High similarity of genetic population structure in the false clown anemonefish (<Emphasis Type="Italic">Amphiprion ocellaris</Emphasis>) found in microsatellite and mitochondrial control region analysis

Many studies, using various marker systems, have been conducted on the genetic population structure of marine organisms to reveal connectivity among locations and dispersal capabilities. Although mitochondrial sequence markers are widely used, their accuracy is controversially discussed in the context of small scale population genetic discrimination. In the present study, the genetic population structure of the False Clown Anemonefish (Amphiprion ocellaris) in the Indo-Malay Archipelago was revealed by screening six microsatellite loci. Results were congruent to previous mitochondrial control region results, with three major genetic breaks within the Indo-Malay Archipelago. Similar to the mitochondrial DNA (mtDNA) analysis, microsatellite data showed a correlation of genetic structure to historical ocean basin separation during Pleistocene sea level low stands, geographic distance, and dominant current patterns. However, microsatellite divergences are not as deep as the mtDNA divergence, suggesting either that admixture of mtDNA lineages is slower than that of nuclear microsatellites, providing a rather historic picture of separation, or the stronger differentiation signal is due to lower effective population sizes presented by mtDNA. As well, the microsatellite analysis did not give a better resolution on the small scale as expected. This study showed that depending on the genetic markers used, different stages of population separation might be illuminated.     

Matrilineal genetic structure and female-mediated gene flow in red grouse (Lagopus lagopus scoticus): an analysis using mitochondrial DNA

Abstract.— DNA sequence variation at the hypervariable 5'end of the mitochondrial control region was examined in 247 individuals to detect genetic divergence among 14 populations of red grouse ( Lagopus lagopus scoticus ) in northeastern Scotland. Ten haplotypes were resolved, several of which were shared among populations. Analysis of molecular variance, Nei's yST, and a cladistic estimate of the amount of gene flow indicated a lack of overall population differentiation. Patterns of overall panmixia are in stark contrast to previous reports of localized subdivision among the same set of populations detected using hypervariable microsatellite markers. Because grouse cocks are territorial and show extreme natal philopatry and females are the dispersing sex, such discordance could be explained by sexbiased dispersal, with extensive female-mediated gene flow preventing mitochondrial DNA divergence. However, it is difficult to reconcile how effective dispersal of females would not homogenize both mitochondrial and nuclear structure simultaneously. We use a model that examines the spatial and temporal dynamics of diparentally and uniparentally inherited genes to show that, under realistic ecological scenarios and with specific differences in the dispersal of males and females, the local effective size of the nuclear genome can be less than that of the mitochondrial and the patterns of structuring we observe are meaningful.     

Genetic evidence for spatio‐temporal changes in the dispersal patterns of two sympatric African colobine monkeys

Western black‐and‐white colobus and Temmink's red colobus are two forest‐dependent African primates with similar ecological requirements, often found in sympatry. Their most striking difference lies in their social system: black‐and‐white colobus live in small groups with mainly male‐mediated dispersal but where females can also disperse, whereas red colobus live in larger groups with males described as philopatric. To investigate whether genetic evidence supports the reported patterns of dispersal based on observational data, we examined eight black‐and‐white and six red colobus social groups from Cantanhez National Park, Guinea‐Bissau. Microsatellite markers revealed a lack of sex‐biased dispersal for black‐and‐white colobus. Gene flow, mainly mediated by females, better explained the genetic patterns found in red colobus, with some evidence for less extensive male dispersal. In contrast to the microsatellite data, low mitochondrial diversity for the black‐and‐white colobus suggests that historical and/or long‐range male‐mediated gene flow might have been favored. In red colobus, the co‐existence of three divergent mitochondrial haplogroups suggests that the Cantanhez population contains a secondary contact zone between divergent lineages that evolved in allopatry. Female‐biased dispersal in this species may be a major factor contributing to the colonization by such differentiated mitochondrial lineages in the region. Overall, we find evidence for a spatio‐temporal change in the dispersal patterns of the colobus monkeys of Cantanhez, with mitochondrial DNA indicating dispersal by mainly a single sex and microsatellite data suggesting that recently both sexes appear to be dispersing within the population. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.     

Weak large‐scale population genetic structure in a philopatric seabird,the European Shag Phalacrocorax aristotelis

Quantifying population genetic structure is fundamental to testing hypotheses regarding gene flow, population divergence and dynamics across large spatial scales. In species with highly mobile life‐history stages, where it is unclear whether such movements translate into effective dispersal among discrete philopatric breeding populations, this approach can be particularly effective. We used seven nuclear microsatellite loci and mitochondrial DNA (ND2) markers to quantify population genetic structure and variation across 20 populations (447 individuals) of one such species, the European Shag, spanning a large geographical range. Despite high breeding philopatry, rare cross‐sea movements and recognized subspecies, population genetic structure was weak across both microsatellites and mitochondrial markers. Furthermore, although isolation‐by‐distance was detected, microsatellite variation provided no evidence that open sea formed a complete barrier to effective dispersal. These data suggest that occasional long‐distance, cross‐sea movements translate into gene flow across a large spatial scale. Historical factors may also have shaped contemporary genetic structure: cluster analyses of microsatellite data identified three groups, comprising colonies at southern, mid‐ and northern latitudes, and similar structure was observed at mitochondrial loci. Only one private mitochondrial haplotype was found among subspecies, suggesting that this current taxonomic subdivision may not be mirrored by genetic isolation.     

Intraspecific variation,sex-biased dispersal and phylogeography of the eastern grey kangaroo (Macropus giganteus)

Genetic information has played an important role in the development of management units by focusing attention on the evolutionary properties and genetics of populations. Wildlife authorities cannot hope to manage species effectively without knowledge of geographical boundaries and demic structure. The present investigation provides an analysis of mitochondrial DNA and microsatellite data, which is used to infer both historical and contemporary patterns of population structuring and dispersal in the eastern grey kangaroo (Macropus giganteus) in Australia. The average level of genetic variation across sample locations was one of the highest observed for marsupials (h=0.95, HE=0.82). Contrary to ecological studies, both genic and genotypic analyses reveal weak genetic structure of populations, where high levels of dispersal may be inferred up to 230 km. The movement of individuals was predominantly male-biased (average Nem=22.61, average Nfm=2.73). However, neither sex showed significant isolation by distance. On a continental scale, there was strong genetic differentiation and phylogeographic distinction between southern (TAS, VIC and NSW) and northern (QLD) populations, indicating a current and/or historical restriction of gene flow. In addition, it is evident that northern populations are historically more recent, and were derived from a small number of southern founders. Phylogenetic comparisons between M. g. giganteus and M. g. tasmaniensis indicated that the current taxonomic status of these subspecies should be revised as there was a lack of genetic differentiation between the populations sampled.     

Effects of habitat fragmentation and changes of dispersal behaviour after a recent population decline on the genetic variability of noncoding and coding DNA of a monogamous Malagasy rodent

While interactions among demography, behaviour and genetic structure are well-documented for neutral genetic markers, the role of these parameters and the effects of genetic drift and selection are considerably less well understood in functional genes, such as the major histocompatibility complex (MHC). In this study, the consequences of habitat fragmentation and the effects of a current population decline on noncoding (mitochondrial DNA) and two coding MHC loci (DQA, DRB) with different functional importance were investigated in the small remnant subdivided population of the endangered Malagasy giant jumping rat (Hypogeomys antimena). Both neutral and selective markers revealed a significant genetic differentiation between the two remnant subpopulations. The FST values were much lower in the MHC DQA and DRB genes than in the mitochondrial data. The MHC DRB loci display the effects of both balancing selection (high sequence diversity, four times higher nonsynonymous than synonymous substitutions in the functionally important antigen-binding site positions, twice the average heterozygosity of individual amino acids at the positions identified as part of the antigen-binding site (ABS) than those outside the ABS and nonselective forces including genetic drift. Simultaneously with a current population decline offspring reduced their dispersal distances. No substantial effects were detected within the first 6 years of reduced gene flow in either mitochondrial or MHC markers.     

Loss of genetic diversity in an outbreeding species: small population effects in the African wild dog <Emphasis Type="Italic">(Lycaon pictus</Emphasis>)

Genetic studies on the endangered African wild dog (Lycaon pictus) have primarily focused on the few remaining large and viable populations. However, investigations on the many isolated small African wild dog populations might also be informative for species management because the majority of extant populations are small and may contain genetic variability that is important for population persistence and for species conservation. Small populations are at higher risk of extinction from stochastic and deterministic demographic processes than larger populations and this is often of more immediate conservation concern than loss of genetic diversity, particularly for species that exhibit out-breeding behaviour such as long distance dispersal which may maintain gene flow. However, the genetic advantages of out-breeding behaviour may be reduced if dispersal is compromised beyond reserve borders (edge effects), further weakening the integrity of small populations. Mitochondrial DNA and 11 microsatellite genetic markers were used to investigate population genetic structure in a small population of out-breeding African wild dogs in Zambia, which occupies an historical dispersal corridor for the species. Results indicated the Zambian population suffered from low allelic richness, and there was significant evidence of a recent population bottleneck. Concurrent ecological data suggests these results were due to habitat fragmentation and restricted dispersal which compromised natural out-breeding mechanisms. This study recommends conservation priorities and management units for the African wild dog that focus on conserving remaining levels of genetic diversity, which may also be applicable for a range of out-breeding species.     

Habitat structure and the dispersal of male and female bottlenose dolphins (Tursiops truncatus)

Bottlenose dolphins (Tursiops truncatus) are widely distributed and a high degree of morphometric and genetic differentiation has been found among both allopatric and parapatric populations. We analysed 145 samples along a contiguous distributional range from the Black Sea to the eastern North Atlantic for mitochondrial and nuclear genetic diversity, and found population structure with boundaries that coincided with transitions between habitat regions. These regions can be characterized by ocean floor topography, and oceanographic features such as surface salinity, productivity and temperature. At the extremes of this range there was evidence for the directional emigration of females. Bi-parentally inherited markers did not show this directional bias in migration, suggesting a different dispersal strategy for males and females at range margins. However, comparative assessment based on mitochondrial DNA and nuclear markers indicated that neither sex showed a strong bias for greater dispersal on average. These data imply a mechanism for the evolutionary structuring of populations based on local habitat dependence for both males and females.     

Phylogeography of a host-specific insect: genetic structure of Ips typographus in Europe does not reflect past fragmentation of its host

The phylogeography of the bark beetle Ips typographus was assessed using five microsatellite markers. Twenty-eight populations were sampled throughout Europe on the host tree Picea abies . I. typographus showed very low levels of genetic diversity, and the study revealed a lack of genetic structure across Europe. No significant barrier to gene flow was found, even though P. abies has a fragmented distribution. A weak but significant effect of isolation by distance was found. These results suggest a high dispersal capacity of I. typographus , which leads to low genetic differentiation between populations. Its high dispersal capacity is likely to have prevented I. typographus from developing important local adaptations to its host, which would have influenced its genetic structure. The nuclear data was compared to previously published mitochondrial data that showed strong differentiation between Central–Northern European populations and Russian–Baltic populations, and a founder effect in Scandinavia, probably reflecting the postglacial history of I. typographus . Discrepancies between nuclear and mitochondrial markers could be due to the maternal inheritance of mitochondrial DNA, and to sex-biased dispersal in I. typographus . The overall low genetic diversity observed on both markers on a large geographical scale is discussed. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 239–246.     

Spatial structure of lemming populations (Dicrostonyx groenlandicus) fluctuating in density

The pattern and scale of the genetic structure of populations provides valuable information for the understanding of the spatial ecology of populations, including the spatial aspects of density fluctuations. In the present paper, the genetic structure of periodically fluctuating lemmings (Dicrostonyx groenlandicus) in the Canadian Arctic was analysed using mitochondrial DNA (mtDNA) control region sequences and four nuclear microsatellite loci. Low genetic variability was found in mtDNA, while microsatellite loci were highly variable in all localities, including localities on isolated small islands. For both genetic markers the genetic differentiation was clear among geographical regions but weaker among localities within regions. Such a pattern implies gene flow within regions. Based on theoretical calculations and population census data from a snap-trapping survey, we argue that the observed genetic variability on small islands and the low level of differentiation among these islands cannot be explained without invoking long distance dispersal of lemmings over the sea ice. Such dispersal is unlikely to occur only during population density peaks.     

Very low genetic variability in the Indian queenless ant Diacamma indicum

Abstract We developed microsatellite markers and combined them with mitochondrial markers to analyse the population genetic structure of the queenless ant Diacamma indicum. This species, lacking winged queens, is likely to have a restricted female dispersal but exhibits various life history traits suggesting higher dispersal abilities than the other Diacamma species. Only 4 of 11 microsatellites were polymorphic and only 1 had more than 4 alleles over 166 individuals originating from 7 populations from the south of India. Only one mitochondrial DNA (mtDNA) haplotype was detected throughout India (including one population in the north) and Sri Lanka. Such a level of polymorphism is particularly low compared with other Diacamma species having much smaller ranges in the south of India. A strong genetic differentiation was observed between populations separated by more than a few kilometres. We also analysed the genetic differentiation between the Indian populations and two populations from the Japanese island of Okinawa, which are morphologically similar and might belong to the same species. The genetic differentiation was high for both markers, suggesting an absence of ongoing gene flow between these populations.     

Genetic diversity and spatial structure of the Rufous‐throated Antbird (Gymnopithys rufigula), an Amazonian obligate army‐ant follower

Amazonian understory antbirds are thought to be relatively sedentary and to have limited dispersal ability; they avoid crossing forest gaps, and even narrow roads through a forest may limit their territories. However, most evidence for sedentariness in antbirds comes from field observations and plot‐based recapture of adult individuals, which do not provide evidence for lack of genetic dispersal, as this often occurs through juveniles. In this study, we used microsatellite markers and mitochondrial control‐region sequences to investigate contemporary and infer historical patterns of genetic diversity and structure of the Rufous‐throated Antbird (Gymnopithys rufigula) within and between two large reserves in central Amazonia. Analyses based on microsatellites suggested two genetically distinct populations and asymmetrical gene flow between them. Within a population, we found a lack of genetic spatial autocorrelation, suggesting that genotypes are randomly distributed and that G. rufigula may disperse longer distances than expected for antbirds. Analyses based on mitochondrial sequences did not recover two clear genetic clusters corresponding to the two reserves and indicated the whole population of the Rufous‐throated Antbird in the region has been expanding over the last 50,000 years. Historical migration rates were low and symmetrical between the two reserves, but we found evidence for a recent unilateral increase in gene flow. Recent differentiation between individuals of the two reserves and a unilateral increase in gene flow suggest that recent urban expansion and habitat loss may be driving changes and threatening populations of Rufous‐throated Antbird in central Amazonia. As ecological traits and behavioral characteristics affect patterns of gene flow, comparative studies of other species with different behavior and ecological requirements will be necessary to better understand patterns of genetic dispersal and effects of urban expansion on Amazonian understory antbirds.     

Dispersal and population structure of a New World predator, the army ant Eciton burchellii

The army ant Eciton burchellii is probably the most important arthropod predator in the Neotropics, and many animal species depend upon it. Sex-biased dispersal with winged males and permanently wingless queens may render this species especially sensitive to habitat fragmentation and natural barriers, which might have severe impacts on population structure and lead to population decline. Using nuclear microsatellite markers and mitochondrial sequences, we investigated genetic differentiation in a fragmented population in the Panama Canal area. While nuclear markers showed little differentiation between subpopulations (F(ST) = 0.017), mitochondrial differentiation was maximal in some cases (Phi(ST) = 1). This suggests that, while females are not capable of crossing barriers such as large rivers, flying males are able to promote nuclear gene flow between the studied forest patches. Consistent with this interpretation, we did not find any evidence for inbreeding or genetic deterioration on Barro Colorado Island over the last 90 years since its formation.     

Genetic evidence for dispersal by both sexes in the Central American Squirrel Monkey, Saimiri oerstedii citrinellus

Sex-biased dispersal (SBD) is common in many vertebrates, including primates. However, dispersal patterns in New World primates may vary among closely related taxa or populations in different local environments. Here, we test for SBD in an endangered New World primate, the Central American Squirrel Monkey (Saimiri oerstedii citrinellus). Previous studies of behavioral ecology suggest predominantly female dispersal in S.o. oerstedii in the Southern Pacific region of Costa Rica. However, our genetic data do not support strongly female-biased dispersal in S.o. citrinellus in the Central Pacific region. Our tests for SBD using microsatellite data including comparisons of isolation-by-distance, AI(c) , and F(ST) values between males and females were not significant. Also, we found greater population genetic structure in mitochondrial markers than in microsatellite markers, indicative of predominantly male dispersal. We conclude that both sexes disperse in S.o. citrinellus, and that males probably disperse over longer distances. We discuss how spatial and temporal variation among local populations should be taken into account when studying dispersal patterns and especially sex bias.     

Population genetic structure, gene flow and sex-biased dispersal in frillneck lizards (Chlamydosaurus kingii)

By using both mitochondrial and nuclear multiloci markers, we explored population genetic structure, gene flow and sex-specific dispersal of frillneck lizards ( Chlamydosaurus kingii ) sampled at three locations, separated by 10 to 50 km, in a homogenous savannah woodland in tropical Australia. Apart from a recombinant lizard, the mitochondrial analyses revealed two nonoverlapping haplotypes/populations, while the nuclear markers showed that the frillneck lizards represented three separate clusters/populations. Due to the small population size of the mtDNA, fixation may occur via founder effects and/or drift. We therefore suggest that either of these two processes, or a combination of the two, are the most likely causes of the discordant results obtained from the mitochondrial and the nuclear markers. In contrast to the nonoverlapping mitochondrial haplotypes, in 12 out of 74 lizards, mixed nuclear genotypes were observed, hence revealing a limited nuclear gene flow. Although gene flow should ultimately result in a blending of the populations, we propose that the distinct nuclear population structure is maintained by frequent fires resulting in local bottlenecks, and concomitant spatial separation of the frillneck lizard populations. Limited mark–recapture data and the difference in distribution of the mitochondrial and nuclear markers suggest that the mixed nuclear genotypes were caused by juvenile male-biased dispersal.     

Population genetic structure and male-biased dispersal in the queenless ant Diacamma cyaneiventre

In this study we investigated the population genetic structure of the queenless ant Diacamma cyaneiventre. This species, lacking winged queens, is likely to have a restricted female dispersal. We used both mitochondrial and microsatellite markers to assess the consequence of such restricted female dispersal at three geographical scales: within a given locality (< 1 km), between localities within a given region (< 10 km) and between regions (> 36 km). Within a locality, a strong population structure was observed for mitochondrial DNA (mtDNA) whereas weak or nonexistent population genetic structure was observed for the microsatellites (around 5% of the value for mtDNA). Male gene flow was estimated to be about 20-30 times higher than female gene flow at this scale. At a larger spatial scale, very strong genetic differentiation for both markers was observed between localities - even within a single region. Female dispersal is nonexistent at these scales and male dispersal is very restricted, especially between regions. The phylogeographical structure of the mtDNA haplotypes as well as the very low genetic diversity of mtDNA within localities indicate that new sites are colonized by a single migration event from adjacent localities, followed by successive colony fissions. These patterns of genetic variability and differentiation agree with what is theoretically expected when colonization events are kin-structured and when, following colonization, dispersion is mainly performed by males.     

Genetic structure among remnant populations of a migratory passerine,the Northern Wheatear Oenanthe oenanthe

Continuous animal populations often become fragmented due to anthropogenic habitat alterations. These small, fragmented populations are fragile due to demographic and genetic factors, whereas immigration can enhance their long‐term viability. Previously, we showed that high philopatry affected the local dynamics of three small and remnant subpopulations of Northern Wheatears in The Netherlands. Here, we show that these three populations together with an additional larger population in the European lowlands are highly genetically differentiated based on 22 microsatellite markers. In contrast, we found no evidence for differentiation using two mitochondrial DNA markers. An IMa2 analysis indicates that gene flow has occurred regularly among our sampled populations. As immigration of colour‐ringed birds among our sampled populations is rare at best, our results suggest that the populations have recently become isolated from one another. Low dispersal rates in highly mobile birds may occur when suitable habitat becomes highly fragmented, and will accentuate stochastic demographic processes and inbreeding, both reducing population viability. As dispersal rates are low among populations of Northern Wheatears in The Netherlands, there is only a small probability of recolonization of habitat patches where populations have become locally extinct.     

Extensive local‐scale gene flow and long‐term population stability in the intertidal mollusc Katharina tunicata (Mollusca: Polyplacophora)

The dispersal capabilities of intertidal organisms may represent a key factor to their survival in the face of global warming, as species that cannot adapt to the various effects of climate change will have to migrate to track suitable habitat. Although species with pelagic larval phases might be expected to have a greater capacity for dispersal than those with benthic larvae, interspecies comparisons have shown that this is not always the case. Consequently, population genetic approaches are being increasingly used to gain insights into dispersal through studying patterns of gene flow. In the present study, we used nuclear single‐nucleotide polymorphisms (SNPs) and mitochondrial DNA (mtDNA) sequencing to elucidate fine‐scale patterns of genetic variation between populations of the Black Katy Chiton, Katharina tunicata, separated by 15–150 km in south‐west Vancouver Island. Both the nuclear and mitochondrial data sets revealed no genetic differentiation between the populations studied, and an isolation‐with‐migration analysis indicated extensive local‐scale gene flow, suggesting an absence of barriers to dispersal. Population demographic analysis also revealed long‐term population stability through previous periods of climate change associated with the Pleistocene glaciations. Together, the findings of the present study suggest that this high potential for dispersal may allow K. tunicata to respond to current global warming by tracking suitable habitat, consistent with its long‐term demographic stability through previous changes in the Earth's climate. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 589–597.     

Patterns of population subdivision and gene flow in the ant Nothomyrmecia macrops reflected in microsatellite and mitochondrial DNA markers

The Australian endemic ant Nothomyrmecia macrops is renowned for having retained a large proportion of 'primitive' morphological and behavioural characters. Another less studied peculiarity of this species is the production of short-winged (brachypterous) female sexuals, which presumably are poor dispersers. The males, in contrast, bear a full set of normally developed wings and thus may disperse widely. We investigated patterns of genetic differentiation within and among three distantly separated populations in South Australia using nine polymorphic microsatellite loci and four regions of mitochondrial DNA (COI, COII, Cytb, lrRNA). We sampled eight subpopulations, one in the Lake Gilles CP, two near Penong and five around Poochera where distances ranged from 360 km to sites separated by 2-10 km. Only little differentiation was found at the local scale (within the assumed dispersal distance of males) using nuclear markers, whereas the three distant locations were moderately differentiated (FST = 0.06). Mitochondrial DNA genetic structure was much more pronounced on all scales (phiST = 0.98), with regular differences in both haplotype composition and frequency even occurring among closely located sites. This lack of congruence between nuclear and mitochondrial markers strongly suggests limited female dispersal and male-biased gene flow among populations. As to the conservation status of the species there is no evidence for severe population reductions in the recent past, which would have left populations genetically depauperate.     

Genetic structure in the European endemic seabird,Phalacrocorax aristotelis,shaped by a complex interaction of historical and contemporary,physical and nonphysical drivers

Geographically separated populations tend to be less connected by gene flow, as a result of physical or nonphysical barriers preventing dispersal, and this can lead to genetic structure. In this context, highly mobile organisms such as seabirds are interesting because the small effect of physical barriers means nonphysical ones may be relatively more important. Here, we use microsatellite and mitochondrial data to explore the genetic structure and phylogeography of Atlantic and Mediterranean populations of a European endemic seabird, the European shag, Phalacrocorax aristotelis, and identify the primary drivers of their diversification. Analyses of mitochondrial markers revealed three phylogenetic lineages grouping the North Atlantic, Spanish/Corsican and eastern Mediterranean populations, apparently arising from fragmentation during the Pleistocene followed by range expansion. These traces of historical fragmentation were also evident in the genetic structure estimated by microsatellite markers, despite significant contemporary gene flow among adjacent populations. Stronger genetic structure, probably promoted by landscape, philopatry and local adaptation, was found among distant populations and those separated by physical and ecological barriers. This study highlights the enduring effect of Pleistocene climatic changes on shag populations, especially within the Mediterranean Basin, and suggests a role for cryptic northern refugia, as well as known southern refugia, on the genetic structure of European seabirds. Finally, it outlines how contemporary ecological barriers and behavioural traits may maintain population divergence, despite long‐distance dispersal triggered by extreme environmental conditions (e.g. population crashes).