Gaetano Aloise

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.

Birth of a hotspot of intraspecific genetic diversity: notes from the underground.

Hotspots of intraspecific diversity have been observed in most species, often within areas of putative Pleistocene refugia. They have thus mostly been viewed as the outcome of prolonged stability of large populations within the refugia. However, recent evidence has suggested that several other microevolutionary processes could also be involved in their formation. Here, we investigate the contribution of these processes to current range‐wide patterns of genetic diversity in the Italian endemic mole Talpa romana, using both nuclear (30 allozyme loci) and mitochondrial markers (cytochrome b sequences). Southern populations of this species showed an allozyme variation that is amongst the highest observed in small mammals (most populations had an expected heterozygosity of 0.10 or above), which was particularly unexpected for a subterranean species. Population genetic, phylogeographic and historical demographic analyses indicated that T. romana populations repeatedly underwent allopatric differentiations followed by secondary admixture within the refugial range in southern Italy. A prolonged demographic stability was reliably inferred from the mitochondrial DNA data only for a population group located north and east of the Calabrian peninsula, showing comparatively lower levels of allozyme variability, and lacking evidence of secondary admixture with other groups. Thus, our results point to the admixture between differentiated lineages as the main cause of the higher levels of diversity of refugial populations. When compared with the Pleistocene evolutionary history recently inferred for species from both the same and other geographic regions, these results suggest the need for a reappraisal of the role of gene exchange in the formation of intraspecific hotspots of genetic diversity.

Systematics of the Microtus savii complex (Rodentia, Cricetidae) via mitochondrial DNA analyses: paraphyly and pattern of sex chromosome evolution.

The genus Microtus underwent a rapid evolutionary radiation that resulted in the extant 59 species distributed throughout the Palaearctic and Nearctic regions (Musser and Carleton, 2005; Conroy and Cook, 1999). The rapidity of speciation events within the genus is reflected in the widespread low interspecific morphological divergence, with the presence of many sibling species (Musser and Carleton, 2005). However, high intraspecific morphological variation of dental and other skull characters has led to the proliferation of subspecific names, causing even more confusing systematics of the genus (Koenigswald, 1980). Studies on karyotypes and DNA sequences have revealed extensive variation among species. Hence, a genetic approach is essential to delimit species and assess the phylogenetic relationships of the groups (Conroy and Cook, 1999, 2000; Mazurok et al., 2001; Jaarola et al., 2004; Li et al., 2006). The Italian endemic voles belonging to the Microtus savii complex represent another case of this systematic uncertainty. The taxa of this species complex are slightly different morphologically and have a variable karyotype. The diploid number is 2n = 54, with a constant autosomal set and variation in the shape and size of the sex chromosomes. This chromosomal and morphological polytypism has led to the identification of five taxa (see Table 1 and

Habitat use and population density of the red squirrel, Sciurus vulgaris meridionalis, in the Sila Grande mountain range (Calabria, South Italy)

Abstract Counts of squirrel nests (dreys) and vegetation surveys in 32 1‐ha census stations were carried out to estimate densities in different forest types and determine habitat selection of the subspecies of red squirrel Sciurus vulgaris meridionalis in the Sila Grande forests, Calabria, South Italy. Dreys were not built randomly, but the majority was constructed at 60–70% of the total height of the nest‐tree, pines and oaks being the preferred tree species. Mean drey densities, 2.75/ha, 2.78/ha, and 2.00/ha in, respectively, Cal‐abrian black pine forest, beech dominated mixed forest, and chestnut woodlands, did not differ between forest types and extrapolated to estimated squirrel densities ranging from 0.44 to 0.61 squirrels/ha. Variation between stations in a tree species diversity index and in distance from the nearest plot of pine woodland significantly affected variation in drey density: squirrels preferred forest habitats dominated by beech, with also black pine and oak available, or chestnut woodlands that were within the range of one (male) squirrel home range diameter (310 m) of a plot of pine forest (mean drey density 5.4/ha). Fewer dreys were found in deciduous (beech or chestnut) woodland >310 m away from areas with pine forest (1.1 dreys/ha). Hence, the availability, at least in the vicinity of the census station, of pine seeds of the Calabrian black pine as main food resource strongly influenced habitat choice.

Integrative taxonomy of the Italian pine voles, Microtus savii group (Cricetidae, Arvicolinae)

The Italian endemic voles belonging to the Microtus savii group (de Sélys‐Longchamps, 1838) include five controversial taxa, namely M. savii savii, M. s. niethammericus Contoli ; M. s. tolfetanus Contoli , M. s. nebrodensis (Minà‐Palumbo, 1868) and M. brachycercus (Lehamann, 1961). A previous mtDNA phylogenetic analysis revealed three main mtDNA lineages that do not correspond to the recognized taxa. Here, we perform a comprehensive univariate and multivariate analysis of craniodental measurements in 151 specimens from 54 geographic samples belonging to the three main phylogroups. Qualitative data on the skull of 126 specimens were also obtained from 54 localities. Moreover, we sequenced the nuclear DNA β‐fibrinogen intron 7 (β‐fibint7) of 23 specimens from 12 localities and Cyt b sequences of 11 new specimens from seven localities. The pattern of morphological and cytogenomic divergence does not corroborate the current taxonomic framework and indicates that M. nebrodensis is a Sicilian endemic species.

Extreme Feeding Behaviours in the Italian Wall Lizard, Podarcis siculus.

In the present paper the occurrence of cannibalism, unusual predation on small reptiles (Hemidactylus turcicus (Reptilia, Gekkonidae)), and foraging on small mammal carrion (Suncus etruscus (Mammalia, Soricidae)) by P. siculus is reported.

Mitochondrial phylogeography of the black rat supports a single invasion of the western Mediterranean basin

Abstract The black rat Rattus rattus is recognized as one of the world’s most harmful invasive species. It has spread across the globe by passive human transport and the dynamics of colonization have been investigated in several areas of the world. However, data for the Mediterranean basin are still lacking. We investigated the black rat colonization of the western Mediterranean basin by means of mitochondrial genes. Mitochondrial control region and cytochrome b gene were sequenced in order to quantify genetic diversity of western Mediterranean black rats. Maximum likelihood phylogenetic analysis based on cytochrome b was used to assign specimens to a specific lineage of the R. rattus species complex. The mitochondrial control region was used to reconstruct phylogeographic pattern by statistical parsimony network and to asses historical demography of western Mediterranean black rats. The results show an unexpectedly low diversity considering that the Mediterranean basin has been a trade route since very ancient times. The results mtDNA analysis are compatible with a single event of invasions of western Mediterranean by R. rattus.

Scale-dependent environmental variables affecting red squirrel (Sciurus vulgaris meridionalis) distribution

We investigated the effects of habitat fragmentation on the endemic subspecies of red squirrel Sciurus vulgaris meridionalis in the Pollino National Park, Calabria, Southern Italy. Presence/absence of squirrels was monitored using drey (nest) counts in 51 1‐ha census plots. Squirrel dreys were found in 16 plots (31%). Patch size was not correlated to squirrel presence. Squirrels were found in patches ranging from 3.19 to 6051 ha. Small‐scale forest structure significantly affected the probability of occurrence. The proportion of conifers and average tree height positively predict squirrel presence; furthermore, nest density was positively correlated with high tree species diversity and the proportion of deciduous oaks (Quercus cerris, Q. ilex). Also at the home‐range scale the proportion of conifer forest and oak‐dominated deciduous forests positively predicted squirrel presence (200–300 m radius). At the even larger scale, corresponding with potential dispersal distances (3000 m radius), landscape parameters indicating a lower degree of fragmentation and proportion of oak seemed to favour squirrel presence. Our results emphasize that multi‐scale analyses can enhance our understanding of red squirrel distribution, and that their distribution and abundance were mainly determined by forest structure components, such as food availability, at the home‐range scale. We underline the importance of protection, and eventually increasing conifer and deciduous oak woods range in the Pollino National Park for the management and conservation of endemic Calabrian red squirrels.

A combination of long term fragmentation and glacial persistence drove the evolutionary history of the Italian wall lizard Podarcis siculus

BackgroundThe current distribution of genetic diversity is the result of a vast array of microevolutionary processes, including short-term demographic and ecological mechanisms and long-term allopatric isolation in response to Quaternary climatic fluctuations. We investigated past processes that drove the population differentiation and spatial genetic distribution of the Italian wall lizard Podarcis siculus by means of sequences of mitochondrial cytb (n = 277 from 115 localities) and nuclear mc1r and β-fibint7genes (n = 262 and n = 91, respectively) from all its distribution range. The pattern emerging from the genetic data was compared with current and past (last glacial maximum) species distribution modeling (SDM).ResultsWe identified seven deeply divergent parapatric clades which presumably remained isolated in different refugia scattered mainly throughout the Tyrrhenian coast. Conversely, the Adriatic coast showed only two haplogroups with low genetic variability. These results appear to agree with the SDM prediction at the last glacial maximum (LGM) indicating a narrow area of habitat suitability along the Tyrrhenian coast and much lower suitability along the Adriatic one. However, the considerable land exposure of the Adriatic coastline favored a glacial colonization of the Balkan Peninsula.ConclusionsOur population-level historical demography showed a common trend consistent with glacial expansions and regional persistence during the last glacial maximum. This complex genetic signature appears to be inconsistent with the expectation of the expansion-contraction model and post-LGM (re)colonizations from southern refugia. Hence it is one of an increasing number of cases in which these assumptions are not met, indicating that long-term fragmentation and pre-LGM events such as glacial persistence were more prominent in shaping genetic variation in this temperate species.

The use of species‐specific cone remains of sympatric arboreal rodents to monitor their distribution

The red squirrel (Sciurus vulgaris) is threatened with local extinction in those parts of its distribution range colonised by introduced alien squirrel species. Therefore, developing fast and economic monitoring techniques is becoming of increasing importance in relation to conservation and/or management of this species as well as for developing early‐warning systems for undesired species (e.g. non‐native, invasive species). We present a detailed description of cone‐feeding techniques by edible dormouse (Glis glis), black rat (Rattus rattus) and Finlaysons squirrel (Callosciurus finlaysonii), that recently colonised a small area in the south of Italy, and compare these with signs left by red squirrels in conifer forests dominated by different tree species (Pinus halepensis, P. nigra, P. laricio, P. pinaster and P. leucodermis) in southern Italy. A total of 15,777 consumed cones were collected in 1997–2005 from 33 localities in Calabria and Lucania. Exact determination of consumer species of 100 cone remains by five trained observers was high (98.8%). We conclude that determination of consumed cones on cone feeding transects is an accurate and economic method for monitoring presence/absence of red squirrels in those parts of their range where they are sympatric with either edible dormice and/or black rats.