Unlinked Mendelian inheritance of red and black pigmentation in snakes: Implications for Batesian mimicry

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135324/1/evo12902_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135324/2/evo12902.pd

Anolis lizards as biocontrol agents in mainland and island agroecosystems

Our knowledge of ecological interactions that bolster ecosystem function and productivity has broad applications to the management of agricultural systems. Studies suggest that the presence of generalist predators in agricultural landscapes leads to a decrease in the abundance of herbivorous pests, but our understanding of how these interactions vary across taxa and along gradients of management intensity and eco‐geographic space remains incomplete. In this study, we assessed the functional response and biocontrol potential of a highly ubiquitous insectivore (lizards in the genus Anolis) on the world’s most important coffee pest, the coffee berry borer (Hypothalemus hampei). We conducted field surveys and laboratory experiments to examine the impact of land‐use intensification on species richness and abundance of anoles and the capacity of anoles to reduce berry borer infestations in mainland and island coffee systems. Our results show that anoles significantly reduce coffee infestation rates in laboratory settings (Mexico, p = .03, F = 5.13 df = 1, 35; Puerto Rico, p = .014, F = 8.82, df = 1, 10) and are capable of consuming coffee berry borers in high abundance. Additionally, diversified agroecosystems bolster anole abundance, while high‐intensity practices, including the reduction of vegetation complexity and the application of agrochemicals were associated with reduced anole abundance. The results of this study provide supporting evidence of the positive impact of generalist predators on the control of crop pests in agricultural landscapes, and the role of diversified agroecosystems in sustaining both functionally diverse communities and crop production in tropical agroecosystems.The focus of this project was to assess the predatory function of wildlife in tropical coffee agroecosystems (i.e. pest reduction by a generalist insectivore), and the relative impacts of land‐use intensification on species abundance in mainland and island settings. The results of this study are the first to provide evidence that lizards in the genus Anolis are capable of both consuming the coffee berry borer in high numbers and significantly reducing infestations in laboratory settings. Our results show that anole presence is bolstered by vegetative complexity, and significantly reduced by high intensity practices including the application of agrochemicals.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/136386/1/ece32806.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/136386/2/ece32806_am.pd

Direct Fitness Correlates and Thermal Consequences of Facultative Aggregation in a Desert Lizard

Social aggregation is a common behavioral phenomenon thought to evolve through adaptive benefits to group living. Comparing fitness differences between aggregated and solitary individuals in nature – necessary to infer an evolutionary benefit to living in groups – has proven difficult because communally-living species tend to be obligately social and behaviorally complex. However, these differences and the mechanisms driving them are critical to understanding how solitary individuals transition to group living, as well as how and why nascent social systems change over time. Here we demonstrate that facultative aggregation in a reptile (the Desert Night Lizard, Xantusia vigilis) confers direct reproductive success and survival advantages and that thermal benefits of winter huddling disproportionately benefit small juveniles, which can favor delayed dispersal of offspring and the formation of kin groups. Using climate projection models, however, we estimate that future aggregation in night lizards could decline more than 50% due to warmer temperatures. Our results support the theory that transitions to group living arise from direct benefits to social individuals and offer a clear mechanism for the origin of kin groups through juvenile philopatry. The temperature dependence of aggregation in this and other taxa suggests that environmental variation may be a powerful but underappreciated force in the rapid transition between social and solitary behavior

Environmental heterogeneity and not vicariant biogeographic barriers generate community-wide population structure in desert-adapted snakes

Genetic structure can be influenced by local adaptation to environmental heterogeneity and biogeographic barriers, resulting in discrete population clusters. Geographic distance among populations, however, can result in continuous clines of genetic divergence that appear as structured populations. Here, we evaluate the relevant importance of these three factors over a landscape characterized by environmental heterogeneity and the presence of a hypothesized biogeographic barrier in producing population genetic structure within 13 codistributed snake species using a genomic data set. We demonstrate that geographic distance and environmental heterogeneity across western North America contribute to population genomic divergence. Surprisingly, landscape features long thought to contribute to biogeographic barriers play little role in divergence community wide. Our results suggest that isolation by environment is the most important contributor to genomic divergence. Furthermore, we show that models of population clustering that incorporate spatial information consistently outperform nonspatial models, demonstrating the importance of considering geographic distances in population clustering. We argue that environmental and geographic distances as drivers of community-wide divergence should be explored before assuming the role of biogeographic barriers.see also the Perspective by Alencar and QuentalPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/1/mec15182-sup-0004-AppendixS4.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/2/mec15182_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/3/mec15182-sup-0005-AppendixS5.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/4/mec15182-sup-0002-AppendixS2.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/5/mec15182-sup-0010-AppendixS10.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/6/mec15182.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/7/mec15182-sup-0003-AppendixS3.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/8/mec15182-sup-0006-AppendixS6.pd

Environmental heterogeneity and not vicariant biogeographic barriers generate community-wide population structure in desert-adapted snakes

Genetic structure can be influenced by local adaptation to environmental heterogeneity and biogeographic barriers, resulting in discrete population clusters. Geographic distance among populations, however, can result in continuous clines of genetic divergence that appear as structured populations. Here, we evaluate the relevant importance of these three factors over a landscape characterized by environmental heterogeneity and the presence of a hypothesized biogeographic barrier in producing population genetic structure within 13 codistributed snake species using a genomic data set. We demonstrate that geographic distance and environmental heterogeneity across western North America contribute to population genomic divergence. Surprisingly, landscape features long thought to contribute to biogeographic barriers play little role in divergence community wide. Our results suggest that isolation by environment is the most important contributor to genomic divergence. Furthermore, we show that models of population clustering that incorporate spatial information consistently outperform nonspatial models, demonstrating the importance of considering geographic distances in population clustering. We argue that environmental and geographic distances as drivers of community-wide divergence should be explored before assuming the role of biogeographic barriers.see also the Perspective by Alencar and QuentalPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/1/mec15182-sup-0004-AppendixS4.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/2/mec15182_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/3/mec15182-sup-0005-AppendixS5.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/4/mec15182-sup-0002-AppendixS2.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/5/mec15182-sup-0010-AppendixS10.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/6/mec15182.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/7/mec15182-sup-0003-AppendixS3.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/8/mec15182-sup-0006-AppendixS6.pd

Report from the First Snake Genomics and Integrative Biology Meeting

This report summarizes the proceedings of the 1st Snake Genomics and Integrative Biology Meeting held in Vail, CO USA, 5-8 October 2011. The meeting had over twenty registered participants, and was conducted as a single session of presentations. Goals of the meeting included coordination of genomic data collection and fostering collaborative interactions among researchers using snakes as model systems.Organismic and Evolutionary Biolog

A collection and analysis of amphibians and reptiles from Nicaragua with new country and departmental records

Nicaragua is a biodiverse country, but documented herpetological specimens are underrepresented compared to neighboring countries. In 2018 we conducted a collaborative expedition between the University of Michigan Museum of Zoology and Nicaraguan biologists. We visited sites in the Pacific Low‑ lands, Caribbean Lowlands, and the Central Highlands, representing the three major biogeographic regions of Nicaragua. We collected specimens of 100 species from a total of 106 encountered. We provide acces‑ sion numbers and morphological, genetic, and ecological information for these specimens. We recorded 23 new departmental records and the first country record of Metlapilcoatlus indomitus (Smith & Ferrari‑Castro, 2008), filling gaps in the known distribution of the species within Nicaragua and across Central America. When available for each species, we provide range maps and comparative genetic trees including conspecific reference sequences from the region, making this work a significant addition to existing checklists of the herpetofauna in Nicaragua

Natural history bycatch: a pipeline for identifying metagenomic sequences in RADseq data

Background Reduced representation genomic datasets are increasingly becoming available from a variety of organisms. These datasets do not target specific genes, and so may contain sequences from parasites and other organisms present in the target tissue sample. In this paper, we demonstrate that (1) RADseq datasets can be used for exploratory analysis of tissue-specific metagenomes, and (2) tissue collections house complete metagenomic communities, which can be investigated and quantified by a variety of techniques. Methods We present an exploratory method for mining metagenomic “bycatch” sequences from a range of host tissue types. We use a combination of the pyRAD assembly pipeline, NCBI’s blastn software, and custom R scripts to isolate metagenomic sequences from RADseq type datasets. Results When we focus on sequences that align with existing references in NCBI’s GenBank, we find that between three and five percent of identifiable double-digest restriction site associated DNA (ddRAD) sequences from host tissue samples are from phyla to contain known blood parasites. In addition to tissue samples, we examine ddRAD sequences from metagenomic DNA extracted snake and lizard hind-gut samples. We find that the sequences recovered from these samples match with expected bacterial and eukaryotic gut microbiome phyla. Discussion Our results suggest that (1) museum tissue banks originally collected for host DNA archiving are also preserving valuable parasite and microbiome communities, (2) that publicly available RADseq datasets may include metagenomic sequences that could be explored, and (3) that restriction site approaches are a useful exploratory technique to identify microbiome lineages that could be missed by primer-based approaches