Molecular Ecology Resources

Veltman, Margaretha A.; Anthoons, Bastien; Schrøder‐Nielsen, Audun; Gravendeel, Barbara; Boer, Hugo J.

doi: 10.1111/1755-0998.13986pmid: 38899721

Terrestrial orchids are a group of genetically understudied, yet culturally and economically important plants. The Orchidinae tribe contains many species that produce edible tubers that are used for the production of traditional delicacies collectively called ‘salep’. Overexploitation of wild orchids in the Eastern Mediterranean and Western Asia threatens to drive many of these species to extinction, but cost‐effective tools for monitoring their trade are currently lacking. Here we present a custom bait kit for target enrichment and sequencing of 205 novel genetic markers that are tailored to phylogenomic applications in Orchidinae s.l. A subset of 31 markers capture genes putatively involved in the production of glucomannan, a water‐soluble polysaccharide that gives salep its distinctive properties. We tested the kit on 73 taxa native to the area, demonstrating universally high locus recovery irrespective of species identity, that exceeds the total sequence length obtained with alternative kits currently available. Phylogenetic inference with concatenation and coalescent approaches was robust and showed high levels of support for most clades, including some which were previously unresolved. Resolution for hybridizing and recently radiated lineages remains difficult, but could be further improved by analysing multiple haplotypes and the non‐exonic sequences captured by our kit, with the promise to shed new light on the evolution of enigmatic taxa with a complex speciation history. Offering a step‐up from traditional barcoding and universal markers, the genome‐wide custom loci targeted by Orchidinae‐205 are a valuable new resource to study the evolution, systematics and trade of terrestrial orchids.

Doorenweerd, Camiel; San Jose, Michael; Leblanc, Luc; Barr, Norman; Geib, Scott M.; Chung, Arthur Y. C.; Dupuis, Julian R.; Ekayanti, Arni; Fiegalan, Elaida; Hemachandra, Kennantudawage S.; Aftab Hossain, Mohammad; Huang, Chia‐Lung; Hsu, Yu‐Feng; Morris, Kimberly Y.;

Oliveira, Sandra; Marchi, Nina; Excoffier, Laurent

doi: 10.1111/1755-0998.13981pmid: 38775247

Admixture is a common biological phenomenon among populations of the same or different species. Identifying admixed tracts within individual genomes can provide valuable information to date admixture events, reconstruct ancestry‐specific demographic histories, or detect adaptive introgression, genetic incompatibilities, as well as regions of the genomes affected by (associative‐) overdominance. Although many local ancestry inference (LAI) methods have been developed in the last decade, their performance was accessed using large reference panels, which are rarely available for non‐model organisms or ancient samples. Moreover, the demographic conditions for which LAI becomes unreliable have not been explicitly outlined. Here, we identify the demographic conditions for which local ancestries can be best estimated using very small reference panels. Furthermore, we compare the performance of two LAI methods (RFMix and MOSAIC) with the performance of a newly developed approach (simpLAI) that can be used even when reference populations consist of single individuals. Based on simulations of various demographic models, we also determine the limits of these LAI tools and propose post‐painting filtering steps to reduce false‐positive rates and improve the precision and accuracy of the inferred admixed tracts. Besides providing a guide for using LAI, our work shows that reasonable inferences can be obtained from a single diploid genome per reference under demographic conditions that are not uncommon among past human groups and non‐model organisms.

Yi, Xueling; Kemppainen, Petri; Merilä, Juha

doi: 10.1111/1755-0998.13985pmid: 38850116

Despite their critical roles in genetic sex determination, sex chromosomes remain unknown in many non‐model organisms, especially those having recently evolved sex‐linked regions (SLRs). These evolutionarily young and labile sex chromosomes are important for understanding early sex chromosome evolution but are difficult to identify due to the lack of Y/W degeneration and SLRs limited to small genomic regions. Here, we present SLRfinder, a method to identify candidate SLRs using linkage disequilibrium (LD) clustering, heterozygosity and genetic divergence. SLRfinder does not rely on specific sequencing methods or a specific type of reference genome (e.g., from the homomorphic sex). In addition, the input of SLRfinder does not require phenotypic sexes, which may be unknown from population sampling, but sex information can be incorporated and is necessary to validate candidate SLRs. We tested SLRfinder using various published datasets and compared it to the local principal component analysis (PCA) method and the depth‐based method Sex Assignment Through Coverage (SATC). As expected, the local PCA method could not be used to identify unknown SLRs. SATC works better on conserved sex chromosomes, whereas SLRfinder outperforms SATC in analysing labile sex chromosomes, especially when SLRs harbour inversions. Power analyses showed that SLRfinder worked better when sampling more populations that share the same SLR. If analysing one population, a relatively larger sample size (around 50) is needed for sufficient statistical power to detect significant SLR candidates, although true SLRs are likely always top‐ranked. SLRfinder provides a novel and complementary approach for identifying SLRs and uncovering additional sex chromosome diversity in nature.

Nakajima, Souta; Tsuri, Kenji

doi: 10.1111/1755-0998.13990pmid: 38923125

Landscape genetics is a field dealing with local genetic differences and contributes to strategic conservation planning. Recently, environmental DNA (eDNA) metabarcoding has proven useful not only for detecting species but also for assessing genetic diversity and genetic structure on a large scale such as in phylogeography. However, it remains unclear whether eDNA analysis also has sufficient power to perform the landscape genetics, which focuses on a local scale. To reveal the applicability of eDNA to landscape genetics, we conducted an eDNA metabarcoding analysis of the mitochondrial DNA D‐loop region of the fluvial sculpin Cottus nozawae in the upper Sorachi River in Japan and compared the results with inferences based on traditional tissue‐based approaches by the same D‐loop region and genome‐wide SNP data. As a result, the spatial distribution of haplotypes was generally consistent between the eDNA‐ and tissue‐based approaches. In addition, the genetic differentiation statistics calculated using eDNA and tissue samples were highly correlated when comparing both in the D‐loop region. The removal of low‐frequency reads or the conversion to semi‐quantitative rankings of eDNA data did not alter the correlation of genetic diversity and differentiation statistics with tissue‐based approaches much. Finally, we confirmed that analyses using eDNA data can reveal patterns such as isolation‐by‐distance shown in previous studies on this species, indicating the applicability of eDNA to basic landscape genetics. Even though some limitations remain, eDNA may have great potential for conducting basic landscape genetics.

Chen, Wen; Newlands, Nathaniel; Hambleton, Sarah; Laroche, André; Davoodi, Seyyed Mohammadreza; Bakkeren, Guus

doi: 10.1111/1755-0998.13983pmid: 38840549

In the face of evolving agricultural practices and climate change, tools towards an integrated biovigilance platform to combat crop diseases, spore sampling, DNA diagnostics and predictive trajectory modelling were optimized. These tools revealed microbial dynamics and were validated by monitoring cereal rust fungal pathogens affecting wheat, oats, barley and rye across four growing seasons (2015–2018) in British Columbia and during the 2018 season in southern Alberta. ITS2 metabarcoding revealed disparity in aeromycobiota diversity and compositional structure across the Canadian Rocky Mountains, suggesting a barrier effect on air flow and pathogen dispersal. A novel bioinformatics classifier and curated cereal rust fungal ITS2 database, corroborated by real‐time PCR, enhanced the precision of cereal rust fungal species identification. Random Forest modelling identified crop and land‐use diversification as well as atmospheric pressure and moisture as key factors in rust distribution. As a valuable addition to explain observed differences and patterns in rust fungus distribution, trajectory HYSPLIT modelling tracked rust fungal urediniospores' northeastward dispersal from the Pacific Northwest towards southern British Columbia and Alberta, indicating multiple potential origins. Our Canadian case study exemplifies the power of an advanced biovigilance toolbox towards developing an early‐warning system for farmers to detect and mitigate impending disease outbreaks.

Li, Juan; Ulloa, Gabriela M.; Mayor, Pedro; Santolalla Robles, Meddly L.; Greenwood, Alex D.

doi: 10.1111/1755-0998.13979pmid: 38780145

Collecting and preserving biological samples in the field, particularly in remote areas in tropical forests, prior to laboratory analysis is challenging. Blood samples in many cases are used for nucleic acid‐based species determination, genomics or pathogen research. In most cases, maintaining a cold chain is impossible and samples remain at ambient temperature for extended periods of time before controlled storage conditions become available. Dried blood spot (DBS) storage, blood stored on cellulose‐based paper, has been widely applied to facilitate sample collection and preservation in the field for decades. However, it is unclear how long‐term storage on this substrate affects nucleic acid concentration and integrity. We analysed nucleic acid quality from DBS stored on Whatman filter paper no. 3 and FTA cards for up to 15 years in comparison to cold‐chain stored samples using four nucleic acid extraction methods. We examined the ability to identify viral sequences from samples of 12 free‐ranging primates in the Amazon forest, using targeted hybridization capture, and determined if mitochondrial genomes could be retrieved. The results suggest that even after extended periods of storage, DBS will be suitable for some genomic applications but may be of limited use for viral pathogen research, particularly RNA viruses.

Potente, Giacomo; Yousefi, Narjes; Keller, Barbara; Mora‐Carrera, Emiliano; Szövényi, Péter; Conti, Elena

doi: 10.1111/1755-0998.13988pmid: 38946153

Research on supergenes, non‐recombining genomic regions housing tightly linked genes that control complex phenotypes, has recently gained prominence in genomics. Heterostyly, a floral heteromorphism promoting outcrossing in several angiosperm families, is controlled by the S‐locus supergene. The S‐locus has been studied primarily in closely related Primula species and, more recently, in other groups that independently evolved heterostyly. However, it remains unknown whether genetic architecture and composition of the S‐locus are maintained among species that share a common origin of heterostyly and subsequently diverged across larger time scales. To address this research gap, we present a chromosome‐scale genome assembly of Primula edelbergii, a species that shares the same origin of heterostyly with Primula veris (whose S‐locus has been characterized) but diverged from it 18 million years ago. Comparative genomic analyses between these two species allowed us to show, for the first time, that the S‐locus can ‘jump’ (i.e. translocate) between chromosomes maintaining its function in controlling heterostyly. Additionally, we found that four S‐locus genes were conserved but reshuffled within the supergene, seemingly without affecting their expression, thus we could not detect changes explaining the lack of self‐incompatibility in P. edelbergii. Furthermore, we confirmed that the S‐locus is not undergoing genetic degeneration. Finally, we investigated P. edelbergii evolutionary history within Ericales in terms of whole genome duplications and transposable element accumulation. In summary, our work provides a valuable resource for comparative analyses aimed at investigating the genetics of heterostyly and the pivotal role of supergenes in shaping the evolution of complex phenotypes.

Li, Wenhao; Song, Jie; Tu, Huaming; Jiang, Shouwen; Pan, Binbin; Li, Jiazhen; Zhao, Yongpeng; Chen, Liangbiao; Xu, Qianghua

doi: 10.1111/1755-0998.13989pmid: 38946220

Abyssal (3501–6500 m) and hadal (>6500 m) fauna evolve under harsh abiotic stresses, characterized by high hydrostatic pressure, darkness and food shortage, providing unique opportunities to investigate mechanisms underlying environmental adaptation. Genomes of several hadal species have recently been reported. However, the genetic adaptation of deep sea species across a broad spectrum of ocean depths has yet to be thoroughly investigated, due to the challenges imposed by collecting the deep sea species. To elucidate the correlation between genetic innovation and vertical distribution, we generated a chromosome‐level genome assembly of the macrourids Coryphaenoides yaquinae, which is widely distributed in the abyssal/hadal zone ranging from 3655 to 7259 m in depth. Genomic comparisons among shallow, abyssal and hadal‐living species identified idiosyncratic and convergent genetic alterations underlying the extraordinary adaptations of deep‐sea species including light perception, circadian regulation, hydrostatic pressure and hunger tolerance. The deep‐sea fishes (Coryphaenoides Sp. and Pseudoliparis swirei) venturing into various ocean depths independently have undergone convergent amino acid substitutions in multiple proteins such as rhodopsin 1, pancreatic and duodenal homeobox 1 and melanocortin 4 receptor which are known or verified in zebrafish to be related with vision adaptation and energy expenditure. Convergent evolution events were also identified in heat shock protein 90 beta family member 1 and valosin‐containing protein genes known to be related to hydrostatic pressure adaptation specifically in fishes found around the hadal range. The uncovering of the molecular convergence among the deep‐sea species shed new light on the common genetic innovations required for deep‐sea adaptation by the fishes.

doi: 10.1111/1755-0998.13994pmid: N/A