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Mei Liu, Yang Zhou, Benjamin D Rosen, Curtis P Van Tassell, Alessandra Stella, Gwenola Tosser-Klopp, Rachel Rupp, Isabelle Palhière, Licia Colli, Brian Sayre, Paola Crepaldi, Lingzhao Fang, Gábor Mészáros, Hong Chen, George E Liu
Goats (Capra hircus) are an important farm animal species. Copy number variation (CNV) represents a major source of genomic structural variation. We investigated the diversity of CNV distribution in goats using CaprineSNP50 genotyping data generated by the ADAPTmap Project. We identified 6286 putative CNVs in 1023 samples from 50 goat breeds using PennCNV. These CNVs were merged into 978 CNV regions, spanning ~262 Mb of total length and corresponding to ~8.96% of the goat genome. We then divided the samples into six subgroups per geographic distribution and constructed a comparative CNV map...
November 6, 2018: Heredity
Václav Janoušek, Jitka Fischerová, Libor Mořkovský, Jiří Reif, Marcin Antczak, Tomáš Albrecht, Radka Reifová
The X and Z sex chromosomes play a disproportionately large role in intrinsic postzygotic isolation. The underlying mechanisms of this large X/Z effect are, however, still poorly understood. Here we tested whether faster rates of molecular evolution caused by more intense positive selection or genetic drift on the Z chromosome could contribute to the large Z effect in two closely related passerine birds, the Common Nightingale (Luscinia megarhynchos) and the Thrush Nightingale (L. luscinia). We found that the two species differ in patterns of molecular evolution on the Z chromosome...
October 29, 2018: Heredity
Valerio Hoyos-Villegas, Vivi N Arief, Wen-Hsi Yang, Mingzhu Sun, Ian H DeLacy, Brent A Barrett, Zulfi Jahufer, Kaye E Basford
Plant breeders are supported by a range of tools that assist them to make decisions about the conduct or design of plant breeding programs. Simulations are a strategic tool that enables the breeder to integrate the multiple components of a breeding program into a number of proposed scenarios that are compared by a range of statistics measuring the efficiency of the proposed systems. A simulation study for the trait growth score compared two major strategies for breeding forage species, among half-sib family selection and among and within half-sib family selection...
October 27, 2018: Heredity
Emily Veltjen, Pieter Asselman, Majela Hernández Rodríguez, Alejandro Palmarola Bejerano, Ernesto Testé Lozano, Luis Roberto González Torres, Paul Goetghebeur, Isabel Larridon, Marie-Stéphanie Samain
Conserving tree populations safeguards forests since they represent key elements of the ecosystem. The genetic characteristics underlying the evolutionary success of the tree growth form: high genetic diversity, extensive gene flow and strong species integrity, contribute to their survival in terms of adaptability. However, different biological and landscape contexts challenge these characteristics. This study employs 63 de novo developed microsatellite or SSR (Single Sequence Repeat) markers in different datasets of nine Neotropical Magnolia species...
October 27, 2018: Heredity
Sara Faggion, Marc Vandeputte, Béatrice Chatain, Pierre-Alexandre Gagnaire, François Allal
Polygenic sex determination (PSD) may show variations in terms of genetic and environmental components between populations of fish species exposed/adapted to different environments. The European sea bass (Dicentrarchus labrax) is an interesting model, combining both a PSD system and a genetic subdivision into an Atlantic and a Mediterranean lineage, with genetic substructures within the Mediterranean Sea. Here, we produced experimental progeny crosses (N = 927) from broodstock sampled in four wild populations (North Atlantic, NAT; Western Mediterranean, WEM; North-Eastern Mediterranean, NEM; South-Eastern Mediterranean, SEM)...
October 24, 2018: Heredity
Enoch Ng'oma, Wilton Fidelis, Kevin M Middleton, Elizabeth G King
The nutritional conditions experienced by a population have a major role in shaping trait evolution in many taxa. Constraints exerted by nutrient limitation or nutrient imbalance can influence the maximal value that fitness components such as reproduction and lifespan attains, and organisms may shift how resources are allocated to different structures and functions in response to changes in nutrition. Whether the phenotypic changes associated with changes in nutrition represent an adaptive response is largely unknown...
October 24, 2018: Heredity
A Paz, Z Spanos, J L Brown, M Lyra, C Haddad, M Rodrigues, A Carnaval
Recent advances in the field of landscape genetics provide ways to jointly analyze the role of present-day climate and landscape configuration in current biodiversity patterns. Expanding this framework into a phylogeographic study, we incorporate information on historical climatic shifts, tied to descriptions of the local topography and river configuration, to explore the processes that underlie genetic diversity patterns in the Atlantic Forest hotspot. We study two montane, stream-associated species of glassfrogs: Vitreorana eurygnatha and V...
October 24, 2018: Heredity
Zhiqiang Wu, Daniel B Sloan
Although mitochondrial genomes are typically thought of as single circular molecules, these genomes are fragmented into multiple chromosomes in many eukaryotes, raising intriguing questions about inheritance and (in)stability of mtDNA in such systems. A previous comparison of mitochondrial genomes from two different individuals of the angiosperm species Silene noctiflora found variation in the presence of entire mitochondrial chromosomes. Here, we expand on this work with a geographically diverse sampling of 25 S...
October 24, 2018: Heredity
Bahar Patlar, Michael Weber, Steven A Ramm
Seminal fluid proteins (SFPs) are crucial mediators of sexual selection and sexual conflict. Recent studies have chiefly focused on environmentally induced plasticity as one source of variation in SFP expression, particularly in response to differing sperm competition levels. However, understanding the evolution of a trait in heterogenous environments requires estimates of both environmental and genetic sources of variation, as well as their interaction. Therefore, we investigated how environment (specifically mating group size, a good predictor of sperm competition intensity), genotype and genotype-by-environment interactions affect seminal fluid expression...
October 24, 2018: Heredity
Junli Xue, Haiguang Zhang, Xin Ning, Wenjun Bu, Xin Yu
Matrona basilaris Selys, 1853 is a damselfly distributed mainly in mainland China. A total of 423 individuals from 48 populations covering almost the entire range were sampled to explore the genetic diversity, phylogeographic structure, and demographic dynamics of the species using sequences of three mitochondrial genes (COI, COII, and ND1) and a nuclear (ITS1 + 5.8 S + ITS2) gene. Phylogenetic tree, median-joining network, and BAPS analyses indicated a four-group division of the entire population, and the divergence event was estimated to have occurred in the middle Pleistocene...
October 24, 2018: Heredity
Mari Suontama, Jaroslav Klápště, Emily Telfer, Natalie Graham, Toby Stovold, Charlie Low, Russell McKinley, Heidi Dungey
Published online: 6 July 2018This article was originally published under standard licence, but has now been made available under a [CC BY 4.0] license. The PDF and HTML versions of the paper have been modified accordingly.
October 22, 2018: Heredity
Joseph M Styga, Thomas M Houslay, Alastair J Wilson, Ryan L Earley
Heritable variation in, and genetic correlations among, traits determine the response of multivariate phenotypes to natural selection. However, as traits develop over ontogeny, patterns of genetic (co)variation and integration captured by the G matrix may also change. Despite this, few studies have investigated how genetic parameters underpinning multivariate phenotypes change as animals pass through major life history stages. Here, using a self-fertilizing hermaphroditic fish species, mangrove rivulus (Kryptolebias marmoratus), we test the hypothesis that G changes from hatching through reproductive maturation...
October 16, 2018: Heredity
Lynette R Strickland, Carlos F Arias, Viterbo Rodriguez, J Spencer Johnston, W Owen McMillan, Donald Windsor
Intraspecific variation maintained in natural populations has long intrigued scientists and naturalists. One form of this variation, color polymorphisms, provide a rich opportunity to connect genotypic and phenotypic diversity within an ecological and evolutionary context. The existence of color polymorphisms in Panamanian populations of the Neotropical tortoise beetle, Chelymorpha alternans, has been suspected but never systematically explored. To characterize geographic distribution and underlying genetics we sampled a total of 3819 beetles from 28 sites across Panama, quantifying five distinct phenotypes...
October 12, 2018: Heredity
Deniz Akdemir, William Beavis, Roberto Fritsche-Neto, Asheesh K Singh, Julio Isidro-Sánchez
The purpose of breeding programs is to obtain sustainable gains in multiple traits while controlling the loss of genetic variation. The decisions at each breeding cycle involve multiple, usually competing, objectives; these complex decisions can be supported by the insights that are gained by applying multi-objective optimization principles to breeding. The discussion in this manuscript includes the definition of several multi-objective optimized breeding approaches within the phenotypic or genomic breeding frameworks and the comparison of these approaches with the standard multi-trait breeding schemes such as tandem selection, independent culling and index selection...
September 27, 2018: Heredity
K Sagonas, A Runemark, A Antoniou, P Lymberakis, P Pafilis, E D Valakos, N Poulakakis, B Hansson
The major histocompatibility complex (MHC) has long served as a model for the evolution of adaptive genetic diversity in wild populations. Pathogen-mediated selection is thought to be a main driver of MHC diversity, but it remains elusive to what degree selection shapes MHC diversity in complex biogeographical scenarios where other evolutionary processes (e.g. genetic drift and introgression) may also be acting. Here we focus on two closely related green lizard species, Lacerta trilineata and L. viridis, to address the evolutionary forces acting on MHC diversity in populations with different biogeographic structure...
September 26, 2018: Heredity
Ceferino Varón-González, Nicolas Navarro
Fluctuating asymmetry is a classic concept linked to organismal development. It has traditionally been used as a measure of developmental instability, which is the inability of an organism to buffer environmental fluctuations during development. Developmental stability has a genetic component that influences the final phenotype of the organism and can lead to congenital disorders. According to alternative hypotheses, this genetic component might be either the result of additive genetic effects or a by-product of developmental gene networks...
September 12, 2018: Heredity
Shannon R Kjeldsen, Herman W Raadsma, Kellie A Leigh, Jennifer R Tobey, David Phalen, Andrew Krockenberger, William A Ellis, Emily Hynes, Damien P Higgins, Kyall R Zenger
The Australian koala is an iconic marsupial with highly specific dietary requirements distributed across heterogeneous environments, over a large geographic range. The distribution and genetic structure of koala populations has been heavily influenced by human actions, specifically habitat modification, hunting and translocation of koalas. There is currently limited information on population diversity and gene flow at a species-wide scale, or with consideration to the potential impacts of local adaptation. Using species-wide sampling across heterogeneous environments, and high-density genome-wide markers (SNPs and PAVs), we show that most koala populations display levels of diversity comparable to other outbred species, except for those populations impacted by population reductions...
September 12, 2018: Heredity
Matthew G Orton, Jacqueline A May, Winfield Ly, David J Lee, Sarah J Adamowicz
The evolutionary speed hypothesis (ESH) suggests that molecular evolutionary rates are higher among species inhabiting warmer environments. Previously, the ESH has been investigated using small numbers of latitudinally-separated sister lineages; in animals, these studies typically focused on subsets of Chordata and yielded mixed support for the ESH. This study analyzed public DNA barcode sequences from the cytochrome c oxidase subunit I (COI) gene for six of the largest animal phyla (Arthropoda, Chordata, Mollusca, Annelida, Echinodermata, and Cnidaria) and paired latitudinally-separated taxa together informatically...
September 10, 2018: Heredity
Shaoxiong Ding, Mrinal Mishra, Haohao Wu, Shuang Liang, Michael M Miyamoto
Following the publication of this article, the authors have requested that the Acknowledgements section be amended to thank Weidi Yang for his assistance with their Bostrychus sinensis photograph that was chosen for the front cover of the January 2018 issue of the journal. This error has been corrected in both the PDF and HTML versions of the paper. Also, the legends for Supplementary Figures 1 and 2 were not posted online. This error has been corrected in the HTML version of the paper.
September 6, 2018: Heredity
Elena Torres, María-Lorena Riofrío, José M Iriondo
Orchid seeds are presumably dispersed by wind due to their very small size and thus can potentially travel long distances. However, the few related studies indicate that seeds fall close to their mother plants. Because seed dispersal and colonization patterns can have relevant consequences for long-term species persistence, we assessed the fine-scale genetic structure of the epiphytic orchid Epidendrum rhopalostele to provide insight into these patterns. All individuals in the studied population were georeferenced and genotyped with AFLP-markers...
September 5, 2018: Heredity
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