Land use conversion from peat swamp forest to oil palm agriculture greatly modifies microclimate and soil conditions.

Oil palm (Elaeis guineensis) agriculture is rapidly expanding and requires large areas of land in the tropics to meet the global demand for palm oil products. Land cover conversion of peat swamp forest to oil palm (large- and small-scale oil palm production) is likely to have negative impacts on microhabitat conditions. This study assessed the impact of peat swamp forest conversion to oil palm plantation on microclimate conditions and soil characteristics. The measurement of microclimate (air temperature, wind speed, light intensity and relative humidity) and soil characteristics (soil surface temperature, soil pH, soil moisture, and ground cover vegetation temperature) were compared at a peat swamp forest, smallholdings and a large-scale plantation. Results showed that the peat swamp forest was 1.5-2.3 °C cooler with significantly greater relative humidity, lower light intensities and wind speed compared to the smallholdings and large-scale plantations. Soil characteristics were also significantly different between the peat swamp forest and both types of oil palm plantations with lower soil pH, soil and ground cover vegetation surface temperatures and greater soil moisture in the peat swamp forest. These results suggest that peat swamp forests have greater ecosystem benefits compared to oil palm plantations with smallholdings agricultural approach as a promising management practice to improve microhabitat conditions. Our findings also justify the conservation of remaining peat swamp forest as it provides a refuge from harsh microclimatic conditions that characterize large plantations and smallholdings.

Logged peat swamp forest supports greater macrofungal biodiversity than large-scale oil palm plantations and smallholdings.

Intensive land expansion of commercial oil palm agricultural lands results in reducing the size of peat swamp forests, particularly in Southeast Asia. The effect of this land conversion on macrofungal biodiversity is, however, understudied. We quantified macrofungal biodiversity by identifying mushroom sporocarps throughout four different habitats; logged peat swamp forest, large-scale oil palm plantation, monoculture, and polyculture smallholdings. We recorded a total of 757 clusters of macrofungi belonging to 127 morphospecies and found that substrates for growing macrofungi were abundant in peat swamp forest; hence, morphospecies richness and macrofungal clusters were significantly greater in logged peat swamp forest than converted oil palm agriculture lands. Environmental factors that influence macrofungi in logged peat swamp forests such as air temperature, humidity, wind speed, soil pH, and soil moisture were different from those in oil palm plantations and smallholdings. We conclude that peat swamp forests are irreplaceable with respect to macrofungal biodiversity. They host much greater macrofungal biodiversity than any of the oil palm agricultural lands. It is imperative that further expansion of oil palm plantation into remaining peat swamp forests should be prohibited in palm oil producing countries. These results imply that macrofungal distribution reflects changes in microclimate between habitats and reduced macrofungal biodiversity may adversely affect decomposition in human-modified landscapes.

The systematic position of Hypsugo macrotis (Chiroptera: Vespertilionidae) and a new record from Peninsular Malaysia.

The Southeast Asian species of Hypsugo are rare bats, except for H. cadornae and H. pulveratus, which are distributed throughout the Indomalayan region. Hypsugo macrotis is restricted to Peninsular Malaysia, Sumatra, Java and adjacent islands, and is known only from a handful of specimens. Here we report a new locality record of the species from Seremban, Peninsular Malaysia, which also represents the first known building-dweller colony of any Hypsugo from the region. We discuss the taxonomic status of two morphologically similar species, H. macrotis and H. vordermanni, and provide the first COI and cyt b gene sequences for H. macrotis and reconstruct the species' phylogenetic relationships.

Social organization and genetic structure: insights from codistributed bat populations.

The impact of ecology and social organization on genetic structure at landscape spatial scales, where gene dynamics shape evolution as well as determine susceptibility to habitat fragmentation, is poorly understood. Attempts to assess these effects must take into account the potentially confounding effects of history. We used microsatellites to compare genetic structure in seven bat species with contrasting patterns of roosting ecology and social organization, all of which are codistributed in an ancient forest habitat that has been exceptionally buffered from radical habitat shifts. Over one thousand individuals were captured at foraging sites and genotyped at polymorphic microsatellite loci. Analyses of spatially explicit genotype data revealed interspecies differences in the extent of movement and gene flow and genetic structure across continuous intact forest. Highest positive genetic structure was observed in tree-roosting taxa that roost either alone or in small groups. By comparison, a complete absence of genetic autocorrelation was noted in the cave-roosting colonial species across the study area. Our results thus reveal measurable interspecies differences in the natural limits of gene flow in an unmodified habitat, which we attribute to contrasting roosting ecology and social organization. The consequences of ecology and behaviour for gene flow have important implications for conservation. In particular, tree-roosting species characterized by lower vagility and thus gene flow will be disproportionally impacted by landscape-scale forest clearance and habitat fragmentation, which are prevalent in the study region. Our method also highlights the usefulness of rapid sampling of foraging bats for assaying genetic structure, particularly where roosting sites are not always known.

Molecular phylogeny of hipposiderid bats from Southeast Asia and evidence of cryptic diversity.

Old World leaf-nosed bats (Hipposideridae) are among the most widespread and ecologically diverse groups of insectivorous bats in the Old World tropics. However, phylogenetic relationships in Hipposideridae are poorly resolved at both the generic and species levels, and deep genetic divergence within several Southeast Asian species suggests that current taxonomy underestimates hipposiderid diversity in this region. We used mitochondrial and nuclear sequence data to conduct the first extensive molecular phylogenetic analysis of Southeast Asian hipposiderid bats. Inclusion of multiple samples per taxon allowed testing for evidence of evolutionarily distinct lineages within taxa currently defined as single species. In contrast to earlier phylogenies based on morphometrics, molecular data support monophyly of Hipposideros, but are ambiguous regarding the monophyly of Hipposideridae. With a few exceptions, molecular data also support currently recognized species groups classified by qualitative morphological characters. Widespread paraphyly and polyphyly within many currently recognized species of Hipposideros indicates that evolutionary diversity in the genus is underrepresented by current nomenclature. Comparison of available morphological and echolocation data suggest that both geographic isolation and ecological selection have contributed to the diversification of Southeast Asian hipposiderid bats.

Parallel declines in species and genetic diversity in tropical forest fragments.

The potential for parallel impacts of habitat change on multiple biodiversity levels has important conservation implications. We report on the first empirical test of the 'species-genetic diversity correlation' across co-distributed taxa with contrasting ecological traits in the context of habitat fragmentation. In a rainforest landscape undergoing conversion to oil palm, we show that depauperate species richness in fragments is mirrored by concomitant declines in population genetic diversity in the taxon predicted to be most susceptible to fragmentation. This association, not seen in the other species, relates to fragment area rather than isolation. While highlighting the over-simplification of extrapolating across taxa, we show that fragmentation presents a double jeopardy for some species. For these, conserving genetic diversity at levels of pristine forest could require sites 15-fold larger than those needed to safeguard species numbers. Importantly, however, each fragment contributes to regional species richness, with larger ones tending to contain more species.

Phylogenetic relationships of the Asian palm civets (Hemigalinae & Paradoxurinae, Viverridae, Carnivora).

The Viverridae (Mammalia, Carnivora), one of the least studied groups of carnivorans, include two subfamilies of Asian palm civets: Hemigalinae and Paradoxurinae. The relationships between and within these two subfamilies have never been thoroughly tested using an extensive molecular sample set. In this study, we gathered sequences of four genes (two mitochondrial: Cytochrome b and ND2 and two nuclear: beta-fibrinogen intron 7 and IRBP exon 1) for eight of the eleven extant species representing these two subfamilies. The results showed that: (1) the Asian palm civets (Hemigalinae and Paradoxurinae) have a single origin and form the sister-group of the (Genettinae+Viverrinae) clade, (2) the Hemigalinae (including the otter civet Cynogale bennettii) are monophyletic, (3) the Paradoxurinae are monophyletic and (4) the small-toothed palm civet (Arctogalidia trivirgata) is an early offshoot within the Paradoxurinae. Using a relaxed molecular clock analysis, the differentiation of the (Hemigalinae+Paradoxurinae) was inferred to occur in the Late Oligocene/Early Miocene.

Chemical ecology of fruit bat foraging behavior in relation to the fruit odors of two species of paleotropical bat-dispersed figs (Ficus hispida and Ficus scortechinii).

We investigated the fruit odors of two bat-dispersed fig species in the Paleotropics, in relation to the foraging behavior of fruit bats, to test the following hypotheses: 1) fruit odor plays a critical role for detection and selection of ripe figs by fruit bats; 2) bat-dispersed fig species are characterized by the same, or similar, chemical compounds; and 3) total scent production, in bat-dispersed figs, increases when fruits ripen. We performed bioassays to test the effect of both natural and synthetic fig fruit odors on the foraging behavior of the short-nosed fruit bat (Cynopterus brachyotis)-an important disperser of figs within the study area. Fruit bats responded to both visual and chemical (olfactory) cues when foraging for figs. However, the strongest foraging reaction that resulted in a landing or feeding attempt was almost exclusively associated with the presence of a ripe fruit odor-either in combination with visual cues or when presented alone. Fruit bats also used fruit odors to distinguish between ripe and unripe fruits. By using gas chromatography (GC) and GC/mass spectrometry (MS), a total of 16 main compounds were identified in the ripe fruit odor of Ficus hispida and 13 in the ripe fruit odor of Ficus scortechinii-including alcohols, ketones, esters, and two terpenes. Additional compounds were also recorded in F. hispida, but not identified-four of which also occurred in F. scortechinii. Total scent production increased in both species when fruits ripened. Both natural and synthetic fruit odors resulted in feeding attempts by bats, with no feeding attempts elicited by unscented controls. Reaction rates to natural fruit odors were higher than those to synthetic blends.

Comparative population structure of Cynopterus fruit bats in peninsular Malaysia and southern Thailand.

The extent to which response to environmental change is mediated by species-specific ecology is an important aspect of the population histories of tropical taxa. During the Pleistocene glacial cycles and associated sea level fluctuations, the Sunda region in Southeast Asia experienced concurrent changes in landmass area and the ratio of forest to open habitat, providing an ideal setting to test the expectation that habitat associations played an important role in determining species' response to the opportunity for geographic expansion. We used mitochondrial control region sequences and six microsatellite loci to compare the phylogeographic structure and demographic histories of four broadly sympatric species of Old World fruit bats in the genus, Cynopterus. Two forest-associated species and two open-habitat generalists were sampled along a latitudinal transect in Singapore, peninsular Malaysia, and southern Thailand. Contrary to expectations based on habitat associations, the geographic scale of population structure was not concordant across ecologically similar species. We found evidence for long and relatively stable demographic history in one forest and one open-habitat species, and inferred non-coincident demographic expansions in the second forest and open-habitat species. Thus, while these results indicate that Pleistocene climate change did not have a single effect on population structure across species, a correlation between habitat association and response to environmental change was supported in only two of four species. We conclude that interactions between multiple factors, including historical and contemporary environmental change, species-specific ecology and interspecific interactions, have shaped the recent evolutionary histories of Cynopterus fruit bats in Southeast Asia.

Phylogeny and phylogeography of Old World fruit bats in the Cynopterus brachyotis complex.

Taxonomic relationships within the Old World fruit bat genus, Cynopterus, have been equivocal for the better part of a century. While nomenclature has been revised multiple times on the basis of phenotypic characters, evolutionary relationships among taxa representing the entire geographic range of the genus have not been determined. We used mitochondrial DNA sequence data to infer phylogenetic relationships among the three most broadly distributed members of the genus: C. brachyotis, C. horsfieldi, and C. sphinx, and to assess whether C. brachyotis represents a single widespread species, or a complex of distinct lineages. Results clearly indicate that C. brachyotis is a complex of lineages. C. sphinx and C. horsfieldi haplotypes formed monophyletic groups nested within the C. brachyotis species complex. We identified six divergent mitochondrial lineages that are currently referred to C. brachyotis. Lineages from India, Myanmar, Sulawesi, and the Philippines are geographically well-defined, while in Malaysia two lineages, designated Sunda and Forest, are broadly sympatric and may be ecologically distinct. Demographic analyses of the Sunda and Forest lineages suggest strikingly different population histories, including a recent and rapid range expansion in the Sunda lineage, possibly associated with changes in sea levels during the Pleistocene. The resolution of the taxonomic issues raised in this study awaits combined analysis of morphometric characters and molecular data. However, since both the Indian and Malaysian Forest C. brachyotis lineages are apparently ecologically restricted to increasingly fragmented forest habitat, we suggest that reevaluation of the conservation status of populations in these regions should be an immediate goal.