Cradle of giants: the evolutionary history of elephants and their kin in Africa

Phylogenetic analyses can be used to resolve taxonomic uncertainties and reconstruct a species’ evolutionary history. This can be combined with ecological data to predict missing life history traits which are important for creation of conservation management strategies. We investigated the evolutionary and life history of the ‘Critically Endangered’ Grenada DoveLeptotila wellsiby estimating its phylogenetic placement and using this new phylogeny to test the accuracy of phylogenetic comparative methods for estimating both documented and unknown life history traits. We extracted DNA from two Grenada Dove samples and obtained sequences from three mitochondrial markers: Cytochrome oxidase I (COI), NADH dehydrogenase 2 (ND2) and Cytochrome b (Cyt b); and one nuclear marker: β-Fibrinogen intron 7 (β-FIB). We present the first genetic data obtained for the Grenada Dove. Our data identify the Grey-Chested DoveLeptotila cassiniias the species which shares both a most recent common ancestor, with an estimated divergence of approximately 2.53 million years ago, and the smallest genetic distance (P= 0.0303) with the Grenada Dove. Life history trait values for the Grenada Dove predicted from our analyses using phylogenetic imputation are: clutch size = 2 (± 0.09) eggs; clutches per year = 1.4 (± 0.81); incubation time = 14.2 (± 0.75) days; hatching weight = 3.8 g (± 1.05) and single imputation: fledging age (genus median) = 15.5 days, longevity (genus median) = 8.6 years. This study contributes novel information regarding evolutionary history and life history characteristics to inform long-term conservation actions for a ‘Critically Endangered’ species.

ABSTRACTIt is often claimed that conserving evolutionary history is more efficient than species‐based approaches for capturing the attributes of biodiversity that benefit people. This claim underpins academic analyses and recommendations about the distribution and prioritization of species and areas for conservation, but evolutionary history is rarely considered in practical conservation activities. One impediment to implementation is that arguments related to the human‐centric benefits of evolutionary history are often vague and the underlying mechanisms poorly explored. Herein we identify the arguments linking the prioritization of evolutionary history with benefits to people, and for each we explicate the purported mechanism, and evaluate its theoretical and empirical support. We find that, even after 25 years of academic research, the strength of evidence linking evolutionary history to human benefits is still fragile.Most – but not all – arguments rely on the assumption that evolutionary history is a useful surrogate for phenotypic diversity. This surrogacy relationship in turn underlies additional arguments, particularly that, by capturing more phenotypic diversity, evolutionary history will preserve greater ecosystem functioning, capture more of the natural variety that humans prefer, and allow the maintenance of future benefits to humans. A surrogate relationship between evolutionary history and phenotypic diversity appears reasonable given theoretical and empirical results, but the strength of this relationship varies greatly. To the extent that evolutionary history captures unmeasured phenotypic diversity, maximizing the representation of evolutionary history should capture variation in species characteristics that are otherwise unknown, supporting some of the existing arguments. However, there is great variation in the strength and availability of evidence for benefits associated with protecting phenotypic diversity. There are many studies finding positive biodiversity–ecosystem functioning relationships, but little work exists on the maintenance of future benefits or the degree to which humans prefer sets of species with high phenotypic diversity or evolutionary history. Although several arguments link the protection of evolutionary history directly with the reduction of extinction rates, and with the production of relatively greater future biodiversity via increased adaptation or diversification, there are few direct tests. Several of these putative benefits have mismatches between the relevant spatial scales for conservation actions and the spatial scales at which benefits to humans are realized. It will be important for future work to fill in some of these gaps through direct tests of the arguments we define here.

BackgroundRecent experimental studies have demonstrated the importance of invasion history for evolutionary formation of community. However, only few theoretical studies on community evolution have focused on such views.Methodology and Principal FindingsWe used a tri-trophic food web model to analyze the coevolutionary effects of ecological invasions by a mutant and by a predator and/or resource species of a native consumer species community and found that ecological invasions can lead to various evolutionary histories. The invasion of a predator makes multiple evolutionary community histories possible, and the evolutionary history followed can determine both the invasion success of the predator into the native community and the fate of the community. A slight difference in the timing of an ecological invasion can lead to a greatly different fate. In addition, even greatly different community histories can converge as a result of environmental changes such as a predator trait shift or a productivity change. Furthermore, the changes to the evolutionary history may be irreversible.Conclusions and SignificanceOur modeling results suggest that the timing of ecological invasion of a species into a focal community can largely change the evolutionary consequences of the community. Our approach based on adaptive dynamics will be a useful tool to understand the effect of invasion history on evolutionary formation of community.

Vector-borne microbes necessarily co-occur with their hosts and vectors, but the degree to which they share common evolutionary or biogeographic histories remains unexplored. We examine the congruity of the evolutionary and biogeographic histories of the bacterium and vector of the Lyme disease system, the most prevalent vector-borne disease in North America. In the eastern and midwestern US, Ixodes scapularis ticks are the primary vectors of Borrelia burgdorferi, the bacterium that causes Lyme disease. Our phylogeographic and demographic analyses of the 16S mitochondrial rDNA suggest that northern I. scapularis populations originated from very few migrants from the southeastern US that expanded rapidly in the Northeast and subsequently in the Midwest after the recession of the Pleistocene ice sheets. Despite this historical gene flow, current tick migration is restricted even between proximal sites within regions. In contrast, B. burgdorferi suffers no barriers to gene flow within the northeastern and midwestern regions but shows clear interregional migration barriers. Despite the intimate association of B. burgdorferi and I. scapularis, the population structure, evolutionary history, and historical biogeography of the pathogen are all contrary to its arthropod vector. In the case of Lyme disease, movements of infected vertebrate hosts may play a larger role in the contemporary expansion and homogenization of the pathogen than the movement of tick vectors whose populations continue to bear the historical signature of climate-induced range shifts.

ABSTRACTThis study presents the first comprehensive phylogenetic analysis of Isometopinae (Hemiptera: Miridae) based on both fossil and extant taxa, providing new insights into subfamily classification. Phylogenetic reconstructions were conducted using morphological data from 37 species, including seven fossil species, to evaluate the impact of fossil inclusion on the results. Comparisons between analyses with and without fossils revealed significant differences in inferred relationships. When fossils were excluded, Diphlebini was recovered as the earliest‐diverging lineage of Isometopinae. However, including fossil taxa placed Eocene amber fossils in earlier branching positions, prompting reassessment of tribal classification and evolutionary history. These findings underscore the crucial role of fossils in phylogenetic analyses, demonstrating their importance in refining relationships and reconstructing evolutionary and biogeographic histories. Our results confirm the monophyly of Isometopinae and most recognised tribes but indicate that Myiommini is non‐monophyletic, leading to the transfer of Corticoris to Isometopini. The study also establishes Electroisopini trib. n., a newly recognised tribe comprising Eocene fossils, as an early‐diverging lineage. Based on these results, we propose a revised classification of Isometopinae. This study provides a framework for understanding Isometopinae diversification and emphasises the need for future research incorporating fossil discoveries to refine its classification and evolutionary history.

AimConvergent evolution and environmental filtering are assumed to often result in deterministic patterns of vegetation structure and function in relation to prevailing environmental conditions regardless of differences in evolutionary history among regions. We systematically evaluate the degree to which biomes located in different biogeographic realms converge in environmental space; identifying globally uniform entities and those diverging systematically among realms.LocationGlobal.MethodsTwo global biome distribution maps constructed using contrasting approaches are used to evaluate convergence in the environmental space occupied by biomes across biogeographic realms. Environmental conditions are summarized using nine climatic and two edaphic variables known to directly influence plant distributions. Biome maps are analysed accounting for differences in the availability of environments among realms.ResultsThe same biome located in two different realms often overlaps no more in environmental space than two altogether different biomes, with the average overlap on the two biome maps calculated using Schoener's D metric only 0.42 and 0.36. This suggests that the coarse structural and phenological characteristics used to define biomes conceal important differences in plant functioning and responses to environmental drivers. Nonetheless, some biomes, in particular savannas and boreal forests, show high overlap among realms. Others, like mediterranean‐type ecosystems and treeless biomes, often occur in vastly different regions of environmental space. Within most biomes though overlap varies greatly depending on the specific realms being compared, with historical biogeography and evolutionary history helping to explain this variation.Main conclusionsBiomes often occur under different environmental conditions when comparing regions with distinct evolutionary and environmental histories. The biome concept and efforts to model current and future vegetation patterns needs to be adapted to account for the role of history in determining how vegetation responds to environmental drivers and disturbance.

One day in August 1856, workers digging in search of limestone in a quarry close to Dusseldorf, western Germany, suddenly came across some old bones. At the time, they did not realize that their finding would revolutionize the history of human evolution: the world had found the Neanderthals.1 Vigorous and resistant to extreme environmental conditions, the Neanderthals survived for a long and difficult 150,000 years before they disappeared from the face of the earth; they were one of the most successful species in the history of evolution. Reasons for their extinction are still hazy and another fact contributes to the enigma: Neanderthals died out exactly when they confronted a strange unknown, Homo sapiens.

The Earth's evolutionary history is threatened by species loss in the current sixth mass extinction event in Earth's history. Such extinction events not only eliminate species but also their unique evolutionary histories. Here we review the expected loss of Earth's evolutionary history quantified by phylogenetic diversity (PD) and evolutionary distinctiveness (ED) at risk. Due to the general paucity of data, global evolutionary history losses have been predicted for only a few groups, such as mammals, birds, amphibians, plants, corals and fishes. Among these groups, there is now empirical support that extinction threats are clustered on the phylogeny; however this is not always a sufficient condition to cause higher loss of phylogenetic diversity in comparison to a scenario of random extinctions. Extinctions of the most evolutionarily distinct species and the shape of phylogenetic trees are additional factors that can elevate losses of evolutionary history. Consequently, impacts of species extinctions differ among groups and regions, and even if global losses are low within large groups, losses can be high among subgroups or within some regions. Further, we show that PD and ED are poorly protected by current conservation practices. While evolutionary history can be indirectly protected by current conservation schemes, optimizing its preservation requires integrating phylogenetic indices with those that capture rarity and extinction risk. Measures based on PD and ED could bring solutions to conservation issues, however they are still rarely used in practice, probably because the reasons to protect evolutionary history are not clear for practitioners or due to a lack of data. However, important advances have been made in the availability of phylogenetic trees and methods for their construction, as well as assessments of extinction risk. Some challenges remain, and looking forward, research should prioritize the assessment of expected PD and ED loss for more taxonomic groups and test the assumption that preserving ED and PD also protects rare species and ecosystem services. Such research will be useful to inform and guide the conservation of Earth's biodiversity and the services it provides.

BackgroundPhylogenetic diversity and evolutionary distinctiveness are highly valuable components of biodiversity, but they are rarely considered in conservation practices. Focusing on a biodiversity hotspot, the Mediterranean Basin, we aimed to identify those areas where evolutionary history is highly threatened and range-restricted in the region. Using null models, we first compared the spatial distributions of three indices: two measured threatened evolutionary history—Expected PDloss and Heightened Evolutionary distinctiveness and Global Endangerment—and one measured endemic evolutionary history—Biogeographically Evolutionary Distinctiveness. We focused on three vertebrate groups with high proportions of endemic, threatened species: amphibians, squamates and terrestrial mammals. Second, we estimated the spatial overlap of hotspots of threatened and endemic evolutionary history within the network of protected areas under several conservation scenarios.ResultsAreas that concentrate evolutionary history of conservation interest greatly differed among taxa and indices, although a large proportion of hotspots were identified in the Maghreb, in the East of the Mediterranean Basin as well as in islands. We found that, in a minimum conservation scenario, there was a significant proportion of hotspots for amphibians and squamates that were protected but not for terrestrial mammals. However, in a strong conservation scenario, only few hotspots overlapped with protected areas and they were significantly less protected than in a model where hotspots were chosen randomly.ConclusionsSome sites concentrate highly threatened and range-restricted evolutionary history of the Mediterranean basin and their conservation could be much improved. These sites are relevant for conservation studies aimed at designing new conservation actions to preserve evolutionary history and the option values it represents.Electronic supplementary materialThe online version of this article (doi:10.1186/s12898-016-0099-3) contains supplementary material, which is available to authorized users.

Background. Mutation detection through genetic testing is playing an increasingly important role in personalized precision medicine in cancer. However, current tests identifying driver mutations as therapeutic targets are based on detection of common mutations in cancer genes. These tests are not patient specific and do not address intra-tumor heterogeneity. Ubiquitous intra-tumor genetic heterogeneity is a mechanism of drug resistance and cancer recurrence. Methods. Approximately 16-24 microsamples are acquired to represent the entire cancer cell population for every ovarian tumor. Each microsample consists of a few cells within a clone and is selected to substitute for a single cell and overcome the large allele dropout rate commonly seen in single genome amplification and sequencing. TEAPOT (Tumor Evolution Assay for Personalized Oncology Therapy) algorithm has been developed to reconstruct a tumor's evolutionary history through integration of whole exome sequencing data from the bulk primary tumor and 16-24 microsamples taken from the bulk tumor. The evolutionary history for an individual tumor is expressed as a rooted and binary tumor developmental tree representing the mitotic process starting from an ancestral cancer cell. Individual mutations are assigned to the cells where they originally occur. The offspring size carrying a mutation was estimated based on tumor purity, variant allele frequency and the variant's copy number. Results. TEAPOT algorithm builds a tumor's evolutionary history with the following features: 1) a tumor's evolutionary history is unique for each ovarian cancer patient; 2) the size of a tree is proportional to the number of microsamples selected; 3) 16-24 microsamples builds a tree with 5 or more generations; 4) TEAPOT detects a driver mutation's occurrence at a specific developmental stage such as 1-cell, 2-cell, 4-cell, etc; 5) The size of offspring carrying a mutation thus the intra-tumor prevalence of the mutation can be estimated; 6) multiple driver mutations can be located separately in different clones. Therefore, TEAPOT provides a quantitative description of intra-tumor genetic heterogeneity and identifies sub-clonal driver mutations in a tumor. Conclusion. TEAPOT reconstructs a tumor's developmental process thus providing a patient-specific evolutionary history. Quantitation of intra-tumor prevalence of driver mutations may inform selection of an effective targeted agent and may provide rationale for cocktail treatment targeting multiple driver mutations simultaneously. TEAPOT can be also used for other solid and liquid cancers. A driver mutation's role in a patient may be functionally defined and quantitated based upon the growth advantage (fitness) it confers on its host cells in the reconstructed tumor evolutionary history. Citation Format: Jianshu Zhang, Helaman Escobar, Harshmi Shah, Mickey Miller, Yang Wei, Kristen Schneider, Michelle Knirr, Kenny Day, Christopher Johnson, Baoli Yang, Eric Devor, Kristina Thiel, Lincoln Nadauld, Kimberly Leslie, Donghai Dai. Development of TEAPOT algorithm to reconstruct individual ovarian tumors' evolutionary history based upon bulk and single cell whole exome sequencing data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 219.

THE RISK OF FACIAL FILLINGS DURING AESTHETIC PROCEDURES: A CASE REPORT

The recent evidence that extant cycads are not living fossils triggered a renewed search for a better understanding of their evolutionary history. In this study, we investigated the evolutionary diversification history of the genus Encephalartos, a monophyletic cycad endemic to Africa. We found an antisigmoidal pattern with a plateau and punctual explosive radiation. This pattern is typical of a constant radiation with mass extinction. The rate shift that we found may therefore be a result of a rapid recolonization of niches that have been emptied owing to mass extinction. Because the explosive radiation occurred during the transition Pliocene–Pleistocene, we argued that the processes might have been climatically mediated.

Ancient and modern mitogenomes of red deer reveal its evolutionary history in northern China

We examined sequence variation in the control region of the mitochondrial genome from 778 seals sampled at 161 locations from northern Japan to southeastern Alaska to learn more about the evolutionary history and population structure of, and effects of recent declines on genetic diversity in, harbor seals (Phoca vitulina) in the northern Pacific Ocean. High haplotypic diversity (H = 0.975) and a poorly resolved mitochondrial genome (mtDNA) phylogeny suggest that harbor seals in the Pacific underwent a rapid expansion in population size in their recent evolutionary past, possibly after the retreat of Pleistocene ice sheets. Weak phylogeographic partitioning of lineages attests to a complex evolutionary and demographic history of contemporary Pacific populations. Extensive macrogeographic subdivision was evident among a subset of grouped localities that represent centers of abundance along the distributional continuum. Heterogeneity was influenced by population size and correlated with geographic distance, suggesting that dispersal occurs primarily among neighboring subpopulations. The 2 currently recognized subspecies of harbor seal in the Pacific, P. v. richardii of North America and P. v. stejnegeri of Asia, do not represent phylogenetically discrete mtDNA assemblages. The greatest differentiation detected was along the Commander–Aleutian Island chain, the region of the presumed subspecies boundary and a likely contact zone for expanding refugial populations of a number of marine mammal species after retreat of ice sheets. Differentiation between the Kodiak Archipelago and Prince William Sound, and between Bristol Bay and the Pribilof Islands, indicates that current management stocks are inappropriate and highlights the need for a detailed analysis of population and stock structure in Alaska. A decline in population size in Prince William Sound over the past few decades was accompanied by a discernible reduction in mtDNA diversity, manifested as a loss of rare haplotypes through random drift. A continued population decline will erode genetic diversity further, with potentially adverse effects on evolutionary potential and individual fitness.

The development of genome sequencing techniques has revolutionized evolutionary biology, facilitating the study of adaptation and speciation at the genome level. Genomic data has also become a cornerstone in conservation management, allowing inferences of population demography and genetic diversity. We sequence the genome of the holotype specimen of the elusive lesula (Cercopithecus lomamiensis), a recently described member of the guenons (tribe Cercopithecini), endemic to the Democratic Republic of the Congo. Using published and novel genomic data, we explore the evolutionary and demographic history of C. lomamiensis and its sister species C. hamlyni. We estimate that the two species split ca. 3–4 million years ago, and find that they both show high genetic diversity despite being listed as Vulnerable on the IUCN Red List. We identify signatures of positive selection in genes involved in pelage coloration and immune functions, as well as skeletal morphology and locomotor behavior, potentially related to the terrestrial lifestyle of C. lomamiensis and C. hamlyni, which stand out among the otherwise arboreal Cercopithecus genus. We specifically explore whether introgression from more distantly related terrestrial guenons was involved in the evolution of terrestriality in the hamlyni group, but found low molecular convergence suggesting that putative terrestrial adaptations occurred largely independently. This study provides insights into the demography and evolutionary history in a poorly known, threatened primate lineage. Furthermore, our results suggest that genomic erosion is not an imminent threat to these species, and that conservation management should prioritize actions to prevent further population decline.