Spatial variation in life history reveals insight into connectivity and geographic population structure of a tropical estuarine teleost: king threadfin, Polydactylus macrochir

Understanding the life history of exploited fish species is not only critical in developing stock assessments and productivity models, but has a dual function in the delineation of connectivity and geographical population structure. In this study, patterns in growth and length and age at sex change of Polydactylus macrochir, an ecologically and economically important protandrous estuarine teleost, were examined to provide preliminary information on the species' connectivity and geographic structure across northern Australia. Considerable variation in life history parameters was observed among the 18 locations sampled. Both unconstrained and constrained (t(0) = 0) estimates of von Bertalanffy growth function parameters differed significantly among all neighbouring locations with the exception of two locations in Queensland's east coast and two in Queensland's Gulf of Carpentaria waters, respectively. Comparisons of back-calculated length-at-age 2 provided additional evidence for growth differences among some locations, but were not significantly different among locations in the south-eastern Gulf of Carpentaria or on Queensland's east coast. The length and age at sex change differed markedly among locations, with fish from the east coast of Australia changing sex from males to females at significantly greater lengths and ages than elsewhere. Sex change occurred earliest at locations within Queensland's Gulf of Carpentaria, where a large proportion of small, young females were recorded. The observed differences suggest that P. macrochir likely form a number of geographically and/or reproductively distinct groups in Australian waters and suggest that future studies examining connectivity and geographic population structure of estuarine fishes will likely benefit from the inclusion of comparisons of life history parameters. (C) 2012 Elsevier B.V. All rights reserved.

Regional variation in the composition and structure of mixed-species bird flocks in the Western Ghats and Sri Lanka

Mixed-species bird flocks are attractive models for the investigation of geographical variation in animal communities, as they represent a subset of the avifauna in most forested regions of the world. Yet studies of the regional variation in flock size and the composition of flocks are few, due to the predominance of studies carried out at single study site. Here, we review nine studies of mixed-species flocks conducted at 16 sites along the Western Ghats in India and in Sri Lanka. We find that flock size varies as much within this region as it does globally, with observation time being a confounding variable. Flock composition, however, is predictably related to elevation. Flocks at high elevations (>1200 m) in the Western Ghats strongly resemble flocks at high elevations in the mountain ranges of Sri Lanka in their composition, especially at the family level. We compare these flocks to flocks of other regions and make recommendations on study methodology that can facilitate comparisons across studies.

Structure of ant assemblages in Western Ghats, India: role of habitat, disturbance and introduced species

1. Habitat fragmentation, anthropogenic disturbance and the introduction of invasive species are factors thought to structure ant assemblages. To understand responses of the ant community to changes in the environment, ants are commonly categorised into functional groups, a scheme developed and based on Australian ants. 2. Behaviourally dominant and aggressive ants of the dominant dolichoderinae functional group have been suggested to structure the ant assemblages in arid and semi-arid habitats of these regions. Given the limited geographical distribution of dominant dolichoderinae, it is crucial to determine the responses of the ant community to changes in the environment in their absence. 3. This study addresses this less studied aspect by considering the associations of ants of Western Ghats, India, with habitat, anthropogenic disturbance and introduced ants. We determined how ant functional groups respond to these factors in this region, where dominant dolichoderines are naturally absent, and whether responses are consistent with predictions derived from the ant functional group scheme. 4. This study provides new information on ant assemblages in a little-studied region. As in other parts of the world, ant assemblages in Western Ghats were strongly influenced by habitat and disturbance, with different functional groups associated with different habitats and levels of disturbance. 5. No functional group showed evidence of being influenced by the abundance of introduced species. In addition, predictions of negative interactions between functional groups were not supported. Our findings suggest that abiotic factors are universal determinants of ant assemblage structure, but that competitive interactions may not be.

A comparison of the fine-scale structure of the diurnal cycle of tropical rain and lightning

In this study, the fine-scale structure of the diurnal variability of ground-based lightning is systematically compared with satellite-based rain. At the outset, it is shown that tropical variability of lightning exhibits a prominent diurnal mode, much like rain. A comparison of the geographical distribution of the timing of the diurnal maximum shows that there is very good agreement between the two observables over continental and coastal regions throughout the tropics. Following this global tropical comparison, we focus on two regions, Borneo and equatorial South America, both of which show the interplay between oceanward and landward propagations of the phase of the diurnal maximum. Over Borneo, both rain and lightning clearly show a climatological cycle of ``breathing in'' (afternoon to early morning) and ``breathing out'' (morning to early afternoon). Over the equatorial east coast of South America, landward propagation is noticed in rain and lightning from early afternoon to early morning. Along the Pacific coast of South America, both rain and lightning show oceanward propagation. Though qualitatively consistent, over both regions the propagation is seen to extend further in rainfall. Additionally, given that lightning highlights vigorous convection, the timing of its diurnal maximum often precedes that of rainfall in the convective life cycle. (C) 2015 Elsevier B.V. All rights reserved.

Diel movements of fishes linked to benthic seascape structure in a Caribbean coral reef ecosystem

Many common fishes associated with Caribbean coral reef ecosystems use resources from more than 1 patch type during routine daily foraging activities. Few studies have provided direct evidence of connectivity across seascapes, and the importance of benthic seascape structure on movement behavior is poorly known. To address this knowledge gap, we coupled hydro-acoustic technology to track fish with seafloor mapping and pattern analysis techniques from landscape ecology to quantify seascape structure. Bluestriped grunts Haemulon sciurus and schoolmaster snapper Lutjanus apodus were tracked over 24 h periods using boat-based acoustic telemetry. Movement pathways, and day and night activity spaces were mapped using geographical information system (GIS) tools, and seafloor structure within activity spaces was mapped from high-resolution aerial photography and quantified using spatial pattern metrics. For both fish species, night activity spaces were significantly larger than day activity spaces. Fish exhibited a daytime preference for seascapes with aggregate coral reef and colonized bedrock, then shifted to night activity spaces with lower complexity soft sediment including sand, seagrass, and scattered coral/rock. Movement path complexity was negatively correlated with seascape complexity. This demonstrates direct connectivity across multiple patch types and represents the first study to apply quantitative landscape ecology techniques to examine the movement ecology of marine fish. The spatially explicit approach facilitates understanding to the linkages between biological processes and the heterogeneity of the landscape. Such studies are essential for identifying ecologically relevant spatial scales, delineating essential fish habitat and designing marine protected areas.

Use of allozyme markers to determine the genetic structure of hatchery population of Thai pangas, Pangasius hypophthalmus of Jessore, Bangladesh

Genetic structure of hatchery population of Thai pangas (Pangasius hypophthalmus) of Jessore region, Bangladesh has been investigated from 1 January 2004 to 31 December 2004. Samples for this study were collected from five fish hatcheries viz. Asrom, Banchte Shekha, Chowdhury, Maola and Rezaul Haque. The enzymes were encoded by 15 gene loci: Adh-1*, Est-1*, G3pdh-2*, Gpi-1*, Gpi-2*, Idhp-1*, Idhp-2*, Ldh-1*, Ldh-2*, Mdh-1*, Mdh-2*, Pgm*, Sdh-1*, Sdh-2* and Sod*. Among them four (Est-1*, G3pdh-2*, Gpi-2*and Pgm*) were found to be polymorphic in different populations but only Gpi-2* was polymorphic in all the sampled populations. The mean proportion of polymorphic loci per population was the highest (26.7%) in Banchte Shekha hatchery while the mean proportion of heterozygous loci was 13.33% per individual in Banchte Shekha and Maola hatcheries. The UPGMA dendrogram of Nei's (1972) genetic distances indicated a relationship between the genetic distance and geographical difference. High genetic variability in stocks of Thai pangas was observed in the Banchte Shekha and Maola hatcheries and less variability was found in the other three hatcheries.

Mitochondrial diversity and phylogeographic structure of Chinese domestic goats

China has numerous native domestic goat breeds, but so far there has been no extensive study on genetic diversity, population demographic history, and origin of Chinese goats. Here, we examined the genetic diversity and phylogeographic structure of Chinese domestic goats by determining a 481-bp fragment of the first hypervariable region of mitochondrial DNA (mtDNA) control region from 368 individuals representing 18 indigenous breeds. Phylogenetic analyses revealed that there were four mtDNA lineages (A-D) identified in Chinese goats, in which lineage A was predominant, lineage B was moderate, and lineages C and D were at low frequency. These results further support the multiple maternal origins of domestic goats. The pattern of genetic variation in goat mtDNA sequences indicated that the two larger lineages A and B had undergone population expansion events. In a combined analysis of previously reported sequences and our sequences belonging to lineage B, we detected two subclades, in which one was unique to eastern Asia and another was shared between eastern and southern Asia. A larger genetic variation in eastern Asia than southern Asia and the pattern of phylogeographic variation in lineage B suggest that at least one subclade of lineage B originated from eastern Asia. There was no significant geographical structuring in Chinese goat populations, which suggested that there existed strong gene flow among goat populations caused by extensive transportation of goats in history. (c) 2005 Elsevier Inc. All rights reserved.

Exploring factors shaping population genetic structure of the freshwater fish Sinocyclocheilus grahami (Teleostei, Cyprinidae)

Phylogeographical analyses on Sinocyclocheilus grahami samples from seven localities within the Lake Dianchi Basin in China were conducted to explore the main factors shaping population structure within this species. Phylogenetic and network analyses reve

Molecular phylogeography and population structure of a mid-elevation montane frog Leptobrachium ailaonicum in a fragmented habitat of southwest China

Leptobrachium ailaonicum is a vulnerable anuran restricted to a patchy distribution associated with small mountain streams surrounded by forested slopes at mid-elevations (approximately 2000-2600 m) in the subtropical Mount Wuliang and Mount Ailao ranges in southwest China (Yunnan Province) and northern Vietnam. Given high habitat specificity and lack of suitable habitat in lower elevations between these ranges, we hypothesized limited gene flow between populations throughout its range. We used two mitochondrial genes to construct a phylogeographic pattern within this species in order to test our hypothesis. We also examined whether this phylogeographic pattern is a response to past geological events and/or climatic oscillations. A total of 1989 base pairs were obtained from 81 individuals of nine populations yielding 51 unique haplotypes. Both Bayesian and maximum parsimony phylogenetic analyses revealed four deeply divergent and reciprocally monophyletic mtDNA lineages that approximately correspond to four geographical regions separated by deep river valleys. These results suggest a long history of allopatric separation by vicariance. The distinct geographic distributions of four major clades and the estimated divergence time suggest spatial and temporal separations that coincide with climatic and paleogeographic changes following the orogeny and uplift of Mount Ailao during the late Miocene to mid Pliocene in southwest China. At the southern distribution, the presence of two sympatric yet differentiated clades in two areas are interpreted as a result of secondary contact between previously allopatric populations during cooler Pleistocene glacial cycles. Analysis of molecular variance indicates that most of the observed genetic variation occurs among the four regions implying long-term interruption of maternal gene flow, suggesting that L ailaonicum may represent more than one distinct species and should at least be separated into four management units corresponding to these four geographic lineages for conservation. (C) 2009 Elsevier Inc. All rights reserved.

Population genetic structure of Carchesium polypinum (Ciliophora : Peritrichia) in four chinese lakes inferred from ISSR fingerprinting: High diversity but low differentiation

Although the peritrichous ciliate Carchesium polypinum is common in freshwater, its population genetic structure is largely unknown. We used inter-simple sequence repeat (ISSR) fingerprinting to analyze the genetic structure of 48 different isolates of the species from four lakes in Wuhan, central China. Using eight polymorphic primers, 81 discernible DNA fragments were detected, among which 76 (93.83%) were polymorphic, indicating high genetic diversity at the isolate level. Further, Nei's gene diversity (h) and Shannon's Information index (I) between the different isolates both revealed a remarkable genetic diversity, higher than previously indicated by their morphology. At the same time, substantial gene flow was found. So the main factors responsible for the high level of diversity within populations are probably due to conjugation (sexual reproduction) and wide distribution of swarmers. Analysis of molecular variance (AMOVA) showed that there was low genetic differentiation among the four populations probably due to common ancestry and flooding events. The cluster analysis and principal component analysis (PCA) suggested that genotypes isolated from the same lake displayed a higher genetic similarity than those from different lakes. Both analyses separated C. polypinum isolates into subgroups according to the geographical locations. However, there is only a weak positive correlation between the genetic distance and geographical distance, suggesting a minor effect of geographical distance on the distribution of genetic diversity between populations of C. polypinum at the local level. In conclusion, our studies clearly demonstrated that a single morphospecies may harbor high levels of genetic diversity, and that the degree of resolution offered by morphology as a marker for measuring distribution patterns of genetically distinct entities is too low.

Geographical distribution of testate amoebae in Tibet and northwestern Yunnan and their relationships with climate

In Asia, especially in China, our knowledge of the distribution of testate amoebae is still limited. In this paper, the geographical distribution of testate amoebae in Tibetan Plateau and northwestern Yunnan Plateau, southwest China and their relationships with the climatic factors have been studied. We found testate amoebae shifted in the most dominant species and increased in species (or genus) richness from northwest to southeast. Further, the linear regression analyses revealed that both species richness and genus richness have higher positive correlations with the mean temperature of the warmest month and annual mean precipitation as contrasted with the mean altitude, which showed weak negative correlation. This indicates that the temperature and precipitation are more significant influences on the richness than the altitude. The cluster analysis based on the community structure, defined by Sorenson's coefficient matrix, suggested four groups from the 10 physiographical regions. This geographical distribution pattern was also closely related with the climatic regionalization. The present climatic regionalization pattern of the study area originated from the uplift of Tibetan Plateau and mainly occurred in or after the late Pleistocene. Therefore, the geographical distribution of testate amoebae in our study area may have experienced complicated and drastic changes corresponding to the variation of the climate caused by the geological events.

Population genetic structure of an endemic cyprinid fish, Ancherythroculter nigrocauda, in the upper reaches of the Yangtze River and its implication for conservation

Ancherythroculter nigrocauda is a cyprinid fish endemic to the upper reaches of the Yangtze River, which has been reported to have 2 or 3 chambers to its air bladder. Morphological studies showed no differences between individuals with different types of air bladder, but did demonstrate geographical differences from different sources. After the completion of the Three Gorges Dam, it was expected that the population of this species would decrease, but artificial breeding and stocking is under consideration to protect this species from extinction. In the present study, mtDNA cytochrome b gene sequences were determined and analyzed for A. nigrocauda samples of different morphotypes and sources to identify their genetic differentiations, and thereby guide plans for the artificial propagation and conservation of this species. Haplotype diversity index values (h) and nucleotide diversity values (pi) for all the populations were found to be high indicating their high level genetic diversity. An analysis of molecular variance identified no differentiation among the studied populations. Therefore, we suggested that the individuals of different morphological types and geographical sources belong to the same species. To maintain its high level genetic diversity, it mill he necessary to use large and diverse sources of parental fish for artificial reproduction.

Population genetic structure of crimson snapper Lutjanus erythropterus in East Asia, revealed by analysis of the mitochondrial control region

The population genetic structure of the crimson snapper Lutjanus erythropterus in East Asia was examined with a 427-bp hypervariable portion of the mtDNA control region. A total of 262 samples were collected and 75 haplotypes were obtained. Neutrality tests (Tajima's and Fu's) suggested that Lutjanus erythropterus in East Asia had experienced a bottleneck followed by population expansion since the late Pleistocene. Despite the low phylogeographic structures in mtDNA haplotypes, a hierarchical examination of populations in 11 localities from four geographical regions using analysis of molecular variance (AMOVA) indicated significant genetic differentiation among regions (Phi(CT) = 0.08564, p < 0.01). Limited gene flow between the eastern region (including a locality in the western Pacific Ocean and two localities in the East Sea) and three geographic regions of the South China Sea largely contributed to the genetic subdivision. However, comparisons among three geographic regions of the South China Sea showed little to no genetic difference. Populations of Lutjanus erythropterus in East Asia are inferred to be divided into two major groups: an eastern group, including populations of the western Pacific Ocean and the East Sea, and a South China Sea group, consisting of populations from northern Malaysia to South China. The results suggest that fishery management should reflect the genetic differentiation and diversity in East Asia. (c) 2006 International Council for the Exploration of the Sea. Published by Elsevier Ltd. All rights reserved.

Genetic structure analysis of natural Sargassum muticum (Fucales, Phaeophyta) populations using RAPD and ISSR markers

Sargassum muticum is important in maintaining the structure and function of littoral ecosystems, and is used in aquaculture and alginate production, however, little is known about its population genetic attributes. In this study, random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were used to investigate the genetic structure of four populations of S. muticum and one outgroup of S. fusiforme (Harv.) Setchell from Shandong peninsula of China. The selected 24 RAPD primers and 19 ISSR primers amplified 164 loci and 122 loci, respectively. Estimates of genetic diversity with different indicators (P%, percentage of polymorphic loci; H, the expected heterozygosity; I, Shannon's information index) revealed low or moderate level of genetic variations within each S. muticum population, and a high level of genetic differentiations were determined with pairwise unbiased genetic distance (D) and fixation index (F-ST ) among the populations. The Mantel test showed that two types of matrices of D and F-ST were highly correlated whether from RAPD (r = 0.9706, P = 0.009) or ISSR data (r = 0.9161, P = 0.009). Analysis of molecular variance (AMOVA) was conducted to apportion the variations among and within the S. muticum populations. It indicated that variations among populations were higher than those within populations, being 55.82% verse 44.18% by RAPD and 55.21% verse 44.79% by ISSR, respectively. Furthermore, the Mantel test suggested that genetic differentiations among populations were related to the geographical distances (r > 0.6), namely, conformed to the IBD (isolation by distance) model, as expected from UPGMA (unweighted pair group method with arithmetic averages) cluster analysis. On the whole, the high genetic structuring among the four S. muticum populations along the distant locations was clearly indicated in RAPD and ISSR analyses (r > 0.9, P < 0.05) in our study.

Population genetic structure of Sargassum thunbergii (Fucales, Phaeophyta) detected by RAPD and ISSR markers

Genetic variation of four populations of Sargassum thunbergii (Mert.) O. Kuntze and one outgroup of S. fusiforme (Harv.) Setchell from Shandong peninsula of China was studied with random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. A total of 28 RAPD primers and 19 ISSR primers were amplified, showing 174 loci and 125 loci, respectively. Calculation of genetic diversity with different indicators (P%, percentage of polymorphic loci; H, the expected heterozygosity; I, Shannon's information index) revealed low or moderate levels of genetic variations within each S. thunbergii population. High genetic differentiations were determined with pairwise Nei's unbiased genetic distance (D) and fixation index (F-ST) between the populations. The Mantel test showed that two types of matrices of D and FST were highly correlated, whether from RAPD or ISSR data, r=0.9310 (P = 0.008) and 0.9313 (P=0.009) respectively. Analysis of molecular variance (AMOVA) was used to apportion the variations between and within the S. thunbergii populations. It indicated that the variations among populations were higher than those within populations, being 57.57% versus 42.43% by RAPD and 59.52% versus 40.08% by ISSR, respectively. Furthermore, the Mantel test suggested that the genetic differentiations between the four populations were related to the geographical distances (r > 0.5), i.e., they conformed to the IBD (isolation by distance) model, as expected from UPGMA (unweighted pair group method with arithmetic averages) cluster analysis. As a whole, the high genetic structuring between the four S. thunbergii populations along distant locations was clearly indicated in the RAPD and ISSR analyses (r > 0.8) in our study.