A road map for molecular ecology

Andrew, Rose L.; Bernatchez, Louis; Bonin, Aurélie; Buerkle, C. Alex; Carstens, Bryan C.; Emerson, Brent C.; Garant, Dany; Giraud, Tatiana; Kane, Nolan C.; Rogers, Sean M.; Slate, Jon; Smith, Harry; Sork, Victoria L.; Stone, Graham N.; Vines, Tim; Waits, Lisette P.; Widmer, Alex; Rieseberg, Loren H.

doi:10.1111/mec.12319

Cited by 106 publications

(117 citation statements)

References 290 publications

(489 reference statements)

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“…The current results thus imply that the molecular methods are complementary, and that in future studies, traditional techniques such as rearing should (at the very least) be supported by these faster and less laborious molecular methods (but see SI Text, section 4 for further considerations). By determining the identity of the host (or prey) from the gut contents of the parasitoid (or predator) (30,35,61,62), and/or by directly identifying the parasitoid DNA from the host (36), molecular approaches also circumvent problems associated with the detection of the feeding event (e.g., [63][64][65], or the maturation of the parasitoid (66,67). Given the wide availability of PCR and the rapid advances in sequencing techniques, methods for detecting both hosts within parasitoids and parasitoids within hosts based on DNA barcodes is now an approach within reach for all ecologists (34,43).…”

Section: Discussionmentioning

confidence: 99%

Complementary molecular information changes our perception of food web structure

Wirta

Hebert

Kaartinen

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

145

202

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How networks of ecological interactions are structured has a major impact on their functioning. However, accurately resolving both the nodes of the webs and the links between them is fraught with difficulties. We ask whether the new resolution conferred by molecular information changes perceptions of network structure. To probe a network of antagonistic interactions in the High Arctic, we use two complementary sources of molecular data: parasitoid DNA sequenced from the tissues of their hosts and host DNA sequenced from the gut of adult parasitoids. The information added by molecular analysis radically changes the properties of interaction structure. Overall, three times as many interaction types were revealed by combining molecular information from parasitoids and hosts with rearing data, versus rearing data alone. At the species level, our results alter the perceived host specificity of parasitoids, the parasitoid load of host species, and the webwide role of predators with a cryptic lifestyle. As the northernmost network of host-parasitoid interactions quantified, our data point exerts high leverage on global comparisons of food web structure. However, how we view its structure will depend on what information we use: compared with variation among networks quantified at other sites, the properties of our web vary as much or much more depending on the techniques used to reconstruct it. We thus urge ecologists to combine multiple pieces of evidence in assessing the structure of interaction webs, and suggest that current perceptions of interaction structure may be strongly affected by the methods used to construct them.trophic interaction | Hymenoptera | Lepidoptera | DNA barcode H ow networks of ecological interactions are structured has major implications on how they function (1), how they react to external stressors (2, 3) and how they return to their original state after disturbance (4, 5). Quantitative descriptions of who interacts with whom (e.g., refs. 6 and 7) may then be used to formulate testable hypotheses for basic questions concerning, for example, the fundamental strength of indirect interactions (8, 9), or how a community will respond to invasive species, habitat modification, or climate change (e.g., refs. 10-14). In applied biology, quantifications of interaction structure have increasingly been used to examine the success of, for example, habitat restoration and management, the biological control of pests, and the conservation of biodiversity (6). Global comparisons of food web structure are underway, comparing the linking structure of local webs described from different latitudes with highly different species richness (15, 16).To encapsulate the emergent properties of large networks of interactions, a set of quantitative descriptors has been proposed (e.g., refs. 2, and 17-19) and widely adopted (e.g., refs. 11 and 20-22). Commonly used metrics summarize the specialization of species at different trophic levels, such as the average number of species at a lower trophic level interacting with ea...

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Section: Discussionmentioning

confidence: 99%

Complementary molecular information changes our perception of food web structure

Wirta

Hebert

Kaartinen

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

145

202

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“…Hence, autoregressive integrated moving average with exogenous variables (ARIMAX) model would be utilised. This is because ARIMAX model has a better prediction ability than the Autoregressive Integrated Moving-Average (ARIMA) models (Anggraeni, 2015;Andrew, et al, 2013;Kongcharoen and Kruangpradit, 2013). Thus, the aim of this paper is to examine how ARIMAX can be used in forecasting TPI in the Ghanaian Building Industry.…”

Section: Previous Studiesmentioning

confidence: 99%

Forecasting Construction Tender Price Index in Ghana using Autoregressive Integrated Moving Average with Exogenous Variables Model

Kissi

Adjei-Kumi

Amoah

et al. 2018

CEB

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Prices of construction resources keep on fluctuating due to unstable economic situations that have been experienced over the years. Clients knowledge of their financial commitments toward their intended project remains the basis for their final decision. The use of construction tender price index provides a realistic estimate at the early stage of the project. Tender price index (TPI) is influenced by various economic factors, hence there are several statistical techniques that have been employed in forecasting. Some of these include regression, time series, vector error correction among others. However, in recent times the integrated modelling approach is gaining popularity due to its ability to give powerful predictive accuracy. Thus, in line with this assumption, the aim of this study is to apply autoregressive integrated moving average with exogenous variables (ARIMAX) in modelling TPI. The results showed that ARIMAX model has a better predictive ability than the use of the single approach. The study further confirms the earlier position of previous research of the need to use the integrated model technique in forecasting TPI. This model will assist practitioners to forecast the future values of tender price index. Although the study focuses on the Ghanaian economy, the findings can be broadly applicable to other developing countries which share similar economic characteristics.

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“…Regardless of the genetic marker used, the analytical challenges of combining genetic data across multiple species and inferring influential biological and physical factors persist. Many of these challenges were considered in Chapter Four of this thesis and have also been discussed elsewhere (Andrew et al 2013, Dawson 2014. Some of these challenges can be circumvented via experimental design.…”

Section: Methodological and Analytical Advancesmentioning

confidence: 99%

“…While it has been recognized that ecology is also likely to play an important role in determining spatial genetic patterns in marine systems (e.g. Choat 2006, investigations have been restricted by coarse genetic markers and limited environmental data (Andrew et al 2013). However, with the increased power of hundreds and thousands of loci offered by next--generation methods and newly available environmental databases for marine ecosystems (Sbrocco andBarber 2013, Sbrocco 2014) the field of seascape genetics is now well--placed to address the role of ecology and selection in forming spatial genetic patterns.…”

Section: Technological Advancesmentioning

confidence: 99%

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Seascape genetics of Indo-Pacific reef organisms: methodologies and case studies for an emerging discipline

Liggins¹

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Which factors shape population connectivity and the consistency of their influence across species and seascapes is largely unresolved. This thesis takes a comparative genetic approach to investigate the influences of seascape topology (past sea level changes, contemporary oceanography, and geography) and species biology on the genetic connectivity among coral reefs around Australia, the Indo-Australasian Archipelago (IAA), and the wider Indo-Pacific. I focus on a suite of common, codistributed coral reef fishes and invertebrates that differ in life history characteristics. In the introductory chapter of my thesis I discuss population connectivity in marine systems, the contribution of seascape genetics to marine population connectivity research, and the state of our knowledge in the Indian and Pacific Oceans (Chapter One). Chapters Two and Three review the field of seascape genetics and the methodologies used in seascape genetic studies, respectively. My empirical research (Chapters Four-Six) takes a broad, yet integrated approach to describe and understand the processes underlying seascape genetic patterns around Australia, the IAA, and the Indo-Pacific. First, I investigate historical spatial genetic (mitochondrial DNA, mtDNA) patterns and processes using a comparative, multi-species framework (Chapter Four). I extend typical methods of comparative phylogeography to include: a matrix comparison method that allows the quantitative characterization of spatial genetic patterns; and a multiple regression modeling approach to identify the processes underlying the spatial genetic patterns for each species. I find that despite being subjected to common geographic and seascape influences, spatial genetic patterns differ across four common coral reef fishes (Acanthurus triostegus, Dascyllus trimaculatus, Halichoeres hortulanus, Pomacentrus coelestis). Although species with similar dispersal potential (based on egg type and pelagic larval duration) have the most similar spatial genetic patterns, the seascape features and processes (e.g. previous landbridges and oceanographic distances) underlying the genetic patterns are not always shared among species. Second, I characterize the latitude-wide genetic patterns of one species (P. coelestis) and extend methods typically used in such investigations by borrowing concepts and measures more commonly used for analyses of community composition (Chapter Five). Genealogical analyses reveal that levels of population genetic diversity in the core of the species range are elevated by the co-occurrence of two cryptic clades. Furthermore, the application of partitioned -diversity measures and nestedness analyses reveal that differing demographic processes underlie the genetic patterns observed at the northern and southern latitudinal peripheries of the species range. Last, I focus on edge-of-range genetic patterns for two tropical echinoderm species (Acanthaster planci and Tripneustes gratilla) at a little-studied high latitude peripheral population, Kermadec Islands, New Zea...

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A road map for molecular ecology

Cited by 106 publications

References 290 publications

Complementary molecular information changes our perception of food web structure

Complementary molecular information changes our perception of food web structure

Forecasting Construction Tender Price Index in Ghana using Autoregressive Integrated Moving Average with Exogenous Variables Model

Seascape genetics of Indo-Pacific reef organisms: methodologies and case studies for an emerging discipline

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