Using ecological niche modelling to evaluate niche stability in deep time

Aim To investigate relative niche stability in species responses to various types of environmental pressure (biotic and abiotic) on geological time‐scales using the fossil record. Location The case study focuses on Late Ordovician articulate brachiopods of the Cincinnati Arch in eastern North America. Methods Species niches were modelled for a suite of fossil brachiopod species based on five environmental variables inferred from sedimentary parameters using GARP and Maxent . Niche stability was assessed by comparison of (1) the degree of overlap of species distribution models developed for a time‐slice and those generated by projecting niche models of the previous time‐slice onto environmental layers of a second time‐slice using GARP and Maxent , (2) Schoener’s D statistic, and (3) the similarity of the contribution of each environmental parameter within Maxent niche models between adjacent time‐slices. Results Late Ordovician brachiopod species conserved their niches with high fidelity during intervals of gradual environmental change but responded to inter‐basinal species invasions through niche evolution. Both native and invasive species exhibited similar levels of niche evolution in the invasion and post‐invasion intervals. Niche evolution was related mostly to decreased variance within the former ecological niche parameters rather than to shifts to new ecospace. Main conclusions Although the species examined exhibited morphological stasis during the study interval, high levels of niche conservatism were observed only during intervals of gradual environmental change. Rapid environmental change, notably inter‐basinal species invasions, resulted in high levels of niche evolution among the focal taxa. Both native and invasive species responded with similar levels of niche evolution during the invasion interval and subsequent environmental reorganization. The assumption of complete niche conservatism frequently employed in ecological niche modelling (ENM) analyses to forecast or hindcast species geographical distributions is more likely to be accurate for climate change studies than for invasive species analyses over geological time‐scales.     

Mammalian organogenesis in deep time: tools for teaching and outreach

Mammals constitute a rich subject of study on evolution and development and provide model organisms for experimental investigations. They can serve to illustrate how ontogeny and phylogeny can be studied together and how the reconstruction of ancestors of our own evolutionary lineage can be approached. Likewise, mammals can be used to promote 'tree thinking' and can provide an organismal appreciation of evolutionary changes. This subject is suitable for the classroom and to the public at large given the interest and familiarity of people with mammals and their closest relatives. We present a simple exercise in which embryonic development is presented as a transformative process that can be observed, compared, and analyzed. In addition, we provide and discuss a freely available animation on organogenesis and life history evolution in mammals. An evolutionary tree can be the best tool to order and understand those transformations for different species. A simple exercise introduces the subject of changes in developmental timing or heterochrony and its importance in evolution. The developmental perspective is relevant in teaching and outreach efforts for the understanding of evolutionary theory today.     

Interpreting melanin-based coloration through deep time: a critical review

Colour, derived primarily from melanin and/or carotenoid pigments, is integral to many aspects of behaviour in living vertebrates, including social signalling, sexual display and crypsis. Thus, identifying biochromes in extinct animals can shed light on the acquisition and evolution of these biological traits. Both eumelanin and melanin-containing cellular organelles (melanosomes) are preserved in fossils, but recognizing traces of ancient melanin-based coloration is fraught with interpretative ambiguity, especially when observations are based on morphological evidence alone. Assigning microbodies (or, more often reported, their ‘mouldic impressions’) as melanosome traces without adequately excluding a bacterial origin is also problematic because microbes are pervasive and intimately involved in organismal degradation. Additionally, some forms synthesize melanin. In this review, we survey both vertebrate and microbial melanization, and explore the conflicts influencing assessment of microbodies preserved in association with ancient animal soft tissues. We discuss the types of data used to interpret fossil melanosomes and evaluate whether these are sufficient for definitive diagnosis. Finally, we outline an integrated morphological and geochemical approach for detecting endogenous pigment remains and associated microstructures in multimillion-year-old fossils.     

Darwin Day in deep time: promoting evolutionary science through paleontology

Charles Darwin’s birthday, February 12th, is an international celebration coined Darwin Day. During the week of his birthday, universities, museums, and science-oriented organizations worldwide host events that celebrate Darwin’s scientific achievements in evolutionary biology. The University of Tennessee, Knoxville (UT) has one of the longest running celebrations in the nation, with 2016 marking the 19th year. For 2016, the theme for our weeklong series of events was paleontology, chosen to celebrate new research in the field and to highlight the specific misconceptions of evolution within the context of geologic time. We provide insight into the workings of one of our largest and most successful Darwin Day celebration to date, so that other institutions might also be able to host their own rewarding Darwin Day events in the future.     

生态位模型的基本原理及其在生物多样性保护中的应用

生态位模型是利用物种已知的分布数据和相关环境变量,根据一定的算法来推算物种的生态需求,然后将运算结果投射至不同的空间和时间中来预测物种的实际分布和潜在分布.近年来,该类模型被越来越多地应用在入侵生物学、保护生物学、全球气候变化对物种分布影响以及传染病空间传播的研究中.然而,由于生态位模型的理论基础未被深入理解,导致得出入侵物种生态位迁移等不符合实际的结论.作者从生态位与物种分布的关系、生态位模型构建的基本原理以及生态位模型和生态位的关系等方面探讨了生态位模型的理论基础.非生物的气候因素、物种间的相互作用和物种的迁移能力是影响物种分布的3个主要因素,它们在不同的空间尺度下作用于物种的分布.生态位模型是利用物种分布点所关联的环境变量来模拟物种的分布,这些分布点本身关联着该物种和其他物种间的相互作用,因此生态位模型所模拟的是现实生态位(realized niche)或潜在生态位(potential niche),而不是基础生态位(fundamental niche).Grinnell生态位和Elton生态位均在生态位模型中得到反映,这取决于环境变量类型的选择、所采用环境变量的分辨率以及物种自身的迁移能力.生态位模型在生物多样性保护中的应用主要包括物种的生态需求分析、未知物种或种群的探索和发现、自然保护区的选择和设计、物种入侵风险评价、气候变化对物种分布的影响、近缘物种生态位保守性及基于生态位分化的物种界定等方面.     

Mammalian viviparity: a complex niche in the evolution of genomic imprinting

Evolution of mammalian reproductive success has witnessed a strong dependence on maternal resources through placental in utero development. Genomic imprinting, which has an active role in mammalian viviparity, also reveals a biased role for matrilineal DNA in its regulation. The co-existence of three matrilineal generations as one (mother, foetus and post-meiotic oocytes) has provided a maternal niche for transgenerational co-adaptive selection pressures to operate. In utero foetal growth has required increased maternal feeding in advance of foetal energetic demands; the mammary glands are primed for milk production in advance of birth, while the maternal hypothalamus is hormonally primed by the foetal placenta for nest building and post-natal care. Such biological forward planning resulted from maternal–foetal co-adaptation facilitated by co-expression of the same imprinted allele in the developing hypothalamus and placenta. This co-expression is concurrent with the placenta interacting with the adult maternal hypothalamus thereby providing a transgenerational template on which selection pressures may operate ensuring optimal maternalism in this and the next generation. Invasive placentation has further required the maternal immune system to adapt and positively respond to the foetal allotype. Pivotal to these mammalian evolutionary developments, genomic imprinting emerged as a monoallelic gene dosage regulatory mechanism of tightly interconnected gene networks providing developmental genetic stability for in utero development.     

Requirements for plant coexistence through pollination niche partitioning

Plant–pollinator interactions are often thought to have been a decisive factor in the diversification of flowering plants, but to be of little or no importance for the maintenance of existing plant diversity. In a recent opinion paper, Pauw (2013 Trends Ecol. Evol. 28, 30–37. (doi:10.1016/j.tree.2012.07.019)) challenged this view by proposing a mechanism of diversity maintenance based on pollination niche partitioning. In this article, I investigate under which conditions the mechanism suggested by Pauw can promote plant coexistence, using a mathematical model of plant and pollinator population dynamics. Numerical simulations show that this mechanism is most effective when the costs of searching for flowers are low, pollinator populations are strongly limited by resources other than pollen and nectar, and plant–pollinator interactions are sufficiently specialized. I review the empirical literature on these three requirements, discuss additional factors that may be important for diversity maintenance through pollination niche partitioning, and provide recommendations on how to detect this coexistence mechanism in natural plant communities.     

Microbial minorities modulate methane consumption through niche partitioning

Microbes catalyze all major geochemical cycles on earth. However, the role of microbial traits and community composition in biogeochemical cycles is still poorly understood mainly due to the inability to assess the community members that are actually performing biogeochemical conversions in complex environmental samples. Here we applied a polyphasic approach to assess the role of microbial community composition in modulating methane emission from a riparian floodplain. We show that the dynamics and intensity of methane consumption in riparian wetlands coincide with relative abundance and activity of specific subgroups of methane-oxidizing bacteria (MOB), which can be considered as a minor component of the microbial community in this ecosystem. Microarray-based community composition analyses demonstrated linear relationships of MOB diversity parameters and in vitro methane consumption. Incubations using intact cores in combination with stable isotope labeling of lipids and proteins corroborated the correlative evidence from in vitro incubations demonstrating γ-proteobacterial MOB subgroups to be responsible for methane oxidation. The results obtained within the riparian flooding gradient collectively demonstrate that niche partitioning of MOB within a community comprised of a very limited amount of active species modulates methane consumption and emission from this wetland. The implications of the results obtained for biodiversity–ecosystem functioning are discussed with special reference to the role of spatial and temporal heterogeneity and functional redundancy.     

Mulberry biodiversity conservation through cryopreservation

A 238 mulberry germplasm accession collection from diverse regions maintained under tropical conditions was identified from an ex situ field gene bank. The purpose was to prioritize the in vitro conservation and cryopreservation to develop long-term biodiversity conservation for ensuring sustainable utilization of these valuable resources. Reliable cryo techniques using desiccation and slow freezing of winter-dormant buds were used. Storage potential of bud grafts of different Morus species at −1.5°C for 90 d indicated species-specific variation, and most of the wild species were found sensitive. In vitro regeneration and cryopreservation (−196°C) protocols using differentiated bud meristems, like axillary winter-dormant buds, were worked out for a wide range of landraces, wild, and cultivated varieties of Morus. Buds maintained under subtropical location are also amenable for cryopreservation. Successful cryopreservation of winter-dormant buds belonging to Morus indica, Morus alba, Morus latifolia, Morus cathayana, Morus laevigata, Morus nigra, Morus australis, Morus bombycis, Morus sinensis, Morus multicaulis, and Morus rotundiloba was achieved. Among wild species, Morus tiliaefolia and Morus serrata showed moderate recovery after cryopreservation. Survival rates did not alter after 3 yr of cryopreservation. Inter-simple sequence repeat markers were used to ascertain the genetic stability of cryopreserved mulberry germplasm accessions, which showed no difference detected among the plantlets regenerated from frozen apices in comparison to the nonfrozen material.     

Mammalian hexokinase 1: Evolutionary conservation and structure to function analysis

We have amplified and sequenced the complete coding region of bovine hexokinase isoenzyme 1 (HK1) from brain RNA with PCR primers selected for sequence conservation. The sequence information was analyzed to evaluate the evolutionary and structure-function relationships among the mammalian and yeast HK isoenzymes. Structure to function analysis identified an unduplicated, invariant N-terminal domain involved in HK1 outer mitochondrial membrane targeting, as well as putative carbohydrate and nucleotide-binding sites in the regulatory and catalytic halves of HK1 essential to enzyme function. The ATP-binding site in the catalytic half of the HK1 protein resembles nucleotide-binding regions from protein kinases, with the single amino acid replacement (lysine to glutamate) in the ATP-binding site of the amino half explaining the loss of HK1 catalytic function in the regulatory domain. Sequence comparisons suggest that the 50-kDa mammalian and yeast glucokinases arose separately in evolution. In addition to providing valuable phylogenetic and structure-function insights, this work provides an efficient strategy for rapid cloning and sequencing of the coding regions for other HKs and related proteins.     

Trophoblasts regulate the placental hematopoietic niche through PDGF-B signaling

The placenta is a hematopoietic organ that supports hematopoietic stem/progenitor cell (HSPC) generation and expansion without promoting differentiation. We identified PDGF-B signaling in trophoblasts as a key component of the unique placental hematopoietic microenvironment that protects HSPCs from premature differentiation. Loss of PDGF-B or its receptor, PDGFRβ, induced definitive erythropoiesis in placental labyrinth vasculature. This was evidenced by accumulation of CFU-Es and actively proliferating definitive erythroblasts that clustered around central macrophages, highly reminiscent of erythropoiesis in the fetal liver. Ectopic erythropoiesis was not due to a requirement of PDGF-B signaling in hematopoietic cells but rather in placental trophoblasts, which upregulated Epo in the absence of PDGF-B signaling. Furthermore, overexpression of hEPO specifically in the trophoblasts in vivo was sufficient to convert the placenta into an erythropoietic organ. These data provide genetic evidence of a signaling pathway that is required to restrict erythroid differentiation to specific anatomical niches during development.     

Reconciling niche and neutrality through the Emergent Group approach

Both niche and neutral theories have been suggested as potential frameworks for modelling biodiversity. Niche models assume that biological traits represent evolutionary adaptations and define individuals in terms of functional trade-offs. Neutral models assume that all individuals at a single trophic level are functionally equivalent on a per capita basis with respect to their birth, death, dispersal and speciation. The opinion of many researchers is that neutral and niche processes operate simultaneously to generate diversity without knowing how the unification of both models can be achieved. Recently, several theoretical papers have reported evidence on the evolutionary emergence of niche structures shaping the emergence of groups of similar species. In this way, an Emergent Group is defined as a set of species that have a similar functional niche owing to a convergent ecological strategy. Central to the Emergent Group concept are the assumptions of functional equivalence within and of functional divergence between Emergent Groups. Within an Emergent Group, species richness is subject to a zero-sum rule set by the balance between the rate of individual loss and of immigration. Between Emergent Groups, tradeoffs such as seed size/seedling competitivity, investment in reproductive system/investment in vegetative systems or competitive ability/predator invulnerability are cornerstones of the evolutionary divergence. Delineating Emergent Groups amounts to reaching a compromise between maximizing niche differentiation (i.e. maximizing differences in functional tradeoffs) between Emergent Groups and maximizing neutrality within Emergent Groups. Up to now, the Emergent Group concept has been mostly proposed by theoretical scientists but it should be tested by empirical ecologists. The way in which niche and neutral models could be combined provides a profitable opportunity for theoretical and empirical scientists to collaborate fruitfully.     

Resource-based habitat definition, niche overlap and conservation of two sympatric glacial relict butterflies

The precise knowledge of ecological resources and conditions required by species threatened by rapidly changing environmental conditions is of prime importance for conservation biology. Transferability of this knowledge between species with similar ecological requirements is often assumed, but rarely tested. This is especially the case for glacial relict populations confined to climate‐habitat traps from where they cannot move to rejoin areas with suitable environmental conditions. Using two glacial relict butterflies as model organisms, we first quantitatively define larval and adult resource‐based habitat use of each species. Secondly, we test the transferability of ecological profiles (both habitat and ecological niche) between these two species that share both the same biotope and the same host plant. Our results show that both species have markedly different ecological requirements relating to differences in life history and behavioural traits (i.e. egg‐laying strategies and mate‐locating behaviour). Although the two species share many ecological features, they use different functional habitats within our study site. The high degree of interspecific niche overlap should indicate a high interspecific competition. However, we argue that their co‐existence can be explained by the non‐limiting abundance of some resources (e.g. host plants), by the partial separation in time of adult flight periods and by the territorial behaviour of one of the species. We discuss the following general messages: (1) functional habitat of a (threatened) species should be defined in a spatial context corresponding to individual station keeping, and (2) quick diagnosis based on similar ecological requirements may be misleading for the design of reliable conservation and restoration strategies. Detailed mechanistic and quantitative ecological understanding of resource‐use and environmental tolerances across an organism's life cycle is essential for effective conservation in changing environments, like for glacial relict species.     

Mammalian Bax initiates plant cell death through organelle destruction

Mammalian Bax is known to cause cell death when expressed in plants. We examined transgenic plants expressing both Bax and organelle-targeted green fluorescent protein to determine the cellular changes that occur during Bax-induced cell death. The mitochondria changed morphologically from being bacilli-shaped to being round, eventually becoming swollen. Mitochondria streaming also stopped. The chloroplasts lost membrane function and their contents leaked out, followed by the disruption of the vacuole. Light was not essential for Bax-induced ion leakage or organelle disruption. These results indicate that Bax induces temporal and spatial cell death events at the organelle level in the plant. A heterologous system, using Bax, would therefor be available to investigate cell death, which is commonly conserved in animals and plantsElectronic Supplementary Material Supplementary material is available for this article at     

Evolutionary conservation of equine gc alleles and of Mammalian gc/albumin linkage

Ancient origin of the equine vitamin D binding protein (Gc) polymorphism is suggested by the finding of two alleles, Gc^F and Gc^S, in each of three equine subgenera, Equus, Asinus and Hippotigris. The equine Gc and albumin loci are closely linked (lod score = 6). Although no recombinants were observed, the data are not inconsistent with a map distance similar to the 2 centimorgans reported for the human albumin/Gc linkage relationship. Gametic association between the Gc^F and Alb^F alleles appears probable in the American Standardbred horse, perhaps as a result of population structure. Since Gc and albumin are both polymorphic in rodents and possibly other orders, this linkage group will be useful for studies of the evolution of mammalian linkage groups, as well as for a comparison of meiotic recombination frequencies and linkage disequilibria in different species.     

Energy conservation through recycling of used oil

This study concentrates on the investigation of energy and environmental benefits for used oil pertaining to its reuse through: (i) recovering the heating value of used oils in a combustion process and (ii) re-refining of used oil to produce fresh lube oil products. Tests were made with the used oil samples by ICP technique and the results were compared with standard requirements. We have found that the problems could successfully be solved through used oil management practices including collection centers, transporters, and processors by providing encouragement and financial support towards the re-refining industry. The novelty and value of our work lies in the conclusion that reformulation of motor oil results in lower levels of hazardous elements in used oils.     

Mammalian endemism,range size and conservation status in the southern temperate zone

Aim To examine the taxonomic uniqueness, range sizes, endemism and conservation status of southern temperate zone mammals and how factors impacting their conservation differ across hemispheres. Location Land surfaces of all continents (with the exception of Antarctica) and continental islands with an emphasis on the southern temperate hemisphere (land south of the Tropic of Capricorn). Methods We used data from the 2008 IUCN Red List of Threatened Species to characterize conservation status, threats and range sizes to compare northern and southern temperate zone mammals. We assessed the taxonomic uniqueness of the two regions as derived from the EDGE programme. We also conducted a gap analysis by overlapping mammal ranges with protected area coverages for temperate regions. Results Southern temperate species are phylogenetically more unique than in the Northern Hemisphere. The endemics have significantly smaller range sizes and are at a significantly greater risk of extinction (about 50% greater, with 24.7% of species being threatened versus 15.6% in the Northern Hemisphere). Finally, southern temperate endemics are significantly more likely to exist outside protected areas (13.38% versus 3.65%). Main conclusions The southern temperate zone harbours a unique fauna, attributed to the long isolation from the northern temperate zone. Temperate regions are heavily exploited for human activities, especially grazing and agriculture. The Southern Hemisphere is particularly susceptible to disturbance, given the small range sizes of its species and the low degree of protected area coverage. The scenario now is one of regions with numerous endemics under high threat from human activities.