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Replicated clines across environmental gradients can be strong evidence of adaptation. House mice (Mus musculus domesticus) were introduced to the Americas by European colonizers and are now widely distributed from Tierra del Fuego to Alaska. Multiple aspects of climate, such as temperature, vary predictably across latitude in the Americas. Past studies of North American populations across latitudinal gradients provided evidence of environmental adaptation in traits related to body size, metabolism, and behavior and identified candidate genes using selection scans. Here, we investigate genomic signals of environmental adaptation on a second continent, South America, and ask whether there is evidence of parallel adaptation across multiple latitudinal transects in the Americas. We first identified loci across the genome showing signatures of selection related to climatic variation in mice sampled across a latitudinal transect in South America, accounting for neutral population structure. Consistent with previous results, most candidate SNPs were in putatively regulatory regions. Genes that contained the most extreme outliers relate to traits such as body weight or size, metabolism, immunity, fat, eye function, and the cardiovascular system. We then compared these results with the results of analyses of published data from two transects in North America. While most candidate genes were unique to individual transects, we found significant overlap among candidate genes identified independently in the three transects. These genes are diverse, with functions relating to metabolism, immunity, cardiac function, and circadian rhythm, among others. We also found parallel shifts in allele frequency in candidate genes across latitudinal gradients. Finally, combining data from all three transects, we identified several genes associated with variation in body weight. Overall, our results provide strong evidence of shared responses to selection and identify genes that likely underlie recent environmental adaptation in house mice across North and South America., Competing Interests: The authors have declared that no competing interest exist., (Copyright: © 2024 Gutiérrez-Guerrero et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

In the species-rich family Phyllostomidae, the genus Macrotus ('big eared' bats) contains only two species; Macrotus waterhousii, distributed in western, central, and southern Mexico, Guatemala and some Caribbean Islands, and Macrotus californicus, distributed in the southwestern USA, and in the Baja California peninsula and the state of Sonora in Mexico. In this study, we sequenced and assembled the mitochondrial genome of Macrotus waterhousii and characterized in detail this genome and that of the congeneric M. californicus. Then, we examined the phylogenetic position of Macrotus in the family Phyllostomidae based on protein coding genes (PCGs). The AT-rich mitochondrial genomes of M. waterhousii and M. californicus are 16,792 and 16,691 bp long, respectively, and each encode 13 PCGs, 22 tRNA genes, 2 rRNA genes, and a putative non-coding control region 1,336 and 1,232 bp long, respectively. Mitochondrial synteny in Macrotus is identical to that reported before for all other cofamilial species. In the two studied species, all tRNAs exhibit a 'typical' cloverleaf secondary structure with the exception of trnS1, which lacks the D arm. A selective pressure analysis demonstrated that all PCGs are under purifying selection. The CR of the two species feature three domains previously reported in other mammals, including bats: extended terminal associated sequences (ETAS), central (CD), and conserved sequence block (CSB). A phylogenetic analysis based on the 13 mitochondrial PCGs demonstrated that Macrotus is monophyletic and the subfamily Macrotinae is a sister group of all remaining phyllostomids in our analysis, except Micronycterinae. The assembly and detailed analysis of these mitochondrial genomes represents a step further to continue improving the understanding of phylogenetic relationships within the species-rich family Phyllostomidae., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

The major lineages of nectar-feeding birds (hummingbirds, sunbirds, honeyeaters, flowerpiercers, and lorikeets) are considered examples of convergent evolution. We compared sucrose digestion capacity and sucrase enzymatic activity per unit intestinal surface area among 50 avian species from the New World, Africa, and Australia, including 20 nectarivores. With some exceptions, nectarivores had smaller intestinal surfaces, higher sucrose hydrolysis capacity, and greater sucrase activity per unit intestinal area. Convergence analysis showed high values for sucrose hydrolysis and sucrase activity per unit intestinal surface area in specialist nectarivores, matching the high proportion of sucrose in the nectar of the plants they pollinate. Plants pollinated by generalist nectar-feeding birds in the Old and New Worlds secrete nectar in which glucose and fructose are the dominant sugars. Matching intestinal enzyme activity in birds and nectar composition in flowers appears to be an example of convergent coevolution between plants and pollinators on an intercontinental scale., Competing Interests: The authors declare no conflict of interest. Funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results., (© 2021 The Author(s).)

Despite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first high-quality wild Cucurbita genome. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We found evidence of gene flow between the domesticated and wild subspecies, which likely alleviated the effects of the domestication bottleneck. We uncovered candidate domestication genes that are involved in the regulation of growth hormones, plant defense mechanisms, seed development, and germination. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.

Relative to other vertebrates, birds have unusually high blood glucose levels. In humans, the hyperglycemia observed in birds would be associated with diabetes mellitus and the non-enzymatic glycation of proteins, which leads to the accumulation of advanced glycation products and to a plethora of microvascular pathologies. How do birds avoid the negative effects of hyperglycemia? Anthony-Regnitz et al. (J Mol Evol 88: 653-661, 2020) discovered that birds might have evolved glycation-resistant proteins. Serum albumin is an important multifunctional protein susceptible to glycation. Anthony-Regnitz et al. (J Mol Evol 88: 653-661, 2020) found that chicken albumin is resistant to glycation relative to bovine serum albumin. Protein glycation takes place primarily in lysine residues, which are less abundant in chicken than in bovine serum albumin. A multispecies comparison of serum albumin sequences revealed lower numbers of lysine residues in birds than in mammals. Benign hyperglycemia is a shared derived trait of birds and glycation resistance mechanisms appear to have accompanied its evolution. The evolution of benign hyperglycemia in birds coincided with a genomic upheaval that included the loss of important genes, including the one that codes for GLUT4, the transporter responsible for insulin-dependent glucose transport in other vertebrates' insulin-sensitive cells. This loss seems to have resulted in the remodeling of the insulin-signaling pathway in bird tissues. Avian hyperglycemia has been considered a mystery for a long time. Although we remain ignorant of its origins and its repercussions for the physiology of birds, the discovery of resistance to glycation in bird serum albumin offers a path forward to solve this mystery.

Premise: Past climate fluctuations during the Holocene and Pleistocene shaped the distribution of several plant species in temperate areas over the world. Wild maize, commonly known as teosinte, is a good system to evaluate the effects of historical climate fluctuations on genetic diversity due to its wide distribution in Mexico with contrasting environmental conditions. We explored the influence of contemporary factors and historical environmental shifts on genetic diversity, including present and three historical periods using neutral markers., Methods: We used 22 nuclear microsatellite loci to examine the genetic diversity of 14 populations of Zea mays subsp. parviglumis and 15 populations of Zea mays subsp. mexicana (527 individuals total). We implemented genetic structure analyses to evaluate genetic differentiation between and within subspecies. We applied coalescent-based demographic analysis and species distribution modeling to evaluate the effects of historical environmental shifts., Results: We found 355 alleles in total for the two subspecies and variable levels of diversity in each (Z. mays subsp. parviglumis expected heterozygosity H E = 0.3646-0.7699; Z. mays subsp. mexicana H E = 0.5885-0.7671). We detected significant genetic structure among populations (D EST = 0.4332) with significant heterozygote deficiency (F IS = 0.1796), and variable selfing rates (sg 2 = 0.0-0.3090). The Bayesian assignment analysis differentiated four genetic groups. Demographic and species distribution modeling analysis suggested that environmental shifts were influential in the amount of genetic diversity., Conclusions: Our analyses suggest that the current genetic diversity in teosinte is shaped by factors such as local adaptation and genetic isolation, along with historical environmental fluctuations., (© 2020 Botanical Society of America.)

Background: The New World leaf-nosed bats (Phyllostomids) exhibit a diverse spectrum of feeding habits and innovations in their nutrient acquisition and foraging mechanisms. However, the genomic signatures associated with their distinct diets are unknown., Results: We conducted a genomic comparative analysis to study the evolutionary dynamics related to dietary diversification and specialization. We sequenced, assembled, and annotated the genomes of five Phyllostomid species: one insect feeder (Macrotus waterhousii), one fruit feeder (Artibeus jamaicensis), and three nectar feeders from the Glossophaginae subfamily (Leptonycteris yerbabuenae, Leptonycteris nivalis, and Musonycteris harrisoni), also including the previously sequenced vampire Desmodus rotundus. Our phylogenomic analysis based on 22,388 gene families displayed differences in expansion and contraction events across the Phyllostomid lineages. Independently of diet, genes relevant for feeding strategies and food intake experienced multiple expansions and signatures of positive selection. We also found adaptation signatures associated with specialized diets: the vampire exhibited traits associated with a blood diet (i.e., coagulation mechanisms), whereas the nectarivore clade shares a group of positively selected genes involved in sugar, lipid, and iron metabolism. Interestingly, in fruit-nectar-feeding Phyllostomid and Pteropodids bats, we detected positive selection in two genes: AACS and ALKBH7, which are crucial in sugar and fat metabolism. Moreover, in these two proteins we found parallel amino acid substitutions in conserved positions exclusive to the tribe Glossophagini and to Pteropodids., Conclusions: Our findings illuminate the genomic and molecular shifts associated with the evolution of nectarivory and shed light on how nectar-feeding bats can avoid the adverse effects of diets with high glucose content., (© The Author(s) 2020. Published by Oxford University Press.)

Whole-genome duplications are an important source of evolutionary novelties that change the mode and tempo at which genetic elements evolve within a genome. The Cucurbita genus experienced a whole-genome duplication around 30 million years ago, although the evolutionary dynamics of the coding and noncoding genes in this genus have not yet been scrutinized. Here, we analyzed the genomes of four Cucurbita species, including a newly assembled genome of Cucurbita argyrosperma, and compared the gene contents of these species with those of five other members of the Cucurbitaceae family to assess the evolutionary dynamics of protein-coding and long intergenic noncoding RNA (lincRNA) genes after the genome duplication. We report that Cucurbita genomes have a higher protein-coding gene birth-death rate compared with the genomes of the other members of the Cucurbitaceae family. C. argyrosperma gene families associated with pollination and transmembrane transport had significantly faster evolutionary rates. lincRNA families showed high levels of gene turnover throughout the phylogeny, and 67.7% of the lincRNA families in Cucurbita showed evidence of birth from the neofunctionalization of previously existing protein-coding genes. Collectively, our results suggest that the whole-genome duplication in Cucurbita resulted in faster rates of gene family evolution through the neofunctionalization of duplicated genes., (Copyright © 2019 The Author. Published by Elsevier Inc. All rights reserved.)