INTERMITTENT BREEDING AND CONSTRAINTS ON LITTER SIZE: CONSEQUENCES FOR EFFECTIVE POPULATION SIZE PER GENERATION (Ne) AND PER REPRODUCTIVE CYCLE (Nb)

In iteroparous species, it is easier to estimate N_b (effective number of breeders in one reproductive cycle) than N_e (effective population size per generation). N_b can be used as a proxy for N_e and also can provide crucial insights into eco‐evolutionary processes that occur during reproduction. We used analytical and numerical methods to evaluate effects of intermittent breeding and litter/clutch size on inbreeding N_b and N_e. Fixed or random litter sizes ≥ 3 have little effect on either effective‐size parameter; however, in species (e.g., many large mammals) in which females can produce only one offspring per cycle, female N_b = ∞ and overall N_b = 4N_b(male). Intermittent breeding reduces the pool of female breeders, which reduces both female and overall N_b; reductions are larger in high‐fecundity species with high juvenile mortality and increase when multiple reproductive cycles are skipped. Simulated data for six model species showed that both intermittent breeding and litter‐size constraints increase N_e, but only slightly. We show how to quantitatively account for these effects, which are important to consider when (1) using N_b to estimate N_e, or (2) drawing inferences about male reproductive success based on estimates of female N_b.     

Rating of perceived exertion as a tool for prescribing and self regulating interval training: a pilot study

The aim of the present study was to analyse the usefulness of the 6-20 rating of perceived exertion (RPE) scale for prescribing and self-regulating high-intensity interval training (HIT) in young individuals. Eight healthy young subjects (age = 27.5±6.7 years) performed maximal graded exercise testing to determine their maximal and reserve heart rate (HR). Subjects then performed two HIT sessions (20 min on a treadmill) prescribed and regulated by their HR (HR: 1 min at 50% alternated with 1 min at 85% of reserve HR) or RPE (RPE: 1 minute at the 9-11 level [very light-fairly light] alternated with 1 minute at the 15-17 level [hard-very hard]) in random order. HR response and walking/running speed during the 20 min of exercise were compared between sessions. No significant difference between sessions was observed in HR during low- (HR: 135±15 bpm; RPE: 138±20 bpm) and high-intensity intervals (HR: 168±15 bpm; RPE: 170±18 bpm). Walking/running speed during low- (HR: 5.7±1.2 km · h⁻¹; RPE: 5.7±1.3 km · h⁻¹) and high-intensity intervals (HR: 7.8±1.9 km · h⁻¹; RPE: 8.2±1.7 km · h⁻¹) was also not different between sessions. No significant differences were observed in HR response and walking/running speed between HIT sessions prescribed and regulated by HR or RPE. This finding suggests that the 6-20 RPE scale may be a useful tool for prescribing and self-regulating HIT in young subjects.     

Estimating contemporary effective population size on the basis of linkage disequilibrium in the face of migration

Effective population size (Ne) is an important genetic parameter because of its relationship to loss of genetic variation, increases in inbreeding, accumulation of mutations, and effectiveness of selection. Like most other genetic approaches that estimate contemporary Ne, the method based on linkage disequilibrium (LD) assumes a closed population and (in the most common applications) randomly recombining loci. We used analytical and numerical methods to evaluate the absolute and relative consequences of two potential violations of the closed-population assumption: (1) mixture LD caused by occurrence of more than one gene pool, which would downwardly bias Ne and (2) reductions in drift LD (and hence upward bias in Ne) caused by an increase in the number of parents responsible for local samples. The LD method is surprisingly robust to equilibrium migration. Effects of mixture LD are small for all values of migration rate (m), and effects of additional parents are also small unless m is high in genetic terms. LD estimates of Ne therefore accurately reflect local (subpopulation) Ne unless m>～5-10%. With higher m, Ne converges on the global (metapopulation) Ne. Two general exceptions were observed. First, equilibrium migration that is rare and hence episodic can occasionally lead to substantial mixture LD, especially when sample size is small. Second, nonequilibrium, pulse migration of strongly divergent individuals can also create strong mixture LD and depress estimates of local Ne. In both cases, assignment tests, Bayesian clustering, and other methods often will allow identification of recent immigrants that strongly influence results. In simulations involving equilibrium migration, the standard LD method performed better than a method designed to jointly estimate Ne and m. The above results assume loci are not physically linked; for tightly linked loci, the LD signal from past migration events can persist for many generations, with consequences for Ne estimates that remain to be evaluated.     

Red flags: correlates of impaired species recovery

Conservation biology research exhibits a striking but unhelpful dichotomy. Analyses of species decline, extinction risk, and threat mitigation typically encompass broad taxonomic and spatial scales. By contrast, most studies of recovery lack generality, pertaining to specific species, populations, or locales. Narrowly focused analyses offer a weak empirical basis for identifying generic recovery correlates across species, particularly in cases where recovery is not effected by an abatement of threats. We present a research framework for multi-species meta-analyses to identify early-warning signals - 'red flags' - of impaired recovery that can be used as predictors of recovery potential before recovery efforts are initiated. An empirically comprehensive understanding of the demographic, ecological, evolutionary, and threat-related factors affecting the rate and trajectory of species recovery will strengthen conservation efforts to set recovery priorities, targets, and timelines.     

Making sense of genetic estimates of effective population size

The last decade has seen an explosion of interest in use of genetic markers to estimate effective population size, N_e. Effective population size is important both theoretically (N_e is a key parameter in almost every aspect of evolutionary biology) and for practical application (N_e determines rates of genetic drift and loss of genetic variability and modulates the effectiveness of selection, so it is crucial to consider in conservation). As documented by Palstra & Fraser ( 2012 ), most of the recent growth in N_e estimation can be attributed to development or refinement of methods that can use a single sample of individuals (the older temporal method requires at least two samples separated in time). As with other population genetic methods, performance of new N_e estimators is typically evaluated with simulated data for a few scenarios selected by the author(s). Inevitably, these initial evaluations fail to fully consider the consequences of violating simplifying assumptions, such as discrete generations, closed populations of constant size and selective neutrality. Subsequently, many researchers studying natural or captive populations have reported estimates of N_e for multiple methods; often these estimates are congruent, but that is not always the case. Because true N_e is rarely known in these empirical studies, it is difficult to make sense of the results when estimates differ substantially among methods. What is needed is a rigorous, comparative analysis under realistic scenarios for which true N_e is known. Recently, Gilbert & Whitlock ( 2015 ) did just that for both single‐sample and temporal methods under a wide range of migration schemes. In the current issue of Molecular Ecology, Wang ( 2016 ) uses simulations to evaluate performance of four single‐sample N_e estimators. In addition to assessing effects of true N_e, sample size, and number of loci, Wang also evaluated performance under changing abundance, physical linkage and genotyping errors, as well as for some alternative life histories (high rates of selfing; haplodiploids). Wang showed that the sibship frequency (SF) and linkage disequilibrium (LD) methods perform dramatically better than the heterozygote excess and molecular coancestry methods under most scenarios (see Fig. 1, modified from figure 2 in Wang 2016 ), and he also concluded that SF is generally more versatile than LD. This article represents a truly Herculean effort, and results should be of considerable value to researchers interested in applying these methods to real‐world situations.     

Effective population size of steelhead trout: influence of variance in reproductive success, hatchery programs, and genetic compensation between life-history forms

The effective population size is influenced by many biological factors in natural populations. To evaluate their relative importance, we estimated the effective number of breeders per year (Nb) and effective population size per generation (Ne) in anadromous steelhead trout (Oncorhynchus mykiss) in the Hood River, Oregon (USA). Using demographic data and genetic parentage analysis on an almost complete sample of all adults that returned to the river over 15 years (>15,000 individuals), we estimated Nb for 13 run years and Ne for three entire generations. The results are as follows: (i) the ratio of Ne to the estimated census population size (N) was 0.17-0.40, with large variance in reproductive success among individuals being the primary cause of the reduction in Ne/N; (ii) fish from a traditional hatchery program (Htrad: nonlocal, multiple generations in a hatchery) had negative effects on Nb, not only by reducing mean reproductive success but also by increasing variance in reproductive success among breeding parents, whereas no sign of such effects was found in fish from supplementation hatchery programs (Hsupp: local, single generation in a hatchery); and (iii) Nb was relatively stable among run years, despite the widely fluctuating annual run sizes of anadromous adults. We found high levels of reproductive contribution of nonanadromous parents to anadromous offspring when anadromous run size is small, suggesting a genetic compensation between life-history forms (anadromous and nonanadromous). This is the first study showing that reproductive interaction between different life-history forms can buffer the genetic impact of fluctuating census size on Ne.     

Spatial-temporal stratifications in natural populations and how they affect understanding and estimation of effective population size

The concept of effective population size (N(e) ) is based on an elegantly simple idea which, however, rapidly becomes very complex when applied to most real-world situations. In natural populations, spatial and temporal stratifications create different classes of individuals with different vital rates, and this in turn affects (generally reduces) N(e) in complex ways. I consider how these natural stratifications influence our understanding of effective size and how to estimate it, and what the consequences are for conservation and management of natural populations. Important points that emerge include the following: 1 The relative influences of local vs metapopulation N(e) depend on a variety of factors, including the time frame of interest. 2 Levels of diversity in local populations are strongly influenced by even low levels of migration, so these measures are not reliable indicators of local N(e) . 3 For long-term effective size, obtaining a reliable estimate of mutation rate is the most important consideration; unless this is accomplished, estimates can be biased by orders of magnitude. 4 At least some estimators of contemporary N(e) appear to be robust to relatively high (approximately 10%) equilibrium levels of migration, so under many realistic scenarios they might yield reliable estimates of local N(e) . 5 Age structure probably has little effect on long-term estimators of N(e) but can strongly influence contemporary estimates. 6 More research is needed in several key areas: (i) to disentangle effects of selection and drift in metapopulations connected by intermediate levels of migration; (ii) to elucidate the relationship between N(b) (effective number of breeders per year) and N(e) per generation in age-structured populations; (iii) to perform rigorous sensitivity analyses of new likelihood and coalescent-based methods for estimating demographic and evolutionary histories.     

Loss of meiosis in Aspergillus

If strictly mitotic asexual fungi lack recombination, the conventional view predicts that they are recent derivatives from older meiotic lineages. We tested this by inferring phylogenetic relationships among closely related meiotic and strictly mitotic taxa with Aspergillus conidial (mitotic) states. Phylogenies were constructed by using DNA sequences from the mitochondrial small ribosomal subunit, the nuclear ribosomal internal transcribed spacers, and the nuclear 5.8S ribosomal gene. Over 920 bp of sequence was analyzed for each taxon. Phylogenetic analysis of both the mitochondrial and nuclear data sets showed at least four clades that possess both meiotic and strictly mitotic taxa. These results support the hypothesis that strictly mitotic lineages arise frequently from more ancient meiotic lineages with Aspergillus conidial states. Many of the strictly mitotic species examined retained characters that may be vestiges of a meiotic state, including the production of sclerotia, sclerotium-like structures, and hulle cells.