scholarly journals Genome sequencing and morphometric analysis of alpine bumblebees experiencing climate change reveal ongoing phenotypic shifts and a lack of population structure

2021 ◽  
Author(s):  
Matthew J. Christmas ◽  
Julia C. Jones ◽  
Anna Olsson ◽  
Ola Wallerman ◽  
Ignas Bunikis ◽  
...  
Keyword(s):  
Climate Change ◽  
Population Structure ◽  
Body Size ◽  
Morphological Change ◽  
Genome Sequencing ◽  
Digestive Enzyme ◽  
Size Variation ◽  
Genetic Associations ◽  
Genetic Substructure ◽  
Tongue Length

ABSTRACTPopulations of the bumblebees Bombus sylvicola and Bombus balteatus in Colorado have experienced decreases in tongue length, a trait important for plant-pollinator mutualisms, in the last six decades. It is hypothesized that this reflects selection exerted by changes in floral composition under climate change. Here we combine extensive morphometric and population genomic data to investigate population structure, whether morphological change is ongoing, and the genetic basis of morphological change. We generate highly-contiguous genome assemblies of both species using long-read sequencing. We then perform whole-genome sequencing and morphometric measurements of 580 samples of these species from seven high-altitude localities. Out of 281 samples originally identified as B. sylvicola, 67 formed a separate genetic cluster comprising the newly-discovered cryptic species B. incognitus. However, there is very little additional genetic substructure, suggesting that gene flow occurs readily between mountains. We find a significant decrease in tongue length between bees collected between 2008-2014 and in 2017, indicating that morphological shifts are ongoing. We did not discover any genetic associations with tongue length, but a SNP related to production of a proteolytic digestive enzyme is implicated in body size variation. We identify evidence of covariance between kinship and both tongue length and body size, which is suggestive of a genetic component of these traits, although it is not possible to rule out shared environmental effects between colonies. Our results provide evidence for ongoing evolution of a morphological trait important for pollination and indicate that this trait likely has a complex genetic and environmental basis.

scholarly journals High-Arctic butterflies become smaller with rising temperatures

2015 ◽  
Vol 11 (10) ◽  
pp. 20150574 ◽  
Author(s):  
Joseph J. Bowden ◽  
Anne Eskildsen ◽  
Rikke R. Hansen ◽  
Kent Olsen ◽  
Carolyn M. Kurle ◽  
...  
Keyword(s):  
Climate Change ◽  
Body Size ◽  
Wing Length ◽  
Size Variation ◽  
Metabolic Cost ◽  
High Arctic ◽  
Similar Rate ◽  
Butterfly Species ◽  
Dispersal Capacity ◽  
Growing Seasons

The response of body size to increasing temperature constitutes a universal response to climate change that could strongly affect terrestrial ectotherms, but the magnitude and direction of such responses remain unknown in most species. The metabolic cost of increased temperature could reduce body size but long growing seasons could also increase body size as was recently shown in an Arctic spider species. Here, we present the longest known time series on body size variation in two High-Arctic butterfly species: Boloria chariclea and Colias hecla . We measured wing length of nearly 4500 individuals collected annually between 1996 and 2013 from Zackenberg, Greenland and found that wing length significantly decreased at a similar rate in both species in response to warmer summers. Body size is strongly related to dispersal capacity and fecundity and our results suggest that these Arctic species could face severe challenges in response to ongoing rapid climate change.

scholarly journals Body Size Variation in Italian Lesser Horseshoe Bats Rhinolophus hipposideros over 147 Years: Exploring the Effects of Climate Change, Urbanization and Geography

Biology ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 16
Author(s):  
Valeria B. Salinas-Ramos ◽  
Paolo Agnelli ◽  
Luciano Bosso ◽  
Leonardo Ancillotto ◽  
Víctor Sánchez-Cordero ◽  
...  
Keyword(s):  
Climate Change ◽  
Body Size ◽  
Species Interactions ◽  
Spatial Scales ◽  
Size Variation ◽  
Environmental Drivers ◽  
Detectable Effect ◽  
Time And Space ◽  
Body Size Variation ◽  
Rhinolophus Hipposideros

Body size in animals commonly shows geographic and temporal variations that may depend upon several environmental drivers, including climatic conditions, productivity, geography and species interactions. The topic of body size trends across time has gained momentum in recent years since this has been proposed as a third universal response to climate change along with changes in distribution and phenology. However, disentangling the genuine effects of climate change from those of other environmental factors is often far from trivial. In this study, we tested a set of hypotheses concerning body size variation across time and space in Italian populations of a rhinolophid bat, the lesser horseshoe bat Rhinolophus hipposideros. We examined forearm length (FAL) and cranial linear traits in a unique historical collection of this species covering years from 1869 to 2016, representing, to the best of our knowledge, the longest time series ever considered in a morphological assessment of a bat species. No temporal changes occurred, rejecting the hypotheses that body size varied in response to climate change or urbanization (light pollution). We found that FAL increased with latitude following a Bergmann’s rule trend, whereas the width of upper incisors, likely a diet-related trait, showed an opposite pattern which awaits explanation. We also confirmed that FAL is sexually dimorphic in this species and ruled out that insularity has any detectable effect on the linear traits we considered. This suggests that positive responses of body size to latitude do not mean per se that concurring temporal responses to climate change are also expected. Further investigations should explore the occurrence of these patterns over larger spatial scales and more species in order to detect the existence of general patterns across time and space.

scholarly journals Whole Genome Sequencing Refines Knowledge on the Population Structure of Mycobacterium bovis from a Multi-Host Tuberculosis System

2021 ◽  
Vol 9 (8) ◽  
pp. 1585
Author(s):  
Ana C. Reis ◽  
Liliana C. M. Salvador ◽  
Suelee Robbe-Austerman ◽  
Rogério Tenreiro ◽  
Ana Botelho ◽  
...  
Keyword(s):  
Population Structure ◽  
Whole Genome Sequencing ◽  
Wild Boar ◽  
Genome Sequencing ◽  
Mycobacterium Bovis ◽  
Red Deer ◽  
Variable Number Tandem Repeat ◽  
Variant Calling ◽  
Whole Genome ◽  
Network Analyses

Classical molecular analyses of Mycobacterium bovis based on spoligotyping and Variable Number Tandem Repeat (MIRU-VNTR) brought the first insights into the epidemiology of animal tuberculosis (TB) in Portugal, showing high genotypic diversity of circulating strains that mostly cluster within the European 2 clonal complex. Previous surveillance provided valuable information on the prevalence and spatial occurrence of TB and highlighted prevalent genotypes in areas where livestock and wild ungulates are sympatric. However, links at the wildlife–livestock interfaces were established mainly via classical genotype associations. Here, we apply whole genome sequencing (WGS) to cattle, red deer and wild boar isolates to reconstruct the M. bovis population structure in a multi-host, multi-region disease system and to explore links at a fine genomic scale between M. bovis from wildlife hosts and cattle. Whole genome sequences of 44 representative M. bovis isolates, obtained between 2003 and 2015 from three TB hotspots, were compared through single nucleotide polymorphism (SNP) variant calling analyses. Consistent with previous results combining classical genotyping with Bayesian population admixture modelling, SNP-based phylogenies support the branching of this M. bovis population into five genetic clades, three with apparent geographic specificities, as well as the establishment of an SNP catalogue specific to each clade, which may be explored in the future as phylogenetic markers. The core genome alignment of SNPs was integrated within a spatiotemporal metadata framework to further structure this M. bovis population by host species and TB hotspots, providing a baseline for network analyses in different epidemiological and disease control contexts. WGS of M. bovis isolates from Portugal is reported for the first time in this pilot study, refining the spatiotemporal context of TB at the wildlife–livestock interface and providing further support to the key role of red deer and wild boar on disease maintenance. The SNP diversity observed within this dataset supports the natural circulation of M. bovis for a long time period, as well as multiple introduction events of the pathogen in this Iberian multi-host system.

scholarly journals Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaoting Xia ◽  
Shunjin Zhang ◽  
Huaju Zhang ◽  
Zijing Zhang ◽  
Ningbo Chen ◽  
...  
Keyword(s):  
Population Structure ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
System Response ◽  
Whole Genome ◽  
Population Structure Analysis ◽  
Native Cattle ◽  
Genomic Regions

Abstract Background Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle. Results The population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (FST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6). Conclusion We provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.

scholarly journals Independent evolution towards larger body size in the distinctive Faroe Island mice

2021 ◽  
Author(s):  
Ricardo Wilches ◽  
William H Beluch ◽  
Ellen McConnell ◽  
Diethard Tautz ◽  
Yingguang Frank Chan
Keyword(s):  
Body Size ◽  
Meta Analysis ◽  
Small Body ◽  
Laboratory Mouse ◽  
Large Body ◽  
Natural Populations ◽  
Size Variation ◽  
Phenotypic Traits ◽  
Island Population ◽  
Multiple Loci

Abstract Most phenotypic traits in nature involve the collective action of many genes. Traits that evolve repeatedly are particularly useful for understanding how selection may act on changing trait values. In mice, large body size has evolved repeatedly on islands and under artificial selection in the laboratory. Identifying the loci and genes involved in this process may shed light on the evolution of complex, polygenic traits. Here, we have mapped the genetic basis of body size variation by making a genetic cross between mice from the Faroe Islands, which are among the largest and most distinctive natural populations of mice in the world, and a laboratory mouse strain selected for small body size, SM/J. Using this F2 intercross of 841 animals, we have identified 111 loci controlling various aspects of body size, weight and growth hormone levels. By comparing against other studies, including the use of a joint meta-analysis, we found that the loci involved in the evolution of large size in the Faroese mice were largely independent from those of a different island population or other laboratory strains. We hypothesize that colonization bottleneck, historical hybridization, or the redundancy between multiple loci have resulted in the Faroese mice achieving an outwardly similar phenotype through a distinct evolutionary path.

scholarly journals Mammalian body size is determined by interactions between climate, urbanization, and ecological traits

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Maggie M. Hantak ◽  
Bryan S. McLean ◽  
Daijiang Li ◽  
Robert P. Guralnick
Keyword(s):  
Body Size ◽  
Resource Availability ◽  
Critical Role ◽  
Size Variation ◽  
Ecological Factors ◽  
Species Traits ◽  
Body Size Variation ◽  
Resource Availability Hypothesis ◽  
Urban Heat ◽  
Thermal Buffering

AbstractAnthropogenically-driven climate warming is a hypothesized driver of animal body size reductions. Less understood are effects of other human-caused disturbances on body size, such as urbanization. We compiled 140,499 body size records of over 100 North American mammals to test how climate and human population density, a proxy for urbanization, and their interactions with species traits, impact body size. We tested three hypotheses of body size variation across urbanization gradients: urban heat island effects, habitat fragmentation, and resource availability. Our results demonstrate that both urbanization and temperature influence mammalian body size variation, most often leading to larger individuals, thus supporting the resource availability hypothesis. In addition, life history and other ecological factors play a critical role in mediating the effects of climate and urbanization on body size. Larger mammals and species that utilize thermal buffering are more sensitive to warmer temperatures, while flexibility in activity time appears to be advantageous in urbanized areas. This work highlights the value of using digitized, natural history data to track how human disturbance drives morphological variation.

scholarly journals Advances in Cereal Crop Genomics for Resilience under Climate Change

Life ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 502
Author(s):  
Tinashe Zenda ◽  
Songtao Liu ◽  
Anyi Dong ◽  
Huijun Duan
Keyword(s):  
Climate Change ◽  
Genome Sequencing ◽  
Gene Editing ◽  
Agronomic Traits ◽  
Cereal Crops ◽  
Agricultural System ◽  
Plant Genomics ◽  
Crop Species ◽  
Underutilized Species ◽  
Recent Developments

Adapting to climate change, providing sufficient human food and nutritional needs, and securing sufficient energy supplies will call for a radical transformation from the current conventional adaptation approaches to more broad-based and transformative alternatives. This entails diversifying the agricultural system and boosting productivity of major cereal crops through development of climate-resilient cultivars that can sustainably maintain higher yields under climate change conditions, expanding our focus to crop wild relatives, and better exploitation of underutilized crop species. This is facilitated by the recent developments in plant genomics, such as advances in genome sequencing, assembly, and annotation, as well as gene editing technologies, which have increased the availability of high-quality reference genomes for various model and non-model plant species. This has necessitated genomics-assisted breeding of crops, including underutilized species, consequently broadening genetic variation of the available germplasm; improving the discovery of novel alleles controlling important agronomic traits; and enhancing creation of new crop cultivars with improved tolerance to biotic and abiotic stresses and superior nutritive quality. Here, therefore, we summarize these recent developments in plant genomics and their application, with particular reference to cereal crops (including underutilized species). Particularly, we discuss genome sequencing approaches, quantitative trait loci (QTL) mapping and genome-wide association (GWAS) studies, directed mutagenesis, plant non-coding RNAs, precise gene editing technologies such as CRISPR-Cas9, and complementation of crop genotyping by crop phenotyping. We then conclude by providing an outlook that, as we step into the future, high-throughput phenotyping, pan-genomics, transposable elements analysis, and machine learning hold much promise for crop improvements related to climate resilience and nutritional superiority.

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