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      The phylogeny of Empis and Rhamphomyia (Diptera, Empididae) investigated using UCEs including an over 150 years old museum specimen

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      Evolutionary Systematics

      Pensoft Publishers

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          Abstract

          The genera Empis Linneus, 1758 and Rhamphomyia Meigen, 1822 (Empidoidea, Empididae Latreille, 1809) are two large genera of flies commonly named dagger flies. They are widely distributed in the world with most species described from the Palearctic Region. Empis comprises about 810 described species and Rhamphomyia comprises about 610 described species, together they represent one third of the known species diversity in Empididae. Two recent studies on the phylogeny of the two genera using Sanger sequencing on a few genetic markers, did not support monophyly of them. In this study high throughput sequencing of target enriched molecular data of ultraconserved elements or UCEs was used to investigate the phylogenetic relationships of included representatives of the genera. This method has proven useful on old and dry museum specimens with high amounts of degraded DNA, which was also tested herein. For this purpose, a commercially synthesized bait kit has previously been developed for Diptera which this study was the first one to test. Three out of nine old and dry museum specimens were successfully sequenced, one with an age of at least 154 years. Higher DNA concentration yielded a greater number of reads. Analyses conducted in the study confirmed that both Empis and Rhamphomyia are non-monophyletic.

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          Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales.

          Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, non-model avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.
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            The evolution and significance of male mate choice.

            The distinct reproductive roles of males and females, which for many years were characterised in terms of competitive males and choosy females, have remained a central focus of sexual selection since Darwin's time. Increasing evidence now shows that males can be choosy too, even in apparently unexpected situations, such as under polygyny or in the absence of male parental care. Here, we provide a synthesis of the theory on male mate choice and examine the factors that promote or constrain its evolution. We also discuss the evolutionary significance of male mate choice and the contrasts in male versus female mate choice. We conclude that mate choice by males is potentially widespread and has a distinct role in how mating systems evolve. Copyright © 2011 Elsevier Ltd. All rights reserved.
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              PHYLUCE is a software package for the analysis of conserved genomic loci.

              Targeted enrichment of conserved and ultraconserved genomic elements allows universal collection of phylogenomic data from hundreds of species at multiple time scales ( 300 Ma). Prior to downstream inference, data from these types of targeted enrichment studies must undergo preprocessing to assemble contigs from sequence data; identify targeted, enriched loci from the off-target background data; align enriched contigs representing conserved loci to one another; and prepare and manipulate these alignments for subsequent phylogenomic inference. PHYLUCE is an efficient and easy-to-install software package that accomplishes these tasks across hundreds of taxa and thousands of enriched loci.
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                Author and article information

                Journal
                Evolutionary Systematics
                EvolSyst
                Pensoft Publishers
                2535-0730
                February 04 2020
                February 04 2020
                : 4
                : 1
                : 21-33
                Article
                10.3897/evolsyst.4.49537
                © 2020

                http://creativecommons.org/licenses/by/4.0/

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