Origin of, and conservation units in, the Irish red squirrel (Sciurus vulgaris) population

Knowledge of genetic relationships among wildlife populations is fundamental to their conservation, particularly where translocations are concerned. This study involved a survey of mitochondrial DNA variation in the Irish red squirrel population. Our main aims were: (1) to determine whether the Irish red squirrel population is distinct from that found in Britain, given known translocations that took place from Britain in the 1800’s; and (2) whether inclusion of Irish data into a reanalysis of European red squirrel data could reveal patterns of postglacial spread in Ireland. We found evidence that the current Irish red squirrel population may be a mixture of native and translocated stock, and relationships between Irish and European haplotypes supported a number of colonisation events of the island. Although only one haplotype was common to both Ireland and Britain, it is probable that the most common haplotypes in Ireland are British introductions that have since become extinct in Britain. There was a significant regional genetic structure in Ireland (P < 0.001), as well as between all Irish and British regions. Although it is likely that the red squirrel will not be fundamental in tracing the colonisation of Ireland by mammals, the data demonstrated that individual regions within Ireland, as well as the Irish population as a whole, are distinct both from the British population and from each other and, therefore, these populations should be treated as separate Management Units (MU) in conservation strategies.     

Retracing the history and planning the future of the red squirrel (<Emphasis Type="Italic">Sciurus vulgaris</Emphasis>) in Ireland using non-invasive genetics

The Eurasian red squirrel’s (Sciurus vulgaris) history in Ireland is largely unknown, but the original population is thought to have been driven to extinction by humans in the seventeenth century, and multiple records exist for its subsequent reintroduction in the nineteenth century. However, it is currently unknown how these reintroductions affect the red squirrel population today, or may do so in the future. In this study, we report on the development of a DNA toolkit for the non-invasive genetic study of the red squirrel. Non-invasively collected red squirrel samples were combined with other samples collected throughout Ireland and previously published mitochondrial DNA (mtDNA) data from Ireland, Great Britain and Continental Europe to give an insight into population genetics and historical introductions of the red squirrel in Ireland. Our findings demonstrate that the Irish red squirrel population is on a national scale quite genetically diverse, but at a local level contains relatively low levels of genetic diversity, and there is also evidence of genetic structure. This is likely an artefact of the introduction of a small number of genetically similar animals to specific sites. A lack of continuous woodland cover in Ireland has prevented further mixing with animals of different origins that may have been introduced even to neighbouring sites. Consequently, some of these genetically isolated populations are or may in the future be at risk of extinction. The Irish red squirrel population contains mtDNA haplotypes of both a British and Continental European origin, the former of which are now extinct or simply not recorded in contemporary Great Britain. The Irish population is therefore important in terms of red squirrel conservation not only in Ireland, but also for Great Britain, and should be appropriately managed.     

Museum samples provide novel insights into the taxonomy and genetic diversity of Irish red grouse

The taxonomic status of red grouse in Ireland has been the subject of considerable debate over the past century. Irish red grouse are usually classified as Lagopus lagopus scoticus, which is the same subspecies as that found in Britain, but some ornithologists believe that native Irish red grouse constitute an endemic subspecies, namely L. lagopus hibernicus. The considerable decline of Irish red grouse over the past century, along with possible hybridization with introduced grouse from Britain, have highlighted the need to resolve their taxonomic status as part of a biodiversity management plan. However, genetic analysis of samples from a single point in time will provide limited insight into potentially confounding historical events such as hybridization and introgression. We therefore compared mtDNA sequences from both current and historical samples of the two putative subspecies, scoticus and hibernicus, to see if they are or were genetically distinct. Red grouse from Britain and Ireland shared mitochondrial haplotypes, and our historical data suggest that this is unlikely to be the result of recent hybridization and introgression. These findings, combined with a general lack of documented differences in behaviour and ecology, suggest that Irish red grouse should remain classified as L. lagopus scoticus. At the same time, we found evidence that a significant amount of genetic diversity has been lost from Irish red grouse over the past century, presumably as a result of diminishing population sizes and fragmentation of extant populations. A loss of habitat, combined with the declining numbers and genetic diversity of Irish red grouse, justify their designation as an All-Ireland Priority (Red List) species and a Northern Ireland Priority Species for conservation.     

Grey squirrels in central Italy: a new threat for endemic red squirrel subspecies

A new population of the invasive American Eastern grey squirrel (Sciurus carolinensis) has recently settled in central Italy from an accidental release in Perugia, Umbria in the early 2000s. The grey squirrel is known to compete with and exclude native red squirrels (S. vulgaris) in the British Isles and Northern Italy, so it represents a potentially important new conservation threat to the red squirrel subspecies of south and central Italy, S. vulgaris italicus and S. v. meridionalis, which are endemic to peninsular Italy. The grey squirrel population range in Perugia is currently expanding at a rate of about 0.29 km/year (SD 0.19), slower than grey squirrel invasions elsewhere in Europe. Nuclear DNA analysed at 12 different microsatellite loci revealed that the grey squirrels in Perugia have extremely low genetic diversity, consistent with a small founder size. Genetic assignment tests indicate that the Perugia population was founded by translocations from an established population in Piedmont, Italy. No genetic substructure is evident yet in the Perugia population. These results together have serious consequences for the management of the grey squirrel invasion in Perugia and the conservation of the red squirrel subspecies: the Perugia grey squirrel population should be eradicated if politically feasible; otherwise new releases of grey squirrels, especially from sources other than the Piedmont population, should be prevented because such introductions could increase genetic diversity, thereby potentially increasing population range expansion rate to the much higher levels seen for more diverse grey squirrel populations elsewhere in Europe.     

Population crash in an invasive species following the recovery of a native predator: the case of the American grey squirrel and the European pine marten in Ireland

In Ireland, the UK and Italy, the invasive North American grey squirrel, Sciurus carolinensis, threatens the survival of the Eurasian red squirrel, Sciurus vulgaris, as the effects of competition and disease almost inevitably lead to total replacement of red squirrel populations. However the results of a recent national squirrel survey suggested that the normally invasive grey squirrel had gone into decline in the Irish midlands, which was anecdotally attributed to an increase in European pine marten, Martes martes, range and numbers. This study aimed to quantify changes in squirrel distribution in Ireland and to investigate the role, if any, of the pine marten in red and grey squirrel population dynamics. A distribution survey of the midlands was carried out which confirmed the grey squirrel population has crashed in approximately 9,000 km² of its former range and the red squirrel is common after an absence of up to 30 years. At landscape level, pine marten and red squirrel abundance were positively correlated, whereas a strong negative correlation between pine marten and grey squirrel presence at woodland level was found to exist. Squirrel demographics were determined by means of live trapping programs which confirmed that the red squirrel in the midlands is now in competitive release and the grey squirrel is present at unusually low density. This study provides the first evidence of a regional grey squirrel population crash and suggests that European pine marten abundance may be a critical factor in the American grey squirrel’s success or failure as an invasive species.     

A genetic analysis of grey squirrel (Sciurus carolinensis) populations in Ireland

Biological Invasions - The grey squirrel (Sciurus carolinensis) is an invasive rodent in Ireland that has had detrimental impacts on the native Irish red squirrel (S. vulgaris) as well as on...     

Patterns of genetic diversity in the red squirrel (Sciurus vulgaris L.): Footprints of biogeographic history and artificial introductions

British S. vulgaris are classified as aseparate subspecies, S. v. leucourus, tomainland Europe. While S. vulgaris is notunder threat across most of its Eurasian range,in Britain, Ireland and Italy populations aredeclining, mainly due to the introduction ofthe American grey squirrel (S.carolinensis). In this study, we conducted anextensive survey of mitochondrial DNA variationin British S. vulgaris populations and apreliminary survey of continental Europeanpopulations. Our main aims were to determinethe extent to which any populations of S.vulgaris in Britain are partially or whollythe product of artificial translocation of redsquirrels from continental Europe, and whethercontinental population variation will provideinformation on post-glacial reafforestationpatterns in Europe. We found that the majorityof extant populations of British S.vulgaris are of continental ancestry, manywith a very recent (last 40 years) Scandinavianancestry. The Scandinavian haplotype hasrapidly become the most dominant innortheastern Britain, despite not appearing innorthern English populations until 1966. Thissuggests that these squirrels may have anadaptive advantage in the non-native sprucedominated conifer plantations of northernEngland. Our preliminary examination ofcontinental populations demonstrated that theyare sufficiently differentiated to allow aphylogeographic study of this species.     

Geographic variation in the Japanese white-toothed shrew<Emphasis Type="Italic">Crocidura dsinezumi</Emphasis>

I investigated geographic variation in the Japanese white-toothed shrewCrocidura dsinezumi (Temminck, 1842) (Insectivora, Soricidae) from the Japanese Archipelago and the northern part of the Ryukyu Archipelago. Univariate and multivariate analyses were conducted based on 11 cranial measurements from 14 sampling localities. Overall size variation seemed to follow clinal changes correlated with latitude and longitude of localities, such that northeastern populations were smaller than southwestern ones. The Hokkaido population and the Kuchinoerabujima population were larger than expected based on estimated values, likely due to changes reflecting environmental factors. In contrast, the Tanegashima population was smaller than its estimated value. The northern Ryukyu populations were divergent from the Kyushu population and from each other. Based on patterns of geographic variation, I suggest that all previously described subspecies ofC. dsinezumi are junior synonyms ofC. dsinezumi; and that the Kuchinoerabujima population and the Nakanoshima population likely represent un- described subspecies.     

Genetic variation among endangered Irish red grouse (<Emphasis Type="Italic">Lagopus lagopus hibernicus</Emphasis>) populations: implications for conservation and management

Extant populations of Irish red grouse (Lagopus lagopus hibernicus) are both small and fragmented, and as such may have an increased risk of extinction through the effects of inbreeding depression and compromised adaptive potential. Here we used 19 microsatellite markers to assay genetic diversity across 89 georeferenced samples from putatively semi-isolated areas throughout the Republic of Ireland and we also genotyped 27 red grouse from Scotland using the same markers. The genetic variation within Ireland was low in comparison to previously published data from Britain and the sample of Scottish red grouse, and comparable to threatened European grouse populations of related species. Irish and Scottish grouse were significantly genetically differentiated (F_ST = 0.07, 95% CI = 0.04–0.10). There was evidence for weak population structure within Ireland with indications of four distinct genetic clusters. These correspond approximately to grouse populations inhabiting suitable habitat patches in the North West, Wicklow Mountains, Munster and Cork, respectively, although some admixture was detected. Pair-wise F_ST values among these populations ranged from 0.02 to 0.04 and the overall mean allelic richness was 5.5. Effective population size in the Munster area was estimated to be 62 individuals (95% CI = 33.6–248.8). Wicklow was the most variable population with an AR value of 5.4 alleles/locus. Local (Munster) neighbourhood size was estimated to 31 individuals corresponding to an average dispersal distance of 31 km. In order to manage and preserve Irish grouse we recommend that further fragmentation and destruction of habitats need to be prevented in conjunction with population management, including protection of the integrity of the existing population by refraining from augmenting it with individuals from mainland Britain to maximise population size.     

Molecular phylogeography of European Sciurus vulgaris: refuge within refugia?

The red squirrel ( Sciurus vulgaris ) is a well-known forest animal distributed all over Europe. Still, we are far from having a firm knowledge of the species' phylogeography. This study investigates the genetic differentiation of S. vulgaris across the species' Eurasian range, using sequence data from the mitochondrial DNA gene (D-loop, 252 base pairs, cytochrome b , 359 base pairs), and eight variable autosomal microsatellite loci genotyped for 236 individuals. The results reveal the presence of two main mitochondrial phylogroups. The first clade comprises the individuals from the region of Calabria in southern Italy, belonging to the subspecies S. v . meridionalis , while the second clade contains the remainder of the studied individuals. Bayesian analysis of microsatellite genotypes resulted in three main clusterings corresponding to the three S. vulgaris subspecies: infuscatus, meridionalis and fuscoater . Geographical distribution of mtDNA haplotypes and mismatch analysis suggest a common refugium for the red squirrel across most of its present range from which expansion happened rather rapidly. The genotype mixing of italicus with northern populations could be a residual of postglacial expansion. The lack of mixing between the Calabrian lineage and the rest of European red squirrel haplotypes can be seen as evidence for distinct histories throughout the Pleistocene. Calabrian mtDNA probably diverged in an ice age contraction and remained isolated from the neighbouring squirrel populations until very recent times.     

Floral trait differentiation in Anacamptis coriophora: Phenotypic selection on scents,but not on colour

Current divergent selection may promote floral trait differentiation among conspecific populations in flowering plants. However, whether this applies to complex traits such as colour or scents has been little studied, even though these traits often vary within species. In this study, we compared floral colour and odour as well as selective pressures imposed upon these traits among seven populations belonging to three subspecies of the widespread, generalist orchid Anacamptis coriophora. Colour was characterized using calibrated photographs, and scents were sampled using dynamic headspace extraction and analysed using gas chromatography–mass spectrometry. We then quantified phenotypic selection exerted on these traits by regressing fruit set values on floral trait values. We showed that the three studied subspecies were characterized by different floral colour and odour, with one of the two predominant floral volatiles emitted by each subspecies being taxon‐specific. Plant size was positively correlated with fruit set in most populations, whereas we found no apparent link between floral colour and female reproductive success. We detected positive selection on several taxon‐specific compounds in A. coriophora subsp. fragrans, whereas no selection was found on floral volatiles of A. coriophora subsp. coriophora and A. coriophora subsp. martrinii. This study is one of the first to document variation in phenotypic selection exerted on floral scents among conspecific populations. Our results suggest that selection could contribute to ongoing chemical divergence among A. coriophora subspecies.     

Genetic differentiation,hybridization and adaptive divergence in two subspecies of the acorn barnacle Tetraclita japonica in the northwestern Pacific

Two acorn barnacles, Tetraclita japonica japonica and Tetraclita japonica formosana, have been recently reclassified as two subspecies, because they are morphologically similar and genetically indistinguishable in mitochondrial DNA sequences. The two barnacles are distinguishable by parietes colour and exhibit parapatric distributions, coexisting in Japan, where T. j. formosana is very low in abundance. Here we investigated the genetic differentiation between the subspecies using 209 polymorphic amplified fragment length polymorphism markers and 341 individuals from 12 locations. The subspecies are genetically highly differentiated (Φ_CT = 0.267). Bayesian analysis and principal component analysis indicate the presence of hybrids in T. j. formosana samples from Japan. Strong differentiation between the northern and southern populations of T. j. japonica was revealed, and a break between Taiwan and Okinawa was also found in T. j. formosana. The differentiation between the two taxa at individual loci does not deviate from neutral expectation, suggesting that the oceanographic pattern which restricts larval dispersal is a more important factor than divergent selection in maintaining genetic and phenotypic differentiation. The T. j. formosana in Japan are probably recent migrants from Okinawa, and their presence in Japan may represent a poleward range shift driven by global warming. This promotes hybridization and might lead to a breakdown of the boundary between the subspecies. However, both local adaptation and larval dispersal are crucial in determining the population structure within each subspecies. Our study provides new insights into the interplay of local adaptation and dispersal in determining the distribution and genetic structure of intertidal biota and the biogeography of the northwestern Pacific.     

韩国与中国东北地区松鼠线粒体DNA控制区的序列变异

为了研究松鼠东北亚种(Sciurus vulgaris manchuricusThomas)不同种群的序列变异水平并进一步确定分类地位,我们分析了韩国5个地点和中国东北2个地点的松鼠标本的线粒体DNA控制区的全序列(1 058 bp)。39个韩国松鼠标本显示出21种单倍型,这些单倍型间的平均Tamura-Nei距离为1·0%; 24个中国松鼠标本显示21种单倍型,单倍型间的平均Tamura-Nei距离为1·4% (1 058 bp的全序列中发生变异的位点有119个,占11·2%)。韩国松鼠和中国松鼠间的平均距离为1·3%。并且韩国和中国松鼠的所有42个单倍型形成了一个单系分支,Fst值为0·04,表明在两个国家的松鼠间没有发生遗传分化。因此,序列分析的分子生物学的结果支持现行的分类,即来自韩国的朝鲜亚种(S·v·coreae)是中国北部地区松鼠东北亚种(S·v·manchuricus)的同物异名。这还需要进一步对北朝鲜和中国东北其它地区更多标本的分子和形态学分析来验证这一结论。     

Genetic structure of Eurasian badgers Meles meles (Carnivora: Mustelidae) and the colonization history of Ireland

The present study examined the contemporary genetic composition of the Eurasian badger, Meles meles, in Ireland, Britain and Western Europe, using six nuclear microsatellite loci and a 215‐bp fragment of the mitochondrial DNA control region. Significant population structure was evident within Europe (global multilocus microsatellite F_ST = 0.205, P < 0.001; global mitochondrial control region Φ_ST = 0.399, P < 0.001). Microsatellite‐based cluster analyses detected one population in Ireland, whereas badgers from Britain could be subdivided into several populations. Excluding the island populations of Ireland and Britain, badgers from Western Europe showed further structuring, with evidence of discrete Scandinavian, Central European, and Spanish populations. Mitochondrial DNA cluster analysis grouped the Irish population with Scandinavia and Spain, whereas the majority of British haplotypes grouped with those from Central Europe. The findings of the present study suggest that British and Irish badger populations colonized from different refugial areas, or that there were different waves of colonization from the source population. There are indications for the presence of an Atlantic fringe element, which has been seen in other Irish species. We discuss the results in light of the controversy about natural versus human‐mediated introductions. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Adaptive and neutral genetic differentiation among Scottish and endangered Irish red grouse (<Emphasis Type="Italic">Lagopus lagopus scotica</Emphasis>)

Studying patterns of intra-specific genetic variation among populations allows for a better understanding of population structure and local adaptation. However, those patterns may differ according to the genetic markers applied, as neutral genetic markers reflect demographic processes and random genetic drift, whereas adaptive markers also carry the footprint of selection. In combination, neutral and adaptive genetic markers permit to assess the relative roles of drift and selection in shaping population structure. Among the best understood adaptive genetic loci are the genes of the major histocompatibility complex (MHC). We here study variation and differentiation at neutral SNP markers and MHC class II genes in red grouse (Lagopus lagopus scotica) from Ireland and Scotland. Irish red grouse populations are fragmented and drastically declining, but red grouse are abundant in Scotland. We find evidence for positive selection acting on the MHC genes and variation in MHC gene copy numbers among Irish individuals. Furthermore, there was significant population differentiation among red grouse from Ireland and Scotland at the neutral SNP markers (F_ST = 0.084) and the MHC-BLB genes (F_ST: BLB1 = 0.116, BLB2 = 0.090, BLB3 = 0.104). Differentiation at the MHC-BLB1 was significantly higher than at the neutral SNP markers, suggesting that selection plays an important role in shaping MHC variation, in addition to genetic drift. We speculate that the observed differentiation pattern might be due to local adaptation to different parasite regimes. These findings have strong conservation implications and we advise against the introduction of Scottish red grouse to supplement Irish populations.     

Genetic and geographic structure of an insect resistant and a susceptible type of <Emphasis Type="Italic">Barbarea vulgaris</Emphasis> in western Europe

Interactions between herbivores and plants are believed to have been important drivers of biodiversity. However, to drive an initial resistance divergence into different evolutionary lineages and taxa, these interactions have probably been embedded in other processes of divergence, like allopatric isolation. The cruciferous plant Barbarea vulgaris ssp. arcuata occurs in Denmark in two types: one (G) is resistant to most genotypes of the flea beetle Phyllotreta nemorum, the other (P) is susceptible. The two types additionally differ in hairiness and glucosinolates, they are genetically strongly divergent, and reproduction between them is reduced. To determine whether the two plant types and their resistance polymorphisms are also present outside Denmark, and to understand how they have evolved, we analysed 33 European populations of B. vulgaris for resistance, hairiness, glucosinolates, and microsatellite markers. Most populations had traits indicative of the G type, including the already characterized Danish G populations. In contrast, only two populations outside Denmark were of the P type; one from northern Sweden and one from Estonia. Genetically, the G populations formed two genetic clusters that were strongly divergent from a genetic cluster containing P populations. A fourth genetic cluster, which contained only a single population and no Danish plants, belonged morphologically to the subspecies ssp. vulgaris. The divergence found in Denmark between a resistant G and a susceptible P type is thus part of a larger divergence in Europe. Judging from the trait correlations, genetic divergence, and partial reproductive incompatibility, the plant types must have been isolated from each other for quite some time. The two P populations outside Denmark came from the north and east, suggesting a more eastern distribution. If so, resistant and susceptible types could have diverged during the ice age and later met in Scandinavia. However, more samples from Eastern Europe are needed to clarify this.     

Geographic variation in the long-nosed snake, Rhinocheilus lecontei (Colubridae): beyond the subspecies debate

Scalation, colour pattern, linear and geometric morphometrics were used to quantify geographical differentiation in the long-nosed snake, Rhinocheilus lecontei, and to test the hypothesis that all four subspecies are morphologically distinct. Also investigated were potential associations between morphological (scalation, colour pattern, linear measurements) and environmental variables (climate, vegetation, soil). Sexual dimorphism was weakest for geometric and strongest for linear morphometric variables. Morphological variables differed widely in their ability to differentiate subspecies. Linear morphometric variables achieved the most statistically significant pairwise Mahalanobis distances between subspecies, while geometric morphometrics largely failed to differentiate them. Colour pattern showed the strongest and linear morphometrics the weakest correlation with environment. Several characters varied continuously along latitudinal or longitudinal gradients, such that, in some cases, the clines for closely related traits were discordant. No one subspecies was consistently divergent in all analyses, leading to the conclusion that the three mainland subspecies are not sufficiently distinct to warrant separate subspecies status. The island subspecies, though not always statistically distinct, is geographically separate from other populations and differs in characters related to size. Given the small number of specimens available, a decision regarding its taxonomic status (i.e. elevation to species level) is best deferred until additional specimens can be examined and data on molecular variation can be analysed.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 65–85.     

Genetic diversity and population divergence in fragmented habitats: Conservation of Idaho ground squirrels

The Idaho ground squirrel, which consists of a northern (Spermophilus brunneus brunneus) and a southern subspecies (S. b. endemicus), has suffered from habitat loss and fragmentation, resulting in a reduction in both numbers and geographic range of the species. The northern Idaho ground squirrel (NIDGS) is listed as a threatened subspecies under the Endangered Species Act, and the southern Idaho ground squirrel (SIDGS) is a candidate. Because Idaho ground squirrel populations are small and often isolated, they are susceptible to inbreeding and loss of genetic diversity through drift. This research evaluates levels of genetic diversity and patterns of population divergence in both subspecies of Idaho ground squirrels. We hypothesized that NIDGS would exhibit lower genetic diversity and greater population divergence due to a longer period of population isolation relative to most SIDGS populations. Genetic diversity and divergence were quantified using 8 microsatellite loci. Contrary to expectations, SIDGS populations exhibited consistently lower levels of microsatellite diversity. Additionally, NIDGS exhibited only modest divergence among populations, while divergence levels among SIDGS populations were highly varied. Preliminary evaluations of mitochondrial DNA diversity and structure revealed lower diversity in NIDGS and some differences in gene flow that warrant further study. Based on our results, we suggest different management strategies for the two subspecies. Habitat restoration appears to be the most desirable conservation strategy for NIDGS populations. In contrast, low genetic diversity observed in SIDGS may warrant supplementation of isolated populations through translocations or captive breeding to mitigate further loss of genetic variability.     

Male–male aggression is unlikely to stabilize a poison frog polymorphism

Phenotypic polymorphism is common in animals, and the maintenance of multiple phenotypes in a population requires forces that act against homogenizing drift and selection. Male–male competition can contribute to the stability of a polymorphism when males compete primarily with males of the same phenotype. In and around a contact zone between red and blue lineages of the poison frog Oophaga pumilio, we used simulated territorial intrusions to test the nonexclusive predictions that males would direct more aggression towards males of (i) their own phenotype and/or (ii) the phenotype that is most common in their population. Males in the monomorphic red and blue populations that flank the contact zone were more aggressive towards simulated intruders that matched the local coloration. However, males in the two polymorphic populations biased aggression towards neither their own colour nor the colour most common in their population. In sympatry, the rarer colour morph gains no advantage via reduced male–male aggression from territorial males in these O. pumilio populations, and so male aggression seems unlikely to stabilize colour polymorphism on its own. More broadly, these results suggest that the potential for divergent male aggression biases to maintain phenotypic diversity depends on the mechanism(s) that generate the biases and the degree to which these mechanisms persist in sympatry.