea as estimated by flow cytometry indicates complex evolutionary history of fenugreek.

The determination of genome size is a fundamental step which provides a basis to initiate studies aimed at deciphering the genetic similarity of a species and to carry out other genomics based investigations. Fenugreek (Trigonella spp.) is an important spice crop which has numerous health promoting phytochemicals. Many species within this genus are known for their various health benefits owing to the presence of a wide diversity of important phytochemicals like diosgenin, trigonelline, fenugreekine, galactomannan, 4-hydroxy isoleucine, etc. It is a multipurpose crop being cultivated for food, animal feed and industrial purposes. Despite its importance, research on the genomics aspect of fenugreek remains scant. In the absence of sufficient genomic information, crop improvement in fenugreek is severely lagging. Estimation of genome size of a species is the preliminary step for initiation of any genomic studies and therefore in the present study we have estimated the genome size for fenugreek. Here, we have determined the genome sizes of three different Trigonella spp. namely T. foenum-graecum, T. corniculata and T. caerulea through flow cytometry (FC). The 2C DNA content values were found to be 6.05 pg (T. foenum-graecum), 1.83 pg (T. corniculata) and 1.96 pg (T. caerulea). The genome size of T. foenum-graecum is approximately three times the genome size of T. corniculata and T. caerulea. This variation in genome size of more than three-fold indicates the level of genetic divergence among the three species, though within the same genus. The differences observed in the genome sizes of the three species provide conclusive evidence of their genetic divergence. Additionally, the information about the genome size would provide an impetus to the structural and functional genomics-based research in this crop.

Museum Skins Enable Identification of Introgression Associated with Cytonuclear Discordance.

Increased sampling of genomes and populations across closely related species has revealed that levels of genetic exchange during and after speciation are higher than previously thought. One obvious manifestation of such exchange is strong cytonuclear discordance, where the divergence in mitochondrial DNA (mtDNA) differs from that for nuclear genes more (or less) than expected from differences between mtDNA and nuclear DNA (nDNA) in population size and mutation rate. Given genome-scale data sets and coalescent modeling, we can now confidently identify cases of strong discordance and test specifically for historical or recent introgression as the cause. Using population sampling, combining exon capture data from historical museum specimens and recently collected tissues we showcase how genomic tools can resolve complex evolutionary histories in the brachyotis group of rock-wallabies (Petrogale). In particular, applying population and phylogenomic approaches we can assess the role of demographic processes in driving complex evolutionary patterns and assess a role of ancient introgression and hybridization. We find that described species are well supported as monophyletic taxa for nDNA genes, but not for mtDNA, with cytonuclear discordance involving at least 4 operational taxonomic units across 4 species which diverged 183-278 kya. ABC modeling of nDNA gene trees supports introgression during or after speciation for some taxon pairs with cytonuclear discordance. Given substantial differences in body size between the species involved, this evidence for gene flow is surprising. Heterogenous patterns of introgression were identified but do not appear to be associated with chromosome differences between species. These and previous results suggest that dynamic past climates across the monsoonal tropics could have promoted reticulation among related species.

Fifty shades of white: morphological and molecular diversity of the Cadlina laevis species complex (Gastropoda: Nudibranchia) in the North-West Pacific

We provide a morphological examination and a barcoding study to investigate the species identity and variation limits within the Cadlina laevis species complex. Our molecular analysis based on the COI marker revealed seven new clades in the North-West Pacific Cadlina diversity. The distances between these clades are low in some cases (2.08-7.51% overall), and the species delimitation tests gave controversial results (1, 2, 13, 14 groups, depending on the analysis method). This does not allow to conclusively classify this diversity as interspecific or intraspecific. Morphological analysis showed a significant similarity of all examined groups, with minor differences found in the morphology of the central tooth of the radula and the reproductive system. However, these variations fit into the morphological variability of the North Atlantic species Cadlina laevis s.str. and cannot serve as evidence of the isolation of these identified groups. The discovered diversity may represent both a complex of at least 11 very close and cryptic species with not well-established species boundaries, or be a part of a single amphiboreal species Cadlina laevis s.l. This indicates an extremely complex evolutionary history of Cadlina laevis species complex, making this group is an interesting model object for studying speciation in boreal and Arctic communities.

High-Voltage Toxin'Roll: Electrostatic Charge Repulsion as a Dynamic Venom Resistance Trait in Pythonid Snakes.

The evolutionary interplay between predator and prey has significantly shaped the development of snake venom, a critical adaptation for subduing prey. This arms race has spurred the diversification of the components of venom and the corresponding emergence of resistance mechanisms in the prey and predators of venomous snakes. Our study investigates the molecular basis of venom resistance in pythons, focusing on electrostatic charge repulsion as a defense against α-neurotoxins binding to the alpha-1 subunit of the postsynaptic nicotinic acetylcholine receptor. Through phylogenetic and bioactivity analyses of orthosteric site sequences from various python species, we explore the prevalence and evolution of amino acid substitutions that confer resistance by electrostatic repulsion, which initially evolved in response to predatory pressure by Naja (cobra) species (which occurs across Africa and Asia). The small African species Python regius retains the two resistance-conferring lysines (positions 189 and 191) of the ancestral Python genus, conferring resistance to sympatric Naja venoms. This differed from the giant African species Python sebae, which has secondarily lost one of these lysines, potentially due to its rapid growth out of the prey size range of sympatric Naja species. In contrast, the two Asian species Python brongersmai (small) and Python bivittatus (giant) share an identical orthosteric site, which exhibits the highest degree of resistance, attributed to three lysine residues in the orthosteric sites. One of these lysines (at orthosteric position 195) evolved in the last common ancestor of these two species, which may reflect an adaptive response to increased predation pressures from the sympatric α-neurotoxic snake-eating genus Ophiophagus (King Cobras) in Asia. All these terrestrial Python species, however, were less neurotoxin-susceptible than pythons in other genera which have evolved under different predatory pressure as: the Asian species Malayopython reticulatus which is arboreal as neonates and juveniles before rapidly reaching sizes as terrestrial adults too large for sympatric Ophiophagus species to consider as prey; and the terrestrial Australian species Aspidites melanocephalus which occupies a niche, devoid of selection pressure from α-neurotoxic predatory snakes. Our findings underline the importance of positive selection in the evolution of venom resistance and suggest a complex evolutionary history involving both conserved traits and secondary evolution. This study enhances our understanding of the molecular adaptations that enable pythons to survive in environments laden with venomous threats and offers insights into the ongoing co-evolution between venomous snakes and their prey.

Was the Lanyu pig independently domesticated in the Philippines? A meta-analysis review on the prehistoric expansion of the unique Lanyu pigs

Due to the paucity of molecular studies, the origin of the unique Lanyu pigs has been described as “cryptic.” Recent evidence of the presence of Lanyu pigs with Type I signatures spanning from Northern Luzon (NL) through the western and central Philippine regions suggests the possibility of independent domestication of Lanyu pigs in the Philippines. To clarify the spatio-temporal dispersal of Lanyu pigs, this study meta-analyzed all D-loop sequences of Lanyu pigs with Type I signatures (n=323) from Taiwan and the Philippines and elucidated the role of humans in their expansion. The result supported the existence of two subclades of Type I Lanyu pigs, the Taiwanese Lanyu and the Philippine Lanyu subclades. While the two subclades shared certain morphological traits, the latter had signs of morphological patterns that had undergone feralization. Long-distance movement of these pigs during the post-Neolithic era may have been facilitated by the known back-and-forth migration between the islanders of Lanyu (Orchid Island) and the Batanes Archipelago, the northernmost region of the Philippines. Due to the absence of Lanyu pig signatures in Borneo and the fascinating presence of Lanyu signatures in Palawan, two possible scenarios are being proposed. First, the Lanyu pig originated in Taiwan and was introduced by humans (e.g., through trade after domestication into the Philippines) moving to the west of the Philippines where a new population later became established. Secondly, the ancestral origin of the Lanyu pig radiated from mainland Southeast Asia into the Philippines but was extirpated, leaving the subsequent population. The latter suggests the allopatric expansion of the unique Lanyu pigs, which could likely support that Sus scrofa is native to the Philippines. This finding provides new perspectives on the complex evolutionary and anthropogenic history of pig dispersal into Island Southeast Asia.

New insights into Cenozoic evolution of the Shijiutuo uplift, Bohai Bay basin, China: Constraints from apatite fission track analysis and seismic data

The Shijiutuo Uplift within the Bohai Bay Basin(BBB)has experienced a complex evolutionary history since the Cenozoic. Studies of the Cenozoic evolution of the Shijiutuo Uplift are important for basin tectonics and petroleum geology. The formation of uplifts in rift basins is generally controlled by regional tectonic event and fault-block tilting. In this study, apatite fission track (AFT) data from fourteen samples and seismic data analysis were used to study the processes of regional uplift and fault-block tilting. We further investigated the Cenozoic evolution and formation mechanism of the Shijiutuo Uplift. The results indicated that the Shijiutuo Uplift experienced a two-phase differential tectonic uplift and erosion history (1) Widespread rapid uplift and erosion during the early Cenozoic (65–55 Ma) (2) Widespread uplift and erosion from 40 Ma to 16 Ma. The uplift and erosion substages of 40–38 Ma and 26–16 Ma were mainly caused by regional uplift, whereas those of 38–26 Ma resulted from fault-block tilting. Since the end of the third member from the Eocene Shahejie Formation, the Shijiutuo Uplift began to rise, causing the greater Bozhong Depression to be separated into the independent Qinnan and Bozhong Sags. These tectonic uplift and erosion events have a wide range of responses and regional dynamics in eastern China. The findings of this study will lead to a better understanding of the evolution and formation of uplifts within the BBB.

An updated infrageneric classification based on phylogenomics and character evolution in Hydrangea (Hydrangeaceae)

AbstractThe genus Hydrangea s.l. (Hydrangeaceae), a favorite among gardeners, comprises more than 80 species that are important understory plants in natural temperate and subtropical forests of the Northern Hemisphere. These species are hypervariable in morphology, especially in indumentum and floral characters, warranting a thorough exploration of the complex evolutionary history of morphological characters of the genus. Ideally, this is done within a robust phylogenetic framework with extensive taxon sampling. In this study, we propose a comprehensive taxonomic reassessment of Hydrangea based on a reconstruction of its molecular phylogeny based mainly on the chloroplast genome (plastome) and the most representative taxon sampling reported to date. Phylogenomic reconstruction yielded five well‐resolved major clades and three newly recognized subclades. Inspection of the 28 characters employed in traditional taxonomic revisions revealed homoplasy in many of these traits. Our results show that characters such as growth habit, woody stem type, number of enlarged marginal sepals, style and stamen number, fruit shape, and ovary position are useful for circumscribing infrageneric divisions. Unique synapomorphies are limited. For example, herb and subshrub growth habits are associated with all the species in H. sect. Deinanthe and sect. Cardiandra, respectively. Character state combinations are proposed for distinguishing infrageneric taxa. Based on a robust phylogenetic framework, our findings suggest a complex evolutionary history of Hydrangea morphological characters. Following the criterion of monophyly and considering the morphological consistency and synapomorphy of single and combined characters to diagnose relevant lineages, we update the classification of Hydrangea into 5 subgenera and 19 sections. Our proposed taxonomic scheme, based on a robust phylogenetic framework and in‐depth character study, provides an updated perspective on the infrageneric subdivision of Hydrangea s.l.

The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi.

Fungi biosynthesize diverse secondary metabolites, small organic bioactive molecules with key roles in fungal ecology. Fungal secondary metabolites are often encoded by physically clustered genes known as biosynthetic gene clusters (BGCs). Fungi in the genus Penicillium produce a cadre of secondary metabolites, some of which are useful (e.g. the antibiotic penicillin and the cholesterol-lowering drug mevastatin) and others harmful (e.g. the mycotoxin patulin and the immunosuppressant gliotoxin) to human affairs. Fungal genomes often also encode resistance genes that confer protection against toxic secondary metabolites. Some Penicillium species, such as Penicillium decumbens, are known to produce gliotoxin, a secondary metabolite with known immunosuppressant activity. To investigate the evolutionary conservation of homologs of the gliotoxin BGC and of genes involved in gliotoxin resistance in Penicillium, we analyzed 35 Penicillium genomes from 23 species. Homologous, lesser fragmented gliotoxin BGCs were found in 12 genomes, mostly fragmented remnants of the gliotoxin BGC were found in 21 genomes, whereas the remaining 2 Penicillium genomes lacked the gliotoxin BGC altogether. In contrast, broad conservation of homologs of resistance genes that reside outside the BGC across Penicillium genomes was observed. Evolutionary rate analysis revealed that BGCs with higher numbers of genes evolve slower than BGCs with few genes, suggestive of constraint and potential functional significance or more recent decay. Gene tree-species tree reconciliation analyses suggested that the history of homologs in the gliotoxin BGC across the genus Penicillium likely involved multiple duplications, losses, and horizontal gene transfers. Our analyses suggest that genes encoded in BGCs can have complex evolutionary histories and be retained in genomes long after the loss of secondary metabolite biosynthesis.

A Dusty Locale: evolution of galactic dust populations from Milky Way to dwarf-mass galaxies

ABSTRACT Observations indicate dust populations vary between galaxies and within them, suggesting a complex life cycle and evolutionary history. Here we investigate the evolution of galactic dust populations across cosmic time using a suite of cosmological zoom-in simulations from the Feedback in Realistic Environments project, spanning $M_{\rm vir}=10^{9-12}{M}_{\odot };\, M_{*}=10^{6-11}\, {M}_{\odot }$. Our simulations incorporate a dust evolution model that accounts for the dominant sources of dust production, growth, and destruction and follows the evolution of specific dust species. All galactic dust populations in our suite exhibit similar evolutionary histories, with gas–dust accretion being the dominant producer of dust mass for all but the most metal-poor galaxies. Similar to previous works, we find the onset of efficient gas–dust accretion occurs above a ‘critical’ metallicity threshold (Zcrit). Due to this threshold, our simulations reproduce observed trends between galactic D/Z and metallicity and element depletion trends in the interstellar medium. However, we find Zcrit varies between dust species due to differences in key element abundances, dust physical properties, and life cycle processes resulting in $Z_{\rm crit}\sim 0.05{\rm Z}_{\odot },\, 0.2{\rm Z}_{\odot },\, 0.5{\rm Z}_{\odot }$ for metallic iron, silicates, and carbonaceous dust, respectively. These variations could explain the lack of small carbonaceous grains observed in the Magellanic Clouds. We also find a delay between the onset of gas–dust accretion and when a dust population reaches equilibrium, which we call the equilibrium time-scale (τequil). The relation between τequil and the metal enrichment time-scale of a galaxy, determined by its recent evolutionary history, can contribute to the scatter in the observed relation between galactic D/Z and metallicity.

Geochemical fingerprinting of continental crust trapped in Cadomian volcanic arcs along northern Gondwana

During the Ediacaran to Cambrian periods, the extensive Avalonian–Cadomian accretionary orogen formed along the northern margin of the Gondwana (Pannotia) supercontinent. One of the best-preserved magmatic arcs within this orogenic system is the Davle volcanic complex (DVC) in the Teplá–Barrandian unit of the Bohemian Massif. Using detailed field observations, petrography, major/trace element concentrations, Nd–Hf isotopic compositions as well as U–Pb zircon dating, we interpret a complex evolutionary history of the DVC as comprising three main stages. The first stage (∼610–570 Ma) is represented by a volcano-plutonic association of andesite, dacite, rhyolite and tonalite–trondhjemite–granodiorite (metamorphosed to orthogneiss). A wide range of major/trace element contents together with highly variable εNd values (+3.6 to –5.1) suggest derivation from a juvenile (mantle-derived) source with subsequent assimilation of cratonic crust during magma emplacement, also supported by the modelling of the assimilation–fractional crystallization (AFC) process. The second stage (∼580–560 Ma) is characterized by a gradual termination of the volcanic arc activity, followed by a deposition of marine siliciclastic succession comprising, from the bottom to the top, laminated tuffs, silicified black shales (Lečice Member), and a thick turbidite greywacke–shale–conglomerate sequence (Štěchovice Group). The third stage of poorly constrained age (∼570–500 Ma) is represented by an intra-arc extension and intrusion of juvenile trondhjemite and related rhyolite dykes (εNd +4.8 to +8.4). Finally, we compare these findings with zircon U–Pb ages and whole-rock Nd isotopic data from other Cadomian terranes and propose that the cratonic crust played an important role in recycling along the whole orogenic belt. Thus, we conclude that the Cadomian Orogen formed as a collage of fringing (such as modern Japan, Taiwan, or Philippines) and continental (as modern Andes) arcs of variable evolutionary stages rather than as a belt dominated by intra-oceanic island arcs.

Geochemistry of high temperature initial geothermal fluids in the Dabie orogenic belt

Analyzing the genesis and resource potential of orogenic geothermal systems poses significant challenges due to their complex geological backgrounds and evolutionary histories. This paper presents a novel synthesis of hydrogeochemical and isotope geochemical data, coupled with geological and geophysical results, to comprehensively understand the origins of deep, high-temperature orogenic geothermal systems. This understanding is achieved through the utilization of advanced geochemical modeling techniques to analyze the geochemical attributes of initial geothermal fluids. The hydrochemical and H/O/S isotopic composition of a total of 67 geothermal and non-geothermal water samples from the Dabie orogenic belt (DOB) were analyzed. Integrated multicomponent geothermometry (IMG) was employed to reconstruct the characteristics of the initial geothermal fluids, and PHREEQC inverse simulations creatively determined the most likely pathways of their genesis and evolution. The findings indicate that all geothermal waters from the three major geothermal fields of Luotian, Yingshan, and Yuexi are alkali-sulfate type waters. The initial geothermal fluids are acidic sulfate type with reservoir temperatures of 156–222 °C, 115–179 °C, and 100–189 °C, respectively. The primary processes responsible for the formation of these initial geothermal fluids are the dissolution of anhydrite from sulfide oxidation and, to a lesser extent, direct sulfide oxidation. Generally, the formation of geothermal systems in the investigated geothermal fields is associated with the extensional collapse and lithospheric thinning of the Dabie orogen since the Early Cretaceous Period. The spatial distribution of the three geothermal fields in this study corresponds to the tectonic-magmatic framework of magmatic intrusion-induced domes (Luotian and Yuexi) in the DOB. The reactivation of the Tan-Lu Fault during the Cenozoic Era suggests the presence of a deep heat source comprising magmatic and metamorphic components. This heat source, combined with the infiltration of paleo-atmospheric and modern atmospheric precipitation water along regional fault systems, results in the formation and gradual dilution of initial geothermal fluids. Neutralization occurs through interactions with calcite and fine-grained sodium aluminosilicates, ultimately leading to the formation of the collected geothermal water. The conceptual model established in this study elucidates the distinctive genesis and formation mechanism of the orogenic geothermal system exemplified by the DOB.