Two-step closure of the Miocene Indian Ocean Gateway to the Mediterranean

Central Asia revealed as a key area in evolution of Eremurus (Asphodelaceae)

Eremurus was described at the beginning of the 19th century. However, due to limited sampling and the small number of gene markers to date, its phylogeny and evolution are largely unknown. In this study, we analyzed plastomes from 27 species belonging to 2 subgenera and 3 sections of Eremurus, which are found in Central Asia (its center of diversity) and China. We also analyzed nuclear DNA ITS of 33 species, encompassing all subgenera and sections of the genus in Central Asia, southwest Asia and China. Our findings revealed that the genus was monophyletic, although both subgenera Eremurus and Henningia were found to be paraphyletic. Both plastome and nrDNA-based phylogenetic trees had three clades that did not reflect the current taxonomy of the genus. Our biogeographical and time-calibrated trees suggest that Eremurus originated in the ancient Tethyan area in the second half of the Eocene. Diversification of Eremurus occurred from the early Oligocene to the late Miocene. Paratethys Sea retreat and several orogenetic events, such as the progressive uplift of the Qinghai-Tibet Plateau and surrounding mountain belts (Altai, Pamir, Tian Shan), caused serious topographic and climate (aridification) changes in Central Asia that may have triggered a split of clades and speciation. In this transformed Central Asia, speciation proceeded rapidly driven mainly by vicariance caused by numerous mountain chains and specialization to a variety of climatic, topographic and soil conditions that exist in this region.

Deep-sea hiatus record reveals orbital pacing by 2.4 Myr eccentricity grand cycles

Astronomical forcing of Earth's climate is embedded in the rhythms of stratigraphic records, most famously as short-period (104-105 year) Milankovitch cycles. Astronomical grand cycles with periods of millions of years also modulate climate variability but have been detected in relatively few proxy records. Here, we apply spectral analysis to a dataset of Cenozoic deep-sea hiatuses to reveal a ~2.4 Myr eccentricity signal, disrupted by episodes of major tectonic forcing. We propose that maxima in the hiatus cycles correspond to orbitally-forced intensification of deep-water circulation and erosive bottom current activity, linked to eccentricity maxima and peaks in insolation and seasonality. A prominent episode of cyclicity disturbance coincides with the Paleocene-Eocene Thermal Maximum (PETM) at ~56 Myr ago, and correlates with a chaotic orbital transition in the Solar System evident in several astronomical solutions. This hints at a potential intriguing coupling between the PETM and Solar System chaos.

Impact of the climatic changes in the Pliocene-Pleistocene transition on Irano-Turanian species. The radiation of genus Jurinea (Compositae)

The Irano-Turanian region is one of the world's richest floristic regions and the centre of diversity for numerous xerophytic plant lineages. However, we still have limited knowledge on the timing of evolution and biogeographic history of its flora, and potential drivers of diversification remain underexplored. To fill this knowledge gap, we focus on the Eurasian genus Jurinea (ca. 200 species), one of the largest plant radiations that diversified in the region. We applied a macroevolutionary integrative approach to explicitly test diversification hypotheses and investigate the relative roles of geography vs. ecology and niche conservatism vs. niche lability in speciation processes. To do so, we gathered a sample comprising 77% of total genus richness and obtained data about (1) its phylogenetic history, recovering 502 nuclear loci sequences; (2) growth forms; (3) ecological niche, compiling data of 21 variables for more than 2500 occurrences; and (4) paleoclimatic conditions, to estimate climatic stability. Our results revealed that climate was a key factor in the evolutionary dynamics of Jurinea. The main diversification and biogeographic events that occurred during past climate changes, which led to colder and drier conditions, are the following: (1) the origin of the genus (10.7 Ma); (2) long-distance dispersals from the Iranian Plateau to adjacent regions (∼7-4 Ma); and (3) the diversification shift during Pliocene-Pleistocene Transition (ca. 3 Ma), when net diversification rate almost doubled. Our results supported the pre-adaptation hypothesis, i.e., the evolutionary success of Jurinea was linked to the retention of the ancestral niche adapted to aridity. Interestingly, the paleoclimatic analyses revealed that in the Iranian Plateau long-term climatic stability favoured old-lineage persistence, resulting in current high species richness of semi-arid and cold adapted clades; whereas moderate climate oscillations stimulated allopatric diversification in the lineages distributed in the Circumboreal region. In contrast, growth form lability and high niche disparity among closely related species in the Central Asian clade suggest adaptive radiation to mountain habitats. In sum, the radiation of Jurinea is the result of both adaptive and non-adaptive processes influenced by climatic, orogenic and ecological factors.

Minuca panema (Coelho, 1972): Resurrection of a Fiddler Crab Species from Brazil Closely Related to Minuca burgersi (Holthuis, 1967) (Crustacea, Decapoda, Brachyura, Ocypodidae)

We redescribe a species of fiddler crab, Minuca panema (Coelho, 1972), from the Atlantic coast of South America. It is closely related to M. mordax (Smith, 1870), and until now, the taxon has been considered to be synonymous with another closely related species Minuca burgersi (Holthuis, 1967). However, we found that two clades of M. burgersi sensu lato were restricted to the Caribbean Basin. This distribution differs from than that of M. panema, which occurs primarily along the eastern coast of South America, ranging from the island of Trinidad to Praia da Armação, Santa Catarina, Brazil. Based on our field studies, the geographical boundary between M. burgersi sensu stricto and M. panema is the Tobago Basin, north of Trinidad. Since the two species diverged only 3 to 4 million years ago, as dated from the phylogeny of the genus Minuca Bott 1954, there are few reliable morphological features that can be used to distinguish them clearly. In live crabs, there is a striking difference in coloration between the cherryred South American M. panema and the rusty-red Caribbean M. burgersi sensu lato. In males, the pattern of tubercles on the inner surface of the major cheliped varies between the two species. In females, the vulva is slightly larger in M. burgersi sensu stricto. Ocean tides and currents together with siltation owing to freshwater outflow from the Amazon and Orinoco rivers most likely have driven the divergence of these species. In the Caribbean, small tidal amplitudes have minimized long-distance gene flow in M. burgersi sensu stricto from isolated insular lagoons. In contrast, large tidal amplitudes and exposed habitats on riverbanks along the eastern Atlantic coast of South America have enabled long-distance dispersal in M. panema. DNA analysis reveals that haplotypes of cytochrome c oxidase subunit 1 are not shared between the species. Since natural selection and/or genetic drift have yet to produce extensive morphological divergences between M. panema and M. burgersi sensu stricto, we speculate that changes in the genes regulating mitochondrial DNA functions have led to speciation at the molecular level. According to the mitonuclear compatibility concept, we propose that mitochondrial DNA may be at the forefront of speciation events and that co-evolved mitonuclear interactions are responsible for some of the earliest genetic incompatibilities arising among isolated populations.

Evolutionary norm-breaking and extinction in the marine tropics

Evolutionary innovations, defined as character states that transcend clade norms, are often studied in an exclusively phylogenetic context, but their distribution in time and space indicates that geography also influences the evolution of new ecological, morphological, and physiological traits. In an analysis of 99 fossillzable, norm-breaking innovations in tropical marine Neogene molluscan clades that arose uniquely in either (but not in both) the Indo-West Pacific (IWP) or Atlantic-East Pacific (AEP) realms, I show that there are far more innovations in the IWP (79%) than those in the AEP (21%). Most of the innovations are interpretable as defensive or competitive adaptations or as indicators of extreme habitat specialization. Although the innovations arose in taxonomically rich biotas, only 9% are associated with subclades comprising 10 or more species each, indicating that they contributed little to overall taxonomic richness. Compilations of extant species in 30 pantropical molluscan clades show that the IWP accounts for 71% of tropical shallow-water species, implying that the per-species incidence of norm-breaking innovations is higher there than in the AEP. Only 5% of innovations became extinct in the IWP as compared with 38% in the AEP, mirroring a similar difference in the magnitudes of Late Miocene and later taxonomic extinction in the two realms. These data imply that large-scale disruption strongly limits norm-breaking innovation. Opportunities for adaptive innovation are therefore likely to be few in today's heavily overexploited and disturbed biosphere.

Modern-like deep water circulation in Indian Ocean caused by Central American Seaway closure

Global overturning circulation underwent significant changes in the late Miocene, driven by tectonic forcing, and impacted the global climate. Prevailing hypotheses related to the late Miocene deep water circulation (DWC) changes driven by the closure of the Central American Seaways (CAS) and its widespread impact remains untested due to the paucity of suitable records away from the CAS region. Here, we test the hypothesis of the large-scale circulation changes by providing a high-resolution record of DWC since the late Miocene (11.3 to ~2 Ma) from the north-western Indian Ocean. Our investigation reveals a progressive shift from Pacific-dominated DWC before ~9.0 Ma to the onset of a modern-like DWC system in the Indian Ocean comprising of Antarctic bottom water and northern component water during the Miocene-Pliocene transition (~6 Ma) caused by progressive shoaling of the CAS and suggests its widespread impact.

Genome-wide SNPs in the spiny lobster Panulirus homarus reveal a hybrid origin for its subspecies

Background

Evolutionary divergence and speciation often occur at a slower rate in the marine realm due to the higher potential for long-distance reproductive interaction through larval dispersal. One common evolutionary pattern in the Indo-Pacific, is divergence of populations and species at the peripheries of widely-distributed organisms. However, the evolutionary and demographic histories of such divergence are yet to be well understood. Here we address these issues by coupling genome-wide SNP data with mitochondrial DNA sequences to test the patterns of genetic divergence and possible secondary contact among geographically distant populations of the highly valuable spiny lobster Panulirus homarus species complex, distributed widely through the Indo-Pacific, from South Africa to the Marquesas Islands.

Result

After stringent filtering, 2020 SNPs were used for population genetic and demographic analyses, revealing strong regional structure (FST = 0.148, P < 0001), superficially in accordance with previous analyses. However, detailed demographic analyses supported a much more complex evolutionary history of these populations, including a hybrid origin of a North-West Indian Ocean (NWIO) population, which has previously been discriminated morphologically, but not genetically. The best-supported demographic models suggested that the current genetic relationships among populations were due to a complex series of past divergences followed by asymmetric migration in more recent times.

Conclusion

Overall, this study suggests that alternating periods of marine divergence and gene flow have driven the current genetic patterns observed in this lobster and may help explain the observed wider patterns of marine species diversity in the Indo-Pacific.

Enhanced ocean oxygenation during Cenozoic warm periods

Dissolved oxygen (O₂) is essential for most ocean ecosystems, fuelling organisms’ respiration and facilitating the cycling of carbon and nutrients. Oxygen measurements have been interpreted to indicate that the ocean’s oxygen-deficient zones (ODZs) are expanding under global warming^1,2. However, models provide an unclear picture of future ODZ change in both the near term and the long term^3–6. The paleoclimate record can help explore the possible range of ODZ changes in warmer-than-modern periods. Here we use foraminifera-bound nitrogen (N) isotopes to show that water-column denitrification in the eastern tropical North Pacific was greatly reduced during the Middle Miocene Climatic Optimum (MMCO) and the Early Eocene Climatic Optimum (EECO). Because denitrification is restricted to oxygen-poor waters, our results indicate that, in these two Cenozoic periods of sustained warmth, ODZs were contracted, not expanded. ODZ contraction may have arisen from a decrease in upwelling-fuelled biological productivity in the tropical Pacific, which would have reduced oxygen demand in the subsurface. Alternatively, invigoration of deep-water ventilation by the Southern Ocean may have weakened the ocean’s ‘biological carbon pump’, which would have increased deep-ocean oxygen. The mechanism at play would have determined whether the ODZ contractions occurred in step with the warming or took centuries or millennia to develop. Thus, although our results from the Cenozoic do not necessarily apply to the near-term future, they might imply that global warming may eventually cause ODZ contraction.

By using foraminifera-bound nitrogen isotopes, it is shown that, during two warm periods of the Cenozoic, oxygen-deficient zones contracted rather than expanded, suggesting that global warming may not necessarily lead to increased oceanic anoxia.

Ancient Tethyan Vicariance and Long-Distance Dispersal Drive Global Diversification and Cryptic Speciation in the Red Seaweed Pterocladiella

We investigated the globally distributed red algal genus Pterocladiella, comprising 24 described species, many of which are economically important sources of agar and agarose. We used DNA-based species delimitation approaches, phylogenetic, and historical biogeographical analyses to uncover cryptic diversity and infer the drivers of biogeographic patterns. We delimited 43 species in Pterocladiella, of which 19 are undescribed. Our multigene time-calibrated phylogeny and ancestral area reconstruction indicated that Pterocladiella most likely originated during the Early Cretaceous in the Tethys Sea. Ancient Tethyan vicariance and long-distance dispersal have shaped current distribution patterns. The ancestor of Eastern Pacific species likely arose before the formation of the formidable Eastern Pacific Barrier-a first confirmation using molecular data in red algae. Divergences of Northeast and Southeast Pacific species have been driven by the Central American Seaway barrier, which, paradoxically, served as a dispersal pathway for Atlantic species. Both long- and short-distance dispersal scenarios are supported by genetic relationships within cosmopolitan species based on haplotype analysis. Asymmetrical distributions and the predominance of peripatry and sympatry between sister species suggest the importance of budding speciation in Pterocladiella. Our study highlights the underestimation of global diversity in these crucial components of coastal ecosystems and provides evidence for the complex evolution of current species distributions.

Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates

Background

Seahorses, seadragons, pygmy pipehorses, and pipefishes (Syngnathidae, Syngnathiformes) are among the most recognizable groups of fishes because of their derived morphology, unusual life history, and worldwide distribution. Despite previous phylogenetic studies and recent new species descriptions of syngnathids, the evolutionary relationships among several major groups within this family remain unresolved.

Results

Here, we provide a reconstruction of syngnathid phylogeny based on genome-wide sampling of 1314 ultraconserved elements (UCEs) and expanded taxon sampling to assess the current taxonomy and as a basis for macroevolutionary insights. We sequenced a total of 244 new specimens across 117 species and combined with published UCE data for a total of 183 species of Syngnathidae, about 62% of the described species diversity, to compile the most data-rich phylogeny to date. We estimated divergence times using 14 syngnathiform fossils, including nine fossils with newly proposed phylogenetic affinities, to better characterize current and historical biogeographical patterns, and to reconstruct diversification through time. We present a phylogenetic hypothesis that is well-supported and provides several notable insights into syngnathid evolution. We found nine non-monophyletic genera, evidence for seven cryptic species, five potentially invalid synonyms, and identified a novel sister group to the seahorses, the Indo-Pacific pipefishes Halicampus macrorhynchus and H. punctatus. In addition, the morphologically distinct southwest Pacific seahorse Hippocampus jugumus was recovered as the sister to all other non-pygmy seahorses. As found in many other groups, a high proportion of syngnathid lineages appear to have originated in the Central Indo-Pacific and subsequently dispersed to adjoining regions. Conversely, we also found an unusually high subsequent return of lineages from southern Australasia to the Central Indo-Pacific. Diversification rates rose abruptly during the Middle Miocene Climate Transition and peaked after the closure of the Tethys Sea.

Conclusions

Our results reveal a previously underappreciated diversity of syngnathid lineages. The observed biogeographic patterns suggest a significant role of the southern Australasian region as a source and sink of lineages. Shifts in diversification rates imply possible links to declining global temperatures, the separation of the Atlantic and Pacific faunas, and the environmental changes associated with these events.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01271-w.

Phylogeography, colouration, and cryptic speciation across the Indo-Pacific in the sea urchin genus Echinothrix

The sea urchins Echinothrix calamaris and Echinothrix diadema have sympatric distributions throughout the Indo-Pacific. Diverse colour variation is reported in both species. To reconstruct the phylogeny of the genus and assess gene flow across the Indo-Pacific we sequenced mitochondrial 16S rDNA, ATPase-6, and ATPase-8, and nuclear 28S rDNA and the Calpain-7 intron. Our analyses revealed that E. diadema formed a single trans-Indo-Pacific clade, but E. calamaris contained three discrete clades. One clade was endemic to the Red Sea and the Gulf of Oman. A second clade occurred from Malaysia in the West to Moorea in the East. A third clade of E. calamaris was distributed across the entire Indo-Pacific biogeographic region. A fossil calibrated phylogeny revealed that the ancestor of E. diadema diverged from the ancestor of E. calamaris ~ 16.8 million years ago (Ma), and that the ancestor of the trans-Indo-Pacific clade and Red Sea and Gulf of Oman clade split from the western and central Pacific clade ~ 9.8 Ma. Time since divergence and genetic distances suggested species level differentiation among clades of E. calamaris. Colour variation was extensive in E. calamaris, but not clade or locality specific. There was little colour polymorphism in E. diadema.

Diversity, biogeography, evolutionary relationships, and conservation of Eastern Mediterranean freshwater mussels (Bivalvia: Unionidae)

Located at the junction between Europe, Africa, and Asia, with distinct evolutionary origins and varied ecological and geographical settings, together with a marked history of changes in orogeny and configuration of the main river basins, turned the Eastern Mediterranean into a region of high diversity and endemism of freshwater taxa. Freshwater mussels (Bivalvia, Unionidae) from the Western Palearctic have been widely studied in their European range, but little attention has been dedicated to these taxa in the Eastern Mediterranean region and their diversity and phylogeography are still poorly understood. The present study aims to resolve the diversity, biogeography, and evolutionary relationships of the Eastern Mediterranean freshwater mussels. To that end, we performed multiple field surveys, phylogenetic analyses, and a thorough taxonomic revaluation. We reassessed the systematics of all Unionidae species in the region, including newly collected specimens across Turkey, Israel, and Iran, combining COI + 16S + 28S and COI phylogenies with molecular species delineation methods. Phylogeographical patterns were characterized based on published molecular data, newly sequenced specimens, and species distribution data, as well as ancestral range estimations. We reveal that Unionidae species richness in the Eastern Mediterranean is over 70% higher than previously assumed, counting 19 species within two subfamilies, the Unioninae (14) and Gonideinae (5). We propose two new species, Anodonta seddonisp. nov. and Leguminaia anatolicasp. nov. Six additional taxa, Unio delicatusstat. rev., Unio eucirrusstat. rev., Unio huetistat. rev., Unio sesirmensisstat. rev., Unio terminalisstat. rev. removed from the synonymy of Unio tigridis, as well as Unio damascensisstat. rev. removed from the synonymy of Unio crassus, are re-described. The nominal taxa Unio rothi var. komarowi O. Boettger, 1880 and Unio armeniacus Kobelt, 1911 are proposed as new synonyms of Unio bruguierianus, and Anodonta cyrea Drouët, 1881 and Anodonta cilicica Kobelt & Rolle, 1895 as new synonyms of Anodonta anatina. Also, the presence of Unio tumidus in the Maritza River is confirmed. The phylogeographic patterns described here are interpreted concerning major past geological events. Conservation needs and implications are presented, together with populations and species conservation priorities.

Revisiting the sedimentary record of the rise of diatoms

Diatoms are a major primary producer in the modern oceans and play a critical role in the marine silica cycle. Their rise to dominance is recognized as one of the largest shifts in Cenozoic marine ecosystems, but the timing of this transition is debated. Here, we use a diagenetic model to examine the effect of sedimentation rate and temperature on the burial efficiency of biogenic silica over the past 66 million years (i.e., the Cenozoic). We find that the changing preservation potential of siliceous microfossils during that time would have overprinted the primary signal of diatom and radiolarian abundance. We generate a taphonomic null hypothesis of the diatom fossil record by assuming a constant flux of diatoms to the sea floor and having diagenetic conditions driven by observed shifts in temperature and sedimentation rate. This null hypothesis produces a late Cenozoic (∼5 Ma to 20 Ma) increase in the relative abundance of fossilized diatoms that is comparable to current empirical records. This suggests that the observed increase in diatom abundance in the sedimentary record may be driven by changing preservation potential. A late Cenozoic rise in diatoms has been causally tied to the rise of grasslands and baleen whales and to declining atmospheric CO₂ levels. Here we suggest that the similarity among these records primarily arises from a common driver-the cooling climate system-that drove enhanced diatom preservation as well as the rise of grasslands and whales, rather than a causal link among them.

Using past interglacial temperature maxima to explore transgressions in modern Maldivian coral and Amphistegina bleaching thresholds

Tropical corals and Amphistegina, an example genus of symbiont-bearing larger benthic foraminifera, are presently living close to their thermal bleaching thresholds. As such, these essential reef-building organisms are vulnerable to the future prospect of more frequent sea surface temperature (SST) extremes. Exploring the earth's paleo-climatic record, including interglacials warmer than present, may provide insights into future oceanographic conditions. We analyse foraminiferal shell geochemical compositions, from Recent surface sediments and Marine Isotope stage (MIS) 9e and MIS11c aged sediments, from the International Ocean Discovery Program Expedition 359 Site U1467 drilled in the Inner Sea of the Maldives. We illustrate through traditional (pooled) geochemical analysis (δ¹⁸O, Mg/Ca) that tropical temperatures were indeed marginally warmer during MIS9e and MIS11c in comparison to the modern ocean. Individual foraminiferal analysis (IFA) from the Recent (representing the last few hundred years) and MIS9e samples shows SSTs occasionally breached the coral bleaching threshold similarly to the modern-day. Significantly, the number of transgressions was four times higher during MIS11c, a recognised analogue for a warmer modern world. This new knowledge and novel IFA insight and application is invaluable given thermal stress is already obvious today with an increasing number of bleaching events over the last few decades.

Improved adulticidal activity against Aedes aegypti (L.) and Aedes albopictus (Skuse) from synergy between Cinnamomum spp. essential oils

Improved natural adulticidal agents against mosquito vectors are in urgent need, and essential oils from Cinnamomum plants can assume this role quite readily. Cinnamomum verum, C. cassia, and C. loureiroi essential oils (EOs) were extracted from the barks and evaluated for their chemical composition by GC–MS. The major constituent of the three EOs was cinnamaldehyde. WHO susceptibility tests on individual and combined EOs as well as cinnamaldehyde were conducted against female adults of Aedes aegypti and Aedes albopictus. All EO combinations exhibited a synergistic effect, manifesting a higher toxicity, with a synergistic value ranging from 2.9 to 6.7. Their increasing mortality value was improved between 16.0 to 41.7%. The highest synergistic effect was achieved by an EO combination of 0.5% C. cassia + 0.5% C. loureiroi, while the highest insecticidal activity was achieved by 2.5% C. verum + 2.5% C. cassia and 1% cinnamaldehyde, with a knockdown and mortality rate of 100% and a KT₅₀ between 0.7 and 2.1 min. This combination was more toxic to both mosquito species than 1% w/v cypermethrin. These findings demonstrate that cinnamaldehyde and synergistic combinations of C. verum + C. cassia EOs and C. cassia + C. loureiroi EOs have a high insecticidal efficacy against Aedes populations.

Phylogenetic relationships, genetic diversity and biogeography of menhadens, genus Brevoortia (Clupeiformes, Clupeidae)

Brevoortia Gill 1861 is a genus of the Clupeidae (Teleostei) that includes six species of fishes commonly known as menhadens in eastern North America and "savelhas" or "saracas" in southeastern South America. Species of Brevoortia are important components of the marine food web of coastal ecosystems in the Atlantic and contribute significantly to fisheries. In this study, the first phylogenetic and biogeographic hypotheses including all species of Brevoortia are presented. A total of 113 specimens were analyzed using three molecular markers (two mitochondrial: COI and 16s; and one nuclear: RAG2). Maximum Parsimony, Maximum Likelihood and Bayesian Inference were employed to estimate phylogenetic relationships. A Bayesian multispecies coalescent approach was used to estimate a dated phylogeny, which supported biogeographic analyses of ancestral geographic ranges. Results corroborate previous hypotheses that the four North Atlantic species are grouped in two clades, one composed of B. tyrannus (Latrobe, 1802) and B. patronus Goode, 1878, and the second including B. smithi Hildebrand, 1941 and B. gunteri Hildebrand, 1948. The South Atlantic B. aurea (Spix and Agassiz, 1829) and B. pectinata (Jenyns, 1842) form a third clade, which is sister to the clade composed of B. smithi and B. gunteri. The monophyly and validity of the six nominal species of Brevoortia were not supported. Results also indicate that Brevoortia originated in the North Atlantic during the middle Miocene (about 15 Mya). A cooling event of the tropical Atlantic at around 10 Mya likely facilitated the range expansion of the genus to the South Atlantic, whereas a significant warming of the tropical Atlantic waters during the late Miocene at 6-7 Mya possibly promoted the isolation between the northern and southern counterparts of that ancestral lineage. The relevance of the Florida Peninsula in association with sea level fluctuations for the diversification within Brevoortia is also discussed.

Contemporary Distribution, Estimated Age, and Prehistoric Migrations of Old World Monkey Retroviruses

Old World monkeys (OWM), simians inhabiting Africa and Asia, are currently affected by at least four infectious retroviruses, namely, simian foamy virus (SFV), simian immunodeficiency virus (SIV), simian T-lymphotropic virus (STLV), and simian type D retrovirus (SRV). OWM also show chromosomal evidence of having been infected in the past with four more retroviral species, baboon endogenous virus (BaEV), Papio cynocephalus endogenous virus (PcEV), simian endogenous retrovirus (SERV), and Rhesus endogenous retrovirus-K (RhERV-K/SERV-K1). For some of the viruses, transmission to other primates still occurs, resulting, for instance, in the HIV pandemic. Retroviruses are intimately connected with their host as they are normally spread by close contact. In this review, an attempt to reconstruct the distribution and history of OWM retroviruses will be made. A literature overview of the species infected by any of the eight retroviruses as well as an age estimation of the pathogens will be given. In addition, primate genomes from databases have been re-analyzed for the presence of endogenous retrovirus integrations. Results suggest that some of the oldest retroviruses, SERV and PcEV, have travelled with their hosts to Asia during the Miocene, when a higher global temperature allowed simian expansions. In contrast, younger viruses, such as SIV and SRV, probably due to the lack of a primate continuum between the continents in later times, have been restricted to Africa and Asia, respectively.

The Oligo-Miocene closure of the Tethys Ocean and evolution of the proto-Mediterranean Sea

The tectonically driven Cenozoic closure of the Tethys Ocean invoked a significant reorganization of oceanic circulation and climate patterns on a global scale. This process culminated between the Mid Oligocene and Late Miocene, although its exact timing has remained so far elusive, as does the subsequent evolution of the proto-Mediterranean, primarily due to a lack of reliable, continuous deep-sea records. Here, we present for the first time the framework of the Oligo–Miocene evolution of the deep Levant Basin, based on the chrono-, chemo- and bio- stratigraphy of two deep boreholes from the Eastern Mediterranean. The results reveal a major pulse in terrigeneous mass accumulation rates (MARs) during 24–21 Ma, reflecting the erosional products of the Red Sea rifting and subsequent uplift that drove the collision between the Arabian and Eurasian plates and the effective closure of the Indian Ocean-Mediterranean Seaway. Subsequently, the proto-Mediterranean experienced an increase in primary productivity that peaked during the Mid-Miocene Climate Optimum. A region-wide hiatus across the Serravallian (13.8–11.6 Ma) and a crash in carbonate MARs during the lower Tortonian reflect a dissolution episode that potentially marks the earliest onset of the global middle to late Miocene carbonate crash.