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      Molecular and morphological studies on Contracaecum rudolphii A and C. rudolphii B in great cormorants ( Phalacrocorax carbo sinensis) from Italy and Israel

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          Abstract

          Abstract

          The distribution of parasites is shaped by a variety of factors, among which are the migratory movements of their hosts. Israel has a unique position to migratory routes of several bird species leaving Europe to winter in Africa, however, detailed studies on the parasite fauna of birds from this area are scarce. Our study investigates occurrence and distribution of sibling species among Contracaecum rudolphii complex in Phalacrocorax carbo sinensis from Italy and Israel, to acquire further information on the geographical range of these species to gain deeper knowledge on the ecology of these parasites and their bird host. A total of 2383 Contracaecum were collected from the gastric mucosa of 28 great cormorants (18 from Israel and 10 from Italy). A subsample was processed for morphological analyses in light and scanning electron microscopy (SEM), and for molecular analyses through amplification and sequencing of the ITS rDNA and the cox2 mtDNA, and through PCR-RFLP. All the 683 Contracaecum subjected to molecular identification belonged to C. rudolphii s.l., (300 C. rudolphii A and 383 C. rudolphii B). SEM micrographs provided, for the first time, details of taxonomic structures in male specimens from both sibling species, and the first SEM characterization of C. rudolphii B. This work presents the first data on the occurrence of sibling species of C. rudolphii in Israel and provides additional information on the distribution of C. rudolphii A and B in Italy, confirming the high prevalence and intensity of infection observed in Ph. carbo sinensis from other Italian areas.

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          MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

          We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
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            MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

            Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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              DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets.

              We present version 6 of the DNA Sequence Polymorphism (DnaSP) software, a new version of the popular tool for performing exhaustive population genetic analyses on multiple sequence alignments. This major upgrade incorporates novel functionalities to analyze large data sets, such as those generated by high-throughput sequencing technologies. Among other features, DnaSP 6 implements: 1) modules for reading and analyzing data from genomic partitioning methods, such as RADseq or hybrid enrichment approaches, 2) faster methods scalable for high-throughput sequencing data, and 3) summary statistics for the analysis of multi-locus population genetics data. Furthermore, DnaSP 6 includes novel modules to perform single- and multi-locus coalescent simulations under a wide range of demographic scenarios. The DnaSP 6 program, with extensive documentation, is freely available at http://www.ub.edu/dnasp.
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                Author and article information

                Journal
                Parasitology
                Parasitology
                PAR
                Parasitology
                Cambridge University Press (Cambridge, UK )
                0031-1820
                1469-8161
                September 2023
                21 September 2023
                : 150
                : 11
                : 1040-1051
                Affiliations
                [1 ]Department of Veterinary Medical Sciences (DIMEVET), Alma Mater Studiorum University of Bologna , Bologna, Italy
                [2 ]Israeli Veterinary Services , Bet Dagan, Israel
                [3 ]Experimental Zooprophylactic Institute of Lombardy and Emilia Romagna , Brescia, Italy
                Author notes
                Corresponding author: Monica Caffara; Email: monica.caffara@ 123456unibo.it
                [*]

                These authors contributed equally.

                Author information
                https://orcid.org/0000-0003-3429-6121
                Article
                S0031182023000902
                10.1017/S0031182023000902
                10941213
                37859396
                addf9674-a78a-4ff9-97c9-ea1747a7f988
                © The Author(s) 2023

                This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited.

                History
                : 01 August 2023
                : 15 September 2023
                : 16 September 2023
                Page count
                Figures: 9, Tables: 2, References: 43, Pages: 12
                Funding
                Funded by: Italian Ministry of Education, Universities and Research
                Award ID: Department of Excellence Project 2018-2022
                Funded by: Israeli Veterinary Services
                Categories
                Research Article

                Parasitology
                contracaecum rudolphii a,c. rudolphii b,israel,italy,phalacrocorax carbo sinensis,taxonomy

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