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Mitochondrial genome evolution(MGE) in flowering plants is quasi-intertwined-dynamic. MGE is driven via mutational pressures, translational selection, and functional constraints. However, unveiling the intra- and inter-genomic interplay governing evolutionary drives remains challenging. We investigate MGE-dynamic across twelve Gentianales species, revealing distinct codon usage patterns influenced by opposing evolutionary forces. While the first and second codon positions are highly conserved, the third codon positions show significant variability (27.7% – 45.8%), reflecting diverse selective pressures. Multi-dimensional analyses, including ENc-GC3s plots, neutrality plots, and PR2 bias, indicate that natural selection predominantly governs codon usage, outweighing mutational biases. Key findings include, non-significant correlations between GC12 and GC3 (R 2  ≤ 0.21), suggesting minimal mutational impact on genome composition; ENc-GC12 analysis showing codon optimization results from both selection and mutation; and PR2-plot analysis highlighting a preference for T- and G-ending codons, indicative of translational efficiency constraints. Gene-specific analyses of substitution rates ( dN , dS , and dN/dS ) uncover heterogeneous selective landscapes, with genes such as atp , ccm , nad , and rps exhibiting signatures of positive selection. Substantial mutually offsetting dynamics between T3s and C3s ( r = − 0.73), coupled with strong correlations between G3s and translational-efficiency indices (CAI: r  = 0.69; CBI: r  = 0.65), underscore that third-codon biases optimize translation. Evolutionary rates ( dS and dN/dS ) show positive correlations with GC3 content ( r  = 0.45 and r  = 0.33, respectively), indicating the influence of nucleotide composition on synonymous substitutions. Thus, these results reveal the interplay of the mutation–selection balance in non-recombining genomes and offer new perspectives on mitochondrial diversity in flowering plants.

Background The large and diverse Coffeeae alliance clade of subfamily Ixoroideae (Rubiaceae) consists of 10 tribes, > 90 genera, and > 2000 species. Previous molecular phylogenetics using limited numbers of markers were often unable to fully resolve the phylogenetic relationships at tribal and generic levels. Also, the structural variations of plastomes (PSVs) within the Coffeeae alliance tribes have been poorly investigated in previous studies. To fully understand the phylogenetic relationships and PSVs within the clade, highly reliable and sufficient sampling with superior next-generation analysis techniques is required. In this study, 71 plastomes (40 newly sequenced and assembled and the rest from the GenBank) were comparatively analyzed to decipher the PSVs and resolve the phylogenetic relationships of the Coffeeae alliance using four molecular data matrices. Results All plastomes are typically quadripartite with the size ranging from 153,055 to 155,908 bp and contained 111 unique genes. The inverted repeat (IR) regions experienced multiple contraction and expansion; five repeat types were detected but the most abundant was SSR. The size of the Coffeeae alliance clade plastomes and its elements are affected by the IR boundary shifts and the repeat types. However, the emerging PSVs had no taxonomic and phylogenetic implications. Eight highly divergent regions were identified within the plastome regions ndhF, ccsA, ndhD, ndhA, ndhH, ycf1 , rps16-trnQ-UUG, and psbM-trnD . These highly variable regions may be potential molecular markers for further species delimitation and population genetic analyses for the clade. Our plastome phylogenomic analyses yielded a well-resolved phylogeny tree with well-support at the tribal and generic levels within the Coffeeae alliance. Conclusions Plastome data could be indispensable in resolving the phylogenetic relationships of the Coffeeae alliance tribes. Therefore, this study provides deep insights into the PSVs and phylogenetic relationships of the Coffeeae alliance and the Rubiaceae family as a whole.

The red ironwood ( Lophira alata ) is a relic tropical African tree species that is increasingly threatened by human activities driven by its high economic value and its vulnerability is further heightened by climate change. However, the impact of these factors on the population distribution dynamics remains unassessed, creating an urgent conservation need. We leveraged geographic occurrence records from in situ assessments and global repositories, together with environmental predictors and human footprint indices, to evaluate the distribution dynamics of L. alata across its range in Nigeria (West Africa) under current and future (2050 and 2090) climatic scenarios. Results showed that precipitation of the coldest quarter and the human footprint index are the main climatic and non-climatic factors influencing the distribution of L. alata in Nigeria, respectively. The model predicted anthropic landscapes, swamp forests, and tropical lowland forests zones in southern Nigeria as the climatically stable and suitable habitats. Substantial habitat shifts are expected under future climate scenarios, with the greatest shrinkage predicted under the worst-case scenario (SSP5-8.5) by the end of the century. A significant conservation gap exists because the predicted suitable habitats lie mostly outside designated protected areas. Our integrative conservation assessment suggests that the species would likely qualify for an “Endangered” status in Nigeria, indicating a higher regional risk despite evidence of natural succession. Collectively, our study identified the factors affecting the population trend and highlights the urgent need for site-specific conservation measures to prevent potential local extinction of L. alata in Nigeria.

The Millettioid/Phaseoloid (MP) clade from the subfamily Papilionoideae (Leguminosae) consists of six tribes and ca. 3,000 species. Previous studies have revealed some plastome structural variations (PSVs) within this clade. However, many deep evolutionary relationships within the clade remain unresolved. Due to limited taxon sampling and few genetic markers in previous studies, our understanding of the evolutionary history of this clade is limited. To address this issue, we sampled 43 plastomes (35 newly sequenced) representing all the six tribes of the MP clade to examine genomic structural variations and phylogenetic relationships. Plastomes of the species from the MP clade were typically quadripartite (size ranged from 140,029 to 160,040 bp) and contained 109–111 unique genes. We revealed four independent gene losses ( ndhF , psbI , rps16 , and trnS-GCU ), multiple IR-SC boundary shifts, and six inversions in the tribes Desmodieae, Millettieae, and Phaseoleae. Plastomes of the species from the MP clade have experienced significant variations which provide valuable information on the evolution of the clade. Plastid phylogenomic analyses using Maximum Likelihood and Bayesian methods yielded a well-resolved phylogeny at the tribal and generic levels within the MP clade. This result indicates that plastome data is useful and reliable data for resolving the evolutionary relationships of the MP clade. This study provides new insights into the phylogenetic relationships and PSVs within this clade.

Aim The African Guineo‐Congolian (GC) region is a global biodiversity hotspot with high species endemism, bioclimatic heterogeneity, complex landscape features, and multiple biogeographic barriers. Bioclimatic and geographic variables influence global patterns of species richness and endemism, but their relative importance varies across taxa and regions and is poorly understood for many faunas. Here, we test the hypothesis that turnover in endemic amphibians of the GC biodiversity hotspot is influenced mainly by the geographic distance between grid cells and secondarily by rainfall‐ and temperature‐related variables. Location West and Central Africa. Major Taxa Studied Amphibians. Methods We compiled species‐occurrence records via field sampling, online databases, and taxonomic literature. Our study used 1205 unique georeferenced records of 222 amphibian species endemic to the GC region. Patterns of species richness were mapped onto a grid with a spatial resolution of 0.5° × 0.5°. We estimated weighted endemism and tested whether endemism was higher than the expected species richness (randomization test). We quantified species turnover using generalized dissimilarity modelling to evaluate the processes underlying observed patterns of species richness in GC endemic amphibians. We explored bioregionalization using agglomerative hierarchical clustering based on the unweighted pair group method with arithmetic averages. Results We identified seven areas within the lower GC region – forests in Cameroon, Gabon, Southern Nigeria, Equatorial Guinea, Republic of Congo, Democratic Republic of Congo, and Cote d'Ivoire – as having high species richness of endemic amphibians. The randomization test returned four major areas of significant weighted endemism: Nigeria‐Cameroon mountains, forest regions of the Democratic Republic of Congo, Cote d'Ivoire, and Ghana. Our analysis revealed five bioregions for amphibian endemism, four of which were located within the lower Guineo‐Congolian forest. Species turnover was strongly related to the geographic distance between grid cells; contributing bioclimatic variables included precipitation of the warmest quarter, mean temperature of the wettest quarter, and mean diurnal temperature range. Main Conclusions Our results indicate that geographic distance between grid cells is the primary determinant of turnover in GC endemic amphibians, with secondary but significant effects of rainfall‐ and temperature‐related variables. Our study identifies key areas of endemic amphibian richness that could be prioritized for conservation actions.

Urticeae s.l. , a tribe of Urticaceae well-known for their stinging trichomes, consists of more than 10 genera and approximately 220 species. Relationships within this tribe remain poorly known due to the limited molecular and taxonomic sampling in previous studies, and chloroplast genome (CP genome/plastome) evolution is still largely unaddressed. To address these concerns, we used genome skimming data—CP genome and nuclear ribosomal DNA (18S-ITS1-5.8S-ITS2-26S); 106 accessions—for the very first time to attempt resolving the recalcitrant relationships and to explore chloroplast structural evolution across the group. Furthermore, we assembled a taxon rich two-locus dataset of trnL-F spacer and ITS sequences across 291 accessions to complement our genome skimming dataset. We found that Urticeae plastomes exhibit the tetrad structure typical of angiosperms, with sizes ranging from 145 to 161 kb and encoding a set of 110–112 unique genes. The studied plastomes have also undergone several structural variations, including inverted repeat (IR) expansions and contractions, inversion of the trnN-GUU gene, losses of the rps19 gene, and the rpl2 intron, and the proliferation of multiple repeat types; 11 hypervariable regions were also identified. Our phylogenomic analyses largely resolved major relationships across tribe Urticeae, supporting the monophyly of the tribe and most of its genera except for Laportea , Urera , and Urtica , which were recovered as polyphyletic with strong support. Our analyses also resolved with strong support several previously contentious branches: (1) Girardinia as a sister to the Dendrocnide - Discocnide - Laportea - Nanocnide - Zhengyia - Urtica - Hesperocnide clade and (2) Poikilospermum as sister to the recently transcribed Urera sensu stricto . Analyses of the taxon-rich, two-locus dataset showed lower support but was largely congruent with results from the CP genome and nuclear ribosomal DNA dataset. Collectively, our study highlights the power of genome skimming data to ameliorate phylogenetic resolution and provides new insights into phylogenetic relationships and chloroplast structural evolution in Urticeae.

[This corrects the article DOI: 10.3389/fpls.2020.00151.].

The genus Dalbergia has a pantropical distribution and comprises approximately 250 species. Previous phylogenetic studies on the genus revealed that Dalbergia is monophyletic and is sister to Machaerium and Aeschynomene sect. Ochopodium. However, due to limited samples or DNA regions in these studies, relationships among the major clades are still unresolved, and divergence dates and biogeographical history of the genus have not been addressed. In this study, phylogenetic analyses of Dalbergia were conducted using broad taxon sampling and a combined dataset of two plastid DNA markers (matK and rbcL) and one nuclear marker (ITS). We evaluated the infrageneric classification of the genus based on the reconstructed tree, and investigated biogeographical history of this genus through molecular dating and ancestral area reconstruction analyses. The monophyly of Dalbergia was strongly supported and the genus was resolved into five major clades with high support, several of which correspond to the previous recognized sections. We inferred that Dalbergia originated in South America during the Early Miocene (c. 22.9 Ma) and achieved its current pantropical distribution through multiple recent transoceanic long-distance dispersals (LDD). We highlighted the important historical events which may explain the pantropical distribution pattern of Dalbergia.

Fontitrygon garouaensis (Smooth Freshwater Stingray) is an evolutionarily distinct and globally endangered species and is currently the only stingray known to be strictly adapted to African freshwater systems. Lack of a reference genome has limited studies of its adaptive evolution and genomic architecture. Here, we present the first chromosome-level genome assembly of F. garouaensis using a hybrid approach that integrates PacBio HiFi long reads, Illumina short reads, and Hi-C chromatin conformation capture. The assembly spans 4.19 Gb with 41 anchored chromosomes, a scaffold N50 of 86.49 Mb, and a contig N50 of 16.58 Mb. Overall, 84.07% of the genome was assigned to chromosomes, with 65.27% repetitive elements. BUSCO analysis showed 93.3% completeness, confirming a highly contiguous genome. We annotated 29,804 protein-coding genes, with 98.28% functionally annotated. Repetitive elements comprised 65.27% of the genome, including lineage-specific expansions of DNA transposons (7.13%) and LTRs (19.31%). This genomic resource establishes a foundation for systematic, evolutionary, and conservation research on this threatened species.

Rapid degradation of wetlands and habitat fragmentation are major threats to species diversity and ecological paradigm in Lagos state, Nigeria. Best to our knowledge, no empirical study has explored the effects of seasonal changes on covering three major cities in the statewithin the major cities in Lagos state. For this, we carried out a study covering the three major cities in Lagos: Badagry, Epe and Ikorodu. Permanent plots were randomly established for monthly data collection (quadrat method; size=10 x 10 m), that span across one-year period covering the wet and dry season). We observed two major vegetation types (secondary forest and mangrove) in the studied areas. Additionally, we documented 107 species belonging to 90 genera and 40 families. Species diversity analysis indicated higher diversity, abundance, species richness and evenness in Ikorodu and Epe during the wet has a greater while high species diversity was observed in Badagry during the dry season. The Dahomey gap phenomenon have greater implication on the Badagry vegetation while the coastal nature of Epe and Badagry negatively influenced their vegetation structure. Analyses inferred that species diversity pattern in the studied area seem to be determined by seasonal changes alongside anthropogenic activities and as a environmental factors (rainfall, geomorphology and geology). Further, our result suggests that Ikorodu could be regarded potential biodiversity hotspot area for conservation purposes because of its high floral composition and diversity. Therefore, improved management and conservation of the vegetation of the Ikorodu area is hereby recommended. The findings from this study will be useful in guiding the Physical Planning and Urban Development and Environment ministries in Lagos state for appropriate management and monitoring of developmental projects for sustainable development.