Collagen sequence analysis reveals evolutionary history of extinct West Indies Nesophontes (‘island shrews’)

Ancient biomolecule analyses are proving increasingly useful in the study of evolutionary patterns, including extinct organisms. Proteomic sequencing techniques complement genomic approaches, having the potential to examine lineages further back in time than achievable using ancient DNA, given the less stringent preservation requirements. In this study, we demonstrate the ability to use collagen sequence analyses via proteomics to provide species delimitation as a foundation for informing evolutionary patterns. We uncover biogeographic information of an enigmatic and recently extinct lineage of Nesophontes across their range on the Caribbean islands. First, evolutionary relationships reconstructed from collagen sequences reaffirm the affinity of Nesophontes and Solenodon as sister taxa within Solenodonota. This relationship helps lay the foundation for testing geographical isolation hypotheses across islands within the Greater Antilles, including movement from Cuba towards Hispaniola. Second, our results are consistent with Cuba having just two species of Nesophontes (N. micrus and N. major) that exhibit intrapopulation morphological variation. Finally, analysis of the recently described species from the Cayman Islands (N. hemicingulus) indicates that it is a closer relative to the Cuban species, N. major rather than N. micrus as previously speculated. Our proteomic sequencing improves our understanding of the origin, evolution, and distribution of this extinct mammal lineage, particularly with respect to approximate timing of speciation. Such knowledge is vital for this biodiversity hotspot, where the magnitude of recent extinctions may obscure true estimates of species richness in the past

Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals

Venom systems are key adaptations that have evolved throughout the tree of life and typically facilitate predation or defense. Despite venoms being model systems for studying a variety of evolutionary and physiological processes, many taxonomic groups remain understudied, including venomous mammals. Within the order Eulipotyphla, multiple shrew species and solenodons have oral venom systems. Despite morphological variation of their delivery systems, it remains unclear whether venom represents the ancestral state in this group or is the result of multiple independent origins. We investigated the origin and evolution of venom in eulipotyphlans by characterizing the venom system of the endangered Hispaniolan solenodon (Solenodon paradoxus). We constructed a genome to underpin proteomic identifications of solenodon venom toxins, before undertaking evolutionary analyses of those constituents, and functional assessments of the secreted venom. Our findings show that solenodon venom consists of multiple paralogous kallikrein 1 (KLK1) serine proteases, which cause hypotensive effects in vivo, and seem likely to have evolved to facilitate vertebrate prey capture. Comparative analyses provide convincing evidence that the oral venom systems of solenodons and shrews have evolved convergently, with the 4 independent origins of venom in eulipotyphlans outnumbering all other venom origins in mammals. We find that KLK1s have been independently coopted into the venom of shrews and solenodons following their divergence during the late Cretaceous, suggesting that evolutionary constraints may be acting on these genes. Consequently, our findings represent a striking example of convergent molecular evolution and demonstrate that distinct structural backgrounds can yield equivalent functions

Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals

Venom systems are key adaptations that have evolved throughout the tree of life and typically facilitate predation or defense. Despite venoms being model systems for studying a variety of evolutionary and physiological processes, many taxonomic groups remain understudied, including venomous mammals. Within the order Eulipotyphla, multiple shrew species and solenodons have oral venom systems. Despite morphological variation of their delivery systems, it remains unclear whether venom represents the ancestral state in this group or is the result of multiple independent origins. We investigated the origin and evolution of venom in eulipotyphlans by characterizing the venom system of the endangered Hispaniolan solenodon (Solenodon paradoxus). We constructed a genome to underpin proteomic identifications of solenodon venom toxins, before undertaking evolutionary analyses of those constituents, and functional assessments of the secreted venom. Our findings show that solenodon venom consists of multiple paralogous kallikrein 1 (KLK1) serine proteases, which cause hypotensive effects in vivo, and seem likely to have evolved to facilitate vertebrate prey capture. Comparative analyses provide convincing evidence that the oral venom systems of solenodons and shrews have evolved convergently, with the 4 independent origins of venom in eulipotyphlans outnumbering all other venom origins in mammals. We find that KLK1s have been independently coopted into the venom of shrews and solenodons following their divergence during the late Cretaceous, suggesting that evolutionary constraints may be acting on these genes. Consequently, our findings represent a striking example of convergent molecular evolution and demonstrate that distinct structural backgrounds can yield equivalent functions

Micro methods for megafauna: novel approaches to late quaternary extinctions and their contributions to faunal conservation in the anthropocene

Drivers of Late Quaternary megafaunal extinctions are relevant to modern conservation policy in a world of growing human population density, climate change, and faunal decline. Traditional debates tend toward global solutions, blaming either dramatic climate change or dispersals of Homo sapiens to new regions. Inherent limitations to archaeological and paleontological data sets often require reliance on scant, poorly resolved lines of evidence. However, recent developments in scientific technologies allow for more local, context-specific approaches. In the present article, we highlight how developments in five such methodologies (radiocarbon approaches, stable isotope analysis, ancient DNA, ancient proteomics, microscopy) have helped drive detailed analysis of specific megafaunal species, their particular ecological settings, and responses to new competitors or predators, climate change, and other external phenomena. The detailed case studies of faunal community composition, extinction chronologies, and demographic trends enabled by these methods examine megafaunal extinctions at scales appropriate for practical understanding of threats against particular species in their habitats today

Biogeographic problem-solving reveals the Late Pleistocene translocation of a short-faced bear to the California Channel Islands

An accurate understanding of biodiversity of the past is critical for contextualizing biodiversity patterns and trends in the present. Emerging techniques are refining our ability to decipher otherwise cryptic human-mediated species translocations across the Quaternary, yet these techniques are often used in isolation, rather than part of an interdisciplinary hypothesis-testing toolkit, limiting their scope and application. Here we illustrate the use of such an integrative approach and report the occurrence of North America’s largest terrestrial mammalian carnivore, the short-faced bear, Arctodus simus, from Daisy Cave (CA-SMI-261), an important early human occupation site on the California Channel Islands. We identified the specimen by corroborating morphological, protein, and mitogenomic lines of evidence, and evaluated the potential natural and anthropogenic mechanisms of its transport and deposition. While representing just a single specimen, our combination of techniques opened a window into the behavior of an enigmatic species, suggesting that A. simus was a wide-ranging scavenger utilizing terrestrial and marine carcasses. This discovery highlights the utility of bridging archaeological and paleontological datasets to disentangle complex biogeographic scenarios and reveal unexpected biodiversity for island systems worldwide.Open Access fees paid for in whole or in part by the University of Oklahoma Libraries Radiocarbon and isotope laboratory work was supported in part by the NSF Archaeometry Program BCS-1460369 (to D.J.K. and B.J.C). M.B was supported by a Royal Society fellowship. Additional funding was provided by the University of Oklahoma, the University of Oregon, and the Smithsonian Institution.Ye

Relationship between hippocampal volume and frequency of event retrieval using the historic events memory test in people with Alzheimer's disease

Core symptom in Alzheimer's disease (AD) is a retrograde amnesia, where recent events are often significantly more affected than remote events. The hippocampus which is considered as a crucial neuroanatomical structure for memory consolidation is early impaired in this neurodegenerative disease. In the standard model of consolidation it is assumed that this temporal gradient in memory performance is due to a time-limited role of the hippocampus in memory storage. Remote events become stored in the neocortex and are therefore not affected by the hippocampal damage

Influence of the Retrieval Frequency on the Memory Performance in Elderly Healthy Subjects and patients with Alzheimer's Disease

Background There is controversial discussion regarding the influence of retrieval frequency or remoteness of an event on the memory performance and their dependence on the neurodegenerative processes in Alzheimer's disease (AD). Regarding this issue we conducted several studies with neuropsychological and imaging methods in terms of memory performance in autobiographical and historical events. Methods In healthy controls (HC) and AD patients, we examined the recall performance of historical events, depending on the remoteness to the event or its retrieval frequency. The ranking of the retrieval frequency was operationalized through a paired comparison of all events. Furthermore, we investigated in HC subjects and patients with AD the memory performance of autobiographical events depending on the remoteness of the event or its retrieval frequency. With functional magnetic resonance imaging, we then examined in HC subjects and patients with AD the influence of the remoteness to the event or its retrieval frequency on brain activity. In a fourth study, we correlated the dependence of the retrieval frequency for the memory of historical events with the hippocampal degeneration in HC subjects and patients with AD using voxel-based morphometry. Results The behavioral data showed that as well in the HC as in the AD groups the memory performance for historical and autobiographical events depended on the retrieval frequency. The memory was accompanied by bilateral activation in the hippocampus, medial temporal lobe, angular gyrus, precuneus and medial prefrontal regions. The activation in this network was reduced in patients with AD, whereas in HC and AD subjects activity in the hippocampus increased with the retrieval frequency. In contrast to rarely retrieved events the memory performance for frequently accessed events was independent of the degree of atrophy of the hippocampus. Conclusions In summary, our studies have shown that the memory performance for historical and autobiographical events depends on retrieval frequency and this is associated with an increase in brain activity in the hippocampus. Moreover, the memory performance of frequently retrieved events appears to be less affected by the atrophy of the hippocampus in AD, either by compensatory hyperactivity in this region of the brain, or by additional activity in other brain regions

Memory performance of past public events depends on retrieval frequency but not remoteness in Alzheimer's disease

Background Patients with Alzheimer's disease (AD) typically develop retrograde amnesia. But whereas some studies found a better preservation of older memories than more recent ones, others could not detect such a temporal gradient (TG). Therefore the views of involvement of the in AD early affected hippocampus in the storage and retrieval of declarative knowledge are ambiguous. In two previous studies we investigated autobiographical memory and remembrance of historic events in patients with AD. While we could show a clear TG in recall of autobiographical information, we did not find a TG for knowledge concerning public events in the same patients with AD. We concluded that recall of more frequently retrieved memories as older autobiographical incidents becomes more independent of the hippocampal formation than more seldomly retrieved remembrances. Consequently, we investigated memory retrieval of past public events in patients with AD in dependency of retrieval frequency with functional magnetic resonance imaging (fMRI). Methods In 28 healthy controls (HC) and 26 patients with AD we assessed the remembrance of historic events of the last 60 years divided in 4 time segments. Retrieval frequency was operationalized by a paired comparison analysis. The events were matched head-to-head with each other and the subjects were required to estimate which of the two events was more often remembered during lifetime. In the scanner an imagination task was chosen as control task. Results As well for the HC group as for the patients with AD we could show a better remembrance of frequently retrieved historic events. No influence of time segment was found. Neuronal network of memory of historic events comprised hippocampus, parts of the medial temporal cortex, precuneus, gyrus angularis and medial prefrontal cortex. Brain activity in this network was reduced in AD. In both groups activity in hippocampus and precuneus increased with retrieval frequency but did not differ with time period. Conclusions The results of the present study suggest a dependency of memory performance on retrieval frequency accompanied by enhancement of brain activity in hippocampus and precuneus in HC and AD. Thus, we conclude that cognitive activities can delay the onset of memory decline in persons who develop AD