Population Differentiation Research Articles

Cryophilic Tardigrada have disjunct and bipolar distribution and establish long-term stable, low-density demes

Glaciers are inhabited by various cryophilic organisms ranging from single celled to multicellular, like Tardigrada (water bears). Owing to their scattered distribution, glaciers represent extremely fragmented habitats, and it remains unclear how their inhabitants survive and disperse among such isolated patches. This study investigates the biogeography of the tardigrade genus Cryoconicus, whose distribution, population stability, and interregional connectivity are examined by screening the collections from ~ 60 glaciers worldwide and by a phylogeographic analysis. We found that two Cryoconicus species occur at low densities on two Arctic glaciers in Svalbard, far from their previously reported Antarctic and Central Asian ranges. Screening of worldwide databases and DNA metabarcoding indicated that these species are absent or rare in the intermediate areas, suggesting large disjunctions in their ranges. In particular, the genetic data and multiyear resampling showed that Cryoconicus kaczmareki established a stable population on the Ebba Glacier (Svalbard), which has been isolated from its Asian core range since before the last glacial maximum. Our findings suggest that glacial invertebrates may possess wide yet largely disjunctive ranges. Interpolar- or intercontinental-scale movements of cryophilic meiofauna may occur, but migration connectivity is not sufficient to mitigate the differentiation of the local population. Revealed biogeographic patterns further demonstrate that inhabitants of extreme environments may establish isolated and highly fragmented populations that persist long term, even if at very low densities.

Limited hybridisation and introgression despite stocking among endemic Interior Highlands black basses (Centrarchidae: Micropterus)

AbstractAimSmallmouth Bass (Micropterus dolomieu; SMB) are globally popular among anglers and have been widely introduced (i.e. stocked) for population management and sportfishing. Importantly, stocking was prevalent before cryptic diversity within the SMB complex was known, which now includes three newly elevated species: Neosho Bass (M. velox; NB), Little River Bass (M. sp. cf. dolomieu Little River; LRB) and Ouachita Bass (M. sp. cf. dolomieu Ouachita River; OB). We sought to quantify population structure and hybridisation and introgression in these three recently described species.LocationSpecies‐level diversity, particularly in the basin‐restricted LRB and OB in the Ouachita Mountains within the Central Interior Highlands (CIH), North America, suggests the presence of distinct genetic variation that could be eroded by introgression.MethodsWe estimated interspecific introgression and intraspecific population differentiation in the Smallmouth Bass species complex (SMB‐C) using 472 specimens comprising SMB, NB, LRB and OB, including the naturally sympatric Spotted Bass (M. punctulatus; SPB). Genomic samples were genotyped on a SNP panel of 192 loci designed to detect allele‐sharing on multiple hierarchical levels.ResultsWe found low range‐wide hybridisation between species in the SMB‐C and SPB (mostly SMB‐C backcrosses), and interspecific heterozygosity varied, indicating differential introgression. Range‐wide hybridisation between species in the CIH and SMB was similar overall (but mostly F2 and CIH backcrosses) and was observed in streams with known SMB stocking in connected reservoirs. Interspecific heterozygosity in SMB hybrids was also generally lower, indicating later‐generation backcrosses. We found strong population structure in the Ouachita Mountains (LRB and OB).Main ConclusionsDespite isolated incidences of natural (SPB) and human‐mediated (SMB) introgression, genomic identity appears intact in endemic LRB and OB, suggesting potential ecological or behavioural isolating mechanisms preventing cross‐species reproduction. Our findings reveal that genetic variation remains in cryptic, basin‐restricted species in the Ouachita Mountains ecoregion that may be managed for long‐term conservation.

Population variation and sexual dimorphism in the deep-sea crab Parilia alcocki (Brachyura, Leucosiidae)

ABSTRACT Parilia alcocki is a deep-sea crab inhabiting the continental shelves and slopes of the eastern Arabian Sea and western Bay of Bengal at a depth of 128–457 m. No published information is available on its population characteristics and sexual dimorphism. The present study provides the first-ever insight into the population differentiation and sexual dimorphism in P. alcocki using Geometric Morphometric Analysis (GMA) of carapace and chela shapes. The Arabian Sea population possessed carapaces with a more pointed anterior and a rounded posterior margin as compared with the Bay of Bengal population. When chela shapes are compared, the Arabian Sea crabs possess an elongated, narrower arm, and shorter pollex. The observed shape variations could be attributed to heterogeneous habitat conditions in these regions which influence feeding and predation. Sexual dimorphism in carapace shapes was indiscernible. However, males exhibited wider intra-specific variations in carapace shape and show a larger average and maximum size for linear carapace measurements. Also, male crabs possess elongated and narrow arms and shorter pollex, whereas the females have a broader and shorter arm and longer pollex, indicative of classical sexual size dimorphism. Our study confirmed the suitability of GMA to understand the ecological and biological characteristics and trait-habitat linkages of P. alcocki.

Genetic variation at innate and adaptive immune genes - contrasting patterns of differentiation and local adaptation in a wild gull.

Immunogenetic variation in natural vertebrate populations is expected to respond to spatial and temporal fluctuations in pathogen assemblages. While spatial heterogeneity in pathogen-driven selection enhances local immunogenetic adaptations and population divergence, different immune genes may yield contrasting responses to the environment. Here, we investigated population differentiation at the key pathogen recognition genes of the innate and adaptive immune system in a colonial bird species, the black-headed gull Chroicocephalus ridibundus. We assessed genetic variation at three toll-like receptor (TLR) genes (innate immunity) and the major histocompatibility complex (MHC) class I and II genes (adaptive immunity) in gulls from seven colonies scattered across Poland. As expected, we found much greater polymorphism at the MHC than TLRs. Population differentiation at the MHC class II, but not MHC-I, was significantly stronger than at neutral microsatellite loci, suggesting local adaptation. This could reflect spatial variation in the composition of extracellular parasite communities (e.g., helminths), possibly driven by sharp differences in habitat structure between colonies. Despite contrasting patterns of population differentiation, both MHC classes showed similar regimes of diversifying selection. Some significant population differentiation was also observed at TLRs, suggesting that innate immune receptors may respond to fine-scale spatial variation in pathogen pressure, although this pattern could have been enhanced by drift. Our results suggested that local adaptation at the pathogen recognition immune genes can be maintained at relatively small or moderate spatial scales in species with high dispersal potential and they highlighted the complexity of immunogenetic responses of animals to heterogeneous environments.

The SSR Genetic Diversity of Wild Red Fruit Lycium (Lycium barbarum) in Northwest China

Through a comprehensive regional systematic collection, we conducted a genetic diversity analysis of wild red-fruited Lycium resources across the entire northwest region of China. This study provides a valuable genetic basis for germplasm exploration and the selection of new Lycium varieties. Utilizing fluorescence capillary electrophoresis, we carefully screened 16 pairs of SSR primers exhibiting high polymorphism. Subsequently, we inferred the genetic diversity of Lycium germplasm through structure clustering, UPGMA analysis, and molecular AMOVA. The 113 Lycium barbarum samples collected from northwest China exhibited distinct subgroups, namely the Qinghai–Gansu–Ningxia subgroup and the Xinjiang subgroup. These subgroups were clearly distinguishable based on genetic clustering. The genetic diversity within the samples was remarkably rich, as indicated by a mean I value of 1.04, He value of 0.57, and PIC value of 0.73. Notably, the majority of genetic diversity (72.99%) was found within populations, signifying substantial intrapopulation variation. Furthermore, our findings revealed significant genetic differentiation among populations, with a substantial Fst value of 0.27 and gene flow Nm estimated at 0.68. This suggests that the genetic variation levels in northwest Lycium were notably high, primarily driven by pronounced genetic differentiation among populations. Nonetheless, it is important to note that genetic diversity predominantly persists within populations. The observed subpopulation structure of Qinghai–Gansu–Ningxia and Xinjiang regions in northwest China can be primarily attributed to geographical isolation. These geographical barriers have played a pivotal role in shaping the genetic differentiation and structure of Lycium populations in the region. Consequently, our study sheds light on the complex genetic landscape of Northwest Lycium and highlights the significance of considering both within-population diversity and population differentiation in conservation and breeding programs.

Host genetic variation guides hepacivirus clearance, chronicity, and liver fibrosis in mice.

Human genetic variation is thought to guide the outcome of HCV infection, but model systems within which to dissect these host genetic mechanisms are limited. Norway rat hepacivirus, closely related to HCV, causes chronic liver infection in rats but causes acute self-limiting hepatitis in typical strains of laboratory mice, which resolves in 2 weeks. The Collaborative Cross (CC) is a robust mouse genetics resource comprised of a panel of recombinant inbred strains, which model the complexity of the human genome and provide a system within which to understand diseases driven by complex allelic variation. We infected a panel of CC strains with Norway rat hepacivirus and identified several that failed to clear the virus after 4 weeks. Strains displayed an array of virologic phenotypes ranging from delayed clearance (CC046) to chronicity (CC071, CC080) with viremia for at least 10 months. Body weight loss, hepatocyte infection frequency, viral evolution, T-cell recruitment to the liver, liver inflammation, and the capacity to develop liver fibrosis varied among infected CC strains. These models recapitulate many aspects of HCV infection in humans and demonstrate that host genetic variation affects a multitude of viruses and host phenotypes. These models can be used to better understand the molecular mechanisms that drive hepacivirus clearance and chronicity, the virus and host interactions that promote chronic disease manifestations like liver fibrosis, therapeutic and vaccine performance, and how these factors are affected by host genetic variation.

Selection on standing genetic variation mediates convergent evolution in extremophile fish.

Hydrogen sulfide is a toxic gas that disrupts numerous biological processes, including energy production in the mitochondria, yet fish in the Poecilia mexicana species complex have independently evolved sulfide tolerance several times. Despite clear evidence for convergence at the phenotypic level in these fishes, it is unclear if the repeated evolution of hydrogen sulfide tolerance is the result of similar genomic changes. To address this gap, we used a targeted capture approach to sequence genes associated with sulfide processes and toxicity from five sulfidic and five nonsulfidic populations in the species complex. By comparing sequence variation in candidate genes to a reference set, we identified similar population structure and differentiation, suggesting that patterns of variation in most genes associated with sulfide processes and toxicity are due to demographic history and not selection. But the presence of tree discordance for a subset of genes suggests that several loci are evolving divergently between ecotypes. We identified two differentiation outlier genes that are associated with sulfide detoxification in the mitochondria that have signatures of selection in all five sulfidic populations. Further investigation into these regions identified long, shared haplotypes among sulfidic populations. Together, these results reveal that selection on standing genetic variation in putatively adaptive genes may be driving phenotypic convergence in this species complex.

Genetic drift versus natural selection affecting the evolution of spectral and functional traits of two key macrophytes: Phragmites australis and Nuphar lutea

Abstract Both genetic and phenotypic intraspecific diversity play a crucial role in the ecological and evolutionary dynamics of organisms. Several studies have compared phenotypic divergence (Pst) and differentiation of neutral loci (Fst) to infer the relative roles of genetic drift and natural selection in population differentiation (Pst–Fst comparison). For the first time, we have assessed and compared the genetic variation and differentiation at the leaf trait level in two key macrophytes, Phragmites australis and Nuphar lutea. To this aim, we quantified and described the genetic structure and phenotypic diversity of both species in five lake systems in north‐central Italy. We then investigated the relative roles of genetic drift and natural selection on leaf trait differentiation (Pst–Fst), assuming that Fst reflects divergence caused only by genetic drift while Pst also incorporates the effects of selective dynamics on the phenotype. In terms of genetic structure, the results for P. australis were in line with those observed for other Italian and European conspecific populations. Conversely, N. lutea showed a more complex genetic structure than expected at the site level, probably due to the combined effect of genetic isolation and its mixed mating system. Both species exhibited high variability in leaf functional traits within and among sites, highlighting a high degree of phenotypic plasticity. Pst–Fst comparisons showed a general tendency towards directional selection in P. australis and a more complex pattern in N. lutea. Indeed, the drivers of phenotypic differentiation in N. lutea showed a variable mix of stabilising and directional selection or neutral divergence at most sites. The prevalence of vegetative over generative reproduction leads P. australis populations to be dominated by a few clones that are well adapted to local conditions, including phenotypes that respond plastically to the environment. In contrast, in N. lutea, the interaction of a mixed mating system and geographical isolation among distant sites tends to reduce the effect of outbreeding depression and provides the genetic basis for adaptive capacity. The first joint analysis of the genetic structure of these two key macrophytes allowed a better understanding of the relative roles of genetic drift and natural selection in the diversification of phenotypic traits within habitats dominated by P. australis and N. lutea.

Africa-specific human genetic variation near CHD1L associates with HIV-1 load.

HIV-1 remains aglobal health crisis1, highlighting the need to identify new targets for therapies. Here, given the disproportionate HIV-1 burden and marked human genome diversity in Africa2, we assessed the genetic determinants of control of set-point viral load in 3,879 people of African ancestries living with HIV-1 participating in the international collaboration for the genomics of HIV3. We identify a previously undescribed association signal on chromosome 1 where the peak variant associates with an approximately 0.3 log10-transformed copies per ml lower set-point viral load per minor allele copy and is specific to populations of African descent. The top associated variant is intergenic and lies between a long intergenic non-coding RNA (LINC00624) and the coding gene CHD1L, which encodes a helicase that is involved in DNA repair4. Infection assays in iPScell-derived macrophages and other immortalized cell lines showed increased HIV-1 replication in CHD1L-knockdown and CHD1L-knockout cells. We provide evidence from population genetic studies that Africa-specific genetic variation near CHD1L associates with HIV replication in vivo. Although experimental studies suggest that CHD1L is able to limit HIV infection in some cell types in vitro, further investigation is required to understand the mechanisms underlying our observations, including any potential indirect effects of CHD1L on HIV spread in vivo that our cell-based assays cannot recapitulate.

NCOurd: modelling length distributions of NCO events and gene conversion tracts.

Meiotic recombination is the main driving force of human genetic diversity, along with mutations. Recombinations split into crossovers, separating large chromosomal regions originating from different homologous chromosomes, and non-crossovers (NCOs), where a small segment from one chromosome is embedded in a region originating from the homologous chromosome. NCOs are much less studied than mutations and crossovers as NCOs are short and can only be detected at markers heterozygous in the transmitting parent, leaving most of them undetectable. The detectable NCOs, known as gene conversions, hide information about NCOs, including their number and length, waiting to be unveiled. We introduce NCOurd, software, and algorithm, based on an expectation-maximization algorithm, to estimate the number of NCOs and their length distribution from gene conversion data. https://github.com/DecodeGenetics/NCOurd.

Molecular characterization and genetic diversity of three Stomoxys flies S. bengalensis, S. calcitrans, and S. sitiens (Diptera: Muscidae) in Central Thailand.

Stomoxys flies (Diptera: Muscidae) are hematophagous ectoparasites of medical and veterinary importance. In this study, three Stomoxys species, i.e. S. bengalensis, S. calcitrans, and S. sitiens, were collected from three provinces in Central Thailand with the aim of estimating the genetic divergence between species, for species identification, as well as within species, for a genetic diversity study based on the cytochrome c oxidase subunit I (COI) gene. Our results showed that the average intraspecific genetic divergences of Stomoxys flies ranged from 0.11% in S. sitiens to 0.98% in S. calcitrans, whereas the average interspecific genetic divergences ranged from 5.24% between S. sitiens and S. bengalensis to 6.69% between S. calcitrans and S. bengalensis. In addition, there was no overlap between the intraspecific and interspecific genetic divergences. The COI sequence analysis revealed a high haplotype diversity and low nucleotide diversity, reflecting a rapid population expansion after past bottlenecks. Moreover, there was no significant difference (P>0.05) in the pairwise population differentiation (Fst) among Stomoxys flies in Central Thailand, because of the lack of natural barriers, thus allowing genetic exchange between them. The monitoring of the haplotype network revealed that two lineages of S. calcitrans in Central Thailand were distributed in all study areas, including the Nakhon Pathom, Pathum Thani, and Saraburi Provinces. These findings may improve our understanding of the genetic patterns of these three Stomoxys flies, as well as the underlying biological mechanisms, which is knowledge that can be used for further effective control of these flies.

Repeat polymorphisms underlie top genetic risk loci for glaucoma and colorectal cancer

Many regions in the human genome vary in length among individuals due to variable numbers of tandem repeats (VNTRs). To assess the phenotypic impact of VNTRs genome-wide, we applied a statistical imputation approach to estimate the lengths of 9,561 autosomal VNTR loci in 418,136 unrelated UK Biobank participants and 838 GTEx participants. Association and statistical fine-mapping analyses identified 58 VNTRs that appeared to influence a complex trait in UK Biobank, 18 of which also appeared to modulate expression or splicing of a nearby gene. Non-coding VNTRs at TMCO1 and EIF3H appeared to generate the largest known contributions of common human genetic variation to risk of glaucoma and colorectal cancer, respectively. Each of these two VNTRs associated with a >2-fold range of risk across individuals. These results reveal a substantial and previously unappreciated role of non-coding VNTRs in human health and gene regulation.

Genetic diversity and climatic suitability over time of Baetodes huaico (Ephemeroptera: Baetidae)

In the Neotropical region, the genetic diversity and bioclimatic preferences of Ephemeroptera are poorly known mainly due to the lack of studies. We used the 16S rRNA mitochondrial gene to examine the genetic structure of Baetodes huaico, an aquatic insect distributed in the Northwest of Argentina. Also, we performed an ecological niche modeling (ENM) to understand bioclimatic preferences and combine with the genetic data to understand historical dynamic distribution of B. huaico. We found that B. huaico populations are genetically structured into two distinct geographic groups. The ENM showed a distributional shift from south to north through time. Also, we recovered a stable region over time in the Southwest of Tucumán with the highest value of suitability and high genetic diversity; this region was previously proposed as a Pleistocene refuge. Our result suggests that the northern group was stable over time and underwent a recent demographic expansion coincident with a glacial refugium, whereas the southern group could have been affected by climatic fluctuations during. The results emphasize possible climatic influences in genetic population differentiation, and contributes to the knowledge of the genetic diversity of Ephemeroptera from subtropical Argentina laying the groundwork for future work for other freshwater insects in our region.

A novel antisense lncRNA, ARBAG harboring an RNA destabilizing GWAS variant for C-peptide dictates the transcript isoforms of GABRA6 in cerebellum.

Human disease-associated genetic variations often map to long non-coding RNA (lncRNA) genes; however, elucidation of their functional impact is challenging. We previously identified a new genetic variant rs4454083 (A/G) residing in exon of an uncharacterized lncRNA ARBAG that strongly associates with plasma levels of C-peptide, a hormone that regulates insulin bioavailability. On the opposite strand, rs4454083 also corresponds to an intron of a cerebellum-specific GABA receptor subunit gene GABRA6 that mediates strengthening of inhibitory synapses by insulin. Here, we show that alleles of rs4454083 modulate transcript levels of the antisense gene, ARBAG, which then controls the expression of the sense gene, GABRA6. Predisposing to low C-peptide, GG (a minor allele genotype across ethnicities) stabilizes ARBAG lncRNA causing higher transcript levels in cerebellum. ARBAG lncRNA abundance leads to cleavage of GABRA6 mRNA at the complementary region, resulting in a dysfunctional GABRA6 protein that would not be recruited for synapse strengthening. Together, our findings in human cerebellar cell-line and induced Pluripotent Stem Cells (iPSCs) demonstrate biological role of a novel lncRNA in determining the ratio of mRNA isoforms of a protein-coding gene and the ability of an embedded variant in modulating lncRNA stability leading to inter-individual differences in protein expression.

Variabilidad genética del pez Lutjanus guttatus (Perciformes: Lutjanidae) mediante el uso de microsatélites en Costa Rica

Introduction: The rose spotted snapper (Lutjanus guttatus) is a highly consumed marine fish and of commercial interest in Costa Rica, under a strong fishing pressure that can affect the genetic diversity of the population creating problems related to inbreeding depression. Objective: To evaluate the genetic diversity of the spotted snapper (Lutjanus guttatus) population in Costa Rica using microsatellites. Methodology: Samples were collected from two locations (Golfo Dulce and Golfo de Nicoya) in 2019, and 44 individuals from each site were studied. DNA extraction and amplification of 10 microsatellites by PCR were carried out for subsequent genotyping for genetic diversity and population structure analysis. Results: The genetic diversity parameters show a high polymorphism, associated to a high number of alleles per locus, but low levels of observed heterozygosity in comparison to the expected heterozygosity (Ho = 0,774 and 0,800 and He = 0,948 and 0,954 for Gulf of Nicoya and Gulf Dulce, respectively). The study of population differentiation indicates that there is not enough evidence to ensure the two populations are different (FST = 0,00264, p > 0.05). The significant deviation from Hardy-Weinberg Equilibrium obtained indicated the possible presence of organisms in the population that does not come from the wild. Conclusions: The rose spotted snapper in Costa Rica shows high levels of genetic diversity, without evidence of differentiation in genetic subpopulations, that should be considered as a single panmictic population for fishery management purposes. The possible mix of individuals of a distinct origin found in the wild suggests the presence of organisms that come from a stock enhancement program or from commercial aquaculture carried out in the region. The use of genetic markers is recommended to keep track of the genetic characteristics of the wild population, to follow-up stock enhancement programs, and eventually, asses their effect.

Genetic diversity and differentiation of coexisting populations of Quercus robur L.and Q. petraea (Matt.) Liebl.

Genetic diversity and differentiation of coexisting populations of Quercus robur L.and Q. petraea (Matt.) Liebl.

Ecological differences among hydrothermal vent symbioses may drive contrasting patterns of symbiont population differentiation.

The intra-host composition of horizontally transmitted microbial symbionts can vary across host populations due to interactive effects of host genetics, environmental, and geographic factors. While adaptation to local habitat conditions can drive geographic subdivision of symbiont strains, it is unknown how differences in ecological characteristics among host-symbiont associations influence the genomic structure of symbiont populations. To address this question, we sequenced metagenomes of different populations of the deep-sea mussel Bathymodiolus septemdierum, which are common at Western Pacific deep-sea hydrothermal vents and show characteristic patterns of niche partitioning with sympatric gastropod symbioses. Bathymodiolus septemdierum lives in close symbiotic relationship with sulfur-oxidizing chemosynthetic bacteria but supplements its symbiotrophic diet through filter-feeding, enabling it to occupy ecological niches with little exposure to geochemical reductants. Our analyses indicate that symbiont populations associated with B. septemdierum show structuring by geographic location, but that the dominant symbiont strain is uncorrelated with vent site. These patterns are in contrast to co-occurring Alviniconcha and Ifremeria gastropod symbioses that exhibit greater symbiont nutritional dependence and occupy habitats with higher spatial variability in environmental conditions. Our results suggest that relative habitat homogeneity combined with sufficient symbiont dispersal and genomic mixing might promote persistence of similar symbiont strains across geographic locations, while mixotrophy might decrease selective pressures on the host to affiliate with locally adapted symbiont strains. Overall, these data contribute to our understanding of the potential mechanisms influencing symbiont population structure across a spectrum of marine microbial symbioses that occupy contrasting ecological niches. IMPORTANCE Beneficial relationships between animals and microbial organisms (symbionts) are ubiquitous in nature. In the ocean, microbial symbionts are typically acquired from the environment and their composition across geographic locations is often shaped by adaptation to local habitat conditions. However, it is currently unknown how generalizable these patterns are across symbiotic systems that have contrasting ecological characteristics. To address this question, we compared symbiont population structure between deep-sea hydrothermal vent mussels and co-occurring but ecologically distinct snail species. Our analyses show that mussel symbiont populations are less partitioned by geography and do not demonstrate evidence for environmental adaptation. We posit that the mussel's mixotrophic feeding mode may lower its need to affiliate with locally adapted symbiont strains, while microhabitat stability and symbiont genomic mixing likely favors persistence of symbiont strains across geographic locations. Altogether, these findings further our understanding of the mechanisms shaping symbiont population structure in marine environmentally transmitted symbioses.

Integrative revision of the Blommersia wittei complex, with description of a new species of frog from western and north-western Madagascar.

Frogs of the Blommersia wittei complex are widespread in western and northern Madagascar, and are one of two clades of the family Mantellidae that have colonized the Comoran island of Mayotte. Based on a comprehensive set of DNA sequences of the mitochondrial 16S rRNA gene and the nuclear-encoded RAG1 and SACS genes, integrated with morphological and bioacoustic data, we here analyze the genetic differentiation of populations of this complex across Madagascar. We confirm that a candidate species named B. sp. Ca5 in previous studies represents a genetically well-defined evolutionary lineage distributed over much of western Madagascar, which we describe herein as Blommeria bara sp. nov. based on its molecular and bioacoustic differentiation. Blommersia wittei occurs across northern Madagascar but its type locality Ambanja, at the lower Sambirano river, is very close to the range of another, newly discovered microendemic lineage that was only found at two sites along the upper Sambirano river (here named as candidate species B. sp. Ca12). The B. wittei complex thus provides an example of a clade of closely related Malagasy frogs that contains species widespread over hundreds of kilometers, as well as extreme microendemics. For a full resolution of this species complex, more data need to be collected on the geographical contact among these two lineages, on the morphology and bioacoustics of B. sp. Ca12, and on the north-eastern populations of B. wittei at Sambava, which are weakly differentiated in mitochondrial genes but differ in bioacoustics and possibly in the extent of foot webbing.

Genomics and inclusion of Indigenous peoples in high income countries

Genomics research related to Indigenous people has been at worst exploitative and at best, retrospectively on a journey to improve effective engagement of Indigenous individuals and communities. Genomics can positively impact all stages of clinical management, and to improve genomic effectiveness researchers aggregate genomic data from diverse global sub-populations, such as shared ancestry groupings, as people within these groupings will have a greater proportion of shared DNA traits. While genomics is already being used worldwide to improve lives, its utility and effectiveness has not been maximized for individuals with Indigenous ancestry. Several large datasets of human genetic variation have been made publicly available, of which the most widely used is the Genome Aggregation Database (gnomAD), but none of these databases currently contain any population-specific data for Indigenous populations. There are many reasons why Indigenous people have been largely left out of genomics research and, because of this, miss out on the benefits offered. It is also clear that if research is to be effective, it needs to be done ‘with’ and not ‘on’ Indigenous communities. This systematic review of the literature regarding Indigenous peoples (in high income countries) and genomics aims to review the existing literature and identify areas of strength and weakness in study design and conduct, focusing on the effectiveness of Indigenous community engagement.

Demographic history of Ryukyu islanders at the southern part of the Japanese Archipelago inferred from whole-genome resequencing data

The Ryukyu Islands are located in the southernmost part of the Japanese Archipelago and consist of several island groups. Each island group has its own history and culture, which differ from those of mainland Japan. People of the Ryukyu Islands are genetically subdivided; however, their detailed demographic history remains unclear. We report the results of a whole-genome sequencing analysis of a total of 50 Ryukyu islanders, focusing on genetic differentiation between Miyako and Okinawa islanders. We confirmed that Miyako and Okinawa islanders cluster differently in principal component analysis and ADMIXTURE analysis and that there is a population structure among Miyako islanders. The present study supports the hypothesis that population differentiation is primarily caused by genetic drift rather than by differences in the rate of migration from surrounding regions, such as the Japanese main islands or Taiwan. In addition, the genetic cline observed among Miyako and Okinawa islanders can be explained by recurrent migration beyond the bounds of these islands. Our analysis also suggested that the presence of multiple subpopulations during the Neolithic Ryukyu Jomon period is not crucial to explain the modern Ryukyu populations. However, the assumption of multiple subpopulations during the time of admixture with mainland Japanese is necessary to explain the modern Ryukyu populations. Our findings add insights that could help clarify the complex history of populations in the Ryukyu Islands.