Species Detection and Identification in Sexual Organisms Using Population Genetic Theory and DNA Sequences

Phylogenetic trees of DNA sequences of a group of specimens may include clades of two kinds: those produced by stochastic processes (random genetic drift) within a species, and clades that represent different species. The ratio of the mean pairwise sequence difference between a pair of clades (K) to the mean pairwise sequence difference within a clade (θ) can be used to determine whether the clades are samples from different species (K/θ≥4) or the same species (K/θ<4) with probability ≥0.95. Previously I applied this criterion to delimit species of asexual organisms. Here I use data from the literature to show how it can also be applied to delimit sexual species using four groups of sexual organisms as examples: ravens, spotted leopards, sea butterflies, and liverworts. Mitochondrial or chloroplast genes are used because these segregate earlier during speciation than most nuclear genes and hence detect earlier stages of speciation. In several cases the K/θ ratio was greater than 4, confirming the original authors'' intuition that the clades were sufficiently different to be assigned to different species. But the K/θ ratio split each of two liverwort species into two evolutionary species, and showed that support for the distinction between the common and Chihuahuan raven species is weak. I also discuss some possible sources of error in using the K/θ ratio; the most significant one would be cases where males migrate between different populations but females do not, making the use of maternally inherited organelle genes problematic. The K/θ ratio must be used with some caution, like all other methods for species delimitation. Nevertheless, it is a simple theory-based quantitative method for using DNA sequences to make rigorous decisions about species delimitation in sexual as well as asexual eukaryotes.     

Defining null expectations for animal site fidelity

Site fidelity—the tendency to return to previously visited locations—is widespread across taxa. Returns may be driven by several mechanisms, including memory, habitat selection, or chance; however, pattern-based definitions group different generating mechanisms under the same label of ‘site fidelity’, often assuming memory as the main driver. We propose an operational definition of site fidelity as patterns of return that deviate from a null expectation derived from a memory-free movement model. First, using agent-based simulations, we show that without memory, intrinsic movement characteristics and extrinsic landscape characteristics are key determinants of return patterns and that even random movements may generate substantial probabilities of return. Second, we illustrate how to implement our framework empirically to establish ecologically meaningful, system-specific null expectations for site fidelity. Our approach provides a conceptual and operational framework to test hypotheses on site fidelity across systems and scales.     

SEQUENCES OF THE RRN18 GENES OF CHLAMYDOMONAS HUMICOLA AND C. DYSOSMOS ARE IDENTICAL,IN AGREEMENT WITH THEIR COMBINATION IN THE SPECIES C. APPLANATA (CHLOROPHYTA)1

The nuclear Rrn18 gene coding for small-subunit ribosomal RNA was amplified from Chlamydomonas humicola and C. dysosmos. The sequences were identical, in agreement with the combination of these two species under the name C. applanata on morphological and physiological grounds by Ettl and Schlösser (1992).     

A phylogenetic network of wild Ussurian pears (Pyrus ussuriensis Maxim.) in China revealed by hypervariable regions of chloroplast DNA

In order to understand the genetic diversity of wild Ussurian pears in China, chloroplast DNA (cpDNA) of 186 wild accessions from 12 populations in Inner Mongolia, Heilongjiang and Jilin Provinces and 51 Chinese and European pear cultivars including Pyrus ussuriensis, Pyrus pyrifolia, Pyrus bretschneideri, Pyrus sinkiangensis and Pyrus communis were investigated. Each accession was classified into one of three types (types A, B and C) based on two large deletions in the hypervariable regions between the accD–psaI and rps16–trnQ genes. Thirty haplotypes were identified by 32 mutations including 17 gaps (in/dels) and 15 base changes. Haplotype network analysis revealed that wild Chinese Ussurian pears could be grouped into subgroup I of type A. A haplotype, Hcp3, in subgroup I detected in Heilongjiang and Jilin Provinces was considered to be a divergent centre in Chinese Ussurian pears. However, the genetic diversity of wild accessions revealed by the two hypervariable regions was quite low. In particular, 98 % of wild Ussurian accessions in Inner Mongolia shared an identical haplotype Hcp1 and are, therefore, monomorphic. In comparison, Chinese pear cultivars were more divergent. These results suggest that the cpDNAs from wild Ussurian pears in Inner Mongolia have specifically differentiated compared to those from pears of other areas. The number of wild Ussurian pears has been decreasing because of desertification and land development, therefore conservation is needed.     

Effectiveness of Partial Sedation to Reduce Stress in Captured Mule Deer

Information garnered from the capture and handling of free-ranging animals helps advance understanding of wildlife ecology and can aid in decisions on wildlife management. Unfortunately, animals may experience increased levels of stress, injuries, and death resulting from captures (e.g., exertional myopathy, trauma). Partial sedation is a technique proposed to alleviate stress in animals during capture, yet efficacy of partial sedation for reducing stress and promoting survival post-capture remains unclear. We evaluated the effects of partial sedation on physiological, biochemical, and behavioral indicators of acute stress and probability of survival post-capture for mule deer (Odocoileus hemionus) that were captured via helicopter net-gunning in the eastern Greater Yellowstone Ecosystem, Wyoming, USA. We administered 10–30 mg of midazolam and 15 mg of azaperone intramuscularly (IM) to 32 mule deer in 2016 and 53 mule deer in 2017, and maintained a control group (captured but not sedated) of 38 mule deer in 2016 and 54 mule deer in 2017. To evaluate indicators of acute stress, we measured heart rate, blood-oxygen saturation, body temperature, respiration rate, and levels of serum cortisol. We recorded number of kicks and vocalizations of deer during handling and evaluated behavior during release. We also measured levels of fecal glucocorticoids as an indicator of baseline stress. Midazolam and azaperone did not reduce physiological, biochemical, or behavioral indicators of acute stress or influence probability of survival post-capture. Mule deer that were administered midazolam and azaperone, however, were more likely to hesitate, stumble or fall, and walk during release compared with individuals in the control group, which were more likely to trot, stot, or run without stumbling or falling. Our findings suggest that midazolam (10–30 mg IM) and azaperone (15 mg IM) may not yield physiological or demographic benefits for captured mule deer as previously assumed and may pose adverse effects that can complicate safety for captured animals, including drug-induced lethargy. Although we failed to find efficacy of midazolam and azaperone as a method for reducing stress in captured mule deer, the efficacy of midazolam and azaperone or other combinations of partial sedatives in reducing stress may depend on the dose of tranquilizer, study animal, capture setting, and how stress is defined. © 2020 The Wildlife Society.     

Variation in habitat use along the freshwater–marine continuum by grey mullet Mugil cephalus at the southern limits of its distribution

In this study, habitat use by Mugil cephalus was investigated in the waters of the west coast of the North Island of New Zealand by analysing microchemical composition of otoliths (laser‐ablation inductively coupled plasma mass spectrometry) obtained from individuals from commercial fish stocks and research surveys. Results of this study show that M. cephalus at the southern limits of its distribution display highly flexible migratory behaviour with extensive use of freshwater and brackish habitats, potentially enabling them to maximize foraging opportunities. Mugil cephalus can tolerate a wide range of salinities and can therefore utilize higher productivity areas, such as estuaries and eutrophic riverine lakes. Finally, M. cephalus populations across a range of climates and latitudes appear to differ in the extent to which they utilize freshwater and brackish habitats, possibly with increasing penetration of fresh waters with increasing latitude.     

Variation in leaf litter nutrients of a Costa Rican rain forest is related to precipitation

By assessing current leaf litter nutrient dynamics, we may be able to predict responses of nutrient cycling in tropical ecosystems to future environmental change. The goal of this study was to assess whether nutrient cycling is related to seasonal variation in rainfall in a wet tropical forest. We examined leaf litter of an old-growth tropical rain forest in N.E. Costa Rica over a 4-year period to explore seasonal and inter-annual changes in leaf litter nutrient concentrations, and to evaluate potential short- and long-term drivers of variation in litter nutrient concentration, particularly that of phosphorus (P) and nitrogen (N). We also examined the temporal dynamics of calcium, potassium, and magnesium in the leaf litter. Leaf litter [P] and %N changed significantly with time, both seasonally and inter-annually. Seasonal changes in leaf litter [P] were strongly positively correlated with rainfall from the previous 2 weeks; cations, however, were inversely related to this measure of current rainfall, while %N was not related to rainfall. We propose that the positive relationship between current rainfall and leaf litter [P] is due to a response by the vegetation to an increase in nutrient availability and uptake. In contrast, given the negative relationship between current rainfall and cation concentrations, leaching from live leaf tissue is a more likely driver of short-term changes in cations. Should global climate change include altered rainfall patterns in this biome, one class of ecosystem-level responses could be significant changes in P and cation cycling.     

Determinants of Leaf Litter Nutrient Cycling in a Tropical Rain Forest: Soil Fertility Versus Topography

We investigated the influence of landscape-level variation in soil fertility and topographic position on leaf litter nutrient dynamics in a tropical rain forest in Costa Rica. We sampled across the three main edaphic conditions (ultisol slope, ultisol plateau, and inceptisol) to determine the effect of soil nutrients on leaf litter nutrient concentrations while controlling for topography, and to examine topographic effects while controlling for soil nutrients. Both leaf litter macronutrient [phosphorus (P), nitrogen (N), sulfur (S), calcium (Ca), potassium (K), magnesium (Mg)] and micronutrient concentrations were quantified throughout a 4-year period. Leaf litter [P], [N] and [K] varied significantly among soil types. The variation in [P], [N], and [K] was explained by soil fertility alone. Leaf litter [S], [Ca], and [Mg] did not vary among the three soil types. Macronutrient (P, K, Mg, S, Ca) concentrations in the leaf litter were much less variable than those of Fe and Al. Lower variability in essential plant nutrients suggests a great deal of plant control over the amount of nutrients resorbed before senescense. Leaf litter macronutrient concentrations varied significantly over the 4-year period, but the temporal variation did not differ among the three edaphic types as anticipated. Hence, although the magnitude of nutrient fluxes may be controlled by local factors such as soil fertility, temporal patterns are likely regulated by a common environmental variable such as precipitation or temperature.