A chromosomal inversion drives evolution of multiple adaptive traits in deer mice

AbstractA long-standing question in evolutionary biology is how differences in multiple traits can evolve quickly and be maintained together during local adaptation. Using forest and prairie ecotypes in deer mice, which differ in both tail length and coat color, we discovered a 41 Mb chromosomal inversion that is strongly linked to variation in both traits. The inversion maintains highly divergent loci in strong linkage disequilibrium and likely originated ~170 kya, long before the forest-prairie divergence ~10 kya. Consistent with a role in local adaptation, inversion frequency is associated with phenotype and habitat across both a local transect and the species range. Still, although eastern and western forest subspecies share similar phenotypes, the inversion is absent in eastern North America. This work highlights the significance of inversion polymorphisms for the establishment and maintenance of multiple locally adaptive traits in mammals, and demonstrates that, even within a species, parallel phenotypes may evolve through nonparallel genetic mechanisms.

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Transcriptomic responses to drought stress among natural populations provide insights into local adaptation of weeping forsythia

BMC Plant Biology ◽

10.1186/s12870-021-03075-6 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yong Li ◽

Long-Chen Shi ◽

Nan-Cai Pei ◽

Samuel A. Cushman ◽

Yu-Tao Si

Keyword(s):

Drought Stress ◽

Differential Expression ◽

Local Adaptation ◽

Evolutionary Biology ◽

Molecular Ecology ◽

Evolutionary Process ◽

Reduction Process ◽

Heterogeneous Environments ◽

Significant Differential Expression ◽

Genetic Mechanisms

Abstract Background Understanding the genetic mechanisms of local adaptation is an important emerging topic in molecular ecology and evolutionary biology. Results Here, we identify the physiological changes and differential expression of genes among different weeping forsythia populations under drought stress in common garden experiments. Physiological results showed that HBWZ might have higher drought tolerance among four populations. RNA-seq results showed that significant differential expression in the genes responding to the synthesis of flavonoids, aromatic substances, aromatic amino acids, oxidation–reduction process, and transmembrane transport occured among four populations. By further reanalysis of results of previous studies, sequence differentiation was found in the genes related to the synthesis of aromatic substances among different weeping forsythia populations. Conclusions Overall, our study supports the hypothesis that the dual differentiation in gene efficiency and expression increases among populations in response to heterogeneous environments and is an important evolutionary process of local adaptation. Here, we proposed a new working model of local adaptation of weeping forsythia populations under different intensities of drought stress, which provides new insights for understanding the genetic mechanisms of local adaptation for non-model species.

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Multiple genetic changes underlie the evolution of long-tailed forest deer mice

10.1101/041699 ◽

2016 ◽

Cited By ~ 1

Author(s):

Evan P Kingsley ◽

Krzysztof M Kozak ◽

Susanne Pfeifer ◽

Dou-Shuan Yang ◽

Hopi E Hoekstra

Keyword(s):

Evolutionary Biology ◽

Morphological Changes ◽

Deer Mouse ◽

Tail Length ◽

Deer Mice ◽

Phenotypic Change ◽

Skeletal Morphology ◽

Genetic Changes ◽

The North ◽

Caudal Vertebrae

Understanding both the role of selection in driving phenotypic change and its underlying genetic basis remain major challenges in evolutionary biology. Here we focus on a classic system of local adaptation in the North American deer mouse,Peromyscus maniculatus, which occupies two main habitat types, prairie and forest. Using historical collections we demonstrate that forest-dwelling mice have longer tails than those from non-forested habitats, even when we account for individual and population relatedness. Based on genome-wide SNP capture data, we find that mice from forested habitats in the eastern and western parts of their range form separate clades, suggesting that increased tail length evolved independently from a short-tailed ancestor. Two major changes in skeletal morphology can give rise to longer tails--increased number and increased length of vertebrae--and we find that forest mice in the east and west have both more and longer caudal vertebrae, but not trunk vertebrae, than nearby prairie forms. Using a second-generation intercross between a prairie and forest pair, we show that the number and length of caudal vertebrae are not correlated in this recombinant population, suggesting that variation in these traits is controlled by separate genetic loci. Together, these results demonstrate convergent evolution of the long-tailed forest phenotype through multiple, distinct genetic mechanisms (controlling vertebral length and vertebral number), thus suggesting that these morphological changes--either independently or together--are adaptive.

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Whole genome sequences reveal multiple functions of PAT1 gene on environment adaptation and coat coloration in Tibetan sheep populations

10.21203/rs.2.11247/v1 ◽

2019 ◽

Author(s):

Jianbin Liu ◽

Xuezhi Ding ◽

Chao Yuan ◽

Yufeng Zeng ◽

Tingting Guo ◽

...

Keyword(s):

Candidate Genes ◽

Coat Color ◽

Body Height ◽

Multiple Traits ◽

Adaptive Traits ◽

Environment Adaptation ◽

Tibetan Sheep ◽

Genomic Regions ◽

The Tropics ◽

Productive Trait

Abstract Background: Most sheep breeding programs designed for the tropics and sub-tropics have to take into account the impacts of both productive and adaptive traits. However, the genetic mechanism regulating the multiple biological process remain unclear. Results: In this study, we report a novel PAT1 gene that simultaneously explained the variations of productive trait (coat color), adaptive traits (altitude and geography response) in 15 indigenous Tibetan sheep populations. Overlapped genomic regions harboring 6 candidate genes across three traits were identified at 27 chromosomes, with the top 1% of Fst and |Zph| values. The SNP/INDELs and expression of these candidate genes were further analyzed, and we find that only PAT1 gene, a CSDE1 homologue was consistent with the variation of multiple traits regarding. Haplotype analysis of PAT1 reveal that Tibetan sheep breeds with C-type of PAT1 have significantly greater body weight, shear amount, chest width and body length, but have lower body height, than those with CA-type of PAT1. Conclusions: We emphasized that PAT1 gene could be a potentially selective target used for the improvements of environmental adaption and coat coloration in the future. These results contribute to the knowledge of adaptive response in Tibetan sheep populations and will help to guide future conservation programs for Tibetan sheep native to Qinghai-Tibetan Plateau.

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Shifts in morphology, gene expression, and selection underlie web loss in Hawaiian Tetragnatha spiders

BMC Ecology and Evolution ◽

10.1186/s12862-021-01779-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Cory A. Berger ◽

Michael S. Brewer ◽

Nobuaki Kono ◽

Hiroyuki Nakamura ◽

Kazuharu Arakawa ◽

...

Keyword(s):

Genetic Basis ◽

Adaptive Traits ◽

Deep Time ◽

Selective Pressures ◽

Silk Production ◽

Silk Glands ◽

Genetic Mechanisms ◽

Orb Web ◽

Short Time ◽

Web Building

Abstract Background A striking aspect of evolution is that it often converges on similar trajectories. Evolutionary convergence can occur in deep time or over short time scales, and is associated with the imposition of similar selective pressures. Repeated convergent events provide a framework to infer the genetic basis of adaptive traits. The current study examines the genetic basis of secondary web loss within web-building spiders (Araneoidea). Specifically, we use a lineage of spiders in the genus Tetragnatha (Tetragnathidae) that has diverged into two clades associated with the relatively recent (5 mya) colonization of, and subsequent adaptive radiation within, the Hawaiian Islands. One clade has adopted a cursorial lifestyle, and the other has retained the ancestral behavior of capturing prey with sticky orb webs. We explore how these behavioral phenotypes are reflected in the morphology of the spinning apparatus and internal silk glands, and the expression of silk genes. Several sister families to the Tetragnathidae have undergone similar web loss, so we also ask whether convergent patterns of selection can be detected in these lineages. Results The cursorial clade has lost spigots associated with the sticky spiral of the orb web. This appears to have been accompanied by loss of silk glands themselves. We generated phylogenies of silk proteins (spidroins), which showed that the transcriptomes of cursorial Tetragnatha contain all major spidroins except for flagelliform. We also found an uncharacterized spidroin that has higher expression in cursorial species. We found evidence for convergent selection acting on this spidroin, as well as genes involved in protein metabolism, in the cursorial Tetragnatha and divergent cursorial lineages in the families Malkaridae and Mimetidae. Conclusions Our results provide strong evidence that independent web loss events and the associated adoption of a cursorial lifestyle are based on similar genetic mechanisms. Many genes we identified as having evolved convergently are associated with protein synthesis, degradation, and processing, which are processes that play important roles in silk production. This study demonstrates, in the case of independent evolution of web loss, that similar selective pressures act on many of the same genes to produce the same phenotypes and behaviors.

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

Genome Biology and Evolution ◽

10.1093/gbe/evab050 ◽

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.

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Evolution of stickleback spines through independent cis-regulatory changes at HOXDB

10.1101/2021.12.14.472698 ◽

2021 ◽

Author(s):

Julia I Wucherpfennig ◽

Timothy R Howes ◽

Jessica N Au ◽

Eric H Au ◽

Garrett A Roberts Kingman ◽

...

Keyword(s):

Gene Expression ◽

Evolutionary Biology ◽

Gasterosteus Aculeatus ◽

Molecular Mechanisms ◽

Wild Populations ◽

Gene Variation ◽

Regulatory Changes ◽

Fundamental Goal ◽

Apeltes Quadracus ◽

Genetic Mechanisms

Understanding the genetic mechanisms leading to new traits is a fundamental goal of evolutionary biology. We show that HOXDB regulatory changes have been used repeatedly in different stickleback fish species to alter the length and number of bony dorsal spines. In Gasterosteus aculeatus, a variant HOXDB allele is genetically linked to shortening an existing spine and adding a spine. In Apeltes quadracus, a variant allele is associated with lengthening an existing spine and adding a spine. The alleles alter the same conserved non-coding HOXDB enhancer by diverse molecular mechanisms, including SNPs, deletions, and transposable element insertions. The independent cis-acting regulatory changes are linked to anterior expansion or contraction of HOXDB expression. Our findings support the long-standing hypothesis that natural Hox gene variation underlies key morphological patterning changes in wild populations and illustrate how different mutational mechanisms affecting the same region may produce opposite gene expression changes with similar phenotypic outcomes.

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Tail length evolution in deer mice: linking morphology, behavior and function

Integrative and Comparative Biology ◽

10.1093/icb/icab030 ◽

2021 ◽

Author(s):

Emily R Hager ◽

Hopi E Hoekstra

Keyword(s):

Computational Models ◽

Deer Mouse ◽

Center Of Mass ◽

Tail Length ◽

Single Species ◽

Deer Mice ◽

Length Variation ◽

Caudal Vertebrae ◽

Long Tails ◽

And Function

Abstract Determining how variation in morphology affects animal performance (and ultimately fitness) is key to understanding the complete process of evolutionary adaptation. Long tails have evolved many times in arboreal and semi-arboreal rodents; in deer mice, long tails have evolved repeatedly in populations occupying forested habit even within a single species (Peromyscus maniculatus). Here we use a combination of functional modeling, laboratory studies, and museum records to test hypotheses about the function of tail-length variation in deer mice. First, we use computational models, informed by museum records documenting natural variation in tail length, to test whether differences in tail morphology between forest and prairie subspecies can influence performance in behavioral contexts relevant for tail use. We find that the deer mouse tail plays little role in statically adjusting center of mass or in correcting body pitch and yaw, but rather it can affect body roll during arboreal locomotion. In this context, we find that even intraspecific tail-length variation could result in substantial differences in how much body rotation results from equivalent tail motions (i.e., tail effectiveness), but the relationship between commonly-used metrics of tail-length variation and effectiveness is non-linear. We further test whether caudal vertebra length, number, and shape are associated with differences in how much the tail can bend to curve around narrow substrates (i.e., tail curvature) and find that, as predicted, the shape of the caudal vertebrae is associated with intervertebral bending angle across taxa. However, although forest and prairie mice typically differ in both the length and number of caudal vertebrae, we do not find evidence that this pattern is the result of a functional trade-off related to tail curvature. Together, these results highlight how even simple models can both generate and exclude hypotheses about the functional consequences of trait variation for organismal-level performance.

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Transgressive segregation and maternal genetic effects of non–target site fluazifop-P-butyl tolerance in Zoysia spp.

Weed Science ◽

10.1017/wsc.2019.26 ◽

2019 ◽

Vol 67 (05) ◽

pp. 504-509

Author(s):

Wenwen Liu ◽

Kevin E. Kenworthy ◽

Gregory E. MacDonald ◽

J. Bryan Unruh ◽

Laurie E. Trenholm ◽

...

Keyword(s):

Genetic Factors ◽

Breeding Population ◽

Transgressive Segregation ◽

Target Site ◽

Multiple Traits ◽

Intermediate Phenotypes ◽

Wide Range ◽

Genetic Mechanisms ◽

Tolerant Line ◽

Biomass Reduction

AbstractZoysia germplasm exhibit different levels of sensitivity to fluazifop-P-butyl, but the genetic factors responsible for such differences are unknown. Segregation patterns of the fluazifop-P-butyl tolerance trait were studied under greenhouse conditions. In total, 244 F1 lines were generated from multiple crosses between the tolerant line 5337-2 (non–target site tolerance) and three more-sensitive lines (123, 252, and 5330-23). Progeny segregation showed that fluazifop-P-butyl tolerance within zoysiagrass (Zoysia spp.) is expressed as a quantitative trait with a wide range of intermediate phenotypes between parental phenotypes. Transgressive segregation was extensive and largely favored susceptibility in most families, but was especially evident for 5337-2 × 123 and 5337-2 × 5330-23. The segregation patterns for biomass reduction and percent injury were different within reciprocal crosses and among three different family crosses. Reciprocal effects were observed in growth reduction for 5337-2 × 5330-23, in percent injury at 3 wk after the treatment (WAT), and for 5337-2 × 252 at 6 WAT. This indicated that fluazifop-P-butyl tolerance was not completely controlled by nuclear genetic factors in 5337-2 and maternal/cytoplasmic inheritance was also partially responsible. These results suggested that fluazifop-P-butyl tolerance may be attributed to multiple genetic mechanisms, which could present a challenge for future breeding efforts because of the difficulty of fixing multiple traits within a breeding population.

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BIOLOGY AND ECOLOGICAL ADAPTATIONS OF BLACKBUCK (Antilope cervicapra): A REVIEW

Agrobiological Records ◽

10.47278/journal.abr/2020.023 ◽

2021 ◽

Vol 4 ◽

pp. 23-31

Author(s):

Abdul Ghaffar

Keyword(s):

Coat Color ◽

Tail Length ◽

Conservation Strategies ◽

Reproductive Disorders ◽

Ecological Adaptations ◽

Desert Areas ◽

Antilope Cervicapra ◽

Average Body Length ◽

Average Body ◽

Average Body Weight

Blackbuck is the existing members of genus Antilope which is most elegant and graceful among all Antelopes of Asia with distinct sexual dimorphism. Blackbuck show endemism in Pakistan, Nepal and India occupying mainly the semi-arid grassland areas. The name of species attributes towards the dark brownish to blackish coat color of male species. While female and the young ones are tawny or yellow. Chin undersides of legs and chest are white in both male and female individuals. Males have whorled horns with 79cm length with absence in females. The average body length of this animal is 100-150cm with the tail length of 10-17cm. The average body weight for male is 20-57kg and for female 19-33kg. Thin grassy forests, open and semi-desert areas are good habitat for it. Being diurnal and herbivorous, it acts as both grazers and browsers. It is the fastest animal with an average speed of 80km/h. It remains reproductively functional whole year. Reproductive disorders including dystocia and different infectious diseases due to ectoparasites, endoparasites, bacteria and viruses affect these species. Habitat loss, stress, illegal killing and genetic troubles cause the species to be ‘Extinct in the Wildlife’ in Pakistan so conservation strategies are underway for species protection. It is indispensable for zoologists and conservational biologists to observe the species for its conservation and confronting threats. Review article highlighted necessary information about species, which will clear the way for further research on species.

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Linking genomic signatures of selection to expression variation and direct evidence of local adaptation

10.1101/2020.08.22.262394 ◽

2020 ◽

Author(s):

Nicholas Price ◽

Jack L. Mullen ◽

Junjiang Lin ◽

Christina Boucher ◽

John K. McKay

Keyword(s):

Cold Acclimation ◽

Local Adaptation ◽

Freezing Tolerance ◽

Evolutionary Biology ◽

Species Conservation ◽

Selective Constraint ◽

Expression Variation ◽

Genomic Signatures ◽

Genome Wide ◽

Signatures Of Selection

AbstractUnderstanding how genomic and expression variation is linked to adaptation of plants to local environments is fundamental to the fields of evolutionary biology and species conservation. Using locally adapted Arabidopsis thaliana Italy and Sweden populations, we examine how variation in gene expression under control and cold acclimation conditions, is linked to allele frequency differentiation (AFD); linkage disequilibrium (LD); selective constraint at nonsynonymous sites; and genetic-tradeoff quantitative trait loci (GT-QTL). Our results indicate that contrary to genes showing a main effect in environment (E), expression genotype by environment interactions (GxE) show significantly higher AFD along cis-regulatory and nonsynonymous sites than the neutral expectation; and interestingly, highly differentiated GxE genes show higher expression and inter-species selective constraint than the rest of the genes. When examining the association between genomic signatures of selection along GxE/E genes and GT-QTL, we find that GxE genes showing a high AFD and LD, display a significant and much higher enrichment along GT-QTL than the genome-wide/E set of genes. Nonetheless, E genes show a higher enrichment than the genome-wide control. In summary, our results suggest, that these highly expressed and selectively constrained GxE genes, may have been part of a cold-responsive regulon of E genes that experienced recent selection when migrating to new environments. Candidate GxE genes underlying GT-QTL reveal interesting biological processes that may underlie local adaptation to temperature, including flowering time, light-dependent cold acclimation, freezing tolerance, and response to hypoxia. Finally, we find no evidence linking lower expression of the CBF-dependent freezing tolerance pathway to genetic-tradeoffs and adaptation to warmer climates.

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