Genome assembly, structural variants, and genetic differentiation between Lake Whitefish young species pairs (Coregonus sp.) with long and short reads

The parallel evolution of nascent pairs of ecologically differentiated species offers an opportunity to get a better glimpse at the genetic architecture of speciation. Of particular interest is our recent ability to consider a wider range of genomic variants, not only single-nucleotide polymorphisms (SNPs), thanks to long-read sequencing technology. We can now identify structural variants (SVs) like insertions, deletions, and other structural rearrangements, allowing further insights into the genetic architecture of speciation and how different variants are involved in species differentiation. Here, we investigated genomic patterns of differentiation between sympatric species pairs (Dwarf and Normal) belonging to the Lake Whitefish (Coregonus clupeaformis) species complex. We assembled the first reference genomes for both Dwarf and Normal Lake Whitefish, annotated the transposable elements, and analysed the genome in the light of related coregonid species. Next, we used a combination of long-read and short-read sequencing to characterize SVs and genotype them at population-scale using genome-graph approaches, showing that SVs cover five times more of the genome than SNPs. We then integrated both SNPs and SVs to investigate the genetic architecture of species differentiation in two different lakes and highlighted an excess of shared outliers of differentiation. In particular, a large fraction of SVs differentiating the two species was driven by transposable elements (TEs), suggesting that TE accumulation during a period of allopatry predating secondary contact may have been a key process in the speciation of the Dwarf and Normal Whitefish. Altogether, our results suggest that SVs play an important role in speciation and that by combining second and third generation sequencing we now have the ability to integrate SVs into speciation genomics.

Development and characterization of microsatellite markers for the French endemic Angelica heterocarpa (Apiaceae) and congeneric sympatric species

Objective Angelica heterocarpa (Apiaceae) is a wild endemic French species with special conservation interest in the European Union. It belongs to Angelica complex genus which is widespread throughout the north temperate zone, and is sympatric with other congeneric species. The objective of this work is to develop and characterize microsatellite markers as a new tool for understanding the ecology and evolution of Angelica species complex. Results We identified simple sequence repeat (SSR) regions in a microsatellite‐enriched library from A. heterocarpa and A. sylvestris. All 16 selected SSR regions were found to amplify in these species and were highly polymorphic. Marker transferability was validated in A. razulii and A. archangelica. These markers will help us to better understand the evolutionary dynamic between rare endemics and widespread sister species, and be useful for conservation of the endemic species. Moreover, they can provide new tools for studying the numerous traditional medicinal herbs of the Angelica genus.

A Quantitative Framework for Identifying Patterns of Route-Use in Animal Movement Data

Animal movement along repeatedly used, “habitual” routes could emerge from a variety of cognitive mechanisms, as well as in response to a diverse set of environmental features. Because of the high conservation value of identifying wildlife movement corridors, there has been extensive work focusing on environmental factors that contribute to the emergence of habitual routes between protected habitats. In parallel, significant work has focused on disentangling the cognitive mechanisms underlying animal route use, as such movement patterns are of fundamental interest to the study of decision making and navigation. We reviewed the types of processes that can generate routine patterns of animal movement, suggested a new methodological workflow for classifying one of these patterns—high fidelity path reuse—in animal tracking data, and compared the prevalence of this pattern across four sympatric species of frugivorous mammals in Panama. We found the highest prevalence of route-use in kinkajous, the only nocturnal species in our study, and propose that further development of this method could help to distinguish the processes underlying the presence of specific routes in animal movement data.

Asymmetric habitat isolation and sexual isolation predicted by the cost of migration and hybridization generate novel signatures of reinforcing selection

Reinforcement is an evolutionary process whereby increased prezygotic reproductive isolation evolves in response to the cost of hybridization. Despite theory predicting that multiple prezygotic barriers can evolve via reinforcement, most empirical studies examine a single barrier. We test novel predictions for the reinforcement of both habitat isolation and sexual isolation between ecologically divergent lineages under asymmetric migration: the lineage that emigrates more should evolve stronger habitat isolation due to the lower fitness of immigrants in the alternative habitat, while the lineage that receives more immigrants should exhibit stronger sexual isolation due to the lower fitness of hybrids. We found both signatures of reinforcement in two sympatric sister species of gall wasps that are host specific to the southern live oaks, Quercus virginiana and Q. geminata, respectively. Specifically, we observed stronger habitat isolation in the species with higher emigration rates, Belonocnema treatae, and stronger sexual isolation in the species facing more immigrants, B. fossoria. In contrast, comparisons of both species to a third, allopatric, species showed that B. kinseyi exhibited both lower habitat isolation and sexual isolation than the sympatric species, consistent with the classic predictions of reinforcement. Our study provides a rare examination of the interplay of ecology and geography in the evolution of multiple reproductive barriers to gene flow. Given that asymmetric migration between ecologically divergent lineages increasingly appears to be the rule rather than the exception, concomitant asymmetries in the strength of habitat and sexual isolation could be more widespread than currently understood.

Species-Specific Flash Patterns Track the Nocturnal Behavior of Sympatric Taiwanese Fireflies

It is highly challenging to evaluate the species’ content and behavior changes in wild fireflies, especially for a sympatric population. Here, the flash interval (FI) and flash duration (FD) of flying males from three sympatric species (Abscondita cerata, Luciola kagiana, and Luciola curtithorax) were investigated for their potentials in assessing species composition and nocturnal behaviors during the A. cerata mating season. Both FI and FD were quantified from the continuous flashes of adult fireflies (lasting 5–30 s) via spatiotemporal analyses of video recorded along the Genliao hiking trail in Taipei, Taiwan. Compared to FD patterns and flash colors, FI patterns exhibited the highest species specificity, making them a suitable reference for differentiating firefly species. Through the case study of a massive occurrence of A. cerata (21 April 2018), the species contents (~85% of the flying population) and active periods of a sympatric population comprising A. cerata and L. kagiana were successfully evaluated by FI pattern matching, as well as field specimen collections. Our study suggests that FI patterns may be a reliable species-specific luminous marker for monitoring the behavioral changes in a sympatric firefly population in the field, and has implication values for firefly conservation.

Acoustic and vibrational signaling in true katydid Nesoecia nigrispina: three means of sound production in the one species

The males of Mexican katydids Nesoecia nigrispina (Stal) produce calling songs and protest sounds using the same stridulatory apparatus as in most of the other Ensifera at the base of the elytra. It includes pars stridens on the upper elytron and plectrum on the lower. Calling sounds are 2−pulse series, repeated with a frequency of 2−3 per sec. Protest signals in the form of short trills from the same pulse duration males produce with tactile stimulation. The pulse repetition rate is almost three times higher than that of the calling sounds - up to 10 per sec. The frequency spectra of these signals have maxima in the band of 14−15 kHz. However, in addition to the sounds described, both males and females are capable to produce protest signals of the second type with the help of another sound apparatus, namely with the help of the wings. Insects with removed elytra are unable to produce an audible sound. Thus, the sound is produced by the friction of the wings on the elytra, but there are no specialized stridulatory structures on them. In females, in response to tactile stimulation, short clicks are recorded, which they make, apparently, by the mandibles. Vibrational signals at tremulation are emitted by individuals of both sexes during courtship and males, completing the calling signal cycle and after copulation. It is possible that vibrational signals are an additional factor in reproductive isolation in sympatric species, since the calling sound signals in representatives of the genus Nesoecia are similar and exhibit significant variability.

A pheromone bouquet controls the reproductive behaviour of the male shore crab, Carcinus maenas

The reproduction of many brachyuran crustaceans involves the formation of mating pairs often around the time of the female moult with attraction of a sexual partner and mating behaviour controlled by sex pheromones. In shore crabs, Carcinus maenas, females produce sex pheromones that are released in the urine. High Performance Liquid Chromatography analysis (HPLC) of female urine shows that the pheromone, identified as the nucleotide uridine diphosphate (UDP), elutes as an unresolved peak with structurally related nucleotides. We examined female urine samples over the moult cycle and detected UDP as well as uridine triphosphate (UTP). Bioassays were conducted to establish the possibility of a blend of nucleotides forming a sex pheromone bouquet in C. maenas. Whilst UDP induced the male mate guarding behaviour (cradling), a mixture of the two nucleotides at a ratio of 4:1 UDP:UTP elicited an even stronger mating response than either UDP or UTP individually. The urine concentration and composition of these nucleotides changes over the moult period pre and post ecdysis, providing evidence that a pheromone bouquet composition is not always constant. The change of the bouquet is related to the physiological state of the sender, here the moult cycle. Our study unravels the functionality of reaction-specific molecules in a pheromone bouquet. Whilst UDP is the mating signal, UTP acts as an attractant and combined they maximise the reproductive response. The use of bouquets provides species-specificity, potentially enabling reproductive isolation of sympatric species, and contains valuable information on the physiological state of the sender.

Source and seasonality of epizootic mycoplasmosis in free-ranging pronghorn (Antilocapra americana)

Mycoplasma bovis is an economically important bacterial pathogen of cattle and bison that most commonly causes pneumonia, polyarthritis and mastitis. M. bovis is prevalent in cattle and commercial bison; however, infections in other host species are rare. In early 2019, we identified the first known cases of M. bovis in free-ranging pronghorn (Antilocapra americana). Here we report on additional pronghorn mortalities caused by M. bovis occurring in the same geographic region of northeastern Wyoming one year later. Genetic analysis by multilocus sequence typing (MLST) revealed that the mortalities were caused by the same M. bovis sequence type, which is unique among all sequence types documented in North America. To determine if pronghorn maintain chronic infections and to assess M. bovis status in other sympatric species, we performed surveillance in free-ranging ungulates. We found no evidence of subclinical infections in pronghorn (n=231) or mule deer (Odocoileus hemionus) (n=231) based on PCR testing of nasal swabs. To assess the likelihood of environmental transmission from livestock to pronghorn, we examined persistence of M. bovis in various substrates and conditions, revealing that M. bovis remains viable for 6 hours following inoculation of shaded water, and up to 3 hours in direct sunlight substrates. Our results indicate that environmental transmission of M. bovis from livestock to pronghorn is possible, and seasonality of infection could be due to shared resources during the late winter. This study also highlights the importance of further investigations to better understand transmission dynamics, to assess population level impacts to pronghorn, and to determine disease risks among other ungulate taxa.

Endogenous biomarkers reveal diet partitioning among three sympatric species of swallows

Since the early 1990s, aerial insectivorous birds have shown serious population declines in North America, but it is not clear if factors common to all species within this guild account for these declines. Among sympatric swallows, population trends differ, and this may be due to differences in ecology operating throughout the annual cycle. Although these species all feed on aerial insects, prey taxa can differ tremendously in their “aeroecology” and use by swallows. We examined the potential for dietary differences among three species of swallows, Barn Swallow (Hirundo rustica), Cliff Swallow (Petrochelidon pyrrhonota), and Tree Swallow (Tachycineta bicolor), breeding sympatrically in southern Ontario, Canada. Potential interspecific differences in nestling diet were examined using two endogenous biomarkers, DNA barcoding of nestling feces and stable isotope analysis (δ 2H, δ 13C, δ 15N) of nestling feathers. We found evidence for differences in dietary sources of provisioned young where Barn Swallows provisioned more terrestrial-based prey, Cliff Swallows provisioned an intermediate diet, and Tree Swallows the most aquatic-emergent insect diet. We suggest this information may help to identify potential factors contributing to differential declines of aerial insectivores operating on the breeding grounds, including diet quality.