Ecomorphological and phylogenetic controls on sympatry across extant bats

AimMacroecological patterns of sympatry can inform our understanding of how ecological and evolutionary processes govern species distributions. Following speciation, both intrinsic and extrinsic factors may determine how readily sympatry occurs. One possibility is that sympatry most readily occurs with ecological divergence, especially if broad‐scale co‐occurrence is mediated by niche differentiation. Time since divergence may also predict sympatry if hybridization and gene flow lead to the collapse of species boundaries between closely related taxa. Here, we test for ecological and phylogenetic predictors of sympatry across the global radiation of extant bats.LocationGlobal.TaxonBats (Order Chiroptera).MethodsWe used a combination of linear mixed‐modelling, simulations and maximum‐likelihood modelling to test whether phylogenetic and ecomorphological divergence between species predict sympatry. We further assess how these relationships vary based on biogeographic realm.ResultsWe find that time since divergence does not predict sympatry in any biogeographic realm. Morphological divergence is negatively related to sympatry in the Neotropics, but shows no relationship with sympatry elsewhere.Main conclusionsWe find that bats in most biogeographic realms co‐occur at broad spatial scales regardless of phylogenetic similarity. Neotropical bats, however, appear to co‐occur most readily when morphologically similar. To the extent that pairwise phylogenetic and morphological divergence reflect ecological differentiation, our results suggest that abiotic and environmental factors may be more important than species interactions in determining patterns of sympatry across bats.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/144581/1/jbi13353-sup-0005-FigureS5.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144581/2/jbi13353.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144581/3/jbi13353-sup-0006-FigureS6.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144581/4/jbi13353-sup-0003-FigureS3.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144581/5/jbi13353-sup-0004-FigureS4.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144581/6/jbi13353_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144581/7/jbi13353-sup-0002-FigureS2.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144581/8/jbi13353-sup-0001-FigureS1.pd

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

Data from: Digitizing extant bat diversity: an open-access repository of 3D μCT-scanned skulls for research and education

Biological specimens are primary records of organismal ecology and history. As such, museum collections are invaluable repositories for testing ecological and evolutionary hypotheses across the tree of life. Digitizing and broadly sharing the phenotypic data from these collections serves to expand the traditional reach of museums, enabling widespread data sharing, collaboration, and education at an unprecedented scale. In recent years, μCT-scanning has been adopted as one way for efficiently digitizing museum specimens. Here, we describe a large repository of 3D, μCT-scanned images and surfaces of skulls from 359 extant species of bats, a highly diverse clade of modern vertebrates. This digital repository spans much of the taxonomic, biogeographic, and morphological diversity present across bats. All data have been published to the MorphoSource platform, an online database explicitly designed for the archiving of 3D morphological data. We demonstrate one potential use of this repository by testing for convergence in skull shape among one particularly diverse group of bats, the superfamily Noctilionoidea. Beyond its intrinsic utility to bat biologists, our digital specimens represent a resource for educators and for any researchers seeking to broadly test theories of trait evolution, functional ecology, and community assembly

A test for rate‐coupling of trophic and cranial evolutionary dynamics in New World bats

Morphological evolution is often assumed to be causally related to underlying patterns of ecological trait evolution. However, few studies have directly tested whether evolutionary dynamics of—and major shifts in—ecological resource use are coupled with morphological shifts that may facilitate trophic innovation. Using diet and multivariate cranial (microCT) data, we tested whether rates of trophic and cranial evolution are coupled in the radiation of New World bats. We developed a generalizable information‐theoretic method for describing evolutionary rate heterogeneity across large candidate sets of multirate evolutionary models, without relying on a single best‐fitting model. We found considerable variation in trophic evolutionary dynamics, in sharp contrast to a largely homogeneous cranial evolutionary process. This dichotomy is surprising given established functional associations between overall skull morphology and trophic ecology. We suggest that assigning discrete trophic states may underestimate trophic generalism and opportunism, and that this radiation could be characterized by labile crania and a homogeneous dynamic of generally high morphological rates. Overall, we discuss how trophic classifications could substantively impact our interpretation of how these dynamics covary in adaptive radiations.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/167529/1/evo14188.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/167529/2/evo14188_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/167529/3/evo14188-sup-0001-FigureS8.pd

What makes a fang? Phylogenetic and ecological controls on tooth evolution in rear-fanged snakes

Abstract Background Fangs are a putative key innovation that revolutionized prey capture and feeding in snakes, and – along with their associated venom phenotypes – have made snakes perhaps the most medically-significant vertebrate animals. Three snake clades are known for their forward-positioned fangs, and these clades (Elapidae, Viperidae, and Atractaspidinae) contain the majority of snakes that are traditionally considered venomous. However, many other snakes are “rear-fanged”: they possess potentially venom-delivering teeth situated at the rear end of the upper jaw. Quantification of fang phenotypes – and especially those of rear-fanged species – has proved challenging or impossible owing to the small size and relative rarity of many such snakes. Consequently, it has been difficult to understand the evolutionary history of both venom and prey-capture strategies across extant snakes. We quantified variation in the dentition of 145 colubriform (“advanced”) snake species using microCT scanning and compared dental characters with ecological data on species’ diet and prey capture method(s) to understand broader patterns in snake fang evolution. Results Dental traits such as maxilla length, tooth number, and fang size show strong phylogenetic signal across Colubriformes. We find extreme heterogeneity and evolutionary lability in the rear-fanged phenotype in colubrid (colubrine, dipsadine, and natricine lineages) and lamprophiid snakes, in contrast to relative uniformity in the front fanged phenotypes of other groups (vipers and, to a lesser extent, elapids). Fang size and position are correlated with venom-use in vipers, elapids, and colubrid snakes, with the latter group shifting fangs anteriorly by shortening the entire maxillary bone. We find that maxilla length and tooth number may also be correlated with the evolution of dietary specialization. Finally, an ancestral state reconstruction suggests that fang loss is a recurring phenomenon in colubrid snakes, likely accompanied by shifts in diet and prey capture mode. Conclusions Our study provides a framework for quantifying the complex morphologies associated with venom use in snakes. Our results suggest that fang phenotypes, and particularly the rear-fanged phenotype, in snakes are both diverse and labile, facilitating a wide range of ecological strategies and contributing to spectacular radiations of these organisms in tropical and subtropical biomes worldwide.http://deepblue.lib.umich.edu/bitstream/2027.42/173460/1/12862_2020_Article_1645.pd

Data from: Ecomorphological and phylogenetic controls on sympatry across extant bats

Aim: Macroecological patterns of sympatry can inform our understanding of how ecological and evolutionary processes govern species distributions. Following speciation, both intrinsic and extrinsic factors may determine how readily sympatry occurs. One possibility is that sympatry most readily occurs with ecological divergence, especially if broad-scale co-occurrence is mediated by niche differentiation. Time since divergence may also predict sympatry if hybridization and gene flow lead to the collapse of species boundaries between closely-related taxa. Here, we test for ecological and phylogenetic predictors of sympatry across the global radiation of extant bats. Location: Global Taxon: Bats (Order Chiroptera) Methods: We used a combination of linear mixed modeling, simulations, and maximum-likelihood modeling to test whether phylogenetic and ecomorphological divergence between species predict sympatry. We further assess how these relationships vary based on biogeographic realm. Results: We find that time since divergence does not predict sympatry in any biogeographic realm. Morphological divergence is negatively related to sympatry in the Neotropics, but shows no relationship with sympatry elsewhere. Main conclusions: We find that bats in most biogeographic realms co-occur at broad spatial scales regardless of phylogenetic similarity. Neotropical bats, however, appear to co-occur most readily when morphologically similar. To the extent that pairwise phylogenetic and morphological divergence reflect ecological differentiation, our results suggest that abiotic and environmental factors may be more important than species interactions in determining patterns of sympatry across bats

Dietary niche partitioning of three Sky Island Sceloporus lizards as revealed through DNA metabarcoding

Abstract Lizard diets are highly diverse and have contributed to the diversification, biogeographical distributions, and evolution of novel traits across this global radiation. Many parts of a lizard's ecology—including habitat preferences, foraging modes, predation risks, interspecific competition, and thermal constraints, among others—interact to shape diets, and dietary niche partitioning simultaneously contributes to co‐occurrence within communities. We used DNA metabarcoding of fecal samples to identify prey items in the diets of three sympatric Sceloporus lizards in the Madrean Sky Islands of Arizona, USA. We found evidence for dietary niche partitioning between interacting species concomitant with their respective ecologies. We also compared diet composition between populations to understand how conserved or plastic species' diets are between different environments. Our findings suggest that habitat generalists are also diet generalists in this system, while the same may be true for specialists. The identification of prey items to much lower taxonomic levels than previously documented further reveals hidden diversity in the diets of these species and underscores the utility of metabarcoding for understanding the full complexity of lizard diets

A set of principles and practical suggestions for equitable fieldwork in biology

Field biology is an area of research that involves working directly with living organisms in situ through a practice known as fieldwork. Conducting fieldwork often requires complex logistical planning within multiregional or multinational teams, interacting with local communities at field sites, and collaborative research led by one or a few of the core team members. However, existing power imbalances stemming from geopolitical history, discrimination, and professional position, among other factors, perpetuate inequities when conducting these research endeavors. After reflecting on our own research programs, we propose four general principles to guide equitable, inclusive, ethical, and safe practices in field biology: be collaborative, be respectful, be legal, and be safe. Although many biologists already structure their field programs around these principles or similar values, executing equitable research practices can prove challenging and requires careful consideration, especially by those in positions with relatively greater privilege. Based on experiences and input from a diverse group of global collaborators, we provide suggestions for action-oriented approaches to make field biology more equitable, with particular attention to how those with greater privilege can contribute. While we acknowledge that not all suggestions will be applicable to every institution or program, we hope that they will generate discussions and provide a baseline for training in proactive, equitable fieldwork practices

A genome assembly for the southern Pacific rattlesnake, Crotalus oreganus helleri, in the western rattlesnake species complex

Rattlesnakes play important roles in their ecosystems by regulating prey populations, are involved in complex coevolutionary dynamics with their prey, and exhibit a variety of unusual adaptations, including maternal care, heat-sensing pit organs, hinged fangs, and medically-significant venoms. The western rattlesnake (Crotalus oreganus) is one of the widest ranging rattlesnake species, with a distribution from British Columbia, where it is listed as threatened, to Baja California and east across the Great Basin to western Wyoming, Colorado and New Mexico. Here, we report a new reference genome assembly for one of six currently recognized subspecies, C. oreganus helleri, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomic sequencing strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 698 scaffolds spanning 1,564,812,557 base pairs, has a contig N50 of 64.7 Mb, a scaffold N50 of 110.8 Mb, and BUSCO complete score of 90.5%. This reference genome will be valuable for studies on the genomic basis of venom evolution and variation within Crotalus, in resolving the taxonomy of C. oreganus and its relatives, and for the conservation and management of rattlesnakes in general

Shi_etal_2018_JBI_data_code

This compressed file contains all data and code associated with Shi et al. (2018), J. Biogeog