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opencc-by-4.0May 2022View details →

Data from: Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry

Abstract: When sex chromosomes stop recombining, they start to accumulate differences. The sex-limited chromosome (Y or W) especially is expected to degenerate via the loss of nucleotide sequence and the accumulation of repetitive sequences. However, how early signs of degeneration can be detected in a new sex chromosome is still unclear. The sex determining region (SDR) of the octoploid strawberries is young, small, and dynamic. Using PacBio HiFi reads, we obtained a chromosome scale assembly of a female (ZW) Fragaria chiloensis plant carrying the youngest and largest of the known SDR on the W in strawberries. We fully characterized the previously incomplete SDR, confirming its gene content, genomic location and evolutionary history. Resolution of gaps in the previous characterization of the SDR added 10 kbp of sequence including a non-canonical LTR-retrotransposon; whereas the Z sequence revealed a Harbinger transposable element adjoining the SDR insertion site. Limited genetic differentiation of the sex chromosomes coupled with structural variation may indicate an early stage of W degeneration. The sex chromosomes have a similar percentage of repeats but differ in their repeat distribution. Differences in the pattern of repeats (transposable element polymorphism) apparently precede sex chromosome differentiation, thus potentially contributing to recombination cessation as opposed to being a consequence of it. Repository content: data (sequence alignments, phylogenetic trees, genome assembly, and vcf files) and scripts associated with the manuscript "Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry"

Figure 4 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.

Figure 4 Holotype of Andrias jiangxiensis sp. nov. (KIZ 037731) in preservative A–C: Holotype of A. jiangxiensis sp. nov., in dorsal (A), lateral (B), and ventral (C) views. D, E: Dorsal (D) and ventral (E) views of head of holotype of A. jiangxiensis sp. nov. F, G: Ventral view of the left hand (F) and left foot (G) of the holotype of A. jiangxiensis sp. nov. Photos by Chen-Qi Lu.

Figure 7 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.

Figure 7 The habitat of Andrias jiangxiensis sp. nov. in Daqi Mountain, Jing'an County, Jiangxi, China A, B: Summer (A) and winter (B) scene of 8–10 meters-wide stream with excellent vegetation coverage. C: Abreeding cave for A. jiangxiensis sp. nov. found in a backwater bay of the stream. Red arrow indicates the exit of the cave. D: Enlarged area near the exit of the cave. Dashed circles in cyan indicate six larvae of A. jiangxiensis sp. nov., and the ones in white indicate the co-occurring shrimps and fishes. Photos by Mu-Rong Yi.

Figure 3 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.

Figure 3 Genetic distinctiveness of CGS from clade U2 found in Jing'an County, Jiangxi, China A: Asimplified phylogeny based on COI of mtDNA modified from Yan et al. (2018), in which clade U2 represents haplotypes found in Jing'an County, Jiangxi. The clade to which A. davidianus belongs remains uncertain. Clade Dindicates the haplotypes of A. sligoi according to the analyses by Turvey et al. (2019). B: Maximum Likelihood (ML) network based on genomic SNPs for six clades. Light purple background marks the 28 individuals of clade U2. C, D: PcoA plots based on genomic SNPs for six clades. E: Genetic clustering (K=2–8, best K=7) based on genomic SNPs from six clades by ADMIXTURE analysis. Asterisks label 18 wild-caught individuals including larvae, juveniles, and adults from Daqi Mountain, diamonds in light purple indicate 10 farm-bred individuals. Colors in all figures correspond with the mtDNA clades.

Figure 2 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.

Figure 2 Results of field-monitoring surveys in Daqi Mountain, Jiangxi Jiulingshan National Nature Reserve (Sep. 2020–Mar. 2022) A: Capture per person-hour of juveniles and adults during Sep. 2020–Mar. 2022. B, C: Activity periods of newborn larvae displayed by capture per person-hour in 2021 and 2022.

Figure 6 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.

Figure 6 Ontogenetic variation in coloration pattern A: Coloration of dorsum with spotted pattern in a juvenile with body length of ~20 cm. B: Coloration of dorsum having larger patch patterns in an adult with body length over 50 cm. Photos by Mu-Rong Yi.

Figure 5 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.

Figure 5 The holotype of Andrias jiangxiensis sp. nov. (KIZ 037731) in life A–C: Coloration of dorsum of whole body (A), head (B), and enlarged view (C) of left periocular area. Photos by Chen-Qi Lu.

Figure 1 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.

Figure 1 Map of survey localities in Jing'an County, northwest of Jiangxi, China The west part of black dashed line displays the historical distribution areas of CGS, upstream of River Liao. Red dashed line circles Daqi Mountain, which is closed to the public. Grey triangles indicate 16 sites surveyed without detection of individuals, while the red triangle and red line display the searching sites with detections.

opencc-zeroJun 2022View details →

Interspecific coprophagia by wild red foxes: DNA metabarcoding reveals a potentially widespread form of commensalism among animals

Vertebrate animals are known to consume other species' faeces, yet the role of such coprophagy in species dynamics remains unknown, not least due to the methodological challenges of documenting it. In a large-scale metabarcoding study of red fox and pine marten scats, we document a high occurrence of domestic dog DNA in red fox scats and investigate if it can be attributed to interspecific coprophagia. We tested whether experimental artifacts or other sources of DNA could account for dog DNA, regressed dog occurrence in the diet of fox against that of the fox' main prey, short-tailed field voles, and consider whether predation or scavenging could explain the presence of dog DNA. Additionally, we determined the calorific value of dog faeces through calorimetric explosion. The high occurrence of dog DNA in the diet of fox, the timing of its increase, and the negative relationship between dog and the fox's main prey, point to dog faeces as the source of DNA in fox scats. Dog faeces being highly calorific, we found that foxes, but not pine martens, regularly exploit them, seemingly as an alternative resource to fluctuating prey. Scattered accounts from the literature may suggest that interspecific coprophagia is a potentially frequent and widespread form of interaction among vertebrates. However, further work should address its prevalence in other systems as well as the implications for ecological communities. Tools such as metabarcoding offer a way forward.

opencc-zeroJun 2022View details →

Cumulative cultural evolution and mechanisms for cultural selection in wild bird songs

Cumulative cultural evolution, the accumulation of sequential changes within a single socially learned behaviour that results in improved function, is prominent in humans and has been documented in experimental studies of captive animals and managed wild populations. Here, we provide evidence that cumulative cultural evolution has occurred in the learned songs of Savannah sparrows. In a first step, "click trains" replaced "high note clusters" over a period of three decades. We use mathematical modeling to show that this replacement is consistent with the action of selection, rather than drift or frequency-dependent learning biases. Generations later, young birds elaborated the "click train" song form by adding more clicks. We show that the new songs with more clicks elicit stronger behavioural responses from both males and females. Therefore, we suggest that a combination of social learning, innovation, and sexual selection favoring a specific discrete trait was followed by directional sexual selection that resulted in naturally occurring cumulative cultural evolution in the songs of this wild animal population.

opencc-zeroJun 2022View details →

Code: A model of wild bee populations accounting for spatial heterogeneity and climate induced temporal variability of food resources at the landscape level

The viability of wild bee populations and the pollination services that they provide are driven by the availability of food resources during their activity period and within the surroundings of their nesting sites. Changes in climate and land use influence the availability of these resources and are major threats to declining bee populations. Because wild bees may be vulnerable to interactions between these threats, spatially explicit models of population dynamics that capture how bee populations jointly respond to land use at a landscape scale and weather are needed. Here, we developed a spatially and temporally explicit theoretical model of wild bee populations aiming for a middle ground between the existing mapping of visitation rates using foraging equations and more refined agent-based modelling. The model is developed for Bombus sp. and captures within-season colony dynamics. The model describes mechanistically foraging at the colony level and temporal population dynamics for an average colony at the landscape level. Stages in population dynamics are temperature-dependent triggered with a theoretical generalized seasonal progression, which can be informed by growing degree days (GDD). The purpose of the LandscapePhenoBee model is to evaluate the impact of systematic changes and within-season variability in resources on bee population sizes and crop visitation rates. In a simulation study, we used the model to evaluate the impact of the shortage of food resources in the landscape arising from extreme drought events in different types of landscapes (ranging from different proportions of semi-natural habitats and early and late flowering crops) on bumblebee populations.

opencc-zeroJul 2022View details →

Can disease resistance evolve independently at different ages? Genetic variation in age-dependent resistance to disease in three wild plant species

1. Juveniles are typically less resistant (more susceptible) to infectious disease than adults, and this difference in susceptibility can help fuel the spread of pathogens in age-structured populations. However evolutionary explanations for this variation in resistance across age remain to be tested. 2. One hypothesis is that natural selection has optimized resistance to peak at ages where disease exposure is greatest. A central assumption of this hypothesis is that hosts have the capacity to evolve resistance independently at different ages. This would mean that hosts populations have a) standing genetic variation in resistance at both juvenile and adult stages, and b) that this variation is not strongly correlated between age-classes so that selection acting at one age does not produce a correlated response at the other age 3. Here we evaluated the capacity of three wild plant species (Silene latifolia, S. vulgaris, and Dianthus pavonius) to evolve resistance to their anther-smut pathogens (Microbotryum fungi), independently at different ages. The pathogen is pollinator-transmitted, and thus exposure risk is considered to be highest at the adult flowering stage. 4. Within each species we grew families to different ages, inoculated individuals with anther smut, and evaluated the effects of age, family and their interaction on infection. 5. In two of the plant species, S. latifolia and D. pavonius, resistance to smut at the juvenile stage was not correlated with resistance to smut at the adult stage. In all three species, we show there are significant age*family interaction effects, indicating that age-specificity of resistance varies among the plant families. 6. Synthesis: These results indicate that different mechanisms likely underlie resistance at juvenile and adult stages and support the hypothesis that resistance can evolve independently in response to differing selection pressures as hosts age. Taken together our results provide new insight into the structure of genetic variation in age-dependent resistance in three well-studied wild host-pathogen systems.

opencc-zeroJul 2022View details →

Anthropogenic noise and light alter temporal but not spatial breeding behavior in a wild frog

Increasing urbanization has led to large scale land-use changes, exposing persistent populations to drastically altered environments. Sensory pollutants, including low-frequency anthropogenic noise and artificial light at night (ALAN), are typically associated with urban environments and known to impact animal populations in a variety of ways. Both ALAN and anthropogenic noise can alter behavioral and physiological processes important for survival and reproduction, including communication and circadian rhythms. Although noise and light pollution typically co-occur in urbanized areas, few studies have addressed their combined impact on species' behavior. Here we assessed how anthropogenic noise and ALAN can influence spatial and temporal variation in breeding activity of a wild frog population. By exposing artificial breeding sites inside a tropical rainforest to multiple sensory environments, we found that both anthropogenic noise and ALAN impact breeding behavior of túngara frogs (Engystomops pustulosus), albeit in different ways. Males arrived later in the night at their breeding sites in response to anthropogenic noise. ALAN, on the other hand, led to an increase in calling effort. We found no evidence that noise or light pollution either attracted frogs to or repelled frogs from breeding sites. Thus, anthropogenic noise may negatively affect calling males by shifting the timing of sexual signaling. Conversely, ALAN may increase the attractiveness of calling males. These changes in breeding behavior highlight the complex ways that urban multisensory pollution can influence behavior and suggest that such changes may have important ecological implications for the wildlife that are becoming increasingly exposed to urban multisensory pollution.

opencc-by-4.0Aug 2022View details →

Data on the abundance of wild ungulates and large carnivores in the Roztocze National Park (south-east Poland), 2007-2022

Data on the abundance of wild ungulates and large carnivores in the Roztocze National Park (south-east Poland), 2007-2022

opencc-zeroSep 2022View details →

Incorporating evolutionary and threat processes into crop wild relatives conservation

Crop wild relatives (CWR) intra- and interspecific diversity is essential for crop breeding and food security. However, intraspecific genetic diversity, which is central given the idiosyncratic threats to species in landscapes, is usually not considered in planning frameworks. Here, we introduce an approach to develop proxies of genetic differentiation to identify conservation areas, applying systematic conservation planning tools that produce hierarchical prioritizations of the landscape. It accounts for: (i) evolutionary processes, including historical and environmental drivers of genetic diversity, and (ii) threat processes, considering taxa-specific tolerance to human-modified habitats, and their extinction risk status. Our results support the development of national strategies for the conservation and use of CWR in Mexico and inform public policy to mitigate threat processes to CWR. Although we focus on Mesoamerican CWR within Mexico, our methodology offers opportunities to effectively guide conservation and monitoring strategies to safeguard the evolutionary resilience of any taxa, including in regions of complex evolutionary histories and mosaic landscapes.

opencc-zeroSep 2022View details →

Temporal change in the contribution of immigration to population growth in a wild seabird experiencing rapid population decline

The source-sink paradigm predicts that populations in poorer-quality habitats ("sinks") persist due to continued immigration from more-productive areas ("sources"). However, this categorisation of populations assumes that habitat quality is fixed through time. Globally, we are in an era of wide-spread habitat degradation, and consequently, there is a pressing need to examine dispersal dynamics in relation to local population change. We used an integrated population model to quantify immigration dynamics in a long-lived colonial seabird, the black-legged kittiwake Rissa tridactyla, that is classified as globally "Vulnerable". We then used a transient life table response experiment to evaluate the contribution of temporal variation in vital rates, immigration rates, and population structure to realised population growth. Finally, we used a simulation analysis to examine the importance of immigration to population dynamics. We show that the contribution of immigration changed as the population declined. This study demonstrates that immigration is unlikely to maintain vulnerable sink populations indefinitely, emphasising the need for temporal analyses of dispersal to identify shifts that may have dramatic consequences for population viability.

Fig. 4 in A new Copelatus with small eyes from the Eastern Cape Wild Coast, South Africa (Coleoptera: Dytiscidae)

Fig. 4. Southern African Copelatus species compound eyes, all to same scale. A – C. mkambati sp. nov., paratype male; B – C. capensis Sharp, 1882 (Groote River, South Africa); C – C. erichsoni Guérin-Méneville, 1847 (St Lucia, South Africa); D – C. pulchellus (Klug, 1834) (St Lucia, South Africa).

Fig. 1. Copelatus species. A – C in A new Copelatus with small eyes from the Eastern Cape Wild Coast, South Africa (Coleoptera: Dytiscidae)

Fig. 1. Copelatus species. A – C. mkambati sp. nov. holotype male habitus; B – C. mkambati sp. nov., paratype female habitus; C – C. macellus Guignot, 1950, holotype male habitus; D – C. macellus, holotype labels. Scale bar applies to A–C. Figs C & D: © MNHN/Christophe Rivier.

Fig. 3. Copelatus species male genitalia. A – C. macellus Guignot, 1950 in A new Copelatus with small eyes from the Eastern Cape Wild Coast, South Africa (Coleoptera: Dytiscidae)

Fig. 3. Copelatus species male genitalia. A – C. macellus Guignot, 1950, median lobe; B – C. basilewskyi Bilardo & Pederzani, 1979, median lobe; C – C. mkambati sp. nov., median lobe and paramere. Scale bar in C = 0.5 mm. Note that lines on the paramere represent musculature, not surface ridges. A & B after GඎංGඇඈඍ (1961) and Bංඅൺඋൽඈ & Pൾൽൾඋඓൺඇං (1979), respectively.