For several decades, economists have been warning the academic community that graduate training has been too tightly focused on careers in higher education, using the apprenticeship model in which students are trained to become tenure-track faculty at research-focused institutions. These jobs are simply not growing at the same rate as graduate admissions. In biomedical research, the mismatch in supply and demand has now been widely recognized. Other disciplines have begun these discussions, but for smaller fields, employment trends are more difficult to identify because they are subsumed in aggregated national statistics. For non-biomedical biological fields in particular, such as ecology, using biology statistics may be inappropriate since trends within the field may be obscured by the strong signal from biomedical disciplines. Here, we use the 2013 Survey of Doctorate Recipients (SDR) to investigate career paths for ecology Ph.D. recipients in the United States, and present the first fine-scale national profile of careers in ecology. Our results demonstrate that while involuntary unemployment is low for ecology Ph.D. recipients (3.3%) and job satisfaction is high, the assumptions of the prevailing apprenticeship model are inappropriate: Less than 20% of employed recent ecology Ph.D. graduates are in tenure-track positions at a Ph.D.-granting university. Accordingly, proactive steps could be taken to create more realistic expectations about graduate training and preparation for diverse careers. Further, the SDR data provide demographic profiles for ecology. Ethnic diversity has remained low in ecology (7.5% non-Caucasian for Ph.D. recipients since 2000). Gender balance in career-track positions appears to have improved by multiple metrics. However, women are overrepresented in non-tenure-track academic positions, where access to resources that support professional advancement may be limited relative to tenure-track jobs, and salary disparities appear for women in private academic institutions. Thus, while there is much good news in these data, we suggest that ecology as a field would benefit from (1) a broad analysis of the training required to make Ph.D.s best prepared for jobs outside of the research-oriented tenure track and (2) continued attention to increasing diversity and equity.

Ras converting enzyme 1 (Rce1) is an integral membrane endoprotease localized to the endoplasmic reticulum that mediates the cleavage of the carboxyl-terminal three amino acids from CaaX proteins, whose members play important roles in cell signaling processes. Examples include the Ras family of small GTPases, the gamma-subunit of heterotrimeric GTPases, nuclear lamins, and protein kinases and phosphatases. CaaX proteins, especially Ras, have been implicated in cancer, and understanding the post-translational modifications of CaaX proteins would provide insight into their biological function and regulation. Many proteolytic mechanisms have been proposed for Rce1, but sequence alignment, mutational studies, topology, and recent crystallographic data point to a novel mechanism involving a glutamate-activated water and an oxyanion hole. Studies using in vivo and in vitro reporters of Rce1 activity have revealed that the enzyme cleaves only prenylated substrates and the identity of the a(2) amino residue in the Ca(1)a(2)X sequence is most critical for recognition, preferring Ile, Leu, or Val. Substrate mimetics can be somewhat effective inhibitors of Rce1 in vitro. Small-molecule inhibitor discovery is currently limited by the lack of structural information on a eukaryotic enzyme, but a set of 8-hydroxyquinoline derivatives has demonstrated an ability to mislocalize all three mammalian Ras isoforms, giving optimism that potent, selective inhibitors might be developed. Much remains to be discovered regarding cleavage specificity, the impact of chemical inhibition, and the potential of Rce1 as a therapeutic target, not only for cancer, but also for other diseases.

Elevated allochthonous inputs of organic matter are increasingly recognized as a driver of ecosystem change in lakes, particularly when concurrent with eutrophication. Evaluation of lakes in a nutrient-color paradigm (i.e., based on total phosphorus and true color) enables a more robust approach to research and management. To assess temporal and spatial patterns in nutrient-color status for U.S. lakes and associated food web attributes, we analyzed the U.S. Environmental Protection Agency's National Lakes Assessment (NLA) data. With 1000+ lakes sampled in 2007 and 2012 in a stratified random sampling design, the NLA enables rigorous assessment of lake condition across the continental U.S. We demonstrate that many U.S. lakes are simultaneously experiencing eutrophication and brownification to produce an abundance of "murky" lakes. Overall, "blue" lakes decreased by similar to 18% (46% of lakes in 2007 to 28% in 2012) while "murky" lakes increased by almost 12% (24% of lakes in 2007 to 35.4% in 2012). No statistical differences were observed in the proportions of "green" or "brown" lakes. Regionally, murky lakes significantly increased in the Northern Appalachian, Southern Plains, and Xeric ecoregions. Murky lakes exhibited the highest epilimnetic chlorophyll a concentrations, cyanobacterial densities, and microcystin concentrations. Total zooplankton biomass was also highest in murky lakes, primarily due to increased rotifer and copepod biomass. However, zooplankton : phytoplankton biomass ratios were low, suggesting reduced energy transfer to higher trophic levels. These results emphasize that many lakes in the U.S. are simultaneously "greening" and "browning", with potentially negative consequences for water quality and food web structure.

Winter is an important season for many limnological processes, which can range from biogeochemical transformations to ecological interactions. Interest in the structure and function of lake ecosystems under ice is on the rise. Although limnologists working at polar latitudes have a long history of winter work, the required knowledge to successfully sample under winter conditions is not widely available and relatively few limnologists receive formal training. In particular, the deployment and operation of equipment in below 0 degrees C temperatures pose considerable logistical and methodological challenges, as do the safety risks of sampling during the ice-covered period. Here, we consolidate information on winter lake sampling and describe effective methods to measure physical, chemical, and biological variables in and under ice. We describe variation in snow and ice conditions and discuss implications for sampling logistics and safety. We outline commonly encountered methodological challenges and make recommendations for best practices to maximize safety and efficiency when sampling through ice or deploying instruments in ice-covered lakes. Application of such practices over a broad range of ice-covered lakes will contribute to a better understanding of the factors that regulate lakes during winter and how winter conditions affect the subsequent ice-free period.

Reproducibility is a key tenet of the scientific process that dictates the reliability and generality of results and methods. The complexities of ecological observations and data present novel challenges in satisfying needs for reproducibility and also transparency. Ecological systems are dynamic and heterogeneous, interacting with numerous factors that sculpt natural history and that investigators cannot completely control. Observations may be highly dependent on spatial and temporal context, making them very difficult to reproduce, but computational reproducibility can still be achieved. Computational reproducibility often refers to the ability to produce equivalent analytical outcomes from the same data set using the same code and software as the original study. When coded workflows are shared, authors and editors provide transparency for readers and allow other researchers to build directly and efficiently on primary work. These qualities may be especially important in ecological applications that have important or controversial implications for science, management, and policy. Expectations for computational reproducibility and transparency are shifting rapidly in the sciences. In this work, we highlight many of the unique challenges for ecology along with practical guidelines for reproducibility and transparency, as ecologists continue to participate in the stewardship of critical environmental information and ensure that research methods demonstrate integrity.

Ancient lakes are among the best archivists of past environmental change, having experienced more than one full glacial cycle, a wide range of climatic conditions, tectonic events, and long association with human settlements. These lakes not only record long histories of environmental variation and human activity in their sediments, but also harbor very high levels of biodiversity and endemism. Yet, ancient lakes are faced with a familiar suite of anthropogenic threats, which may degrade the unusual properties that make them especially valuable to science and society. In all ancient lakes for which data exist, significant warming of surface waters has occurred, with a broad range of consequences. Eutrophication threatens both native species assemblages and regional economies reliant on clean surface water, fisheries, and tourism. Where sewage contributes nutrients and heavy metals, one can anticipate the occurrence of less understood emerging contaminants, such as pharmaceuticals, personal care products, and microplastics that negatively affect lake biota and water quality. Human populations continue to increase in most of the ancient lakes' watersheds, which will exacerbate these concerns. Further, human alterations of hydrology, including those produced through climate change, have altered lake levels. Co-occurring with these impacts have been intentional and unintentional species introductions, altering biodiversity. Given that the distinctive character of each ancient lake is strongly linked to age, there may be few options to remediate losses of species or other ecosystem damage associated with modern ecological change, heightening the imperative for understanding these systems.

The ice-covered period on lakes in the northern hemisphere has often been neglected or assumed to have less importance relative to the open water season. However, recent studies challenge this convention, suggesting that the winter period is more dynamic than previously thought. In this review, we synthesize the current understanding of under-ice carbon dioxide (CO2) and methane (CH4) dynamics, highlighting the annual importance of CO2 and CH4 emissions from lakes at ice-melt. We compiled data from 25 studies that showed that the ice-melt period represents 17% and 27% of the annual CO2 and CH4 emissions, respectively. We also found evidence that the magnitude and type of emission (i.e., CO2 and CH4) varies with characteristics of lakes including geographic location, lake morphometry, and physicochemical conditions. The scarcity of winter and spring carbon data from northern lakes represents a major gap in our understanding of annual budgets in these lakes and calls for future research during this key period.

Food production hinges largely upon access to phosphorus (P) fertilizer. Most fertilizer P used in the global agricultural system comes from mining of nonrenewable phosphate rock deposits located within few countries. However, P contained in livestock manure or urban wastes represents a recyclable source of P. To inform development of P recycling technologies and policies, we examined subnational, national, and global spatial patterns for two intersections of land use affording high P recycling potential: (a) manure-rich cultivated areas and (b) populous cultivated areas. In turn, we examined overlap between P recycling potential and nation-level P fertilizer import dependency. Populous cultivated areas were less abundant globally than manure-rich cultivated areas, reflecting greater segregation between crops and people compared to crops and livestock, especially in the Americas. Based on a global hexagonal grid (290-km(2) grid cell area), disproportionately large shares of subnational "hot spots" for P recycling potential occurred in India, China, Southeast Asia, Europe, and parts of Africa. Outside of China, most of the remaining manure-rich or pulous cultivated areas occurred within nations that had relatively high imports of P fertilizer (net P import:consumption ratios >= 0.4) or substantial increases in fertilizer demand between the 2000s (2002-2006) and 2010s (2010-2014). Manure-rich cultivated grid cells (those above the 75th percentiles for both manure and cropland extent) represented 12% of the global grid after excluding cropless cells. Annually, the global sum of animal manure P was at least 5 times that contained in human excreta, and among cultivated cells the ratio was frequently higher (median = 8.9). The abundance of potential P recycling hot spots within nations that have depended on fertilizer imports or experienced rising fertilizer demand could prove useful for developing local P sources and maintaining agricultural independence.