The rails (Family Rallidae) are the most diverse and widespread group in the Gruiformes. Their extensive fossil history, global geographic distribution, and tendency to rapidly evolve flightless species on islands make them an attractive subject of evolutionary studies, but the rarity of modern museum specimens of so many rail species has, until recently, limited the scope of molecular phylogenetics studies. As a result, the classification of rails remains one of the most unsettled among major bird radiations. We extracted DNA from museum specimens of 82 species, including 27 from study skins collected as long ago as 1875, and generated nucleotide sequences from thousands of homologous ultra-conserved elements (UCEs). Our phylogenetic analyses, using both concatenation and multispecies coalescent approaches, resulted in well-supported and highly congruent phylogenies that resolve the major lineages of rails and reveal several currently recognized genera to be polyphyletic. A fossil-calibrated time tree is well-resolved and supports the hypothesis that rails split into 2 major lineages (subfamilies Himantornithinae and Rallinae) ~34 mya, but clade age estimates have wide confidence intervals. Our results, combined with results of other recently published phylogenomics studies of rails and other Gruiformes, form the basis for a proposed classification of the Rallidae that recognizes 40 genera in 9 tribes.• Rails are a diverse, globally distributed group of birds that are of great interest to ornithologists that study fossil birds and the evolution of flightless species on islands. But because so many rail species are rare or extinct, studying rail evolution using genomic data requires that DNA be obtained from very old museum specimens.• We extracted DNA from museum specimens, including study skins of rare and extinct species collected as long ago as 1875, and generated DNA sequences from thousands of genes.• The DNA-based phylogeny indicates that rails underwent an initial split into 2 groups ~34 mya, and that 9 major extant rail lineages have evolved since then.• Our genetic analyses clarify the relationships of some enigmatic species that have not been studied with DNA before and are the basis for a revised taxonomic classification of rails.

Reports of P. vivax infections among Duffy-negative hosts have accumulated throughout sub-Saharan Africa. Despite this growing body of evidence, no nationally representative epidemiological surveys of P. vivax in sub-Saharan Africa have been performed. To overcome this gap in knowledge, we screened over 17,000 adults in the Democratic Republic of the Congo (DRC) for P. vivax using samples from the 2013-2014 Demographic Health Survey. Overall, we found a 2.97% (95% CI: 2.28%, 3.65%) prevalence of P. vivax infections across the DRC. Infections were associated with few risk-factors and demonstrated a relatively flat distribution of prevalence across space with focal regions of relatively higher prevalence in the north and northeast. Mitochondrial genomes suggested that DRC P. vivax were distinct from circulating non-human ape strains and an ancestral European P. vivax strain, and instead may be part of a separate contemporary clade. Our findings suggest P. vivax is diffusely spread across the DRC at a low prevalence, which may be associated with long-term carriage of low parasitemia, frequent relapses, or a general pool of infections with limited forward propagation.

Reliable estimation of phylogeny is central to avoid inaccuracy in downstream macroevolutionary inferences. However, limitations exist in the implementation of concatenated and summary coalescent approaches, and Bayesian and full coalescent inference methods may not yet be feasible for computation of phylogeny using complicated models and large data sets. Here, we explored methodological (e.g., optimality criteria, character sampling, model selection) and biological (e.g., heterotachy, branch length heterogeneity) sources of systematic error that can result in biased or incorrect parameter estimates when reconstructing phylogeny by using the gadiform fishes as a model clade. Gadiformes include some of the most economically important fishes in the world (e.g., Cods, Hakes, and Rattails). Despite many attempts, a robust higher-level phylogenetic framework was lacking due to limited character and taxonomic sampling, particularly from several species-poor families that have been recalcitrant to phylogenetic placement. We compiled the first phylogenomic data set, including 14,208 loci ($>$2.8 M bp) from 58 species representing all recognized gadiform families, to infer a time-calibrated phylogeny for the group. Data were generated with a gene-capture approach targeting coding DNA sequences from single-copy protein-coding genes. Species-tree and concatenated maximum-likelihood (ML) analyses resolved all family-level relationships within Gadiformes. While there were a few differences between topologies produced by the DNA and the amino acid data sets, most of the historically unresolved relationships among gadiform lineages were consistently well resolved with high support in our analyses regardless of the methodological and biological approaches used. However, at deeper levels, we observed inconsistency in branch support estimates between bootstrap and gene and site coefficient factors (gCF, sCF). Despite numerous short internodes, all relationships received unequivocal bootstrap support while gCF and sCF had very little support, reflecting hidden conflict across loci. Most of the gene-tree and species-tree discordance in our study is a result of short divergence times, and consequent lack of informative characters at deep levels, rather than incomplete lineage sorting. We use this phylogeny to establish a new higher-level classification of Gadiformes as a way of clarifying the evolutionary diversification of the order. We recognize 17 families in five suborders: Bregmacerotoidei, Gadoidei, Ranicipitoidei, Merluccioidei, and Macrouroidei (including two subclades). A time-calibrated analysis using 15 fossil taxa suggests that Gadiformes evolved $sim $79.5 Ma in the late Cretaceous, but that most extant lineages diverged after the Cretaceous–Paleogene (K-Pg) mass extinction (66 Ma). Our results reiterate the importance of examining phylogenomic analyses for evidence of systematic error that can emerge as a result of unsuitable modeling of biological factors and/or methodological issues, even when data sets are large and yield high support for phylogenetic relationships. [Branch length heterogeneity; Codfishes; commercial fish species; Cretaceous-Paleogene (K-Pg); heterotachy; systematic error; target enrichment.]