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Research products from students and faculty in the Center.  Student co-authors are indicated with (§) for undergraduates and (‡) for graduates; postdocs are indicated by (*).

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Uetz, P., and E. Pohl (2021) Protein-DNA and Protein-Protein-Interactions. Wink, W. (ed.), An Introduction to Molecular Biotechnology: Fundamentals, Methods and Applications, 3rd Edition :261-276.,+Methods+and+Applications,+3rd+Edition-p-9783527344147

Chowdhury, S., S. Hepper, M.K. Lodi, M.H. Saier, Jr., and P. Uetz (2021) The protein interactome of glycolysis in Escherichia coli. Proteomes 9:16.

Glycolysis is regulated by numerous mechanisms including allosteric regulation, post-translational modification or protein-protein interactions (PPI). While glycolytic enzymes have been found to interact with hundreds of proteins, the impact of only some of these PPIs on glycolysis is well understood. Here we investigate which of these interactions may affect glycolysis in E. coli and possibly across numerous other bacteria, based on the stoichiometry of interacting protein pairs (from proteomic studies) and their conservation across bacteria. We present a list of 339 protein-protein interactions involving glycolytic enzymes but predict that ~70% of glycolytic interactors are not present in adequate amounts to have a significant impact on glycolysis. Finally, we identify a conserved but uncharacterized subset of interactions that are likely to affect glycolysis and deserve further study.

Rivera, J.A., H.N. Rich, A.M. Lawling, M.S. Rosenberg, and E.P. Martins (2021) Occurrence data uncover patterns of allopatric divergence and interspecies interactions in the evolutionary history of Sceloporus lizards. Ecology and Evolution 11:2796-2813.

As shown from several long‐term and time‐intensive studies, closely related, sympatric species can impose strong selection on one another, leading to dramatic examples of phenotypic evolution. Here, we use occurrence data to identify clusters of sympatric Sceloporus lizard species and to test whether Sceloporus species tend to coexist with other species that differ in body size, as we would expect when there is competition between sympatric congeners. We found that Sceloporus species can be grouped into 16 unique bioregions. Bioregions that are located at higher latitudes tend to be larger and have fewer species, following Rapoport’s rule and the latitudinal diversity gradient. Species richness was positively correlated with the number of biomes and elevation heterogeneity of each bioregion. Additionally, most bioregions show signs of phylogenetic underdispersion, meaning closely related species tend to occur in close geographic proximity. Finally, we found that although Sceloporus species that are similar in body size tend to cluster geographically, small‐bodied Sceloporus species are more often in sympatry with larger‐bodied Sceloporus species than expected by chance alone, whereas large‐bodied species cluster with each other geographically and phylogenetically. These results suggest that community composition in extant Sceloporus species is the result of allopatric evolution, as closely related species move into different biomes, and interspecies interactions, with sympatry between species of different body sizes. Our phyloinformatic approach offers unique and detailed insights into how a clade composed of ecologically and morphologically disparate species are distributed over large geographic space and evolutionary time.

Uetz, P. (2020) Six reasons why (and how) you should digitize your herp library. Bibliotheca Herpetologica 14:47-50.

Uetz, P., A. Slavenko, S. Meira, and M. Heinicke (2020) Gecko diversity: A history of global discovery. Israel Journal of Ecology & Evolution 6:117-125.

1935 gecko species (and 224 subspecies) were known in December 2019 in seven families and 124 genera. These nearly 2000 species were described by ~950 individuals of whom more than 100 described more than 10 gecko species each. Most gecko species were discovered during the past 40 years. The primary type specimens of all currently recognized geckos (including subspecies) are distributed over 161 collections worldwide, with 20 collections having about two thirds of all primary types. The primary type specimens of about 40 gecko taxa have been lost or unknown. The phylogeny of geckos is well studied, with DNA sequences being available for ~76% of all geckos (compared to ~63% in other reptiles) and morphological characters now being collected in databases. Geographically, geckos occur on five continents and many islands but are most species-rich in Australasia (which also houses the greatest diversity of family-level taxa), Southeast Asia, Africa, Madagascar, and the West Indies. Among countries, Australia has the highest number of geckos (241 species), with India, Madagascar, and Malaysia being the only other countries with more than 100 described species each. As expected, when correcting for land area, countries outside the tropics have fewer geckos.

Venanzi Rullo, E., M.R. Pinzone, L. Cannon, S. Weissman, M. Ceccarelli, R. Zurakowski, G. Nunnari, and U. O'Doherty (2020) Persistence of an intact HIV reservoir in phenotypically naive T cells. JCI Insight 5:e133157.

Despite the efficacy of antiretroviral therapy (ART), HIV persists in a latent form and remains a hurdle to eradication. CD4+ T lymphocytes harbor the majority of the HIV reservoir, but the role of individual subsets remains unclear. CD4+ T cells were sorted into central, transitional, effector memory, and naive T cells. We measured HIV DNA and performed proviral sequencing of more than 1900 proviruses in 2 subjects at 2 and 9 years after ART initiation to estimate the contribution of each subset to the reservoir. Although our study was limited to 2 subjects, we obtained comparable findings with publicly available sequences. While the HIV integration levels were lower in naive compared with memory T cells, naive cells were a major contributor to the intact proviral reservoir. Notably, proviral sequences isolated from naive cells appeared to be unique, while those retrieved from effector memory cells were mainly clonal. The number of clones increased as cells differentiated from a naive to an effector memory phenotype, suggesting naive cells repopulate the effector memory reservoir as previously shown for central memory cells. Naive T cells contribute substantially to the intact HIV reservoir and represent a significant hurdle for HIV eradication.

Arruda A., A. dos Santos Jr., G.E.M. Ferreira, J.C. Sobrinho, L.S. Ozaki, and A. Almeida e Silva (2020) Leveduras do trato digestório de Anopheles darlingi como alternativa para o desenvolvimento de paratransgênese para o controle da malária [Yeast from the digestive tract of Anopheles darlingi as an alternative to develop the paratransgenesis for the control of malaria]. da Silva, E. (ed.), Consolidação do potencial científico e tecnológico das ciências biológicas :pp. 54-65.

Microorganisms living in insects’ digestive tract have been isolated and identified for developing biotechnological tools to fight vector-born diseases. In this context, mosquitoes Anopheles from different regions of the world have been studied about their midgut microbiota focused on paratransgenesis. However, we started to understand the information about microorganisms living in neotropical midgut, specially about Anopheles darlingi. The first step for paratransgenesis is to isolate culturable microorganisms naturally associated to the insect vector, and thus amenable to experimentation in laboratory. The objectives of this work were to isolate and to identify culturable yeasts isolated from feces of Anopheles darlingi, the main vector of malaria in Brazil; to estimate the frequency distribution of the sampled yeasts and to characterize and to select among the yeasts isolated from feces of An. darlingi those with potential for paratansgenesis. The female mosquitoes of An. darlingi were captured in two rural places of Porto Velho, Rondônia, Brasil. For improving the yeast growth, mosquito feces were collected on YPD agar medium with chloramphenicol and cultivated at 3o° C for 48 hours. Sixty pure yeast colonies were sampled. The isolates were preserved in -80° C freezer. PCR reactions with genomic DNA from each isolate were performed using the primers of 26S and ITS for yeasts. From 60 yeast isolates, just 27 samples were identified. The fragments were sequenced with the Sanger method and the sequences with similarities above of 97% with sequences in reference database were deposited in Genbank (NCBI). The identified yeast fall into 9 genera: Candida, Diutina, Hanseniaspora, Metschnikowia, Meyerozyma (=Pichia), Moesziomyces, Papiliotrema (=Cryptococcus), Pseudozyma and Rhodotorula. We suggest as candidates to paratransgenesis to control of malaria in An. darlingi those yeasts belonging to the genera Meyeroyzma (=Pichia), Metschnikowia, Hanseniaspora, and Pseudozyma.

Des Roches, S., K.I. Brans, M. Lambert, L.R. Rivkin, A. Savage, C.J. Schell, C. Correa, L. De Meester, S.E. Diamond, L. Govaert, N.B. Grimm, N.C. Harris, A.P. Hendry, M.T.J. Johnson, J. Munshi-South, E.P. Palkovacs, M. Szulkin, M.C. Urban, B.C. Verrelli, and M. Alberti (2021) Socio-eco-evolutionary dynamics in cities. Evolutionary Applications 14:248-267.

Cities are uniquely complex systems regulated by interactions and feedbacks between natural and social processes. Characteristics of human society – including culture, economics, technology, and politics – underlie social patterns and activity, creating a heterogeneous environment that can influence and be influenced by both ecological and evolutionary processes. Increasing interest in urban ecology and evolutionary biology has coincided with growing interest in eco‐evolutionary dynamics, which encompasses the interactions and reciprocal feedbacks between evolution and ecology. Research on both urban evolutionary biology and eco‐evolutionary dynamics frequently focuses on contemporary evolution of species that have potentially substantial ecological – and even social – significance. Still, little research fully integrates urban evolutionary biology and eco‐evolutionary dynamics, and rarely do researchers in either of these fields fully consider the role of human social patterns and processes. Because cities are fundamentally regulated by human activities, are inherently interconnected, and are frequently undergoing social and economic transformation, they represent an opportunity for ecologists and evolutionary biologists to study urban “socio‐eco‐evolutionary dynamics.” Through this new framework, we encourage researchers of urban ecology and evolution to fully integrate human social drivers and feedbacks to increase understanding and conservation of ecosystems, their functions, and their contributions to people within and outside cities.

Marshall, B.M., P. Freed, L.J. Vitt, P. Bernardo, G. Vogel, S. Lotzkat, M. Franzen, J. Hallermann, R.D. Sage, B. Bush, M.R. Duarte, L.J. Avila, D. Jandzik, B. Klusmeyer, B. Maryan, J. Hošek, and P. Uetz (2020) An inventory of online reptile images. Zootaxa 4896:251-264.

No central online repository exists for the collection of animal images; hence it remains unclear how extensively species have been illustrated in the published literature or online. Here we compiled a list of more than 8000 reptile species (out of 11,341) that have photos in one of six popular online repositories, namely iNaturalist (6,349 species), the Reptile Database (5,144), Flickr (4,386), CalPhotos (3,071), Wikimedia (2,952), and Herpmapper (2,571). These sites have compiled over one million reptile photos, with some species represented by tens of thousands of images. Despite the number of images, many species have only one or a few images. This suggests that a considerable fraction of morphological and geographic variation is under documented or difficult to access. We highlight prominent gaps in amphisbaenians, lizards, and snakes, with geographic hotspots for species without images in Central Africa, Pacific Islands, and the Andes Mountains. We present a list of ~3,000 species without photos in any of the six databases and ask the community to fill the gaps by depositing images on one of these sites (preferably with minimal copyright restrictions).

Tassone, E.E., L.S. Miles, R.J. Dyer, M.S. Rosenberg, R.M. Cowling, and B.C. Verrelli (2021) Evolutionary stability, landscape heterogeneity, and human land-usage shape population genetic connectivity in the Cape Floristic Region biodiversity hotspot. Evolutionary Applications 14:in press.

As human‐induced change eliminates natural habitats, it impacts genetic diversity and population connectivity for local biodiversity. The South African Cape Floristic Region (CFR) is the most diverse extratropical area for plant biodiversity, and much of its habitat is protected as a UNESCO World Heritage site. There has long been great interest in explaining the underlying factors driving this unique diversity, especially as much of the CFR is endangered by urbanization and other anthropogenic activity. Here, we use a population and landscape genetic analysis of SNP data from the CFR endemic plant Leucadendron salignum or “common sunshine conebush” as a model to address the evolutionary and environmental factors shaping the vast CFR diversity. We found that high population structure, along with relatively deeper and older genealogies, are characteristic of the southwestern CFR, whereas, low population structure and more recent lineage coalescence depicts the eastern CFR. Population network analyses show genetic connectivity is facilitated in areas of lower elevation and higher seasonal precipitation. These population genetic signatures corroborate CFR species‐level patterns consistent with high Pleistocene biome stability and landscape heterogeneity in the southwest, but with coincident instability in the east. Finally, we also find evidence of human land‐usage as a significant gene flow barrier, especially in severely‐threatened lowlands where genetic connectivity has been historically the highest. These results help identify areas where conservation plans can prioritize protecting high genetic diversity threatened by contemporary human activities within this unique cultural UNESCO site.

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