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The ability to bear live offspring, viviparity, has evolved multiple times across the tree of life and is a remarkable adaptation with profound life-history and ecological implications. Within amphibians the ancestral reproductive mode is oviparity followed by a larval life stage, but viviparity has evolved independently in all three amphibian orders. Two types of viviparous reproduction can be distinguished in amphibians; larviparity and pueriparity. Larviparous amphibians deliver larvae into nearby ponds and streams, while pueriparous amphibians deliver fully developed juveniles and thus do not require waterbodies for reproduction. Among amphibians, the salamander genus Salamandra is remarkable as it exhibits both inter- and intraspecific variation in the occurrence of larviparity and pueriparity. While the evolutionary relationships among Salamandra lineages have been the focus of several recent studies, our understanding of how often and when transitions between modes occurred is still incomplete. Furthermore, in species with intraspecific variation, the reproductive mode of a given population can only be confirmed by direct observation of births and thus the prevalence of pueriparous populations is also incompletely documented. We used sequence capture to obtain 1,326 loci from 94 individuals from across the geographic range of the genus, focusing on potential reproductive mode transition zones. We also report additional direct observations of pueriparous births for 20 new locations and multiple lineages. We identify at least five independent transitions from the ancestral mode of larviparity to pueriparity among and within species, occurring at different evolutionary timescales ranging from the Pliocene to the Holocene. Four of these transitions occurred within species. Based on a distinct set of markers and analyses, we also confirm previous findings of introgression between species and the need for taxonomic revisions in the genus. We discuss the implication

The radiation of Palearctic green toads (Bufotes) holds great potential to evaluate the role of hybridization in phylogeography at multiple stages along the speciation continuum. With fifteen species representing three ploidy levels, this model system is particularly attractive to examine the causes and consequences of allopoly-ploidization, a prevalent yet enigmatic pathway towards hybrid speciation. Despite substantial efforts, the evolutionary history of this species complex remains largely blurred by the lack of consistency among the corresponding literature. To get a fresh, comprehensive view on Bufotes phylogeography, here we combined genome-wide multilocus analyses (RAD-seq) with an extensive compilation of mitochondrial, genome size, niche modelling, distribution and phenotypic (bioacoustics, morphometrics, toxin composition) datasets, representing hundreds of populations throughout Eurasia. We provide a fully resolved nuclear phylogeny for Bufotes and highlight exceptional cyto-nuclear discordances characteristic of complete mtDNA replacement (in 20% of species), mitochondrial surfing during post-glacial expansions, and the formation of homoploid hybrid populations. Moreover, we traced the origin of several allopolyploids down to species level, showing that all were exclusively fathered by the West Himalayan B. latastii but mothered by several diploid forms inhabiting Central Asian lowlands, an asymmetry consistent with hypotheses on mate choice and Dobzhansky-Muller incompatibilities. Their intermediate call phenotypes potentially allowed for rapid reproductive isolation, while toxin compositions converged towards the ecologically-closest parent. Across the radiation, we pinpoint a stepwise progression of reproductive isolation through time, with a threshold below which hybridizability is irrespective of divergence (< 6My), above which species barely admix and eventually evolve different mating calls (6-10My), or can successfully cross-breed through all

Effective conservation and management of pond‐breeding amphibians depends on the accurate estimation of population structure, demographic parameters, and the influence of landscape features on breeding‐site connectivity. Population‐level studies of pond‐breeding amphibians typically sample larval life stages because they are easily captured and can be sampled nondestructively. These studies often identify high levels of relatedness between individuals from the same pond, which can be exacerbated by sampling the larval stage. Yet, the effect of these related individuals on population genetic studies using genomic data is not yet fully understood. Here, we assess the effect of within‐pond relatedness on population and landscape genetic analyses by focusing on the barred tiger salamanders (Ambystoma mavortium) from the Nebraska Sandhills. Utilizing genome‐wide SNPs generated using a double‐digest RADseq approach, we conducted standard population and landscape genetic analyses using datasets with and without siblings. We found that reduced sample sizes influenced parameter estimates more than the inclusion of siblings, but that withinpond relatedness led to the inference of spurious population structure when analyses depended on allele frequencies. Our landscape genetic analyses also supported different models across datasets depending on the spatial resolution analyzed. We recommend that future studies not only test for relatedness among larval samples but also remove siblings before conducting population or landscape genetic analyses. We also recommend alternative sampling strategies to reduce sampling siblings before sequencing takes place. Biases introduced by unknowingly including siblings can have significant implications for population and landscape genetic analyses, and in turn, for species conservation strategies and outcomes.

The Major Histocompatibility Complex (MHC) is a genomic region encoding immune loci that are important and frequently used markers in studies of adaptive genetic variation and "disease resistance. Given the primary role of infectious diseases in contributing to global amphibian declines, we characterized the hypervariable exon 2 and flanking introns of the MHC Class II beta chain for 17 species of frogs in the Ranidae, a speciose and cosmopolitan family facing widespread pathogen infections and declines. We find high levels of genetic variation concentrated in the Peptide Binding Region (PBR) of the exon. Ten codons are under positive selection, nine of which are located in the mammal-defined PBR. We hypothesize that the tenth codon (residue 21) is an amphibian-specific PBR site that may be important in disease resistance. Trans-species and trans-generic polymorphisms are evident from exon-based genealogies, and co-phylogenetic analyses between intron, exon and mitochondrial based reconstructions reveal incongruent topologies, likely due to different locus histories. We developed two sets of barcoded adapters that reliably amplify a single and likely functional locus in all screened species using both 454 and Illumina based sequencing methods. These primers provide a resource for multiplexing and directly sequencing hundreds of samples in a single sequencing run, avoiding the labour and chimeric sequences associated with cloning, and enabling MHC population genetic analyses. Although the primers are currently limited to the 17 species we tested, these sequences and protocols provide a useful genetic resource and can serve as a starting point for future disease, adaptation and conservation studies across a range of anuran taxa.

U.S. Department of Transportation, Bureau of Transportation Statistics, Port Performance Freight Statistics Annual Report to Congress 2018 (Washington, DC: 2018). https://doi.org/10.21949/1502601 Note: publication date derived from PDF. Port Performance Profiles: Appendix A, This is the third edition of the Port Performance Freight Statistics Program Annual Report, which builds on the foundation of the inaugural 2016 Annual Report. In the first edition, BTS published existing, nationally consistent measures of port capacity and throughput and explained the criteria used to define ports and the measures used to define the top 25 ports in each category. The report included recommendations of the advisory working group to the Port Performance Freight Statistics Program (2016 Working Group) and was delivered to the BTS Director prior to publication as specified in FAST Act Section 6018. This 2018 Annual Report expands on previous editions in several ways. The throughput and capacity statistics included in previous editions have been updated with the most recently available annual data and, in many cases, have been enhanced with additional detail. This edition also expands the number of published throughput and capacity measures (included in the online port profiles) and incorporates new and improved methodologies. For example, the expanded 2018 port profiles are available online at https://www.bts.dot.gov/ports a new index of liquid bulk vessel (tanker) dwell times using automatic vessel location data builds on the container vessel dwell time index added in the previous Annual Report. This edition includes additional descriptions of global and national maritime trends to provide a more robust context for understanding port performance and the emerging issues and topics, including: waterborne transport of food and farm products, and use of Automatic Identification System (AIS) data to measure the impacts of weather disruptions on ports. The Port Performance Freight Statistics Program Definitions and Methods Handbook (PPFSP Definitions and Methods Handbook), available separately, details the process used to identify the top 25 ports and calculate their capacity and throughput.

This is the second edition of the Port Performance Freight Statistics Program Annual Report, which builds on the foundation of the 2016 Annual Report. In the inaugural edition, BTS published existing, nationally consistent measures of port capacity and throughput, and explained the criteria used to define ports and the measures used to define the top 25 ports in each category. The report included recommendations of the advisory working group to the Port Performance Freight Statistics Program (2016 Working Group), and was delivered to the BTS Director prior to publication as specified in FAST Act Section 6018. This 2017 Annual Report expands upon the first edition in several ways. The throughput and capacity statistics included in the 2016 edition have been updated with the most recently available annual data and, in many cases, have been enhanced with additional detail. This edition also expands the number of throughput and capacity measures published and incorporates new and improved methodologies. For example, a new measure of container vessel dwell times uses locational data transmitted continuously from ships, and represents the first application by BTS of automated data collection to port performance measurement. The supporting zip file contains port profile and port vicinity map datasets, a README.txt with a data dictionary, and a .json metadata file in Project Open Data format, for Port Performance Freight Statistics Program : Annual Report to Congress 2017, https://rosap.ntl.bts.gov/view/dot/36212 The data files are in Adobe Acrobat PDF format. The compressed zip file is 50.63 MB. These files can be unzipped using any zip decompression software. The PDF files can be opened by web browsers or with PDF readers. The README.txt file is a plain-text file and can be opened with any basic text editor. The metadata file is in .json format and can be opened with any basic text editor, but is better viewed in a metadata editor or more advance text editor, such as Note

This is the second edition of the Port Performance Freight Statistics Program Annual Report, which builds on the foundation of the 2016 Annual Report. In the inaugural edition, BTS published existing, nationally consistent measures of port capacity and throughput, and explained the criteria used to define ports and the measures used to define the top 25 ports in each category. The report included recommendations of the advisory working group to the Port Performance Freight Statistics Program (2016 Working Group), and was delivered to the BTS Director prior to publication as specified in FAST Act Section 6018. This 2017 Annual Report expands upon the first edition in several ways. The throughput and capacity statistics included in the 2016 edition have been updated with the most recently available annual data and, in many cases, have been enhanced with additional detail. This edition also expands the number of throughput and capacity measures published and incorporates new and improved methodologies. For example, a new measure of container vessel dwell times uses locational data transmitted continuously from ships, and represents the first application by BTS of automated data collection to port performance measurement.