Genetic structuring in Andean landlocked populations of Galaxias maculatus: effects of biogeographic history

Aim To test whether the genetic diversity of diadromous and landlocked populations of the small puyen Galaxias maculatus (known as jollytail in Australia and inanga in New Zealand) follow the same structuring patterns observed for migratory and non‐migratory species of the genus Galaxias. This work also aimed to test whether the genetic structuring of a group of populations could be predicted from differences in the geomorphologic history of the region they inhabit. Location Eight landlocked populations were sampled from cold‐temperate lakes in north‐western Patagonia. The study area could be split latitudinally into two sectors that differed in their geomorphology, each of them hosting four populations. The southern sector shows evidence of a higher degree of glacial coverage, and the lakes are probably remnants of a big proglacial palaeolake. Lakes in the northern sector, on the other hand, suggest no common origin. Results Significant genetic structuring was found among the studied populations (Θ = 0.188), being the highest value reported to date for the species. Significant correlation was found between genetic diversity and lake area and perimeter. Diversity also showed a slight latitudinal variation suggesting the presence of genetically distinct groups of populations. The comparison of populations from the two geographical sectors showed that those from the north had a higher diversity, more private alleles and strong structuring, while those from the south were less diverse and much more homogeneous. Main conclusions Non‐migratory populations of G. maculatus show much higher values of genetic structuring than those reported for diadromous populations. This follows the pattern seen when comparing migratory and non‐migratory species of Galaxias. This agrees with population genetics theory which predicts that restricted gene flow would result in greater among‐population divergence. Also, differences between northern and southern populations agreed with what was predicted by the geomorphologic history of the study area. During the Last Glacial Maximum ice cover in that region may have reduced the habitat of G. maculatus to a refuge with an impoverished gene pool. When the ice receded, leaving a great proglacial lake, that former population expanded and became fragmented after water levels descended. This resulted in present day lakes harbouring homogeneous populations with reduced diversity. The northern sector, in contrast, was less affected by glaciers, resulting in more geomorphologically stable lakes holding genetically diverse populations.     

The effects of diadromy and its loss on genomic divergence: The case of amphidromous Galaxias maculatus populations

Understanding the evolutionary mechanisms that affect the genetic divergence between diadromous and resident populations across heterogeneous environments is a challenging task. While diadromy may promote gene flow leading to a lack of genetic differentiation among populations, resident populations tend to be affected by local adaptation and/or plasticity. Studies on these effects on genomic divergence in nonmodel amphidromous species are scarce. Galaxias maculatus, one of the most widespread fish species in the Southern Hemisphere, exhibits two life histories, an ancestral diadromous, specifically, amphidromous form, and a derived freshwater resident form. We examined the genetic diversity and divergence among 20 estuarine and resident populations across the Chilean distribution of G. maculatus and assessed the extent to which selection is involved in the differentiation among resident populations. We obtained nearly 4,400 SNP markers using a RADcap approach for 224 individuals. As expected, collections from estuarine locations typically consist of diadromous individuals. Diadromous populations are highly differentiated from their resident counterparts by both neutral and putative adaptive markers. While diadromous populations exhibit high gene flow and lack site fidelity, resident populations appear to be the product of different colonization events with relatively low genetic diversity and varying levels of gene flow. In particular, the northernmost resident populations were clearly genetically distinct and reproductively isolated from each other suggesting local adaptation. Our study provides insights into the role of life history differences in the maintenance of genetic diversity and the importance of genetic divergence in species evolution.     

Genetic footprints of habitat fragmentation in the extant populations of Sinojackia (Styracaceae): implications for conservation

Sinojackia, a member of the family Styracaceae, is an endangered genus endemic to China. The number of populations and population size of Sinojackia have decreased sharply because of habitat fragmentation and destruction. We studied the genetic diversity of extant populations in two different cohorts (adult and seedling) using eight microsatellite markers to investigate the genetic footprints of habitat fragmentation in four recognized Sinojackia spp. and to develop appropriate conservation measures. Data on intrapopulational genetic diversity suggest that Sinojackia populations have maintained relatively high levels of genetic diversity and low levels of genetic differentiation despite severe fragmentation. The high genetic diversity may be explained by the outcrossing mating system and high longevity of Sinojackia spp. The amount of genetic variation is not associated with population size, which was also supported by bottleneck analysis. In the species studied, there was no significant difference in the genetic diversity between the two cohorts analysed. However, inbreeding increased from adult trees to seedling populations, suggesting that the higher proportion of biparental inbreeding in the recent generations of seedlings is the result of restricted current genetic flow caused by habitat fragmentation. Average seed set per population was not significantly correlated with either population size or genetic diversity. Conservation management should aim to monitor inbreeding and outbreeding depression carefully to ensure the in situ and ex situ conservation of Sinojackia spp. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ?? , ??–??.     

The impact of habitat fragmentation on fitness‐related traits in a native prairie plant,Chamaecrista fasciculata (Fabaceae)

Loss and fragmentation of the native prairies in the Midwestern United States have resulted in isolated and smaller habitats and populations. The populations remaining in these prairies are expected to show a decline in the extent of genetic variation and an increase in genetic drift load (accumulation of deleterious recessive alleles due to genetic drift) in fitness‐related traits. Using complementary greenhouse experiments, we tested whether these expected changes have occurred in the native annual prairie plant Chamaecrista fasciculata. In the first experiment, open pollinated C. fasciculata seeds from 12 prairie fragments representing a range in area of habitat were grown in competition with Schizachyrium scoparium to determine if there are changes in plant vigour with changes in fragment size and corresponding changes in population size. Plants from smaller prairie fragments exhibited a slight but significant decline in biomass, suggesting an increase in genetic drift load. In the second experiment, a formal genetic crossing design of four prairie fragment populations was used to estimate quantitative genetic diversity and genetic drift load. We did not find extensive quantitative genetic variation, but we did find a strong effect of genetic drift load on five traits in this experiment. Our overall conclusion is that a decline in relative‐fitness traits in smaller prairie fragments is probably associated with fixation of deleterious alleles due to more isolated and smaller populations, i.e. genetic drift load. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Watershed characteristics shape the landscape genetics of brook stickleback (Culaea inconstans) in shallow prairie lakes

Investigating the consequences of landscape features on population genetic patterns is increasingly important to elucidate the ecological factors governing connectivity between populations and predicting the evolutionary consequences of landscapes. Small prairie lakes in Alberta, Canada, and the brook stickleback (Culaea inconstans) that inhabit them, provide a unique aquatic system whereby populations are highly isolated from one another. These heterogeneous and extreme environments are prone to winterkills, an event whereby most of the fish die and frequent bottlenecks occur. In this study, we characterized the genetic population structure of brook stickleback among several lakes, finding that the species is hierarchically influenced by within‐lake characteristics in small‐scale watersheds. Landscape genetic analyses of the role of spatial features found support for basin characteristics associated with genetic diversity and bottlenecks in 20% of the sampled lakes. These results suggest that brook stickleback population genetic patterns may be driven, at least in part, by ecological processes that accelerate genetic drift and landscape patterns associated with reduced dispersal. Collectively, these results reinforce the potential importance of connectivity in the maintenance of genetic diversity, especially in fragmented landscapes.     

Hierarchical population structure and genetic diversity of lake trout (Salvelinus namaycush) in a dendritic system in Northern Labrador

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Genetic and phenotypic variation among Galaxias maculatus populations reflects contrasting landscape effects between northern and southern Patagonia

1. Understanding the influence of landscape characteristics on genetic and phenotypic intraspecific variability can yield insights into how evolutionary processes work as well as provide essential information for the conservation of biodiversity. 2. Our aim was to compare the genetic structure and phenotypic variation among Galaxias maculatus populations inhabiting two Atlantic Ocean river basins in Patagonia in relation to historical and contemporary landscape characteristics associated with latitude. 3. Population genetic analysis (based on eight microsatellite loci, 505 individuals) indicates that genetic structure is more pronounced in the Río Negro basin (RN) at 39–41°S (10 localities) than in the southernmost Santa Cruz River basin (SCR) at 49–50°S (seven localities). Spatial autocorrelation analysis showed different effects of geographic distance in shaping population differentiation patterns in the two basins. 4. While in northern Patagonia, fragmented populations could have survived the severity of Quaternary climate cycles, at higher latitudes G. maculatus populations were probably extirpated by extensive ice sheets. Extant populations in the upper reaches of the southernmost basin probably originated from refugia close to the Atlantic Ocean. 5. Based on otolith microchemistry, we have documented facultative diadromy for the first time for the species in the SCR basin, while no evidence of migration to the sea was found in individuals from the RN basin. Vertebral number increased with latitude, and within the SCR basin, the higher counts are possibly associated with a migratory life style.     

Metapopulation dynamics of a diadromous galaxiid fish and potential effects of salmonid aquaculture

1. Direct ecological effects of biological invasions have been widely documented, but indirect genetic effects on native species are poorly known. In many cases, this is because of the lack of information on the genetic structure of species affected by invasions. 2. We used microsatellite DNA loci to estimate the genetic structure and gene flow patterns of Galaxias maculatus, a galaxiid fish endemic to the southern hemisphere, which is increasingly being threatened by salmonid invasions. 3. Analysis of nine diadromous populations of G. maculatus in Chilean Patagonia (an area heavily impacted by farming of non‐native salmonids) indicates that dispersal is mostly a passive process, seemingly driven by wind and currents and resulting in high gene flow and weak population structuring. 4. Gene flow was asymmetrical, with three populations acting as sources and six populations acting as sinks. Sinks had lower habitat quality and had a greater incidence of adults than sources, which consisted mostly of juveniles. 5. Rivers invaded by salmonid escapees experienced significantly higher aquaculture pressure than rivers where salmonid escapees were apparently absent, but no effect on genetic diversity of G. maculatus could be detected. 6. We discuss whether salmonid aquaculture might affect the demography and connectivity of galaxiid metapopulations: indirectly through habitat alteration and directly through escapes of predatory fish.     

The interplay of dispersal limitation,rivers, and historical events shapes the genetic structure of an Amazonian frog

Disentangling the impact of landscape features such as rivers and historical events on dispersal is a challenging but necessary task to gain a comprehensive picture of the evolution of diverse biota such as that found in Amazonia. Adenomera andreae, a small, territorial, terrestrial frog species of the Amazonian forest represents a good model for such studies. We combined cytochrome b sequences with 12 microsatellites to investigate the genetic structure at two contrasted spatial scales in French Guiana: along a ～6‐km transect, to evaluate dispersal ability, and between paired bank populations along a ～65‐km stretch of the Approuague river, to test the effect of rivers as barriers to dispersal. We observed significant spatial genetic structure between individuals at a remarkably small geographical scale, and conclude that the species has a restricted dispersal ability that is probably tied to its life‐history traits. Mitochondrial and microsatellite data also indicate a high level of differentiation among populations on opposite banks of the river, and, in some cases, among populations on the same riverbank. These results suggest that the observed population structure in A. andreae is the result of restricted dispersal abilities combined with the action of rivers and Quaternary population isolation. Given that Amazonia hosts a great portion of anurans, as well as other small vertebrates, that display life‐history traits comparable with A. andreae, we argue that our analyses provide new insights into the complex interactions among evolutionary processes shaping Amazonian biodiversity. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 356–373.     

A wide geographical survey of mitochondrial DNA variation in the great spotted woodpecker complex,Dendrocopos major (Aves: Picidae)

One of the fundamental goals of phylogeographical studies should be to achieve a comprehensive geographical sampling of any investigated group. In this study, we conducted the most comprehensive geographical investigation to date for the great spotted woodpecker complex (Dendrocopos major), including populations from North Africa and Eurasia [including specimens from China, Japan and southern Caucasia (Anatolia, Azerbaijan and Iran)], in order to evaluate its genetic structure and population history. At the same time, we tested species limits within the D. major complex, which currently includes 14 recognized subspecies based on morphology and coloration. We based our study on haplotypes for the mitochondrial gene NADH dehydrogenase subunit 2 (ND2). Most haplotypes were obtained from museum toe pads, although we also used some previously published data. We also tested gene flow through MDIV, and estimated divergence dates among lineages using BEAST. The analysis of 352 base pairs of the ND2 gene from 155 individuals sampled from 33 populations showed significant phylogeographical structure across the breeding range. Our results found four distinct and reciprocally monophyletic clades: China, Japan, Iran–Azerbaijan and Eurasia–North Africa, with no phylogeographical structure within them. Coalescent‐based gene flow analysis showed restricted gene flow between China and Japan and between Japan and Eurasia. On the basis of the gene flow and phylogenetic analysis results, we propose the recognition of at least four different species within the complex. We also propose that, within the Eurasia–North Africa clade, a rapid population expansion through ‘leading edge expansion’ from refugia in Iberia, Kursk and North Africa, as well as irruptive and loop migration, can explain the lack of phylogeographical structure. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Where do you come from,where do you go? Directional migration rates in landscape genetics

Identifying landscape elements that influence gene flow and migration in wild species is the current main topic of landscape genetics. Most landscape genetic studies infer gene flow and migration from genetic distances among populations or individuals and statistically relate these measurements to landscape composition and configuration. This approach assumes symmetrical gene flow between pairs of populations. Such an assumption, however, will often be violated, especially in source–sink systems. Source populations provide more emigrants than they receive immigrants, and sink populations get many immigrants, but release few emigrants. Source–sink dynamics cannot be explored using common landscape genetic approaches relying on genetic distances. In this issue of Molecular Ecology, Andreasen et al. ( 2012 ) apply an alternative approach allowing them to infer asymmetrical migration. They use a Bayesian assignment test among objectively defined populations of mountain lions (Puma concolor) in western USA to estimate recent and directional migration rates. The study shows that an area with a high amount of wildlife refuges and low hunting pressure harbours a source population for mountain lion dispersal, while areas with high hunting pressures form sink populations; a result helpful in making informed decisions in conservation management.     

Inferring the evolutionary history of divergence despite gene flow in a lizard species,Scincella lateralis (Scincidae), composed of cryptic lineages

Although recent radiations are fruitful for studying the process of speciation, they are difficult to characterize and require the use of multiple loci and analytical methods that account for processes such as gene flow and genetic drift. Using multilocus sequence data, we combine hierarchical cluster analysis, coalescent species tree inference, and isolation‐with‐migration analysis to investigate evolutionary relationships among cryptic lineages of North American ground skinks. We also estimate the extent that gene flow has accompanied or followed diversification, and also attempt to account for and minimize the influence of gene flow when reconstructing relationships. The data best support seven largely parapatric populations that are broadly concordant with mitochondrial (mt)DNA phylogeography throughout most of the species range, although they fail to fully represent extensive mtDNA divergence along the Gulf Coast. Relationships within and among three broad geographical groups are well supported, despite evidence of gene flow among them. Rejection of an allopatric divergence model partially depends on the inclusion of samples from near parapatric boundaries in the analyses, suggesting that allopatric divergence followed by recent migration may best explain migration rate estimates. Accounting for geographical variation in patterns of gene flow can improve estimates of migration–divergence parameters and minimize the influence of contemporary gene flow on phylogenetic inference. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Variation in Life History of Land-Locked Lacustrine and Riverine Populations of Galaxias maculatus (Jenyns 1842) in Western Australia

Galaxias maculatus is one of the most naturally widely distributed species in the world yet there is no published literature on the biology of Western Australian populations. Galaxias maculatus in the rivers of the south coast of Western Australia inhabit an environment that is variable and at times unpredictable. By examining trends in gonadal development, lengths at first maturity, growth and appearance and persistence of larvae of G. maculatus in two saline rivers (Jerdacuttup River and Oldfield River) and one freshwater lake (Moates Lake), the life histories of populations in contrasting environments were determined. The stable conditions that prevail in the low salinity, cool waters of Moates Lake have fostered an extremely protracted breeding and larval recruitment period (year round) in comparison to limited recruitment in the riverine environments which experience less predictable flow events and water quality (salinity). An upstream migration for breeding in the Jerdacuttup and Oldfield rivers is similar to land-locked G. maculatus in south-eastern Australia and is a reversal of the downstream migration in Moates Lake or populations with marine larval dispersal, i.e. diadromous populations. Differences in population demographics existed between these habitats, with smaller maximum sizes and significantly smaller sizes at maturation occurring in the rivers compared to the lake. In Moates Lake approximately 93, 6 and 1% were 0+, 1+ and 2+, respectively; while cohort progression in the rivers suggests that most fish do not live beyond their first year. As an adaptable opportunist, G. maculatus can modify its life history strategy at a local level to persist in varied and sometimes unpredictable environments.     

Phenotypic and genetic differentiation between diadromous and landlocked puyen Galaxias maculatus

This study reports the phenotypic and genetic differences between individuals of puyen Galaxias maculatus from two sites in the same river basin in Tierra del Fuego National Park, southern South America. Individuals from the two sampling sites presented morphometric and genetic differences. The morphometric differences indicated that individuals from Laguna Negra (LN) were short and more robust and had large eyes, whereas those from Arroyo Negro (AN) were thin and elongated and had small eyes. Genetic differences showed that AN individuals had a greater genetic structuration and an older demographic history than LN individuals. The results of this study affirmed that the individuals from the two sampling sites belong to different populations with a high degree of isolation. The demographic history could indicate that the individuals of G. maculatus which migrated to northern areas during the last glaciation settled in the Beagle Channel after its formation. The LN population could have originated after the retreat of the glaciers, migrating from AN.     

Genetic variation,population structure and cryptic species within the black mudfish,Neochanna diversus,an endemic galaxiid from New Zealand

To investigate the phylogenetic relationships and geographical structure among landlocked populations of the black mudfish, Neochanna diversus, mitochondrial DNA nucleotide sequence data were sampled from seven populations from the Waikato and Northland regions of New Zealand. The complete D-loop region was sequenced from 70 individuals, with 913 bp from the tRNA-pro end used in population and phylogenetic analysis. A tandem repeat array, which ranged in size up to 200 bp, was found in most populations at the 3′ end of the D-loop that was not able to be aligned for analysis. Of the seven sites sampled, two from Northland exhibited significant sequence divergence from all other sites. There was also a clear distinction among remaining Northland sites and those from the Waikato. An additional 518 bp segment of the 16S region was sequenced from all sites and compared with the other New Zealand mudfish species, N. apoda, N. burrowsius and the Tasmanian mudfish Galaxias (Neochanna) cleaveri using Galaxias maculatus as an outgroup. Both D-loop and 16S sequence data provided strong evidence for a cryptic species of mudfish present in Northland. The significant genetic structure apparent in the black mudfish appears most probably to be attributed to geological conditions during the Pliocene, where peat wetlands became apparent in the Waikato while Northland consisted of disjunct ‘islands’. Conservation and management of these populations must take into account the historical processes that have shaped these patterns of genetic diversity.     

How genetically variable are Neottia ovata (Orchidaceae) populations in northeast Poland?

Using 32 allozyme loci, we examined the genetic diversity of ten populations of Neottia ovata differing in size and located in different regions of northeast Poland. Within‐population genetic variation was low (P_pl = 9.4–31.2%, A = 1.09–1.34 and H_E = 0.044–0.128) relative to taxa with similar life histories. In the majority of N. ovata populations (excluding those in Biebrza), we noted high genotypic diversity (0.49?1.00) and high proportions of unique genotypes (86–100%). Neottia ovata shows a strong pattern of genetic differentiation among populations in northeast Poland, reflected in the high overall F_ST value (0.409). There was a weak, but significant, relationship between genetic and geographical distance (r = 0.09, P < 0.05). We discuss the breeding system, small population sizes and population subdivision as the most important factors affecting the genetic diversity of this species. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 170 , 40–49     

Testing the ‘Pleistocene species pump’ in alpine habitats: lineage diversification of flightless ground beetles (Coleoptera: Carabidae: Nebria) in relation to altitudinal zonation

Alpine species often have similar demographic responses to Pleistocene climate changes, but exhibit different spatial patterns of genetic diversity. Using a comparative phylogeographical approach, we examined the factors influencing lineage formation in three alpine carabid beetles of the genus Nebria Latreille inhabiting the California Sierra Nevada. These flightless beetles differ in altitudinal zonation and habitat preferences, but overlap spatially, have limited dispersal capacities and share life history characteristics. Species distribution modelling predicted decreasing population connectivity in relation to increasing altitudinal preferences. Diversity patterns at the cytochrome oxidase subunit I gene revealed north–south genetic structure and recent population growth in all three species. The high‐elevation‐restricted species, Nebria ingens Horn, exhibited a deep phylogeographical split, morphological divergence and evidence of limited, unidirectional gene flow towards the south. This was supported by additional data from three nuclear genes and isolation with migration analysis. Nebria spatulata Van Dyke, inhabiting an intermediate altitudinal range, exhibited fixed morphological differences between northern and southern populations, but showed limited structure. The broadly distributed Nebria ovipennis LeConte showed less structure and lacked morphological variation. Diversification of these Nebria species supports the role of altitudinal zonation in lineage formation and is consistent with the Pleistocene species pump model. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

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, ?? , ??–??.     

Effects of ultraviolet radiation on the eggs of landlocked Galaxias maculatus (Galaxiidae, Pisces) in northwestern Patagonia

• 1 Ultraviolet radiation (UVR) damages early life stages of several fish species. Galaxias maculatus is a small catadromous fish, with landlocked forms occurring in many lakes within the Nahuel Huapi National Park (Patagonia, Argentina). In this work, the vulnerability of G. maculatus eggs exposed to both natural and artificial UVR was investigated in relation to water transparency.
• 2 Field experiments were performed in two lakes differing in UVR attenuation. Galaxias maculatus eggs were exposed to in situ levels of UVR in quartz tubes incubated at various depths. For laboratory experiments, the eggs were exposed to five levels of artificial UVB radiation.
• 3 Exposure to natural UVR causes various degrees of egg mortality depending on water transparency and incubation depth. In the less transparent lake (K_d320 = 3.08 m^‐1), almost complete mortality was observed near the surface. At a depth of 43 cm the observed mortality was only 22%, but was still significantly different from the dark control. In the most transparent lake (K_d320 = 0.438 m^‐1), almost total mortality was observed in tubes incubated at 2.56 m or shallower. A gradual decline in mortality was recorded from that depth to 3.78 m where the values approached those in the dark control treatments.
• 4 A monotonic relationship between mortality and UV exposure could be observed both in field and laboratory experiments. Using the results from field incubations, a LD₅₀ of 2.5 J cm^‐2 nm^‐1 was estimated. In a few mountain lakes, this value would be exceeded even if the eggs were laid at the maximum depth of the lake. Thus UVR seems a sufficient cause to explain the absence of G. maculatus populations in some mountain lakes. For most lakes, however, UVR is probably one of several important environmental factors, which together determine the habitat suitability.

     

Cranial distinctiveness in the Apennine brown bear: genetic drift effect or ecophenotypic adaptation?

Molecular studies highlighted a strong genetic affinity between the remnant and isolated population of the Apennine brown bear and other southern European populations. Despite this genetic closeness a recent morphometric study revealed a marked phenotypic distinctiveness of the Apennine population, supporting the reinstatement of a distinct taxon (Ursus arctos marsicanus). By building upon previous morphological analyses, we adopted geometric morphometrics to better investigate the skull morphology of the Apennine brown bear with reference to the other, closely related southern European populations. Both skull shape and size differences confirmed the strong divergence of U. arctos marsicanus. In particular, the Apennine bears are characterized by an enlargement of the supraorbital apophysis and a larger distance across the zygomatic arches. Furthermore, our analyses highlighted significant shape differences of the first upper molar in the Apennine bears. Our results suggest that the Apennine bears underwent a rapid morphological change, possibly driven by genetic drift and local selective pressures. Because the greatest morphological differentiation is likely to be related to the muscles involved in mastication, we hypothesize that local selective pressures might be related to a shift in food habits, with highly reduced depredation and feeding on large carcasses in favour of vegetation and hard mast (beech nuts and acorns). These results suggest an adaptive distinctiveness of the Apennine bears, which should be carefully considered in any management and conservation action addressed to this highly endangered population. Although more in‐depth molecular studies are required to better assess the taxonomic and genetic status of the Apennine brown bear population, our study emphasizes the importance of morphological analyses as a complementary tool for a more thorough characterization of variation and divergence in endangered taxa. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.