Arid ecosystems, characterized by severe water scarcity, play a crucial role in preserving Earth’s biodiversity and resources. The Tarim Basin in Northwestern China, a typical arid region isolated by the Tianshan Mountains and expansive deserts, provides a special study area for investigating how plant response and adaptation to such environments. Tamarix hispida, a species well adapted to saline-alkaline and drought conditions, dominates in the saline-alkali lands of the Tarim Basin. This study aims to examine the genetic diversity and environmental adaptation of T. hispida in the Tarim Basin. Genomic SNPs for a total of 160 individuals from 17 populations were generated using dd-RAD sequencing approach. Population genetic structure and genetic diversity were analyzed by methods including ADMIXTURE, PCA, and phylogenetic tree. Environmental association analysis (EAA) was performed using LFMM and RDA analyses. The results revealed two major genetic lineages with geographical substitution patterns from west to east, indicating significant gene flow and hybridization. Environmental factors such as Precipitation Seasonality (bio15) and Topsoil Sand Fraction (T_SAND) significantly shaped allele frequencies, supporting the species’ genetic adaptability. Several genes associated with environmental adaptation were identified and annotated, highlighting physiological and metabolic processes crucial for survival in arid conditions. The study highlights the role of geographical isolation and environmental factors in shaping genetic structure and adaptive evolution. The identified adaptive genes related to stress tolerance emphasize the species’ resilience and highlight the importance of specific physiological and metabolic pathways.
{"title":"Population genetic diversity and environmental adaptation of Tamarix hispida in the Tarim Basin, arid Northwestern China","authors":"Haowen Tian, Hongxiang Zhang, Xiaojun Shi, Wenhui Ma, Jian Zhang","doi":"10.1038/s41437-024-00714-0","DOIUrl":"10.1038/s41437-024-00714-0","url":null,"abstract":"Arid ecosystems, characterized by severe water scarcity, play a crucial role in preserving Earth’s biodiversity and resources. The Tarim Basin in Northwestern China, a typical arid region isolated by the Tianshan Mountains and expansive deserts, provides a special study area for investigating how plant response and adaptation to such environments. Tamarix hispida, a species well adapted to saline-alkaline and drought conditions, dominates in the saline-alkali lands of the Tarim Basin. This study aims to examine the genetic diversity and environmental adaptation of T. hispida in the Tarim Basin. Genomic SNPs for a total of 160 individuals from 17 populations were generated using dd-RAD sequencing approach. Population genetic structure and genetic diversity were analyzed by methods including ADMIXTURE, PCA, and phylogenetic tree. Environmental association analysis (EAA) was performed using LFMM and RDA analyses. The results revealed two major genetic lineages with geographical substitution patterns from west to east, indicating significant gene flow and hybridization. Environmental factors such as Precipitation Seasonality (bio15) and Topsoil Sand Fraction (T_SAND) significantly shaped allele frequencies, supporting the species’ genetic adaptability. Several genes associated with environmental adaptation were identified and annotated, highlighting physiological and metabolic processes crucial for survival in arid conditions. The study highlights the role of geographical isolation and environmental factors in shaping genetic structure and adaptive evolution. The identified adaptive genes related to stress tolerance emphasize the species’ resilience and highlight the importance of specific physiological and metabolic pathways.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 5","pages":"298-307"},"PeriodicalIF":3.1,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141975597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-06DOI: 10.1038/s41437-024-00713-1
Sylvine Durand, Romain Pigeault, Isabelle Giraud, Anaïs Loisier, Nicolas Bech, Frédéric Grandjean, Thierry Rigaud, Jean Peccoud, Richard Cordaux
In the terrestrial isopod Armadillidium vulgare, many females produce progenies with female-biased sex ratios due to two feminizing sex ratio distorters (SRD): Wolbachia endosymbionts and a nuclear non-mendelian locus called the f element. To investigate the potential impact of these SRD on the evolution of host sex determination, we analyzed their temporal distribution in six A. vulgare populations sampled between 2003 and 2017, for a total of 29 time points. SRD distribution was heterogeneous among populations despite their close geographic locations, so that when one SRD was frequent in a population, the other SRD was rare. In contrast with spatial heterogeneity, our results overall did not reveal substantial temporal variability in SRD prevalence within populations, suggesting equilibria in SRD evolutionary dynamics may have been reached or nearly so. Temporal stability was also generally reflected in mitochondrial and nuclear variation. Nevertheless, in a population, a Wolbachia strain replacement coincided with changes in mitochondrial composition but no change in nuclear composition, thus constituting a typical example of mitochondrial sweep caused by endosymbiont rise in frequency. Rare incongruence between Wolbachia strains and mitochondrial haplotypes suggested the occurrence of intraspecific horizontal transmission, making it a biologically relevant parameter for Wolbachia evolutionary dynamics in A. vulgare. Overall, our results provide an empirical basis for future studies on SRD evolutionary dynamics in the context of multiple sex determination factors co-existing within a single species, to ultimately evaluate the impact of SRD on the evolution of host sex determination mechanisms and sex chromosomes.
{"title":"Temporal stability of sex ratio distorter prevalence in natural populations of the isopod Armadillidium vulgare","authors":"Sylvine Durand, Romain Pigeault, Isabelle Giraud, Anaïs Loisier, Nicolas Bech, Frédéric Grandjean, Thierry Rigaud, Jean Peccoud, Richard Cordaux","doi":"10.1038/s41437-024-00713-1","DOIUrl":"10.1038/s41437-024-00713-1","url":null,"abstract":"In the terrestrial isopod Armadillidium vulgare, many females produce progenies with female-biased sex ratios due to two feminizing sex ratio distorters (SRD): Wolbachia endosymbionts and a nuclear non-mendelian locus called the f element. To investigate the potential impact of these SRD on the evolution of host sex determination, we analyzed their temporal distribution in six A. vulgare populations sampled between 2003 and 2017, for a total of 29 time points. SRD distribution was heterogeneous among populations despite their close geographic locations, so that when one SRD was frequent in a population, the other SRD was rare. In contrast with spatial heterogeneity, our results overall did not reveal substantial temporal variability in SRD prevalence within populations, suggesting equilibria in SRD evolutionary dynamics may have been reached or nearly so. Temporal stability was also generally reflected in mitochondrial and nuclear variation. Nevertheless, in a population, a Wolbachia strain replacement coincided with changes in mitochondrial composition but no change in nuclear composition, thus constituting a typical example of mitochondrial sweep caused by endosymbiont rise in frequency. Rare incongruence between Wolbachia strains and mitochondrial haplotypes suggested the occurrence of intraspecific horizontal transmission, making it a biologically relevant parameter for Wolbachia evolutionary dynamics in A. vulgare. Overall, our results provide an empirical basis for future studies on SRD evolutionary dynamics in the context of multiple sex determination factors co-existing within a single species, to ultimately evaluate the impact of SRD on the evolution of host sex determination mechanisms and sex chromosomes.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 5","pages":"287-297"},"PeriodicalIF":3.1,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-02DOI: 10.1038/s41437-024-00711-3
Hui Zhen Tan, Phoebe Scherer, Katarina C. Stuart, Sarah Bailey, Kate D. Lee, Patricia Brekke, John G. Ewen, Annabel Whibley, Anna W. Santure
Recombination, the process of DNA exchange between homologous chromosomes during meiosis, plays a major role in genomic diversity and evolutionary change. Variation in recombination rate is widespread despite recombination often being essential for progression of meiosis. One such variation is heterochiasmy, where recombination rates differ between sexes. Heterochiasmy has been observed across broad taxonomic groups, yet it remains an evolutionary enigma. We used Lep-MAP3, a pedigree-based software that is efficient in handling large datasets, to generate linkage maps for the hihi or stitchbird (Notiomystis cincta), utilising information from >36 K SNPs and 36 families. We constructed 29 linkage maps, including for the previously unscaffolded Z chromosome. The hihi is an endangered passerine endemic to Aotearoa New Zealand that is sexually dimorphic and exhibits high levels of sexual conflict, including sperm competition. Patterns in recombination in the hihi are consistent with those in other birds, including higher recombination rates in micro-chromosomes. Heterochiasmy in the hihi is male-biased, in line with predictions of the Haldane-Huxley rule, with the male linkage map being 15% longer. Micro-chromosomes exhibit heterochiasmy to a greater extent, contrary to that reported in other birds. At the intra-chromosomal level, heterochiasmy is higher nearer to chromosome ends and in gene-rich regions. Regions of extreme heterochiasmy are enriched for genes implicated in cell structure. This study adds an important contribution in assessing evolutionary theories of heterochiasmy and provides a framework for future studies investigating fine-scale heterochiasmy.
重组是减数分裂过程中同源染色体之间的 DNA 交换过程，在基因组多样性和进化变化中发挥着重要作用。尽管重组通常对减数分裂的进展至关重要，但重组率的变异却很普遍。其中一种变异是 "异性畸变"（heterochiasmy），即不同性别之间的重组率不同。在广泛的分类群中都观察到了异性重组，但它仍然是一个进化之谜。我们利用基于谱系的软件 Lep-MAP3（该软件可高效处理大型数据集），利用来自超过 36 K SNPs 和 36 个科的信息，生成了绣眼鸟（Notiomystis cincta）的连接图。我们构建了 29 个连接图，其中包括以前没有褶皱的 Z 染色体。喜鹊是新西兰奥特亚罗瓦特有的一种濒临灭绝的雀形目鸟类，具有性二型，并表现出高度的性冲突，包括精子竞争。喜鹊的重组模式与其他鸟类一致，包括微染色体的重组率较高。喜鹊的异花授粉是雄性偏向的，这与霍尔丹-赫胥黎规则的预测一致，雄性的连接图长15%。微染色体在更大程度上表现出异型性，这与其他鸟类的报道相反。在染色体内水平上，靠近染色体末端和基因丰富区域的异染色性更高。与细胞结构有关的基因富集在极端杂合的区域。这项研究为评估异染色体进化理论做出了重要贡献，并为今后研究精细异染色体提供了一个框架。
{"title":"A high-density linkage map reveals broad- and fine-scale sex differences in recombination in the hihi (stitchbird; Notiomystis cincta)","authors":"Hui Zhen Tan, Phoebe Scherer, Katarina C. Stuart, Sarah Bailey, Kate D. Lee, Patricia Brekke, John G. Ewen, Annabel Whibley, Anna W. Santure","doi":"10.1038/s41437-024-00711-3","DOIUrl":"10.1038/s41437-024-00711-3","url":null,"abstract":"Recombination, the process of DNA exchange between homologous chromosomes during meiosis, plays a major role in genomic diversity and evolutionary change. Variation in recombination rate is widespread despite recombination often being essential for progression of meiosis. One such variation is heterochiasmy, where recombination rates differ between sexes. Heterochiasmy has been observed across broad taxonomic groups, yet it remains an evolutionary enigma. We used Lep-MAP3, a pedigree-based software that is efficient in handling large datasets, to generate linkage maps for the hihi or stitchbird (Notiomystis cincta), utilising information from >36 K SNPs and 36 families. We constructed 29 linkage maps, including for the previously unscaffolded Z chromosome. The hihi is an endangered passerine endemic to Aotearoa New Zealand that is sexually dimorphic and exhibits high levels of sexual conflict, including sperm competition. Patterns in recombination in the hihi are consistent with those in other birds, including higher recombination rates in micro-chromosomes. Heterochiasmy in the hihi is male-biased, in line with predictions of the Haldane-Huxley rule, with the male linkage map being 15% longer. Micro-chromosomes exhibit heterochiasmy to a greater extent, contrary to that reported in other birds. At the intra-chromosomal level, heterochiasmy is higher nearer to chromosome ends and in gene-rich regions. Regions of extreme heterochiasmy are enriched for genes implicated in cell structure. This study adds an important contribution in assessing evolutionary theories of heterochiasmy and provides a framework for future studies investigating fine-scale heterochiasmy.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 4","pages":"262-275"},"PeriodicalIF":3.1,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00711-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141878593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
How frequently hybridisation and gene flow occur in the contact zones of diverging taxa is important for understanding the speciation process. Stigmaeopsis sabelisi and Stigmaeopsis miscanthi high-aggression form (hereafter, S. miscanthi HG) are haplodiploid, social spider mites that infest the Chinese silver grass, Miscanthus sinensis. These two species are closely related and parapatrically distributed in Japan. In mountainous areas, S. sabelisi and S. miscanthi HG are often found in the highlands and lowlands, respectively, suggesting that they are in contact at intermediate altitudes. It is estimated that they diverged from their common ancestors distributed in subtropical regions (south of Japan) during the last glacial period, expanded their distribution into the Japanese Archipelago, and came to have such a parapatric distribution (secondary contact). As their reproductive isolation is strong but incomplete, hybridisation and genetic introgression are expected at their distributional boundaries. In this study, we investigated their spatial distribution patterns along the elevation on Mt. Amagi using male morphological differences, and investigated their hybridisation status using single-nucleotide polymorphisms by MIG-seq. We found their contact zone at altitudes of 150–430 m, suggesting that their contact zone is prevalent in the parapatric area, which is in line with a previous study. Interspecific mating was predicted based on the sex ratio in the contact zone. No obvious hybrids were found, but genetic introgression was detected although it was extremely low.
在不同类群的接触区发生杂交和基因流动的频率对于了解物种的演化过程非常重要。Stigmaeopsis sabelisi 和 Stigmaeopsis miscanthi highaggression form（以下简称 S. miscanthi HG）是侵扰中国银草的单倍体社会性蜘蛛螨。这两个物种亲缘关系很近，在日本同域分布。在山区，S. sabelisi 和 S. miscanthi HG 经常分别出现在高地和低地，这表明它们在中海拔地区有接触。据估计，在上一个冰川期，它们从分布在亚热带地区（日本南部）的共同祖先那里分化出来，扩展到日本列岛，并形成了这种同域分布（次生接触）。由于它们的生殖隔离很强，但并不完全，因此预计在它们的分布边界会发生杂交和基因导入。在本研究中，我们利用雄性的形态差异研究了它们在天木山沿海拔高度的空间分布模式，并通过 MIG-seq 利用单核苷酸多态性研究了它们的杂交状况。我们在海拔150-430米处发现了它们的接触区，表明它们的接触区普遍存在于准同域地区，这与之前的研究结果一致。根据接触区的性别比例预测了种间交配。虽然没有发现明显的杂交种，但发现了基因导入现象，尽管其程度极低。
{"title":"Secondary contact zone and genetic introgression in closely related haplodiploid social spider mites","authors":"Shota Konaka, Shun K. Hirota, Yukie Sato, Naoki Matsumoto, Yoshihisa Suyama, Yoshihiko Tsumura","doi":"10.1038/s41437-024-00708-y","DOIUrl":"10.1038/s41437-024-00708-y","url":null,"abstract":"How frequently hybridisation and gene flow occur in the contact zones of diverging taxa is important for understanding the speciation process. Stigmaeopsis sabelisi and Stigmaeopsis miscanthi high-aggression form (hereafter, S. miscanthi HG) are haplodiploid, social spider mites that infest the Chinese silver grass, Miscanthus sinensis. These two species are closely related and parapatrically distributed in Japan. In mountainous areas, S. sabelisi and S. miscanthi HG are often found in the highlands and lowlands, respectively, suggesting that they are in contact at intermediate altitudes. It is estimated that they diverged from their common ancestors distributed in subtropical regions (south of Japan) during the last glacial period, expanded their distribution into the Japanese Archipelago, and came to have such a parapatric distribution (secondary contact). As their reproductive isolation is strong but incomplete, hybridisation and genetic introgression are expected at their distributional boundaries. In this study, we investigated their spatial distribution patterns along the elevation on Mt. Amagi using male morphological differences, and investigated their hybridisation status using single-nucleotide polymorphisms by MIG-seq. We found their contact zone at altitudes of 150–430 m, suggesting that their contact zone is prevalent in the parapatric area, which is in line with a previous study. Interspecific mating was predicted based on the sex ratio in the contact zone. No obvious hybrids were found, but genetic introgression was detected although it was extremely low.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 4","pages":"227-237"},"PeriodicalIF":3.1,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141874669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-02DOI: 10.1038/s41437-024-00712-2
Ivan Jakovlić, Tong Ye, Hong Zou, Fengyue Zhu, Yuying Shi, Yiwen Ma, Gui-Tang Wang, Wen-Xiang Li, Dong Zhang
Studies of forces driving interlineage variability in the evolutionary rates (both sequence and architecture) of mitochondrial genomes often produce contradictory results. Flatworms (Platyhelminthes) exhibit the fastest-evolving mitogenomic sequences among all bilaterian phyla. To test the effects of multiple factors previously associated with different aspects of mitogenomic evolution, we used mitogenomes of 223 flatworm species, phylogenetic multilevel regression models, and causal inference. Thermic host environment (endothermic vs. ectothermic) had nonsignificant impacts on both sequence evolution and mitogenomic size. Mitogenomic gene order rearrangements (GORR) were mostly positively correlated with mitogenomic size (R2 ≈ 20–30%). Longevity was not (negatively) correlated with sequence evolution in flatworms. The predominantly free-living “turbellaria” exhibited much shorter branches and faster-evolving mitogenomic architecture than parasitic Neodermata. As a result, “parasitism” had a strong explanatory power on the branch length variability (>90%), and there was a negative correlation between GORR and branch length. However, the stem branch of Neodermata comprised 63.6% of the total average branch length. This evolutionary period was also marked by a high rate of gene order rearrangements in the ancestral Neodermata. We discuss how this period of rapid evolution deep in the evolutionary history may have decoupled sequence evolution rates from longevity and GORR, and overestimated the explanatory power of “parasitism”. This study shows that impacts of variables often vary across lineages, and stresses the importance accounting for the episodic nature of evolutionary patterns in studies of mitogenomic evolution.
{"title":"Drivers of interlineage variability in mitogenomic evolutionary rates in Platyhelminthes","authors":"Ivan Jakovlić, Tong Ye, Hong Zou, Fengyue Zhu, Yuying Shi, Yiwen Ma, Gui-Tang Wang, Wen-Xiang Li, Dong Zhang","doi":"10.1038/s41437-024-00712-2","DOIUrl":"10.1038/s41437-024-00712-2","url":null,"abstract":"Studies of forces driving interlineage variability in the evolutionary rates (both sequence and architecture) of mitochondrial genomes often produce contradictory results. Flatworms (Platyhelminthes) exhibit the fastest-evolving mitogenomic sequences among all bilaterian phyla. To test the effects of multiple factors previously associated with different aspects of mitogenomic evolution, we used mitogenomes of 223 flatworm species, phylogenetic multilevel regression models, and causal inference. Thermic host environment (endothermic vs. ectothermic) had nonsignificant impacts on both sequence evolution and mitogenomic size. Mitogenomic gene order rearrangements (GORR) were mostly positively correlated with mitogenomic size (R2 ≈ 20–30%). Longevity was not (negatively) correlated with sequence evolution in flatworms. The predominantly free-living “turbellaria” exhibited much shorter branches and faster-evolving mitogenomic architecture than parasitic Neodermata. As a result, “parasitism” had a strong explanatory power on the branch length variability (>90%), and there was a negative correlation between GORR and branch length. However, the stem branch of Neodermata comprised 63.6% of the total average branch length. This evolutionary period was also marked by a high rate of gene order rearrangements in the ancestral Neodermata. We discuss how this period of rapid evolution deep in the evolutionary history may have decoupled sequence evolution rates from longevity and GORR, and overestimated the explanatory power of “parasitism”. This study shows that impacts of variables often vary across lineages, and stresses the importance accounting for the episodic nature of evolutionary patterns in studies of mitogenomic evolution.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 4","pages":"276-286"},"PeriodicalIF":3.1,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00712-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141878594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-01DOI: 10.1038/s41437-024-00709-x
Dieu - Merci Assumani Angbonda, Crispin M. Ilunga-Mulala, Nils Bourland, Hans Beeckman, Faustin Boyemba, Hulda Hatakiwe, Jean Pierre Ngongo, Olivier J. Hardy
Selfing or mating between related individuals can lead to inbreeding depression (ID), which can influence the survival, growth and evolution of populations of tree species. As selective logging involves a decrease in the density of congeneric partners, it could lead to increasing biparental inbreeding or self-fertilization, exposing the population to higher ID. We assessed the influence of inbreeding on the growth of a commercial timber species, Pericopsis elata (Fabaceae), which produced about 54% of self-fertilized seedlings in a natural population of the Congo basin. We followed the survival and growth of 540 plants raised in a plantation along a gradient of plant density (0.07–15.9 plants per m2). Parentage analysis allowed us distinguishing selfed and outcrossed seedlings. The annual growth was higher for outcrossed than selfed plants, on average by 10.8% for diameter and 12.9% for height growth. Based on the difference in above ground biomass between selfed and outcrossed seedlings after 41 months, we estimated the level of ID at δ = 0.33, while a lifetime estimate of ID based on the proportions of selfed plants at seedling and adult stages led to δ = 0.7. The level of ID on growth rate did not change significantly with age but tended to vanish under high competition. Pericopsis elata is a particularly interesting model because inbreeding depression is partial, with about 26% of reproducing adults resulting from selfing, contrary to most tropical tree species where selfed individuals usually die before reaching adulthood. Hence, the risks of ID must be considered in the management and conservation of the species.
{"title":"Inbreeding depression affects the growth of seedlings of an African timber species with a mixed mating reproductive system, Pericopsis elata (Harms) Meeuwen","authors":"Dieu - Merci Assumani Angbonda, Crispin M. Ilunga-Mulala, Nils Bourland, Hans Beeckman, Faustin Boyemba, Hulda Hatakiwe, Jean Pierre Ngongo, Olivier J. Hardy","doi":"10.1038/s41437-024-00709-x","DOIUrl":"10.1038/s41437-024-00709-x","url":null,"abstract":"Selfing or mating between related individuals can lead to inbreeding depression (ID), which can influence the survival, growth and evolution of populations of tree species. As selective logging involves a decrease in the density of congeneric partners, it could lead to increasing biparental inbreeding or self-fertilization, exposing the population to higher ID. We assessed the influence of inbreeding on the growth of a commercial timber species, Pericopsis elata (Fabaceae), which produced about 54% of self-fertilized seedlings in a natural population of the Congo basin. We followed the survival and growth of 540 plants raised in a plantation along a gradient of plant density (0.07–15.9 plants per m2). Parentage analysis allowed us distinguishing selfed and outcrossed seedlings. The annual growth was higher for outcrossed than selfed plants, on average by 10.8% for diameter and 12.9% for height growth. Based on the difference in above ground biomass between selfed and outcrossed seedlings after 41 months, we estimated the level of ID at δ = 0.33, while a lifetime estimate of ID based on the proportions of selfed plants at seedling and adult stages led to δ = 0.7. The level of ID on growth rate did not change significantly with age but tended to vanish under high competition. Pericopsis elata is a particularly interesting model because inbreeding depression is partial, with about 26% of reproducing adults resulting from selfing, contrary to most tropical tree species where selfed individuals usually die before reaching adulthood. Hence, the risks of ID must be considered in the management and conservation of the species.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 4","pages":"238-248"},"PeriodicalIF":3.1,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00709-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141870882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-29DOI: 10.1038/s41437-024-00699-w
Marc-Alexander Gose, Emily Humble, Andrew Brownlow, Dave Wall, Emer Rogan, Guðjón Már Sigurðsson, Jeremy J. Kiszka, Charlotte Bie Thøstesen, Lonneke L. IJsseldijk, Mariel ten Doeschate, Nicholas J. Davison, Nils Øien, Rob Deaville, Ursula Siebert, Rob Ogden
{"title":"Correction: Population genomics of the white-beaked dolphin (Lagenorhynchus albirostris): implications for conservation amid climate-driven range shifts","authors":"Marc-Alexander Gose, Emily Humble, Andrew Brownlow, Dave Wall, Emer Rogan, Guðjón Már Sigurðsson, Jeremy J. Kiszka, Charlotte Bie Thøstesen, Lonneke L. IJsseldijk, Mariel ten Doeschate, Nicholas J. Davison, Nils Øien, Rob Deaville, Ursula Siebert, Rob Ogden","doi":"10.1038/s41437-024-00699-w","DOIUrl":"10.1038/s41437-024-00699-w","url":null,"abstract":"","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 3","pages":"206-206"},"PeriodicalIF":3.1,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00699-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141792333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-24DOI: 10.1038/s41437-024-00706-0
Elizabeth Tapanes, Diana J. Rennison
Pigmentation is an excellent trait to examine patterns of evolutionary change because it is often under natural selection. Benthic and limnetic threespine stickleback (Gasterosteus aculeatus) exhibit distinct pigmentation phenotypes, likely an adaptation to occupation of divergent niches. The genetic architecture of pigmentation in vertebrates appears to be complex. Prior QTL mapping of threespine stickleback pigmentation phenotypes has identified several candidate loci. However—relative to other morphological phenotypes (e.g., spines or lateral plates)—the genetic architecture of threespine stickleback pigmentation remains understudied. Here, we performed QTL mapping for two melanic pigmentation traits (melanophore density and lateral barring) using benthic-limnetic F2 crosses. The two traits mapped to different chromosomes, suggesting a distinct genetic basis. The resulting QTLs were additive, but explained a relatively small fraction of the total variance (~6%). QTLs maps differed by F1 family, suggesting variation in genetic architecture or ability to detect loci of small effect. Functional analysis identified enriched pathways for candidate loci. Several of the resulting candidate loci for pigmentation, including three loci in enriched pathways (bco1, sulf1, and tyms) have been previously indicated to affect pigmentation in other vertebrates. These findings add to a growing body of evidence suggesting pigmentation is often polygenic.
{"title":"The genetic basis of divergent melanic pigmentation in benthic and limnetic threespine stickleback","authors":"Elizabeth Tapanes, Diana J. Rennison","doi":"10.1038/s41437-024-00706-0","DOIUrl":"10.1038/s41437-024-00706-0","url":null,"abstract":"Pigmentation is an excellent trait to examine patterns of evolutionary change because it is often under natural selection. Benthic and limnetic threespine stickleback (Gasterosteus aculeatus) exhibit distinct pigmentation phenotypes, likely an adaptation to occupation of divergent niches. The genetic architecture of pigmentation in vertebrates appears to be complex. Prior QTL mapping of threespine stickleback pigmentation phenotypes has identified several candidate loci. However—relative to other morphological phenotypes (e.g., spines or lateral plates)—the genetic architecture of threespine stickleback pigmentation remains understudied. Here, we performed QTL mapping for two melanic pigmentation traits (melanophore density and lateral barring) using benthic-limnetic F2 crosses. The two traits mapped to different chromosomes, suggesting a distinct genetic basis. The resulting QTLs were additive, but explained a relatively small fraction of the total variance (~6%). QTLs maps differed by F1 family, suggesting variation in genetic architecture or ability to detect loci of small effect. Functional analysis identified enriched pathways for candidate loci. Several of the resulting candidate loci for pigmentation, including three loci in enriched pathways (bco1, sulf1, and tyms) have been previously indicated to affect pigmentation in other vertebrates. These findings add to a growing body of evidence suggesting pigmentation is often polygenic.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 4","pages":"207-215"},"PeriodicalIF":3.1,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00706-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141758404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-22DOI: 10.1038/s41437-024-00707-z
Fernando H. S. Souza, Manolo F. Perez, Pedro H. N. Ferreira, Luiz A. C. Bertollo, Tariq Ezaz, Deborah Charlesworth, Marcelo B. Cioffi
Neotropical fishes exhibit remarkable karyotype diversity, whose evolution is poorly understood. Here, we studied genetic differences in 60 individuals, from 11 localities of one species, the wolf fish Hoplias malabaricus, from populations that include six different “karyomorphs”. These differ in Y-X chromosome differentiation, and, in several cases, by fusions with autosomes that have resulted in multiple sex chromosomes. Other differences are also observed in diploid chromosome numbers and morphologies. In an attempt to start understanding how this diversity was generated, we analyzed within- and between-population differences in a genome-wide sequence data set. We detect clear genotype differences between karyomorphs. Even in sympatry, samples with different karyomorphs differ more in sequence than samples from allopatric populations of the same karyomorph, suggesting that they represent populations that are to some degree reproductively isolated. However, sequence divergence between populations with different karyomorphs is remarkably low, suggesting that chromosome rearrangements may have evolved during a brief evolutionary time. We suggest that the karyotypic differences probably evolved in allopatry, in small populations that would have allowed rapid fixation of rearrangements, and that they became sympatric after their differentiation. Further studies are needed to test whether the karyotype differences contribute to reproductive isolation detected between some H. malabaricus karyomorphs.
{"title":"Multiple karyotype differences between populations of the Hoplias malabaricus (Teleostei; Characiformes), a species complex in the gray area of the speciation process","authors":"Fernando H. S. Souza, Manolo F. Perez, Pedro H. N. Ferreira, Luiz A. C. Bertollo, Tariq Ezaz, Deborah Charlesworth, Marcelo B. Cioffi","doi":"10.1038/s41437-024-00707-z","DOIUrl":"10.1038/s41437-024-00707-z","url":null,"abstract":"Neotropical fishes exhibit remarkable karyotype diversity, whose evolution is poorly understood. Here, we studied genetic differences in 60 individuals, from 11 localities of one species, the wolf fish Hoplias malabaricus, from populations that include six different “karyomorphs”. These differ in Y-X chromosome differentiation, and, in several cases, by fusions with autosomes that have resulted in multiple sex chromosomes. Other differences are also observed in diploid chromosome numbers and morphologies. In an attempt to start understanding how this diversity was generated, we analyzed within- and between-population differences in a genome-wide sequence data set. We detect clear genotype differences between karyomorphs. Even in sympatry, samples with different karyomorphs differ more in sequence than samples from allopatric populations of the same karyomorph, suggesting that they represent populations that are to some degree reproductively isolated. However, sequence divergence between populations with different karyomorphs is remarkably low, suggesting that chromosome rearrangements may have evolved during a brief evolutionary time. We suggest that the karyotypic differences probably evolved in allopatry, in small populations that would have allowed rapid fixation of rearrangements, and that they became sympatric after their differentiation. Further studies are needed to test whether the karyotype differences contribute to reproductive isolation detected between some H. malabaricus karyomorphs.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 4","pages":"216-226"},"PeriodicalIF":3.1,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141748029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-12DOI: 10.1038/s41437-024-00703-3
Cleiton A. Wartha, Aaron J. Lorenz
Parental selection is perhaps the most critical decision a breeder makes, establishing the foundation of the entire program for years to come. Cross selection based on predicted mean and genetic variance can be further expanded to multiple-trait improvement by predicting the genetic correlation ( $${r}_{G}$$ ) between pairs of traits. Our objective was to empirically assess the ability to predict the family mean, genetic variance, superior progeny mean and genetic correlation through genomic prediction in a soybean population. Data made available through the Soybean Nested Association Mapping project included phenotypic data on seven traits (days to maturity, lodging, oil, plant height, protein, seed size, and seed yield) for 39 families. Training population composition followed a leave-one-family-out cross-validation scheme, with the validation family genetic parameters predicted using the remaining families as the training set. The predictive abilities for family mean and superior progeny mean were significant for all traits while predictive ability of genetic variance was significant for four traits. We were able to validate significant predictive abilities of $${r}_{G}$$ for 18 out of 21 (86%) pairwise trait combinations (P < 0.05). The findings from this study support the use of genome-wide marker effects for predicting $${r}_{G}$$ in soybean biparental crosses. If successfully implemented in breeding programs, this methodology could help to increase the rate of genetic gain for multiple correlated traits.
亲本选择可能是育种者做出的最关键的决定，它奠定了整个育种计划未来几年的基础。基于预测平均值和遗传变异的杂交选育可通过预测成对性状之间的遗传相关性（r G）进一步扩展到多性状改良。我们的目标是通过大豆群体的基因组预测，对预测家系平均值、遗传变异、优良后代平均值和遗传相关性的能力进行实证评估。大豆嵌套关联图谱项目提供的数据包括 39 个家系的七个性状（成熟天数、结实率、油分、株高、蛋白质、种子大小和种子产量）的表型数据。训练群体的组成采用了 "留一族不留 "的交叉验证方案，以其余族为训练集预测验证族的遗传参数。对所有性状而言，家系平均值和优系后代平均值的预测能力都是显著的，而对四个性状而言，遗传变异的预测能力是显著的。在大豆双亲杂交的 21 个配对性状组合（P r G）中，我们验证了 18 个（86%）配对性状组合的 r G 具有显著的预测能力。如果能在育种计划中成功实施，该方法将有助于提高多个相关性状的遗传增益率。
{"title":"Genomic predictions of genetic variances and correlations among traits for breeding crosses in soybean","authors":"Cleiton A. Wartha, Aaron J. Lorenz","doi":"10.1038/s41437-024-00703-3","DOIUrl":"10.1038/s41437-024-00703-3","url":null,"abstract":"Parental selection is perhaps the most critical decision a breeder makes, establishing the foundation of the entire program for years to come. Cross selection based on predicted mean and genetic variance can be further expanded to multiple-trait improvement by predicting the genetic correlation ( $${r}_{G}$$ ) between pairs of traits. Our objective was to empirically assess the ability to predict the family mean, genetic variance, superior progeny mean and genetic correlation through genomic prediction in a soybean population. Data made available through the Soybean Nested Association Mapping project included phenotypic data on seven traits (days to maturity, lodging, oil, plant height, protein, seed size, and seed yield) for 39 families. Training population composition followed a leave-one-family-out cross-validation scheme, with the validation family genetic parameters predicted using the remaining families as the training set. The predictive abilities for family mean and superior progeny mean were significant for all traits while predictive ability of genetic variance was significant for four traits. We were able to validate significant predictive abilities of $${r}_{G}$$ for 18 out of 21 (86%) pairwise trait combinations (P < 0.05). The findings from this study support the use of genome-wide marker effects for predicting $${r}_{G}$$ in soybean biparental crosses. If successfully implemented in breeding programs, this methodology could help to increase the rate of genetic gain for multiple correlated traits.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 3","pages":"173-185"},"PeriodicalIF":3.1,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00703-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141599259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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