Climate influences a population through a variety of processes, including reproduction, growth, migration patterns and phenology. Climate may operate either directly through metabolic and reproductive processes or indirectly through prey, predators, and competitors. One mechanism that may be particularly important, and which is the focus of this review, is the role of climate in affecting the reproductive success of a predator through its effect on the relative timing of food requirement and food availability during early life stages. This principle -the match or mismatch of predators' requirement with resource availability -originated in the marine literature, where it initially referred to how growth and survival of fish larvae (predator) depends on this production being synchronous with that of their main food items, i.e. early stage zooplankton (prey). Here we review how the match/mismatch hypothesis (MMH) is used to describe climate effects on ecological patterns and processes in both marine and terrestrial systems. In addition to studying match/mismatch sensu stricto, we expand on it to include effects of overall production level and the spatial aspect. Possible impacts of climate change on match/mismatch are examined in the context of one of the most apparent effects of global warming: an advancement of spring phenology. As a consequence of different species reacting dissimilarly, even minor changes in climate may invoke non-linear responses unbalancing established patterns of synchrony. All components of a food chain cannot be expected to shift their phenology at the same rate, and thus are unlikely to remain synchronous.

With over 32,000 extant species 1 , teleost fishes comprise the majority of vertebrate species. Their taxonomic diversity is matched by extensive genetic and phenotypic variation, including novel immunological strategies. Although the functionality of the adaptive immune system has been considered to be conserved since its emergence in the ancestor of all jawed vertebrates 2,3 , fundamental modifications of the immune gene repertoire have recently been reported in teleosts [4][5][6][7] . One of the most dramatic changes has occurred in Atlantic cod (Gadus morhua), involving complete loss of the MHC II pathway that is otherwise responsible for the detection of bacterial pathogens in vertebrates 4 . Moreover, this loss is accompanied by a substantially enlarged repertoire of MHC I genes, which normally encode molecules for protection against viral pathogens. It has thus been hypothesized that the expanded MHC I repertoire of cod evolved as a compensatory mechanism, whereby broader MHC I functionality makes up for the initial loss of MHC II (refs. 4,6). However, the questions of how and when MHC II was lost relative to the MHC I expansion, and whether these genomic modifications are causally related, have so far remained unresolved.As key components of the vertebrate adaptive immune system, the complex MHC pathways and their functionality are now well characterized 8-10 , but less is known about the causes of MHC copy number variation, which poses an immunological tradeoff 11,12 . Although an increase in the number of MHC genes facilitates pathogen detection, it will also decrease the number of circulating T cells [13][14][15][16] , resulting in an immune system that can detect a large number of pathogens at the expense of being less efficient in removing them. The evolution of MHC copy numbers is therefore likely driven toward intermediate optima determined by a tradeoff between detection and elimination of pathogens-as suggested by selection for 5-10 copies inferred in case studies of fish 17,18 and birds 19 . Because pathogen load and the associated selective pressures vary between habitats, the optimal number of MHC copies depends on the environment [20][21][22] . As a result, interbreeding between different locally adapted populations is expected to produce hybrids with excess (above optimal) MHC diversity that are characterized by T cell deprivation and low fitness. This process would introduce postzygotic reproductive isolation and promote reinforcement of premating isolation between the populations. Consequently, MHC genes have been suggested to have an important role in speciation 22,23 , but, to our knowledge, this role has never been tested comparatively in a macroevolutionary context.Here we report comparative analyses of 76 teleost species, of which 66 were sequenced to produce partial draft genome assemblies, including 27 representatives of cod-like fishes within the order Gadiformes. First, we use phylogenomic analysis to resolve standing controversy regarding early-teleost divergences and to firmly ...

Conservation of species and ecosystems is increasingly difficult because anthropogenic impacts are pervasive and accelerating. Under this rapid global change, maximizing conservation success requires a paradigm shift from maintaining ecosystems in idealized past states toward facilitating their adaptive and functional capacities, even as species ebb and flow individually. Developing effective strategies under this new paradigm will require deeper understanding of the long-term dynamics that govern ecosystem persistence and reconciliation of conflicts among approaches to conserving historical versus novel ecosystems. Integrating emerging information from conservation biology, paleobiology, and the Earth sciences is an important step forward on the path to success. Maintaining nature in all its aspects will also entail immediately addressing the overarching threats of growing human population, overconsumption, pollution, and climate change.

Dengue, a viral infection transmitted between people by mosquitoes, is one of the most rapidly spreading diseases in the world. Here, we report the analyses covering 11 y (2005)(2006)(2007)(2008)(2009)(2010)(2011)(2012)(2013)(2014)(2015) from the city of Guangzhou in southern China. Using the first 8 y of data to develop an ecologically based model for the dengue system, we reliably predict the following 3 y of dengue dynamics-years with exceptionally extensive dengue outbreaks. We demonstrate that climate conditions, through the effects of rainfall and temperature on mosquito abundance and dengue transmission rate, play key roles in explaining the temporal dynamics of dengue incidence in the human population. Our study thus contributes to a better understanding of dengue dynamics and provides a predictive tool for preventive dengue reduction strategies.D engue is one of the most rapidly spreading diseases in the world (1), including within the Guangdong province of southern China (2). During the last 50 y, the incidence of dengue has increased 30-fold with increasing geographic expansion to new countries (1). In 2010, an estimated 390 million dengue infections occurred, of which around 96 million showed symptoms (3). Dengue outbreaks in China were previously thought to be imported and initiated by people traveling to China from dengue-endemic areas elsewhere (4); however, recent studies suggest that dengue may now be endemic to China as well (2). The epidemiological triangle of both dengue fever and dengue hemorrhagic fever, which is the more serious form of dengue, includes hosts (humans), pathogens (one or more of five dengue virus serotypes) (5), and mosquito vectors (Aedes albopictus and Aedes aegypti) with their ecological interactions (6). The dengue outbreaks are qualitatively known to be strongly influenced by temperature (7), humidity, rainfall, and socioeconomic factors like urbanization (8). However, a full understanding of the quantitative nature of such effects is largely lacking. With this paper, we provide such a quantitative understanding of dengue dynamics.In 2014, an extensive dengue outbreak hit China, with 47,127 dengue cases diagnosed, a new record since 1986 (9). Since the 1990s, dengue epidemics have gradually spread from Guangdong, Hainan, and Guangxi provinces (9). We present here a time series analysis of dengue dynamics, using dengue surveillance data for the years 2005−2015 from Guangzhou, the largest city in Guangdong and the city with the most dengue cases in China. We split the main analysis by using the first 8 y to develop a model, and the three remaining years to test that model, as these latter years encompass exceptionally extensive dengue outbreaks.Monthly human dengue incidence data (number of diagnosed cases) were obtained from the China National Notifiable Disease Surveillance System (10) (Fig. 1). Monthly surveillance data of A. albopictus density, the only dengue vector species in Guangzhou, were obtained from local Centers for Disease Control and Prevention (11) (Metho...

Adaptation to local conditions is a fundamental process in evolution; however, mechanisms maintaining local adaptation despite high gene flow are still poorly understood. Marine ecosystems provide a wide array of diverse habitats that frequently promote ecological adaptation even in species characterized by strong levels of gene flow. As one example, populations of the marine fish Atlantic cod (Gadus morhua) are highly connected due to immense dispersal capabilities but nevertheless show local adaptation in several key traits. By combining population genomic analyses based on 12K single nucleotide polymorphisms with larval dispersal patterns inferred using a biophysical ocean model, we show that Atlantic cod individuals residing in sheltered estuarine habitats of Scandinavian fjords mainly belong to offshore oceanic populations with considerable connectivity between these diverse ecosystems. Nevertheless, we also find evidence for discrete fjord populations that are genetically differentiated from offshore populations, indicative of local adaptation, the degree of which appears to be influenced by connectivity. Analyses of the genomic architecture reveal a significant overrepresentation of a large~5 Mb chromosomal rearrangement in fjord cod, previously proposed to comprise genes critical for the survival at low salinities. This suggests that despite considerable connectivity with offshore populations, local adaptation to fjord environments may be enabled by suppression of recombination in the rearranged region. Our study provides new insights into the potential of local adaptation in high gene flow species within fine geographical scales and highlights the importance of genome architecture in analyses of ecological adaptation. K E Y W O R D Schromosomal inversion, ecological adaptation, Gadus morhua, gene flow, population divergence ----------------------------------------------------------------------------------------------------------------------------------------------------------------------This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. | INTRODUCTIONLocal adaptation characterizes populations that experience higher inherited fitness in their native habitat compared to members of other populations transferred to the same environment (Kawecki & Ebert, 2004). The degree of such ecological adaptation depends on the directional selection of advantageous traits and is counteracted by high connectivity and resulting homogenizing gene flow, implicating a limited potential for local adaptation in populations experiencing high gene flow (Dobzhansky, 1937;Mayr, 1942;Wright, 1931).Although environmental adaptation can also involve gene expression-induced plastic responses such as morphological, physiological or behavioural changes, these occur without genotypic changes (Reusch, 2014;Via et al., 1995).Most marine fish populations have traditionally been regar...

Dengue is a climate-sensitive mosquito-borne disease with increasing geographic extent and human incidence. Although the climate–epidemic association and outbreak risks have been assessed using both statistical and mathematical models, local mosquito population dynamics have not been incorporated in a unified predictive framework. Here, we use mosquito surveillance data from 2005 to 2015 in China to integrate a generalized additive model of mosquito dynamics with a susceptible–infected–recovered (SIR) compartmental model of viral transmission to establish a predictive model linking climate and seasonal dengue risk. The findings illustrate that spatiotemporal dynamics of dengue are predictable from the local vector dynamics, which in turn, can be predicted by climate conditions. On the basis of the similar epidemiology and transmission cycles, we believe that this integrated approach and the finer mosquito surveillance data provide a framework that can be extended to predict outbreak risk of other mosquito-borne diseases as well as project dengue risk maps for future climate scenarios.

Knowledge of the range and chronology of historic trade and long-distance transport of natural resources is essential for determining the impacts of past human activities on marine environments. However, the specific biological sources of imported fauna are often difficult to identify, in particular if species have a wide spatial distribution and lack clear osteological or isotopic differentiation between populations. Here, we report that ancient fishbone remains, despite being porous, brittle, and light, provide an excellent source of endogenous DNA (15-46%) of sufficient quality for whole-genome reconstruction. By comparing ancient sequence data to that of modern specimens, we determine the biological origin of 15 Viking Age (800-1066 CE) and subsequent medieval (1066-1280 CE) Atlantic cod (Gadus morhua) specimens from excavation sites in Germany, Norway, and the United Kingdom. Archaeological context indicates that one of these sites was a fishing settlement for the procurement of local catches, whereas the other localities were centers of trade. Fish from the trade sites show a mixed ancestry and are statistically differentiated from local fish populations. Moreover, Viking Age samples from Haithabu, Germany, are traced back to the North East Arctic Atlantic cod population that has supported the Lofoten fisheries of Norway for centuries. Our results resolve a long-standing controversial hypothesis and indicate that the marine resources of the North Atlantic Ocean were used to sustain an international demand for protein as far back as the Viking Age.genomics | high-throughput sequencing | trade | chromosomal inversion | fish bone

SignificanceWhile our knowledge of modern plague reservoirs and their hosts is extensive, we have little to no knowledge about the origin of the Medieval plague pandemics or the routes of transmission involved in their spread. Prior genomic data provide a patchy low-resolution picture of the transmission dynamics involved during the Second Plague Pandemic, with only five distinct genomes. We have reevaluated all Medieval strains under the light of archaeological and historical evidence to carefully discuss the involvement of different transmission routes during the Second Plague Pandemic. Our interpretation showcases the importance of trade routes and human movements and further supports the identification of Yersinia pestis as the pathogenic agent of the so-called pestis secunda (1357–1366).