The closure of the Isthmus of Panama has long been considered to be one of the best defined biogeographic calibration points for molecular divergence-time estimation. However, geological and biological evidence has recently cast doubt on the presumed timing of the initial isthmus closure around 3 Ma but has instead suggested the existence of temporary land bridges as early as the Middle or Late Miocene. The biological evidence supporting these earlier land bridges was based either on only few molecular markers or on concatenation of genome-wide sequence data, an approach that is known to result in potentially misleading branch lengths and divergence times, which could compromise the reliability of this evidence. To allow divergence-time estimation with genomic data using the more appropriate multispecies coalescent (MSC) model, we here develop a new method combining the single-nucleotide polymorphism-based Bayesian species-tree inference of the software SNAPP with a molecular clock model that can be calibrated with fossil or biogeographic constraints. We validate our approach with simulations and use our method to reanalyze genomic data of Neotropical army ants (Dorylinae) that previously supported divergence times of Central and South American populations before the isthmus closure around 3 Ma. Our reanalysis with the MSC model shifts all of these divergence times to ages younger than 3 Ma, suggesting that the older estimates supporting the earlier existence of temporary land bridges were artifacts resulting at least partially from the use of concatenation. We then apply our method to a new restriction-site associated DNA-sequencing data set of Neotropical sea catfishes (Ariidae) and calibrate their species tree with extensive information from the fossil record. We identify a series of divergences between groups of Caribbean and Pacific sea catfishes around 10 Ma, indicating that processes related to the emergence of the isthmus led to vicariant speciation already in the Late Miocene, millions of years before the final isthmus closure.

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BackgroundIn horses, the morphological changes induced by the process of domestication are reportedly less pronounced than in other species, such as dogs or pigs – although the horses’ disparity has rarely been empirically tested. We investigated shape differences and modularity of domesticated horses, Przewalski’s horses, donkeys and zebras. Mandibular and tooth shape have been shown to be valuable features for differentiating wild and domesticated forms in some mammals.ResultsBoth mandible and teeth, show a pattern of shape space occupation analogous to that of the cranium, with domesticated horses occupying a similar extension in shape space to that of wild equids. Only cranial shape data exhibit a tendency to separate domesticated horses and Przewalski’s horses from donkeys and zebras. Maximum likelihood model-based tests confirm the horse cranium is composed of six developmental modules, as reported for placental mammals in general. The magnitude of integration in domesticated horse skull was lower than in wild equids across all six cranial modules, and lower values of integration were associated with higher disparity values across all modules.ConclusionThis is the first study that combines different skeletal features for the description and comparison of shape changes in all living equid groups using geometric morphometrics. We support Darwin’s hypothesis that the shape variation in the skull of domesticated horses is similar to the shape variation of all wild equid species existing today. Lower magnitudes of module integration are recovered in domesticated horses compared to their wild relatives.Electronic supplementary materialThe online version of this article (10.1186/s12983-018-0258-9) contains supplementary material, which is available to authorized users.

Lampreys, together with hagfishes, are the only extant representatives of jawless vertebrates and thus of prime interest for the study of vertebrate evolution [1]. Most lamprey genera occur in two forms with divergent life histories: a parasitic, anadromous and a non-parasitic, freshwater resident form [2-8]. The taxonomic status of such 'paired species' is disputed, however. While indistinguishable at larval stages, but clearly distinct as adults, they cannot be differentiated with available genetic data [6,7], which has fuelled speculations that the two forms may in fact represent products of phenotypic plasticity within a single species. Here, we use restriction site-associated DNA sequencing (RADseq) to examine the genetic population structure of sympatric European river (Lampetra fluviatilis L., 1758) and brook (Lampetra planeri Bloch, 1784) lampreys. We find strong genetic differentiation and identify numerous fixed and diagnostic single nucleotide polymorphisms (SNPs) between the two species, 12 of which can be unequivocally assigned to specific genes.

Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Background In December 2020, the United Kingdom (UK) reported a SARS-CoV-2 Variant of Concern (VoC) which is now named B.1.1.7. Based on initial data from the UK and later data from other countries, this variant was estimated to have a transmission fitness advantage of around 40–80 % (Volz et al., 2021; Leung et al., 2021; Davies et al., 2021). Aim This study aims to estimate the transmission fitness advantage and the effective reproductive number of B.1.1.7 through time based on data from Switzerland. Methods We generated whole genome sequences from 11.8 % of all confirmed SARS-CoV-2 cases in Switzerland between 14 December 2020 and 11 March 2021. Based on these data, we determine the daily frequency of the B.1.1.7 variant and quantify the variant’s transmission fitness advantage on a national and a regional scale. Results We estimate B.1.1.7 had a transmission fitness advantage of 43–52 % compared to the other variants circulating in Switzerland during the study period. Further, we estimate B.1.1.7 had a reproductive number above 1 from 01 January 2021 until the end of the study period, compared to below 1 for the other variants. Specifically, we estimate the reproductive number for B.1.1.7 was 1.24 [1.07–1.41] from 01 January until 17 January 2021 and 1.18 [1.06–1.30] from 18 January until 01 March 2021 based on the whole genome sequencing data. From 10 March to 16 March 2021, once B.1.1.7 was dominant, we estimate the reproductive number was 1.14 [1.00–1.26] based on all confirmed cases. For reference, Switzerland applied more non-pharmaceutical interventions to combat SARS-CoV-2 on 18 January 2021 and lifted some measures again on 01 March 2021. Conclusion The observed increase in B.1.1.7 frequency in Switzerland during the study period is as expected based on observations in the UK. In absolute numbers, B.1.1.7 increased exponentially with an estimated doubling time of around 2–3.5 weeks. To monitor the ongoing spread of B.1.1.7, our plots are available online.

The first case of SARS-CoV-2 in Basel, Switzerland was detected on February 26th 2020. We present a phylogenetic study to explore viral introduction and evolution during the exponential early phase of the local COVID-19 outbreak from February 26th until March 23rd. We sequenced SARS-CoV-2 naso-oropharyngeal swabs from 746 positive tests that were performed at the University Hospital Basel during the study period. We successfully generated 468 high quality genomes from unique patients and called variants with our COVID-19 Pipeline (COVGAP), and analysed viral genetic diversity using PANGOLIN taxonomic lineages. To identify introduction and dissemination events we incorporated global SARS-CoV-2 genomes and inferred a time-calibrated phylogeny. Epidemiological data from patient questionnaires was used to facilitate the interpretation of phylogenetic observations. The early outbreak in Basel was dominated by lineage B.1 (83·6%), detected first on March 2nd, although the first sample identified belonged to B.1.1. Within B.1, 68·2% of our samples fall within a clade defined by the SNP C15324T (‘Basel cluster’), including 157 identical sequences at the root of the ‘Basel cluster’, some of which we can specifically trace to regional spreading events. We infer the origin of B.1-C15324T to mid-February in our tri-national region. The other genomes map broadly over the global phylogenetic tree, showing several introduction events from and/or dissemination to other regions of the world via travellers. Family transmissions can also be traced in our data. A single lineage variant dominated the outbreak in the Basel area while other lineages, such as the first (B.1.1), did not propagate. A mass gathering event was the predominant initial source of cases, with travel returners and family transmissions to a lesser extent. We highlight the importance of adding specific questions to epidemiological questionnaires, to obtain data on attendance of large gatherings and their locations, as well as travel history, to effectively identify routes of transmissions in up-coming outbreaks. This phylogenetic analysis in concert with epidemiological and contact tracing data, allows connection and interpretation of events, and can inform public health interventions. Trial Registration: ClinicalTrials.gov NCT04351503.

The process of domestication has long fascinated evolutionary biologists, yielding insights into the rapidity with which selection can alter behaviour and morphology. Previous studies on dogs, cattle and pigeons have demonstrated that domesticated forms show greater magnitudes of morphological variation than their wild ancestors. Here, we quantify variation in skull morphology, modularity and integration in chickens and compare those to the wild fowl using three-dimensional geometric morphometrics and multivariate statistics. Similar to other domesticated species, chickens exhibit a greater magnitude of variation in shape compared with their ancestors. The most variable part of the chicken skull is the cranial vault, being formed by dermal and neural crest-derived bones, its form possibly related to brain shape variation in chickens, especially in crested breeds. Neural crest-derived portions of the skull exhibit a higher amount of variation. Further, we find that the chicken skull is strongly integrated, confirming previous studies in birds, in contrast to the presence of modularity and decreased integration in mammals.