John Marshall Bates

John Marshall Bates
Field Museum of Natural History · Integrative Research Center

PHD

About

326
Publications
53,815
Reads
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4,748
Citations
Additional affiliations
March 2000 - present
University of Chicago
Position
  • Member
October 1993 - October 1995
American Museum of Natural History
Position
  • Chapman Post-doctoral Fellow

Publications

Publications (326)
Article
Using raw geographic distributions for Neotropical species and subspecies of the perching birds (Order Passeriformes), we present an hypothesis of area-relationships for twelve avian areas of endemism in the lowland Neotropics. With 1717 characters (distributions of species and subspecies) we find a single most parsimonious tree of area-relationshi...
Article
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Populations of ten Amazonian bird species were sampled on opposite banks of the Rio Teles Pires, a headwater stream of the Rio Tapajs, in the Alta Floresta region, northern Mato Grosso, Brazil. The river is 100–300m wide in this region. We found a range of genetic differentiation from none to relatively high levels; six of the ten species studied e...
Article
We use the small-bodied toucan genus Pteroglossus to test hypotheses about diversification in the lowland Neotropics. We sequenced three mitochondrial genes and one nuclear intron from all Pteroglossus species and used these data to reconstruct phylogenetic trees based on maximum parsimony, maximum likelihood, and Bayesian analyses. These phylogene...
Article
The glacial refugia paradigm has been broadly applied to patterns of species dynamics and population diversification. However, recent geological studies have demonstrated striking Pleistocene climate changes in currently semiarid northeastern Brazil at time intervals much more frequent than the climatic oscillations associated with glacial and inte...
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Weir and Schluter (Reports, 16 March 2007, p. 1574) used variation in the age distribution of sister species to estimate that recent rates of speciation decline toward the tropics. However, this conclusion may be undermined by taxonomic biases, sampling artifacts, and the sister-species method, all of which tend to underestimate diversification rat...
Article
1. Global climate change impacts species and ecosystems in potentially harmful ways. For migratory bird species, earlier spring warm-up could lead to a mis-match between nesting activities and food availability. CO 2 provides a useful proxy for temperature and an environmental indicator of climate change when temperature data are not available for...
Article
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Macroevolutionary patterns, often inferred from metrics of community relatedness, are often used to ascertain major evolutionary processes shaping communities. These patterns have been shown to be informative of biogeographic barriers, of habitat suitability and invasibility (especially with regard to environmental filtering), and of regions that f...
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The Philippine endemic genus Bullimus is currently considered to include three species, one each from the Late Pleistocene islands of Greater Mindanao, Greater Luzon, and Camiguin. We describe a fourth species, Bullimus carletoni, new species, from the Caramoan Peninsula in southern Luzon based on analyses of molecular and craniodental data. Molecu...
Article
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Context Amazonian white-sand ecosystems ( campinas ) are open vegetation patches which form a natural island-like system in a matrix of tropical rainforest. Due to a clear distinction from the surrounding matrix, the spatial characteristics of campina patches may affect the genetic diversity and composition of their specialized organisms, such as t...
Article
Migratory animals experiencing substantial change in diet and habitat across the annual cycle may have corresponding shifts in host‐associated microbial diversity. Using automated telemetry and radio tags to recapture birds, we examined gut microbiota structure in the same population and often same individual of Kirtland's Warblers (Setophaga kirtl...
Article
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The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic reveals a major gap in global biosecurity infrastructure: a lack of publicly available biological samples representative across space, time, and taxonomic diversity. The shortfall, in this case for vertebrates, prevents accurate and rapid identification and monitoring of emer...
Article
Africa’s montane ecosystems are noteworthy not only for their isolation but for their morphologically similar bird populations that inhabit geographically disparate localities. Many species possess range disjunctions in excess of 2,000 km and appear to represent populations that have been isolated since at least the last Ice Age, including the Nort...
Article
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Megascops is the most species-rich owl genus in the New World, with 21 species currently recognized. Phylogenetic relationships within this genus are notoriously difficult to establish due to the considerable plumage similarity among species and polymorphism within species. Previous studies have suggested that the widespread lowland Amazonian M. wa...
Article
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Geographic turnover in community composition is created and maintained by eco-evolutionary forces that limit the ranges of species. One such force may be antagonistic interactions among hosts and parasites, but its general importance is unknown. Understanding the processes that underpin turnover requires distinguishing the contributions of key abio...
Preprint
Full-text available
Context Amazonian white-sand ecosystems (campinas) are open vegetation patches which form a natural island-like system in a matrix of tropical rainforest. Due to their clear distinction from the surrounding matrix, the spatial characteristics of campina patches may affect the genetic diversity and composition of their specialized organisms such as...
Article
Understanding how species attain their geographical distributions and identifying traits correlated with range size are important objectives in biogeography, evolutionary biology and biodiversity conservation. Despite much effort, results have been varied and general trends have been slow to emerge. Studying species pools that occupy specific habit...
Article
Synopsis Sonations are sounds that animals produce with structures other than the vocal apparatus for communication. In birds, many sonations are usually produced with modified flight feathers through diverse kinematic mechanisms. For instance, aeroelastic fluttering of feathers produces tonal sound when airflow exceeds a threshold velocity and ind...
Article
Full-text available
The ~1.97 million egg sets (~5 million eggs) housed in museums have not been used in proportion to their availability. We highlight the wide variety of scientific disciplines that have used egg collections and the geographic locations and sizes of these collections, to increase awareness of the importance of egg collections, improve their visibilit...
Article
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https://www.researchgate.net/deref/https%3A%2F%2Facademic.oup.com%2Fbioscience%2Farticle%2Fdoi%2F10.1093%2Fbiosci%2Fbiaa064%2F5857068
Chapter
Full-text available
We identify key interdisciplinary questions and approaches to understanding the paleogeographic and biotic history of Amazonia. We discuss the importance of comparing evolutionary taxonomic units across groups and considering their particular environmental affinities as a framework for a mechanistic understanding of how the diversity of Amazonia wa...
Chapter
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White sand ecosystems (WSE) occur in nutrient-poor sandy soils patchily distributed throughout the lowlands of Amazonia. The diversification and current patterns of diversity of birds and plants specialized to the WSE were likely affected by abiotic conditions in very different ways relative to those in the upland Terra Firme forest, which has been...
Article
1. Functional traits are the essential phenotypes that underlie an organism's life history and ecology. Although biologists have long recognized that intraspecific variation is consequential to an animals’ ecology, studies of functional variation are often restricted to species‐level comparisons, ignoring critical variation within species. In birds...
Article
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For more than two centuries, biodiversity collections have served as the foundation for scientific investigation of and education about life on Earth (Melber and Abraham 2002, Cook et al. 2014, Funk 2018). The collections that have been assembled in the past and continue to grow today are a cornerstone of our national heritage that have been treate...
Article
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The Amazonian landscape evolution is the result of the combined effect of Andean tectonism, climate and the Earth’s interior dynamics. To reconstruct the landscape evolution and its influence on paleoenvironmental variations within Amazonia since the Oligocene, we conducted numerical experiments that incorporate different surface and geodynamic pro...
Article
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Abyssinian Crimsonwing Cryptospiza salvadorii and Red-faced Crimsonwing C. reichenovii occur in Tanzania and a few other countries in sub-Saharan Africa. C. salvadorii is found from Ethiopia south to northern Tanzania and eastern Democratic Republic of Congo (Zimmerman et al. 1996, Keith 2004, Payne 2010). C. reichenovii occurs in East Africa from...
Article
We gathered molecular data to assess phylogenetic and phylogeographic patterns for widespread lineages of Neotropical forest falcons in the genus Micrastur to: (1) investigate the comparative phylogeography of four species from the M. ruficollis complex (M. ruficollis, M. gilvicollis, M. plumbeus and M. mintoni), to identify the temporal and spatia...
Article
Avian endemism in the Albertine Rift is among the highest of any region in Africa. Conservation of these forests is a high priority, but informed prioritization has been hampered by limited data for most endemic bird species. We employed ecological niche models, coupled with remote sensing and field data, to present a case study of 2 Albertine Rift...
Article
Jacamar species occur throughout Amazonia, with most species occupying forested habitats. One species-complex, Galbula leucogastra / chalcothorax, is associated to white sand ecosystems (WSE). Previous studies of WSE bird species recovered shallow genetic structure in mtDNA coupled with signs of gene flow among WSE patches. Here, we characterize di...
Article
For two centuries evolutionary biologists have sought to explain elevated biodiversity in the Neotropics. Although different process are known to be important, it is still not uncommon for researchers to emphasize a single mechanism. Recently, arguments have highlighted the importance of dispersal shaping community structure and evolution across th...
Article
To investigate patterns of genetic and morphological differentiation in a ‘New Endemic’ Philippine rodent (Bullimus) and examine the dynamics on intra-island speciation on oceanic islands. The Philippine archipelago, focusing on Luzon Island. We examined patterns of genetic differentiation by sequencing one mitochondrial and three nuclear loci for...
Article
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Parasites of the genera Plasmodium and Haemoproteus (Apicomplexa: Haemosporida) are a diverse group of pathogens that infect birds nearly worldwide. Despite their ubiquity, the ecological and evolutionary factors that shape the diversity and distribution of these protozoan parasites among avian communities and geographic regions are poorly understo...
Article
Weaverbirds are a diverse passerine group with species diversity concentrated in sub-Saharan Africa. No comprehensive phylogenetic hypothesis regarding relationships of weaverbirds has been produced, however, so we developed a first extensive phylogeny for the family Ploceidae, based on a multilocus dataset of three mitochondrial loci and four nucl...
Article
The endangered warbler Bradypterus graueri is endemic to the Albertine Rift, where it is restricted to montane swamps above 1900 m across the region. We studied genetic structure among six populations sampled across the species' distribution in northern Burundi, Rwanda, Uganda and the eastern Democratic Republic of Congo. A total of 2117 base pairs...
Article
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Thirteen novel polymorphic microsatellite loci were isolated and characterized from the Amazonian Black Manakin, Xenopipo atronitens. The loci were screened using 30 samples from Brazil. A total of 13 loci were variable with number of alleles per locus ranging from 2 to 17, whilst the observed and expected heterozygosities varied from 0.067–0.900 a...
Article
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Peregrine falcons (Falco peregrinus) were extirpated from most of the continental United States by widespread use of the pesticide DDT in the 1960s. Populations have rebounded with banning of the pesticide and successful implementation of captive breeding and hacking programs. An essentially new population of Midwestern peregrines now exists that i...
Data
S1 File contains: Table A in S1 File. List of all specimens used in the study with their US Fish and Wildlife identification number (USFWS#), birth year, sex, and locality information from the Bell Museum of Natural History in Minneapolis. Additional samples (n = 39) not shown in Table 1 used in the study to calculate population allele frequencies...
Article
Species boundaries within the African Batises, small forest and savanna dwelling insectivorous birds, remain a challenge given complex distributions of plumage, call, and eye color phenotypes throughout their distributional range. The relatively recent delineation of two species within Batis mixta: B. mixta and Batis crypta based on morphological a...
Article
Mosesia ovalis n. sp. (Digenea: Phaneropsolidae) is described based on one specimen found in the intestine of a green manakin (Pipridae: Xenopipo holochlora Sclater, 1888) collected in the Cordillera Azul National Park, Peru. Mosesia ovalis n. sp. differs from the morphologically similar species Mosesia mosesi (Travassos, 1921) and Mosesia chordeil...
Article
Full-text available
In the Andes, humid-forest organisms frequently exhibit pronounced genetic structure and geographic variation in phenotype, often coincident with physical barriers to dispersal. However, phylogenetic relationships of clades have often been difficult to resolve due to short internodes. Consequently, even in taxa with well-defined genetic structure,...
Article
The effects of climate fluctuations on seasonally dry forests and their fauna are important to a holistic understanding of diversification in the South American lowlands. We document the intraspecific genetic structure of the burnished-buff tanager (Tangara cayana), a species common in seasonally dry tropical forests throughout South America. Using...
Article
Full-text available
Megascops screech-owls are endemic to the New World and range from southern Canada to the southern cone of South America. The 21 currently recognized Megascops species occupy a wide range of habitats and elevations, from desert to humid montane forest, and from sea level to the Andean tree line. Species and subspecies diagnoses of Megascops are not...
Data
Materials and methods. Table S1. Genetic diversity statistics of eight microsatellite loci for each mtDNA clade of X. zosterops. Table S2. Pairwise genetic differentiation statistics for X. zosterops mtDNA clades, based on 8 microsatellite loci. Figure S1. ΔK values calculated from 10 Structure runs each of K = 1–8. Figure S2. The average negative...
Article
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The merger of formerly isolated lineages is hypothesized to occur in vertebrates under certain conditions. However, despite many demonstrated instances of introgression between taxa in secondary contact, examples of lineage mergers are rare. Preliminary mtDNA sequencing of a Malagasy passerine, Xanthomixis zosterops (Passeriformes: Bernieridae), in...
Article
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Background Peripatric speciation and peripheral isolation have uncertain importance in species accumulation, and are largely overshadowed by assumed dominance of allopatric modes of speciation. Understanding the role of different speciation mechanisms within biodiversity hotspots is central to understanding the generation of biological diversity. H...
Article
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We present a response to Dowsett-Lemaire et al. regarding their contention that there is a “new threat” posed by scientific collecting in Malawi and elsewhere.
Article
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Avian host life history traits have been hypothesized to predict rates of infection by haemosporidian parasites. Using molecular techniques, we tested this hypothesis for parasites from three haemosporidian genera (Plasmodium, Haemoproteus, and Leucocytozoon) collected from a diverse sampling of birds in northern Malawi. We found that host life his...
Article
Full-text available
Geographic isolation is considered essential to most speciation events, but our understanding of what controls the pace and degree of phenotypic divergence among allopatric populations remains poor. Why do some taxa exhibit phenotypic differentiation across barriers to dispersal, whereas others do not? To test factors controlling phenotypic diverge...