Contributors: Bélouard, Nadège, Paillisson, Jean-Marc, Oger, Adrien, Besnard, Anne-Laure, Petit, Eric
... Recent theoretical and experimental models have evidenced the role played by evolution during species spread, and particularly question the influence of genetic drift at range edges. By investigating the spread of an aquatic invader in patchy habitats, we quantified genetic drift and explored its consequences on genetic diversity and fitness. We examined the interplay of gene flow and genetic drift in 36 populations of the red swamp crayfish, Procambarus clarkii, in a relatively recently invaded wetland area (30 years, Brière, northwestern France). Despite the small spatial scale of our study (15 km²), populations were highly structured according to the strong barrier of land surfaces and revealed a clear pattern of colonisation through watercourses. Isolated populations exhibited small effective sizes and low dispersal rates that depended on water connectivity, suggesting that genetic drift dominated in the evolution of allele frequencies in these populations. We also observed a significant decrease in the genetic diversity of isolated populations over only a two-year period, but failed to demonstrate an associated fitness cost using fluctuating asymmetry. This study documents the possible strong influence of genetic drift during the spread of a species, and such findings provide critical insights in the current context of profound rearrangements in species distributions due to global change.
Data from: Genetics of adaptation: experimental test of a biotic mechanism driving divergence in traits and genes
Contributors: Rennison, Diana, Rudman, Seth, Schluter, Dolph
... The genes underlying adaptations are becoming known, yet the causes of selection on genes -- a key step in the study of the genetics of adaptation -- remains uncertain. We address this issue experimentally in a threespine stickleback species pair showing exaggerated divergence in bony defensive armor in association with competition-driven character displacement. We used semi-natural ponds to test the role of a native predator in causing divergent evolution of armor and two known underlying genes. Predator presence/absence altered selection on dorsal spines and allele frequencies at the Msx2a gene across a generation. Evolutionary trajectories of alleles at a second gene, Pitx1, and the pelvic spine trait it controls, were more variable. Our experiment demonstrates how manipulation of putative selective agents help to identify causes of evolutionary divergence at key genes, rule out phenotypic plasticity as a sole determinant of phenotypic differences, and eliminate reliance on fitness surrogates. Divergence of predation regimes in sympatric stickleback is associated with coevolution in response to resource competition, implying a cascade of biotic interactions driving species divergence. We suggest that as divergence proceeds, an increasing number of biotic interactions generate divergent selection, causing more evolution in turn. In this way, biotic adaptation perpetuates species divergence through time during adaptive radiation in an expanding number of traits and genes.
Data from: Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers
Contributors: Stankowski, Sean, Chase, Madeline A., Fuiten, Allison M., Rodrigues, Murillo F., Ralph, Peter L., Streisfeld, Matthew A.
... Speciation genomic studies aim to interpret patterns of genome-wide variation in light of the processes that give rise to new species. However, interpreting the genomic ‘landscape’ of speciation is difficult, because many evolutionary processes can impact levels of variation. Facilitated by the first chromosome-level assembly for the group, we use whole-genome sequencing and simulations to shed light on the processes that have shaped the genomic landscape during a radiation of monkeyflowers. After inferring the phylogenetic relationships among the nine taxa in this radiation, we show that highly similar diversity (π) and differentiation (FST) landscapes have emerged across the group. Variation in these landscapes was strongly predicted by the local density of functional elements and the recombination rate, suggesting that the landscapes have been shaped by widespread natural selection. Using the varying divergence times between pairs of taxa, we show that the correlations between FST and genome features arose almost immediately after a population split and have become stronger over time. Simulations of genomic landscape evolution suggest that background selection (i.e., selection against deleterious mutations) alone is too subtle to generate the observed patterns, but scenarios that involve positive selection and genetic incompatibilities are plausible alternative explanations. Finally, tests for introgression among these taxa reveal widespread evidence of heterogeneous selection against gene flow during this radiation. Combined with previous evidence for adaptation in this system, we conclude that the correlation in FST among these taxa informs us about the processes contributing to adaptation and speciation during a rapid radiation.
Data from: Divergence of tropical pitvipers promoted by independent colonization events of dry montane Andean habitats
Contributors: Salazar-Valenzuela, David, Kuch, Ulrich, Torres-Carvajal, Omar, Valencia, Jorge H., Gibbs, H. Lisle
... Aim: One aspect that is still poorly explored about the origin and maintenance of Neotropical biodiversity is how the evolutionary dynamics of colonization and differentiation in relation to lowland and highland habitats has impacted lineage formation. Most speciation models for this region have focused on vicariant events, and the need to assess the influence of demographic processes has been recognized only recently. We evaluate if the origin of Andean montane lineages of terciopelo pitvipers is explained by either of two historical processes that represent fundamental phylogeographic mechanisms: differentiation by isolation within the highlands or different dispersal events from the lowlands. Location: Western Ecuador. Taxon: Terciopelo pitvipers (Bothrops asper species complex). Methods: We use genomic data and genetic clustering analyses, evaluation of historical migration between genetic clusters, and demographic model selection to investigate recent diversification events in South America using a vertebrate group rarely explored in phylogeographic studies: tropical Andean snakes. Specifically, the origin of two Ecuadorian montane lineages of terciopelo pitvipers was evaluated given ambiguous phylogenetic relationships with the presumably ancestral Pacific lowland lineage. Results: Discrepancies of evolutionary relationships previously obtained with tree-like methods are resolved through the use of modeling approaches. We found strong support for the independent origin of montane lineages based on topologies inferred by maximum-likelihood trees and modeling approaches that take into account possible gene flow. Main conclusions: Recent large-scale studies have found support for identifying dispersal events as important drivers of diversification in the Neotropical region. We contribute to these ideas by identifying a fine-scale case in a rarely explored group of animals -Andean snakes- in which river valleys acted as an entrance for the upward colonization of montane dry habitats and subsequent ecological diversification.
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).
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.