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Dynamic shifts in social network structure and composition within a breeding hybrid population

1. Mating behavior and the timing of reproduction can inhibit genetic exchange between closely related species; however, these reproductive barriers are challenging to measure within natural populations. Social network analysis provides promising tools for studying the social context of hybridization, and the exchange of genetic variation, more generally. 2. We test how social networks within a hybrid population of California (Callipepla californica) and Gambel's quail (Callipepla gambelii) change over discrete periods of a breeding season. We assess patterns of phenotypic and genotypic assortment, and ask whether altered associations between individuals (association rewiring), or changes to the composition of the population (individual turnover) drive network dynamics. We use genetic data to test whether social associations and relatedness between individuals correlate with patterns of parentage within the hybrid population. 3. To achieve these aims, we combine RFID association data, phenotypic data, and genomic measures with social network analyses. We adopt methods from the ecological network literature to quantify shifts in network structure and to partition changes into those due to individual turnover and association rewiring. We integrate genomic data into networks as node-level attributes (ancestry) and edges (relatedness, parentage) to test links between social and parentage networks. 4. We show that rewiring of associations between individuals that persist across network periods, rather than individual turnover, drives the majority of the changes in network structure throughout the breeding season, and that the traits involved in phenotypic/genotypic assortment were highly dynamic over time. Social networks were randomly assorted based upon genetic ancestry, suggesting weak behavioral reproductive isolation within this hybrid population. Finally, we show that the strength of associations within the social network, but not levels of genetic relatedness, predict patterns of parentage. 5. Social networks play an important role in population processes such as the transmission of disease and information, yet there has been less focus on how networks influence the exchange of genetic variation. By integrating analyses of social structure, phenotypic assortment, and reproductive outcomes within a hybrid zone, we demonstrate the utility of social networks for analyzing links between social context and gene flow within wild populations. 08-Jul-2020

opencc-zeroDec 2019View details →

First come, first served: possible role for priority effects in marine populations under different degrees of dispersal potential

Aim Studying clearly delineated populations in marine lakes, islands of sea, we investigate the interplay of habitat size, immigration, and priority effects in shaping marine population genetic structure. Location Marine lakes and coastal locations in Indonesia, Palau, Papua New-Guinea and Australia. Taxon Mussels (Mytillidae, Brachidontes spp.) Methods Populations were sampled from four coastal locations and 22 marine lakes of similar age (~8,000 years), yet differing in size (0.04 - 4.7 km2) and degree of connection to the adjacent sea. While some lakes are highly connected, allowing potential influx of larvae from the sea, others have very limited water exchange. We assessed the phylogeographic structure and demographic history using mitochondrial and nuclear DNA sequence data, and combined this with geometric morphometrics. The effects of lake characteristics on population genetic diversity and structure were tested using linear regression and Mantel tests. Results Each lake contained one of six distinct genetic lineages, which were characterized by deep phylogenetic splits and significant morphometric differences. These lineages likely represent separate species. The lineages showed similar demographic patterns, with lakes containing founder populations that rapidly expanded and diverged. Genetic diversity within lake populations was significantly correlated with lake area, but not with physical connection to the adjacent sea. Within lineages that occurred in multiple lakes there was strong population structure (average ΦST 0.65), which did not conform to an isolation-by-distance pattern or to the degree of dispersal potential. Main Conclusions Marine lakes across a gradient of physical isolation show strong population structure and evidence for in situ divergence. We hypothesize that the observed genetic structure is the result of priority effects. In addition, reduction of habitat size appears to reduce genetic diversity, even at very small spatial scales. Our findings are relevant in the context of ongoing alterations to coastal hydrodynamics, which lead to habitat reduction and influence migration among populations at fine spatial scales.

Population genomic analyses of the sea urchin Echinometra sp. EZ across an extreme environmental gradient

Extreme environmental gradients represent excellent study systems to better understand the variables that mediate patterns of genomic variation between populations. They also allow for more accurate predictions of how future environmental change might affect marine species. The Persian/Arabian Gulf is extreme in both temperature and salinity, whereas the adjacent Gulf of Oman has conditions more typical of tropical oceans. The sea urchin Echinometra sp. EZ inhabits both of these seas and plays a critical role in coral reef health as a grazer and bioeroder, but, to date, there have been no population genomic studies on this or any urchin species in this unique region. E. sp. EZ's life history traits (e.g., large population sizes, large reproductive clutches, and long life spans), in theory, should homogenize populations unless nonneutral processes are occurring. Here, we generated a draft genome and a restriction site-associated DNA sequencing data set from seven populations along an environmental gradient across the Persian/Arabian Gulf and the Gulf of Oman. The estimated genome size of E. sp. EZ was 609 Mb and the heterozygosity was among the highest recorded for an echinoderm at 4.5%. We recovered 918 high-quality SNPs from 85 individuals which we then used in downstream analyses. Population structure analyses revealed a high degree of admixture between all sites, although there was population differentiation and significant pairwise FST values between the two seas. Preliminary results suggest migration is bidirec- tional between the seas and nine candidate loci were identified as being under putative natural selection, including one collagen gene. This study is the first to investigate the population genomics of a sea urchin from this extreme environmental gradient and is an important contribution to our understanding of the complex spatial patterns that drive genomic divergence.

Data from: Curation: heat stress responses and population genetics of the kelp Laminaria digitata (Phaeophyceae) across latitudes reveal differentiation among North Atlantic populations

We aim to understand the thermal plasticity of a coastal foundation species across its latitudinal distribution by assessing physiological responses to high temperature stress in the kelp Laminaria digitata in combination with population genetic characteristics. We <a>hypothesize</a> that Arctic and cold-temperate populations are less heat resilient than warm-temperate populations. Using meristems of natural L. digitata populations from six locations ranging between Kongsfjorden, Spitsbergen (79°N), and Quiberon, France (47°N), we performed a common-garden heat stress experiment applying 15°C to 23°C over eight days. We assessed growth, quantum yield, carbon and nitrogen storage, and xanthophyll pigment contents as response traits. Population connectivity and genetic diversity were analysed with microsatellite markers to relate heat resilience to genetic features and phylogeography. Microsatellite genotyping revealed all sampled populations to be genetically distinct, underlying strong hierarchical structuring between and within southern and northern clades. Genetic diversity was lowest in the isolated population of the North Sea island of Helgoland and highest in Roscoff in the English Channel. Results from the heat stress experiment suggest that the upper temperature limit of L. digitata is nearly identical across its distribution range, but subtle differences we<a>re </a>revealed for the two populations currently at their warm limits. They respectively <a>show</a> a significant advantage in growth at 19°C and 21°C (Quiberon) and a lack of stress responses in photosynthetic quantum yield and xanthophyll pigments at 23°C (Helgoland). In addition, quantum yield indicated the highest heat sensitivity in L. digitata from the northernmost population in Spitsbergen. All together, these results support the hypothesis of moderate local differentiation across L. digitata's European distribution, whereas effects are likely too weak to ameliorate the species' capacity to withstand ocean warming and marine heatwaves at the southern range edge.

Heat stress responses of the kelp Laminaria digitata (Phaeophyceae) across Northeast Atlantic populations: growth, biochemistry, chlorophyll fluorescence, pigments

To understand the thermal plasticity of a coastal foundation species across its latitudinal distribution, we assess physiological responses to high temperature stress in the kelp Laminaria digitata in combination with population genetic characteristics and relate heat resilience to genetic features and phylogeography. We hypothesize that populations from Arctic and cold-temperate locations are less heat resilient than populations from warm distributional edges. Using meristems of natural L. digitata populations from six locations ranging between Kongsfjorden, Spitsbergen (79°N), and Quiberon, France (47°N), we performed a common-garden heat stress experiment applying 15°C to 23°C over eight days. We assessed growth, photosynthetic quantum yield, carbon and nitrogen storage, and xanthophyll pigment contents as response traits. Population connectivity and genetic diversity were analysed with microsatellite markers. Results from the heat stress experiment suggest that the upper temperature limit of L. digitata is nearly identical across its distribution range, but subtle differences in growth and stress responses were revealed for three populations from the species' ecological range margins. Two populations at the species' warm distribution limit showed higher temperature tolerance compared to other populations in growth at 19°C and recovery from 21°C (Quiberon, France), and photosynthetic quantum yield and xanthophyll pigment responses at 23°C (Helgoland, Germany). In L. digitata from the northernmost population (Spitsbergen, Norway), quantum yield indicated the highest heat sensitivity. Microsatellite genotyping revealed all sampled populations to be genetically distinct, with a strong hierarchical structure between southern and northern clades. Genetic diversity was lowest in the isolated population of the North Sea island of Helgoland and highest in Roscoff in the English Channel. All together, these results support the hypothesis of moderate local differentiation across L. digitata's European distribution, whereas effects are likely too weak to ameliorate the species' capacity to withstand ocean warming and marine heatwaves at the southern range edge.

How butterflies keep their cool: physical and ecological traits influence thermoregulatory ability and population trends.

Understanding which factors influence the ability of individuals to respond to changing temperatures is fundamental to species conservation under climate change. We investigated how a community of butterflies responded to fine-scale changes in air temperature, and whether species-specific responses were predicted by ecological or morphological traits. Using data collected across a UK reserve network, we investigated the ability of 29 butterfly species to buffer thoracic temperature against changes in air temperature. First, we tested whether differences were attributable to taxonomic family, morphology or habitat association. We then investigated the relative importance of two buffering mechanisms: behavioural thermoregulation versus fine-scale microclimate selection. Finally, we tested whether species' responses to changing temperatures predicted their population trends from a UK-wide dataset. We found significant interspecific variation in buffering ability, which varied between families and increased with wing length. We also found interspecific differences in the relative importance of the two buffering mechanisms, with species relying on microclimate selection suffering larger population declines over the last 40 years than those that could alter their temperature behaviourally. Our results highlight the importance of understanding how different species respond to fine-scale temperature variation, and the value of taking microclimate into account in conservation management to ensure favourable conditions are maintained for temperature-sensitive species.

Artificial night light helps account for observer bias in citizen science monitoring of an expanding large mammal population

1. The integration of citizen scientists into ecological research is transforming how, where, and when data are collected, and expanding the potential scales of ecological studies. Citizen-science projects can provide numerous benefits for participants, while educating and connecting professionals with lay audiences, potentially increasing acceptance of conservation and management actions. However, for all the benefits, collection of citizen-science data is often biased towards areas that are easily accessible (e.g. developments and roadways), and thus data are usually affected by issues typical of opportunistic surveys (e.g. uneven sampling effort). These areas are usually illuminated by artificial light at night (ALAN), a dynamic sensory stimulus that alters the perceptual world for both humans and wildlife. 2. Our goal was to test whether satellite-based measures of ALAN could improve our understanding of the detection process of citizen scientist-reported sightings of a large mammal. 3. We collected observations of American black bears (Ursus americanus; n = 1,315) outside their primary range in Minnesota, USA, as part of a study to gauge population expansion. Participants from the public provided sighting locations of bears on a website. We used an occupancy modelling framework to determine how well ALAN accounted for observer metrics when compared to other commonly used metrics (e.g. housing density). 4. Citizen scientists reported 17% of bear sightings were under artificially-lit conditions and monthly ALAN estimates did the best job accounting for spatial bias in detection of all observations, based on AIC values and effect sizes (β ^ = 0.81, 0.71 – 0.90 95% CI). Bear detection increased with elevated illuminance; relative abundance was positively associated with natural cover, closer proximity to primary bear range and lower road density. Although the highest counts of bear sightings occurred in the highly illuminated suburbs of the Minneapolis-St. Paul metropolitan region, we estimated substantially higher bear abundance in another region with plentiful natural cover and low ALAN (up to 275% increased predicted relative abundance) where observations were sparse. 5. We demonstrate the importance of considering ALAN radiance when analyzing citizen scientist-collected data, and we highlight the ways that ALAN data provides a dynamic snapshot of human activity. 31-Jul-2020

opencc-zeroOct 2019View details →

Data from: New and Old World phylogeography of pumpkinseed (Lepomis gibbosus): the North American origin of introduced populations in Europe

To determine the origin of introduced European populations of pumpkinseed (Lepomis gibbosus) – a freshwater sunfish, native to eastern North America that has spread across western and central Europe – we investigated the phylogeography of the species by sequencing the mitochondrial NADH subunit 1 gene. A total of 543 pumpkinseed were sampled from 32 sites across the native range of the species, and from 19 sites covering much of its introduced European range. The presence and geographic distribution of two distinct clades in North American populations were discovered, suggesting that pumpkinseed survived the Pleistocene glaciations in two refugia (Atlantic and Mississippian). Analyses of mitochondrial variation revealed that European pumpkinseed may have been introduced to Europe from at least two distinct sources, but from the Atlantic drainages of North America only, which is consistent with historical records. Within Europe, haplotype distributions of pumpkinseed lend support to the entry of non-native fishes into Iberia via the so-called 'Perpignan–Barcelona corridor'. European populations possessed lower genetic diversity than populations from North America, suggesting that low genetic diversity may not preclude a species from establishing and spreading into new environments outside of their native range.

Data from: Selection on multiple sexual signals in two Central- and Eastern-European populations of the barn swallow

Variation in intensity and targets of sexual selection on multiple traits has been suggested to play a major role in promoting phenotypic differentiation between populations, although the divergence in selection may depend on year, local conditions or age. In this study, we quantified sexual selection for two putative sexual signals across two Central- and East-European barn swallow (Hirundo rustica rustica) populations from Czech Republic and Romania over multiple years. We then related these differences in selection to variation in sexual characters among barn swallow populations. Our results show that tail length and ventral colouration vary between populations, sexes and age classes (first-time breeders vs. experienced birds). We found that selection on tail length was stronger in first-time breeders than in experienced birds and in males than in females in the Romanian population, while these differences between age groups and sexes were weak in Czech birds. We suggest that the populational difference in selection on tail length might be related to the differences in breeding conditions. Our results show that ventral colouration is darker (i.e. has lower brightness) in the Romanian than in the Czech population, and in experienced birds and males compared with first-time breeders and females, respectively. The sexual difference in ventral colouration may suggest sexual selection on this trait, which is supported by the significant directional selection of ventral colouration in first-time breeding males on laying date. However, after controlling for the confounding effect of wing length and tarsus length, the partial directional selection gradient on this trait turned non-significant, suggesting that the advantage of dark ventral colouration in early breeding birds is determined by the correlated traits of body size. These findings show that ventral colouration may be advantageous over the breeding season, but the underlying mechanism of this relationship is not clarified.

Character displacement in the midst of background evolution in island populations of Anolis lizards: a spatiotemporal perspective

Negative interactions between species can generate divergent selection that causes character displacement. However, other processes cause similar divergence. We use spatial and temporal replication of island populations of Anolis lizards to assess the importance of negative interactions in driving trait shifts. Previous work showed that the establishment of Anolis sagrei drove resident Anolis carolinensis to perch higher and evolve larger toepads. To further test the interaction's causality and predictability, we resurveyed a subset of islands nine years later. Anolis sagrei had established on one island between surveys. We found that A. carolinensis on this island now perch higher and have larger toepads. However, toepad morphology change on this island was not distinct from shifts on six other islands whose Anolis community composition had not changed. Thus, the presence of A. sagrei only partly explains A. carolinensis trait variation across space and time. We also find that A. carolinensis on islands with previously established A. sagrei now perch higher than a decade ago, and that current A. carolinensis perch height is correlated with A. sagrei density. Our results suggest that character displacement likely interacts with other evolutionary processes in this system, and that temporal data are key to detecting such interactions.

Monitoring Plasmodium falciparum and Plasmodium vivax using microsatellite markers indicates limited changes in population structure after substantial transmission decline in Papua New Guinea

Monitoring the genetic structure of pathogen populations may be an economical and sensitive approach to quantify the impact of control on transmission dynamics, highlighting the need for a better understanding of changes in population genetic parameters as transmission declines. Here we describe the first population genetic analysis of the major human malaria parasites, Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) populations following nationwide distribution of long-lasting insecticide treated nets (LLIN) in Papua New Guinea (PNG). Parasite isolates from pre- (2005-6) and post-LLIN (2010-2014) were genotyped using microsatellite markers. Despite parasite prevalence declining substantially (East Sepik: Pf=54.9-8.5%, Pv=35.7-5.6%, Madang: Pf=38.0-9.0%, Pv: 31.8-19.7%), genetically diverse and intermixing parasite populations remained. Pf diversity declined modestly post-LLIN relative to pre-LLIN (East Sepik: Rs = 7.1-6.4, He = 0.77-0.71; Madang: Rs= 8.2-6.1, He = 0.79-0.71). Unexpectedly, population structure present in pre-LLIN populations was lost post-LLIN, suggesting that more frequent human movement between provinces may have contributed to higher gene flow. Pv prevalence initially declined but increased again in one province, yet diversity remained high throughout the study period (East Sepik: Rs=11.4-9.3, He=0.83-0.80; Madang: Rs=12.2-14.5, He=0.85-0.88). Although genetic differentiation values increased between provinces over time, no significant population structure was observed at any time point. For both species, a decline in multiple infections and increasing clonal transmission and significant multilocus linkage disequilibrium (mLD) post-LLIN was a positive indicator of impact on the parasite population using microsatellite markers. These parameters may be useful adjuncts to traditional epidemiological tools in the early stages of transmission reduction.

Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches

Simultaneous molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics, and species delimitation studies. In these investigations, multiple sequence alignments consist of both intra- and inter-species samples (mixed samples). As a result, the phylogenetic trees contain inter-species, inter-population, and within-population divergences. Bayesian relaxed clock methods are often employed in these analyses, but they assume the same tree prior for both inter- and intra-species branching processes and require specification of a clock model for branch rates (independent vs. autocorrelated rates models). We evaluated the impact of a single tree prior onBayesian divergence time estimates by analyzing computer-simulated datasets. We also examined the effectof the assumption of independence of evolutionary rate variation among branches when the branch rates are autocorrelated. Bayesian approach with coalescent tree priors generally produced excellent molecular dates and highest posterior densities with high coverage probabilities. We also evaluated the performance of a non-Bayesian method, RelTime, which does not require the specification of a tree prior or a clock model. RelTime's performance was similar to that of the Bayesian approach, suggesting that it is also suitable to analyze datasets containing both populations and species variation when its computational-efficiency is needed.

opencc-zeroMar 2020View details →

ISSR analysis of Tulipa suaveolens (Liliaceae) populations in the European part of the species range

Tulipa suaveolens Roth is a decorative bulbous, polycarpic species in the Liliaceae family. Currently, the species populations are declining due to the degradation of natural steppes. In the present article, we evaluated the genetic diversity of 216 specimens from 22 natural T. suaveolens localities in the European part of the species range using 10 inter simple sequence repeat (ISSR) markers. The polymerase chain reaction (PCR) yielded 250 unambiguous and reproducible polymorphic bands with a mean polymorphism information content (PIC) value of 0.27. Neither the principal component analysis nor the clustering method split the dataset. However, the Bayesian model-based STRUCTURE analysis detected two genetic clusters of T. suaveolens. The analysis of the biogeographical distributional pattern of the revealed genetic groups confirmed our hypothesis that the evolution and distribution of T. suaveolens were likely affected by the Early Khvalynian transgression of the Caspian Sea and the following Enotayevsk regression. Furthermore, this hypothesis was supported by the results of the NEW HYBRIDS analysis identifying the specimens from the populations located outside the Early Khvalynian flooding limit as pure parents, while the specimens of the populations within the flooding limit were classified as backcrosses and second generation hybrids.

opencc-by-4.0Jun 2020View details →

A genomic data set of single‐nucleotide polymorphisms (SNPs) generated by ddRAD tag sequencing in Q. petraea (Matt.) Liebl. populations from Central-Eastern Europe and Balkan Peninsula

This genomic dataset provides highly variable single-nucleotide polymorphism (SNP) markers from georeferenced natural Quercus petraea (Matt.) Liebl. populations collected in Bulgaria, Hungary, Romania, Serbia, Bosnia and Herzegovina, Kosovo and Albania. These SNP loci can be used to assess genetic diversity, differentiation, population structure, and can also be used to detect signatures of selection and local adaptation.

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The last moves: the effect of hunting and culling on the risk of disease spread from a population of reindeer

1. Hunting and culling are frequently used to combat infectious wildlife diseases. The aim is to markedly lower population density in order to limit disease transmission or to eradicate the host. Massive host culling can yield a trade-off when combating wildlife disease; it follows that intrusive actions may have unintended behavioural side-effects, leading to the geographic spread of disease. The manner in which such excessive hunting and culling of hosts can affect the movement and dispersion of cervids has not been studied. 2. In this study, we quantified the behaviour (daily movements and habitat use) and dispersion of GPS-marked reindeer (n = 24) before and during the eradication of an entire population (>2000 reindeer) infected with chronic wasting disease (CWD) in Norway. We compared behaviour and dispersion during 10 ordinary hunting seasons (2007-16), an extended hunt in 2017 and marksmen culling (2017/18). 3. Seasonality had a major impact on movements. Reindeer movements during the early hunting season (20 August–20 September) did not increase the overall movements compared to that in the pre-hunt season (20 July–19 August), while extended hunting into October (as in 2017) and marksmen culling from November to February markedly increased daytime movements relative to that normally observed in this time of the year. Towards the end of the eradication, the remaining reindeer sought refuge at restricted high-elevation areas with limited forage production. Reindeer used novel areas towards the perimeter of the range, but active herding during culling stopped one herd from leaving the CWD zone. 4. Synthesis and applications: With emerging wildlife diseases, host culling is becoming a more frequently used tool for managers in Europe. Our study highlights the potential trade-off between combating disease transmission within a population and the risk of geographic spread. Such insight is important to design mitigation measures, such as perimeter fencing or herding, to avoid the risk of the geographic spread of disease in cases of severe and economically important wildlife diseases.

Inbreeding and disease avoidance in a free‐ranging koala population

Habitat destruction and fragmentation are increasing globally, forcing surviving species into small, isolated populations. Isolated populations typically experience heightened inbreeding risk, and associated inbreeding depression and population decline; although individuals in these populations may mitigate these risks through inbreeding avoidance strategies. For koalas, as dietary specialists already under threat in the northern parts of their range, increased habitat fragmentation and associated inbreeding costs are of great conservation concern. Koalas are known to display passive inbreeding avoidance through sex-biased dispersal, although population isolation will reduce dispersal pathways. We tested whether free-ranging koalas display active inbreeding avoidance behaviours. We used VHF tracking data, parentage reconstruction, and veterinary examination results to test whether female koalas make mate choices based on [1] relatedness, and [2] chlamydial disease in available mates. We found no evidence that female koalas based their mate choice on the relative relatedness of available mates. In fact, as the relatedness of potential mates increases, so did inbreeding events. We also found no evidence that female koalas based their mate choice on the chlamydial disease status of available mates. The absence of active inbreeding avoidance mechanisms in koalas is concerning from a conservation perspective, as small, isolated populations may be at even higher risk of inbreeding depression than expected. At-risk koala populations may require urgent conservation interventions to augment gene flow and reduce inbreeding risks. Similarly, if koalas are not avoiding mating with individuals with chlamydial disease, populations may be at higher risk from disease than anticipated, further impacting population viability.

High elevation increases the risk of Y chromosome loss in Alpine skink populations with sex reversal

The view genotypic sex determination (GSD) and environmental sex determination (ESD) are mutually exclusive states has been contradicted by the discovery that chromosomal sex and environmental influences can co-exist within the same species, hinting at a continuum of intermediate states. Systems where genes and the environment interact to determine sex present the opportunity for sex reversal to occur, where the phenotypic sex is the opposite of that predicted by their sex chromosome complement. The skink Bassiana duperreyi has XX:XY sex chromosomes with sex reversal of the XX genotype to a male phenotype in response to exposure to cold incubation temperatures. Here we studied the frequency of sex reversal in B. duperreyi in response to climatic variation, using elevation as a surrogate for environmental temperatures. We demonstrate sex reversal for the first time in free-ranging adults of a reptile species with XX/XY sex determination. The highest frequency of sex reversal occurred at the highest elevation location, Mount Ginini (18.64%) and decreases in frequency with elevation. We model the impact of this under Fisher's frequency dependent selection to show that, only at the highest elevations, populations risk the loss of the Y chromosome and a transition to TSD. This study contributes to our understanding of the risks of extinction from climate change in species subject to sex reversal by temperature, and will provide focus for future research to test on-the-ground management strategies to mitigate the effects of climate in local populations. <div> <div> <div class="msocomtxt"> </div> </div> </div>