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Clare, Elizabeth L.; Fazekas, Aron J.; Ivanova, Natalia V.; Floyd, Robin M.; Hebert, Paul D.N.; Adams, Amanda M.; Nagel, Juliet; Girton, Rebecca; Newmaster, Steven G.; Fenton, M. Brock; Hebert, Paul D. N. — 2018-10-31 As molecular tools for assessing trophic interactions become common, research is increasingly focused on the construction of interaction networks. Here we demonstrate three key methods for incorporating DNA data into network ecology and discuss analytical considerations using a model consisting of plants, insects, bats and their parasites from the Costa Rican dry forest. The simplest method involves the use of Sanger sequencing to acquire long sequences to validate or refine field identifications, for example of bats and their parasites, where one specimen yields one sequence and one identification. This method can be fully quantified and resolved and these data resemble traditional ecological networks. For more complex taxonomic identifications, we target multiple DNA loci e.g. from a seed or fruit pulp sample in faeces. These networks are also well resolved but gene targets vary in resolution and quantification is difficult. Finally for mixed templates such as faecal contents of insectivorous bats we use DNA metabarcoding targeting two sequence lengths (157bp, 407bp) of one gene region and a MOTU, BLAST and BIN association approach to resolve nodes. This network type is complex to generate and analyse and we discuss the implications of this type of resolution on network analysis. Using these data we construct the first molecular-based network of networks containing 3304 interactions between 762 nodes of 8 trophic functions and involving parasitic, mutualistic, and predatory interactions. We provide a comparison of the relative strengths and weaknesses of these data types in network ecology. https://creativecommons.org/publicdomain/zero/1.0/

Rapai, Sean B.; Collis, Brianna; Henry, Thomas; Lyle, Kimberly; Newmaster, Steven G.; Raizman, Veronika; Hanner, Robert — 2021-06-16 Early successional plant community assemblage within a reclamation field trial at the Detour Lake Mine in northeastern Ontario is assessed, and compared with reference forested and historically reclaimed sites. The reclamation field trial examines eight amendment treatment combinations that include treatments with a winter kill cover crop of oats, fertilizer, biosolids, peat, and combinations thereof. The objectives of this study are to: (1) Investigate how soil amendments influence plant functional group establishment and growth in mine overburden; and (2) Explore the amendment properties that best support the establishment and growth of a plant community that resembles the baseline reference sites. Currently, the presence of non-native species and a dominant woody plant community explains the largest proportion of variance between the forested upland and lowland reference sites and all reclaimed sites. Similar to non-native species, graminoids were absent from the upland forested reference sites. The difference in the graminoid community explains much of the variance between the forested reference sites and all reclaimed sites. The cumulative additions of fertilizer and peat increased alpha diversity of non-native and graminoid plants within the amendment treatments, which had greater alpha diversity of these plant functional groups than the forested reference sites. Within the amendment treatments, non-native and graminoid alpha diversity was initially greater in the nutrient treatments, but by 2019 there was no significant difference in non-native or graminoid alpha diversity between amendment treatments. The results indicate that applications of nutrients through fertilizer or biosolids may increase graminoid alpha diversity and abundance within reclamation units in year 1. The results also confirm that the vascular plant community composition present within the historically reclaimed sites and amendment treatments does not resemble the forested reference sites. The plant community present within the amendment treatment sites is best described as early successional, with the presence of non-native herbaceous legumes dominating the historically reclaimed sites. Despite this, the results indicate that fertilizer and biosolids-based treatments have developed a vascular plant community, excluding woody species that is more similar to the forested reference sites than the peat-based treatments. Further research and long-term monitoring are needed to determine which amendment treatment will best support a plant community that resembles the forested reference sites. In addition, future studies of this nature might consider including wildfire affected and post-harvested forest stands as additional reference sites, to better capture possible plant community trajectories of a severely disturbed environment.

Avgar, Tal; Brown, Glen S.; Thompson, Ian; Rodgers, Art R.; Mosser, Anna; Fryxell, John M.; Patterson, Brent R.; Newmaster, Steven G.; Reid, Doug E. B.; Turetsky, Merritt; Hagens, Jevon S.; Reid, Douglas E. B.; Shuter, Jennifer; Baker, James A.; Kittle, Andrew M.; Mallon, Erin E.; McGreer, Madeleine T.; Street, Garrett M.; Turetsky, Merritt J. — 2016-01-20 1. Movement patterns offer a rich source of information on animal behaviour and the ecological significance of landscape attributes. This is especially useful for species occupying remote landscapes where direct behavioural observations are limited. In this study, we fit a mechanistic model of animal cognition and movement to GPS positional data of woodland caribou (Rangifer tarandus caribou; Gmelin 1788) collected over a wide range of ecological conditions. 2. The model explicitly tracks individual animal informational state over space and time, with resulting parameter estimates that have direct cognitive and ecological meaning. Three biotic landscape attributes were hypothesized to motivate caribou movement: forage abundance (dietary digestible biomass), wolf (Canis lupus; Linnaeus, 1758) density and moose (Alces alces; Linnaeus, 1758) habitat. Wolves are the main predator of caribou in this system and moose are their primary prey. 3. Resulting parameter estimates clearly indicated that forage abundance is an important driver of caribou movement patterns, with predator and moose avoidance often having a strong effect, but not for all individuals. From the cognitive perspective, our results support the notion that caribou rely on limited sensory inputs from their surroundings, as well as on long-term spatial memory, to make informed movement decisions. Our study demonstrates how sensory, memory and motion capacities may interact with ecological fitness covariates to influence movement decisions by free-ranging animals.

McMullin, Richard Troy; Lendemer, James C.; Braid, Heather E.; Newmaster, Steven G. — 2016-11-20 Alectoria is a genus of fruticose lichen characterised by the presence of usnic acid and conspicuous raised pseudocyphellae. This genus is particularly diverse and abundant in montane, boreal, and Arctic regions of North America. Because intermediate forms have been reported for several species of Alectoria on the continent, it has been suggested that these species were initially delimited based on the extremes of morphological gradients. Here, we use the results of molecular phylogenetic analyses of two nuclear genes, ITS and Mcm7, with 48 representatives of 9 taxa to examine the delineation of 5 taxa that have been previously shown to be related to, or confused with, A. sarmentosa: A. fallacina, A. imshaugii, A. sarmentosa var. sorediosa, A. sarmentosa subsp. vexillifera, and A. vancouverensis. Alectoria fallacina was found to be well-supported and distantly related to A. sarmentosa. Conversely, the other four taxa were recovered as a single monophyletic group with little internal structure, which did not support the presently defined morphological species. A provisional taxonomic treatment is proposed pending more detailed study at the population level. Alectoria sarmentosa var. sorediosa is recognized at the species level, which necessitates the new combination: A. sorediosa. An updated key to the North American species of Alectoria is also provided.

Percy, Diana M.; Argus, George W.; Cronk, Quentin C.; Fazekas, Aron J.; Kesanakurti, Prasad R.; Burgess, Kevin S.; Husband, Brian C.; Newmaster, Steven G.; Barrett, Spencer C. H.; Graham, Sean W.; Barrett, Spencer C.H. — 2014-06-17 Willows (Salix: Salicaceae) form a major ecological component of Holarctic floras, and consequently are an obvious target for a DNA-based identification system. We surveyed two to seven plastid genome regions (~3.8 kb; ~3% of the genome) from 71 Salix species across all five subgenera, to assess their performance as DNA barcode markers. Although Salix has a relatively high level of interspecific hybridization, this may not sufficiently explain the near complete failure of barcoding that we observed: only one species had a unique barcode. We recovered 39 unique haplotypes, from more than 500 specimens, that could be partitioned into six major haplotype groups. A unique variant of group I (haplotype 1*) was shared by 53 species in three of five Salix subgenera. This unusual pattern of haplotype sharing across infrageneric taxa is suggestive of either a massive non-random coalescence failure (incomplete lineage sorting), or of repeated plastid capture events, possibly including a historical selective sweep of haplotype 1* across taxonomic sections. The former is unlikely as molecular dating indicates that haplotype 1* originated recently, and is nested in the oldest major haplotype group in the genus. Further, we detected significant non-neutrality in the frequency spectrum of mutations in group I, but not outside group I, and demonstrated a striking absence of geographic structure to the haplotype distributions in this group. The most likely explanation for the patterns we observed involves recent repeated plastid capture events, aided by widespread hybridization and long-range seed dispersal, but primarily propelled by one or more trans-species selective sweeps.