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      At the confluence of vicariance and dispersal: Phylogeography of cavernicolous springtails (Collembola: Arrhopalitidae, Tomoceridae) codistributed across a geologically complex karst landscape in Illinois and Missouri

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          Abstract

          The processes of vicariance and dispersal are central to our understanding of diversification, yet determining the factors that influence these processes remains a significant challenge in evolutionary biology. Caves offer ideal systems for examining the mechanisms underlying isolation, divergence, and speciation. Intrinsic ecological differences among cavernicolous organisms, such as the degree of cave dependence, are thought to be major factors influencing patterns of genetic isolation in caves. Using a comparative phylogeographic approach, we employed mitochondrial and nuclear markers to assess the evolutionary history of two ecologically distinct groups of terrestrial cave‐dwelling springtails (Collembola) in the genera Pygmarrhopalites (Arrhopalitidae) and Pogonognathellus (Tomoceridae) that are codistributed in caves throughout the Salem Plateau—a once continuous karst region, now bisected by the Mississippi River Valley in Illinois and Missouri. Contrasting phylogeographic patterns recovered for troglobiotic Pygmarrhopalites sp. and eutroglophilic Pogonognathellus sp. suggests that obligate associations with cave habitats can restrict dispersal across major geographic barriers such as rivers and valleys, but may also facilitate subterranean dispersal between neighboring cave systems. Pygmarrhopalites sp. populations spanning the Mississippi River Valley were estimated to have diverged 2.9–4.8 Ma, which we attribute to vicariance resulting from climatic and geological processes involved in Mississippi River Valley formation beginning during the late Pliocene/early Pleistocene. Lastly, we conclude that the detection of many deeply divergent, morphologically cryptic, and microendemic lineages highlights our poor understanding of microarthropod diversity in caves and exposes potential conservation concerns.

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          Revisiting the insect mitochondrial molecular clock: the mid-Aegean trench calibration.

          Phylogenetic trees in insects are frequently dated by applying a "standard" mitochondrial DNA (mtDNA) clock estimated at 2.3% My(-1), but despite its wide use reliable calibration points have been lacking. Here, we used a well-established biogeographic barrier, the mid-Aegean trench separating the western and eastern Aegean archipelago, to estimate substitution rates in tenebrionid beetles. Cytochrome oxidase I (cox1) for six codistributed genera across 28 islands (444 individuals) on both sides of the mid-Aegean trench revealed 60 independently coalescing entities delimited with a mixed Yule-coalescent model. One representative per entity was used for phylogenetic analysis of mitochondrial (cox1, 16S rRNA) and nuclear (Mp20, 28S rRNA) genes. Six nodes marked geographically congruent east-west splits whose separation was largely contemporaneous and likely to reflect the formation of the mid-Aegean trench at 9-12 Mya. Based on these "known" dates, a divergence rate of 3.54% My(-1) for the cox1 gene (2.69% when combined with the 16S rRNA gene) was obtained under the preferred partitioning scheme and substitution model selected using Bayes factors. An extensive survey suggests that discrepancies in mtDNA substitution rates in the entomological literature can be attributed to the use of different substitution models, the use of different mitochondrial gene regions, mixing of intraspecific with interspecific data, and not accounting for variance in coalescent times or postseparation gene flow. Different treatments of these factors in the literature confound estimates of mtDNA substitution rates in opposing directions and obscure lineage-specific differences in rates when comparing data from various sources.
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            GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

            Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and comparative genomics studies. However, from the same set of sequences different MSAs are often inferred, depending on the methodologies used and the assumed parameters. Much effort has recently been devoted to improving the ability to identify unreliable alignment regions. Detecting such unreliable regions was previously shown to be important for downstream analyses relying on MSAs, such as the detection of positive selection. Here we developed GUIDANCE2, a new integrative methodology that accounts for: (i) uncertainty in the process of indel formation, (ii) uncertainty in the assumed guide tree and (iii) co-optimal solutions in the pairwise alignments, used as building blocks in progressive alignment algorithms. We compared GUIDANCE2 with seven methodologies to detect unreliable MSA regions using extensive simulations and empirical benchmarks. We show that GUIDANCE2 outperforms all previously developed methodologies. Furthermore, GUIDANCE2 also provides a set of alternative MSAs which can be useful for downstream analyses. The novel algorithm is implemented as a web-server, available at: http://guidance.tau.ac.il.
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              Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution

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                Author and article information

                Contributors
                aronkatz@illinois.edu
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                24 September 2018
                October 2018
                : 8
                : 20 ( doiID: 10.1002/ece3.2018.8.issue-20 )
                : 10306-10325
                Affiliations
                [ 1 ] Department of Entomology University of Illinois at Urbana‐Champaign Urbana Illinois USA
                [ 2 ] Illinois Natural History Survey Prairie Research Institute University of Illinois at Urbana‐Champaign Champaign Illinois USA
                [ 3 ]Present address: Office of General Studies Colorado College Colorado Springs Colorado USA
                Author notes
                [*] [* ] Correspondence

                Aron D. Katz, Department of Entomology, University of Illinois at Urbana‐Champaign, Urbana, Illinois, USA.

                Email: aronkatz@ 123456illinois.edu

                Author information
                http://orcid.org/0000-0002-7810-9773
                Article
                ECE34507
                10.1002/ece3.4507
                6206200
                baa10146-0812-40f3-bd03-f6e119afebff
                © 2018 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 19 June 2018
                : 06 August 2018
                : 08 August 2018
                Page count
                Figures: 7, Tables: 6, Pages: 20, Words: 15842
                Funding
                Funded by: Cave Conservancy Foundation
                Funded by: University of Illinois at Urbana‐Champaign
                Funded by: Illinois Natural History Survey
                Funded by: National Speleological Society
                Funded by: Subterranean Ecology Institute
                Categories
                Original Research
                Original Research
                Custom metadata
                2.0
                ece34507
                October 2018
                Converter:WILEY_ML3GV2_TO_NLMPMC version:version=5.5.1 mode:remove_FC converted:30.10.2018

                Evolutionary Biology
                biospeleology,cryptic diversity,ecology,evolution,mississippi river,short‐range endemism

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