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      Genetic architecture facilitates then constrains adaptation in a host–parasite coevolutionary arms race

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          Validating an almost century-old hypothesis, we show that a critical host-specific adaptation in a brood-parasitic bird, mimicry of host egg coloration, is maternally inherited, allowing mothers to transmit specialized mimicry to their daughters irrespective of the father’s host species. This genetic architecture, however, is a double-edged sword for parasites: the loss of recombination and heterozygosity as sources of evolutionary novelty likely constrains the parasite from mimicking the full range of color polymorphisms that hosts have evolved as an escalated defense against parasitism. This important tradeoff of asexual inheritance may have relevance for understanding coevolution in other host–parasite systems.

          Abstract

          In coevolutionary arms races, interacting species impose selection on each other, generating reciprocal adaptations and counter adaptations. This process is typically enhanced by genetic recombination and heterozygosity, but these sources of evolutionary novelty may be secondarily lost when uniparental inheritance evolves to ensure the integrity of sex-linked adaptations. We demonstrate that host-specific egg mimicry in the African cuckoo finch Anomalospiza imberbis is maternally inherited, confirming the validity of an almost century-old hypothesis. We further show that maternal inheritance not only underpins the mimicry of different host species but also additional mimetic diversification that approximates the range of polymorphic egg “signatures” that have evolved within host species as an escalated defense against parasitism. Thus, maternal inheritance has enabled the evolution and maintenance of nested levels of mimetic specialization in a single parasitic species. However, maternal inheritance and the lack of sexual recombination likely disadvantage cuckoo finches by stifling further adaptation in the ongoing arms races with their individual hosts, which we show have retained biparental inheritance of egg phenotypes. The inability to generate novel genetic combinations likely prevents cuckoo finches from mimicking certain host phenotypes that are currently favored by selection (e.g., the olive-green colored eggs laid by some tawny-flanked prinia, Prinia subflava, females). This illustrates an important cost of coding coevolved adaptations on the nonrecombining sex chromosome, which may impede further coevolutionary change by effectively reversing the advantages of sexual reproduction in antagonistic coevolution proposed by the Red Queen hypothesis.

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          Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

          Abstract Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) plays a central role in understanding evolutionary history from molecular sequence data. Visualizing and analyzing the MCMC-generated samples from the posterior distribution is a key step in any non-trivial Bayesian inference. We present the software package Tracer (version 1.7) for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more. Tracer is open-source and available at http://beast.community/tracer.
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            jModelTest 2: more models, new heuristics and parallel computing.

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              Inference of Population Structure Using Multilocus Genotype Data

              We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
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                Author and article information

                Journal
                Proc Natl Acad Sci U S A
                Proc Natl Acad Sci U S A
                pnas
                PNAS
                Proceedings of the National Academy of Sciences of the United States of America
                National Academy of Sciences
                0027-8424
                1091-6490
                12 April 2022
                26 April 2022
                12 October 2022
                : 119
                : 17
                : e2121752119
                Affiliations
                [1] aDepartment of Zoology, University of Cambridge , Cambridge CB2 3EJ, United Kingdom;
                [2] bFitzPatrick Institute of African Ornithology, Department of Science and Technology–National Research Foundation Centre of Excellence, University of Cape Town , Rondebosch 7701, South Africa;
                [3] cDepartment of Biology, Boston University , Boston, MA 02215;
                [4] dBiology Department, Boston College , Chestnut Hill, MA 02467;
                [5] eChenga Farm , Choma, Southern Province, Zambia;
                [6] fMusumanene Farm , Choma, Southern Province, Zambia;
                [7] gBuffalo Farm , Choma, Southern Province, Zambia
                Author notes
                1To whom correspondence may be addressed. Email: cns26@ 123456cam.ac.uk or msoren@ 123456bu.edu .

                Edited by Douglas Futuyma, Stony Brook University, Stony Brook, NY; received November 30, 2021; accepted February 11, 2022

                Author contributions: C.N.S. and M.D.S. designed research; C.N.S., W.T., G.A.J., K.F.S., J.M.D., E.R.K., A.G., S.H., I.G.T., C.M., and M.D.S. performed research; C.N.S. and M.D.S. analyzed data; C.N.S. and M.D.S. wrote the paper; and all authors contributed to revisions.

                Author information
                https://orcid.org/0000-0002-2766-7687
                https://orcid.org/0000-0001-5375-2917
                Article
                202121752
                10.1073/pnas.2121752119
                9170059
                35412865
                29daeb48-d8ca-4ac2-8d3f-f95a9e1568f9
                Copyright © 2022 the Author(s). Published by PNAS.

                This article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).

                History
                : 11 February 2022
                Page count
                Pages: 8
                Funding
                Funded by: RCUK | Biotechnology and Biological Sciences Research Council (BBSRC) 501100000268
                Award ID: BB/J014109/1
                Award Recipient : Claire N Spottiswoode Award Recipient : Wenfei Tong Award Recipient : Gabriel Jamie
                Funded by: Royal Society 501100000288
                Award ID: Dorothy Hodgkin Fellowship
                Award Recipient : Claire N Spottiswoode
                Funded by: National Research Foundation (NRF) 501100001321
                Award ID: DST-NRF Centre of Excellence at the FitzPatrick Institute
                Award Recipient : Claire N Spottiswoode
                Funded by: National Science Foundation (NSF) 100000001
                Award ID: DEB 0640759
                Award Recipient : Michael D Sorenson
                Categories
                Biological Sciences
                Evolution

                coevolution,gentes,maternal inheritance,mimicry,w chromosome

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