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Motivation Haplotype networks are a routine approach to visualize relationships among alleles. Such visual analysis of single-locus data is still of importance, especially in species diagnosis and delimitation, where a limited amount of sequence data usually are available and sufficient, along with other data sets in the framework of integrative taxonomy. In diploid organisms, this often requires separating (‘phasing’) sequences with heterozygotic positions, and typically separate programs are required for phasing, reformatting of input files, and haplotype network construction. We therefore developed Hapsolutely, a user-friendly program with an ergonomic graphical user interface (GUI) that integrates haplotype phasing from single-locus sequences with five approaches for network/genealogy reconstruction. Results Among the novel options implemented, Hapsolutely integrates phasing and graphical reconstruction steps of haplotype networks, supports input of species partition data in the common SPART and SPART-XML formats, and calculates and visualizes haplowebs and fields for recombination, thus allowing graphical comparison of allele distribution and allele sharing among subsets for the purpose of species delimitation. The new tool has been specifically developed with a focus on the workflow in alpha-taxonomy, where exploring fields for recombination across alternative species partitions may help species delimitation. Availability and implementation Hapsolutely is written in Python, and integrates code from Phase, SeqPHASE and PopART in C ++ and Haxe. Compiled stand-alone executables for MS Windows and Mac OS along with a detailed manual can be downloaded from https://www.itaxotools.org; the source code is openly available on GitHub (https://github.com/iTaxoTools/Hapsolutely).
Motivation Haplotype networks are a routine approach to visualize relationships among alleles. Such visual analysis of single-locus data is still of importance, especially in species diagnosis and delimitation, where a limited amount of sequence data usually are available and sufficient, along with other data sets in the framework of integrative taxonomy. In diploid organisms, this often requires separating (‘phasing’) sequences with heterozygotic positions, and typically separate programs are required for phasing, reformatting of input files, and haplotype network construction. We therefore developed Hapsolutely, a user-friendly program with an ergonomic graphical user interface (GUI) that integrates haplotype phasing from single-locus sequences with five approaches for network/genealogy reconstruction. Results Among the novel options implemented, Hapsolutely integrates phasing and graphical reconstruction steps of haplotype networks, supports input of species partition data in the common SPART and SPART-XML formats, and calculates and visualizes haplowebs and fields for recombination, thus allowing graphical comparison of allele distribution and allele sharing among subsets for the purpose of species delimitation. The new tool has been specifically developed with a focus on the workflow in alpha-taxonomy, where exploring fields for recombination across alternative species partitions may help species delimitation. Availability and implementation Hapsolutely is written in Python, and integrates code from Phase, SeqPHASE and PopART in C ++ and Haxe. Compiled stand-alone executables for MS Windows and Mac OS along with a detailed manual can be downloaded from https://www.itaxotools.org; the source code is openly available on GitHub (https://github.com/iTaxoTools/Hapsolutely).
A recent revision of the anacondas (Serpentes: Boidae: Eunectes), with the description of a new species of green anaconda, generated extensive publicity, but also provoked considerable controversy due to inadequacies of the evidence used and errors in nomenclature. We here use the case of this problematic publication to: (i) highlight common issues affecting species delimitations, especially an over-reliance on mitochondrial DNA data, and reiterate best practices; (ii) reanalyse the data available for anacondas to establish the true current state of knowledge and to highlight lines of further research; and (iii) analyse the nomenclatural history and status of the genus. While our analysis reveals significant morphological variation in both green and yellow anacondas, denser sampling and an analysis of informative nuclear markers are required for meaningful species delimitation in Eunectes. Tracing the history of name-bearing types establishes Trinidad as the type locality for Boa murina Linnaeus, 1758 and allows identification of the extant lectotype for the species. Finally, we emphasize the responsibility of both journals and authors to ensure that published taxonomic work meets the burden of evidence required to substantiate new species descriptions and that species are named in compliance with the rules of zoological nomenclature.
Valettietta Lincoln & Thurston, 1983 (Amphipoda: Alicelloidea) is an infrequently sampled genus of scavenging amphipod, with a known bathymetric range from 17–5467 m encompassing a variety of habitats from anchialine caves to abyssal plains. Molecular systematics studies have uncovered cryptic speciation in specimens collected from the abyssal Pacific, highlighting uncertainty in the description of Valettietta anacantha (Birstein & Vinogradov, 1963). Here, we apply an integrative taxonomic approach and describe two new species, Valettietta trottarum sp. nov. and Valettietta synchlys sp. nov., collected at abyssal depths in the Clarion-Clipperton Zone, Pacific Ocean. Both species can be distinguished by characters of the gnathopods, uropod 3, and the inner plate of the maxilliped. Further, molecular phylogenetic analyses of two mitochondrial (16S rDNA and COI) and two nuclear (Histone 3 and 28S rRNA) regions found both new species to form well-supported clades and allowed us to re-identify previously published records based on genetic species delimitation. The biogeography of Valettietta is discussed in light of these re-evaluated records, and a new taxonomic key to the genus is provided. These new taxa highlight the strength of applying an integrated taxonomic approach to uncover biodiversity, which is critical in regions being explored for potential industrial purposes.
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