Molecular Ecology最新文献_第8页

Delimiting Species—Prospects and Challenges for DNA Barcoding

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-02-06 DOI: 10.1111/mec.17677

Brent C. Emerson

{"title":"Delimiting Species—Prospects and Challenges for DNA Barcoding","authors":"Brent C. Emerson","doi":"10.1111/mec.17677","DOIUrl":"10.1111/mec.17677","url":null,"abstract":"Discovering, describing and cataloguing global species diversity remains a fundamental challenge both for biodiversity research and for the management and conservation of biodiversity. Among animals, the challenge is particularly acute within the arthropods, which comprise approximately 85% of all described animals, with approximately 1 million described species. The true number of arthropod species is estimated to be in excess of 10 million species. This estimate is likely to be revised upward in the light of global DNA barcode sequencing initiatives that are cataloguing unprecedented levels of cryptic or overlooked diversity. The scale of diversity that is being recovered with barcode sequencing places further strain on a taxonomic system confronted by ever-limited global taxonomic capacity to verify and describe new species. It is predicted that the number of novel operational taxonomic units delimited by barcode sequencing is likely to eclipse the number of species described by Linnean taxonomy by as early as 2029. Unless addressed, this may see an increasing proportion of arthropod species falling outside of protective legislative frameworks as a consequence of their lack of formal description. Confronted with this challenge, there is increasing, but controversial, acceptance of species delimitation and species description based on barcode sequence clustering thresholds. In response to the evolving controversy surrounding this issue, it is both timely and important to identify and clarify prospects and challenges for DNA barcoding, with a specific focus on species delimitation to address important shortfalls and impediments in biodiversity research.","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 5","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17677","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143253970","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomes of Galápagos Mockingbirds Reveal the Impact of Island Size and Past Demography on Inbreeding and Genetic Load in Contemporary Populations

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-02-06 DOI: 10.1111/mec.17665

Jakub Vlček, Sebastian Espinoza-Ulloa, Sarah A. Cowles, Luis Ortiz-Catedral, Cathy Coutu, Jaime A. Chaves, Jose Andrés, Jan Štefka

{"title":"Genomes of Galápagos Mockingbirds Reveal the Impact of Island Size and Past Demography on Inbreeding and Genetic Load in Contemporary Populations","authors":"Jakub Vlček, Sebastian Espinoza-Ulloa, Sarah A. Cowles, Luis Ortiz-Catedral, Cathy Coutu, Jaime A. Chaves, Jose Andrés, Jan Štefka","doi":"10.1111/mec.17665","DOIUrl":"10.1111/mec.17665","url":null,"abstract":"Restricted range size brings about noteworthy genetic consequences that may affect the viability of a population and eventually its extinction. Particularly, the question if an increase in inbreeding can avert the accumulation of genetic load via purging is hotly debated in the conservation genetic field. Insular populations with limited range sizes represent an ideal setup for relating range size to these genetic factors. Leveraging a set of eight differently sized populations of Galápagos mockingbirds (Mimus), we investigated how island size shaped effective population size (Ne), inbreeding and genetic load. We assembled a genome of M. melanotis and genotyped three individuals per population by whole-genome resequencing. Demographic inference showed that the Ne of most populations remained high after the colonisation of the archipelago 1–2 Mya. Ne decline in M. parvulus happened only 10–20 Kya, whereas the critically endangered M. trifasciatus showed a longer history of reduced Ne. Despite these historical fluctuations, the current island size determines Ne in a linear fashion. In contrast, significant inbreeding coefficients, derived from runs of homozygosity, were identified only in the four smallest populations. The index of additive genetic load suggested purging in M. parvulus, where the smallest populations showed the lowest load. By contrast, M. trifasciatus carried the highest genetic load, possibly due to a recent rapid bottleneck. Overall, our study demonstrates a complex effect of demography on inbreeding and genetic load, providing implications in conservation genetics in general and in a conservation project of M. trifasciatus in particular.","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 5","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17665","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143253973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Macroalgal Biofilm Harbours a Wide Diversity of Parasitic Protists With Distinct Temporal Dynamics

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-02-05 DOI: 10.1111/mec.17666

Elisabet Alacid, Albert Reñé, Natàlia Timoneda, Esther Garcés

{"title":"Macroalgal Biofilm Harbours a Wide Diversity of Parasitic Protists With Distinct Temporal Dynamics","authors":"Elisabet Alacid, Albert Reñé, Natàlia Timoneda, Esther Garcés","doi":"10.1111/mec.17666","DOIUrl":"10.1111/mec.17666","url":null,"abstract":"<div>\u0000 \u0000 Marine macroalgae surfaces create a nutrient-rich environment that promotes the formation of epiphyte biofilms. Biofilms are complex systems that facilitate ecological interactions within the community, yet parasitism remains largely unexplored. This study describes the diversity and temporal dynamics of the microeukaryotic community in the biofilm of Mediterranean macroalgae during summer, focusing on parasitic groups. Protist diversity was assessed using metabarcoding sequencing of the V4 region of the 18S rDNA gene using primers biased against metazoans. The macroalgal biofilm exhibited dynamic shifts in the microeukaryotic community structure associated to three phases of biofilm formation. Each phase was characterised by the dominance of specific eukaryotic and parasitic groups with clear successions between them. Our study revealed a high diversity of parasitic protists from different lineages in the macroalgal biofilm. These parasites can infect a wide variety of hosts, including the basibiont, species within the biofilm (micro- and macrocolonizers), nearby marine hosts and terrestrial organisms. The highest diversity and abundance of parasites were found in the mature phase of the biofilm, where the complexity and stability of the system seem to favour parasitism. The parasite assemblage was dominated by Apicomplexa, with many corresponding to unknown diversity, demonstrating that biofilms are a hotspot of unknown parasitic interactions. These parasites could potentially affect the dynamics of these communities and facilitate ecological interactions between the biofilm and surrounding organisms, suggesting that parasitism play a key, but still unexplored role, in shaping complex marine biofilms network.\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 5","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143187514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Damsels in Disguise: Development of Ultraviolet Sensitivity and Colour Patterns in Damselfishes (Pomacentridae)

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-02-05 DOI: 10.1111/mec.17680

Valerio Tettamanti, N. Justin Marshall, Karen L. Cheney, Fabio Cortesi

{"title":"Damsels in Disguise: Development of Ultraviolet Sensitivity and Colour Patterns in Damselfishes (Pomacentridae)","authors":"Valerio Tettamanti, N. Justin Marshall, Karen L. Cheney, Fabio Cortesi","doi":"10.1111/mec.17680","DOIUrl":"10.1111/mec.17680","url":null,"abstract":"Damselfishes (Pomacentridae) are widespread and highly abundant on tropical coral reefs. They exhibit diverse body colouration within and between the ~250 species and across ontogenetic stages. In addition to human-visible colours (i.e., 400–700 nm), most adult damselfishes reflect ultraviolet (UV, 300–400 nm) colour patches. UV sensitivity and UV colour signals are essential for feeding and form the basis for a secret communication channel invisible to the many UV-blind predatory fish on the reef; however, how these traits develop across ontogenetic stages and their distribution across the damselfish family is poorly characterised. Here, we used UV photography, phylogenetic reconstructions of opsin genes, and differential gene expression analysis (DGE) of retinal samples to investigate the development of UV vision and colour patterns in three ontogenetic stages (pre-settlement larval, juvenile, and adult) of 11 damselfish species. Using DGE, we found similar gene expression between juveniles and adults, which strongly differed from larvae. All species and all stages expressed at least one UV-sensitive sws1 opsin gene. However, UV body colour patterns only started to appear at the juvenile stage. Moreover, Pomacentrus species displayed highly complex UV body patterns that were correlated with the expression of two sws1 copies. This could mean that some damselfishes can discriminate colours that change only in their UV component. We demonstrate dramatic shifts in both UV sensitivity and UV colouration across the development stages of damselfish while highlighting the importance of considering ontogeny when studying the coevolution of visual systems and colour signals.","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 6","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17680","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143187874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Worker Survival and Egg Production—But Not Transcriptional Activity—Respond to Queen Number in the Highly Polygynous, Invasive Ant Tapinoma magnum

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-02-04 DOI: 10.1111/mec.17679

Anna Lenhart, Megha Majoe, Sibel Selvi, Thomas J. Colgan, Romain Libbrecht, Susanne Foitzik

{"title":"Worker Survival and Egg Production—But Not Transcriptional Activity—Respond to Queen Number in the Highly Polygynous, Invasive Ant Tapinoma magnum","authors":"Anna Lenhart, Megha Majoe, Sibel Selvi, Thomas J. Colgan, Romain Libbrecht, Susanne Foitzik","doi":"10.1111/mec.17679","DOIUrl":"10.1111/mec.17679","url":null,"abstract":"In social animals, reproductive activity and ageing are influenced by group composition. In monogynous (single-queen) insect societies, queen presence affects worker fecundity and longevity, but less is known about worker responses to queen number variation in polygynous (multi-queen) species or how queens age in these systems. We created queenless, one-queen and two-queen colonies of the invasive, polygynous ant Tapinoma magnum to examine the effect of queen number on worker survival, ovary and oocyte development, oxidative stress resistance and fat body gene expression. We also compared the fecundity and brain and fat body transcriptomes between young and old queens. Queenless workers experienced the highest mortality, contrasting with monogynous species, where queen removal typically extends lifespan. Workers lived longer and had more developing oocytes in their ovaries in single-queen than in two-queen colonies. Queen number did not directly affect oxidative stress resistance or fat body gene expression, though its effect on the latter differed between inside and outside workers. Furthermore, inside—likely younger—workers produced more oocytes, showed higher oxidative stress resistance and upregulated antioxidant genes compared to outside—likely older—workers. Minimal shifts in fecundity and gene expression of differently aged queens indicated their physiological stability. Our research highlights distinct caste- and tissue-specific responses to varying queen numbers in workers of a highly polygynous species.","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 6","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17679","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143121876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Impacts of Body Colour, Symbionts and Genomic Regions on the Pea Aphid Wing Plasticity Variation

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-02-04 DOI: 10.1111/mec.17660

Lauren E. Gregory, Rose M. H. Driscoll, Benjamin J. Parker, Jennifer A. Brisson

{"title":"Impacts of Body Colour, Symbionts and Genomic Regions on the Pea Aphid Wing Plasticity Variation","authors":"Lauren E. Gregory, Rose M. H. Driscoll, Benjamin J. Parker, Jennifer A. Brisson","doi":"10.1111/mec.17660","DOIUrl":"10.1111/mec.17660","url":null,"abstract":"<div>\u0000 \u0000 Adaptive phenotypic plasticity describes the phenomenon in which a single genotype can produce a variety of phenotypes that match their environments. Like any trait, plasticity is a phenotype that can exhibit variation, but despite the ecological importance of plasticity variation, little is known about its genetic basis. Here we use the pea aphid to investigate the genetic basis of wing plasticity variation. Previous reports have suggested an ecological association between body coloration and wing plasticity strength in the pea aphid, so we tested the hypothesis that the body colour determination locus (tor) associated with wing plasticity variation. We discover that there is no relationship between body colour and wing plasticity in natural populations or in a genetic mapping population. We also localise the tor locus to the third autosome, whereas it was previously thought to be on the first autosome, a finding that will be important for future studies of the locus. We find that the presence of the bacterial symbiont Regiella is associated with higher levels of wing plasticity. Genome-wide association analysis of wing plasticity variation did not reveal an impact of the tor locus, consistent with independence of body colour and wing plasticity. This analysis implicated one possible candidate gene—a Hox gene, abdominal-A—underlying wing plasticity variation, although SNPs do not reach the level of genome-wide significance and therefore will require further study. Our study highlights that plasticity variation is complex, impacted by a bacterial symbiont and genetic variation, but not influenced by body colour.\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 5","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143187875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Footprints of Human Migration in the Population Structure of Wild Baker's Yeast.

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-02-04 DOI: 10.1111/mec.17669

Jacqueline J Peña, Eduardo F C Scopel, Audrey K Ward, Douda Bensasson

{"title":"Footprints of Human Migration in the Population Structure of Wild Baker's Yeast.","authors":"Jacqueline J Peña, Eduardo F C Scopel, Audrey K Ward, Douda Bensasson","doi":"10.1111/mec.17669","DOIUrl":"https://doi.org/10.1111/mec.17669","url":null,"abstract":"Humans have a long history of fermenting food and beverages that led to domestication of the baker's yeast, Saccharomyces cerevisiae. Despite their tight companionship with humans, yeast species that are domesticated or pathogenic can also live on trees. Here we used over 300 genomes of S. cerevisiae from oaks and other trees to determine whether tree-associated populations are genetically distinct from domesticated lineages and estimate the timing of forest lineage divergence. We found populations on trees are highly structured within Europe, Japan, and North America. Approximate estimates of when forest lineages diverged out of Asia and into North America and Europe coincide with the end of the last ice age, the spread of agriculture, and the onset of fermentation by humans. It appears that migration from human-associated environments to trees is ongoing. Indeed, patterns of ancestry in the genomes of three recent migrants from the trees of North America to Europe could be explained by the human response to the Great French Wine Blight. Our results suggest that human-assisted migration affects forest populations, albeit rarely. Such migration events may even have shaped the global distribution of S. cerevisiae. Given the potential for lasting impacts due to yeast migration between human and natural environments, it seems important to understand the evolution of human commensals and pathogens in wild niches.","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17669"},"PeriodicalIF":4.5,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143121873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comparative Population Genomics Reveal the Determinants of Genome Erosion in Two Sympatric Neotropical Falcons

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-02-03 DOI: 10.1111/mec.17686

Nicolas Dussex

{"title":"Comparative Population Genomics Reveal the Determinants of Genome Erosion in Two Sympatric Neotropical Falcons","authors":"Nicolas Dussex","doi":"10.1111/mec.17686","DOIUrl":"10.1111/mec.17686","url":null,"abstract":"Studying genetic diversity in endangered species has become an important component of conservation science over the past decades. Thanks to recent developments in sequencing technologies and bioinformatics, genetic parameters of conservation relevance such as neutral and functional genome-wide variation are now routinely estimated. Since inbreeding and deleterious mutations represent significant threats to small and declining populations, assessing the dynamics of these parameters has received particular attention in many recent conservation genomics studies. In this issue of Molecular Ecology, Martin et al. analyse the genomes of two Neotropical falcon species to assess the impact of their contrasting population histories on genome-wide diversity. They show that the Orange-breasted falcon which has had a low long-term population size and has experienced recent population bottlenecks is more inbred but has relatively fewer deleterious variations compared to its sister taxon, the Bat falcon, which is characterised by a larger long-term population size. This study not only provides insights into the role of past demography on the dynamics of deleterious variation in two species with contrasting population histories but also highlights the increasing importance of comparative approaches in population and conservation genomics.","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 5","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17686","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evolution of Hybrid Inviability Associated With Chromosome Fusions.

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-02-03 DOI: 10.1111/mec.17672

Jesper Boman, Karin Näsvall, Roger Vila, Christer Wiklund, Niclas Backström

{"title":"Evolution of Hybrid Inviability Associated With Chromosome Fusions.","authors":"Jesper Boman, Karin Näsvall, Roger Vila, Christer Wiklund, Niclas Backström","doi":"10.1111/mec.17672","DOIUrl":"https://doi.org/10.1111/mec.17672","url":null,"abstract":"Chromosomal rearrangements, such as inversions, have received considerable attention in the speciation literature due to their hampering effects on recombination. Less is known about how other rearrangements, such as chromosome fissions and fusions, can affect the evolution of reproductive isolation. Here, we use crosses between populations of the wood white butterfly (Leptidea sinapis) with different karyotypes to identify genomic regions associated with hybrid inviability. We map hybrid inviability candidate loci by contrasting allele frequencies between F2 hybrids that survived until the adult stage with individuals of the same cohort that succumbed to hybrid incompatibilities. Hybrid inviability candidate regions have high genetic differentiation between parental populations, reduced recombination rates, and are enriched near chromosome fusions. By analysing sequencing coverage, we exclude aneuploidies as a direct link between hybrid inviability and chromosome fusions. Instead, our results point to an indirect relationship between hybrid inviability and chromosome fusions, possibly related to reduced recombination in fused chromosomes. Thus, we map postzygotic isolation to chromosomal rearrangements, providing crucial empirical evidence for the idea that chromosome number differences between taxa can contribute to speciation.","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17672"},"PeriodicalIF":4.5,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction to “Resistance, Resilience, and Functional Redundancy of Freshwater Bacterioplankton Communities Facing a Gradient of Agricultural Stressors in a Mesocosm Experiment”

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-02-03 DOI: 10.1111/mec.17673

引用次数: 0