Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The Theory of Island Biogeography

Genotyping errors occur when the genotype determined after molecular analysis does not correspond to the real genotype of the individual under consideration. Virtually every genetic data set includes some erroneous genotypes, but genotyping errors remain a taboo subject in population genetics, even though they might greatly bias the final conclusions, especially for studies based on individual identification. Here, we consider four case studies representing a large variety of population genetics investigations differing in their sampling strategies (noninvasive or traditional), in the type of organism studied (plant or animal) and the molecular markers used [microsatellites or amplified fragment length polymorphisms (AFLPs)]. In these data sets, the estimated genotyping error rate ranges from 0.8% for microsatellite loci from bear tissues to 2.6% for AFLP loci from dwarf birch leaves. Main sources of errors were allelic dropouts for microsatellites and differences in peak intensities for AFLPs, but in both cases human factors were non-negligible error generators. Therefore, tracking genotyping errors and identifying their causes are necessary to clean up the data sets and validate the final results according to the precision required. In addition, we propose the outline of a protocol designed to limit and quantify genotyping errors at each step of the genotyping process. In particular, we recommend (i) several efficient precautions to prevent contaminations and technical artefacts; (ii) systematic use of blind samples and automation; (iii) experience and rigor for laboratory work and scoring; and (iv) systematic reporting of the error rate in population genetics studies.

/pdf/how-to-track-and-assess-genotyping-errors-in-population-1ccjofq7qv.pdf

How to track and assess genotyping errors in population genetics studies.

Time is divided by geologists according to marked shifts in Earth's state. Recent global environmental changes suggest that Earth may have entered a new human-dominated geological epoch, the Anthropocene. Here we review the historical genesis of the idea and assess anthropogenic signatures in the geological record against the formal requirements for the recognition of a new epoch. The evidence suggests that of the various proposed dates two do appear to conform to the criteria to mark the beginning of the Anthropocene: 1610 and 1964. The formal establishment of an Anthropocene Epoch would mark a fundamental change in the relationship between humans and the Earth system.

Defining the Anthropocene

The authors attempted a complete review of the empirical literature on effects of roads and traffic on animal abundance and distribution. They found 79 studies, with results for 131 species and 30 species groups. Overall, the number of documented negative effects of roads on animal abundance outnumbered the number of positive effects by a factor of 5; 114 responses were negative, 22 were positive, and 56 showed no effect. Amphibians and reptiles tended to show negative effects. Birds showed mainly negative or no effects, with a few positive effects for some small birds and for vultures. Small mammals generally showed either positive effects or no effect, mid-sized mammals showed either negative effects or no effect, and large mammals showed predominantly negative effects. The authors synthesized this information, along with information on species attributes, to develop a set of predictions of the conditions that lead to negative or positive effects or no effect of roads on animal abundance. Four species types are predicted to respond negatively to roads: (i) species that are attracted to roads and are unable to avoid individual cars; (ii) species with large movement ranges, low reproductive rates, and low natural densities; and (iii and iv) small animals whose populations are not limited by road-affected predators and either (a) avoid habitat near roads due to traffic disturbance or (b) show no avoidance of roads or traffic disturbance and are unable to avoid oncoming cars. Two species types are predicted to respond positively to roads: (i) species that are attracted to roads for an important resource (e.g., food) and are able to avoid oncoming cars, and (ii) species that do not avoid traffic disturbance but do avoid roads, and whose main predators show negative population-level responses to roads. Other conditions lead to weak or non-existent effects of roads and traffic on animal abundance. The authors identify areas where further research is needed, but they also argue that the evidence for population-level effects of roads and traffic is already strong enough to merit routine consideration of mitigation of these effects in all road construction and maintenance projects.

/pdf/effects-of-roads-on-animal-abundance-an-empirical-review-and-1lbgf8c4mw.pdf

Effects of Roads on Animal Abundance: an Empirical Review and Synthesis

Facilitation between species is thought to be a key mechanism by which biodiversity affects the rates of resource use that govern the efficiency and productivity of ecosystems; however, there is no direct empirical evidence to support this hypothesis. Here we show that increasing the species diversity of a functional group of aquatic organisms induces facilitative interactions, leading to non-additive changes in resource consumption. We increased the richness and evenness of suspension-feeding caddisfly larvae (Insecta, Trichoptera) in stream mesocosms and found that the increased topographical complexity of the benthic habitat alters patterns of near-bed flow such that the feeding success of individuals is enhanced. Species diversity reduces 'current shading' (that is, the deceleration of flow from upstream to downstream neighbours), allowing diverse assemblages to capture a greater fraction of suspended resources than is caught by any species monoculture. The fundamental nature of this form of hydrodynamic facilitation suggests that it is broadly applicable to freshwater and marine habitats; in addition, it has several analogues in terrestrial ecosystems where fluxes of energy and matter can be influenced by biophysical complexity. Thus, changes in species diversity may alter the probability of positive species interactions, resulting in disproportionately large changes in the functioning of ecosystems.

Species diversity enhances ecosystem functioning through interspecific facilitation

We used DNA analysis to estimate grizzly bear (Ursus arctos) population size in a 9.866-km 2 area in southeast British Columbia and a 5,030-km 2 area in southwest Alberta. We sampled bears by removing hair at bait sites surrounded by a single strand of barbed wire. DNA profiling with microsatellites of the root portion of the hair was used to identify individuals. We collected hair from 109 different bears and had 25 recaptures in 5 10-day trapping sessions in British Columbia. In Alberta we collected hair from 37 bears and had 9 recaptures in 4 14-day sessions. A model in program CAPTURE (M h ) that acconmodates heterogeneity in (individual capture probaluilities estimated the population size in British Columbia as 262 (95% CI = 224-313) and in Alberta as 71 (60 100), We believe that hair capture combined with DNA profiling is a promising technique for estimating distribution and abundance of bears and potentially many other species. This approach is of special interest to management biologists because it can be applied at the scale conservation and management decisions are made.

Estimating population size of grizzly bears using hair capture, DNA profiling, and mark-recapture analysis

We measured stable carbon and nitrogen isotope ratios in guard hair of 81 populations of grizzly bears (Ursus arctos L., 1758) across North America and used mixing models to assign diet fractions of salmon, meat derived from terrestrial sources, kokanee (Oncorhynchus nerka (Walbaum in Artedi, 1792)), and plants. In addition, we examined the relationship between skull size and diet of bears killed by people in British Columbia. The majority of carbon and nitrogen assimilated by most coastal grizzly bear populations was derived from salmon, while interior populations usually derived a much smaller fraction of their nutrients from salmon, even in areas with relatively large salmon runs. Terrestrial prey was a large part of the diet where ungulates were abundant, with the highest fractions observed in the central Arctic, where caribou (Rangifer tarandus (L., 1758)) were very abundant. Bears in some boreal areas, where moose (Alces alces (L., 1758)) were abundant, also ate a lot of meat. Bears in dryer areas w...

Major components of grizzly bear diet across North America

Population fragmentation compromises population viability, reduces a species ability to respond to climate change, and ultimately may reduce biodiversity. We studied the current state and potential causes of fragmentation in grizzly bears over approximately 1,000,000 km 2 of western Canada, the northern United States (US), and southeast Alaska. We compiled much of our data from projects undertaken with a variety of research objectives including population estimation and trend, landscape fragmentation, habitat selection, vital rates, and response to human development. Our primary analytical techniques stemmed from genetic analysis of 3,134 bears, supplemented with radiotelemetry data from 792 bears. We used 15 locus microsatellite data coupled with measures of genetic distance, isolation-by-distance (IBD) analysis, analysis of covariance (ANCOVA), linear multiple regression, multi-factorial correspondence analysis (to identify population divisions or fractures with no a priori assumption of group membership), and population-assignment methods to detect individual migrants between immediately adjacent areas. These data corroborated observations of inter-area movements from our telemetry database. In northern areas, we found a spatial genetic pattern of IBD, although there was evidence of natural fragmentation from the rugged heavily glaciated coast mountains of British Columbia (BC) and the Yukon. These results contrasted with the spatial pattern of fragmentation in more southern parts of their distribution. Near the Canada-US border area, we found extensive fragmentation that corresponded to settled mountain valleys and major highways. Genetic distances across developed valleys were elevated relative to those across undeveloped valleys in central and northern BC. In disturbed areas, most inter-area movements detected were made by male bears, with few female migrants identified. North-south movements within mountain ranges (Mts) and across BC Highway 3 were more common than east-west movements across settled mountain valleys separating Mts. Our results suggest that relatively distinct subpopulations exist in this region, including the Cabinet, Selkirk South, and the decades- isolated Yellowstone populations. Current movement rates do not appear sufficient to consider the subpopulations we identify along the Canada-US border as 1 inter-breeding unit. Although we detected enough male movement to mediate gene flow, the current low rate of female movement detected among areas is insufficient to provide a demographic rescue effect between areas in the immediate future (0-15 yr). In Alberta, we found fragmentation corresponded to major east-west highways (Highways 3, 11, 16, and 43) and most inter-area movements were made by males. Gene flow and movement rates between Alberta and BC were highest across the Continental Divide

http://igbconline.org/wp-content/uploads/2016/02/2012_Proctoretal_Fragmentation_Monograph.pdf

Population fragmentation and inter-ecosystem movements of grizzly bears in western Canada and the northern United States

Refugia from trapping are believed to be important to support a long-term sustainable harvest of Canada lynx (Lynx lynx), but long-term studies in unharvested areas are lacking. We studied lynx population characteristics in relation to snowshoe hare (Lepus americanus) densities in a 301 km 2 refugium in the Yukon Territory between 1986 and 1994. Lynx carcasses were collected from adjacent trapping concessions for analysis of attributes of the harvested population. Hare density peaked in summer 1990 and began to decline in the winter of 1990-91. Lynx density in March varied with hare density from 2.7/100 km 2 in 1987 to 44.9/ 100 km 2 in 1991-92. The lynx population doubled annually for 4 years when reproduction and kit and adult survival were high, and immigration balanced or exceeded emigration. High mortality and emigration characterized the lynx decline. Proportions of breeding adults were 100% most years, including the first year of declining hare densities, but zero in the following 2 years. Yearling females reproduced only in the 2 years of highest hare numbers. Kit survival, which was 0% in 1986-87, peaked at 75% for kits of adult females and 26% for kits of yearlings in 1990-91. Emigration peaked annually from March-June, was lowest Sept.-Oct., and was not sex-biased. At least 16% (n= 22) of emigrants were trapped or shot. Seventeen lynx (14M, 3F) emigrated 100-1100 km. Annual natural mortality rates were under 11% for the first 6 years of study, including 2 years of hare decline, 60% in 1992-93 and 25% in 1993-94. The carcass sample contained 36% fewer kits, 40% more yearlings, and 4% fewer adults than were present on the study area, reflecting the lower birth and survival rates of kits of yearling females and trapping bias. Mean annual lynx home range size did not vary with hare density, until 1992-93 when male ranges increased markedly, and 1993-94 when female ranges increased. We recommend a network of permanently assigned untrapped areas to facilitate normal lynx population responses to changing snowshoe hare densities, to prevent local extinctions, and to maximize lynx harvests over a complete population cycle.

Lynx population dynamics in an untrapped refugium

We tested non-invasive genetic methods for estimating the abundance of marten Martes americana using baited glue-patch traps to pull hair samples from individual animals We divided our 800–km2 study area into 3 × 3 km cells and put one hair trap in each cell We trapped 309 sites for an average of 15 days each between 15 January and 14 March 1997 Based on tracks in snow and hair morphology, we captured hair from marten, red squirrels Tamiasciurus hudsonicus, flying squirrels Glaucomys sabrinus, short or long-tailed weasels Mustela erminea and Mfrenata, and several unidentified mouse and vole species Of 309 sites, 58% collected a marten hair sample while 8% of sites removed weasel hair When roots were embedded in adhesive, a xylene wash was used to remove them before extracting DNA All marten samples were genotyped at six microsatellite loci to identify individuals Xylene-washed samples yielded similar genotyping success to samples that had never been exposed to xylene, and genotyping success increased with the number of hairs in the sample Genetic data allowed 139 samples to be assigned to 88 individual marten, constituting 124 capture events during the four trapping sessions The population estimate for our study area was 213 (95% Cl: 148–348) and the average capture probability was 015 The density of marten in our study area was 033/km2 when inhospitable habitat was removed from the calculation We believe hair sampling and genetic analysis could be used to measure population distribution, trend and size for marten, and perhaps also for other carnivores

https://bioone.org/journals/wildlife-biology/volume-8/issue-1/wlb.2002.034/Estimating-marten-Martes-americana-population-size-using-hair-capture-and/10.2981/wlb.2002.034.pdf

Garth Mowat

Papers

Estimating population size of grizzly bears using hair capture, DNA profiling, and mark-recapture analysis

Major components of grizzly bear diet across North America

Population fragmentation and inter-ecosystem movements of grizzly bears in western Canada and the northern United States

Lynx population dynamics in an untrapped refugium

Estimating marten Martes americana population size using hair capture and genetic tagging