The brown bear () is an iconic carnivoran species of the Northern Hemisphere. Its population history has been studied extensively using mitochondrial markers, which demonstrated signatures of multiple waves of migration, arguably connected with glaciation periods. Among Eurasian brown bears, Siberian populations remain understudied. We have sequenced complete mitochondrial genomes of four ancient (~4.5-40 kya) bears from South Siberia and 19 modern bears from South Siberia and the Russian Far East. Reconstruction of phylogenetic relationships between haplotypes and evaluation of modern population structure have demonstrated that all the studied samples belong to the most widespread Eurasian clade 3. One of the ancient haplotypes takes a basal position relative to the whole of clade 3; the second is basal to the haplogroup 3a (the most common subclade), and two others belong to clades 3a1 and 3b. Modern Siberian bears retain at least some of this diversity; apart from the most common haplogroup 3a, we demonstrate the presence of clade 3b, which was previously found mainly in mainland Eurasia and Northern Japan. Our findings highlight the importance of South Siberia as a refugium for northern Eurasian brown bears and further corroborate the hypothesis of several waves of migration in the Pleistocene.

How developmental modifications produce key innovations, which subsequently allow for rapid diversification of a clade into new adaptive zones, has received much attention. However, few studies have used a robust comparative framework to investigate the influence of evolutionary and developmental constraints on the origin of key innovations, such as the adhesive toe pad of lizards. Adhesive toe pads evolved independently at least 16 times in lizards, allowing us to examine whether the patterns observed are general evolutionary phenomena or unique, lineage-specific events. We performed a high-resolution comparison of plantar scale development in 14 lizard species in and geckos, encompassing five independent origins of toe pads (one in , four in geckos). Despite substantial evolutionary divergence between and geckos, we find that these clades have undergone similar developmental modifications to generate their adhesive toe pads. Relative to the ancestral plantar scale development, in which scale ridges form synchronously along the digit, both padded geckos and exhibit scansor formation in a distal-to-proximal direction. Both clades have undergone developmental repatterning and, following their origin, modifications in toe pad morphology occurred through relatively minor developmental modifications, suggesting that developmental constraints governed the diversification of the adhesive toe pad in lizards.

The Northern Rocky Mountain ecosystem supports rich biological diversity with many endemic and rare species. Extant endemics display two biogeographic patterns: widespread species with fragmented populations, and narrow-range endemics. These distributions are shown by the congeneric snails and . These two taxa are disjunct from the remaining species of the genus, which achieves its greatest diversity in eastern North America. Given the disjunct nature of and , we here present a mtDNA phylogeny of the genus that includes both eastern and western species to assess the phylogenetic position of and . We then reconstruct the demographic history of and by analysing current patterns of genetic variation and interpreting the results considering the historical biogeography of the region. Both and represent unique taxa that are genetically and geographically distinct from their congeners. The current distribution and genetic structure of has been shaped by both historical isolation in refugia and more recent northward shifts, whereas is represented by two populations with shallow divergence in an area of long-term habitat stability.

Heterosis, Haldane and Bateson-Dobzhansky-Muller effects have been widely documented amongst a range of plants and animals. However, typically these effects are shown by taking parents of known genotype into the laboratory and measuring components of the F progeny under laboratory conditions. This leaves in doubt the real significance of such effects in the field. Here we use the well-known colour pattern genotypes of the African monarch or queen (), which also control wing length, to test these effects both in the laboratory and in a contact zone in the field. By measuring the wing lengths in animals of known colour pattern genotype we show clear evidence for all three hybrid effects at the A and BC colour patterning loci, and importantly, that these same effects persist in the same presumptive Fs when measured in hybrid populations in the field. This demonstrates the power of a system in which genotypes can be directly inferred in the field and highlights that all three hybrid effects can be seen in the East African contact zone of this fascinating butterfly.

Divergence in mating signals typically accompanies speciation. We examine two ecologically divergent sibling species of crickets to assess the degree and timing of the evolution of prezygotic reproductive isolation. occurs in rocky habitats throughout western North America with long-winged individuals capable of long-distance dispersal; is endemic to red-rock sandstone areas of south-eastern Utah and north-eastern Arizona and has short-winged individuals only capable of limited dispersal. Previous genetic work suggested some degree of introgression and/or incomplete lineage sorting is likely. Here we: (1) use restriction site associated DNA sequencing (RAD-seq) genetic data to describe the degree of genetic divergence among species and populations; (2) examine the strength of prezygotic isolation by (i) quantifying differences among male mating songs, and (ii) testing whether females prefer or calling songs. Our results show that genetically distinct "pure" species populations and genetically intermediate populations exist. Male mating songs are statistically distinguishable, but the absolute differences are small. In playback experiments, females from pure populations had no preference based on song; however, females from a genetically intermediate population preferred song. Together these results suggest that prezygotic isolation is minimal, and mediated by female behaviour in admixed populations.

Phylogeographical studies of Philippine vertebrates have demonstrated that genetic variation is broadly partitioned by Pleistocene island aggregation. Contemporary island discontinuity is expected to influence genetic differentiation but remains relatively undocumented, perhaps because the current episode of island isolation started in relatively recent times. We investigated inter- and intra-island population structure in a Philippine endemic bird genus () to determine whether genetic differentiation has evolved during the recent period of isolation. We sequenced thousands of genome-wide restriction site associated DNA (RAD) markers from throughout the Mindanao group to assess fine-scale genetic structure across islands. Specifically, we investigated patterns of gene flow and connectivity within and between taxonomic and geographical bounds. A previous assessment of mitochondrial DNA detected deep structure between and a sister species, , but was insufficient to detect differentiation within either species. Analysis of RAD markers, however, revealed structure within between the islands of Samar/Leyte and Bohol. This genetic differentiation probably demonstrates an effect of recent geographical isolation (after the Last Glacial Maximum) on the genetic structure of Philippine avifauna. We suggest that the general lack of evidence for differentiation between recently isolated populations is a failure to detect subtle population structure owing to past genetic sampling constraints, rather than the absence of such structure.

Agassiz, L. (1862) Contributions to the natural history of the United States of America. Vol. 4. Little Brown, Boston, 380 pp.Aguirrezabalaga, F., Altuna, A., Borja, A., Feliu, J., GarcíaCarrascosa, A.M., Romero, A., San Vicente, C., Torres-Gómez-de-Cádiz, J.A., Uriz, M.J. Ibánez, M. (1984) Contribución al conocimiento de la fauna marina de la costa Vasca. Π. Lurralde, Investigación y espacio, 1984, pp. 83-133.Alder, J. (1856) A notice of some new genera and species of British hydroid zoophytes. Annals and Magazine of Natural History, Series 2, 18, 353-362.        https://doi.org/10.1080/00222935608697652Allman, G.J. (1873) Interim report on the hydroids collected by L.F. de Pourtalès during the Gulf Stream exploration of United States coast survey. Bulletin of the Museum of Comparative Zoology at Harvard College, 3 (7), 185-186.Allman, G.J. (1874) Report on the Hydroida collected during the expeditions of H.M.S. 'Porcupine.' Transactions of the Zoological Society of London, 8, 469-481.        https://doi.org/10.1111/j.1096-3642.1874.tb00566.xAllman, G.J. (1877) Report on the Hydroida collected during the exploration of the Gulf Stream by L.F. de Pourtalès, assistant United States Coast Survey. Memoirs of the Museum of Comparative Zoology at Harvard College, 5 (2), 1-66.        https://doi.org/10.5962/bhl.

Differences in avian eggshell pigmentation could be an honest signal of female quality that males use to inform their nestling provisioning effort. We investigated whether among-individual variation in protoporphyrin-based eggshell pigmentation in house wrens () reflects female fitness-associated traits and whether males use that information. Females laying lighter clutches were older and larger than females laying darker clutches. Nestlings hatching from lighter clutches had greater size-corrected mass on post-hatch day 11, a measure that strongly predicts survival and recruitment to the breeding population. To test whether male provisioning effort responds to clutch pigmentation, we used a reciprocal clutch cross-fostering design, swapping dark with light clutches and light with dark; in controls, we swapped light with light clutches and dark with dark. Shortly before hatching, clutches were returned to their original nest to avoid confounding effects of nestling quality on male provisioning. Contrary to the sexual selection hypothesis, clutch pigmentation had no effect on male provisioning. Males were probably able to observe eggshell pigmentation and thus had information about female quality, but they did not use this information to modulate their nestling provisioning. This may be because of constraints on species-specific reproductive opportunities, or because variation in eggshell protoporphyrin serves other functions.

Species such as threespine stickleback () that inhabit divergent selective environments and that have diversified on different time scales can be of value for understanding evolutionary processes. Here we synthesize high-resolution genotypic and phenotypic data to explore a largely unstudied distribution of threespine stickleback populations living in oceanic and freshwater habitats along coastal and inland regions of Oregon. Many inland aquatic habitats of Oregon remained unglaciated during the last ice age, meaning that some extant Oregon lake and river stickleback may have descended from freshwater populations established long before more well-studied, post-glacial freshwater populations. To address the degree of congruence between genetic and phenotypic divergence, we directly compared Oregon stickleback to much younger (post-glacial) Alaskan populations. We found phenotypic variation in Oregon stickleback to be primarily partitioned between oceanic and freshwater habitats, as has been documented in other stickleback systems. However, the main axis of genetic divergence was between coastal and inland regions regardless of habitat type. Furthermore, when comparing patterns between Oregon and Alaska we found similar levels of phenotypic divergence, but much greater genetic divergence among Oregon's populations. The Oregon stickleback system therefore appears well suited for future studies linking genotypic and phenotypic change, further extending the utility of this small fish to provide general insights into evolutionary processes.

The Apennine Mountains in Italy are an important biogeographical region and of particular interest in phylogeographical research, because they have been a refugium during Pleistocene glaciation events for numerous European species. We performed a genetic study on the Eurasian bark beetle (Linnaeus, 1760), focusing on two Apennine (Italian) and two Central European (Austrian) locations to assess the influence of the Apennines in the evolutionary history of the beetle, particularly during the Pleistocene. We analysed a part of the mitochondrial gene and a set of 5470 informative genome-wide markers to understand its biogeography. We found 75 distinct mitochondrial haplotypes, which are structured in three main clades. In general, the Apennine locations harbour a higher number of mitochondrial clades than Central European sites, with one specific clade exclusively detected in the Apennines. Analysis of our genome-wide, multi-locus dataset reveals a clustering of by geography, with Italian individuals clearly separated from Austrian samples. Our data highlight the significance of the Apennines for the genetic diversity of and support the hypothesis that this area was an important refugium during unfavourable conditions in the Pleistocene. We discuss additional life-history traits and processes that shaped the evolution of this widespread beetle.

Paper wasps (genus ) are one of the most species-rich genera of social insect. Prior studies have found that male coloration, male colour pattern, territory choice and female caste are potential drivers of intraspecific mate choice in paper wasps. However, there has been no formal assessment of interspecific mate choice in this group; therefore, the mechanism driving diversification in paper wasps remains an open question. In this study, we measured interspecific and intraspecific mating behaviour between two closely related species of paper wasps, and . These two species have ample opportunity to interbreed because and forage, nest and mate in the same habitats. We tested the strength of reproductive isolation between these species using no-choice and choice mating trials. Our results show strong, symmetric, prezygotic isolation between and . Males discriminated between conspecifics and heterospecifics but attempted to mate with females of the other species in ~10% of heterospecific mating trials. Female wasps were more discriminating than males and probably evaluated species identity and male quality through visual or olfactory cues. We additionally report sexual dimorphism in body size.

Spatial and temporal environmental variation influences evolutionary processes such as divergence among populations and species. Here, we investigate the patterns of niche evolution for the Louisiana irises as well as understanding the phylogenetic relationship between these species. Using BEAST, a species phylogeny was generated for the Louisiana irises in order to test the hypothesis of whether niche conservatism has played an important role for this species complex. Species Distribution Models were constructed for present day distributions to determine the environmental factors, which contribute to species ranges. Tests of niche similarity were performed in order to evaluate if niche conservatism is apparent within this species complex. We demonstrate that the Louisiana iris species complex is a monophyletic clade with and as being sister to each other. The differences observed among the iris species, in regard to associated environmental factors suggest an effect from these components on the distributions and habitats occupied. Furthermore, tests of niche similarity indicate niche conservatism for all species comparisons. Working at the species level and assessing various factors that can influence differentiation, this study assessed a more complete picture of the ecological and evolutionary history of this species complex across their geographic and ecological range.

Parenting strategies can be flexible within a species, and may have varying fitness effects. Understanding this flexibility and its fitness consequences is important for understanding why parenting strategies evolve. Here, we investigate the fitness consequences of flexible parenting in the burying beetle , a species known for its advanced provisioning behaviour of regurgitated vertebrate carrion to offspring by both sexes. We show that even when a parent is freely allowed to abandon the carcass at any point in time, biparental post-hatching care is the most common pattern of care adopted in . Furthermore, two parents together raised more offspring than single parents of either sex, showing that the presence of the male can directly influences parental fitness even in the absence of competitors. This contrasts with studies in other species of burying beetle, where biparental families do not differ in offspring number. This may explain why biparental care is more common in than in other burying beetles. We suggest how fitness benefits of two parents may play a role in the evolution and maintenance of flexible biparental care in .

Climate and host demographic cycling often shape both parasite genetic diversity and host distributions, processes that transcend a history of strict host-parasite association. We explored host associations and histories based on an evaluation of mitochondrial and nuclear sequences to reveal the underlying history and genetic structure of a pinworm, , infecting 10 species of western North American chipmunks (Rodentia:, subgenus ). contains divergent lineages influenced by the diversity of hosts and variation across the complex topography of western North America. We recovered six reciprocally monophyletic mitochondrial clades, largely supported by nuclear gene trees, exhibiting divergence levels comparable to intraspecific variation reported for other nematodes. Phylogenetic relationships among pinworm clades suggest that colonized an ancestral lineage of western chipmunks and lineages persisted during historical isolation in diverging species or species groups. Pinworm diversification, however, is incongruent and asynchronous relative to host diversification. Secondarily, patterns of shallow divergence were shaped by geography through events of episodic colonization reflecting an interaction of taxon pulses and ecological fitting among assemblages in recurrent sympatry. Pinworms occasionally infect geographically proximal host species; however, host switching may be unstable or ephemeral, as there is no signal of host switching in the deeper history of .

Functional tool use requires the selection of appropriate raw materials. New Caledonian crows are known for their extraordinary tool-making behaviour, including the crafting of hooked stick tools from branched vegetation. We describe a surprisingly strong between-site difference in the plant materials used by wild crows to manufacture these tools: crows at one study site use branches of the non-native shrub , whereas only approximately 7 km away, birds apparently ignore this material in favour of the terminal twigs of an as-yet-unidentified tree species. Although it is likely that differences in local plant communities drive this striking pattern, it remains to be determined how and why crows develop such strong site-specific preferences for certain raw materials.

Phylogenetic comparative methods are increasingly used to give new insights into the dynamics of trait evolution in deep time. For continuous traits the core of these methods is a suite of models that attempt to capture evolutionary patterns by extending the Brownian constant variance model. However, the properties of these models are often poorly understood, which can lead to the misinterpretation of results. Here we focus on one of these models - the Ornstein Uhlenbeck (OU) model. We show that the OU model is frequently incorrectly favoured over simpler models when using Likelihood ratio tests, and that many studies fitting this model use datasets that are small and prone to this problem. We also show that very small amounts of error in datasets can have profound effects on the inferences derived from OU models. Our results suggest that simulating fitted models and comparing with empirical results is critical when fitting OU and other extensions of the Brownian model. We conclude by making recommendations for best practice in fitting OU models in phylogenetic comparative analyses, and for interpreting the parameters of the OU model.

In wild birds, the proximate and ultimate factors that affect circulating carotenoid concentrations remain poorly understood. We studied variation in plasma carotenoid concentrations across several scales: annual, seasonal, pair, territory and individual, and evaluated whether carotenoid levels explained reproductive outcome of wild American kestrels (). We sampled plasma carotenoid concentrations of 99 female and 80 male incubating kestrels from April-June in 2008-2012. Plasma carotenoid concentrations were explained by an interaction between year and sex, date, and random effects for pair and individual identity. In general, plasma carotenoid concentrations of males were significantly higher than females, but this depended on year. Within a breeding season, earlier nesting kestrels had higher carotenoid concentrations than later nesting kestrels, a pattern that is coincident with seasonal trends in local fitness. Pair and individual identity explained variation in carotenoid concentrations suggesting that carotenoid concentrations of mated birds were correlated, and some individuals consistently maintained higher carotenoid levels than others. Male carotenoid concentrations were positively associated with number of young fledged per pair. These results are consistent with the hypothesis that higher quality individuals have higher carotenoid levels compared to lower quality individuals, despite annual variations in carotenoid availability.

Thorough sampling is necessary to delineate lineage diversity for polytypic "species" such as . We conducted extensive mtDNA sampling (cytochrome b and ND4) from the Pecos River, Rio Grande, and South Canadian River, New Mexico. Our study emphasized the Pecos River due to its complex geological history and potential to harbor multiple lineages. We used geometric-morphometric, morphometric, and meristic analyses to test for phenotypic divergence and combined nucDNA with mtDNA to test for cytonuclear disequilibrium and combined our sequences with published data to conduct a phylogenetic re-assessment of the entire clade. We detected five co-occurring mtDNA lineages in the Pecos River, but no evidence for cytonuclear disequilibrium or phenotypic divergence. Recognized species were interspersed amongst divergent lineages of "". Allopatric divergence among drainages isolated in the Late Miocene and Pliocene apparently produced several recognized species and major divisions within "". Pleistocene re-expansion and subsequent re-fragmentation of a centralized lineage founded younger, divergent lineages throughout the Rio Grande basin and Edwards Plateau. There is also evidence of recent introductions to the Rio Grande, Pecos and South Canadian Rivers. Nonetheless, deeply divergent lineages have coexisted since the Pleistocene.

Superfetation is the ability of females to simultaneously carry multiple broods of embryos, with each brood at a different developmental stage. Matrotrophy is the post-fertilization maternal provisioning of nutrients to developing embryos throughout gestation. Several studies have demonstrated that, in viviparous fishes, superfetation and matrotrophy have evolved in a correlated way, such that species capable of bearing several simultaneous broods also exhibit advanced degrees of post-fertilization provisioning. The adaptive value of the concurrent presence of both reproductive modes may be associated with the production of larger newborns, which in turn may result in enhanced offspring fitness. In this study, we tested two hypotheses: (1) species with superfetation and moderate or extensive matrotrophy give birth to larger offspring compared to species without superfetation or matrotrophy; (2) species with higher degrees of superfetation and matrotrophy (i.e. more simultaneous broods and increased amounts of post-fertilization provisioning) give birth to larger offspring compared to species with relatively low degrees of superfetation and matrotrophy (i.e. fewer simultaneous broods and lesser amounts of post-fertilization provisioning). Using different phylogenetic comparative methods and data on 44 species of viviparous fishes of the family Poeciliidae, we found a lack of association between offspring size and the combination of superfetation and matrotrophy. Therefore, the concurrent presence of superfetation and moderate or extensive matrotrophy has not facilitated the evolution of larger offspring. In fact, these traits have evolved differently. Superfetation and matrotrophy have accumulated gradual changes that largely can be explained by Brownian motion, whereas offspring size has evolved fluidly, experiencing changes that likely resulted from selective responses to the local conditions.

The slender filefish is a master of adaptive camouflage and can change its appearance within 1-3 seconds. Videos and photographs of this animal's cryptic body patterning and behavior were collected under natural light on a Caribbean coral reef. We present an ethogram of body patterning components that includes large- and small-scale spots, stripes and bars that confer a variety of cryptic patterns amidst a range of complex backgrounds. Field images were analyzed to investigate two aspects of camouflage effectiveness: (i) the degree of color resemblance between animals and their nearby visual stimuli and (ii) the visibility of each fish's actual body outline versus its illusory outline. Most animals more closely matched the color of nearby visual stimuli than that of the surrounding background. Three-dimensional dermal flaps complement the melanophore skin patterns by enhancing the complexity of the fish's physical skin texture to disguise its actual body shape, and the morphology of these structures was studied. The results suggest that the body patterns, skin texture, postures and swimming orientations putatively hinder both the detection and recognition of the fish by potential visual predators. Overall, the rapid speed of change of multiple patterns, color blending with nearby backgrounds, and the physically complicated edge produced by dermal flaps effectively camouflage this animal among soft corals and macroalgae in the Caribbean Sea.

Sexual traits vary tremendously in static allometry. This variation may be explained in part by body size-related differences in the strength of selection. We tested this hypothesis with in two populations of vervet monkeys, using estimates of the level of condition dependence for different morphological traits as a proxy for body size-related variation in the strength of selection. In support of the hypothesis, we found that the steepness of allometric slopes increased with the level of condition dependence. One trait of particular interest, the penis, had shallow allometric slopes and low levels of condition dependence, in agreement with one of the most consistent patterns yet detected in the study of allometry, that of genitalia exhibitting shallow allometries.