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Chromosomal level reference genome of Tachypleus tridentatus provides insights into evolution and adaptation of horseshoe crabs

Li Gong, Guangyi Fan, Yandong Ren, Yongjiu Chen, więcej

Molecular Ecology Resources > 19 > 3 > 744 - 756

Horseshoe crabs including Tachypleus tridentatus are a group of marine arthropods and living fossil species which have existed on the earth for ~500 million years. However, the genetic mechanisms underlying their unique adaptive ability are still unclear. Here, we assembled the first chromosome‐level T. tridentatus genome, and proved that this genome is of high quality with contig N50 1.69 Mb. By...

artykuł

The rising tide of high‐quality genomic resources

Scott Hotaling, Joanna L. Kelley

Molecular Ecology Resources > 19 > 3 > 567 - 569

artykuł

Chromosomal inversions promote genomic islands of concerted evolution of Hsp70 genes in the Drosophila subobscura species subgroup

Marta Puig Giribets, María Pilar García Guerreiro, Mauro Santos, Francisco J. Ayala, więcej

Molecular Ecology > 28 > 6 > 1316 - 1332

Heat‐shock (HS) assays to understand the connection between standing inversion variation and evolutionary response to climate change in Drosophila subobscura found that “warm‐climate” inversion O₃₊₄ exhibits non‐HS levels of Hsp70 protein like those of “cold‐climate” O_ST after HS induction. This was unexpected, as overexpression of Hsp70 can incur multiple fitness costs. To understand the genetic...

artykuł

Asymmetric assortative mating and queen polyandry are linked to a supergene controlling ant social organization

Amaury Avril, Jessica Purcell, Alan Brelsford, Michel Chapuisat

Molecular Ecology > 28 > 6 > 1428 - 1438

Nonrecombining genomic variants underlie spectacular social polymorphisms, from bird mating systems to ant social organization. Because these “social supergenes” affect multiple phenotypic traits linked to survival and reproduction, explaining their persistence remains a substantial challenge. Here, we investigate how large nonrecombining genomic variants relate to colony social organization, mating...

artykuł

Genotype‐free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data

Vera M. Warmuth, Hans Ellegren

Molecular Ecology Resources > 19 > 3 > 586 - 596

Restriction‐site associated DNA sequencing (RADSeq) facilitates rapid generation of thousands of genetic markers at relatively low cost; however, several sources of error specific to RADSeq methods often lead to biased estimates of allele frequencies and thereby to erroneous population genetic inference. Estimating the distribution of sample allele frequencies without calling genotypes was shown to...

artykuł

DNA barcoding fishes from the Congo and the Lower Guinean provinces: Assembling a reference library for poorly inventoried fauna

Gontran Sonet, Jos Snoeks, Zoltán T. Nagy, Emmanuel Vreven, więcej

Molecular Ecology Resources > 19 > 3 > 728 - 743

The Congolese and Lower Guinean ichthyological provinces are understudied hotspots of the global fish diversity. Here, we barcoded 741 specimens from the Lower and Middle Congo River and from three major drainage basins of the Lower Guinean ichthyological province, Kouilou‐Niari, Nyanga and Ogowe. We identified 194 morphospecies belonging to 82 genera and 25 families. Most morphospecies (92.8%) corresponded...

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A roadmap for high‐throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture

Lauren C. White, Claudia Fontsere, Esther Lizano, David A. Hughes, więcej

Molecular Ecology Resources > 19 > 3 > 609 - 622

Large‐scale genomic studies of wild animal populations are often limited by access to high‐quality DNA. Although noninvasive samples, such as faeces, can be readily collected, DNA from the sample producers is usually present in low quantities, fragmented, and contaminated by microorganism and dietary DNAs. Hybridization capture can help to overcome these impediments by increasing the proportion of...

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Genome‐wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae)

Aude Rogivue, Rimjhim R. Choudhury, Stefan Zoller, Stéphane Joost, więcej

Molecular Ecology Resources > 19 > 3 > 773 - 787

Advances in high‐throughput sequencing have promoted the collection of reference genomes and genome‐wide diversity. However, the assessment of genomic variation among populations has hitherto mainly been surveyed through single‐nucleotide polymorphisms (SNPs) and largely ignored the often major fraction of genomes represented by transposable elements (TEs). Despite accumulating evidence supporting...

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Bioaerosol biomonitoring: Sampling optimization for molecular microbial ecology

Robert M. W. Ferguson, Sonia Garcia‐Alcega, Frederic Coulon, Alex J. Dumbrell, więcej

Molecular Ecology Resources > 19 > 3 > 672 - 690

Bioaerosols (or biogenic aerosols) have largely been overlooked by molecular ecologists. However, this is rapidly changing as bioaerosols play key roles in public health, environmental chemistry and the dispersal ecology of microbes. Due to the low environmental concentrations of bioaerosols, collecting sufficient biomass for molecular methods is challenging. Currently, no standardized methods for...

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A new cost‐effective and fast direct PCR protocol for insects based on PBS buffer

Kantima Thongjued, Wilaiwan Chotigeat, Sara Bumrungsri, Phuvadol Thanakiatkrai, więcej

Molecular Ecology Resources > 19 > 3 > 691 - 701

Insect DNA barcoding is a species identification technique used in biodiversity assessment and ecological studies. However, DNA extraction can result in the loss of up to 70% of DNA. Recent research has reported that direct PCR can overcome this issue. However, the success rates could still be improved, and tissues used for direct PCR could not be reused for further genetic studies. Here, we developed...

artykuł

Ultralong telomeres shorten with age in nestling great tits but are static in adults and mask attrition of short telomeres

Els Atema, Ellis Mulder, Arie J. van Noordwijk, Simon Verhulst

Molecular Ecology Resources > 19 > 3 > 648 - 658

Telomere length (TL) is increasingly being used as a biomarker of senescence, but measuring telomeres remains a challenge. Within tissue samples, TL varies between cells and chromosomes. Class I telomeres are (presumably static) interstitial telomeric sequences, while terminal telomeres have been divided in shorter (Class II) telomeres and ultralong (Class III) telomeres, and the presence of the latter...

artykuł

The genomic pool of standing structural variation outnumbers single nucleotide polymorphism by threefold in the marine teleost Chrysophrys auratus

Andrew Catanach, Ross Crowhurst, Cecilia Deng, Charles David, więcej

Molecular Ecology > 28 > 6 > 1210 - 1223

Recent studies have highlighted an important role of structural variation (SV) in ecological and evolutionary processes, but few have studied nonmodel species in the wild. As part of our long‐term research programme on the nonmodel teleost fish Australasian snapper (Chrysophrys auratus), we aim to build one of the first catalogues of genomic variants (SNPs and indels, and deletions, duplications and...

artykuł

The role of structural genomic variants in population differentiation and ecotype formation in Timema cristinae walking sticks

Kay Lucek, Zachariah Gompert, Patrik Nosil

Molecular Ecology > 28 > 6 > 1224 - 1237

Theory predicts that structural genomic variants such as inversions can promote adaptive diversification and speciation. Despite increasing empirical evidence that adaptive divergence can be triggered by one or a few large inversions, the degree to which widespread genomic regions under divergent selection are associated with structural variants remains unclear. Here we test for an association between...

artykuł

Going beyond SNPs: The role of structural genomic variants in adaptive evolution and species diversification

Maren Wellenreuther, Claire Mérot, Emma Berdan, Louis Bernatchez

Molecular Ecology > 28 > 6 > 1203 - 1209

artykuł

Retention of a chromosomal inversion from an anadromous ancestor provides the genetic basis for alternative freshwater ecotypes in rainbow trout

Martin C. Arostegui, Thomas P. Quinn, Lisa W. Seeb, James E. Seeb, więcej

Molecular Ecology > 28 > 6 > 1412 - 1427

Migratory behaviour patterns in animals are controlled by a complex genetic architecture. Rainbow trout (Oncorhynchus mykiss) is a salmonid fish that spawns in streams but exhibits three primary life history pathways: stream‐resident (fluvial), lake‐migrant (adfluvial) and ocean‐migrant (anadromous). Previous studies examining fluvial and anadromous O. mykiss have identified several genes associated...

artykuł

Impact of polymorphic transposable elements on linkage disequilibrium along chromosomes

Rimjhim Roy Choudhury, Aude Rogivue, Felix Gugerli, Christian Parisod

Molecular Ecology > 28 > 6 > 1550 - 1562

Recombination and selection drive the extent of linkage disequilibrium (LD) among loci and therefore affect the reshuffling of adaptive genetic variation. However, it is poorly known to what extent the enrichment of transposable elements (TEs) in recombinationally‐inert regions reflects their inefficient removal by purifying selection and whether the presence of polymorphic TEs can modify the local...

artykuł

Chromosomal inversions associated with environmental adaptation in honeybees

Matthew J. Christmas, Andreas Wallberg, Ignas Bunikis, Anna Olsson, więcej

Molecular Ecology > 28 > 6 > 1358 - 1374

Chromosomal inversions can facilitate local adaptation in the presence of gene flow by suppressing recombination between well‐adapted native haplotypes and poorly adapted migrant haplotypes. East African mountain populations of the honeybee Apis mellifera are highly divergent from neighbouring lowland populations at two extended regions in the genome, despite high similarity in the rest of the genome,...

artykuł

Population‐specific dynamics and selection patterns of transposable element insertions in European natural populations

Emmanuelle Lerat, Clément Goubert, Sara Guirao‐Rico, Miriam Merenciano, więcej

Molecular Ecology > 28 > 6 > 1506 - 1522

Transposable elements (TEs) are ubiquitous sequences in genomes of virtually all species. While TEs have been investigated for several decades, only recently we have the opportunity to study their genome‐wide population dynamics. Most of the studies so far have been restricted either to the analysis of the insertions annotated in the reference genome or to the analysis of a limited number of populations...

artykuł

Patterns of transposable element variation and clinality in Drosophila

Jeffrey R. Adrion, David J. Begun, Matthew W. Hahn

Molecular Ecology > 28 > 6 > 1523 - 1536

Natural populations often exist in spatially diverse environments and may experience variation in the strength and targets of natural selection across their ranges. Drosophila provides an excellent opportunity to study the effects of spatially varying selection in natural populations, as both Drosophila melanogaster and Drosophila simulans live across a wide range of environments in North America...

artykuł

Association mapping desiccation resistance within chromosomal inversions in the African malaria vector Anopheles gambiae

Diego Ayala, Simo Zhang, Mathieu Chateau, Caroline Fouet, więcej

Molecular Ecology > 28 > 6 > 1333 - 1342

Inversion polymorphisms are responsible for many ecologically important phenotypes and are often found under balancing selection. However, the same features that ensure their large role in local adaptation—especially reduced recombination between alternate arrangements—mean that uncovering the precise loci within inversions that control these phenotypes is unachievable using standard mapping approaches...

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