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Environmental changes since the Pleistocene and commercial whaling in the last few centuries have drastically reduced many whale populations, including gray whales in the North Pacific. Herein we use complete mitogenome sequences from 74 individuals to evaluate gray whale phylogeography and historical demography, then use environmental niche modeling to assess how habitat availability has changed through time for Pacific gray whales. We identify a large degree of haplotype sharing between gray whales sampled in Russian and Mexican waters, coupled with very limited matrilineal population structure. Confirming previous studies, our environmental niche models showed a decrease in available habitat during the Last Glacial Maximum, but we find no genetic signals of recent population declines in mitochondrial genomes despite both sustained habitat loss and a commercial whaling bottleneck. Our results illustrate the complex dynamics of baleen whale biogeography since the Holocene as well as the difficulty in detecting recent demographic bottlenecks from mitochondrial DNA sequences.

Bowhead whales (Balaena mysticetus) are divided into four stocks: the Okhotsk (OKH) Sea stock, the Bering-Chukchi-Beaufort (BCB) Seas stock, the East Canada-West Greenland (ECWG) stock, and the East Greenland-Svalbard-Barents (EGSB) Sea stock. Genetic data have contributed to the understanding of the differentiation among these stocks, rates of migration between them, and have been used to test hypotheses of stock substructure. Moreover, historical and recent demography of the BCB stock has been investigated using multiple genetic markers. No evidence of a genetic bottleneck from commercial whaling has been found, and models of recent population expansion are supported. Population genetic data is one source of data used by the International Whaling Commission (IWC) to issue an aboriginal whaling quota for the BCB stock.

Small-eared shrews of the genus Cryptotis (Mammalia: Eulipotyphla: Soricidae) are widespread in the northern Neotropics. Systematic studies of these shrews over the past two decades have revealed previously undocumented morphological and species diversity, resulting in a quadrupling of the number of recognized species. Unfortunately, a small proportion of the species in the genus have been included in molecular phylogenetic studies, and evolutionary relationships within the genus are incompletely known. Traditionally, species have been assigned to four or five morphologically defined ‘species groups’, but tests of the monophyly of some of these groups show weak support and relationships amongst species groups remain somewhat speculative. The largest species group is the C. mexicanus group inhabiting Mexico and northern Central America. We studied sequences from mitochondrial cytochrome-b and 16S genes, as well as nuclear ApoB and BRCA1 genes from 22 species of Cryptotis, including 15 species in the C. mex...

The effective size of a population (Ne), which determines its level of neutral variability, is a key evolutionary parameter. Ne can substantially depart from census sizes of present-day breeding populations (NC) as a result of past demographic changes, variation in life-history traits and selection at linked sites. Using genome-wide data we estimated the long-term coalescent Ne for 17 pinniped species represented by 36 population samples (total n = 458 individuals). Ne estimates ranged from 8,936 to 91,178, were highly consistent within (sub)species and showed a strong positive correlation with NC ( $${R}_{\mathrm{adj}}^2$$ = 0.59; P = 0.0002). Ne/NC ratios were low (mean, 0.31; median, 0.13) and co-varied strongly with demographic history and, to a lesser degree, with species’ ecological and life-history variables such as breeding habitat. Residual variation in Ne/NC, after controlling for past demographic fluctuations, contained information about recent population size changes during the Anthropocene. Specifically, species of conservation concern typically had positive residuals indicative of a smaller contemporary NC than would be expected from their long-term Ne. This study highlights the value of comparative population genomic analyses for gauging the evolutionary processes governing genetic variation in natural populations, and provides a framework for identifying populations deserving closer conservation attention. Using comparative population genomics across pinnipeds, this study explores how demographic change and life-history traits are correlated to the effective size of a population and conservation status.

Background Commercial whaling caused extensive demographic declines in many great whale species, including gray whales that were extirpated from the Atlantic Ocean and dramatically reduced in the Pacific Ocean. The Eastern Pacific gray whale has recovered since the 1982 ban on commercial whaling, but the Western Pacific gray whale—once considered possibly extinct—consists of only about 200 individuals and is considered critically endangered by some international authorities. Herein, we use whole-genome sequencing to investigate the demographic history of gray whales from the Pacific and use environmental niche modelling to make predictions about future gene flow. Results Our sequencing efforts and habitat niche modelling indicate that: i) western gray whale effective population sizes have declined since the last glacial maximum; ii) contemporary gray whale genomes, both eastern and western, harbor less autosomal nucleotide diversity than most other marine mammals and megafauna; iii) the extent of inbreeding, as measured by autozygosity, is greater in the Western Pacific than in the Eastern Pacific populations; and iv) future climate change is expected to open new migratory routes for gray whales. Conclusion Our results indicate that gray whale genomes contain low nucleotide diversity and have been subject to both historical and recent inbreeding. Population sizes over the last million years likely peaked about 25,000 years before present and have declined since then. Our niche modelling suggests that novel migratory routes may develop within the next century and if so this could help retain overall genetic diversity, which is essential for adaption and successful recovery in light of global environmental change and past exploitation.

This study reports the phylogenetic relationships of 13 species of lasiurine bats using 4 loci from mitochondrial and Y-chromosomal DNA. Our results support a sister taxon relationship between the red and hoary bats, with the yellow bats being more distantly related. Several taxonomic revisions are suggested based on the results of this study. We support the recognition of 3 separate genera: Lasiurus (red bats), Dasypterus (yellow bats), and Aeorestes (hoary bats, including A. egregius which groups more closely to the hoary bats than its traditional placement with the red bats). We recognize L. frantzii as a distinct species and recognize L. blossevillii salinae as a subspecies rather than species. We elevate 3 previously recognized subspecies of A. cinereus to specific status. The phylogeography of the endangered Hawaiian hoary bat is studied in detail, and hoary bats are found to have undergone multiple invasions of the Hawaiian Islands from North America over its evolutionary history. We also report th...

Genetic and genomic approaches have much to offer in terms of ecology, evolution, and conservation. To better understand the biology of the gray whale Eschrichtius robustus (Lilljeborg, 1861), we sequenced the genome and produced an assembly that contains ∼95% of the genes known to be highly conserved among eukaryotes. From this assembly, we annotated 22,711 genes and identified 2,057,254 single-nucleotide polymorphisms (SNPs). Using this assembly, we generated a curated list of candidate genes potentially subject to strong natural selection, including genes associated with osmoregulation, oxygen binding and delivery, and other aspects of marine life. From these candidate genes, we queried 92 autosomal protein-coding markers with a panel of 96 SNPs that also included 2 sexing and 2 mitochondrial markers. Genotyping error rates, calculated across loci and across 69 intentional replicate samples, were low (0.021%), and observed heterozygosity was 0.33 averaged over all autosomal markers. This level of variability provides substantial discriminatory power across loci (mean probability of identity of 1.6 × 10-25 and mean probability of exclusion >0.999 with neither parent known), indicating that these markers provide a powerful means to assess parentage and relatedness in gray whales. We found 29 unique multilocus genotypes represented among our 36 biopsies (indicating that we inadvertently sampled 7 whales twice). In total, we compiled an individual data set of 28 western gray whales (WGSs) and 1 presumptive eastern gray whale (EGW). The lone EGW we sampled was no more or less related to the WGWs than expected by chance alone. The gray whale genomes reported here will enable comparative studies of natural selection in cetaceans, and the SNP markers should be highly informative for future studies of gray whale evolution, population structure, demography, and relatedness.

Mammals vary dramatically in lifespan, by at least two-orders of magnitude, but the molecular basis for this difference remains largely unknown. The bowhead whale Balaena mysticetus is the longest-lived mammal known, with an estimated maximal lifespan in excess of two hundred years. It is also one of the two largest animals and the most cold-adapted baleen whale species. Here, we report the first genome-wide gene expression analyses of the bowhead whale, based on the de novo assembly of its transcriptome. Bowhead whale or cetacean-specific changes in gene expression were identified in the liver, kidney and heart, and complemented with analyses of positively selected genes. Changes associated with altered insulin signaling and other gene expression patterns could help explain the remarkable longevity of bowhead whales as well as their adaptation to a lipid-rich diet. The data also reveal parallels in candidate longevity adaptations of the bowhead whale, naked mole rat and Brandt's bat. The bowhead whale transcriptome is a valuable resource for the study of this remarkable animal, including the evolution of longevity and its important correlates such as resistance to cancer and other diseases.

A phylogenetic analysis of partial sequences of 2 mitochondrial genes, NADH dehydrogenase subunit 4 (ND4) and cytochrome b (cyt b), supports the generic distinction and sister taxon relationship of Platemys and a monophyletic Acanthochelys. Acanthochelys radiolata is the most distinct member of the genus Acanthochelys and is sister to a clade that includes A. spixii, A. pallidipectoris, and A. macrocephala. Parsimony and maximum likelihood analyses suggested A. spixii (A. pallidipectoris, A. macrocephala), but this was not strongly supported in bootstrap analysis parsimony and maximum likelihood analyses and low Bayesian posterior probabilities. Evidence of molecular diversity within morphologically defined species suggests that there may be additional cryptic species in this group.

Patterns of genetic variation observed within species reflect evolutionary histories that include signatures of past demography. Understanding the demographic component of species' history is fundamental to informed management because changes in effective population size affect response to environmental change and evolvability, the strength of genetic drift, and maintenance of genetic variability. Species experiencing anthropogenic population reductions provide valuable case studies for understanding the genetic response to demographic change because historic changes in the census size are often well documented. A classic example is the bowhead whale, Balaena mysticetus, which experienced dramatic population depletion due to commercial whaling in the late 19th and early 20th centuries. Consequently, we analyzed a large multi-marker dataset of bowhead whales using a variety of analytical methods, including extended Bayesian skyline analysis and approximate Bayesian computation, to characterize genetic signatures of both ancient and contemporary demographic histories. No genetic signature of recent population depletion was recovered through any analysis incorporating realistic mutation assumptions, probably due to the combined influences of long generation time, short bottleneck duration, and the magnitude of population depletion. In contrast, a robust signal of population expansion was detected around 70,000 years ago, followed by a population decline around 15,000 years ago. The timing of these events coincides to a historic glacial period and the onset of warming at the end of the last glacial maximum, respectively. By implication, climate driven long-term variation in Arctic Ocean productivity, rather than recent anthropogenic disturbance, appears to have been the primary driver of historic bowhead whale demography.

Interest in bowhead whale stock structure has been high due to the species’ extreme historical depletion, differential rates of recovery, the potential effects of climate change, and the need to set appropriate quotas for aboriginal hunts. We present an analysis of 42 linked and unlinked single nucleotide polymorphisms (SNPs) among 3 bowhead whale stocks and within the Bering/Chukchi/Beaufort Seas (BCB) stock, and compare results with previously published results of mtDNA control region sequences and 22 microsatellites. We performed tests of population structure (FST, χ2, STRUCTURE), population assignment, and estimates of effective population size (Ne), and evaluated different numbers of loci and samples to estimate the relative statistical power of SNPs and microsatellites. Results indicate that this number of SNPs provides similar power to microsatellites to detect low levels of differentiation (FST = 0.005−0.03) between bowhead populations with sample sizes of at least 20 per population. Neither marker performed well for Bayesian analysis of population structure (STRUCTURE) for the strata that had high diversity coupled with low differentiation. This example is valuable in cautioning against use of STRUCTURE to exclude demographic independence of relatively abundant populations. Microsatellites provided greater precision for estimates of Ne and for assignment tests. All 3 genetic marker types are consistent with the BCB stock being a single population. For microsatellites, differences were found between individuals born before 1949 and those born after 1979. SNPs are continuing to prove valuable as tools for understanding structure and demography of populations, and are likely to prove beneficial for long-term monitoring of bowhead whales.

Evolutionary toxicology is a young field that has grown rapidly in the past two decades. The potential of this field comes from the ability to link chemical contamination to multigenerational and population‐wide effects in various species. The advancements and rapidly decreasing costs of ‐omic tools are improving the power and resolution of evolutionary toxicology studies. In this manuscript, we aim to address the trajectories and perspectives for conducting evolutionary toxicology studies with ‐omic approaches. We discuss the complementarity of using multiple ‐omic tools (genomics, eDNA, transcriptomics, proteomics, and metabolomics) for utility in understanding the toxicological relevance of adaptive responses in populations. In addition, we discuss phenotypic plasticity and its relevance to transcriptomic studies in toxicology. As evolutionary toxicology grows and expands its capacity to link toxicology with population‐wide end points, we emphasize the applications of such studies in answering questions about ecological and population health, as well as future applicability to regulation. Thus, we aim to emphasize the enormous potential for evolutionary toxicology in an ‐omics world and give perspectives on the directions of future investigations.

This study focused on several wetlands in Laguna del Tigre National Park (Guatemala) as part of Conservation International's Rapid Assessment Program. Sediment and water samples were collected from a laguna near Xan field, Guatemala's largest oil facility, and three other sites for determination of levels of polycyclic aromatic hydrocarbons (PAHs). Cichlid fish (Thorichthys meeki and Vieja synspila) were collected for determination of DNA strand breakage (by gel electrophoresis), chromosomal breakage (flow cytometry), and fin erosion. For T. meeki from Xan field, chromosomal breakage and strand breakage was greater than in at least two of the three reference sites. For V. synspila, chromosomal breakage and strand breakage were greater in Xan than one of the two reference sites. Fin erosion was observed only at the Xan laguna. Genetic biomarker effects and fin erosion, along with patterns of aqueous PAH concentrations, indicate that fish are affected by anthropogenic contaminants. PAHs were elevated at some reference sites, but environmental forensic analysis suggested a pyrogenic or diagenic origin. It is possible that oil field brines injected into the ground water caused fin erosion and genotoxicity in fish at Xan field, and it is also possible that pyrogenic PAHs influence levels of DNA damage in reference sites. These analyses represent one of the first efforts to examine genotoxicity in native Mesoamerican cichlids.

The biology of the Steller sea lion (Eumetopias jubatus) has been the subject of intense scientific investigation. This is primarily due to the rapid decline of population size in the western part of the species’ range since the 1970s and the subsequent Threatened and Endangered species listings that had direct impact on the management of one of the world’s largest fisheries. The Steller sea lion has emerged as an indicator species representing the environmental health of the North Pacific Ocean and Bering Sea. In this study, to better understand the historical processes that have culminated in the extant populations of E. jubatus, a large genetic data set consisting of 3 mitochondrial regions for .1,000 individuals was analyzed from multiple phylogeographic and demographic perspectives. The results describe the role of climate change in shaping the population structure of E. jubatus. Climatically associated historical processes apparently involved differential demographic responses to ice ages (and putative glacial vicariance) dependent on population size. Ice ages during times of small effective population size promoted restricted gene flow and fragmentation, and ice ages occurring during times of large population size promoted gene flow and dispersal. These results illustrate that effective population size has a profound effect on how species respond to climate change, an observation with obvious implications for large mammals and endangered species under the present conditions of imminent anthropogenically caused climate change. In addition, the results confirm previous observations of strongly biased historic and contemporary gene flow involving dispersal from west to east. Furthermore, phylogenetic patterns in combination with available fossil data suggest the potential of an Asian origin of E. jubatus. The results of this study provide a detailed scenario for the history that has shaped contemporary populations of E. jubatus.

The Atlantic Wood Industries Superfund site (AWI) on the Elizabeth River in Portsmouth, VA is heavily contaminated with polycyclic aromatic hydrocarbons (PAHs) from a wood treatment facility. Atlantic killifish, or mummichog (Fundulus heteroclitus), at this Superfund site are exposed to very high concentrations of several carcinogens. In this study, we measured PAH concentrations in both fish tissues and sediments. Concurrently, we assessed different aspects of genotoxicity in the killifish exposed in situ. Both sediment and tissue PAH levels were significantly higher in AWI samples, relative to a reference site, but the chemistry profile was different between sediments and tissues. Killifish at AWI exhibited higher levels of DNA damage compared to reference fish, as measured via the flow cytometric method (FCM), and the damage was consistent with sediment PAH concentrations. Covalent binding of benzo[a]pyrene (BaP) metabolites to DNA, as measured via LC-MS/MS adduct detection methods, were also elevated and could be partially responsible for the DNA damage. Using similar LC-MS/MS methods, we found no evidence that oxidative DNA adducts had a role in observed genotoxicity.

Gray whales (Eschrichtius robustus) in the Western Pacific are critically endangered, whereas in the Eastern Pacific, they are relatively common. Holocene environmental changes and commercial whaling reduced their numbers, but gray whales in the Eastern Pacific now outnumber their Western counterparts by more than 100-fold. Herein, we investigate the genetic diversity and population structure within the species using a panel of genic single nucleotide polymorphisms. Results indicate the gray whale gene pool is differentiated into two substocks containing similar levels of genetic diversity, and that both our Eastern and Western geographical samples represent mixed-stock aggregations. Ongoing or future gene flow between the stocks may conserve genetic diversity overall, but admixture has implications for conservation of the critically endangered Western gray whale.

Reig's short-tailed opossum (Monodelphis reigi) was recently described morphologically, based on a single specimen from southeastern Venezuela. It was considered most similar to M. adusta, which is allopatrically distributed in the Andes and surrounding areas, but there has not been an explicit study of systematic relationships with other species of Monodelphis. We report the first occurrence from Guyana of this rare species that was previously known by only the holotype. In a molecular phylogenetic analysis of mitochondrial cytochrome b sequence variation, it groups within a well-supported monophyletic clade that includes M. adusta, M. handleyi, M. osgoodi, and M. peruviana. M. adusta was found to be the sister taxon to the rest of the adusta-complex. M. reigi is the basal taxon (sister species) of remaining adusta-complex forms. This corroborates earlier morphological studies suggesting close affinity of these taxa. As presently known, M. reigi is endemic to the highland regions (>1,000 m asl) of the Guiana Shield of northern South America, and is the only taxon within the M. adusta species complex that does not occur in the Andes or adjacent lowland regions. Based on previous molecular dating of Didelphidae, this suggests that there was a dispersal event from the Andes to the Guiana Highlands in the Miocene that gave rise to M. reigi.

Nanoparticles are being used in many commercial applications. We describe the toxicity of two commercial silver (Ag) nanoparticle (NP) products, NanoAmor and Sigma on Pimephales promelas embryos. Embryos were exposed to varying concentrations of either sonicated or stirred NP solutions for 96 h. LC(50) values for NanoAmor and Sigma Ag NPs were 9.4 and 10.6 mg/L for stirred and 1.25 and 1.36 mg/L for sonicated NPs, respectively. Uptake of Ag NPs into the embryos was observed after 24 h using Transmission Electron Microscopy and Ag NPs induced a concentration-dependent increase in larval abnormalities, mostly edema. Dissolved Ag released from Ag NPs was measured using Inductively Coupled-Mass Spectrometry and the effects tested were found to be three times less toxic when compared to Ag nitrate (AgNO(3)). The percentage of dissolved Ag released was inversely proportional to the concentration of Ag NPs with the lowest (0.625 mg/L) and highest (20 mg/L) concentrations tested releasing 3.7 and 0.45% dissolved Ag, respectively and percent release was similar regardless if concentrations were stirred or sonicated. Thus increased toxicity after sonication cannot be solely explained by dissolved Ag. We conclude that both dissolved and particulate forms of Ag elicited toxicity to fish embryos.

Scotophilus occurs throughout sub-Saharan Africa, parts of southern and southeastern Asia, a majority of the Indomalayan Islands, Reunion Island, and Madagascar. The genus is in the family Vespertilionidae, subfamily Vespertilioninae, and tribe Scotophilini (Hoofer and Van Den Bussche 2003). The type specimen of the genus (S. kuhlii) was 1st described by Leach (1821) based on a single immature specimen. However, the holotype still retained its deciduous milk teeth, which prompted debate on the validity of the genus. Nonetheless, earlier zoologists were applying the name Scotophilus to almost every bat in the family Vespertilionidae with fewer than 38 teeth, resulting in taxonomic confusion (Dobson 1875).

Microsatellite genotyping from samples with varying quality can result in an uneven distribution of errors. Previous studies reporting error rates have focused on estimating the effects of both randomly distributed and locus-specific errors. Sample-specific errors, however, can also significantly affect results in population studies despite a large sample size. From two studies including six microsatellite markers genotyped from 272 sperm whale DNA samples, and 33 microsatellites genotyped from 213 bowhead whales, we investigated the effects of sample- and locus-specific errors on calculations of Hardy–Weinberg equilibrium. The results of a jackknife analysis in these two studies identified seven individuals that were highly influential on estimates of Hardy–Weinberg equilibrium for six different markers. In each case, the influential individual was homozygous for a rare allele. Our results demonstrate that Hardy–Weinberg P values are very sensitive to homozygosity in rare alleles for single individuals, and that > 50% of these cases involved genotype errors likely due to low sample quality. This raises the possibility that even small, normal levels of laboratory errors can result in an overestimate of the degree to which markers are out of Hardy–Weinberg equilibrium and hence overestimate population structure. To avoid such bias, we recommend routine identification of influential individuals and multiple replications of those samples.

The twist-necked turtle, Platemys platycephala, is 1 of only 2 known species to possess sexual reproduction and diploid-triploid mosaicism. Previous studies have shown that mosaics occur in Suriname and French Guiana but only diploids are known from Bolivia and Brazil. In this paper, the frequency of ploidy mosaicism was studied in a large sample of P. platycephala from Suriname to more fully explore the diversity of ploidy levels within and among individuals. Flow-cytometric analysis of blood revealed a wide diversity of conditions including diploids, diploid-triploid mosaics, triploids, and triploid-tetraploid mosaics. The largest frequency class was 100% diploid, and the second largest was 100% triploid. However, mosaic individuals were observed from the entire spectrum of mixtures ranging from nearly all-diploid to nearly all-triploid and 2 individuals were triploid-tetraploid mosaics. It appears likely that diploids, triploids and mosaics do not represent distinct biotypes, but simply different conditions within a spectrum of possible ploidy mixtures. Studies of multiple tissues from 5 individuals showed blood alone is a good indicator of ploidy, but subtle differences were found among tissues for some individuals, and some individuals that were all-diploid or all-triploid in blood were found to be mosaic in other tissues. Triploidy was statistically associated with males, and we hypothesize that genome size plays a role in sex determination in this species.

We quantified the level of dietary mercury (Hg), delivered as methylmercury chloride (CH3HgCl), associated with negative effects on organ and plasma biochemistries related to glutathione (GSH) metabolism and oxidative stress, and chromosomal damage in captive-reared common loon (Gavia immer) chicks reared from hatch to 105 days. Mercury-associated effects related to oxidative stress and altered glutathione metabolism occurred at 1.2 microg Hg/g and 0.4 microg Hg/g, an ecologically relevant dietary mercury level, but not at 0.08 microg Hg/g. Among the variables that contributed most to dissimilarities in tissue chemistries between control and treatment groups were increased levels of oxidized glutathione (GSSG), GSH peroxidase, and the ratio of GSSG to GSH in brain tissue; increased levels of hepatic GSH; and decreased levels of hepatic glucose-6-phosphate dehydrogenase (G-6-PDH). Our results also suggest that chronic exposure to environmentally relevant dietary Hg levels did not result in statistically significant somatic chromosomal damage in common loon chicks.

We studied molecular and morphological variation in small fruit-eating bats (Artibeus) in northern South America to establish species boundaries, evolutionary relationships, and distributional limits. Although this is a speciose genus with some of the most common bats in Neotropical forests, resolution of taxonomy and their identification has been difficult. Our molecular phylogeny based on Bayesian and parsimony analyses of cytochrome b variation includes a well supported topology of A. glaucus glaucus sister to a clade of A. gnomus and A. glaucus bogotensis indicating that A. glaucus is a paraphyletic amalgam. A re-assessment of morphology corroborates differences between A. g. bogotensis from the Andean valleys of Colombia east into the Guianas and A. g. glaucus from western Amazonia. Thus, we recognize A. bogotensis and A. glaucus as distinct and allopatrically occurring species. Based on a Kimura-2 parameter model of substitution for cytochrome b, there was 1.2% sequence divergence within A....

Cliff swallows (Petrochelidon pyrrhonota) and cave swallows (P. fulva) were sampled during the breeding season at several locations in the Rio Grande, Texas, to evaluate the potential effects of environmental contaminants on P450 aromatase activity in brain and gonads and DNA damage in blood cells. The tritiated water-release aromatase assay was used to measure aromatase activity and flow cytometry was used to measure DNA damage in nucleated blood cells. There were no significant differences in brain and gonadal aromatase activities or in estimates of DNA damage (HPCV values) among cave swallow colonies from the Lower Rio Grande Valley (LRGV) and Somerville. However, both brain and gonadal aromatase activities were significantly higher (P < 0.05) in male cliff swallows from Laredo than in those from Somerville. Also, DNA damage estimates were significantly higher (P < 0.05) in cliff swallows (males and females combined) from Laredo than in those from Somerville. Contaminants of current high use in the LRGV, such as atrazine, and some of the highly persistent organochlorines, such as toxaphene and DDE, could be potentially associated with modulation of aromatase activity in avian tissues. Previous studies have indicated possible DNA damage in cliff swallows. We did not observe any differences in aromatase activity or DNA damage in cave swallows that could be associated with contaminant exposure. Also, the differences in aromatase activity and DNA damage between male cliff swallows from Laredo and Somerville could not be explained by contaminants measured at each site in previous studies. Our study provides baseline information on brain and gonadal aromatase activity in swallows that could be useful in future studies.

Evolutionary relationships among bats of the genus Rhogeessa (Chiroptera: Vespertilionidae) are poorly understood because of the morphological similarity of many of the species and the limited resolution of karyotypes and allozymes in previous studies. Previous karyotypic studies reported several populations that differ by Robertsonian centric fusions, which led to a proposed mechanism of speciation called speciation by monobrachial centric fusions. Here, we present a molecular phylogenetic analysis of 8 of the 10 currently recognized species of Rhogeessa using the mitochondrial DNA gene cytochrome b as well as new karyotypic data. The results are generally consistent with speciation by monobrachial centric fusions because karyotypically distinct populations typically comprise monophyletic maternal lineages. One exception was 2 individuals that were possible hybrids between R. tumida (2n ¼ 34) and R. aeneus (2n ¼ 32). We found ostensible species-level differentiation among 3 karyotypically identical (2n ¼ 34) but geographically separated populations of R. tumida. Examination of new karyotypic data shows a population from western Ecuador to have 2n ¼ 42 and study of molecular data shows it to be phylogenetically distinct from both the karyotypically identical R. genowaysi from Mexico and the South American R. io (2n ¼ 30) to which it was previously allocated. We recognize this population by its available name, R. velilla. We also found an unexpectedly close relationship between Baeodon alleni and R. gracilis.

We examine the evolutionary history and speculate about the evolutionary future of three basic life history ecotypes that contribute to the biocomplexity of sockeye salmon (Oncorhynchus nerka). The ‘recurrent evolution’ (RE) hypothesis claims that the sea/river ecotype is ancestral, a ‘straying’ form with poorly differentiated (meta)population structure, and that highly structured populations of lake-type sockeye and kokanee have evolved repeatedly in parallel adaptive radiations between recurrent glaciations of the Pleistocene Epoch. Basic premises of this hypothesis are consistent with new, independent evidence from recent surveys of genetic variation in mitochondrial and microsatellite DNA: (1) sockeye salmon are most closely related to pink (O. gorbuscha) and chum (O. keta) salmon with sea-type life histories; (2) the sockeye life history ecotypes exist as polyphyletic lineages within large drainages and geographic regions; (3) the sea/river ecotype exhibits less genetic differentiation among populations than the lake or kokanee ecotypes both within and among drainages; and (4) genetic diversity is typically higher in the sea/river ecotype than in the lake and kokanee ecotypes. Anthropogenic modification of estuarine habitat and intensive coastal fisheries have likely reduced and fragmented historic metapopulations of the sea/river ecotype, particularly in southern areas. In contrast, the kokanee ecotype appears to be favoured by marine fisheries and predicted changes in climate.

Multiple unlinked loci are surveyed in a methodological approach for mammalian systematics that uses genes from the four pathways of genetic transmission: mitochondrial, autosomal, and X and Y sex chromosomes. Each of these components has different properties, such as effective population size, mutation rate, and recombination, that result in a robust hypothesis of evolutionary history. The utility of this experimental design is tested with bats in the family Emballonuridae and the hypothesis that the New World taxa are monophyletic. Parsimony and Bayesian analyses of the individual data sets give generally congruent topologies with high bootstrap proportions and posterior probabilities for monophyletic clades representing species and genera. The mitochondrial gene has significantly faster rates of substitution, higher levels of homoplasy, and a greater degree of saturation than the nuclear genes that contributed to the loss of phylogenetic signal at deeper branches of the tree. However, there is better resolution and support for the more slowly evolving nuclear introns including a New World clade, indicating a single origin of emballonurid bats in the Neotropics (tribe Diclidurini). One novel subtribe has a hard basal polytomy that is unresolved for all of the nuclear partitions, suggesting a rapid burst of evolution during the diversification of genera. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 189–209.

We examined a suite of environmental contaminants and exposure endpoints in black-crowned night-heron (Nycticorax nycticorax, BCNH) embryos collected in 2002 from colonies in Illinois, Minnesota, and Virginia. Embryos from the Lake Calumet, IL, colony had greater exposure to polychlorinated biphenyls (PCBs), 4,4′-dichlorodiphenyldichloroethylene (DDE), dieldrin, transnonachlor, oxy-chlordane, cobalt, copper, and selenium than did those from northwest MN and coastal VA. Embryos from IL and VA contained greater concentrations of mercury and zinc than those from MN, whereas the latter had greater accumulation of lead. Greater exposure of IL embryos to PCBs was reflected in greater ethoxyresorufin-O-deethylase and benzyloxyresorufin-O-dealkylase induction. However, measures of oxidative stress and genotoxicity were similar to those in embryos from the other colonies examined, and no overt toxic effects of contaminant exposure such as embryo mortality or malformations were observed. Although efforts t...

We develop a general framework for analysing and testing genetic structure within a migratory assemblage that is based on measures of genetic differences between individuals. We demonstrate this method using microsatellite DNA data from the Bering-Chukchi-Beaufort stock of bowhead whales (Balaena mysticetus), sampled via Inuit hunting during the spring and autumn migration off Barrow, Alaska. This study includes a number of covariates such as whale ages and the time separation between captures. Applying the method to a sample of 117 bowhead whales, we use permutation methods to test for temporal trends in genetic differences that can be ascribed to age-related effects or to timing of catches during the seasons. The results reveal a pattern with elevated genetic differences among whales caught about a week apart, and are statistically significant for the autumn migration. In contrast, we find no effects of time of birth or age-difference on genetic differences. We discuss possible explanations for the results, including population substructuring, demographic consequences of historical overexploitation, and social structuring during migration.

The U.S. Army Corps of Engineers conducted a water drawdown on Navigation Pool 8 of the Upper Mississippi River during the summers of 2001 and 2002 to increase aquatic vegetation production and thereby improve fish and wildlife habitat. Flooding of previously dried wetlands, however, may increase the rate of mercury methylation and make mercury more available to terrestrial vertebrates that feed in aquatic environments. Our objective was to determine if mercury, other elements, and organochlorine contaminants were more available to vertebrates following the 2001 drawdown. Tree swallow (Tachycineta bicolor) eggs and nestlings were collected at two sites on Pool 8 and a nearby Reference site in 2000 (pre-2001 drawdown), 2001 (pre-2001 drawdown) and 2002 (post-2001 drawdown) and tissues were analyzed for mercury, other elements, and organochlorine contaminants. Bioindicator measurements of genetic damage, oxidative stress, ethoxyresorufin-O-dealkylase activity, and the ratio of liver to nestling mass were also measured in nestlings at all sites and all years. Based on a multivariate analysis, the 2001 drawdown of Pool 8 did not influence element concentrations, organochlorine concentrations, or bioindicator response. Concentrations of inorganic and organochlorine contaminants in tree swallow eggs and nestlings were not at toxic levels. Hatching success did not differ among years and was comparable to the nationwide average.

Pocket gophers (Rodentia: Geomyidae) are fossorial herbivores, sister to the New World Heteromyidae, and, with one exception (Orthogeomys), are restricted in distribution to North America. Because they occur in small, isolated demes and possess an overall lack of vagility as well as conservative morphology, these rodents pose many problems with respect to their taxonomy, systematics, evolutionary history, and intrageneric affinities. Members of the genus Geomys are no exception. Species of Geomys occur in the southeastern United States and throughout much of the central and southern Great Plains westward to the eastern slope of the Rocky Mountains and south into northern Mexico (Fig. 1). Considerable uncertainty exists concerning the number of species present and the historical relationships among described taxa. Much of the confusion involves the presence of sibling species, with little or no morphological differentiation and, in some instances, high degrees of chromosomal diversification and allozymic variation. Merriam (1895), in his revision of pocket gophers of the family Geomyidae (exclusive of Thomomys), recognized 3 species groups within Geomys: the tuza (¼ pinetis) group including what is today recognized as G. pinetis; the bursarius

The Steller’s sea lion Eumetopias jubatus is an endangered marine mammal that has experienced dramatic population declines over much of its range during the past five decades. Studies using mitochondrial DNA (mtDNA) have shown that an apparently continuous population includes a strong division, yielding two discrete stocks, western and eastern. Based on a weaker split within the western stock, a third Asian stock has also been defined. While these findings indicate strong female philopatry, a recent study using nuclear microsatellite markers found little evidence of any genetic structure, implying extensive paternal gene flow. However, this result was at odds with mark–recapture data, and both sample sizes and genetic resolution were limited. To address these concerns, we increased analytical power by genotyping over 700 individuals from across the species’ range at 13 highly polymorphic microsatellite loci. We found a clear phylogenetic break between populations of the eastern stock and those of the western and Asian stocks. However, our data provide little support for the classification of a separate Asian stock. Our findings show that mtDNA structuring is not due simply to female philopatry, but instead reflects a genuine discontinuity within the range, with implications for both the phylogeography and conservation of this important marine mammal.

Extremely high concentrations of cadmium (3.5 microg/g dry wgt.) and elevated concentrations of chromium (10 microg/g dry wgt.) and mercury (1.6 microg/g dry wgt.) were reported in waterbird tissues at Agassiz National Wildlife Refuge in northwestern Minnesota in 1994. Tree swallows (Tachycineta bicolor) were studied during 1998-2001 at three drainages into the Refuge, two pools on the Refuge, and at a nearby reference location to document whether high levels of contaminants were still present, and if so to quantify the source and severity of the contamination. Trace elements were measured in tree swallow eggs, livers, and diet. Reproductive success and bioindicator responses were monitored. In 2000, water was drawn down on Agassiz Pool, one of the main pools on the Refuge. This presented an opportunity to evaluate the response of trace element concentrations in the diet and tissues of tree swallows after reflooding. High concentrations of trace elements were not detected in swallow tissues, nor were there differences among locations. Less than 20% of swallow samples had detectable concentrations of cadmium or chromium. Mercury concentrations were low and averaged0.25 microg/g dry wgt. in swallow tissues. Trace elements, including mercury, did not increase in tree swallows following the 2000 drawdown at Agassiz Pool. Hatching success and survival of nestlings to 12 days-of-age for tree swallows on the Refuge were similar to the national average and consistent with background trace element concentrations. Bioindicator measurements were within the normal ranges as well.

We used molecular methods and population genetic analyses to study the effects of chronic contaminant exposure in marsh frogs from Sumgayit, Azerbaijan. Marsh frogs inhabiting wetlands in Sumgayit are exposed to complex mixtures of chemical contaminants, including petroleum products, pesticides, heavy metals, and many other industrial chemicals. Previous results documented elevated estimates of genetic damage in marsh frogs from the two most heavily contaminated sites. Based on mitochondrial DNA (mtDNA) control region sequence data, the Sumgayit region has reduced levels of genetic diversity, likely due to environmental degradation. The Sumgayit region also acts as an ecological sink, with levels of gene flow into the region exceeding gene flow out of the region. Additionally, localized mtDNA heteroplasmy and diversity patterns suggest that one of the most severely contaminated sites in Sumgayit is acting as a source of new mutations resulting from an increased mutation rate. This study provides an integrated method for assessing the cumulative population impacts of chronic contaminant exposure by studying both population genetic and evolutionary effects.

The endangered Sonoran pronghorn (Antilocapra americana sonoriensis) consists of only 2 small populations, 1 in Arizona and 1 in Mexico. Mitochondrial DNA sequence data and 5 microsatellite loci were used to compare levels of genetic diversity and differentiation between the 2 Sonoran pronghorn populations and between this subspecies and other selected pronghorn populations, both proximate and distant to the Sonoran pronghorn's current range. The data support a history of recent isolation of Sonoran pronghorn populations from those in Arizona, New Mexico, and Texas. Loss of genetic diversity due to bottlenecks and drift has been severe in both populations of the Sonoran pronghorn, but is most pronounced in the Arizona population. These results are discussed in terms of conservation management strategies.

We analyzed the phylogenetic relationships of all eleven currently recognized species of large Artibeus using the cytochrome b mitochondrial gene. The topology from a maximum parsimony analysis included: (1) A. obscurus and A. planirostris as sister species with successively basal lineages of (2) A. amplus, (3) a clade with A. lituratus and A. intermedius, (4) A. jamaicensis, (5) a clade of A. inopinatus sister to A. hirsutus and A. fraterculus, (6) A. fimbriatus, and (7) the most basal lineage of A. concolor. The individual species were monophyletic and well supported by bootstrap and decay values. The monophyletic clade of ((((obscurus + planirostris) + amplus) + (lituratus + intermedius)) + jamaicensis) was also highly supported, although some of the interspecific relationships were less so. Contrary to previous hypotheses of species limits based on a presumed intergradation in body size, A. jamaicensis and A. planirostris do not form a monophyletic group, refuting their conspecificity and supporting a...

Genetic variation at 6 nuclear microsatellite loci with biparental inheritance and the maternally inherited mitochondrial DNA (mtDNA) was studied at 3 geographic scales (rookeries, regions, and stocks) in Steller sea lions (Eumetopias jubatus). Genetic variation was high in both nuclear and mtDNA markers as revealed by a near range-wide survey of 21 rookeries. However, population structure was not well defined, and there was no obvious phylogeographic pattern to the distribution of microsatellite alleles. This contrasts with a clear phylogeographic pattern revealed by control-region sequences of mtDNA in which 2 well-differentiated stocks, eastern and western, are defined as well as 2 distinct groups, Asian and central, in the western stock. Effective migration estimates are consistently higher for the nuclear loci than for mtDNA. The difference in patterns between the biparentally and maternally inherited genetic markers can be explained by relatively high male dispersal rates and female philopa...