A stochastic model for estimating sustainable limits to wildlife mortality in a changing world

Human-caused mortality of wildlife is a pervasive threat to biodiversity. Assessing the population-level impact of fisheries bycatch and other human-caused mortality of wildlife has typically relied upon deterministic methods. However, population declines are often accelerated by stochastic factors that are not accounted for in such conventional methods. Building on the widely applied potential biological removal (PBR) equation, we devised a new population modeling approach for estimating sustainable limits to human-caused mortality and applied it in a case study of bottlenose dolphins affected by capture in an Australian demersal otter trawl fishery. Our approach, termed sustainable anthropogenic mortality in stochastic environments (SAMSE), incorporates environmental and demographic stochasticity, including the dependency of offspring on their mothers. The SAMSE limit is the maximum number of individuals that can be removed without causing negative stochastic population growth. We calculated a PBR of 16.2 dolphins per year based on the best abundance estimate available. In contrast, the SAMSE model indicated that only 2.3–8.0 dolphins could be removed annually without causing a population decline in a stochastic environment. These results suggest that reported bycatch rates are unsustainable in the long term, unless reproductive rates are consistently higher than average. The difference between the deterministic PBR calculation and the SAMSE limits showed that deterministic approaches may underestimate the true impact of human-caused mortality of wildlife. This highlights the importance of integrating stochasticity when evaluating the impact of bycatch or other human-caused mortality on wildlife, such as hunting, lethal control measures, and wind turbine collisions. Although population viability analysis (PVA) has been used to evaluate the impact of human-caused mortality, SAMSE represents a novel PVA framework that incorporates stochasticity for estimating acceptable levels of human-caused mortality. It offers a broadly applicable, stochastic addition to the demographic toolbox to evaluate the impact of human-caused mortality on wildlife

Tracking invasion and invasiveness in queensland fruit flies: From classical genetics to ‘omics’

Three Australian tephritid fruit flies (Bactrocera tryoni – Q-fly, Bactrocera neohumeralis – NEO, and Bactrocera jarvisi – JAR) are promising models for genetic studies of pest status and invasiveness. The long history of ecological and physiological studies of the three species has been augmented by the development of a range of genetic and genomic tools, including the capacity for forced multigeneration crosses between the three species followed by selection experiments, a draft genome for Q-fly, and tissue- and stage-specific transcriptomes. The Q-fly and NEO species pair is of particular interest. The distribution of NEO is contained entirely within the wider distribution of Q-fly and the two species are ecologically extremely similar, with no known differences in pheromones, temperature tolerance, or host-fruit utilisation. However there are three clear differences between them: humeral callus colour, complete pre-mating isolation based on mating time-of-day, and invasiveness. NEO is much less invasive, whereas in historical times Q-fly has invaded southeastern Australia and areas of Western Australia and the Northern Territory. In southeastern fruit-growing regions, microsatellites suggest that some of these outbreaks might derive from genetically differentiated populations overwintering in or near the invaded area. Q-fly and NEO show very limited genome differentiation, so comparative genomic analyses and QTL mapping should be able to identify the regions of the genome controlling mating time and invasiveness, to assess the genetic bases for the invasive strains of Q-fly, and to facilitate a variety of improvements to current sterile insect control strategies for that species

Transcript- and annotation-guided genome assembly of the European starling

First published: 28 June 2022The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long- read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second, North American, short- read genome assembly (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterization. S. vulgaris vAU combined 10× genomics linked- reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full- length transcript scaffolding to generate a 1050 Mb assembly on 6222 scaffolds (7.6 Mb scaffold N50, 94.6% busco completeness). Further scaffolding against the high-quality zebra finch (Taeniopygia guttata) genome assigned 98.6% of the assembly to 32 puta-tive nuclear chromosome scaffolds. Species-specific transcript mapping and gene an-notation revealed good gene- level assembly and high functional completeness. Using S. vulgaris vAU, we demonstrate how the multifunctional use of PacBio Iso-Seq tran-script data and complementary homology-based annotation of sequential assembly steps (assessed using a new tool, saaga) can be used to assess, inform, and validate assembly workflow decisions. We also highlight some counterintuitive behaviour in traditional busco metrics, and present buscomp, a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. This work expands our knowledge of avian genomes and the available toolkit for assessing and improving genome quality. The new genomic resources presented will facilitate further global genomic and transcriptomic analysis on this ecologically important species.Katarina C. Stuart, Richard J. Edwards, Yuanyuan Cheng, Wesley C. Warren, David W. Burt, William B. Sherwin, Natalie R. Hofmeister, Scott J. Werner, Gregory F. Ball, Melissa Bateson, Matthew C. Brandley, Katherine L. Buchanan, Phillip Cassey, David F. Clayton, Tim De Meyer, Simone L. Meddle, Lee A. Rollin

Neuropathological Findings In Chronic Relapsing Experimental Allergic Neuritis Induced In The Lewis Rat By Inoculation With Intradural Root Myelin And Treatment With Low Dose Cyclosporin A

Experimental allergic neuritis (EAN) was induced in Lewis rats by inoculation with bovine intradural root myelin and adjuvants. Rats treated with subcutaneous cyclosporin A (CsA) (4mg/kg on 3 days per week from the day of inoculation until day 29) developed a chronic relapsing course. Tissues from the spinal cord, nerve roots, dorsal root ganglia and sciatic nerve of CsA-treated rats sampled during relapses and remissions were studied during or after episodes of acute EAN. Both control and CsA-treated animals studied in the first episode of EAN had evidence of inflammation and primary demyelination of the nerve roots and dorsal root ganglia. In control and CsA-treated animals in the second episode there was severe inflammation and demyelination and remyelination in the spinal nerves and sciatic nerves and dorsal columns of the spinal cord, particularly in later stages of the disease. In later episodes there was less inflammation, but there was continuing demyelination and onion bulbs were present. In animals sampled after recovery from chronic relapsing EAN onion bulbs were present. Occasional small onion bulbs were also observed in control animals that were inoculated with higher doses of myelin. Plasma cells were present in the inflammatory lesions of later episodes. Mast cells were also observed at different stages of the disease. We conclude that the CsA form of chronic relapsing EAN has clinical and pathological similarities with the human disease, chronic inflammatory demyelinating polyradiculoneuropathy

Genes are information, so information theory is coming to the aid of evolutionary biology

Speciation is central to evolutionary biology, and to elucidate it, we need to catch the early genetic changes that set nascent taxa on their path to species status (Via 2009). That challenge is difficult, of course, for two chief reasons: (i) serendipity is required to catch speciation in the act; and (ii) after a short time span with lingering gene flow, differentiation may be low and/or embodied only in rare alleles that are difficult to sample. In this issue of Molecular Ecology Resources, Smouse et al. (2015) have noted that optimal assessment of differentiation within and between nascent species should be robust to these challenges, and they identified a measure based on Shannon's information theory that has many advantages for this and numerous other tasks. The Shannon measure exhibits complete additivity of information at different levels of subdivision. Of all the family of diversity measures (‘0’ or allele counts, ‘1’ or Shannon, ‘2’ or heterozygosity, FST and related metrics) Shannon's measure comes closest to weighting alleles by their frequencies. For the Shannon measure, rare alleles that represent early signals of nascent speciation are neither down-weighted to the point of irrelevance, as for level 2 measures, nor up-weighted to overpowering importance, as for level 0 measures (Chao et al. 2010, 2015). Shannon measures have a long history in population genetics, dating back to Shannon's PhD thesis in 1940 (Crow 2001), but have received only sporadic attention, until a resurgence of interest in the last ten years, as reviewed briefly by Smouse et al. (2015)

Inconsistency between socio-spatial and genetic structure in a coastal dolphin population

Identifying population structure and boundaries among communities of wildlife exposed to anthropogenic threats is key to successful conservation management. Previous studies on the demography, social and spatial structure of Indo-Pacific bottlenose dolphins (Tursiops aduncus) suggested four nearly discrete behavioral communities in Perth metropolitan waters, Western Australia. We investigated the genetic structure of these four communities using highly polymorphic microsatellite markers and part of the hypervariable segment of the mitochondrial control region. Overall, there was no evidence of spatial genetic structure. We found significant, yet very small genetic differentiation between some communities, most likely due to the presence of highly related individuals within these communities. Our findings of high levels of contemporary migration and highly related individuals among communities point toward a panmictic genetic population with continuous gene flow among each of the communities. In species with slow life histories and fission-fusion dynamics, such as Tursiops spp., genetic and socio-spatial structures may reflect different timescales. Thus, despite genetic similarity, each social community should be considered as a distinct ecological unit to be conserved because they are exposed to different anthropogenic threats and occur in different ecological habitats, social structure being as important as genetic information for immediate conservation management. The estuarine community, in particular, is highly vulnerable and appropriate conservation measures are needed in order to maintain its connectivity with the adjacent, semi-enclosed coastal communities

De Novo Assembly of the Liver Transcriptome of the European Starling, Sturnus vulgaris

The European starling, Sturnus vulgaris, is a prolific and worldwide invasive species that also has served as an important model for avian ecological and invasion research. Although the genome sequence recently has become available, no transcriptome data have been published for this species. Here, we have sequenced and assembled the S. vulgaris liver transcriptome, which will provide a foundational resource for further annotation and validation of the draft genome. Moreover, it will be important for ecological and evolutionary studies investigating the genetic factors underlying rapid evolution and invasion success in this global invader

Paternity and male mating strategies of a ground squirrel (Ictidomys parvidens) with an extended mating season

Animal mating systems are driven by the temporal and spatial distribution of sexually receptive females. In mammals, ground-dwelling squirrels represent an ideal clade for testing predictions regarding the effects of these parameters on male reproductive strategies. While the majority of ground squirrel species have a short, highly synchronous annual breeding season that occurs immediately after females emerge from hibernation, the Mexican or Rio Grande ground squirrel (Ictidomys parvidens) differs markedly in having an extended mating season (2 months) and a long delay between emergence from hibernation and female receptivity (1–2 months). Both traits are expected to favor polygyny by increasing the chances that a male can secure matings with multiple females (e.g., females that come into estrus on different days). To test this prediction, we used microsatellite markers to characterize the mating system of a population of Rio Grande ground squirrels from Carlsbad, New Mexico. Our analyses indicated a high frequency of multiple paternity of litters in this population. Paternity was not related to spatial overlap between known mothers and assigned fathers, suggesting that territory defense is unlikely to be an effective male reproductive strategy in the study population. Dominance interactions among males were frequent, with heavier males typically winning dyadic interactions. Surprisingly, however, males with lower dominance scores appeared to have higher reproductive success, as did males that were active over a greater extent of the study site. Collectively, these results suggest that the mating system of the Rio Grande ground squirrel is best described as scramble competition polygyny, with the primary male reproductive strategy consisting of searching for estrous females. Similar patterns of male–male competition have been reported for a few other ground squirrel species, providing potentially important opportunities for comparative studies of the factors favoring this form of male reproductive strategy

Information theory broadens the spectrum of molecular ecology and evolution

Information or entropy analysis of diversity is used extensively in community ecology, and has recently been exploited for prediction and analysis in molecular ecology and evolution. Information measures belong to a spectrum (or q profile) of measures whose contrasting properties provide a rich summary of diversity, including allelic richness (q = 0), Shannon information (q = 1), and heterozygosity (q = 2). We present the merits of information measures for describing and forecasting molecular variation within and among groups, comparing forecasts with data, and evaluating underlying processes such as dispersal. Importantly, information measures directly link causal processes and divergence outcomes, have straightforward relationship to allele frequency differences (including monotonicity that q = 2 lacks), and show additivity across hierarchical layers such as ecology, behaviour, cellular processes, and nongenetic inheritance. Diversity of molecules or species is best summarised as a diversity profile.Such profiles are useful in studies spanning bioinformatics to physical landscapes.Shannon information is a neglected but particularly informative part of the profile.Shannon now has robust theoretical background for molecular ecology and evolution

Pooling hair samples to increase DNA yield for PCR

Hairs are useful non-invasive sources of DNA,but the DNA yield can be very small, thus promoting genotyping errors. Using multiple hairs can counter this problem, but mayintroduce multiple contributors to a sample if collected remotely. With microsatellite genotyping, samples representing multiple animals are obvious if three or more alleles are detected at any locus: these samples canthen be removed from any analyses. However, some multiple-individual samples may have only one or two alleles at each of the loci examined. We investigated the probability of failing to identify mixed pooled samples by simulating pooled samples (10~000 replicates)from microsatellite data from the northern and southern hairy-nosed wombats (NHNW, Lasiorhinus krefftii; SHNW, L.latifrons), species with low and high genetic diversity respectively. The majority (81.7%)of the 40 000 simulated samples had three or four alleles, so were readily identified as mixed. In the remaining 1-or-2-allele SHNW samples, forensic science software (DNAMIX) correctly identified mixed versus single-individual samples for all cases when the probability of locus failure was low(P (LF) = 0.1), and 99% of samples whenlocus failure was high (P (LF) = 0.5). For NHNW however, the probability of failing to identify a mixed sample was too high for population size estimation (0.05), even when the probability of locus failure was low. Incases such as this, pooled samples may beadequate for less demanding tasks, such as estimation of allele proportions. However, for animal populations with at least average levels of genetic variation, pooling of samples could safely be utilised for most applications