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1. Range in the Use and Realization of BIN in African American English

   https://doi.org/10.1177/00238309221111201  

   Green, Lisa; Yu, Kristine M.; Neal, Anissa; Whitmal, Ayana; Powe, Tamira; Özyıldız, Deniz (July 2022, Language and Speech)

   This paper jointly considers syntactic, semantic, and phonological/phonetic factors in approaching an understanding of BIN, a remote past marker in African American English that has been described as “stressed.” It brings together data from the Corpus of Regional African American Language (CORAAL) and a production study in a small African American English-speaking community in southwest Louisiana to investigate the use and phonetic realization of BIN constructions. Only 20 instances of BIN constructions were found in CORAAL. This sparsity was not simply due to a dearth of semantic contexts for BIN in the interviews, since 122 instances of semantically equivalent been + temporal adverbial variants were also found. These results raise questions about the extent to which BIN constructions and been + temporal adverbial variants are used in different pragmatic and discourse contexts as well as in different speech styles. The production study elicited BIN and past participle been constructions in controlled syntactic and semantic environments. The phonetic realization of BIN was found to be distributed over the entire utterance rather than localized to BIN. BIN utterances were distinguished from past participle been utterances by having higher ratios of fundamental frequency (F0), intensity, and duration in BIN/ been relative to preceding and following material in the utterance. In both studies, BIN utterances were generally realized with a high F0 peak on BIN and a reduced F0 range in the post- BIN region, with variability in the presence and kinds of F0 movements utterance-initially and utterance-finally, as well as in F0 downtrends in the post- BIN region. 

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2. De Novo Whole Genome Assemblies for Two Southern African Dwarf Chameleons ( Bradypodion , Chamaeleonidae)

   https://doi.org/10.1093/gbe/evad182  

   Taft, Jody M; Tolley, Krystal A; Alexander, Graham J; Geneva, Anthony J (October 2023, Genome Biology and Evolution)

   Fraser, Bonnie (Ed.)

   Abstract A complete and high-quality reference genome has become a fundamental tool for the study of functional, comparative, and evolutionary genomics. However, efforts to produce high-quality genomes for African taxa are lagging given the limited access to sufficient resources and technologies. The southern African dwarf chameleons (Bradypodion) are a relatively young lineage, with a large body of evidence demonstrating the highly adaptive capacity of these lizards. Bradypodion are known for their habitat specialization, with evidence of convergent phenotypes across the phylogeny. However, the underlying genetic architecture of these phenotypes remains unknown for Bradypodion, and without adequate genomic resources, many evolutionary questions cannot be answered. We present de novo assembled whole genomes for Bradypodion pumilum and Bradypodion ventrale, using Pacific Biosciences long-read sequencing data. BUSCO analysis revealed that 96.36% of single copy orthologs were present in the B. pumilum genome and 94% in B. ventrale. Moreover, these genomes boast scaffold N50 of 389.6 and 374.9 Mb, respectively. Based on a whole genome alignment of both Bradypodion genomes, B. pumilum is highly syntenic with B. ventrale. Furthermore, Bradypodion is also syntenic with Anolis lizards, despite the divergence between these lineages estimated to be nearly 170 Ma. Coalescent analysis of the genomic data also suggests that historical changes in effective population size for these species correspond to notable shifts in the southern African environment. These high-quality Bradypodion genome assemblies will support future research on the evolutionary history, diversification, and genetic underpinnings of adaptation in Bradypodion. 

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3. Molecular evolution of the ependymin-related gene epdl2 in African weakly electric fish

   https://doi.org/10.1093/g3journal/jkac331  

   Losilla, Mauricio; Gallant, Jason R (December 2022, G3 Genes|Genomes|Genetics)

   McCallion, A (Ed.)

   Abstract Gene duplication and subsequent molecular evolution can give rise to taxon-specific gene specializations. In previous work, we found evidence that African weakly electric fish (Mormyridae) may have as many as three copies of the epdl2 gene, and the expression of two epdl2 genes is correlated with electric signal divergence. Epdl2 belongs to the ependymin-related family (EPDR), a functionally diverse family of secretory glycoproteins. In this study, we first describe vertebrate EPDR evolution and then present a detailed evolutionary history of epdl2 in Mormyridae with emphasis on the speciose genus Paramormyrops. Using Sanger sequencing, we confirm three apparently functional epdl2 genes in Paramormyrops kingsleyae. Next, we developed a nanopore-based amplicon sequencing strategy and bioinformatics pipeline to obtain and classify full-length epdl2 gene sequences (N = 34) across Mormyridae. Our phylogenetic analysis proposes three or four epdl2 paralogs dating from early Paramormyrops evolution. Finally, we conducted selection tests which detected positive selection around the duplication events and identified ten sites likely targeted by selection in the resulting paralogs. These sites’ locations in our modeled 3D protein structure involve four sites in ligand binding and six sites in homodimer formation. Together, these findings strongly imply an evolutionary mechanism whereby epdl2 genes underwent selection-driven functional specialization after tandem duplications in the rapidly speciating Paramormyrops. Considering previous evidence, we propose that epdl2 may contribute to electric signal diversification in mormyrids, an important aspect of species recognition during mating. 

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4. Facial and body colouration is linked to social rank in the African cichlid Astatotilapia burtoni

   https://doi.org/10.1101/2024.08.21.608989  

   Peroš, M; Chang, A; Martashvili, A; Alvarado, SG (August 2024, bioRxiv)

   TBD (Ed.)

   Animal colouration is fundamentally important for social communication within conspecifics to advertising threat to competitors or fitness to possible mates. Social status and animal colouration are covarying traits that are plastic in response to dynamic environments. In the African cichlid,Astatotilapia burtoni, body colouration and behaviour have been extensively reported to vary with social rank. However, the nature of the interaction between these two traits is poorly understood. We hypothesise that pigmentation patterns could be linked to the behavioural repertoires underlying social status and can be resolved to regions on the cichlid body plan. To test this hypothesis, we generated Territorial (T) and Non-territorial (NT) males and employed computer vision tools to quantify and visualise patterns/colour enrichment associated with stereotyped T/NT male behaviour. We report colour-behaviour interactions localised in specific areas of the body and face for two colour morphs illustrating a more nuanced view of social behaviour and pigmentation. Since behavioural and morphological variation are key drivers of selection in the East African Great Rift Lakes, we surmise our data may be translatable to other cichlid lineages and underline the importance of trait covariance in sexual selection and male competition. 

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5. Carbon and nitrogen isotope variability in the seeds of two African millet species: Pennisetum glaucum and Eleusine coracana

   https://doi.org/10.1002/rcm.8217  

   Reid, Rachel E.B.; Lalk, Ellen; Marshall, Fiona; Liu, Xinyi (October 2018, Rapid Communications in Mass Spectrometry)