Si Min Lin

Molecular systematics and phylogeography of the gigantic earthworms of the Metaphire formosae species group (Clitellata, Megascolecidae)

The earthworms of the Metaphire formosae species group distributed in Taiwan are members of the Pheretima complex within the Megascolecidae. In this study, the systematics and phylogeography of this species group were investigated using DNA sequences of mitochondrial cytochrome c oxidase subunit I (COI), 16S ribosomal (r)RNA, and NADH dehydrogenase subunit 1 (ND1). The results indicated that the 13 taxa of the M. formosae species group form a clade, including a cryptic species discovered in this study. In addition, Metaphire hengchunensis (James, S.W., Shih, H.-T., Chang, H.-W., 2005. Seven new species of Amynthas (Clitellata: Megascolecidae) and new earthworm records from Taiwan. J. Nat. Hist. 39, 1007-1028) should be regarded as a subspecies of Metaphire paiwanna Tsai, C.-F., Shen, H.-P., Tsai, S.-C., 2000a. Native and exotic species of terrestrial earthworm (Oligochaeta) in Taiwan with reference to Northeast Asia. Zool. Stud. 39, 285-294, Tsai, C.-F., Tsai, S.-C., Liaw, G.-J., 2000b. Two new species of pontandric pheretimoid earthworms belonging to the genus Metaphire (Megascolecidae: Oligochaeta) from Taiwan. J. Nat. Hist. 34, 1731-1741, and Metaphire bununa glareosa Tsai et al. 2000 should be elevated to specific status. Phylogeographical inferences showed that allopatric speciation occurred in this species group during the rapid uplift of the main island of Taiwan between 5.0 and 2.5 million years ago. Our analysis exposes non-monophyly within each of the genera Amynthas and Metaphire, and more generally within the Pheretima complex. Further revisions of this speciose complex are urgently needed.

TWO NEW CRYPTIC SPECIES OF TAKYDROMUS (SQUAMATA: LACERTIDAE) FROM TAIWAN

Two new grass lizard species, previously confused with Takydromus formosanus, were identified in Taiwan using mitochondrial DNA sequences. In the present study, 40 morphological characters and their taxonomic significances were assessed using principal components analysis and discriminant analysis. The three species can be distinguished by morphology of body sizes, dorsal and caudal scales, and most importantly, by male coloration during the breeding seasons. The present study increases the total number of Takydromus to 19 species, of which 10 are insular endemics, with six only occurring in Taiwan.

Strict consistency between genetic and topographic landscapes of the brown tree frog (Buergeria robusta) in Taiwan

Taiwan presents an excellent opportunity to build a phylogeographic paradigm for fine-scaled differentiation occurring within short distances on an single island. Due to the limitation of habitat availability on the island, demographic histories of species in Taiwan were strongly influenced by glacial-interglacial cycles. Nevertheless, there are relatively few studies demonstrating such phylogeographic patterns for islands, especially in subtropical Asia. In this study, we aim to construct the genetic landscape of a philopatric stream frog Buergeria robusta by an intense and fine-scaled collection throughout the island. The deduced genetic landscape of B. robusta presented extremely high congruence with the actual topography of Taiwan. Two major lineages were found on the eastern and the western sides of Taiwan with a non-overlapping distribution, indicating the importance of the Central Mountain Range as the major biogeographic barrier. Both clades showed a strong and congruent tendency of demographic or distributional expansion in recent history based on different analyses. Population expansion of such a subtropical lowland species might be a result from a release of available habitat in post-glacial periods.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 April 2012 - 31 May 2012: PERMANENT GENETIC RESOURCES NOTE

This article documents the addition of 123 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Brenthis ino, Cichla orinocensis, Cichla temensis, Epinephelus striatus, Gobio gobio, Liocarcinus depurator, Macrolophus pygmaeus, Monilinia vaccinii‐corymbosi, Pelochelys cantorii, Philotrypesis josephi, Romanogobio vladykovi, Takydromus luyeanus and Takydromus viridipunctatus. These loci were cross‐tested on the following species: Cichla intermedia, Cichla ocellaris, Cichla pinima, Epinephelus acanthistius, Gobio carpathicus, Gobio obtusirostris, Gobio sp. 1, Gobio volgensis, Macrolophus costalis, Macrolophus melanotoma, Macrolophus pygmaeus, Romanogobio albipinnatus, Romanogobio banaticus, Romanogobio belingi, Romanogobio kesslerii, Romanogobio parvus, Romanogobio pentatrichus, Romanogobio uranoscopus, Takydromus formosanus, Takydromus hsuehshanesis and Takydromus stejnegeri.

Ventral coloration differentiation and mitochondrial sequences of the Chinese Cobra (Naja atra) in Taiwan

Differences in coloration between eastern and western populations of the Chinese cobra (Naja atra) in Taiwan have been noted by snake collectors, snake keepers, and users of Chinese traditional medicine, but have never been verified by scientific research. In this study, we quantified the amount of black pigment on ventral scales, and found prominent differences in ventral coloration of populations across Taiwan; populations in eastern Taiwan have black ventral scales while populations in the west are predominantly white. Previous studies have shown a similar east-west population differentiation in regards to venom components. We supplement these data with mitochondrial control region sequences, which show extremely low nucleotide diversity. Black-ventral and white-ventral snakes share major haplotypes and show no genetic differentiation. Nevertheless, moderate Fst and low Nm values between populations indicate low levels of gene flow. With a morphological fixation earlier than mitochondrial sequences on a relatively short evolutionary time scale, ventral coloration is potentially a result of local adaptation. Based upon the results of this study, along with traditional observations, we strongly recommend treating each of the four populations of the Chinese cobra in Taiwan as distinct ESUs. Reintroducing confiscated snakes from the illegal trade back into the wild needs to be halted to prevent artifical gene flow.

Changes of diet and dominant intestinal microbes in farmland frogs

BackgroundAgricultural activities inevitably result in anthropogenic interference with natural habitats. The diet and the gut microbiota of farmland wildlife can be altered due to the changes in food webs within agricultural ecosystems. In this work, we compared the diet and intestinal microbiota of the frog Fejervarya limnocharis in natural and farmland habitats in order to understand how custom farming affects the health of in vivo microbial ecosystems.ResultsThe occurrence, abundance, and the numbers of prey categories of stomach content were significantly different between the frogs inhabiting natural and farmland habitats. In addition, differences in the abundance, species richness, and alpha-diversity of intestinal microbial communities were also statistically significant. The microbial composition, and particularly the composition of dominant microbes living in intestines, indicated that the land use practices might be one of factors affecting the gut microbial community composition. Although the first three dominant microbial phyla Bacteroidetes, Firmicutes, and Proteobacteria found in the intestines of frogs were classified as generalists among habitats, the most dominant gut bacterial phylum Bacteroidetes in natural environments was replaced by the microbial phylum Firmicutes in farmland frogs. Increased intestinal microbial richness of the farmland frogs, which is mostly contributed by numerous microbial species of Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes, not only reflects the possible shifts in microbial community composition through the alteration of external ecosystem, but also indicates the higher risk of invasion by disease-related microbes.ConclusionsThis study indicates that anthropogenic activities, such as the custom farming, have not only affected the food resources of frogs, but also influenced the health and in vivo microbial ecosystem of wildlife.

Within-island speciation with an exceptional case of distinct separation between two sibling lizard species divided by a narrow stream

Delimitation of genetic and geographic boundaries between species is a focus of evolutionary biology. In this study, we demonstrated fine-scale differentiation of Takydromus formosanus species complex comprising four insular endemics on Taiwan Island. Phylogeny and ancestral range reconstruction based on mitochondrial DNA sequences of 430 Takydromus lizards (405 lizards of this complex throughout their distribution range, and 25 lizards from 11 other species) indicated that the major branching process occurred within Taiwan, which represented a solid evidence of within-island speciation on this small island. We further demonstrated an exceptional case of a pair of sister species, T. viridipunctatus and T. luyeanus, that were separated by a narrow stream with a width of only 15m. This pattern might be one of the narrowest contact zones ever documented in terrestrial vertebrates. To evaluate the level of genetic introgression between these sister species, a fine-scale collection of another 382 lizards was conducted along a transect line across the stream. A total of 13 microsatellite markers and mtDNA genotyping was used to detect a low proportion of hybrids (5.7-9.9% from STRUCTURE, and 2.3% from DAPC). Our results indicated that the two clades are highly differentiated across this extremely short distance.

Breeding performance of Crested Goshawk Accipiter trivirgatus in urban and rural environments of Taiwan

Capsule A Crested Goshawk population recently colonizing an urban area of Taiwan is characterized by earlier egg-laying dates, a higher ratio of mixed-age pairs and higher nesting success. Aims To compare breeding time, productivity and pairing pattern of Crested Goshawk populations between urban and rural areas. Methods A total of 117 nests, comprising 49 rural and 68 urban ones, were monitored in Taichung, central Taiwan over six years. Age of parents, egg-laying date, clutch size and number of fledglings were recorded from each nest. Results The urban Crested Goshawk bred 34 days earlier on average than the rural population with a significantly higher nesting success. Mixed-age pairs occurred in a higher frequency in urban (30.9%) than in rural (14.3%) areas. Predation (55.6%) and inclement weather (27.8%) were the two main factors causing nesting failures in rural areas, whereas neither occurred in the urban area. Conclusion We conclude that the urban Crested Goshawk population benefits from high food supply and low predation risk. The year-round abundance of prey might increase the breeding success of young adults and advance their breeding schedule, which coincidently shifts the brooding period away from the heavy rainy season.

Tail regeneration after autotomy revives survival: a case from a long-term monitored lizard population under avian predation

Caudal autotomy in lizards has intrigued scientists for more than 100 years. Because of the relative lack of literature under natural conditions, the complicated association among field autotomy rate, real predation pressure, the long-term cost of tail loss, and the benefit of regeneration remains equivocal. In this study, we conducted a 7-year capture–mark–recapture (CMR) programme with a wild population of a sexually dichromatic lizard, Takydromus viridipunctatus. We used autotomy indexes and a contemporary bird census mega-dataset of four predatory birds as predictors to examine the association between tail loss and predation pressure. We further estimated the survival cost of tail loss and alleviation by regeneration under natural conditions through CMR modelling. We found that large and small avian predators affect lizard survival through the following two routes: the larger-sized cattle egret causes direct mortality while the smaller shrikes and kestrels are the major causes of autotomy. Following autotomy, the survival rate of tailless individuals over the next month was significantly lower than that of tailed individuals, especially males during the breeding season, which showed a decline of greater than 30%. This sex-related difference further demonstrated the importance of reproductive costs for males in this sexually dichromatic species. However, the risk of mortality returned to baseline after the tails were fully grown. This study indicates the benefit of tail regeneration under natural conditions, which increases our understanding of the cost–benefit dynamics of caudal autotomy and further explains the maintenance of this trait as an evolutionarily beneficial adaption to long-term predator–prey interactions.

Influence of gene flow on divergence dating - implications for the speciation history of Takydromus grass lizards

Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analysed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species‐tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation‐with‐migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favoured over the isolation model, and the initiation of the speciation process was far earlier than the dates estimated by gene‐ and species‐based divergence dating. Due to their limited dispersal ability, it is suggested that geographical isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, this study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating. By using multilocus data and incorporating Bayesian coalescence approaches, we provide a more biologically realistic framework for delineating the divergence history of Takydromus.