We present complete genome sequences of 2 species of African honeyguides.

We present complete genome sequences of 3 species of African sunbirds.

We present complete genome sequences of 3 species of African barbets.

We present complete genome sequences of 3 species of African Woodpeckers.

The immense biodiversity observed in tropical forests has inspired the study of evolution since its inception, and numerous hypotheses have been generated to explain this diversity. One major driver of tropical forest biodiversity has been the repeated climatic fluctuations due to the Pleistocene glacial cycles. The Afrotropics are one region that has seen a particularly rich debate about the origin of its avifauna. Lowland and highland Afrotropical forests responded in different ways to Pleistocene climatic cycling, likely shaping the population genetic structure of species tracking these habitats. Here we study the role of shifting forests throughout the Pleistocene in shaping population genetic structure in a forest generalist, the Yellow-whiskered Greenbul (Eurillas latirostris). We sequenced genomes from individuals across the continent with forest thought to span three Pleistocene refugia. At a coarse scale, we found evidence for three lineages that expanded from these refugia, with a western lineage west of the Dahomey gap, a central lineage across the Congo Basin, and an eastern lineage in the Albertine rift and adjacent rainforest. However, finer scale analysis revealed a more complex story. First, we found that the most stable eastern lineage demonstrated population genetic structure between its montane populations. This included one population that was likely admixed between the sampled Albertine Rift locations and an unsampled region. Second, we found surprisingly strong divergence between the parapatric eastern and central lineages. However, despite this divergence, we found signals of mitochondrial introgression from the eastern lineage far into the eastern sampling localities of the central lineage. This suggests a largely untapped promise for evolutionary genomic research across the Congo Basin, where populations expanding from alternate refugia likely meet and have their species boundaries tested.

We present complete genome sequences of 3 species of African Monarch Flycatchers.

We present complete genome sequences of 8 species of African Bulbuls.

Biodiversity has experienced tremendous shifts in community, species, and genetic diversity during the Anthropocene. Understanding temporal diversity shifts is especially critical in biodiversity hotspots, i.e., regions that are exceptionally biodiverse and threatened. Here, we use museomics and temporal genomics approaches to quantify temporal shifts in genomic diversity in an assemblage of eight generalist highland bird species from the Ethiopian Highlands (part of the Eastern Afromontane Biodiversity Hotspot). With genomic data from contemporary and historical samples, we demonstrate an assemblage-wide trend of increased genomic diversity through time, potentially due to improved habitat connectivity within highland regions. Genomic diversity shifts in these generalist species contrast with general trends of genomic diversity declines in specialist or imperiled species. In addition to genetic diversity shifts, we found an assemblage-wide trend of decreased realized mutational load, indicative of overall trends for potentially deleterious variation to be masked or selectively purged. Across this avian assemblage, we also show that shifts in population genomic structure are idiosyncratic, with species-specific trends. These results are in contrast with other charismatic and imperiled African taxa that have largely shown strong increases in population genetic structure over the recent past. This study highlights that not all taxa respond the same to environmental change, and generalists, in some cases, may even respond positively. Future comparative conservation genomics assessments on species groups or assemblages with varied natural history characteristics would help us better understand how diverse taxa respond to anthropogenic landscape changes.

The impact of preserved museum specimens is transforming and increasing by three-dimensional (3D) imaging that creates high-fidelity online digital specimens. Through examples from the openVertebrate (oVert) Thematic Collections Network, we describe how we created a digitization community dedicated to the shared vision of making 3D data of specimens available and the impact of these data on a broad audience of scientists, students, teachers, artists, and more. High-fidelity digital 3D models allow people from multiple communities to simultaneously access and use scientific specimens. Based on our multiyear, multi-institution project, we identify significant technological and social hurdles that remain for fully realizing the potential impact of digital 3D specimens.

Museum specimens collected prior to cryogenic tissue storage are increasingly being used as genetic resources, and though high-throughput sequencing is becoming more cost-efficient, whole genome sequencing (WGS) of historical DNA (hDNA) remains inefficient and costly due to its short fragment sizes and high loads of exogenous DNA, among other factors. It is also unclear how sequencing efficiency is influenced by DNA sources. We aimed to identify the most efficient method and DNA source for collecting WGS data from avian museum specimens. We analyzed low-coverage WGS from 60 DNA libraries prepared from four American Robin (Turdus migratorius) and four Abyssinian Thrush (Turdus abyssinicus) specimens collected in the 1920s. We compared DNA source (toepad versus incision-line skin clip) and three library preparation methods: (1) double-stranded DNA (dsDNA), single tube (KAPA); (2) single-stranded DNA (ssDNA), multi-tube (IDT); and (3) ssDNA, single tube (Claret Bioscience). We found that the ssDNA, multi-tube method resulted in significantly greater endogenous DNA content, average read length, and sequencing efficiency than the other tested methods. We also tested whether a predigestion step reduced exogenous DNA in libraries from one specimen per species and found promising results that warrant further study. The ~10% increase in average sequencing efficiency of the best-performing method over a commonly implemented dsDNA library preparation method has the potential to significantly increase WGS coverage of hDNA from bird specimens. Future work should evaluate the threshold for specimen age at which these results hold and how the combination of library preparation method and DNA source influence WGS in other taxa.

The aim of this study was to investigate the bird population structure across an altitudinal gradient and assess the effects of human activities on bird diversity in the understorey of the Burhinyi forest, eastern Democratic Republic of Congo (DRC). Mist-netting and opportunistic observations were made at four selected sites in the intact and disturbed forest. Of the 16 most abundant species among the 121 species recorded, the Rwenzori Blue-headed Sunbird Cyanomitra alinae and the Mountain Greenbul Arizelocichla nigriceps stood out with high abundance at the Katasomwa site. Muscicapidae was the richest family with 13 species. Twenty-two Albertine Rift endemic species or subspecies were found, considered of importance for the conservation of this forest, among them Shelley's Crimsonwing Cryptospiza shelleyi (Endangered according to the IUCN Red List) and three genera, Pseudocalyptomena, Hemitesia and Graueria. The presence of Willard's Sooty Boubou Laniarius poensis willardi in the Itombwe Massif is confirmed above 2000 m, in sympatry with the Albertine Sooty Boubou L. holomelas, and the Abyssinian Ground-Thrush Geokichla piaggiae piaggiae in sympatry with the Kivu Ground-Thrush G. p. tanganjicae. Species richness varied between the two types of forest (intact and disturbed), with significantly fewer species in disturbed forests.

AbstractUnlike most bird species, individual kingfisher species (Aves: Alcedinidae) are typically parasitized by only a single genus of louse (Alcedoffula,Alcedoecus, orEmersoniella). These louse genera are typically specific to a particular kingfisher subfamily. Specifically,AlcedoecusandEmersoniellaparasitize Halcyoninae, whereasAlcedoffulaparasitizes Alcedininae and Cerylinae. AlthoughEmersoniellais geographically restricted to the Indo-Pacific region,AlcedoecusandAlcedoffulaare geographically widespread. We used DNA sequences from two genes, the mitochondrial COI and nuclear EF-1αgenes, to infer phylogenies for the two geographically widespread genera of kingfisher lice,AlcedoffulaandAlcedoecus. These phylogenies included 47 kingfisher lice sampled from 11 of the 19 currently recognized genera of kingfishers. We compared louse phylogenies to host phylogenies to reconstruct their cophylogenetic history. Two distinct clades occur withinAlcedoffula, one that infests Alcedininae and a second that infests Cerylinae. All species ofAlcedoecuswere found only on host species of the subfamily Halcyoninae. Cophylogenetic analysis indicated thatAlcedoecus, as well as the clade ofAlcedoffulaoccurring on Alcedininae, do not show evidence of cospeciation. In contrast, the clade ofAlcedoffulaoccurring on Cerylinae showed strong evidence of cospeciation.

Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic data sets can also result in conflicting estimates of phylogeny. Here, we use the early divergences in Neoaves, the largest clade of extant birds, as a "model system" to understand the basis for incongruence among phylogenomic trees. We were motivated by the observation that trees from two recent avian phylogenomic studies exhibit conflicts. Those studies used different strategies: 1) collecting many characters [$\sim$ 42 mega base pairs (Mbp) of sequence data] from 48 birds, sometimes including only one taxon for each major clade; and 2) collecting fewer characters ($\sim$ 0.4 Mbp) from 198 birds, selected to subdivide long branches. However, the studies also used different data types: the taxon-poor data matrix comprised 68% non-coding sequences whereas coding exons dominated the taxon-rich data matrix. This difference raises the question of whether the primary reason for incongruence is the number of sites, the number of taxa, or the data type. To test among these alternative hypotheses we assembled a novel, large-scale data matrix comprising 90% non-coding sequences from 235 bird species. Although increased taxon sampling appeared to have a positive impact on phylogenetic analyses the most important variable was data type. Indeed, by analyzing different subsets of the taxa in our data matrix we found that increased taxon sampling actually resulted in increased congruence with the tree from the previous taxon-poor study (which had a majority of non-coding data) instead of the taxon-rich study (which largely used coding data). We suggest that the observed differences in the estimates of topology for these studies reflect data-type effects due to violations of the models used in phylogenetic analyses, some of which may be difficult to detect. If incongruence among trees estimated using phylogenomic methods largely reflects problems with model fit developing more "biologically-realistic" models is likely to be critical for efforts to reconstruct the tree of life. [Birds; coding exons; GTR model; model fit; Neoaves; non-coding DNA; phylogenomics; taxon sampling.].

Background The Buff-spotted Woodpecker ( Campethera nivosa ) is a resident bird species that is distributed in lowland rainforest habitats from western to eastern Africa. We developed species-specific microsatellite markers to examine the population genetics of this species. Findings Twenty-one microsatellite loci were isolated from C. nivosa . Of these, 15 were found to amplify consistently. These loci were then tested for variability in 15 individuals from different lowland forest localities. The number of alleles ranged from 3 to 13 per locus, with observed and expected heterozygosity ranging from 0.100 to 0.917 and 0.485 to 0.901, respectively. Four loci exhibited significant heterozygote deficiency while one had an excess of heterozygotes. None of the loci exhibited linkage disequilibrium. Conclusion These polymorphic microsatellite markers will be used to study genetic variability in populations of C. nivosa across either sides of the Congo River to evaluate the effect of the river as a barrier to gene flow.

The Democratic Republic of Congo holds the most diverse assemblage of birds in Africa. However, ornithological surveys in its network of reserves are rare. In this paper we pre-sent the first detailed list of birds from the Man and Biosphere Reserve of Luki in the country’s southwestern tip based on collected specimens, photographs, audio recordings, and direct observations from two surveys conducted in 2012–2013. We document a total of 136 species, including the threatened Psittacus erithacus . Range extensions of four species and breeding records for 19 species are also reported. Further surveys in the reserve, which covers the largest remaining forest patch along the Lower Congo River, are highly recommended.

Horseshoe bats of the Rhinolophus maclaudi species group were recently revised by Fahr et al. (2002). Known members of the group are located in the mountainous region of West Africa and the Albertine Rift, east of the Congo River basin with a major gap (4300 km) between the two recognized sub-groups. Here we describe two additional species within this species group from the Albertine Rift center of endemism in the eastern Democratic Republic of Congo. One derives from the Misotschi-Kabogo highlands, a heretofore poorly documented region half-way down the western shore of Lake Tanganyika. Additional bat records from this locality are also documented. The second new taxon was collected in Kahuzi-Biega National Park, a World Heritage Site adjacent to the shore of Lake Kivu.

Horseshoe bats of the Rhinolophus maclaudi species group were recently revised by Fahr et al. (2002). Known members of the group are located in the mountainous region of West Africa and the Albertine Rift, east of the Congo River basin with a major gap (4300 km) between the two recognized sub-groups. Here we describe two additional species within this species group from the Albertine Rift center of endemism in the eastern Democratic Republic of Congo. One derives from the Misotschi-Kabogo highlands, a heretofore poorly documented region half-way down the western shore of Lake Tanganyika. Additional bat records from this locality are also documented. The second new taxon was collected in Kahuzi-Biega National Park, a World Heritage Site adjacent to the shore of Lake Kivu.