Return to Beringia: parasites reveal cryptic biogeographic history of North American pikas

Phylogenomic analysis of Stylops reveals the evolutionary history of a Holarctic Strepsiptera radiation parasitizing wild bees

Holarctic Stylops is the largest genus of the enigmatic insect order Strepsiptera, twisted winged parasites. Members of Stylops are obligate endoparasites of Andrena mining bees and exhibit extreme sexual dimorphism typical of Strepsiptera. So far, molecular studies on Stylops have focused on questions on species delimitation. Here, we utilize the power of whole genome sequencing to infer the phylogeny of this morphologically challenging genus from thousands of loci. We use a species tree method, concatenated maximum likelihood analysis and Bayesian analysis with a relaxed clock model to reconstruct the phylogeny of 46 Stylops species, estimate divergence times, evaluate topological consistency across methods and infer the root position. Furthermore, the biogeographical history and coevolutionary patterns with host species are assessed. All methods recovered a well resolved topology with close to all nodes maximally supported and only a handful of minor topological variations. Based on the result, we find that included species can be divided into 12 species groups, seven of them including only Palaearctic species, three Nearctic and two were geographically mixed. We find a strongly supported root position between a clade formed by the spreta, thwaitesi and gwynanae species groups and the remaining species and that the sister group of Stylops is Eurystylops or Eurystylops + Kinzelbachus. Our results indicate that Stylops originated in the Western Palaearctic or Western Palaearctic and Nearctic in the early Neogene or late Paleogene, with four independent dispersal events to the Nearctic. Cophylogenetic analyses indicate that the diversification of Stylops has been shaped by both significant coevolution with the mining bee hosts and host-shifting. The well resolved and strongly supported phylogeny will provide a valuable phylogenetic basis for further studies into the fascinating world of Strepsipterans.

Putative climate adaptation in American pikas (Ochotona princeps) is associated with copy number variation across environmental gradients

Improved understanding of the genetic basis of adaptation to climate change is necessary for maintaining global biodiversity moving forward. Studies to date have largely focused on sequence variation, yet there is growing evidence that suggests that changes in genome structure may be an even more significant source of adaptive potential. The American pika (Ochotona princeps) is an alpine specialist that shows some evidence of adaptation to climate along elevational gradients, but previous work has been limited to single nucleotide polymorphism based analyses within a fraction of the species range. Here, we investigated the role of copy number variation underlying patterns of local adaptation in the American pika using genome-wide data previously collected across the entire species range. We identified 37-193 putative copy number variants (CNVs) associated with environmental variation (temperature, precipitation, solar radiation) within each of the six major American pika lineages, with patterns of divergence largely following elevational and latitudinal gradients. Genes associated (n = 158) with independent annotations across lineages, variables, and/or CNVs had functions related to mitochondrial structure/function, immune response, hypoxia, olfaction, and DNA repair. Some of these genes have been previously linked to putative high elevation and/or climate adaptation in other species, suggesting they may serve as important targets in future studies.

Phylogenomics of American pika (Ochotona princeps) lineage diversification

Quaternary climate oscillations have profoundly influenced current species distributions. For many montane species, these fluctuations were a prominent driver in species range shifts, often resulting in intraspecific diversification, as has been the case for American pikas (Ochotona princeps). Range shifts and population declines in this thermally-sensitive lagomorph have been linked to historical and contemporary environmental changes across its western North American range, with previous research reconstructing five mitochondrial DNA lineages. Here, we paired genome-wide data (25,244 SNPs) with range-wide sampling to re-examine the number and distribution of intra-specific lineages, and investigate patterns of within- and among-lineage divergence and diversity. Our results provide genomic evidence of O. princeps monophyly, reconstructing six distinct lineages that underwent multiple rounds of divergence (0.809-2.81 mya), including a new Central Rocky Mountain lineage. We further found evidence for population differentiation across multiple spatial scales, and reconstructed levels of standing variation comparable to those found in other small mammals. Overall, our findings demonstrate the influence of past glacial cycles on O. princeps lineage diversification, suggest that current subspecific taxonomy may need to be revisited, and provide an important framework for investigations of American pika adaptive potential in the face of anthropogenic climate change.

Nuclear genetic diversity of head lice sheds light on human dispersal around the world

The human louse, Pediculus humanus, is an obligate blood-sucking ectoparasite that has coevolved with humans for millennia. Given the intimate relationship between this parasite and the human host, the study of human lice has the potential to shed light on aspects of human evolution that are difficult to interpret using other biological evidence. In this study, we analyzed the genetic variation in 274 human lice from 25 geographic sites around the world by using nuclear microsatellite loci and female-inherited mitochondrial DNA sequences. Nuclear genetic diversity analysis revealed the presence of two distinct genetic clusters I and II, which are subdivided into subclusters: Ia-Ib and IIa-IIb, respectively. Among these samples, we observed the presence of the two most common louse mitochondrial haplogroups: A and B that were found in both nuclear Clusters I and II. Evidence of nuclear admixture was uncommon (12%) and was predominate in the New World potentially mirroring the history of colonization in the Americas. These findings were supported by novel DIYABC simulations that were built using both host and parasite data to define parameters and models suggesting that admixture between cI and cII was very recent. This pattern could also be the result of a reproductive barrier between these two nuclear genetic clusters. In addition to providing new evolutionary knowledge about this human parasite, our study could guide the development of new analyses in other host-parasite systems.

Late Cenozoic History And The Role Of Beringia In Assembling A Holarctic Cestode Species Complex

The dynamic climate history that drove sea level fluctuation during past glacial periods mediated the movement of organisms between Asia and North America via the Bering Land Bridge. Investigations of the biogeographic histories of small mammals and their parasites demonstrate facets of a complex history of episodic geographic colonization and refugial isolation that structured diversity across the Holarctic. We use a large multi-locus nuclear DNA sequence dataset to robustly resolve relationships within the cestode genus Arostrilepis (Cyclophyllidea: Hymenolepididae), a widespread parasite of predominantly arvicoline rodents (voles, lemmings). Using this phylogeny, we confirm that several Asian Arostrilepis lineages colonized North America during up to four distinct glacial periods in association with different rodent hosts, consistent with taxon-pulse dynamics. A previously inferred westward dispersal across the land bridge is rejected. We also refine interpretations of past host colonization, providing evidence for several distinct episodes of expanding host range, which probably contributed to diversification by Arostrilepis. Finally, Arostrilepis is shown to be paraphyletic with respect to Hymenandrya thomomyis, a parasite of pocket gophers, confirming that ancient Arostrilepis species colonized new host lineages upon arriving in North America.

Phylogeography of the Plateau Pika (Ochotona curzoniae) in Response to the Uplift of the Qinghai-Tibet Plateau

The evolution and current distribution of species on the Qinghai-Tibet Plateau have been significantly impacted by historical occurrences, including the uplift of the plateau and the Quaternary climate upheaval. As a remnant species, the plateau pika (Ochotona curzoniae) is a great model for researching historical events. In this study, 302 samples from 42 sample sites were utilized to analyze the impact of historical events on the evolution and distribution pattern of plateau pikas. The genetic diversity, patterns of differentiation, and historical dynamics of the plateau pika were investigated using molecular markers that included four mitochondrial genes (COI, D-loop, Cytb, and 12S rRNA) and three nuclear genes (GHR, IRBP, and RAG1). The results showed that: (1) The genetic diversity of the plateau pika was high in the Tibetan Plateau (Hd = 0.9997, π = 0.01205), and the plateau pika evolved into five lineages that occupied different geographical areas, with lineage 1 (Group 1) in the south of the Yarlung Zangbo River, lineage 2 (Group 2) in the hinterland of the plateau, lineage 3 (Group 3) in the northeastern part of the plateau, lineage 4 (Group 4) in the Hengduan Mountains, and lineage 5 (Group 5) in the eastern part of the plateau. (2) The gene flow among the five lineages was low, and the differentiation level was high (Nm < 0.25; Fst > 0.25), indicating that the geographical barriers between the five lineages, such as the Yarlung Zangbo River, the Qaidam-Ghuong-Guide Basin, and the Lancang River, effectively promoted the population differentiation of the plateau pika. (3) The plateau pika first spread from the Hengduan Mountains to the entire Qinghai-Tibet Plateau and then conducted small-scale migration and dispersal in several refuges across the plateau in response to climate changes during the glacial and interglacial periods. (4) Except for Group 1 and Group 4, all the other populations exhibited a rapid expansion between 0.06 and 0.01 Mya, but the expansion was considerably delayed or halted by the effects of climate change during the last glacial maximum (0.02 Mya). Overall, the plateau pika on the Qinghai-Tibet Plateau exhibits high genetic diversity, and topographic obstacles, including mountains, valleys, and basins, created by the uplift of the plateau and climatic changes since the Quaternary period have played an important role in the differentiation and historical dynamics of the plateau pika population.

Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

Background

Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada.

Results

Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θ_W = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θ_W = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θ_W = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide.

Conclusions

Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

When parasites persist: tapeworms survive host extinction and reveal waves of dispersal across Beringia

Investigations of intercontinental dispersal between Asia and North America reveal complex patterns of geographic expansion, retraction and isolation, yet historical reconstructions are largely limited by the depth of the record that is retained in patterns of extant diversity. Parasites offer a tool for recovering deep historical insights about the biosphere, improving the resolution of past community-level interactions. We explored biogeographic hypotheses regarding the history of dispersal across Beringia, the region intermittently linking Asia and North America, through large-scale multi-locus phylogenetic analyses of the genus Schizorchis, an assemblage of host-specific cestodes in pikas (Lagomorpha: Ochotonidae). Our genetic data support palaeontological evidence for two separate geographic expansions into North America by Ochotona in the late Tertiary, a history that genomic evidence from extant pikas does not record. Pikas descending from the first colonization of Miocene age persisted into the Pliocene, subsequently coming into contact with a second wave of Nearctic colonists from Eurasia before going extinct. Spatial and temporal overlap of historically independent pika populations provided a window for host colonization, allowing persistence of an early parasite lineage in the contemporary fauna following the extinction of its ancestral hosts. Empirical evidence for ancient 'ghost assemblages' of hosts and parasites demonstrates how complex mosaic faunas are assembled in the biosphere through episodes of faunal mixing encompassing parasite lineages across deep and shallow time.

Lousy grouse: Comparing evolutionary patterns in Alaska galliform lice to understand host evolution and host-parasite interactions

Understanding both sides of host-parasite relationships can provide more complete insights into host and parasite biology in natural systems. For example, phylogenetic and population genetic comparisons between a group of hosts and their closely associated parasites can reveal patterns of host dispersal, interspecies interactions, and population structure that might not be evident from host data alone. These comparisons are also useful for understanding factors that drive host-parasite coevolutionary patterns (e.g., codivergence or host switching) over different periods of time. However, few studies have compared the evolutionary histories between multiple groups of parasites from the same group of hosts at a regional geographic scale. Here, we used genomic data to compare phylogenomic and population genomic patterns of Alaska ptarmigan and grouse species (Aves: Tetraoninae) and two genera of their associated feather lice: Lagopoecus and Goniodes. We used whole-genome sequencing to obtain hundreds of genes and thousands of single-nucleotide polymorphisms (SNPs) for the lice and double-digest restriction-associated DNA sequences to obtain SNPs from Alaska populations of two species of ptarmigan. We found that both genera of lice have some codivergence with their galliform hosts, but these relationships are primarily characterized by host switching and phylogenetic incongruence. Population structure was also uncorrelated between the hosts and lice. These patterns suggest that grouse, and ptarmigan in particular, share habitats and have likely had historical and ongoing dispersal within Alaska. However, the two genera of lice also have sufficient dissimilarities in the relationships with their hosts to suggest there are other factors, such as differences in louse dispersal ability, that shape the evolutionary patterns with their hosts.

The Invasion Hierarchy: Ecological and Evolutionary Consequences of Invasions in the Fossil Record

Species invasions are pervasive in Earth history, yet the ecological and evolutionary consequences vary greatly. Ancient invasion events can be organized in a hierarchy of increasing invasion intensity from ephemeral invasions to globally pervasive invasive regimes. Each level exhibits emergent properties exceeding the sum of interactions at lower levels. Hierarchy levels correspond to, but do not always exactly correlate with, geographic extent of invasion success. The ecological impacts of lower-level impacts can be negligible or result in temporary community accommodation. Invasion events at moderate to high levels of the hierarchy permanently alter ecological communities, regional faunas, and global ecosystems. The prevalence of invasive species results in evolutionary changes by fostering niche evolution, differential survival of ecologically generalized taxa, faunal homogenization, and suppressing speciation. These impacts can contribute to mass extinctions and biodiversity crises that alter the trajectory of ecological and evolutionary patterns of life. The fossil record provides a long-term record of how invasion impacts may scale up through time, which can augment ecological studies of modern species invasions.

Nematodes and cestodes of rodents in South Africa: baseline data on diversity and geographic distribution

Currently, descriptive information on the host range and geographic distribution of helminth parasites associated with naturally occurring rodents in South and southern Africa is scant. Therefore, we embarked on a countrywide study to: (1) identify gastrointestinal helminths and their host range, and (2) provide baseline data on the geographic distribution of helminths across the country. Altogether, 55 helminth taxa were recovered from at least 13 rodent species (n = 1030) at 26 localities across South Africa. The helminth taxa represented 25 genera (15 nematodes, nine cestodes and one acanthocephalan). Monoxenous nematodes were the most abundant and prevalent group, while the occurrence of heteroxenous nematodes and cestodes was generally lower. The study recorded several novel helminth-host associations. Single-host-species infections were common, although multiple-host-species infections by helminth species were also recorded. Monoxenous nematodes and some cestodes were recovered countrywide, whereas heteroxenous nematodes were restricted to the eastern regions of South Africa. The study highlights the as yet unexplored diversity of helminth species associated with naturally occurring rodent species and provides initial data on their geographical distribution in South Africa.

Beta diversity of gastrointestinal helminths in two closely related South African rodents: species and site contributions

A fundamental aim of parasite ecology is to understand the mechanisms behind spatial variation in diversity and structure of parasite assemblages. To understand the contribution of individual parasite species and their assemblages to spatial variation in parasite communities, we examined species contributions to beta diversity (SCBD) and local contributions to beta diversity (LCBD) of parasitic gastrointestinal helminths (nematodes and cestodes) in two closely related rodents, Rhabdomys dilectus and Rhabdomys pumilio, from 20 localities across South Africa. Although the two Rhabdomys spp. are morphologically similar, they differ substantially in body size, habitat preference, and sociality. We asked whether the variation in life history traits and infection parameters are associated with SCBD of helminths and whether variation in environmental factors, host population density, and species richness of host communities are associated with LCBD of component assemblages of helminths. We also considered spatial factors to test whether LCBD of helminth assemblages demonstrate geographic structure. We found that the contribution of helminth species parasitic in both hosts to beta diversity significantly increased with characteristic prevalence of these species, whereas mean abundance, type of life cycle, and location in the host's gut had no effect on SCBD. The LCBD of helminth assemblages showed a significant positive correlation with environmental factors in both host species. Our results suggest that predictors of variation in SCBD and LCBD may substantially differ between parasites with different infection parameters and/or parasite communities at different hierarchical scales.

Building an integrated infrastructure for exploring biodiversity: field collections and archives of mammals and parasites

Museum specimens play an increasingly important role in predicting the outcomes and revealing the consequences of anthropogenically driven disruption of the biosphere. As ecological communities respond to ongoing environmental change, host-parasite interactions are also altered. This shifting landscape of host-parasite associations creates opportunities for colonization of different hosts and emergence of new pathogens, with implications for wildlife conservation and management, public health, and other societal concerns. Integrated archives that document and preserve mammal specimens along with their communities of associated parasites and ancillary data provide a powerful resource for investigating, anticipating, and mitigating the epidemiological, ecological, and evolutionary impacts of environmental perturbation. Mammalogists who collect and archive mammal specimens have a unique opportunity to expand the scope and impact of their field work by collecting the parasites that are associated with their study organisms. We encourage mammalogists to embrace an integrated and holistic sampling paradigm and advocate for this to become standard practice for museum-based collecting. To this end, we provide a detailed, field-tested protocol to give mammalogists the tools to collect and preserve host and parasite materials that are of high quality and suitable for a range of potential downstream analyses (e.g., genetic, morphological). Finally, we also encourage increased global cooperation across taxonomic disciplines to build an integrated series of baselines and snapshots of the changing biosphere. Los especímenes de museo desempeñan un papel cada vez más importante tanto en la descripción de los resultados de la alteración antropogénica de la biosfera como en la predicción de sus consecuencias. Dado que las comunidades ecológicas responden al cambio ambiental, también se alteran las interacciones hospedador-parásito. Este panorama cambiante de asociaciones hospedador-parásito crea oportunidades para la colonización de diferentes hospedadores y para la aparición de nuevos patógenos, con implicancias en la conservación y manejo de la vida silvestre, la salud pública y otras preocupaciones de importancia para la sociedad. Archivos integrados que documentan y preservan especímenes de mamíferos junto con sus comunidades de parásitos y datos asociados, proporcionan un fuerte recurso para investigar, anticipar y mitigar los impactos epidemiológicos, ecológicos y evolutivos de las perturbaciones ambientales. Los mastozoólogos que recolectan y archivan muestras de mamíferos, tienen una oportunidad única de ampliar el alcance e impacto de su trabajo de campo mediante la recolección de los parásitos que están asociados con los organismos que estudian. Alentamos a los mastozoólogos a adoptar un paradigma de muestreo integrado y holístico y abogamos para que esto se convierta en una práctica estándarizada de la obtención de muestras para museos. Con este objetivo, proporcionamos un protocolo detallado y probado en el campo para brindar a los mastozoólogos las herramientas para recolectar y preservar materiales de parásitos y hospedadores de alta calidad y adecuados para una gran variedad de análisis subsecuentes (e.g., genéticos, morfológicos, etc.). Finalmente, también abogamos por una mayor cooperación global entre las diversas disciplinas taxonómicas para construir una serie integrada de líneas de base y registros actuales de nuestra cambiante biosfera.

The population genetics of parasitic nematodes of wild animals

Parasitic nematodes are highly diverse and common, infecting virtually all animal species, and the importance of their roles in natural ecosystems is increasingly becoming apparent. How genes flow within and among populations of these parasites - their population genetics - has profound implications for the epidemiology of host infection and disease, and for the response of parasite populations to selection pressures. The population genetics of nematode parasites of wild animals may have consequences for host conservation, or influence the risk of zoonotic disease. Host movement has long been recognised as an important determinant of parasitic nematode population genetic structure, and recent research has also highlighted the importance of nematode life histories, environmental conditions, and other aspects of host ecology. Commonly, factors influencing parasitic nematode population genetics have been studied in isolation, such that an integrated view of the drivers of population genetic structure of parasitic nematodes is still lacking. Here, we seek to provide a comprehensive, broad, and integrative picture of these factors in parasitic nematodes of wild animals that will be a useful resource for investigators studying non-model parasitic nematodes in natural ecosystems. Increasingly, new methods of analysing the population genetics of nematodes are becoming available, and we consider the opportunities that these afford in resolving hitherto inaccessible questions of the population genetics of these important animals.

Arctic systems in the Quaternary: ecological collision, faunal mosaics and the consequences of a wobbling climate

Climate oscillations and episodic processes interact with evolution, ecology and biogeography to determine the structure and complex mosaic that is the biosphere. Parasites and parasite–host assemblages are key components in a general explanatory paradigm for global biodiversity. We explore faunal assembly in the context of Quaternary time frames of the past 2.6 million years, a period dominated by episodic shifts in climate. Climate drivers cross a continuum from geological to contemporary timescales and serve to determine the structure and distribution of complex biotas. Cycles within cycles are apparent, with drivers that are layered, multifactorial and complex. These cycles influence the dynamics and duration of shifts in environmental structure on varying temporal and spatial scales. An understanding of the dynamics of high-latitude systems, the history of the Beringian nexus (the intermittent land connection linking Eurasia and North America) and downstream patterns of diversity depend on teasing apart the complexity of biotic assembly and persistence. Although climate oscillations have dominated the Quaternary, contemporary dynamics are driven by tipping points and shifting balances emerging from anthropogenic forces that are disrupting ecological structure. Climate change driven by anthropogenic forcing has supplanted a history of episodic variation and is eliminating ecological barriers and constraints on development and distribution for pathogen transmission. A framework to explore interactions of episodic processes on faunal structure and assembly is the Stockholm Paradigm, which appropriately shifts the focus from cospeciation to complexity and contingency in explanations of diversity.

Temporal and spatial mosaics: deep host association and shallow geographic drivers shape genetic structure in a widespread pinworm, Rauschtineria eutamii

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, Rauschtineria eutamii, infecting 10 species of western North American chipmunks (Rodentia:Tamias, subgenus Neotamias). Rauschtineria eutamii contains divergent lineages influenced by the diversity of hosts and variation across the complex topography of western North America. We recovered six reciprocally monophyletic R. eutamii 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 R. eutamii colonized an ancestral lineage of western chipmunks and lineages persisted during historical isolation in diverging Neotamias 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 R. eutamii.

Target gene enrichment in the cyclophyllidean cestodes, the most diverse group of tapeworms

The Cyclophyllidea is the most diverse order of tapeworms, encompassing species that infect all classes of terrestrial tetrapods including humans and domesticated animals. Available phylogenetic reconstructions based either on morphology or molecular data lack the resolution to allow scientists to either propose a solid taxonomy or infer evolutionary associations. Molecular markers available for the Cyclophyllidea mostly include ribosomal DNA and mitochondrial loci. In this study, we identified 3641 single-copy nuclear coding loci by comparing the genomes of Hymenolepis microstoma, Echinococcus granulosus and Taenia solium. We designed RNA baits based on the sequence of H. microstoma, and applied target enrichment and Illumina sequencing to test the utility of those baits to recover loci useful for phylogenetic analyses. We captured DNA from five species of tapeworms representing two families of cyclophyllideans. We obtained an average of 3284 (90%) of the targets from the test samples and then used captured sequences (2 181 361 bp in total; fragment size ranging from 301 to 6969 bp) to reconstruct a phylogeny for the five test species plus the three species for which genomic data are available. The results were consistent with the current consensus regarding cyclophyllidean relationships. To assess the potential for our method to yield informative genetic variation at intraspecific scales, we extracted 14 074 single nucleotide polymorphisms (SNPs) from alignments of four Arostrilepis macrocirrosa and two A. cooki and successfully inferred their relationships. The results showed that our target gene tools yield data sets that provide robust inferences at a range of taxonomic scales in the Cyclophyllidea.

Natural history collections-based research: progress, promise, and best practices

Specimens and associated data in natural history collections (NHCs) foster substantial scientific progress. In this paper, we explore recent contributions of NHCs to the study of systematics and biogeography, genomics, morphology, stable isotope ecology, and parasites and pathogens of mammals. To begin to assess the magnitude and scope of these contributions, we analyzed publications in the Journal of Mammalogy over the last decade, as well as recent research supported by a single university mammal collection (Museum of Southwestern Biology, Division of Mammals). Using these datasets, we also identify weak links that may be hindering the development of crucial NHC infrastructure. Maintaining the vitality and growth of this foundation of mammalogy depends on broader engagement and support from across the scientific community and is both an ethical and scientific imperative given the rapidly changing environmental conditions on our planet.

Comparative phylogeography between two generalist flea species reveal a complex interaction between parasite life history and host vicariance: parasite-host association matters

Background

In parasitic taxa, life history traits such as microhabitat preference and host specificity can result in differential evolutionary responses to similar abiotic events. The present study investigates the influence of vicariance and host association on the genetic structure of two generalist flea species, Listropsylla agrippinae, and Chiastopsylla rossi. The taxa differ in the time spent on the host (predominantly fur vs. nest) and level of host specificity.

Results

A total of 1056 small mammals were brushed to collect 315 fleas originating from 20 geographically distinct localities in South Africa. Phylogeographic genetic structure of L. agrippinae and C. rossi were determined by making use of 315 mitochondrial COII and 174 nuclear EF1-α sequences. Both parasites show significant genetic differentiation among the majority of the sampling sites confirming limited dispersal ability for fleas. The generalist fur flea with a narrower host range, L. agrippinae, displayed geographic mtDNA spatial genetic structure at the regional scale and this pattern is congruent with host vicariance. The dating of the divergence between the L. agrippinae geographic clades co-insides with paleoclimatic changes in the region approximately 5.27 Ma and this provides some evidence for a co-evolutionary scenario. In contrast, the more host opportunistic nest flea, C. rossi, showed a higher level of mtDNA and nDNA spatial genetic structure at the inter-populational scale, most likely attributed to comparatively higher restrictions to dispersal.

Conclusions

In the present study, the evolutionary history of the flea species could best be explained by the association between parasite and host (time spent on the host). The phylogeographic pattern of the fur flea with a narrower host range correspond to host spatial genetic structures, while the pattern in the host opportunistic nest flea correspond to higher genetic divergences between sampling localities that may also be associated with higher effective population sizes. These findings suggest that genetic exchange among localities are most likely explained by differences in the dispersal abilities and life histories of the flea species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0389-y) contains supplementary material, which is available to authorized users.

Comparative phylogeography highlights the double-edged sword of climate change faced by arctic- and alpine-adapted mammals

Recent studies suggest that alpine and arctic organisms may have distinctly different phylogeographic histories from temperate or tropical taxa, with recent range contraction into interglacial refugia as opposed to post-glacial expansion out of refugia. We use a combination of phylogeographic inference, demographic reconstructions, and hierarchical Approximate Bayesian Computation to test for phylodemographic concordance among five species of alpine-adapted small mammals in eastern Beringia. These species (Collared Pikas, Hoary Marmots, Brown Lemmings, Arctic Ground Squirrels, and Singing Voles) vary in specificity to alpine and boreal-tundra habitat but share commonalities (e.g., cold tolerance and nunatak survival) that might result in concordant responses to Pleistocene glaciations. All five species contain a similar phylogeographic disjunction separating eastern and Beringian lineages, which we show to be the result of simultaneous divergence. Genetic diversity is similar within each haplogroup for each species, and there is no support for a post-Pleistocene population expansion in eastern lineages relative to those from Beringia. Bayesian skyline plots for four of the five species do not support Pleistocene population contraction. Brown Lemmings show evidence of late Quaternary demographic expansion without subsequent population decline. The Wrangell-St. Elias region of eastern Alaska appears to be an important zone of recent secondary contact for nearctic alpine mammals. Despite differences in natural history and ecology, similar phylogeographic histories are supported for all species, suggesting that these, and likely other, alpine- and arctic-adapted taxa are already experiencing population and/or range declines that are likely to synergistically accelerate in the face of rapid climate change. Climate change may therefore be acting as a double-edged sword that erodes genetic diversity within populations but promotes divergence and the generation of biodiversity.

An integrated parasitology: revealing the elephant through tradition and invention

The field of parasitology contributes to the elucidation of patterns and processes in evolution, ecology, and biogeography that are of fundamental importance across the biosphere, leading to a thorough understanding of biodiversity and varied responses to global change. Foundations from taxonomic and systematic information drive biodiversity discovery and foster considerable infrastructure and integration of research programs. Morphological, physiological, behavioral, life-history, and molecular data can be synthesized to discover and describe global parasite diversity, in a timely manner. In fully incorporating parasitology in policies for adaptation to global change, parasites and their hosts should be archived and studied within a newly emergent conceptual universe (the 'Stockholm Paradigm'), embracing the inherent complexity of host-parasite systems and improved explanatory power to understand biodiversity past, present, and future.

Phylogeography analysis and molecular evolution patterns of the nematode parasite Heligmosomum mixtum based on mitochondrial DNA sequences

Mitochondrial DNA was explored to study phylogeography of the nematode parasite Heligmosomum mixtum and elucidate molecular evolution pattern of cytochrome b gene. The size of cyt b gene ranged from 511 bp to 591 bp and the average of GC contents was 28.9%. The overall transition/transversion ratio R was 5.773 indicating that the transitions are more frequent than transversion. The aligned sequences allowed identifying 54 mtDNA haplotypes among the 119 examined individuals. The genetic divergence registered among the populations of H. mixtum was low (0.3% to 1.5%). Neighbor-joining and maximum Likelihood trees evidenced a huge polytomy and unstructured phylogeographic pattern among the studied populations. The demographic analyses tend to evidence a recent and rapid expansion of H. mixtum. Our results imply a positive selection and the genetic hitchhiking effect is unlikely. Parameters performed supported scenario of sweep selection and recent expansion of H.mixtum populations. Both positive selection and demographic histories have jointly contributed to the observed patterns of nucleotide diversity and haplotypes structure. The comparison of the phylogeographical pattern of H. mixtum with the one of its most common rodent host M. glareolus, confirmed a strong incongruence between the two species. These results strongly suggest that the parasite would not be specific to M. glareolus and that it would switch easily from one rodent species to another. The mitochondrial diversity seems to be unstructured with any biogeographic repartition of the variability and that the genetic structure of H. mixtum is probably associated with weak host specificity.

A walk on the tundra: Host-parasite interactions in an extreme environment

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Climate change is altering host–parasite interactions in the Arctic.

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Changing ecological barriers reflect climate warming.

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Metabolic Theory of Ecology advances understanding of host–parasite interactions.

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Diversity emerges from host/parasite biogeographic/ecologic history.

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Insights gained from the Arctic apply to more complex systems.

Climate change is occurring very rapidly in the Arctic, and the processes that have taken millions of years to evolve in this very extreme environment are now changing on timescales as short as decades. These changes are dramatic, subtle and non-linear. In this article, we discuss the evolving insights into host–parasite interactions for wild ungulate species, specifically, muskoxen and caribou, in the North American Arctic. These interactions occur in an environment that is characterized by extremes in temperature, high seasonality, and low host species abundance and diversity. We believe that lessons learned in this system can guide wildlife management and conservation throughout the Arctic, and can also be generalized to more broadly understand host–parasite interactions elsewhere. We specifically examine the impacts of climate change on host–parasite interactions and focus on: (I) the direct temperature effects on parasites; (II) the importance of considering the intricacies of host and parasite ecology for anticipating climate change impacts; and (III) the effect of shifting ecological barriers and corridors. Insights gained from studying the history and ecology of host–parasite systems in the Arctic will be central to understanding the role that climate change is playing in these more complex systems.

Invasion, establishment, and range expansion of two parasitic nematodes in the Canadian Arctic

Climate warming is occurring at an unprecedented rate in the Arctic and is having profound effects on host-parasite interactions, including range expansion. Recently, two species of protostrongylid nematodes have emerged for the first time in muskoxen and caribou on Victoria Island in the western Canadian Arctic Archipelago. Umingmakstrongylus pallikuukensis, the muskox lungworm, was detected for the first time in 2008 in muskoxen at a community hunt on the southwest corner of the island and by 2012, it was found several hundred kilometers east in commercially harvested muskoxen near the town of Ikaluktutiak. In 2010, Varestrongylus sp., a recently discovered lungworm of caribou and muskoxen was found in muskoxen near Ikaluktutiak and has been found annually in this area since then. Whereas invasion of the island by U. pallikuukensis appears to have been mediated by stochastic movement of muskoxen from the mainland to the southwest corner of the island, Varestrongylus has likely been introduced at several times and locations by the seasonal migration of caribou between the island and the mainland. A newly permissive climate, now suitable for completion of the parasite life cycles in a single summer, likely facilitated the initial establishment and now drives range expansion for both parasites.

Northern host-parasite assemblages: history and biogeography on the borderlands of episodic climate and environmental transition

Diversity among assemblages of mammalian hosts and parasites in northern terrestrial ecosystems was structured by a deep history of biotic and abiotic change that overlies a complex geographic arena. Since the Pliocene, Holarctic ecosystems assembled in response to shifting climates (glacial and interglacial stages). Cycles of episodic dispersal/isolation and diversification defined northern diversity on landscape to regional scales. Episodes of geographic expansion and colonisation linked Eurasia and North America across Beringia and drove macroevolutionary structure of host and parasite associations. Asynchronous dispersal from centres of origin in Eurasia into the Nearctic resulted in gradients in parasite diversity in the carnivoran, lagomorph, rodent and artiodactyl assemblages we reviewed. Recurrent faunal interchange and isolation in conjunction with episodes of host colonisation have produced a mosaic structure for parasite faunas and considerable cryptic diversity among nematodes and cestodes. Mechanisms of invasion and geographic colonisation leading to the establishment of complex faunal assemblages are equivalent in evolutionary and ecological time, as demonstrated by various explorations of diversity in these high-latitude systems. Our ability to determine historical responses to episodic shifts in global climate may provide a framework for predicting the cascading effects of contemporary environmental change.

New species of Arostrilepis (Eucestoda: Hymenolepididae) in members of Cricetidae and Geomyidae (Rodentia) from the western Nearctic

Abstract : Specimens originally identified as Arostrilepis horrida from the Nearctic are revised, contributing to the recognition of a complex of cryptic species distributed across the Holarctic region. Previously unrecognized species are described based on specimens in cricetid (Neotominae) and geomyid rodents. Arostrilepis mariettavogeae n. sp. in Peromyscus californicus from Monterey County, California and Arostrilepis schilleri n. sp. in Thomomys bulbivorus from Corvallis, Oregon are characterized. Consistent with recent studies defining diversity in the genus, form, size, and spination (pattern, shape, and size) of the cirrus are diagnostic; species are further distinguished by the relative position and length of the cirrus sac and arrangement of the testes. Species of Arostrilepis have not previously been described in rodents outside of the Arvicolinae or from localities in the Nearctic. These studies emphasize the need for routine deposition of archival specimens and information, from survey, ecological, and biogeographic studies, in museum collections to serve as self-correcting records for biodiversity at local, regional, and continental scales.