Middle Miocene long-term continental temperature change in and out of pace with marine climate records

Enhancing in search of Milankovitch cycles from stratigraphic record using convex optimization algorithm

Accurately identifying Milankovitch cycles has been a significant challenge in cyclostratigraphic studies, as it is essential for improving geochronology. This manuscript focuses on developing a method that distinguishes Milankovitch cycles from sedimentary noise to enhance stratigraphic precision. Despite their often-conspicuous magnitude, these periodicities frequently intertwine with noise, posing a challenge for conventional spectral analysis. Therefore, to address this issue, we have developed an algorithm that enhances the resolution of the Milankovitch signal by employing convex optimization in spectral analysis. To evaluate the effectiveness of this new algorithm, we applied it to four distinct types of local stratigraphy where the Milankovitch signal has been confirmed. These include the stratigraphic sections in the middle Miocene molluscan beds of Java and the Mahakam Delta, Pleistocene sediments of Hominin Flores, and the Towuti Lake in Sulawesi Island, Indonesia. Our findings demonstrate the preservation of all targeted signals, with a confidence level surpassing 99%. By setting the significance level to 1%, we can reject the null hypothesis, which assumes noise or the absence of a Milankovitch signal in the stratigraphic data being tested. The absence of deviations from the identified periodicities further strengthens the Milankovitch signal, underscoring the robustness of our algorithm. However, we acknowledge that achieving optimal results still hinges on the accurate selection of the initial parameters z and λ.

Phylogenomic analysis of target enrichment and transcriptome data uncovers rapid radiation and extensive hybridization in the slipper orchid genus Cypripedium

BACKGROUND AND AIMS

Cypripedium is the most widespread and morphologically diverse genus of slipper orchids. Despite several published phylogenies, the topology and monophyly of its infrageneric taxa remained uncertain. Here, we aimed to reconstruct a robust section-level phylogeny of Cypripedium and explore its evolutionary history using target capture data for the first time.

METHODS

We used the orchid-specific bait set Orchidaceae963 in combination with transcriptomic data to reconstruct the phylogeny of Cypripedium based on 913 nuclear loci, covering all 13 sections. Subsequently, we investigated discordance among nuclear and chloroplast trees, estimated divergence times and ancestral ranges, searched for anomaly zones, polytomies and diversification rate shifts, and identified potential gene (genome) duplication and hybridization events.

KEY RESULTS

All sections were recovered as monophyletic, contrary to the two subsections within sect. Cypripedium. The two subclades within this section did not correspond to its subsections but matched the geographical distribution of their species. Additionally, we discovered high levels of discordance in the short backbone branches of the genus and within sect. Cypripedium, which can be attributed to hybridization events detected based on phylogenetic network analyses, and incomplete lineage sorting caused by rapid radiation. Our biogeographical analysis suggested a Neotropical origin of the genus during the Oligocene (~30 Ma), with a lineage of potentially hybrid origin spreading to the Old World in the Early Miocene (~22 Ma). The rapid radiation at the backbone probably occurred in Southeast Asia around the Middle Miocene Climatic Transition (~15-13 Ma), followed by several independent dispersals back to the New World. Moreover, the glacial cycles of the Pliocene-Quaternary may have contributed to further speciation and reticulate evolution within Cypripedium.

CONCLUSIONS

Our study provides novel insights into the evolutionary history of Cypripedium based on high-throughput molecular data, shedding light on the dynamics of its distribution and diversity patterns from its origin to the present.

Mitogenomic Architecture of Atlantic Emperor Lethrinus atlanticus (Actinopterygii: Spariformes): Insights into the Lineage Diversification in Atlantic Ocean

The evolutionary history of emperors, particularly in the Atlantic and Indo-West Pacific Oceans, remains largely unmapped. This study explores the maternal lineage evolution of Lethrinids by examining the complete mitogenome of Lethrinus atlanticus, which is endemic to the Eastern Atlantic Ocean. Utilizing advanced next-generation sequencing, we found that the mitogenome spans 16,789 base pairs and encompasses 37 genes, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNAs, and an AT-rich control region (CR). Our analysis indicates a preference for AT base pairs in the L. atlanticus mitogenome (53.10%). Most PCGs begin with the ATG codon, except for COI, which starts with GTG. Relative synonymous codon usage reveals high frequencies for alanine, leucine, proline, serine, and threonine. The ratio of nonsynonymous to synonymous substitutions suggests strong negative selection across all PCGs in Lethrinus species. Most transfer RNAs exhibit typical cloverleaf structures, with the exception of tRNA-serine (GCT), which lacks a dihydrouracil stem. Comparative analysis of conserved sequence blocks across the CRs of three Lethrinus species shows notable differences in length and nucleotide composition. Phylogenetic analysis using concatenated PCGs clearly distinguishes all Lethrinus species, including L. atlanticus, and sheds light on the evolutionary relationships among Spariformes species. The estimated divergence time of approximately 20.67 million years between L. atlanticus and its Indo-West Pacific relatives provides insights into their historical separation and colonization during the late Oligocene. The distribution of Lethrinids may be influenced by ocean currents and ecological factors, potentially leading to their speciation across the Eastern Atlantic and Indo-West Pacific. This study enhances our understanding of the genetic diversity and phylogenetic relationships within Lethrinus species. Further exploration of other emperor fish mitogenomes and comprehensive genomic data could provide vital insights into their genetic makeup, evolutionary history, and environmental adaptability in marine ecosystems globally.

Different Evolutionary Trends of Galloanseres: Mitogenomics Analysis

The two existing clades of Galloanseres, orders Galliformes (landfowl) and Anseriformes (waterfowl), exhibit dramatically different evolutionary trends. Mitochondria serve as primary sites for energy production in organisms, and numerous studies have revealed their role in biological evolution and ecological adaptation. We assembled the complete mitogenome sequences of two species of the genus Aythya within Anseriformes: Aythya baeri and Aythya marila. A phylogenetic tree was constructed for 142 species within Galloanseres, and their divergence times were inferred. The divergence between Galliformes and Anseriformes occurred ~79.62 million years ago (Mya), followed by rapid evolution and diversification after the Middle Miocene (~13.82 Mya). The analysis of selective pressure indicated that the mitochondrial protein-coding genes (PCGs) of Galloanseres species have predominantly undergone purifying selection. The free-ratio model revealed that the evolutionary rates of COX1 and COX3 were lower than those of the other PCGs, whereas ND2 and ND6 had faster evolutionary rates. The CmC model also indicated that most PCGs in Anseriformes exhibited stronger selective constraints. Our study suggests that the distinct evolutionary trends and energy requirements of Galliformes and Anseriformes drive different evolutionary patterns in the mitogenome.

High species diversity of Phintella and Phintella-like spiders (Araneae: Salticidae) in Vietnam revealed by DNA-based species delimitation analyses

Salticidae (jumping spiders) usually exhibit pronounced sexual dimorphism in adult morphology, particularly body coloration and size and shape of the first legs. Consequently, the male and female from the same species might be erroneously assigned to different species or even different genera, which could generate synonymies in classification if only morphological data were used. Phintella is a species-rich genus of Salticidae, which currently exhibits 76 named species. However, the male-female counterpart is unknown for nearly half of the species. In this study, we used a molecular approach to delineate the species boundaries for Phintella and Phintella-like specimens collected in Vietnam, using morphological information as supporting data. We used three gene fragments (mitochondrial COI, 16S-ND1, and nuclear 28S) and biogeographical considerations for species delimitation. A total of 22 putative species were recognized: 18 species of the genus Phintella, one species of the genus Lechia (L. squamata), and three species of the genus Phinteloides. Eleven undescribed species were discovered, of which seven have a male-female combination, two species have only males, and two species have only females. The crown age of Phintella was estimated at the Serravallian stage of the Miocene after the increase of species number around 16 MYA. The crown ages of most putative species recognized in this study were estimated in the Pleistocene, and the divergence among sister species likely occurred from the mid-Miocene to the Pliocene. Our ancestral range reconstruction results showed that the diversification of our ingroup was governed by progressive dispersal events, i.e., Phintella and their related species in Vietnam diversified while expanding their range on the continent. Our results provide fundamental biodiversity data for a high-diversity genus in Vietnamese Phintella spiders.

Insights into the Mitochondrial Genetic Makeup and Miocene Colonization of Primitive Flatfishes (Pleuronectiformes: Psettodidae) in the East Atlantic and Indo-West Pacific Ocean

The mitogenomic evolution of the Psettodes flatfishes is still poorly known from their range distribution in eastern Atlantic and Indo-West Pacific Oceans. The study delves into the matrilineal evolutionary pathway of these primitive flatfishes, with a specific focus on the complete mitogenome of the Psettodes belcheri species, as determined through next-generation sequencing. The mitogenome in question spans a length of 16,747 base pairs and comprises a total of 37 genes, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Notably, the mitogenome of P. belcheri exhibits a bias towards AT base pairs, with a composition of 54.15%, mirroring a similar bias observed in its close relative, Psettodes erumei, which showcases percentages of 53.07% and 53.61%. Most of the protein-coding genes commence with an ATG initiation codon, except for Cytochrome c oxidase I (COI), which initiates with a GTG codon. Additionally, four protein-coding genes commence with a TAA termination codon, while seven others exhibit incomplete termination codons. Furthermore, two protein-coding genes, namely NAD1 and NAD6, terminate with AGG and TAG stop codons, respectively. In the mitogenome of P. belcheri, the majority of transfer RNAs demonstrate the classical cloverleaf secondary structures, except for tRNA-serine, which lacks a DHU stem. Comparative analysis of conserved blocks within the control regions of two Psettodidae species unveiled that the CSB-II block extended to a length of 51 base pairs, surpassing the other blocks and encompassing highly variable sites. A comprehensive phylogenetic analysis using mitochondrial genomes (13 concatenated PCGs) categorized various Pleuronectiformes species, highlighting the basal position of the Psettodidae family and showed monophyletic clustering of Psettodes species. The approximate divergence time (35-10 MYA) between P. belcheri and P. erumei was estimated, providing insights into their separation and colonization during the early Miocene. The TimeTree analysis also estimated the divergence of two suborders, Psettodoidei and Pleuronectoidei, during the late Paleocene to early Eocene (56.87 MYA). The distribution patterns of Psettodes flatfishes were influenced by ocean currents and environmental conditions, contributing to their ecological speciation. In the face of climate change and anthropogenic activities, the conservation implications of Psettodes flatfishes are emphasized, underscoring the need for regulated harvesting and adaptive management strategies to ensure their survival in changing marine ecosystems. Overall, this study contributes to understanding the evolutionary history, genetic diversity, and conservation needs of Psettodes flatfishes globally. However, the multifaceted exploration of mitogenome and larger-scale genomic data of Psettodes flatfish will provide invaluable insights into their genetic characterization, evolutionary history, environmental adaptation, and conservation in the eastern Atlantic and Indo-West Pacific Oceans.

An exceptionally well-preserved monodominant fossil forest of Wataria from the lower Miocene of Japan

Byttneriophyllum tiliifolium is a leaf fossil-species of the family Malvaceae that was distributed widely throughout Eurasia from the Miocene to the Pliocene. An affinity to some Malvadendrina subfamilies has been suggested for Byttneriophyllum-bearing plants, but remains to be clarified due to insufficient information on other organs. Here, we report an exceptional lower Miocene fossil locality in Japan where a monodominant forest of the wood fossil-species Wataria parvipora flourished. Notably, the forest floor was covered by a bed consisting almost exclusively of B. tiliifolium. We observed occurrence modes of B. tiliifolium in this bed that confirmed that these leaves were deposited parautochthonously. These observations imply a biological connection between B. tiliifolium and W. parvipora. The wood and leaf characters together might narrow the affinity of Byttneriophyllum-bearing plants down to Helicterioideae within the Malvadendrina, although it is also possible that Byttneriophyllum-bearing plants constitutes an extinct lineage which is characterized by a combination of morphological traits found in several extant lineages. Our results suggest that Byttneriophyllum-bearing plants started to inhabit swamps no later than the end of the early Miocene when the global temperature was getting warmer.

CO2-forced Late Miocene cooling and ecosystem reorganizations in East Asia

In parallel with pronounced cooling in the oceans, vast areas of the continents experienced enhanced aridification and restructuring of vegetation and animal communities during the Late Miocene. Debate continues over whether pCO2-induced global cooling was the primary driver of this climate and ecosystem upheaval on land. Here we present an 8 to 5 Ma land surface temperatures (LST) record from East Asia derived from paleosol carbonate clumped isotopes and integrated with climate model simulations. The LST cooled by ~7 °C between 7.5 and 5.7 Ma, followed by rapid warming across the Miocene-Pliocene transition (5.5 to 5 Ma). These changes occurred synchronously with variations in alkenone and Mg/Ca-based sea surface temperatures and with hydroclimate and ecosystem shifts in East Asia, highlighting a global climate forcing mechanism. Our modeling experiments additionally demonstrate that pCO2-forced cooling would have altered moisture transfer and pathways and driven extensive aridification in East Asia. We, thus, conclude that the East Asian hydroclimate and ecosystem shift was primarily controlled by pCO2-forced global cooling between 8 and 5 Ma.

Event- and biostratigraphic evidence for two independent Ries and Steinheim asteroid impacts in the Middle Miocene

For decades, the Nördlinger Ries and Steinheim Basin in southern Germany have been regarded as a textbook example of a terrestrial impact crater doublet, although the oldest crater lake deposits in both craters suggest a biostratigraphic age difference of ~ 0.5 to 1 Myr. We previously presented stratigraphic arguments that challenged the double impact scenario and favoured a model of two temporally independent impact events in the Mid-Miocene. We here present, for the first time, four localities within a distance of ~ 50-100 km from the Ries and ~ 50-70 km from the Steinheim crater that expose two independent seismite horizons, together unique within the Upper Freshwater Molasse of the North Alpine Foreland Basin, each one featuring impressive water escape structures. The seismite horizons are separated by ~ 10 to 15 m of undisturbed Molasse deposits and, biostratigraphically, by an entire European Land Mammal Zone, thus providing evidence for two independent major seismic events within a time span of ~ 0.5-1 Myr. Both the lower and the upper seismite horizons can be correlated litho- and biostratigraphically with the basal crater lake sediments at the Ries and Steinheim craters, respectively, deposited immediately after the impacts. From a biostratigraphic point of view, the impact event that formed the Steinheim Basin probably occured around 14 Ma, some 0.8 Myr after the ~ 14.81 Ma Ries impact event.

Sand spikes pinpoint powerful palaeoseismicity

Sand spikes, pin-shaped, carbonate-cemented sandstone bodies of variable size widely interpreted as sedimentary concretions, have been enigmatic for nearly two centuries. We here present a high-energy mechanism for their formation. Two classic sand spike occurrences are found in the North Alpine Foreland Basin of Central Europe and at Mount Signal in southern California, USA. A distinct seismite horizon in Mid-Miocene Molasse sediments of southern Germany, genetically linked with the Ries impact event, exhibits dewatering structures and contains numerous sand spikes with tails systematically orientated away from the Ries crater. Sand spikes at Mount Signal, strikingly similar in shape to those found in Germany, have tails that point away from the nearby San Andreas Fault. Based on their structural and stratigraphic context, we interpret sand spikes as a new type of seismite and a promising tool to identify strong impact-induced or tectonic palaeo-earthquakes and their source regions in the geologic record.

Positive Selection of Transcription Factors Is a Prominent Feature of the Evolution of a Plant Pathogenic Genus Originating in the Miocene

Tests based on the d_N/d_S statistic are used to identify positive selection of nonsynonymous polymorphisms. Using these tests on alignments of all orthologs from related species can provide insights into which gene categories have been most frequently positively selected. However, longer alignments have more power to detect positive selection, creating a detection bias that could create misleading results from functional enrichment tests. Most studies of positive selection in plant pathogens focus on genes with specific virulence functions, with little emphasis on broader molecular processes. Furthermore, no studies in plant pathogens have accounted for detection bias due to alignment length when performing functional enrichment tests. To address these research gaps, we analyze 12 genomes of the phytopathogenic fungal genus Botrytis, including two sequenced in this study. To establish a temporal context, we estimated fossil-calibrated divergence times for the genus. We find that Botrytis likely originated 16–18 Ma in the Miocene and underwent continuous radiation ending in the Pliocene. An untargeted scan of Botrytis single-copy orthologs for positive selection with three different statistical tests uncovered evidence for positive selection among proteases, signaling proteins, CAZymes, and secreted proteins. There was also a strong overrepresentation of transcription factors among positively selected genes. This overrepresentation was still apparent after two complementary controls for detection bias due to sequence length. Positively selected sites were depleted within DNA-binding domains, suggesting changes in transcriptional responses to internal and external cues or protein–protein interactions have undergone positive selection more frequently than changes in promoter fidelity.

Complete chloroplast genome sequencing of ten wild Fragaria species in China provides evidence for phylogenetic evolution of Fragaria

Complete chloroplast genomes of ten wild Fragaria species native to China were sequenced. Phylogenetic analysis clustered Fragaria species into two clades: The south clade (F. iinumae, F. chinensis, F. pentaphylla, F. nilgerrensis, F. daltoniana, F. corymbosa, F. moupinensis, F. tibetica, F. nipponica, F. gracilis, and F. nubicola and north clade (F. viridis, F. orientalis, F. moschata, F. mandshurica, F. vesca, F. chiloensis, F. virginiana, and F. × ananassa), while F. iinumae is the oldest extant species. Molecular clock analysis suggested present Fragaria species share a common ancestor 3.57 million years ago (Ma), F. moschata and octoploid species evolve 0.89 and 0.97 Ma, respectively, but F. moschata be not directly involved in current octoploid species formation. Drastic global temperature change since the Palaeocene-Eocene, approx. 55 Ma, especially during uplifting of the Qinghai-Tibet plateau and quaternary glaciation may have driven the formation of Fragaria, separation of two groups and polyploidization.

New discovery of two seismite horizons challenges the Ries-Steinheim double-impact theory

The Nördlinger Ries and the Steinheim Basin are widely perceived as a Middle Miocene impact crater doublet. We discovered two independent earthquake-produced seismite horizons in North Alpine Foreland Basin deposits potentially related to both impacts. The older seismite horizon, demonstrated to be associated with the Ries impact, is overlain by distal impact ejecta in situ, forming a unique continental seismite-ejecta couplet within a distance of up to 180 km from the crater. The younger seismite unit, also produced by a major palaeo-earthquake, comprises clastic dikes that cut through the Ries seismite-ejecta couplet. The clastic dikes may have formed in response to the Steinheim impact, some kyr after the Ries impact, in line with paleontologic results that indicate a time gap of about 0.5 Myr between the Ries and Steinheim events. This interpretation suggests the Ries and Steinheim impacts represent two temporally separate events in Southern Germany that, thus, witnessed a double disaster in the Middle Miocene. The magnitude–distance relationship of seismite formation during large earthquakes suggests the seismic and destructive potential of impact-induced earthquakes may be underestimated.