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1.
Rachel M. Wright Hanaka Mera Carly D. Kenkel Maria Nayfa Line K. Bay Mikhail V. Matz 《Global Change Biology》2019,25(10):3294-3304
Climate change threatens organisms in a variety of interactive ways that requires simultaneous adaptation of multiple traits. Predicting evolutionary responses requires an understanding of the potential for interactions among stressors and the genetic variance and covariance among fitness‐related traits that may reinforce or constrain an adaptive response. Here we investigate the capacity of Acropora millepora, a reef‐building coral, to adapt to multiple environmental stressors: rising sea surface temperature, ocean acidification, and increased prevalence of infectious diseases. We measured growth rates (weight gain), coral color (a proxy for Symbiodiniaceae density), and survival, in addition to nine physiological indicators of coral and algal health in 40 coral genets exposed to each of these three stressors singly and combined. Individual stressors resulted in predicted responses (e.g., corals developed lesions after bacterial challenge and bleached under thermal stress). However, corals did not suffer substantially more when all three stressors were combined. Nor were trade‐offs observed between tolerances to different stressors; instead, individuals performing well under one stressor also tended to perform well under every other stressor. An analysis of genetic correlations between traits revealed positive covariances, suggesting that selection to multiple stressors will reinforce rather than constrain the simultaneous evolution of traits related to holobiont health (e.g., weight gain and algal density). These findings support the potential for rapid coral adaptation under climate change and emphasize the importance of accounting for corals’ adaptive capacity when predicting the future of coral reefs. 相似文献
2.
Yuna Zayasu Yuichi Nakajima Kazuhiko Sakai Go Suzuki Noriyuki Satoh Chuya Shinzato 《Ecology and evolution》2016,6(15):5491-5505
To establish effective locations and sizes of potential protected areas for reef ecosystems, detailed information about source and sink relationships between populations is critical, especially in archipelagic regions. Therefore, we assessed population structure and genetic diversity of Acropora tenuis, one of the dominant stony coral species in the Pacific, using 13 microsatellite markers to investigate 298 colonies from 15 locations across the Nansei Islands in southwestern Japan. Genetic diversity was not significant among sampling locations, even in possibly peripheral locations. In addition, our results showed that there are at least two populations of A. tenuis in the study area. The level of genetic differentiation between these populations was relatively low, but significant between many pairs of sampling locations. Directions of gene flow, which were estimated using a coalescence‐based approach, suggest that gene flow not only occurs from south to north, but also from north to south in various locations. Consequently, the Yaeyama Islands and the Amami Islands are potential northern and southern sources of corals. On the other hand, the Miyako Islands and west central Okinawa Island are potential sink populations. The Kerama Islands and the vicinity of Taketomi Island are potential contact points of genetic subdivision of coral populations in the Nansei Islands. We found that genetic population structure of A. tenuis in the Nansei Islands is more complex than previously thought. These cryptic populations are very important for preserving genetic diversity and should be maintained. 相似文献
3.
Cassidy C. D&#x;Aloia Jose A. Andrs Steven M. Bogdanowicz Amy R. McCune Richard G. Harrison Peter M. Buston 《Molecular ecology》2020,29(12):2189-2203
Marine metapopulations often exhibit subtle population structure that can be difficult to detect. Given recent advances in high‐throughput sequencing, an emerging question is whether various genotyping approaches, in concert with improved sampling designs, will substantially improve our understanding of genetic structure in the sea. To address this question, we explored hierarchical patterns of structure in the coral reef fish Elacatinus lori using a high‐resolution approach with respect to both genetic and geographic sampling. Previously, we identified three putative E. lori populations within Belize using traditional genetic markers and sparse geographic sampling: barrier reef and Turneffe Atoll; Glover's Atoll; and Lighthouse Atoll. Here, we systematically sampled individuals at ~10 km intervals throughout these reefs (1,129 individuals from 35 sites) and sequenced all individuals at three sets of markers: 2,418 SNPs; 89 microsatellites; and 57 nonrepetitive nuclear loci. At broad spatial scales, the markers were consistent with each other and with previous findings. At finer spatial scales, there was new evidence of genetic substructure, but our three marker sets differed slightly in their ability to detect these patterns. Specifically, we found subtle structure between the barrier reef and Turneffe Atoll, with SNPs resolving this pattern most effectively. We also documented isolation by distance within the barrier reef. Sensitivity analyses revealed that the number of loci (and alleles) had a strong effect on the detection of structure for all three marker sets, particularly at small spatial scales. Taken together, these results illustrate empirically that high‐throughput genotyping data can elucidate subtle genetic structure at previously‐undetected scales in a dispersive marine fish. 相似文献
4.
The population structure of benthic marine organisms is of central relevance to the conservation and management of these often threatened species, as well as to the accurate understanding of their ecological and evolutionary dynamics. A growing body of evidence suggests that marine populations can be structured over short distances despite theoretically high dispersal potential. Yet the proposed mechanisms governing this structure vary, and existing empirical population genetic evidence is of insufficient taxonomic and geographic scope to allow for strong general inferences. Here, we describe the range‐wide population genetic structure of an ecologically important Caribbean octocoral, Gorgonia ventalina. Genetic differentiation was positively correlated with geographic distance and negatively correlated with oceanographically modelled dispersal probability throughout the range. Although we observed admixture across hundreds of kilometres, estimated dispersal was low, and populations were differentiated across distances <2 km. These results suggest that populations of G. ventalina may be evolutionarily coupled via gene flow but are largely demographically independent. Observed patterns of differentiation corroborate biogeographic breaks found in other taxa (e.g. an east/west divide near Puerto Rico), and also identify population divides not discussed in previous studies (e.g. the Yucatan Channel). High genotypic diversity and absence of clonemates indicate that sex is the primary reproductive mode for G. ventalina. A comparative analysis of the population structure of G. ventalina and its dinoflagellate symbiont, Symbiodinium, indicates that the dispersal of these symbiotic partners is not coupled, and symbiont transmission occurs horizontally. 相似文献
5.
In the face of predicted climate change, a broader understanding of biotic responses to varying environments has become increasingly important within the context of biodiversity conservation. Local adaptation is one potential option, yet remarkably few studies have harnessed genomic tools to evaluate the efficacy of this response within natural populations. Here, we show evidence of selection driving divergence of a climate‐change‐sensitive mammal, the American pika (Ochotona princeps), distributed along elevation gradients at its northern range margin in the Coast Mountains of British Columbia (BC), Canada. We employed amplified‐fragment‐length‐polymorphism‐based genomic scans to conduct genomewide searches for candidate loci among populations inhabiting varying environments from sea level to 1500 m. Using several independent approaches to outlier locus detection, we identified 68 candidate loci putatively under selection (out of a total 1509 screened), 15 of which displayed significant associations with environmental variables including annual precipitation and maximum summer temperature. These candidate loci may represent important targets for predicting pika responses to climate change and informing novel approaches to wildlife conservation in a changing world. 相似文献
6.
Scott R. Santos 《Molecular ecology》2014,23(17):4185-4187
The modern synthesis was a seminal period in the biological sciences, establishing many of the core principles of evolutionary biology that we know today. Significant catalysts were the contributions of R.A. Fisher, J.B.S. Haldane and Sewall Wright (and others) developing the theoretical underpinning of population genetics, thus demonstrating adaptive evolution resulted from the interplay of forces such as natural selection and mutation within groups of individuals occupying the same space and time (i.e. a population). Given its importance, it is surprising that detailed population genetic data remain lacking for numerous organisms vital to many ecosystems. For example, the coral reef ecosystem is well recognized for its high biodiversity and productivity, numerous ecological services and significant economic and societal values (Moberg & Folke 1999; Cinner 2014). Many coral reef invertebrates form symbiotic relationships with single‐celled dinoflagellates within the genus Symbiodinium Freudenthal (Taylor 1974), with hosts providing these (typically) intracellular symbionts with by‐products of metabolism and in turn receiving photosynthetically fixed carbon capable of meeting hosts’ respiratory demands (Falkowski et al. 1984; Muscatine et al. 1984). Unfortunately, the health and integrity of the coral reef ecosystem has been significantly and negatively impacted by onslaughts like anthropogenic eutrophication and disease in addition to global climate change, with increased incidences of ‘bleaching’ events (characterized as the loss of photosynthetic pigments from the algal cell or massive reduction of Symbiodinium density from hosts’ tissue) and host mortality leading to staggering declines in geographic coverage (Bruno & Selig 2007) that have raised questions on the viability of this ecosystem as we know it (Bellwood et al. 2004; Parmesan 2006). One avenue towards anticipating the future of the coral reef ecosystem is by developing a broader and deeper understanding of the current genotypic diversity encompassed within and between populations of their keystone species, the scleractinian corals and dinoflagellate symbionts, as they potentially possess functional variation (either singularly or in combination) that may come under selection due to the ongoing and rapid environmental changes they are experiencing. However, such studies, especially for members of the genus Symbiodinium, are sparse. In this issue, Baums et al. (2014) provide a significant contribution by documenting the range‐wide population genetics of Symbiodinium ‘fitti’ (Fig. 1 ) in the context of complementary data from its host, the endangered Caribbean elkhorn coral Acropora palmata (Fig. 1 ). Notable results of this study include a single S. ‘fitti’ genotype typically dominates an individual A. palmata colony both spatially and temporally, gene flow among coral host populations is a magnitude higher to that of its symbiont populations, and the partners possess disparate patterns of genetic differentiation across the Greater Caribbean. The implications of such findings are discussed herein. 相似文献
7.
GILLES GUILLOT RAPHAËL LEBLOIS AURÉLIE COULON ALAIN C. FRANTZ 《Molecular ecology》2009,18(23):4734-4756
The joint analysis of spatial and genetic data is rapidly becoming the norm in population genetics. More and more studies explicitly describe and quantify the spatial organization of genetic variation and try to relate it to underlying ecological processes. As it has become increasingly difficult to keep abreast with the latest methodological developments, we review the statistical toolbox available to analyse population genetic data in a spatially explicit framework. We mostly focus on statistical concepts but also discuss practical aspects of the analytical methods, highlighting not only the potential of various approaches but also methodological pitfalls. 相似文献
8.
Marine reserves networks are implemented as a way to mitigate the impact of fishing on marine ecosystems. Theory suggests that a reserve network will function synergistically when connected by dispersal, but the scale of dispersal is often unknown. On the Pacific coast of the United States and Canada, both countries have recently implemented a number of rockfish conservation areas (RCAs) to protect exploited rockfish species, but no study has evaluated the connectivity within networks in each country or between the two countries. We used isolation‐by‐distance theory to estimate the scale of dispersal from microsatellite data in the black rockfish, Sebastes melanops, and compared this estimate with the distance between RCAs that would protect this species. Within each country, we found that the distance between RCAs was generally within the confidence intervals of mean dispersal per generation. The distance between these two RCA networks, however, was greater than the average dispersal per generation. The data were also consistent with a genetic break between southern Oregon and central Oregon. We discuss whether additional nearshore RCAs in southern Oregon and Washington would help promote connectivity between RCA's for shallow‐water rockfishes. 相似文献
9.
Laura E. Timm 《Molecular ecology》2020,29(12):2133-2136
From its inception, population genetics has been nearly as concerned with the genetic data type—to which analyses are brought to bear—as it is with the analysis methods themselves. The field has traversed allozymes, microsatellites, segregating sites in multilocus alignments and, currently, single nucleotide polymorphisms (SNPs) generated by high‐throughput genomic sequencing methods, primarily whole genome sequencing and reduced representation library (RRL) sequencing. As each emerging data type has gained traction, it has been compared to existing methods, based on its relative ability to discern population structural complexity at increasing levels of resolution. However, this is usually done by comparing the gold standard in one data type to the gold standard in the new data type. These gold standards frequently differ in power and in sampling density, both across a genome and throughout a spatial range. In this issue of Molecular Ecology, D’Aloia et al. apply the high‐throughput approach as fully as possible to microsatellites, nuclear loci and SNPs genotyped through an RRL method; this is coupled with a spatially dense sampling scheme. Completing a battery of population genetics analyses across data types (including a series of down‐sampled data sets), the authors find that SNP data are slightly more sensitive to fine‐scale genetic structure, and the results are more resilient to down‐sampling than microsatellites and nonrepetitive nuclear loci. However, their results are far from an unqualified victory for RRL SNP data over all previous data types: the authors note that modest additions to the microsatellites and nuclear loci data sets may provide the necessary analytical power to delineate the fine‐scale genetic structuring identified by SNPs. As always, as the field begins to fully embrace the newest thing, good science reminds us that traditional data types are far from useless, especially when combined with a well‐designed sampling scheme. 相似文献
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11.
Ingrid Spies Kristen M. Gruenthal Daniel P. Drinan Anne B. Hollowed Duane E. Stevenson Carolyn M. Tarpey Lorenz Hauser 《Evolutionary Applications》2020,13(2):362-375
Poleward species range shifts have been predicted to result from climate change, and many observations have confirmed such movement. Poleward shifts may represent a homogeneous shift in distribution, seasonal northward movement of specific populations, or colonization processes at the poleward edge of the distribution. The ecosystem of the Bering Sea has been changing along with the climate, moving from an arctic to a subarctic system. Several fish species have been observed farther north than previously reported and in increasing abundances. We examined one of these fish species, Pacific cod, in the northern Bering Sea (NBS) to assess whether they migrated from another stock in the eastern Bering Sea (EBS), Gulf of Alaska, or Aleutian Islands, or whether they represent a separate population. Genetic analyses using 3,599 single nucleotide polymorphism markers indicated that nonspawning cod collected in August 2017 in the NBS were similar to spawning stocks of cod in the EBS. This result suggests escalating northward movement of the large EBS stock during summer months. Whether the cod observed in the NBS migrate south during winter to spawn or remain in the NBS as a sink population is unknown. 相似文献
12.
Host–parasite interactions are ubiquitous in nature. However, how parasite population genetic structure is shaped by the interaction between host and parasite life history remains understudied. Studies comparing multiple parasites infecting a single host can be used to investigate how different parasite life history traits interplay with host behaviour and life history. In this study, we used 10 newly developed microsatellite loci to investigate the genetic structure of a parasitic bat fly (Basilia nana). Its host, the Bechstein's bat (Myotis bechsteinii), has a social system and roosting behaviour that restrict opportunities for parasite transmission. We compared fly genetic structure to that of the host and another parasite, the wing‐mite, Spinturnix bechsteini. We found little spatial or temporal genetic structure in B. nana, suggesting a large, stable population with frequent genetic exchange between fly populations from different bat colonies. This contrasts sharply with the genetic structure of the wing‐mite, which is highly substructured between the same bat colonies as well as temporally unstable. Our results suggest that although host and parasite life history interact to yield similar transmission patterns in both parasite species, the level of gene flow and eventual spatiotemporal genetic stability is differentially affected. This can be explained by the differences in generation time and winter survival between the flies and wing‐mites. Our study thus exemplifies that the population genetic structure of parasites on a single host can vary strongly as a result of how their individual life history characteristics interact with host behaviour and life history traits. 相似文献
13.
Felipe Torquato Pedro Range Radhouane Ben‐Hamadou Eva E. Sigsgaard Philip F. Thomsen Rodrigo Riera Michael L. Berumen John A. Burt David A. Feary Alyssa Marshell Daniele D'Agostino Joseph D. DiBattista Peter R. Mller 《Ecology and evolution》2019,9(19):11215-11226
Ocean circulation, geological history, geographic distance, and seascape heterogeneity play an important role in phylogeography of coral‐dependent fishes. Here, we investigate potential genetic population structure within the yellowbar angelfish (Pomacanthus maculosus) across the Northwestern Indian Ocean (NIO). We then discuss our results with respect to the above abiotic features in order to understand the contemporary distribution of genetic diversity of the species. To do so, restriction site‐associated DNA sequencing (RAD‐seq) was utilized to carry out population genetic analyses on P. maculosus sampled throughout the species’ distributional range. First, genetic data were correlated to geographic and environmental distances, and tested for isolation‐by‐distance and isolation‐by‐environment, respectively, by applying the Mantel test. Secondly, we used distance‐based and model‐based methods for clustering genetic data. Our results suggest the presence of two putative barriers to dispersal; one off the southern coast of the Arabian Peninsula and the other off northern Somalia, which together create three genetic subdivisions of P. maculosus within the NIO. Around the Arabian Peninsula, one genetic cluster was associated with the Red Sea and the adjacent Gulf of Aden in the west, and another cluster was associated with the Arabian Gulf and the Sea of Oman in the east. Individuals sampled in Kenya represented a third genetic cluster. The geographic locations of genetic discontinuities observed between genetic subdivisions coincide with the presence of substantial upwelling systems, as well as habitat discontinuity. Our findings shed light on the origin and maintenance of genetic patterns in a common coral reef fish inhabiting the NIO, and reinforce the hypothesis that the evolution of marine fish species in this region has likely been shaped by multiple vicariance events. 相似文献
14.
Ying Zhang Min Qiao Jianping Xu Yang Cao Ke‐Qin Zhang Ze‐Fen Yu 《Ecology and evolution》2013,3(2):312-325
Nematophagous fungi can trap and capture nematodes and other small invertebrates. This unique ability has made them ideal organisms from which to develop biological control agents against plant‐ and animal‐parasitic nematodes. However, effective application of biocontrol agents in the field requires a comprehensive understanding about the ecology and population genetics of the nematophagous fungi in natural environments. Here, we genotyped 228 strains of the nematode‐trapping fungus Arthrobotrys oligospora using 12 single nucleotide polymorphic markers located on eight random DNA fragments. The strains were from different ecological niches and geographical regions from China. Our analyses identified that ecological niche separations contributed significantly, whereas geographic separation contributed relatively little to the overall genetic variation in our samples of A. oligospora. Interestingly, populations from stressful environments seemed to be more variable and showed more evidence for recombination than those from benign environments at the same geographic areas. We discussed the implications of our results to the conservation and biocontrol application of A. oligospora in agriculture and forestry. 相似文献
15.
Michael J. Hickerson 《Molecular ecology》2014,23(12):2887-2889
As the field of phylogeography has continued to move in the model‐based direction, researchers continue struggling to construct useful models for inference. These models must be both simple enough to be tractable yet contain enough of the complexity of the natural world to make meaningful inference. Beyond constructing such models for inference, researchers explore model space and test competing models with the data on hand, with the goal of improving the understanding of the natural world and the processes underlying natural biological communities. Approximate Bayesian computation (ABC) has increased in recent popularity as a tool for evaluating alternative historical demographic models given population genetic samples. As a thorough demonstration, Pelletier & Carstens ( 2014 ) use ABC to test 143 phylogeographic submodels given geographically widespread genetic samples from the salamander species Plethodon idahoensis (Carstens et al. 2004 ) and, in so doing, demonstrate how the results of the ABC model choice procedure are dependent on the model set one chooses to evaluate. 相似文献
16.
The endangered Rio Grande silvery minnow persists as a remnant population in a highly fragmented and regulated arid‐land river system. The species is subject to dramatic annual fluctuations in density. Since 2003, the wild population has been supplemented by hatchery‐reared fish. We report on a 12‐year (1999–2010) monitoring study of genetic diversity and effective population size (Ne) of wild and hatchery stocks. Our goals were to evaluate how genetic metrics responded to changes in wild fish density and whether they corresponded to the number and levels of diversity of hatchery‐reared repatriates. Genetic diversity and all measures of Ne in the wild population did not correlate with wild fish density until hatchery supplementation began in earnest. Estimates of variance and inbreeding effective size were not correlated. Our results suggest source–sink dynamics where captive stocks form a genetically diverse source and the wild population behaves as a sink. Nevertheless, overall genetic diversity of silvery minnow has been maintained over the last decade, and we attribute this to a well‐designed and executed propagation management plan. When multiple factors like environmental fluctuation and hatchery supplementation act simultaneously on a population, interpretation of genetic monitoring data may be equally complex and require considerable ecological data. 相似文献
17.
Anna Tammilehto Phillip C. Watts Nina Lundholm 《The Journal of eukaryotic microbiology》2017,64(2):248-256
The arctic phytoplankton spring bloom, which is often diatom‐dominated, is a key event that provides the high latitude communities with a fundamental flux of organic carbon. During a bloom, phytoplankton may increase its biomass by orders of magnitude within days. Yet, very little is known about phytoplankton bloom dynamics, including for example how blooming affects genetic composition and diversity of a population. Here, we quantified the genetic composition and temporal changes of the diatom Fragilariopsis cylindrus, which is one of the most important primary producers in the Arctic, during the spring bloom in western Greenland, using 13 novel microsatellite markers developed for this study. We found that genetic differentiation (quantified using sample‐specific FST) decreased between time points as the bloom progressed, with the most drastic changes in FST occurring at the start of the bloom; thus the genetic structure of the bloom is characterized by isolation by time. There was little temporal variation in genetic diversity throughout the bloom (mean HE = 0.57), despite marked fluctuations in F. cylindrus cell concentrations and the temporal change in sample‐specific FST. On the basis of this novel pattern of genetic differentiation, we suggest that blooming behavior may promote genetic diversity of a phytoplankton population. 相似文献
18.
A fundamental goal of evolutionary biology is to understand how ecological diversity arises and is maintained in natural populations. We have investigated the contributions of gene flow and divergent selection to the distribution of genetic variation in an ecologically differentiated population of a thermophilic cyanobacterium (Mastigocladus laminosus) found along the temperature gradient of a nitrogen‐limited stream in Yellowstone National Park. For most loci sampled, gene flow appears to be sufficient to prevent substantial genetic divergence. However, one locus (rfbC) exhibited a comparatively low migration rate as well as other signatures expected for a gene experiencing spatially varying selection, including an excess of common variants, an elevated level of polymorphism and extreme genetic differentiation along the gradient. rfbC is part of an expression island involved in the production of the polysaccharide component of the protective envelope of the heterocyst, the specialized nitrogen‐fixing cell of these bacteria. SNP genotyping in the vicinity of rfbC revealed a ~5‐kbp region including a gene content polymorphism that is tightly associated with environmental temperature and therefore likely contains the target of selection. Two genes have been deleted both in the predominant haplotype found in the downstream region of White Creek and in strains from other Yellowstone populations of M. laminosus, which may result in the production of heterocysts with different envelope properties. This study implicates spatially varying selection in the maintenance of variation related to thermal performance at White Creek despite on‐going or recent gene flow. 相似文献
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20.
Martha M. Muñoz Nicholas G. Crawford Thomas J. McGreevy Jr Nicholas J. Messana Rebecca D. Tarvin Liam J. Revell Rosanne M. Zandvliet Juanita M. Hopwood Elbert Mock André L. Schneider Christopher J. Schneider 《Molecular ecology》2013,22(10):2668-2682
Adaptive divergence in coloration is expected to produce reproductive isolation in species that use colourful signals in mate choice and species recognition. Indeed, many adaptive radiations are characterized by differentiation in colourful signals, suggesting that divergent selection acting on coloration may be an important component of speciation. Populations in the Anolis marmoratus species complex from the Caribbean island of Guadeloupe display striking divergence in the colour and pattern of adult males that occurs over small geographic distances, suggesting strong divergent selection. Here we test the hypothesis that divergence in coloration results in reduced gene flow among populations. We quantify variation in adult male coloration across a habitat gradient between mesic and xeric habitats, use a multilocus coalescent approach to infer historical demographic parameters of divergence, and examine gene flow and population structure using microsatellite variation. We find that colour variation evolved without geographic isolation and in the face of gene flow, consistent with strong divergent selection and that both ecological and sexual selection are implicated. However, we find no significant differentiation at microsatellite loci across populations, suggesting little reproductive isolation and high levels of contemporary gene exchange. Strong divergent selection on loci affecting coloration probably maintains clinal phenotypic variation despite high gene flow at neutral loci, supporting the notion of a porous genome in which adaptive portions of the genome remain fixed whereas neutral portions are homogenized by gene flow and recombination. We discuss the impact of these findings for studies of colour evolution and ecological speciation. 相似文献