Systematics, biogeography and phylogenomics of northern bog lemmings (Cricetidae), cold-temperate rodents of conservation concern under global change

Northern bog lemmings, Mictomys (Synaptomys) borealis, are currently being assessed for protections under the U.S. Endangered Species Act. A major impediment to comprehensive evaluation is a deficiency of data towards understanding the biology of these rodents. Inherent rarity and scarce specimen sampling, despite a continent-wide distribution, has precluded our ability to implement modern methods for resolving taxonomy, evolutionary history, and investigating multiple other species traits. Here we use a maternally inherited locus (mitochondrial cytochrome b) and between 5,939 and 11,513 nuclear loci from reduced representation sequencing (ddRADseq) to investigate the evolutionary history of northern bog lemmings. We 1) qualify evidence based on morphological and early molecular studies for the genus assignment of Mictomys, 2) test the validity of multiple sub-species designations, 3) provide spatial and temporal historical biogeographic perspectives, and 4) discuss how incomplete sampling might influence conservation efforts. Both mitochondrial and nuclear datasets exhibit deep divergence and paraphyly between two recognized species, the northern (Mictomys borealis) and southern (Synaptomys cooperi) bog lemmings. Based on mtDNA, the geographically isolated subspecies (M. b. sphagnicola) was found to be divergent from all other specimens. The remainder of the species exhibited shallow intra-specific differentiation in mtDNA, however nuclear data supports genetic distinction consistent with four geographic subspecies. Recent coalescence of all northern bog lemmings (except for M. b. sphagnicola) reflects divergence in multiple refugia through the last glacial cycle, including a well-known coastal center of endemism and multiple regions south of continental ice-sheets. Regional lineages across North America suggest strong latitudinal displacement with global climate change, coupled with isolation-reconnection dynamics. This taxon suffers from a lack of modern samples through most of its distribution, severely limiting interpretation of ongoing evolutionary processes, particularly in southern portions of the species' range. Limited voucher specimen sampling of vulnerable populations could aid in rigorous conservation decision-making.

Geography, ecology, and history synergistically shape across-range genetic variation in a calanoid copepod endemic to the north-eastern Oriental

The center-periphery hypothesis (CPH) predicts that peripheral populations will have lower genetic variation than those at the center of a species' distribution. However, ecological margins do not always coincide with geographical edges when topographies are diverse. Historical climate changes can also strongly affect genetic variation. Here, we examined genetic variation in Phyllodiaptomus tunguidus, a calanoid copepod endemic to the north-eastern Oriental. This species was predicted to exhibit a complex pattern of genetic variation across its range due to the diverse topographies and stable climate history of the north-eastern Oriental. To test this, we used geographic distance to the center of the distribution, current ecological suitability, and climate during the last glacial maximum as geographical, ecological, and historical factors, respectively, in our analyses. We measured genetic diversity and population differentiation using mitochondrial and nuclear markers. This showed that P. tunguidus had 3 refugia during the last glacial maximum (LGM). Such a pattern of multiple refugia complicates the determination of the center and periphery of spatial genetic diversity. Both regression models and redundancy analyses failed to support the CPH. Instead, they showed that geographical, ecological, and historical factors together shaped population genetic structure in this species. Ecological factors explained significantly more genetic variation than did geographical and historical factors-however, all three factors interacted significantly to affect the pattern of genetic variation. The results extend our understanding of the CPH and the extent to which it can explain genetic variation across populations.

Pleistocene dynamics of the Eurasian steppe as a driving force of evolution: Phylogenetic history of the genus Capsella (Brassicaceae)

Capsella is a model plant genus of the Brassicaceae closely related to Arabidopsis. To disentangle its biogeographical history and intrageneric phylogenetic relationships, 282 individuals of all five currently recognized Capsella species were genotyped using a restriction digest-based next-generation sequencing method. Our analysis retrieved two main lineages within Capsella that split c. one million years ago, with western C. grandiflora and C. rubella forming a sister lineage to the eastern lineage consisting of C. orientalis. The split was attributed to continuous latitudinal displacements of the Eurasian steppe belt to the south during Early Pleistocene glacial cycles. During the interglacial cycles of the Late Pleistocene, hybridization of the two lineages took place in the southwestern East European Plain, leading to the allotetraploid C. bursa-pastoris. Extant genetic variation within C. orientalis postdated any extensive glacial events. Ecological niche modeling showed that suitable habitat for C. orientalis existed during the Last Glacial Maximum around the north coast of the Black Sea and in southern Kazakhstan. Such a scenario is also supported by population genomic data that uncovered the highest genetic diversity in the south Kazakhstan cluster, suggesting that C. orientalis originated in continental Asia and migrated north- and possibly eastwards after the last ice age. Post-glacial hybridization events between C. bursa-pastoris and C. grandiflora/rubella in the southwestern East European Plain and the Mediterranean gave rise to C. thracica. Introgression of C. grandiflora/rubella into C. bursa-pastoris resulted in a new Mediterranean cluster within the already existing Eurasian C. bursa-pastoris cluster. This study shows that the continuous displacement and disruption of the Eurasian steppe belt during the Pleistocene was the driving force in the evolution of Capsella.

Centre-periphery approaches based on geography, ecology and historical climate stability: what explains the variation in morphological traits of Bulnesia sarmientoi?

BACKGROUND AND AIMS

The centre-periphery hypothesis posits that higher species performance is expected in geographic and ecological centres rather than in peripheral populations. However, this is not the commonly found pattern; therefore, alternative approaches, including the historical dimension of species geographical ranges, should be explored. Morphological functional traits are fundamental determinants of species performance, commonly related to environmental stability and productivity. We tested whether or not historical processes may have shaped variations in tree and leaf traits of the Chaco tree Bulnesia sarmientoi.

METHODS

Morphological variation patterns were analysed from three centre-periphery approaches: geographical, ecological and historical. Tree (stem and canopy) and leaf (leaf size and specific leaf area) traits were measured in 24 populations across the species range. A principal component analysis was performed on morphological traits to obtain synthetic variables. Linear mixed-effects models were used to test which of the implemented centre-periphery approaches significantly explained trait spatial patterns.

KEY RESULTS

The patterns retrieved from the three centre-periphery approaches were not concordant. The historical approach revealed that trees were shorter in centre populations than in the periphery. Significant differences in leaf traits were observed between the geographical centre and the periphery, mainly due to low specific leaf area values towards the geographical centre. We did not find any pattern associated with the ecological centre-periphery approach.

CONCLUSIONS

The decoupled response between leaf and tree traits suggests that these sets of traits respond differently to processes occurring at different times. The geographical and historical approaches showed centres with extreme environments in relation to their respective peripheries, but the historical centre has also been a climatically stable area since the Last Glacial Maximum. The historical approach allowed for the recovery of historical processes underlying variation in tree traits, highlighting that centre-periphery delimitations should be based on a multi-approach framework.

Molecular Phylogeography and Evolutionary History of the Endemic Species Corydalis hendersonii (Papaveraceae) on the Tibetan Plateau Inferred From Chloroplast DNA and ITS Sequence Variation

In response to past climatic changes, the species with different habits or adaptive traits likely have experienced very different evolutionary histories, especially for species that restricted to high mountain areas. In order to trace how Quaternary climatic oscillations affected range distributions and intraspecific divergence of such alpine plants on the Tibetan Plateau, here, we investigated maternally inherited chloroplast DNA (cpDNA) markers and biparentally inherited nuclear ribosomal internal transcribed spacer (ITS) DNA variations and aimed to explore the phylogeographic history of the endemic alpine species Corydalis hendersonii Hemsl. (Papaveraceae). We sequenced four cpDNA fragments (trnS-trnG, trnT-trnL, atpH-atpI, and psbE-petL) and also the nuclear (ITS) region in 368 individuals from 30 populations across the species' range. The network and phylogenetic analysis based on cpDNA variations identified 15 chlorotypes that cluster into three distinct clades. However, our nuclear DNA results demonstrated that there were four genetic/geographical groups within C. hendersonii. Some common and highly divergent cpDNA and ITS haplotypes were distributed in the populations of central and northeastern Tibetan Plateau, and the highest nucleotide diversity and genetic differentiation were detected in the central region. Demographic tests further indicated that the populations of southwestern and western Tibet may have experienced recent range expansion, which most likely occurred during the last glacial maximum (LGM) and continued its expansion after the beginning of the Holocene. These two different groups of this species may have derived from potential refugia that existed in the central and/or northeastern regions of Tibet during recent interglacial periods. In addition, our AMOVA analyses detected high genetic differentiation along with the whole sampling range. Also, distinct phylogeographic structures were detected among populations of C. hendersonii based on both of cpDNA and ITS variation. These findings shed new light on the importance of climatic oscillations during Quaternary and complex local topography as causes of intraspecific diversification and demographic changes within cold-tolerant herbs in the Tibetan Plateau biodiversity hotspot.

[Distribution changes and refugia of three spruce taxa since the last interglacial.]

Based on the current distribution information and 19 environmental variables data, we used the maximum entropy model to simulate the suitable distribution of Picea likiangensis var. likiangensis, P. purpurea and P. wilsonii in the last interglacial, Last Glacial Maximum, Mid- Holocene and present. The results from such modelling were validated by pollen data. We analyzed the relationship between species distribution dynamics and climate change, and then speculated the cryptic refugia of those species. Both the areas under the receiver operating characteristic curves and the verification results from pollen data indicated high accuracy of the model results. Results showed that isothermality was the most important factor influencing the distribution of P. likiangensis var. likiangensis and mean temperature of the warmest quarter was the most important for the distribution of both P. purpurea and P. wilsonii. Temperature was more important than precipitation in driving species distributions. Three species expanded their distribution ranges in Last Glacial Maximum due to their cold-adapted ecological habitat and the deep canyon topography feature which benefited their migration. There might be refugia of both P. wilsonii and P. purpurea in last interglacial, and they respectively located in Shennongjia Mountain in Hubei and Erlang Mountain and its nearby mountains in Sichuan. Our results, to some extent, made accurate prediction of the suitable distribution of three spruce species in the key periods since last interglacial, and speculated refugia of P. purpurea and P. willsonii. Our findings provided reference for better understanding of the formation mechanism of the present distribution of Picea and prediction of distribution changes in the future and sustainable management and protection of three spruce species.

Fish Parasite Dinoflagellates Haidadinium ichthyophilum and Piscinoodinium Share a Recent Common Ancestor

The dinoflagellate Haidadinium ichthyophilum Buckland-Nicks, Reimchen and Garbary 1997 is an ectoparasite of the spine-deficient, three-spine stickleback Gasterosteus aculeatus L. Reimchen 1984, a fish endemic to Rouge Lake, Haida Gwaii. Haidadinium ichthyophilum proved difficult to assign taxonomically because its morphology and complex life cycle exhibited defining characteristics of both autotrophic and heterotrophic dinoflagellates, and was tentatively assigned to the Phytodiniales. Here, we characterized a 492 bp fragment of the small subunit ribosomal RNA (SSU rRNA) from preserved H. ichthyophilum cysts. In SSU phylogeny, H. ichthyophilum branches with the fish parasites, Piscinoodinium sp., strongly supporting the inclusion of H. ichthyophilum within the Suessiales.

A large historical refugium explains spatial patterns of genetic diversity in a Neotropical savanna tree species

BACKGROUND AND AIMS

The relative role of Pleistocene climate changes in driving the geographic distribution and genetic diversity of South American species is not well known, especially from open biomes such as the Cerrado, the most diverse tropical savanna, encompassing high levels of endemism. Here the effects of Quaternary climatic changes on demographic history, distribution dynamics and genetic diversity of Dimorphandra mollis, an endemic tree species widely distributed in the Cerrado, were investigated.

METHODS

A total of 38 populations covering most of the distribution of D. mollis were analysed using internal transcribed spacer (ITS) sequences and nuclear microsatellite variation [simple sequence repeats (SSRs)]. The framework incorporated statistical phylogeography, coalescent analyses and ecological niche modelling (ENM).

KEY RESULTS

Different signatures of Quaternary climatic changes were found for ITS sequences and SSRs corresponding to different time slices. Coalescent analyses revealed large and constant effective population sizes, with high historical connectivity among the populations for ITS sequences and low effective population sizes and gene flow with recent population retraction for SSRs. ENMs indicated a slight geographical range retraction during the Last Glacial Maximum. A large historical refugium across central Brazil was predicted. Spatially explicit analyses showed a spatial cline pattern in genetic diversity related to the paleodistribution of D. mollis and to the centre of its historical refugium.

CONCLUSIONS

The complex genetic patterns found in D. mollis are the result of a slight geographical range retraction during the Last Glacial Maximum followed by population expansion to the east and south from a large refugium in the central part of the Cerrado. This historical refugium is coincident with an area predicted to be climatically stable under future climate scenarios. The identified refugium should be given high priority in conservation polices to safeguard the evolutionary potential of the species under predicted future climatic changes.

High migration rates shape the postglacial history of amphi-Atlantic bryophytes

Paleontological evidence and current patterns of angiosperm species richness suggest that European biota experienced more severe bottlenecks than North American ones during the last glacial maximum. How well this pattern fits other plant species is less clear. Bryophytes offer a unique opportunity to contrast the impact of the last glacial maximum in North America and Europe because about 60% of the European bryoflora is shared with North America. Here, we use population genetic analyses based on approximate Bayesian computation on eight amphi-Atlantic species to test the hypothesis that North American populations were less impacted by the last glacial maximum, exhibiting higher levels of genetic diversity than European ones and ultimately serving as a refugium for the postglacial recolonization of Europe. In contrast with this hypothesis, the best-fit demographic model involved similar patterns of population size contractions, comparable levels of genetic diversity and balanced migration rates between European and North American populations. Our results thus suggest that bryophytes have experienced comparable demographic glacial histories on both sides of the Atlantic. Although a weak, but significant genetic structure was systematically recovered between European and North American populations, evidence for migration from and towards both continents suggests that amphi-Atlantic bryophyte population may function as a metapopulation network. Reconstructing the biogeographic history of either North American or European bryophyte populations therefore requires a large, trans-Atlantic geographic framework.

First Alaskan records and a significant northern range extension for two species of Diplura (Diplura, Campodeidae)

Species in the class Diplura are recorded from Alaska for the first time. Two species, Tricamparileyi Silvestri from Dall and Prince of Wales Islands in the Alexander Archipelago of Southeast Alaska and Metriocampaallocerca Conde & Geeraert from near Quartz Lake, southeast of Fairbanks, both in the family Campodeidae, are documented based on recently collected specimens deposited in the University of Alaska Museum Insect Collection. A brief review of the history of the documentation of the Alaskan soil microarthropod fauna is provided, as well as discussion of possible glacial refugia.

The Arctic: Glacial Refugium or Area of Secondary Contact? Inference from the Population Genetic Structure of the Thick-Billed Murre (Uria lomvia), with Implications for Management

Quaternary glaciations affected the distribution of many species. Here, we investigate whether the Arctic represented a glacial refugium during the Last Glacial Maximum or an area of secondary contact following the ice retreat, by analyzing the genetic population structure of the thick-billed murre (Uria lomvia), a seabird that breeds throughout the North Atlantic, North Pacific and Arctic Oceans. The thick-billed murre is a species of socio-economic importance and faces numerous threats including hunting, oil pollution, gill netting, and climate change. We compared variation in the mitochondrial DNA (mtDNA) control region (n = 424), supplemented by 4 microsatellite loci (n = 445), among thick-billed murres sampled throughout their range. MtDNA data indicated that colonies comprise 4 genetically differentiated groups (Φst = 0.11-0.81): 1) Atlantic Ocean plus New Siberian Islands region, 2) Cape Parry, 3) Chukchi Sea, and 4) Pacific Ocean. Microsatellite variation differed between Atlantic and Pacific populations. Otherwise, little substructure was found within either ocean. Atlantic and Pacific populations appear to have been genetically isolated since the last interglacial period and should be considered separate evolutionary significant units for management. The Chukchi Sea and Cape Parry appear to represent areas of secondary contact, rather than arctic refugial populations.

Insecticide/acaricide resistance in fleas and ticks infesting dogs and cats

This review defines insecticide/acaricide resistance and describes the history, evolution, types, mechanisms, and detection of resistance as it applies to chemicals currently used against fleas and ticks of dogs and cats and summarizes resistance reported to date. We introduce the concept of refugia as it applies to flea and tick resistance and discuss strategies to minimize the impact and inevitable onset of resistance to newer classes of insecticides. Our purpose is to provide the veterinary practitioner with information needed to investigate suspected lack of efficacy, respond to lack of efficacy complaints from their clients, and evaluate the relative importance of resistance as they strive to relieve their patients and satisfy their clients when faced with flea and tick infestations that are difficult to resolve. We conclude that causality of suspected lack of insecticide/acaricide efficacy is most likely treatment deficiency, not resistance.

Taxonomic revision of Madagascan Rhantus (Coleoptera, Dytiscidae, Colymbetinae) with an emphasis on Manjakatompo as a conservation priority

We review the diving-beetle genus Rhantus Dejean of Madagascar (Coleoptera, Dytiscidae, Colymbetinae) based on museum collection holdings and recently collected expedition material. Both morphology and DNA is used to test species boundaries, in particular whether newly collected material from the Tsaratanana mountains in the north represent a new species or are conspecific with Rhantus manjakatompo Pederzani and Rocchi 2009, described based on a single male specimen from the central Ankaratra mountains. DNA of the holotype of R. manjakatompo was successfully extracted in a non-destructive way and sequenced. The general mixed Yule coalescent model applied to an ultrametric tree constructed from mitochondrial cytochrome c oxidase subunit I (COI) sequence data delimited three species. Morphological characters supported the same species unambiguously. We therefore recognise three species of Rhantus to occur in Madagascar: R. latus (Fairmaire, 1869), R. bouvieri Régimbart, 1900 and R. manjakatompo Pederzani and Rocchi, 2009. All three species are endemic to Madagascar and restricted to the highlands of the island. Rhantusstenonychus Régimbart, 1895, syn. n., is considered a junior synonym of R. latus. We designate lectotypes for R. bouvieri and R. goudoti Sharp, 1882, the latter a junior synonym of R. latus. We provide descriptions, a determination key, SEM-images of fine pronotal and elytral structures, distribution maps, habitus photos, and illustrations of male genitalia and pro- and mesotarsal claws. We discuss the role of the Manjakatompo forest as a refugium for Madagascan Rhantus diversity and other endemics of the montane central high plateau.

Could brown bears (Ursus arctos) have survived in Ireland during the Last Glacial Maximum?

Brown bears are recorded from Ireland during both the Late Pleistocene and early-mid Holocene. Although most of the Irish landmass was covered by an ice sheet during the Last Glacial Maximum (LGM), Irish brown bears are known to have hybridized with polar bears during the Late Pleistocene, and it is suggested that the Irish brown bear population did not become extinct but instead persisted in situ through the LGM in a southwestern ice-free refugium. We use historical population modelling to demonstrate that brown bears are highly unlikely to have survived through the LGM in Ireland under any combination of life-history parameters shown by living bear populations, but instead would have rapidly become extinct following advance of the British-Irish ice sheet, and probably recolonized Ireland during the end-Pleistocene Woodgrange Interstadial from a closely related nearby source population. The time available for brown bear-polar bear hybridization was therefore restricted to narrow periods at the beginning or end of the LGM. Brown bears would have been extremely vulnerable to extinction in Quaternary habitat refugia and required areas substantially larger than southwestern Ireland to survive adverse glacial conditions.

Description of Caurinus tlagu, new species, from Prince of Wales Island, Alaska (Mecoptera, Boreidae, Caurininae)

A new species of the cryptic, minute, wingless, and enigmatic taxon Caurinus, and the second for the subfamily Caurininae,is described from Prince of Wales Island in the Alexander Archipelago, Alaska. It is distinguished from its only congener, Caurinus dectes Russell, 1979b, which occurs 1,059 km southeast in Oregon and Washington, based on external morphology and sequences of the mitochondrial gene cytochrome oxidase II. These two species are probably evolutionary relicts - the only known members of a clade dating to the Late Jurassic or older.

Phylogeography of sea oats (Uniola paniculata), a dune-building coastal grass in southeastern North America

We tested the hypothesis that Uniola paniculata populations are divided into eastern and western lineages, with the primary geographic break at the southern tip of Florida, as observed in codistributed animal taxa. We asked whether the geographic distribution of chloroplast DNA (cpDNA) variation in U. paniculata corresponds to 1) genetic structure in nuclear variation reported in previous studies, and 2) the geographic distribution of morphological adaptive traits reported in previous studies. We sampled 66 populations and performed phylogeographic analyses using sequence variations in maternally inherited cpDNA. We reconstructed the intraspecific phylogenetic network with TCS software and identified phylogeographic breaks in the species using Monmonier's algorithm. Analyses identified 6 cpDNA haplotypes and 2 major lineages: eastern (Atlantic) and western (Gulf), with a phylogeographic break at the southern tip of Florida. The data suggest U. paniculata survived the last glacial maximum (LGM) in southern refugia. Following the LGM, differential leading-edge recolonization explains the current distribution of haplotypes into 2 lineages. Populations containing a haplotype from outside its native range are likely due to human-mediated transplantation. The genetic structure of cpDNA variation has weak correlation with nuclear DNA variation, and there is partial concordance between the geographic distribution of cpDNA and morphological variation.

How do temperate bryophytes face the challenge of a changing environment? Lessons from the past and predictions for the future

Bryophytes are a group of early land plants, whose specific ecophysiological and biological features, including poikilohydry, sensitivity to moderately high temperature and high dispersal ability, make them ideal candidates for investigating the impact of climate changes. Employing a combined approach of species distribution modelling (SDM) and molecular phylogeography in the temperate moss Homalothecium sericeum, we explore the significance of the Mediterranean refugia, contrasting the southern and northern refugia hypotheses, determine the extent to which recolonization of previously glaciated areas has been facilitated by the high dispersal ability of the species and make predictions on the extent to which it will be impacted by ongoing climate change. The Mediterranean areas exhibit the highest nucleotidic diversities and host a mixture of ancestral, endemic and more recently derived haplotypes. Extra-Mediterranean areas exhibit low genetic diversities and Euro-Siberian populations display a significant signal of expansion that is identified to be of Euro-Siberian origin, pointing to the northern refugia hypothesis. The SDMs predict a global net increase in range size owing to ongoing climate change, but substantial range reductions in southern areas. Presence of a significant phylogeographical signal at different spatial scales suggests, however, that dispersal limitations might constitute, as opposed to the traditional view of spore-producing plants as efficient dispersers, a constraint for migration. This casts doubts about the ability of the species to face the massive extinctions predicted in the southern areas, threatening their status of reservoir of genetic diversity.

The role of Pleistocene refugia and rivers in shaping gorilla genetic diversity in central Africa

The role of Pleistocene forest refugia and rivers in the evolutionary diversification of tropical biota has been the subject of considerable debate. A range-wide analysis of gorilla mitochondrial and nuclear variation was used to test the potential role of both refugia and rivers in shaping genetic diversity in current populations. Results reveal strong patterns of regional differentiation that are consistent with refugial hypotheses for central Africa. Four major mitochondrial haplogroups are evident with the greatest divergence between eastern (A, B) and western (C, D) gorillas. Coalescent simulations reject a model of recent east-west separation during the last glacial maximum but are consistent with a divergence time within the Pleistocene. Microsatellite data also support a similar regional pattern of population genetic structure. Signatures of demographic expansion were detected in eastern lowland (B) and Gabon/Congo (D3) mitochondrial haplogroups and are consistent with a history of postglacial expansion from formerly isolated refugia. Although most mitochondrial haplogroups are regionally defined, limited admixture is evident between neighboring haplogroups. Mantel tests reveal a significant isolation-by-distance effect among western lowland gorilla populations. However, mitochondrial genetic distances also correlate with the distance required to circumnavigate intervening rivers, indicating a possible role for rivers in partitioning gorilla genetic diversity. Comparative data are needed to evaluate the importance of both mechanisms of vicariance in other African rainforest taxa.