scholarly journals The evolutionary pathways for local adaptation in mountain hares

2021 ◽  
Author(s):  
Iwona Giska ◽  
João Pimenta ◽  
Liliana Farelo ◽  
Pierre Boursot ◽  
Klaus Hackländer ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Evolutionary Biology ◽  
Introgressive Hybridization ◽  
Coat Colour ◽  
Wide Distribution ◽  
Comparative Genomic ◽  
Local Adaptations ◽  
Crucial Component ◽  
Demographic Modelling ◽  
Species Specific

Understanding the evolution of local adaptations is a central aim of evolutionary biology and key for the identification of unique populations and lineages of conservation relevance. By combining RAD sequencing and whole-genome sequencing, we identify genetic signatures of local adaptation in mountain hares (Lepus timidus) from isolated and distinctive habitats of its wide distribution: Ireland, the Alps and Fennoscandia. Demographic modelling suggested that the split of these mountain hares occurred around 20 thousand years ago, providing the opportunity to study adaptive evolution over a short timescale. Using genome-wide scans, we identified signatures of extreme differentiation among hares from distinct geographic areas that overlap with area-specific selective sweeps, suggesting targets for local adaptation. Several identified candidate genes are associated with traits related to the uniqueness of the different environments inhabited by the three groups of mountain hares, including coat colour, ability to live at high altitudes and variation in body size. In Irish mountain hares, a variant of ASIP, a gene previously implicated in introgression-driven winter coat colour variation in mountain and snowshoe hares (L. americanus), may underlie brown winter coats, reinforcing the repeated nature of evolution at ASIP moulding adaptive seasonal colouration. Comparative genomic analyses across several hare species suggested that mountain hares' adaptive variants appear predominantly species-specific. However, using coalescent simulations we also show instances where the candidate adaptive variants have been introduced via introgressive hybridization. Our work shows that standing adaptive variation, including that introgressed from other species, was a crucial component of the post-glacial dynamics of species.

scholarly journals Pan-American Lancehead Pit-Vipers: Coagulotoxic Venom Effects and Antivenom Neutralisation of Bothrops asper and B. atrox Geographical Variants

Toxins ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 78
Author(s):  
Lachlan A. Bourke ◽  
Christina N. Zdenek ◽  
Edgar Neri-Castro ◽  
Melisa Bénard-Valle ◽  
Alejandro Alagón ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Current Knowledge ◽  
Clinical Manifestations ◽  
In Vivo Studies ◽  
Factor X ◽  
Clotting Factors ◽  
Bothrops Asper ◽  
Species Specific

The toxin composition of snake venoms and, thus, their functional activity, can vary between and within species. Intraspecific venom variation across a species’ geographic range is a major concern for antivenom treatment of envenomations, particularly for countries like French Guiana that lack a locally produced antivenom. Bothrops asper and Bothrops atrox are the most medically significant species of snakes in Latin America, both producing a variety of clinical manifestations, including systemic bleeding. These pathophysiological actions are due to the activation by the venom of the blood clotting factors Factor X and prothrombin, thereby causing severe consumptive coagulopathy. Both species are extremely wide-ranging, and previous studies have shown their venoms to exhibit regional venom variation. In this study, we investigate the differential coagulotoxic effects on human plasma of six venoms (four B. asper and two B. atrox samples) from different geographic locations, spanning from Mexico to Peru. We assessed how the venom variation of these venom samples affects neutralisation by five regionally available antivenoms: Antivipmyn, Antivipmyn-Tri, PoliVal-ICP, Bothrofav, and Soro Antibotrópico (SAB). The results revealed both inter- and intraspecific variations in the clotting activity of the venoms. These variations in turn resulted in significant variation in antivenom efficacy against the coagulotoxic effects of these venoms. Due to variations in the venoms used in the antivenom production process, antivenoms differed in their species-specific or geographical neutralisation capacity. Some antivenoms (PoliVal-ICP, Bothrofav, and SAB) showed species-specific patterns of neutralisation, while another antivenom (Antivipmyn) showed geographic-specific patterns of neutralisation. This study adds to current knowledge of Bothrops venoms and also illustrates the importance of considering evolutionary biology when developing antivenoms. Therefore, these results have tangible, real-world implications by aiding evidence-based design of antivenoms for treatment of the envenomed patient. We stress that these in vitro studies must be backed by future in vivo studies and clinical trials before therapeutic guidelines are issued regarding specific antivenom use in a clinical setting.

scholarly journals Transcriptome Expression of Biomineralization Genes in Littoraria flava Gastropod in Brazilian Rocky Shore Reveals Evidence of Local Adaptation

2021 ◽  
Vol 13 (4) ◽  
Author(s):  
Camilla A Santos ◽  
Gabriel G Sonoda ◽  
Thainá Cortez ◽  
Luiz L Coutinho ◽  
Sónia C S Andrade
Keyword(s):  
Local Adaptation ◽  
Differentially Expressed Genes ◽  
Evolutionary Biology ◽  
Rocky Shore ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Marine Species ◽  
Differentially Expressed ◽  
Planktonic Larva ◽  
Structure Changes

Abstract Understanding how selection shapes population differentiation and local adaptation in marine species remains one of the greatest challenges in the field of evolutionary biology. The selection of genes in response to environment-specific factors and microenvironmental variation often results in chaotic genetic patchiness, which is commonly observed in rocky shore organisms. To identify these genes, the expression profile of the marine gastropod Littoraria flava collected from four Southeast Brazilian locations in ten rocky shore sites was analyzed. In this first L. flava transcriptome, 250,641 unigenes were generated, and 24% returned hits after functional annotation. Independent paired comparisons between 1) transects, 2) sites within transects, and 3) sites from different transects were performed for differential expression, detecting 8,622 unique differentially expressed genes. Araçá (AR) and São João (SJ) transect comparisons showed the most divergent gene products. For local adaptation, fitness-related differentially expressed genes were chosen for selection tests. Nine and 24 genes under adaptative and purifying selection, respectively, were most related to biomineralization in AR and chaperones in SJ. The biomineralization-genes perlucin and gigasin-6 were positively selected exclusively in the site toward the open ocean in AR, with sequence variants leading to pronounced protein structure changes. Despite an intense gene flow among L. flava populations due to its planktonic larva, gene expression patterns within transects may be the result of selective pressures. Our findings represent the first step in understanding how microenvironmental genetic variation is maintained in rocky shore populations and the mechanisms underlying local adaptation in marine species.

scholarly journals An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely related Aspergillus fungi

Genetics ◽  
2021 ◽  
Author(s):  
Matthew E Mead ◽  
Jacob L Steenwyk ◽  
Lilian P Silva ◽  
Patrícia A de Castro ◽  
Nauman Saeed ◽  
...  
Keyword(s):  
Human Disease ◽  
Evolutionary Rate ◽  
Fungal Disease ◽  
Comparative Genomic ◽  
Genetic Elements ◽  
Genomic Approach ◽  
Evolutionary Genomic ◽  
Repeated Evolution ◽  
Species Specific ◽  
Encoding Genes

Abstract Aspergillosis is an important opportunistic human disease caused by filamentous fungi in the genus Aspergillus. Roughly 70% of infections are caused by Aspergillus fumigatus, with the rest stemming from approximately a dozen other Aspergillus species. Several of these pathogens are closely related to A. fumigatus and belong in the same taxonomic section, section Fumigati. Pathogenic species are frequently most closely related to non-pathogenic ones, suggesting Aspergillus pathogenicity evolved multiple times independently. To understand the repeated evolution of Aspergillus pathogenicity, we performed comparative genomic analyses on 18 strains from 13 species, including 8 species in section Fumigati, which aimed to identify genes, both ones previously connected to virulence as well as ones never before implicated, whose evolution differs between pathogens and non-pathogens. We found that most genes were present in all species, including approximately half of those previously connected to virulence, but a few genes were section- or species-specific. Evolutionary rate analyses identified over 1,700 genes whose evolutionary rate differed between pathogens and non-pathogens and dozens of genes whose rates differed between specific pathogens and the rest of the taxa. Functional testing of deletion mutants of 17 transcription factor-encoding genes whose evolution differed between pathogens and non-pathogens identified eight genes that affect either fungal survival in a model of phagocytic killing, host survival in an animal model of fungal disease, or both. These results suggest that the evolution of pathogenicity in Aspergillus involved both conserved and species-specific genetic elements, illustrating how an evolutionary genomic approach informs the study of fungal disease.

scholarly journals Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content

BMC Genomics ◽  
2009 ◽  
Vol 10 (1) ◽  
pp. 358 ◽  
Author(s):  
Fumito Maruyama ◽  
Mitsuhiko Kobata ◽  
Ken Kurokawa ◽  
Keishin Nishida ◽  
Atsuo Sakurai ◽  
...  
Keyword(s):  
Streptococcus Mutans ◽  
Comparative Genomic ◽  
Specific Content ◽  
Genomic Analyses ◽  
Species Specific

scholarly journals The role of environment, local adaptation and past climate fluctuation on the amount and distribution of genetic diversity in the teosinte in Mexico

2019 ◽  
Author(s):  
Jaime Gasca-Pineda ◽  
Yocelyn T. Gutiérrez-Guerrero ◽  
Erika Aguirre-Planter ◽  
Luis E. Eguiarte
Keyword(s):  
Genetic Diversity ◽  
Local Adaptation ◽  
Environmental Conditions ◽  
Wide Distribution ◽  
Wide Range ◽  
Significant Genetic Structure ◽  
Nuclear Microsatellite ◽  
Genetic Clusters ◽  
Assignment Analysis ◽  
Climate Fluctuation

AbstractWild maize, commonly known as teosinte, has a wide distribution in central Mexico and inhabits a wide range of environmental conditions. According to previous studies, the environment is a determinant factor for the amount and distribution of genetic diversity. In this study, we used a set of neutral markers to explore the influence of contemporary factors and historical environmental shifts on genetic diversity, including present and three historical periods. Using a set of 22 nuclear microsatellite loci, we genotyped 527 individuals from 29 localities. We found highly variable levels of genetic diversity (Z. m. parviglumis HE= 0.3646–0.7699; Z. m. mexicana HE= 0.5885–0.7671) and significant genetic structure among localities (average DEST= 0.4332). Also, we recovered significant values of heterozygote deficiency (average FIS= 0.1796) and variable levels of selfing (sg2=0.0–0.3090). The Bayesian assignment analysis yielded four genetic clusters dividing the sample into subspecies, that in turn, were separated into two clusters. Environmental conditions played a strong influence in the distribution of genetic diversity, as demographic analysis and changes in species range revealed by modeling analyses were consistent. We conclude that current genetic diversity in teosinte is the result of a mixture of local adaptation and genetic isolation along with historical environmental fluctuations.

scholarly journals Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad

2021 ◽  
Author(s):  
Binia De Cahsan ◽  
Katrin Kiemel ◽  
Michael Westbury ◽  
Maike Lauritsen ◽  
Marijke Autenrieth ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Local Adaptation ◽  
Agricultural Land ◽  
Introgressive Hybridization ◽  
Mitochondrial Control Region ◽  
The Body ◽  
Immune Gene ◽  
Range Margin ◽  
Adaptive Immune ◽  
The Impact

Northern range margin populations of the European fire-bellied toad (Bombina bombina) have rapidly declined during recent decades. Extensive agricultural land use has fragmented the landscape, leading to habitat disruption and loss, as well as eutrophication of ponds. In Northern Germany (Schleswig-Holstein) and Southern Sweden, this decline resulted in decreased gene flow from surrounding populations, low genetic diversity, and a putative reduction in adaptive potential, leaving populations vulnerable to future environmental and climatic changes. Previous studies using mitochondrial control region and nuclear transcriptome-wide SNP data detected introgressive hybridization in multiple northern B. bombina populations after presumed illegal release of toads from Austria. Here, we determine the impact of this introgression by comparing the body conditions (as a proxy for fitness) of introgressed and non-introgressed populations, and the genetic consequences in two candidate genes for putative local adaptation (the MHC II gene as part of the adaptive immune system and the stress response gene HSP70 kDa). We detected regional differences in body condition. We observed significantly elevated levels of within individual MHC allele counts in introgressed Swedish populations, associated with a tendency towards higher body weight, relative to regional non-introgressed populations. These differences were not observed among introgressed and non-introgressed German populations. Genetic diversity in both MHC and HSP was generally lower in northern than southern populations. Our study sheds light on the potential benefits of translocations of more distantly related conspecifics as a means to increase adaptive genetic variability and fitness of struggling range margin populations without distortion of local adaptation.

scholarly journals Nanopore amplicon sequencing reveals molecular convergence and local adaptation of opsin genes

2020 ◽  
Author(s):  
Katherine M. Eaton ◽  
Moisés A. Bernal ◽  
Nathan J.C. Backenstose ◽  
Trevor J. Krabbenhoft
Keyword(s):  
Local Adaptation ◽  
Environmental Gradients ◽  
Parallel Evolution ◽  
Amplicon Sequencing ◽  
Species Flock ◽  
Closely Related Species ◽  
Oxford Nanopore ◽  
Opsin Genes ◽  
Potential Case ◽  
Species Specific

AbstractLocal adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus Coregonus) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle. Five visual opsin genes were amplified for individuals of C. artedi, C. hoyi, C. kiyi, and C. zenithicus. Comparisons revealed species-specific differences in the coding sequence of rhodopsin (Tyr261Phe substitution), suggesting local adaptation by C. kiyi to the blue-shifted depths of Lake Superior. Parallel evolution and “toggling” at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.

scholarly journals The Role of Plasticity and Adaptation in the Incipient Speciation of a Fire Salamander Population

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 875
Author(s):  
Joana Sabino-Pinto ◽  
Daniel J. Goedbloed ◽  
Eugenia Sanchez ◽  
Till Czypionka ◽  
Arne W. Nolte ◽  
...  
Keyword(s):  
Gene Expression ◽  
Phenotypic Plasticity ◽  
Local Adaptation ◽  
Habitat Preferences ◽  
Genetic Change ◽  
Incipient Speciation ◽  
Expression Of Genes ◽  
Species Specific ◽  
Reciprocal Transfer ◽  
High Degree

Phenotypic plasticity and local adaptation via genetic change are two major mechanisms of response to dynamic environmental conditions. These mechanisms are not mutually exclusive, since genetic change can establish similar phenotypes to plasticity. This connection between both mechanisms raises the question of how much of the variation observed between species or populations is plastic and how much of it is genetic. In this study, we used a structured population of fire salamanders (Salamandra salamandra), in which two subpopulations differ in terms of physiology, genetics, mate-, and habitat preferences. Our goal was to identify candidate genes for differential habitat adaptation in this system, and to explore the degree of plasticity compared to local adaptation. We therefore performed a reciprocal transfer experiment of stream- and pond-originated salamander larvae and analyzed changes in morphology and transcriptomic profile (using species-specific microarrays). We observed that stream- and pond-originated individuals diverge in morphology and gene expression. For instance, pond-originated larvae have larger gills, likely to cope with oxygen-poor ponds. When transferred to streams, pond-originated larvae showed a high degree of plasticity, resembling the morphology and gene expression of stream-originated larvae (reversion); however the same was not found for stream-originated larvae when transferred to ponds, where the expression of genes related to reduction-oxidation processes was increased, possibly to cope with environmental stress. The lack of symmetrical responses between transplanted animals highlights the fact that the adaptations are not fully plastic and that some level of local adaptation has already occurred in this population. This study illuminates the process by which phenotypic plasticity allows local adaptation to new environments and its potential role in the pathway of incipient speciation.

scholarly journals Sewall Wright, 21 December 1889 - 3 March 1988

1990 ◽  
Vol 36 ◽  
pp. 567-579 ◽  
Keyword(s):  
Population Genetics ◽  
Evolutionary Biology ◽  
Natural Populations ◽  
Coat Colour ◽  
Balance Theory ◽  
Theory Of Evolution ◽  
Shifting Balance Theory ◽  
Sewall Wright ◽  
Shifting Balance ◽  
Active Research

Sewall Wright's active life spanned the development of genetics from a new discipline when the principles of inheritance were still being elucidated to the technology of recombinant gene construction and insertion. He was one of the major pioneers of population genetics, which gave a quantitative basis to the studies of evolution, of variation in natural populations and of animal and plant breeding. He contributed most significantly to methods and ideas over a long period, indeed his four volume treatise was written long after he formally ‘retired’ and his last paper (211) was published a few days before his death at the age of 98. In the field of population genetics Wright developed the method of path coefficients, which he used to analyse quantitative genetic variation and relationship, but which has been applied to subjects as diverse as economics, the ideas of inbreeding coefficient and F -statistics which form the basis of analysis of population structure, the theory of variation in gene frequency among populations, and the shifting balance theory of evolution, which remains a topic of active research and controversy. Wright contributed to physiological genetics, notably analysis of the inheritance of coat colour in the guinea pig, and in particular the epistatic relationships among the genes involved. There was a critical interplay between his population and physiological work, in that the analysis of finite populations on the one hand and of epistatic interactions on the other are the bases of Wright’s development of the shifting balance theory. A full and enlightening biography of Sewall Wright which traces his influence on evolutionary biology and his interactions with other important workers was published recently (Provine 1986) and shorter appreciations have appeared since his death, notably by Crow (1988), Wright’s long-time colleague. This biography relies heavily on Provine’s volume, and does no more than summarize Wright’s extensive contributions. Many of his important papers have been reprinted recently (1986).

scholarly journals Disentangling Population History and Character Evolution among Hybridizing Lineages

2020 ◽  
Vol 37 (5) ◽  
pp. 1295-1305 ◽  
Author(s):  
Sean P Mullen ◽  
Nicholas W VanKuren ◽  
Wei Zhang ◽  
Sumitha Nallu ◽  
Evan B Kristiansen ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
De Novo ◽  
Balancing Selection ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Character Evolution ◽  
Population History ◽  
Lineage Sorting ◽  
Evolutionary Origins ◽  
Whole Genome Resequencing

Abstract Understanding the origin and maintenance of adaptive phenotypic novelty is a central goal of evolutionary biology. However, both hybridization and incomplete lineage sorting can lead to genealogical discordance between the regions of the genome underlying adaptive traits and the remainder of the genome, decoupling inferences about character evolution from population history. Here, to disentangle these effects, we investigated the evolutionary origins and maintenance of Batesian mimicry between North American admiral butterflies (Limenitis arthemis) and their chemically defended model (Battus philenor) using a combination of de novo genome sequencing, whole-genome resequencing, and statistical introgression mapping. Our results suggest that balancing selection, arising from geographic variation in the presence or absence of the unpalatable model, has maintained two deeply divergent color patterning haplotypes that have been repeatedly sieved among distinct mimetic and nonmimetic lineages of Limenitis via introgressive hybridization.

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