Bioscience Horizons Advance Access originally published online on April 19, 2009
Bioscience Horizons 2009 2(2):147-154; doi:10.1093/biohorizons/hzp017
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Patterns of genetic diversity in populations of two bat species (Sturnira ludovici and Artibeus toltecus) in Cusuco National Park, Honduras
Department of Biology and Environmental Science, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
* Corresponding author: 4 Villiers Walk, Newbury, Berkshire RG14 6SJ, UK. Tel: +44 01635 821316. Email: claireasher13{at}googlemail.com
Supervisors: Professor Adam Eyre-Walker, Department of Biology and Environmental Science, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK and Dr Kimberley Hunter, Department of Biological Sciences, Salisbury University, Salisbury, Maryland 21801, USA.
| Abstract |
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Habitat loss, disturbance and fragmentation are thought to be major threats to many species, particularly those in habitats that are already rare. In this study, we examined whether habitat disturbance, primarily due to the cultivation of coffee, has had a major impact on populations of two species of bats in a Honduran cloud forest, using genetic diversity as a measure of population health. Bats were selected as the study species because they play a major role in seed dispersal within the tropics. I compared the genetic diversity of two frugivorous bat species, Sturnira ludovici and Artibeus toltecus, between two localities within Cusuco National Park; a buffer zone in which some human activity, including coffee plantations, is allowed, and the core zone in which no disturbance is permitted. Genetic diversity was assessed using intersimple sequence repeats, a technique similar to random amplification of polymorphic DNA (RAPD). I also measured various habitat variables including foliage height diversity (FHD), fruit availability, canopy cover, aspect of slope and angle of slope in the two sites. I found that FHD and fruit availability differed significantly between the two localities, with the buffer zone having higher values for both. Despite these differences in habitat, we found no significant differences in the level of genetic diversity between the two locations for either bat species. This may be because effective population sizes of the bats do not differ significantly between the sites, because of a lag between disturbance and population decline or because migration is sufficiently frequent to homogenize allele frequencies between the localities.
Key words: genetic diversity, bat, cloud forest, conservation, habitat disturbance
| Introduction |
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Collectively, the Americas contain 916 million ha of tropical forest, which is being destroyed faster than on any other continent, at a rate of 10 million ha a year.1 Of the 34 hotspots identified by Conservation International, 8 reside within the Americas.2 Of these, the Mesoamerican hotspot is the largest, and the third largest in the world.
The Mesoamerican hotspot includes most of Central America and contains dry forest, lowland moist forest and montane forest.2 It exhibits extremely high endemism of up to 70% in the richest areas,3 where endemism is defined as the percentage of species whose distribution is confined to that area,4 and may contain as much as 7% of the world's biodiversity.5
Honduras is the second largest country in Central America, and approximately half its land5 is covered by a mosaic of pine-oak forest and montane forest.3 It is home to over 5500 vascular plants, of which 108 are listed as endangered.5 In addition to this, there are 410 known bird and mammal species,5 of which 26 appear on the IUCN red list.6 Despite this, it has been relatively overlooked in biodiversity studies within Mesoamerica. All land higher than 1800 m has been designated as protected,3 and
25% of the country's forests lie within protected areas, covering a total of 2.7 million ha.5 However, there has been little enforcement of these areas and illegal logging is a severe problem.5
Tropical forests can contain hundreds or even thousands of tree species,7 a significant proportion of which use animal-mediated seed dispersal. Between 50% and 90% of tropical shrub and tree species are dependent on frugivorous vertebrates for seed dispersal.8 As well as distributing seeds over a wide area, frugivores are important because the passage of a seed through the digestive tract improves both seed viability and rapidity of germination.7 Compared with other frugivores, birds and bats have the greatest positive effect on germination.7 However, bats are responsible for a greater amount of seed dispersal than birds,9 particularly in disturbed areas, where bats have been found to be the primary seed dispersers.10
Bats are members of the order Chiroptera, one of the most diverse and widely distributed groups of animals.11 They are especially important in Neotropical forests, where they constitute
50% of all mammal species.12 Neotropical bats are members of the family Phylostomidae, of which there are
220 species, comprising 24% of the global total.9
The reliance of many tree species on frugivorous bats for seed dispersal has important implications for conservation and forest regeneration. Experimental exclusion of frugivorous bats resulted in a 30% reduction in seed species richness13 and research suggests that forest regeneration may already be being threatened by reduced seed dispersal.10 Furthermore, it appears that there is a threshold bat population density, below which seed dispersal may cease altogether.7
Frugivorous bats have been found to be particularly tolerant of human disturbance, perhaps because they have relatively general habitat requirements.10 Some studies have even found them to be more abundant in disturbed areas because of the greater availability of fruiting plants.14 However, they may rely upon pristine habitat for roosting sites, and studies on temperate bat species have found that many species have very specific roosting preferences.10 If this is the case, then the loss of pristine forest may impair the ability of frugivorous bats to aid regeneration in disturbed areas resulting in a vicious cycle of habitat degradation. Thus, the effects of human activities on bat species need to be carefully monitored to prevent exacerbation of anthropogenic habitat change.
Bats may be considered keystone species,14 not only because of their indispensable role in seed-dispersal, but also because of their involvement in a variety of ecological processes including pollination and insect population regulation.9 Bats may also be useful as indicator species as they are common and relatively easy to capture.9 Furthermore, bat species richness and diversity in Neotropical forests is positively correlated with measures of vegetation structure.9, 14 Bat species richness is highest in undisturbed forest, and the most abundant species is characteristic of particular levels of disturbance.9 Considering their abundance, and invaluable role in a variety of ecosystem processes, understanding how Neotropical bats are affected by habitat disturbance is crucial to understanding how best to preserve the remaining tropical forests.
Although most studies have used species-richness and abundance estimates to determine the affect of human disturbance on animal and plant populations, genetic methods can also be used to assess these questions. Species with small, or declining, populations are likely to suffer from reduced genetic diversity due to inbreeding and genetic drift.15 Inbreeding has been found to have deleterious effects on a variety of characteristics including sperm production, female fecundity, juvenile and adult survival, and mating ability.15 Furthermore, reduced genetic diversity may adversely affect the ability of a species to adapt to environmental changes.15 Small population size is therefore likely to further increase the chances of extinction.15 Experimental evidence supports this, and a recent comparison of genetic diversity in threatened and unthreatened species found that 77% of threatened species had lower genetic diversity, with an average reduction in heterozygosity of 35%.16 Conservation studies that ignore genetic factors are therefore likely to overestimate the probability of survival for threatened species.17
This study uses intersimple sequence repeats (ISSRs), a polymerase chain reaction (PCR)-based technique, to determine the level of polymorphism in populations of bats living in pristine cloud forest, compared with those living in a human-altered habitat. ISSR18 techniques involve amplification of nuclear DNA using a primer that targets the repeating sequence of microsatellites.19 ISSR is identical to RAPD, except that the primer sequence is based only on the repeating sequence,20 and therefore no information about flanking sequences is required to use the technique.19 ISSRs are therefore simpler and less expensive to use21 and may reveal a greater number of polymorphisms than RAPD.22 ISSRs have been used in a variety of different studies in plants,19, 22, 23 but have rarely been used in vertebrates before.24
I have chosen two common species of frugivorous phyllostomid bat, Sturnira ludovici and Artibeus toltecus, to investigate this. A. toltecus has recently been reclassified into the Dermanura genus, and in some of the literature, is now referred to as Dermanura tolteca. For the purposes of this paper, I will use the original, A. toltecus classification. These two species are among the most abundant species of Neotropical bat.14 A. toltecus is a canopy specialist,9 and fruit choice trials have indicated that A. toltecus preferentially feeds on Constegia volcanalis.25 In contrast, S. ludovici is more generalist,9 feeding on a variety of fruits from both canopy and ground-storey plants.25 However, about half of its diet is composed of fruits of Solanum sp. which are found primarily in disturbed forest.9
I hypothesize that if habitat disturbance has had a major impact on bat populations, then the genetic diversity of S. ludovici and A. toltecus will be significantly lower in the buffer zone than in the core zone of Cusuco National Park.
| Materials and Methods |
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Study Site
Cusuco National Park (Fig. 1) is one of the smallest of the country's protected areas, located in the Paraiso valley near San Pedro Sula, in the Northwest of the Country.26 It was established in 1959 and covers 23 440 ha of land.26 The park predominantly consists of cloud forest, a rare type of evergreen montane forest, which occurs only at sufficiently high altitudes, and in climate conditions which cause regular contact between clouds and the vegetation.27 Cloud forest accounts for
2% of the world's tropical forest, but is known to exhibit exceptionally high endemism.27 Furthermore, cloud forests are home to the wild relatives of many crop plants, including tomato, avocado, cucumber and potato.27 They are also essential in maintaining water supply to local people. For example, 40% of the water supply to the capital, Tegucigalpa, is supplied by cloud forests in neighbouring national parks.27
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Data were collected from two sites within Cusuco National Park; Operation Wallacea Base Camp within the core zone and a village called Buenos Aires in the buffer zone. At each site, bats were captured using mist-nets setup on transects surrounding the site. At each transect, six 6 m x 2.5 m mist-nets with five shelves were set up between the hours of 5 pm and 12 midnight.
For each bat, a 1 mm radius wing-punch was taken and stored in ethanol in a 2.5 ml eppendorf tube. These were transferred back to the laboratory located at base camp. Wing-punches of S. ludovici and A. toltecus were then used for genetic analysis. Five wing-punches were collected for each species at each site, producing a total of 20 wing-punch samples for processing.
Habitat Sampling
Habitat data were collected from two circular plots of 20 and 40 m radius surrounding each mist-netting site. A total of 45 samples were collected at each transect. Of these, 30 samples were collected within a 20 m radius, and a further 15 in a 20–40 m radius. The latter points were then combined with 15 randomly selected samples from the 20 m radius, to produce a total of 30 samples within the 40 m radius.
The position of each sample point was determined using random numbers generated in Microsoft Excel. For each point, a random number between 0 and 1 was generated and multiplied by 360 to produce a bearing from North. A second random number between 0 and 1 was generated and multiplied by 20 to produce a distance of up to 20 m. To collect the samples from the 20 to 40 m radius, 20 m was added to the distance value. These two numbers together determined the position of the sample point with relation to the start point. This distance-based sampling method provides an easy way to determine and locate sample points, and the use of random numbers ensures that the points are selected in an unbiased way and are well distributed across the study area. The start point was selected in order to be as central as possible within the area in which the mist-nets were located. Due to the structure of the terrain, some random points were not accessible because of barriers such as rivers and cliffs. When a point arose that was not usable, it was skipped and the next point in the list was selected.
In order to calculate the foliage height diversity (FHD),28 a 3 m pole, marked into 1 m sections, was used. For each 1 m section, a cylinder of radius 1 m was imagined surrounding the pole, and the number of branches intersecting the cylinder was noted. FHD was calculated as:
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The availability of fruit surrounding the sample point was noted on a nominal scale of low to high. In addition to this, the angle of the steepest slope was measured using a clinometer and the aspect of the slope was measured using a compass. These data were collected to assess whether sunlight exposure has any impact on the bat populations, either directly or indirectly through its impact on the vegetation. Finally, a digital photograph was taken of the sky directly above the sample point in order to calculate the canopy cover. This was achieved using Adobe Photoshop 7.0, which was first used to convert the photograph to black and white, and then produced a histogram showing the number of pixels of each colour. The number of white pixels was then divided by the total to produce a percentage sky visibility value. For each variable, a t-test was used to compare the data collected in the buffer and core zones.
Measuring Genetic Diversity
DNA was extracted from each wing-punch using Qiagen DNeasy kits. Briefly, 180 µl of buffer ATL (a tissue lysis buffer), along with 20 µl of proteinase K was added to the wing-punch and incubated at 56°C for
1 h, until the tissue was completely lysed. Two hundred microlitres of buffer AL (a lysis buffer for DNA purification) and 200 µl of ethanol (95%) were then added and the mixture pipetted into a DNeasy mini spin column. This column was centrifuged at 8000 rpm for 1 min, and the flow-through discarded. Next, the spin column was placed into a new collection tube and 500 µl of wash buffer AW1 was added. Centrifugation was then repeated and the flow-through discarded. Next, 500 µl of wash buffer AW2 was added and the column was centrifuged at 13 000 rpm for 3 min. The flow-through was discarded and the spin column placed in a new collection tube. One hundred microlitres of elution buffer (AE) was added and the mixture was incubated at room temperature for 1 min. The column was then centrifuged at 8000 rpm for 1 min, and the elution process was repeated. The resulting purified DNA was then amplified using an ISSR PCR. This technique uses anonymous dominant markers consisting of repeated sequences to amplify small sections of the DNA.
Following amplification, the DNA was run on a cambrex flash gel (2.2%) to produce a visual representation of the genetic constitution of each individual. ISSR primers consist of short repeating sequences, which bind to complementary microsatellite sequences. Since ISSR primers do not include a flanking region, no prior information about a species is required. A number of ISSR primers were available, and these had to be screened to find ones that successfully bind to the DNA and show polymorphism between individuals. Initially, two samples from S. ludovici were amplified with each of three randomly chosen primers, and the resulting DNA was run on a flash gel. Two of these three primers showed polymorphism, both of which consisted of AG repeats. Based on this, a further three primers, also containing AG repeats were selected and used to amplify DNA from the same two individuals. Of these, one primer showed polymorphism. The three primers used in the study were labelled 834 (AGA GAG AGA GAG AGA GYT), 840 (GAG AGA GAG AGA GAG AYT) and 868 (GAA GAA GAA GAA GAA GAA).
It was noted that the bands on the gels being produced showed poor definition. A review of the literature indicated that a lower annealing temperature might be more suitable for amplifying bat DNA. Other genetic studies of Chiroptera have used annealing temperatures ranging from 4529 to 52°C.30 In an attempt to improve the quality of the images, the PCR annealing temperature was therefore changed from 56 to 44°C and this change was successful. PCR amplifications then began for each of the samples using each of the three suitable primers.
Six cambrex flash gels were run, one for each species with each of the three primers. Photographs of the gels were taken under ultraviolet light. The band positions were then scored using Kodak Digital Science Program, which produced a list of molecular weights for the bands present for each individual based on known molecular weights of reference DNA. These data were then transferred into Microsoft Excel and analysed, scoring each individual for the presence or absence of each band. The results of this were entered into Popgene, which calculated percentage of polymorphism, Nei's diversity index, Shannon–Weiner index for each locus. For each species, an analysis of variance (ANOVA) was performed comparing both Nei's and Shannon–Weiner diversity in the core and buffer zones.
| Results and Discussion |
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To investigate whether the habitat differed between the core and buffer zones, I estimated a number of habitat variables around the four mist-netting sites. I found that FHD and fruit availability (Fig. 2) were significantly greater in the buffer zone sites than the core zone sites. However, it is possible that these differences were due to differences in the slope angle of the two collecting sites, since these also differ significantly in the 20 m radius around the mist-netting sites (Fig. 3).
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Given that there do appear to be differences in the habitat of the core and buffer zones, we might expect there to be differences in the population sizes that each zone can sustain, and therefore differences in the level of genetic diversity. However, I found no evidence to support this conjecture, as neither species showed any significant differences in genetic diversity between the buffer and core zones as measured by Nei's diversity index or Shannon–Weiner index (Fig. 4).
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The habitat sampling in this study was relatively superficial, especially the assessment of fruit availability, which used only a very course measure. However, the sample size achieved was relatively large and was therefore able to detect differences between the two sites. The use of a circular plot from which habitat samples were drawn has the benefit of using a single dimension to define the perimeter of the sample area, making it easy to establish.31 However, one disadvantage with the method used in this study is that the density of sample points within the 40 m radius is much higher in the middle. The use of a square plot with randomly generated coordinates would not suffer from this problem and may have provided a better method for sampling the area.
For the genetic data, I was only able to collect a very small sample size, due to the logistical difficulties of transporting DNA equipment to a remote field site. The data presented in this paper are therefore a very crude representation of the total genetic diversity of bat populations in Cusuco National Park, and it is quite plausible that the absence of a significant result is due to this. However, one success of this project is that I was able to perform genetic analysis in the field, where it was not possible to refrigerate DNA or enzymes.
If there is in fact no difference in genetic diversity between bat populations in the buffer and core zones, there are a number of possible explanations for this result. The effect of habitat destruction on animal populations is likely to show a lag,32, 33 although it is not clear how long this might be. One study found that population decline in Caribou showed a 20-year lag behind disturbance,34 while another study found a lag of just 1–4 years between disturbance and lek disappearance in greater sage-grouse.35 The village of Buenos Aires was established in 1921, before which the area is believed to have been fully forested. The majority of the disturbance in the area occurred between 1936 and 1954, during which time logging was undertaken around Buenos Aires and the south east of the park. Cusuco National Park was established in 1959,26 preventing any further disturbance within the core zone and limiting destruction within the buffer zone to shaded coffee plantations. Thus, it is likely that disturbance of some degree has been occurring for 70 years and that conditions should have remained relatively similar for the last 40 years. From the limited data available, it seems likely that the impact of human activities should be evident in the bat populations now.
Another possible explanation for the result is that the two sample sites do not represent distinct populations and that substantial gene flow is occurring maintaining genetic diversity at a relatively constant level. Alternatively, bats caught within the buffer zone may actually be roosting in the core zone, so they represent the same population as that found in the core zone. Investigations into the home range size of Neotropical bats have been fairly limited. However, studies that have been conducted indicate that most phyllostomid bat species have home ranges of just a few kilometres around their roost sites.36 One study looking at home range size for nine phyllostomid bats found that they range from 0.07 to 1.15 km2, 37 and other studies have found similar results.7, 38
The distance between the two sites in my study is
6 km, and so based on the limited data available, it seems reasonable to conclude that bats caught in the buffer and core zones represent samples from two, at least partially independent populations. However, one study on Artibeus jamaicensis found that it can fly up to 8 km to forage.11 It is not clear whether home ranges of this size are wide-spread among Neotropical bats, and whether either S. ludovici or A. toltecus are likely to have home ranges this large. Only a direct investigation of the home ranges of the two species used in this study can conclusively determine whether the buffer zone and core zone samples represent distinct populations.
According to population genetic theory, a single migrating individual per generation is sufficient to homogenize populations.39 It seems likely that this level of migration could be occurring between the populations in the buffer and core zones. The result of genetic analyses can often be used to calculate the level of gene flow between populations using statistics such as FST. However, this is particularly problematic for dominant markers, such as ISSR markers used in this study.40 Estimating the FST for populations requires that allele frequencies can be inferred, which is not possible with dominant markers, because dominant homozyogotes cannot be distinguished from heterozygotes.40 As such it has not been possible to use statistical tests to analyse the level of migration occurring between populations of S. ludovici and A. toltecus in the buffer and core zones of Cusuco National Park.
Finally, the non-significant result of this study may represent a real absence of differences in genetic diversity between the core and buffer zones because habitat disturbance in the buffer zone is not having a significant effect on populations of S. ludovici and A. toltecus. The suggestion that both S. ludovici and A. toltecus may be able to maintain healthy populations within disturbed forest is congruent with the results of some other studies. For instance, one study found that members of the genus Artibeus, Sturnira and Demanura are common in both pristine forest and shaded coffee plantations.14 Several authors have attributed this to generalist habits, which allow foraging in a variety of habitats.10, 14 Furthermore, one study found that even species with specialist foraging and roosting requirements, such as S. ludovici, may cope well with disturbed habitats.12
Research indicates that some species may actually do better in secondary forest. In particular, Estrada et al.14 found that A. toltecus was most common in shaded coffee plantations. This may be explained by the greater availability of fruiting plants and trees found in disturbed forest,8 which is corroborated by the significantly higher fruit availability in the buffer zone found in this study. Fruit availability may also be more continuous in secondary forest, as successional trees have longer fruiting periods and smaller daily crops.8
However, there is substantial evidence to suggest that not all bat species are so tolerant of habitat disturbance. In general, species that are abundant in pristine forest have been found to cope well or even thrive in secondary forest,12 but less common species may be more vulnerable to habitat changes. Furthermore, a study in Guatemala found that small frugivores were captured most often in fragmented forest where there was a high availability of small-fruited successional plants, whereas larger frugivores were most common in continuous forest as they required larger fruits unique to this habitat.41 Thus, dietary preferences may significantly impact on the ability of frugivorous bats to inhabit secondary forest. This is contrary to the expectation that roosting requirements would represent the most limiting factor in terms of bat abundance in disturbed habitat.
It is important to consider that shaded coffee plantations represent a relatively low-level disturbance, when compared with other practices such as logging. They commonly retain the original canopy of trees as shade for the coffee plants, and as such, canopy species may be particularly unaffected by their presence.9 Shaded coffee plantations also contain high plant diversity and a complex vertical vegetation structure similar to that found in pristine forest.14 A mild effect of shaded coffee plantations on bat populations is supported by the finding that traditional coffee plantations in Mexico support a similar level of bat species diversity as in pristine forest.14 More severe disturbance of the habitat would be expected to have a significant effect on bat populations.
The data presented in this paper are insufficient to conclude whether shaded coffee plantations are having a significant impact on bat species in Cusuco National Park. It is quite possible that the small sample size used in this study resulted in a type II error. Alternatively, a lag between disturbance and population decline and inbreeding effects may have meant that the effects of habitat disturbance are not yet evident in measures of genetic diversity, or gene flow may mean that a comparison between sites is meaningless. Even if the result presented here represents a genuine lack of difference between sites, habitat disturbance may be affecting other bat species in the park. However, the results of this study suggest that the inclusion of buffer zones in national parks may represent a good compromise between the needs of local people for land on which to live and farm, and the need to protect the valuable biodiversity present in the area. Clearly, the value of a buffer zone will vary greatly depending on the requirements of the local people, as different land uses are likely to have significantly different impacts on the biodiversity that is able to survive in buffer zones. The impact of buffer zones on other animal species needs to be investigated before this suggestion can be supported. Where traditional farming practices can maintain, or even promote biodiversity, they should be encouraged over more intensive practices.
A more thorough investigation of the bat populations of the park should aim to collect more DNA samples both from the sites included in this study and from other sites within the core and buffer zones of the park.
Any further studies aiming to quantify the effect of habitat disturbance on these species should also include and analysis of the home ranges of the bat species, either used genetic or observational techniques.
| Funding |
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This research was performed as part of an Undergraduate Dissertation at the University of Sussex, with field work organised by Operation Wallacea.
| Acknowledgements |
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I would like to thank Professor Adam Eyre-Walker, Dr Kimberley Hunter, Dr Richard Field and Peter Long for all their help and advice during this project. I would also like to thank Operation Wallacea for hosting my project, and Instituto Nacional de Conservación y Desarrollo Forestal, Areas Protegidas y Vida Silvestre (ICF) [formally known as Administracion Forestal del Estado—Corporación Hondureña de Desarollo Forestal (AFE-COHDEFOR)] for providing a research permit for the study.
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| Author Biography |
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Claire Asher has recently graduated from the University of Sussex with a first-class degree in Biology. She also received the John Maynard Smith award for the best performance in evolutionary biology. Claire's particular fields of interest are evolutionary theory, conservation genetics and animal behaviour. She began an MSc in Evolutionary and Behaviour ecology at the University of Exeter in October 2008, and intends to do a PhD in the future. Ultimately, Claire aims to become a research scientist studying evolution and genetics.
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