Lee, W., T.M. Milewski, M.F. Dwortz, R.L. Young, A.D. Gaudet, L.K. Fonken, F.A. Champagne, and J.P. Curley. “Distinct inflammatory and transcriptomic profiles in dominant versus subordinate males in mouse social hierarchies.” bioRxiv. Publisher's Version
Young*, R.L., B.J. Liebeskind*, D.B. Halling, R.W. Aldrich, and E.M. Marcotte. “Mapping Functional Protein Neighborhoods in the Mouse Brain.” bioRxiv. Publisher's Version
Chan, M.E., P.S. Bhamidipati, H.J. Goldsby, A. Hintze, H.A. Hofmann, and R.L. Young. “Comparative Transcriptomics Reveals Distinct Patterns of Gene Expression Conservation through Vertebrate Embryogenesis.” Genome Biology and Evolution 13 (8). Publisher's Version
Hernandez Scudder*, M.E., R.L. Young*, L.M. Thompson, P. Kore, D. Crews, H.A. Hofmann, and A.C. Gore. “EDCs Reorganize Brain-Behavior Phenotypic Relationships in Rats.” Journal of the Endocrine Society 5 (5). Publisher's Version
Eastman, G., G. Valiño, S. Radío, R.L. Young, L. Quintana, H.H. Zakon, H.A. Hofmann, J. Sotelo-Silveira, and A. Silva. “Brain transcriptomics of agonistic behaviour in the weakly electric fish Gymnotus omarorum, a wild teleost model of non-breeding aggression.” Scientific Reports 10 (1): 1-11. Publisher's Version
Young, R.L., and H.A. Hofmann. “Reply to Jiang and Zhang: Parallel transcriptomic signature of monogamy: What is the null hypothesis anyway?.” Proceeding of the National Academy of Sciences 116 (36): 17629-17630. Publisher's Version
Young, R.L., M.H. Ferkin, N.F. Ockendon, V.N. Orr, S.M. Phelps, Á Pogány, C.L. Richards-Zawacki, et al.Conserved transcriptomic profiles underpin monogamy across vertebrates.” Proceeding of the National Academy of Sciences 116 (4): 1331-1336.
Goldsby, H.J., R.L. Young, J. Schossau, H.A. Hofmann, and A. Hintze. “Serendipitous scaffolding to improve a genetic algorithm's speed and quality..” Proceedings of the Genetic and Evolutionary Computation Conference Companion (GECCO '18), 959-966.
Goldsby, H.J., R.L. Young, H.A. Hofmann, and A. Hintze. “Increasing the complexity of solutions produced by an evolutionary developmental system. .” Proceedings of the 2017 on Genetic and Evolutionary Computation Conference.
Snell-Rood, Emilie C, Eli Swanson, and Rebecca L. Young. “Life history as a constraint on plasticity: developmental timing is correlated with phenotypic variation in birds.” Heredity 115 (4): 379-88.Abstract

Understanding why organisms vary in developmental plasticity has implications for predicting population responses to changing environments and the maintenance of intraspecific variation. The epiphenotype hypothesis posits that the timing of development can constrain plasticity—the earlier alternate phenotypes begin to develop, the greater the difference that can result amongst the final traits. This research extends this idea by considering how life history timing shapes the opportunity for the environment to influence trait development. We test the prediction that the earlier an individual begins to actively interact with and explore their environment, the greater the opportunity for plasticity and thus variation in foraging traits. This research focuses on life history variation across four groups of birds using museum specimens and measurements from the literature. We reasoned that greater phenotypic plasticity, through either environmental effects or genotype-by-environment interactions in development, would be manifest in larger trait ranges (bills and tarsi) within species. Among shorebirds and ducks, we found that species with relatively shorter incubation times tended to show greater phenotypic variation. Across warblers and sparrows, we found little support linking timing of flight and trait variation. Overall, our results also suggest a pattern between body size and trait variation, consistent with constraints on egg size that might result in larger species having more environmental influences on development. Taken together, our results provide some support for the hypothesis that variation in life histories affects how the environment shapes development, through either the expression of plasticity or the release of cryptic genetic variation.

Young, Rebecca L.Linking conceptual mechanisms and transcriptomic evidence of plasticity-driven diversification.” Molecular Ecology 22 (17): 4363 - 4365.Abstract

The East African cichlid fishes provide text book examples of adaptive radiation. Diversification and speciation of cichlids associate with variation in diet and trophic morphologies among other ecological, behavioural and morphological phenotypes (Kocher 2004). Numerous case studies in cichlids reveal a role of developmental plasticity in generating jaw ecomorphs in response to variation in feeding ecology that can facilitate niche exploitation and subsequent diversification (e.g. Meyer 1987). Specifically, genetic divergence among such environmentally induced morphs can occur via reproductive isolation due to divergence in habitat and resource use in combination with genetic assimilation of environmentally induced phenotypes (West-Eberhard 2003; Pfenniget al. 2010). Expansion of this conceptual model has been hampered in part by the limited knowledge of the molecular mechanisms of plasticity in nonstandard model systems and the associated lack of evidence linking the molecular mechanisms of plasticity to those that generate phenotypic divergence among populations and taxa. In this issue of Molecular Ecology, Gunteret al. (2013) identify the transcriptional mechanisms of diet-induced lower pharyngeal jaw (LPJ) plasticity in the cichlid fish Astatoreochromis alluaudi. Natural populations of A. alluaudi exhibit variation in jaw morphology in relation to diet hardness. Among the plastic responses to diet are adjustments to the LPJ ranging from a robust molariform morph in response to a hard diet to a more gracile papilliform morph in response to a soft diet (Fig. 1). Gunter and colleagues induced developmental plasticity of the A. alluaudi jaw using diet manipulations and compared LPJ transcriptomic profiles of the resulting morphs. In this foundational work, the authors identify 187 differentially expressed genes that underlie the development and maintenance of diet-induced LPJ morphologies. This list includes a wide range of genes spanning from broad-acting transcription factors to signalling molecules and structural genes. Here, I examine the ontogeny of the molecular response to mechanical strain imposed by diet hardness and discuss the role of the stages of this response in the evolution of plasticity and plasticity-driven diversification.

Brandley, Matthew C., Rebecca L. Young, Dan L Warren, Michael B. Thompson, and Günter P Wagner. “Uterine Gene Expression in the Live-Bearing Lizard, Chalcides ocellatus, Reveals Convergence of Squamate Reptile and Mammalian Pregnancy Mechanisms.” Genome Biology and Evolution 4 (3): 394 - 411.Abstract
Although the morphological and physiological changes involved in pregnancy in live-bearing reptiles are well studied, the genetic mechanisms that underlie these changes are not known. We used the viviparous African Ocellated Skink, Chalcides ocellatus, as a model to identify a near complete gene expression profile associated with pregnancy using RNA-Seq analyses of uterine transcriptomes. Pregnancy in C. ocellatus is associated with upregulation of uterine genes involved with metabolism, cell proliferation and death, and cellular transport. Moreover, there are clear parallels between the genetic processes associated with pregnancy in mammals and Chalcides in expression of genes related to tissue remodeling, angiogenesis, immune system regulation, and nutrient provisioning to the embryo. In particular, the pregnant uterine transcriptome is dominated by expression of proteolytic enzymes that we speculate are involved both with remodeling the chorioallantoic placenta and histotrophy in the omphaloplacenta. Elements of the maternal innate immune system are downregulated in the pregnant uterus, indicating a potential mechanism to avoid rejection of the embryo. We found a downregulation of major histocompatability complex loci and estrogen and progesterone receptors in the pregnant uterus. This pattern is similar to mammals but cannot be explained by the mammalian model. The latter finding provides evidence that pregnancy is controlled by different endocrinological mechanisms in mammals and reptiles. Finally, 88% of the identified genes are expressed in both the pregnant and the nonpregnant uterus, and thus, morphological and physiological changes associated with C. ocellatus pregnancy are likely a result of regulation of genes continually expressed in the uterus rather than the initiation of expression of unique genes.
Young, Rebecca L., and Günter P Wagner. “Why ontogenetic homology criteria can be misleading: lessons from digit identity transformations..” Journal of experimental zoology. Part B, Molecular and developmental evolution 316B (3): 165 - 70.Abstract
As the basis for comparative biology, correctly assigning character homology is critical. Yet, identifying homologous characters in practice is often challenging. Among the major roadblocks is that the mechanistic bases of character homology remain in question. Thus, investigators must rely on several independent lines of evidence (e.g., character anatomy, phylogenetic distribution, or embryological position); however, these distinct sources of evidence often lead to conflicting diagnoses of character homology. What is more, there is no consensus regarding the relative importance of distinct lines of evidence for determining character homology. Here, we review the difficulties that have hindered the search for the mechanistic bases of character identity, and relate these issues to a recently proposed mechanistic hypothesis of character identity--the Character Identity Network Hypothesis. Next, using two well-studied cases of homology conflict (i.e., avian and skink digit identity), we assess the utility of different lines of evidence in diagnosing homology. We conclude that, when comparing adult structures, because anatomical characters more closely reflect the actions of the developmental genetic mechanisms of character individuation they are more reliable than embryological homology criteria.
Young, Rebecca L., Gabe S Bever, Zhe Wang, and Günter P Wagner. “Identity of the avian wing digits: Problems resolved and unsolved.” Developmental Dynamics 240 (5). Wiley-Liss, Inc.: 1042 - 1053.Abstract

Controversy over bird wing digit identity has been a touchstone for various ideas in the phylogeny of birds, homology, and developmental evolution. This review summarizes the past 10 years of progress toward understanding avian digit identity. We conclude that the sum of evidence supports the Frame Shift Hypothesis, indicating that the avian wing digits have changed anatomical location. Briefly, the derivation of birds from theropod dinosaurs and the positional identities of the avian wing digits as 2, 3, and 41 are no longer in question. Additionally, increasing evidence indicates that the developmental programs for identity of the wing digits are of digits I, II, and III. Therefore, the attention moves from whether the digit identity frame shift occurred, to what the mechanisms of the frame shift were, and when in evolution it happened. There is considerable uncertainty about these issues and we identify exciting new research directions to resolve them. Developmental Dynamics 240:1042–1053, 2011. © 2011 Wiley-Liss, Inc.

Wang, Zhe, Rebecca L. Young, Huiling Xue, and Gunter P Wagner. “Transcriptomic analysis of avian digits reveals conserved and derived digit identities in birds.” Nature 477 (7366). Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.: 583 - 586.Abstract

Morphological characters are the result of developmental gene expression. The identity of a character is ultimately grounded in the gene regulatory network directing development and thus whole-genome gene expression data can provide evidence about character identity. This approach has been successfully used to assess cell-type identity123. Here we use transcriptomic data to address a long-standing uncertainty in evolutionary biology, the identity of avian wing digits45. Embryological evidence clearly identifies the three wing digits as developing from digit positions 2, 3 and 4 (ref. 6), whereas palaeontological data suggest that they are digits I, II and III7. We compare the transcriptomes of the wing and foot digits and find a strong signal that unites the first wing digit with the first foot digit, even though the first wing digit develops from embryological position 2. Interestingly, our transcriptomic data of the posterior digits show a higher degree of differentiation among forelimb digits compared with hindlimb digits. These data show that in the stem lineage of birds the first digit underwent a translocation from digit position 1 to position 2, and further indicate that the posterior wing digits have unique identities contrary to any model of avian digit identity proposed so far58.

Young, Rebecca L., and Alexander V Badyaev. “Developmental plasticity links local adaptation and evolutionary diversification in foraging morphology..” Journal of experimental zoology. Part B, Molecular and developmental evolution 314 (6): 434 - 44.Abstract
Developmental plasticity is thought to reconcile the constraining role of natural selection in maintaining local adaptation with evolutionary diversification under novel conditions, but empirical documentations are rare. In vertebrates, growth and development of bones is partially guided by contractions of attached musculature and such muscle activity changes progressively through embryonic development from sporadic motility to direct functional effects. In species with short generation times, delayed skull maturation extends the guiding effects of muscle activity on formation of foraging morphology into adulthood, providing an opportunity to directly examine the links between plasticity of bone development, ecological adaptations, and evolutionary diversification in foraging morphology. In this case, the morphological consequences of inputs due to local functional requirements should be evident in adaptive divergence across taxa. Here we provide evidence that epigenetic regulation of bone growth in Soricid shrews may enable both development of local adaptations and evolutionary divergence in mandibular morphology. We contrast the effects of muscle stimulation on early- vs. late-maturing components of, foraging apparatus to show that the morphology of late-maturing components is more affected by functional requirements than are early-ossifying traits. Further, the divergence in foraging morphology across shrew species occurs along the directions delineated by inductive effects of muscle loading and bite force on bone formation in late-maturing but not early-maturing mandible components within species. These results support the hypothesis that developmental plasticity can link maintenance of local adaptations with evolutionary diversification in morphology.
Young, Rebecca L., Michael J. Sweeney, and Alexander V Badyaev. “Morphological diversity and ecological similarity: versatility of muscular and skeletal morphologies enables ecological convergence in shrews.” Functional Ecology 24 (3): 556 - 565.Abstract


1. Ecological convergence in morphology among taxa of distinct evolutionary histories is a common illustration of the efficacy of natural selection. Ecological convergence is often enabled by functional redundancy of complex morphological structures, such that modification of existing morphologies in response to similar functional requirements can lead to the development and evolution of morphological diversity. Thus, studies of the mechanisms that enable the development of similar adaptations in taxa with distinct morphologies provide important insights into both the evolution of past adaptations and patterns of future evolutionary divergence.

2. Here, we examine mechanisms that have enabled ecological convergence in foraging morphology among four geographically isolated and morphologically distinct populations of shrews: south-eastern Arizona and north-central New Mexico populations of the montane shrews (Sorex monticolus) and northern California and north-central Montana populations of the vagrant shrew (S. vagrans).

3. We show that despite overlap in diet, populations had distinct skeletal and muscular morphologies of the mandible. This association between ecological convergence and morphological uniqueness among populations was enabled by versatility of foraging morphologies that generated similar functional outputs.

4. In addition, we found that populations exhibited unique skeletal and muscular correlations with diet suggesting that distinct muscular and morphological components of the complex foraging apparatus can be used for a particular resource. This result corroborates a previous finding that extensive modularity in mandibular development allows diverse morphologies to generate equivalent functions and utilize similar resources across taxa.

5.Synthesis. We conclude that the observed functional and ecological convergences resulted from population-specific musculoskeletal interactions, and suggest that the differences in skeletal and muscular morphologies observed among these populations reflect evolved differences in plasticity of the skeletal and muscular components of the mandible.

Evolution of digit identity in the three-toed Italian skink Chalcides chalcides: a new case of digit identity frame shift
Young, Rebecca L., Vincenzo Caputo, Massimo Giovannotti, Tiana Kohlsdorf, Alexander O Vargas, Gemma E May, and Gunter P Wagner. “Evolution of digit identity in the three-toed Italian skink Chalcides chalcides: a new case of digit identity frame shift.” Evol Dev 11: 647 - 658.Abstract

Digit identity in the avian wing is a classical example of conflicting anatomical and embryological evidence regarding digit homology. Anatomical in conjunction with phylogenetic evidence supports the hypothesis that the three remaining digits in the bird wing are digits 1, 2, and 3. At the same time, various lines of embryological evidence support the notion that these digits develop in positions that normally produce digits 2, 3, and 4. In recent years, gene expression as well as experimental evidence was published that supports the hypothesis that this discrepancy arose from a digit identity shift in the evolution of the bird wing. A similar but less well-known controversy has been ongoing since the late 19th century regarding the identity of the digits of the three-toed Italian skink, Chalcides chalcides. Comparative anatomy identifies these digits as 1, 2, and 3, while embryological evidence suggests their derivation from embryological positions 2, 3, and 4. Here we re-examine this evidence and add gene expression data to determine the identity of the three digits of C. chalcides. The data confirm that the adult and the embryological evidence for digit identity are in conflict, and the expression of Hoxd11 suggests that digits 1, 2, and 3 develop in positions 2, 3, and 4. We conclude that in C. chalcides, and likely in its close relatives, a digit identity frame shift has occurred, similar to the one in avian evolution. This result suggests that changes in of digit identity might be a more frequent consequence of digit reduction than previously assumed.

F1000 Recommended

Badyaev, Alexander V, Rebecca L. Young, Geoffery E Hill, and Renee A Duckworth. “Evolution of sex-biased maternal effects in birds. IV. Intra-ovarian growth dynamics can link sex determination and sex-specific acquisition of resources.” Journal of Evolutionary Biology 21: 449 - 460.Abstract

The evolutionary importance of maternal effects is determined by the interplay of maternal adaptations and strategies, offspring susceptibility to these strategies, and the similarity of selection pressures between the two generations. Interaction among these components, especially in species where males and females differ in the costs and requirements of growth, limits inference about the evolution of maternal strategies from their expression in the offspring phenotype alone. As an alternative approach, we examine divergence in the proximate mechanisms underlying maternal effects across three house finch populations with contrasting patterns of sex allocation: an ancestral population that shows no sex-biased ovulation, and two recently established populations at the northern and southern boundaries of the species range that have opposite sequences of ovulation of male and female eggs. For each population, we examined how oocyte acquisition of hormones, carotenoids and vitamins was affected by oocyte growth and overlap with the same and opposite sexes. Our results suggest that sex-specific acquisition of maternal resources and sex determination of oocytes are linked in this system. We report that acquisition of testosterone by oocytes that become males was not related to growth duration, but instead covaried with temporal exposure to steroids and overlap with other male oocytes. In female oocytes, testosterone acquisition increased with the duration of growth and overlap with male oocytes, but decreased with overlap with female oocytes. By contrast, acquisition of carotenoids and vitamins was mostly determined by organism-wide partitioning among oocytes and oocyte-specific patterns of testosterone accumulation, and these effects did not differ between the sexes. These results provide important insights into three unresolved phenomena in the evolution of maternal effects - (i) the evolution of sex-specific maternal allocation in species with simultaneously developing neonates of both sexes; (ii) the link between sex determination and sex-specific acquisition of maternal products; and (iii) the evolution of context-dependent modulation of maternal effects.

Badyaev, Alexander V, Rebecca.L. Young, Kevin P Oh, and Clayton Addison. “Evolution on a local scale: Developmental, functional, and genetic bases of divergence in bill form and associated changes in song structure between adjacent habitats.” Evolution 62 (8): 1951 - 1964.Abstract

Divergent selection on traits involved in both local adaptation and the production of mating signals can strongly facilitate population differentiation. Because of its links to foraging morphologies and cultural inheritance song of birds can contribute particularly strongly to maintenance of local adaptations. In two adjacent habitats2014native Sonoran desert and urban areas2014house finches (Carpodacus mexicanus) forage on seeds that are highly distinct in size and shell hardness and require different bite forces and bill morphologies. Here, we first document strong and habitat-specific natural selection on bill traits linked to bite force and find adaptive modifications of bite force and bill morphology and associated divergence in courtship song between the two habitats. Second, we investigate the developmental basis of this divergence and find that early ontogenetic tissue transformation in bill, but not skeletal traits, is accelerated in the urban population and that the mandibular primordia of the large-beaked urban finches express bone morphogenetic proteins (BMP) earlier and at higher level than those of the desert finches. Further, we show that despite being geographically adjacent, urban and desert populations are nevertheless genetically distinct corroborating findings of early developmental divergence between them. Taken together, these results suggest that divergent selection on function and development of traits involved in production of mating signals, in combination with localized learning of such signals, can be very effective at maintaining local adaptations, even at small spatial scales and in highly mobile animals.