Data from: Local and regional scale habitat heterogeneity contribute to genetic adaptation in a commercially important marine mollusc (Haliotis rubra) from southeastern Australia
Contributors: Miller, Adam, Hoffmann, Ary, Tan, Mun Hua, Young, Mary, Ahrens, Collin, Cocomazzo, Michael, Rattray, Alex, Ierodiaconou, Daniel, Treml, Eric, Sherman, Craig
... Characterising adaptive genetic divergence among conspecific populations is often achieved by studying genetic variation across defined environmental gradients. In marine systems this is challenging due to a paucity of information on habitat heterogeneity at local and regional scales and a dependency on sampling regimes that are typically limited to broad longitudinal and latitudinal environmental gradients. As a result, the spatial scales at which selection processes operate and the environmental factors that contribute to genetic adaptation in marine systems are likely to be unclear. In this study we explore patterns of adaptive genetic structuring in a commercially- harvested abalone species (Haliotis rubra) from south-eastern Australia, using a panel of genome-wide SNP markers (5,239 SNPs), and a sampling regime informed by marine LiDAR bathymetric imagery and 20-year hindcasted oceanographic models. Despite a lack of overall genetic structure across the sampling distribution, significant genotype associations with heterogeneous habitat features were observed at local and regional spatial scales, including associations with wave energy, ocean current, sea surface temperature, and geology. These findings provide insights into the potential resilience of the species to changing marine climates and the role of migration and selection on recruitment processes, with implications for conservation and fisheries management. This study points to the spatial scales at which selection processes operate in marine systems and highlights the benefits of geospatially-informed sampling regimes for overcoming limitations associated with marine population genomic research.
Contributors: Bisht, Shikha, Banerjee, Sudip, Qureshi, Qamar, Jhala, Yadvendradev
... 1.Prioritising conservation of source populations within landscapes is proposed as a strategy for recovering tigers globally. We studied population dynamics of tigers in Corbett National Park (CNP) in Indian Terai, which harbours the largest and highest density tiger population in any protected area of the world. Through population viability models we demonstrate the importance of CNP in tiger recovery of western Terai. 2.We camera trapped 521 km2 of CNP using open population capture‐mark‐recapture framework between 2010‐2015 to estimate annual abundance, spatially explicit density, survival, recruitment, temporary movements, sex ratio and proportion of females breeding. We model metapopulation persistence with and without Corbett as a source within western Terai landscape at different levels of poaching and habitat connectivity. 3.In six years we recorded 6202 photo‐captures of 307 individual tigers. Annual tiger abundance and density were stable at 120 (SE 19) and 14 (SE 3) per 100 km2 respectively. Overall detection probability of tigers was (0.18 SE 0.03) and detection corrected male: female sex ratio was female biased (0.80 SE 0.13). Apparent annual survival probability was 0.79 (SE 0.05) for females and 0.60 (SE 0.04) for males. Overall survival (0.68 SE 0.12) was lower than that reported for other tiger populations. CNP tigers showed high reproduction with 54.8 (SE 5.1) % females breeding and with addition of 35(SE 8)% as new recruits to the population each year. Small tiger populations in the western Terai with moderate poaching could only persist through dispersal from CNP. 4.Synthesis and applications: The Corbett tiger population was characterised by a stable high density, high reproductive rate and low survival resulting in high turnover rates of 32‐48% between successive years. Such source populations could sustain low level poaching and with habitat connectivity recover tiger populations across the landscape. This study establishes potential thresholds that can likely be achieved by tiger populations under optimal natural conditions and highlights the importance of prioritizing conservation of source populations within tiger landscapes. This information can be used to plan and implement realistic tiger recovery programmes globally.
Data from: Genome analysis reveals genetic admixture and signature of selection for productivity and environmental traits in Iraqi cattle
Contributors: Alshawi, Akil Farouk, Essa, Abdulameer, Al-Bayatti, Sahar, Hanotte, Olivier
... The Near East cattle are adapted to different agro-ecological zones including desert areas, mountains habitats as well as humid regions along the Tigris and Euphrates rivers system. The region was one of the earliest and most significant areas of cattle husbandry. Currently four main breeds of Iraqi cattle are recognized. Among these, the Jenoubi is found in the southern more humid part of Iraq while the Rustaqi is found in the middle and drier region of the country. Despite their importance, Iraqi cattle have up to now been poorly characterized at genome level. Here, we report at genome-wide level the diversity and signature of positive selection in these two breeds. Thirty-five unrelated Jenoubi cattle, sampled in the Maysan and Basra regions, and 60 Rustaqi cattle, from around Baghdad and Babylon, were genotyped using the Illumina Bovine HD BeadChip (700K). Genetic population structure and diversity level were studied using principal component analysis (PCA), expected heterozygosity (He), observed heterozygosity (Ho) and admixture. Signatures of selection were studied using Extended Haplotype Homozygosity (EHH) (iHS and Rsb) and inter-population Wright’s Fst. The results of PCA and admixture analysis, including European taurine, Asian indicine, African indicine and taurine indicate that the two breeds are crossbreed zebu x taurine, with more zebu background in Jenoubi cattle compared to Rustaqi. The Rustaqi has the greatest mean heterozygosity (He = 0.37) among all breeds. iHS and Rsb signature of selection analyses identify 68 candidate genes under positive selection in the two Iraqi breeds, while Fst analysis identifies 220 candidate genes including genes related to the innate and acquired immunity responses, different environmental selection pressures (e.g. tick resistance, heat stress) and genes of commercial interest (e.g. marbling score).
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Contributors: Polato, Nicholas R.
... Species richness is greatest in the tropics and much of this diversity is concentrated in mountains. Janzen (1967) proposed that reduced seasonal temperature variation selects for narrower thermal tolerances and limited dispersal along tropical elevation gradients. These locally adapted traits should, in turn, promote reproductive isolation and higher speciation rates in tropical mountains compared to temperate ones. Here we show that tropical and temperate montane stream insects have diverged in thermal tolerance and dispersal capacity, two key traits that are drivers of isolation in montane populations. Tropical species in each of three insect clades have markedly narrower thermal tolerances and lower dispersal than temperate species, resulting in significantly greater population divergence, higher cryptic species diversity, higher tropical speciation rates, and greater accumulation of species over time. Our study also indicates that tropical montane species, with narrower thermal tolerance and reduced dispersal ability, will be especially vulnerable to rapid climate change.
Contributors: Figueirido, Borja, Lautenschlager, Stephan, Perez-Ramos, Alejandro, Van Valkenburgh, Blaire
... Over the Cenozoic, large cat-like forms have convergently evolved into specialized killers of ‘megaherbivores’ that relied on their large, and laterally-compressed (saber-like) canines to rapidly subdue their prey [1-5]. Scimitar- and dirk-toothed sabertooths are distinct ecomorphs that differ in canine tooth length, degree of serration, and postcranial features indicative of dissimilar predatory behavior [6-13]. Despite these differences, it is assumed that they used a similar ‘canine-shear’ bite to kill their prey [14,15]. We investigated the killing behavior of the scimitar-toothed Homotherium serum and the dirk-toothed Smilodon fatalis using a comparative sample of living carnivores and a new quantitative approach to the analysis of skull function. For the first time, we quantified differences in the relative amount and distribution of cortical and trabecular bone in coronal sections of skulls to assess relative skull stiffness and flexibility [16-19]. We also use finite element analysis to simulate various killing scenarios that load skulls in ways that likely favor distinct proportions of cortical versus trabecular bone across the skull. Our data reveal that S. fatalis had an extremely thick skull and relatively little trabecular bone, consistent with a large investment in cranial strength for a stabbing canine-shear-bite. However, H. serum had more trabecular bone, and likely deployed an unusual predatory behavior more similar to the clamp-and-hold technique of the lion than S. fatalis. These data broaden the killing repertoire of sabertooths and highlight the degree of ecological specialization among members of the large carnivore guild during the Late Pleistocene of North America.
Contributors: Burford Reiskind, Martha O., Labadie, Paul E, Bargielowski, Irka, Lounibos, L. Philip, Reiskind, Michael H.
... While few species introduced into a new environment become invasive, those that do provide critical information on ecological mechanisms that determine invasions success and the evolutionary responses that follow invasion. Aedes albopictus (the Asian tiger mosquito) was introduced into the naturalized range of Aedes aegypti (the yellow fever mosquito) in the USA in the mid-1980s, resulting in the displacement of A. aegypti in much of the southeastern USA. The rapid displacement was likely due to the superior competitive ability of A. albopictus as larvae and asymmetric mating interference competition, in which male A. albopictus mate with and sterilize A. aegypti females, a process called “satyrization”. The goal of this study was to examine the genomic responses of a resident species to an invasive species in which the mechanism of character displacement is understood. We used double-digest restriction enzyme DNA sequencing (ddRADseq) to analyze outlier loci between selected and control lines of laboratory-reared A. aegypti females from two populations (Tucson, AZ and Key West, Florida, USA), and individual females classified as either “resisted” or “mated with” A. albopictus males via mating trials of wild-derived females from four populations in Florida. We found significant outlier loci in comparing selected and control lines and between mated and non-mated A. aegypti females in the laboratory and wild-derived populations, respectively. We found overlap in specific outlier loci between different source populations that support consistent genomic signatures of selection within A. aegypti. Our results point to regions of the A. aegypti genome and potential candidate genes that may be involved in mating behavior, and specifically in avoiding interspecific mating choices.
Data from: Sunning themselves in heaps, knots, and snarls: the extraordinary abundance and demography of island watersnakes
Contributors: King, Richard B., Stanford, Kristin M., Jones, Peter C.
... Snakes represent a sizable fraction of vertebrate biodiversity but until recently, data on their demography has been sparse. Consequently, generalizations regarding patterns of variation are weak and the potential for population projections are limited. We address this information gap through an analysis of spatial and temporal variation in demography (population size, annual survival, realized population growth) of the Lake Erie Watersnake, Nerodia sipedon insularum, and a review of snake survival more generally. Our study spans a period during which the Lake Erie Watersnake was listed as threatened under the U.S. Endangered Species Act, recovered and was delisted. We collected capture-mark-recapture data at 14 study sites over 20 years, accruing 20,000 captures of 13,800 individually marked adults. Lake Erie Watersnakes achieve extraordinary abundance, averaging 520 adults/km of shoreline (ca. 260 adult/ha) at our study sites (range = 160-1600 adults/km; ca. 80-800 adults/ha) and surpassing population recovery and post-delisting monitoring criteria. Annual survival averages 0.68 among adult females and 0.76 among adult males, varies among sites, and is positively correlated with body size among study sites. Temporal process variance in annual survival is low, averaging 0.0011 or less than 4% of total variance; thus, stochasticity in annual survival may be of minor significance to snake extinction risk. Estimates of realized population growth indicate that population size has been stable or increasing over the course of our study. More generally, snake annual survival overlaps broadly across continents, climate zones, families, subfamilies, reproductive modes, body size categories, maturation categories, and parity categories. Differences in survival in relation to size, parity, and maturation are in the directions predicted by life history theory but are of small magnitude with much variation around median values. Overall, annual survival appears to be quite plastic, varying with food availability, habitat quality, and other ecological variables
Data from: Genome-wide search for quantitative trait loci controlling important plant and flower traits in petunia using an interspecific recombinant inbred population of Petunia axillaris and Petunia exserta
Contributors: Cao, Zhe, Guo, Yufang, Yang, Qian, He, Yanhong, Fetouh, Mohammed, Warner, Ryan M., Deng, Zhanao
... A major bottleneck in plant breeding has been the much limited genetic base and much reduced genetic diversity in domesticated, cultivated germplasm. Identification and utilization of favorable gene loci or alleles from wild or progenitor species can serve as an effective approach to increasing genetic diversity and breaking this bottleneck in plant breeding. This study was conducted to identify quantitative trait loci (QTL) in wild or progenitor petunia species that can be used to improve important horticultural traits in garden petunia. An F7 recombinant inbred population derived between Petunia axillaris and P. exserta was phenotyped for plant height, plant spread, plant size, flower counts, flower diameter, flower length, and days to anthesis, in Florida in two consecutive years. Transgressive segregation was observed for all seven traits in both years. The broad-sense heritability estimates for the traits ranged from 0.20 (days to anthesis) to 0.62 (flower length). A genome-wide genetic linkage map consisting 368 single nucleotide polymorphism bins and extending over 277 cM was searched to identify QTL for these traits. Nineteen QTL were identified and localized to five linkage groups. Eleven of the loci were identified consistently in both years; several loci explained up to 34.0% and 24.1% of the phenotypic variance for flower length and flower diameter, respectively. Multiple loci controlling different traits are co-localized in four intervals in four linkage groups. These intervals contain desirable alleles that can be introgressed into commercial petunia germplasm to expand the genetic base and improve plant performance and flower characteristics in petunia.
Data from: Urban rat races: spatial population genomics of brown rats (Rattus norvegicus) compared across multiple cities
Contributors: Combs, Matthew, Byers, Kaylee A., Ghersi, Bruno M., Blum, Michael J., Caccone, Adalgisa, Costa, Federico, Himsworth, Chelsea G., Richardson, Jonathan L., Munshi-South, Jason
... Urbanization often substantially influences animal movement and gene flow. However, few studies to date have examined gene flow of the same species across multiple cities. In this study, we examine brown rats (Rattus norvegicus) to test hypotheses about the repeatability of neutral evolution across four cities: Salvador, Brazil; New Orleans, USA; Vancouver, Canada; New York City, USA. At least 150 rats were sampled from each city and genotyped for a minimum of 15,000 genome-wide SNPs. Levels of genome-wide diversity were similar across cities, but varied across neighborhoods within cities. All four populations exhibited high spatial autocorrelation at the shortest distance classes (< 500 m) due to limited dispersal. Coancestry and evolutionary clustering analyses identified genetic discontinuities within each city that coincided with a resource desert in New York City, major waterways in New Orleans, and roads in Salvador and Vancouver. Such replicated studies are crucial to assessing the generality of predictions from urban evolution, and have practical applications for pest management and public health. Future studies should include a range of global cities in different biomes, incorporate multiple species, and examine the impact of specific characteristics of the built environment and human socioeconomics on gene flow.
Data from: Signatures of local adaptation along environmental gradients in a range-expanding damselfly (Ischnura elegans)
Contributors: Dudaniec, Rachael Y., Yong, Chuan Ji, Lancaster, Lesley T., Svensson, Erik I., Hansson, Bengt
... Insect distributions are shifting rapidly in response to climate change and are undergoing rapid evolutionary change. We investigate the molecular signatures underlying local adaptation in the range-expanding damselfly, Ischnura elegans. Using a landscape genomic approach combined with generalized dissimilarity modelling (GDM), we detect selection signatures on loci via allelic frequency change along environmental gradients. We analyse 13,612 Single Nucleotide Polymorphisms (SNPs), derived from Restriction site-Associated DNA sequencing (RADseq), in 426 individuals from 25 sites spanning the I. elegans distribution in Sweden, including its expanding northern range edge. Environmental association analysis (EAA) and the magnitude of allele frequency change along the range expansion gradient revealed significant signatures of selection in relation to high maximum summer temperature, high mean annual precipitation, and low wind speeds at the range edge. SNP annotations with significant signatures of selection revealed gene functions associated with ongoing range expansion, including heat shock proteins (HSP40 and HSP70), ion transport (V-ATPase) and visual processes (long wavelength-sensitive opsin), which have implications for thermal stress response, salinity tolerance and mate discrimination, respectively. We also identified environmental thresholds where climate-mediated selection is likely to be strong, and indicate that I. elegans is rapidly adapting to the climatic environment during its ongoing range expansion. Our findings empirically validate an integrative approach for detecting spatially explicit signatures of local adaptation along environmental gradients.