scholarly journals Highly divergent mussel lineages in isolated Indonesian marine lakes

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2496 ◽  
Author(s):  
Leontine E. Becking ◽  
Christiaan A. de Leeuw ◽  
Bram Knegt ◽  
Diede L. Maas ◽  
Nicole J. de Voogd ◽  
...  
Keyword(s):  
Sequence Data ◽  
Spatial Scales ◽  
Sequence Divergence ◽  
Shell Shape ◽  
Marine Biodiversity ◽  
Geometric Morphometric ◽  
East Kalimantan ◽  
Coastal Marine ◽  
Marine Lakes ◽  
Founder Populations

Marine lakes, with populations in landlocked seawater and clearly delineated contours, have the potential to provide a unique model to study early stages of evolution in coastal marine taxa. Here we ask whether populations of the musselBrachidontesfrom marine lakes in Berau, East Kalimantan (Indonesia) are isolated from each other and from the coastal mangrove systems. We analyzed sequence data of one mitochondrial marker (Cytochrome Oxidase I (COI)), and two nuclear markers (18S and 28S). In addition, we examined shell shape using a geometric morphometric approach. The Indonesian populations ofBrachidontesspp. harbored four deeply diverged lineages (14–75% COI corrected net sequence divergence), two of which correspond to previously recorded lineages from marine lakes in Palau, 1,900 km away. These four lineages also showed significant differences in shell shape and constitute a species complex of at least four undescribed species. Each lake harbored a different lineage despite the fact that the lakes are separated from each other by only 2–6 km, while the two mangrove populations, at 20 km distance from each other, harbored the same lineage and shared haplotypes. Marine lakes thus represent isolated habitats. As each lake contained unique within lineage diversity (0.1–0.2%), we suggest that this may have resulted fromin situdivergence due to isolation of founder populations after the formation of the lakes (6,000–12,000 years before present). Combined effects of stochastic processes, local adaptation and increased evolutionary rates could produce high levels of differentiation in small populations such as in marine lake environments. Such short-term isolation at small spatial scales may be an important contributing factor to the high marine biodiversity that is found in the Indo-Australian Archipelago.

scholarly journals Biogeography of acoustic biodiversity of NW Mediterranean coralligenous reefs

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lucia Di Iorio ◽  
Manon Audax ◽  
Julie Deter ◽  
Florian Holon ◽  
Julie Lossent ◽  
...  
Keyword(s):  
Large Scale ◽  
Spatial Scales ◽  
Western Mediterranean ◽  
Ecosystem Functions ◽  
Marine Biodiversity ◽  
Predator Species ◽  
The North ◽  
Mediterranean Habitats ◽  
Geographical Regions ◽  
Nw Mediterranean

AbstractMonitoring the biodiversity of key habitats and understanding the drivers across spatial scales is essential for preserving ecosystem functions and associated services. Coralligenous reefs are threatened marine biodiversity hotspots that are challenging to monitor. As fish sounds reflect biodiversity in other habitats, we unveiled the biogeography of coralligenous reef sounds across the north-western Mediterranean using data from 27 sites covering 2000 km and 3 regions over a 3-year period. We assessed how acoustic biodiversity is related to habitat parameters and environmental status. We identified 28 putative fish sound types, which is up to four times as many as recorded in other Mediterranean habitats. 40% of these sounds are not found in other coastal habitats, thus strongly related to coralligenous reefs. Acoustic diversity differed between geographical regions. Ubiquitous sound types were identified, including sounds from top-predator species and others that were more specifically related to the presence of ecosystem engineers (red coral, gorgonians), which are key players in maintaining habitat function. The main determinants of acoustic community composition were depth and percentage coverage of coralligenous outcrops, suggesting that fish-related acoustic communities exhibit bathymetric stratification and are related to benthic reef assemblages. Multivariate analysis also revealed that acoustic communities can reflect different environmental states. This study presents the first large-scale map of acoustic fish biodiversity providing insights into the ichthyofauna that is otherwise difficult to assess because of reduced diving times. It also highlights the potential of passive acoustics in providing new aspects of the correlates of biogeographical patterns of this emblematic habitat relevant for monitoring and conservation.

scholarly journals A developmentally descriptive method for quantifying shape in gastropod shells

2020 ◽  
Vol 17 (163) ◽  
pp. 20190721
Author(s):  
J. Larsson ◽  
A. M. Westram ◽  
S. Bengmark ◽  
T. Lundh ◽  
R. K. Butlin
Keyword(s):  
Empirical Studies ◽  
Three Dimensional ◽  
Shell Shape ◽  
Large Set ◽  
Littorina Saxatilis ◽  
Shape Variation ◽  
Gastropod Shell ◽  
Geometric Morphometric ◽  
Wide Range ◽  
Descriptive Method

The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods.

scholarly journals Achieving sustainable coastal environment in Langkawi, Malaysia

2017 ◽  
Author(s):  
Mazlin Mokhtar ◽  
Minhaz Farid Ahmed ◽  
Khai Ern Lee ◽  
Lubna Alam ◽  
Choo Ta Goh ◽  
...  
Keyword(s):  
Anthropogenic Activities ◽  
Sediment Quality ◽  
Pollution Index ◽  
Quality Standard ◽  
Coastal Environment ◽  
Coastal Pollution ◽  
Marine Biodiversity ◽  
Average Value ◽  
Spanish Mackerel ◽  
Coastal Marine

Despite many good policies and institutions, the coastal environment of Langkawi continues to deteriorate. This could be due to lack of effective governance as well as unregulated waste discharge. Evidences collected from the literature during 1996 to 2013 also revealed a significant increase in the concentrations of Zn (R2 = 0.78) and Pb (R2 = 0.12) in the sediment. This appears to be the result of large volume of terrestrial runoff that brings these metals originating from extensive anthropogenic activities. It is a vital indicator of coastal pollution. It is a matter of concern that in many cases Pb concentration in the sediment exceeded the world average value 20 μg/g as well as Canadian Interim Sediment Quality Standard of 35 μg/g for the coastal areas. Similarly, the metal pollution index (MPI) measured over a period of 2007 to 2009 in fish also indicated an increasing trend of pollution in Langkawi. The maximum MPI value (4.87) was recorded in Spanish mackerel. Since pollution of coastal environment has serious implications for marine biodiversity and health of seafood consumers, measures are required to address this problem. Use of constructed wetland might be effective in reducing the coastal pollution as this will filter the effluent and waste before their mixing with the coastal water. Furthermore, enabling the stakeholders to play the environmental stewardship role will ensure better governance of coastal ecosystem and effective implementation of policies, envisaging an improved monitoring of waste/effluent discharge into the coastal marine environment. These measures are among the actions necessary for achieving a sustainable coastal environment of Langkawi.

scholarly journals Characterization of an unusually conserved AluI highly reiterated DNA sequence family from the honeybee, Apis mellifera.

Genetics ◽  
1993 ◽  
Vol 134 (4) ◽  
pp. 1195-1204
Author(s):  
S Tarès ◽  
J M Cornuet ◽  
P Abad
Keyword(s):  
Apis Mellifera ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Repeated Sequence ◽  
Consensus Sequences ◽  
Dna Sequence Data ◽  
Repeat Class ◽  
Honeybee Subspecies

Abstract An AluI family of highly reiterated nontranscribed sequences has been found in the genome of the honeybee Apis mellifera. This repeated sequence is shown to be present at approximately 23,000 copies per haploid genome constituting about 2% of the total genomic DNA. The nucleotide sequence of 10 monomers was determined. The consensus sequences is 176 nucleotides long and has an A + T content of 58%. There are clusters of both direct and inverted repeats. Internal subrepeating units ranging from 11 to 17 nucleotides are observed, suggesting that it could have evolved from a shorter sequence. DNA sequence data reveal that this repeat class is unusually homogeneous compared to the other class of invertebrate highly reiterated DNA sequences. The average pairwise sequence divergence between the repeats is 2.5%. In spite of this unusual homogeneity, divergence has been found in the repeated sequence hybridization ladder between four different honeybee subspecies. Therefore, the AluI highly reiterated sequences provide a new probe for fingerprinting in A. m. mellifera.

scholarly journals Phylogeography of two Andean frogs: Test of vicariance versus elevational gradient models of diversification

2019 ◽  
Author(s):  
Daria Koscinski ◽  
Paul Handford ◽  
Pablo L. Tubaro ◽  
Peiwen Li ◽  
Stephen C. Lougheed
Keyword(s):  
Sequence Data ◽  
Environmental Gradients ◽  
Spatial Scales ◽  
Elevational Gradient ◽  
Northwestern Argentina ◽  
Dna Sequence Data ◽  
The Andes ◽  
Common Causes ◽  
History Of ◽  
Historical Range

ABSTRACTThe tropical and subtropical Andes have among the highest levels of biodiversity in the world. Understanding the forces that underlie speciation and diversification in the Andes is a major focus of research. Here we tested two hypotheses of species origins in the Andes: 1. Vicariance mediated by orogenesis or shifting habitat distribution. 2. Parapatric diversification along elevational environmental gradients. We also sought insights on the factors that impacted the phylogeography of co-distributed taxa, and the influences of divergent species ecology on population genetic structure. We used phylogeographic and coalescent analyses of nuclear and mitochondrial DNA sequence data to compare genetic diversity and evolutionary history of two frog species: Pleurodema borellii (Family: Leiuperidae, 130 individuals; 20 sites), and Hypsiboas riojanus (Family: Hyllidae, 258 individuals; 23 sites) across their shared range in northwestern Argentina. The two showed concordant phylogeographic structuring, and our analyses support the vicariance model over the elevational gradient model. However, Pleurodema borellii exhibited markedly deeper temporal divergence (≥4 Ma) than H. riojanus (1-2 Ma). The three main mtDNA lineages of P. borellii were nearly allopatric and diverged between 4-10 Ma. At similar spatial scales, differentiation was less in the putatively more habitat-specialized H. riojanus than in the more generalist P. borellii. Similar allopatric distributions of major lineages for both species implies common causes of historical range fragmentation and vicariance. However, different divergence times among clades presumably reflect different demographic histories, permeability of different historical barriers at different times, and/or difference in life history attributes and sensitivities to historical environmental change. Our research enriches our understanding of the phylogeography of the Andes in northwestern Argentina.

scholarly journals Phenotypic plasticity at fine-grained spatial scales: the scorched mussel Perumytilus purpuratus growing on Patagonian rocky salt-marshes

2020 ◽  
Vol 84 (4) ◽  
pp. 393-401
Author(s):  
Yamila Gonzalez Giorgis ◽  
María Cruz Sueiro ◽  
Federico Márquez
Keyword(s):  
Phenotypic Plasticity ◽  
Environmental Conditions ◽  
Range Expansion ◽  
Salt Marshes ◽  
Spatial Scales ◽  
Shell Shape ◽  
Patch Type ◽  
Fine Grained ◽  
Perumytilus Purpuratus ◽  
Ecological Range

Understanding phenotypic plasticity of species at different spatial scales is vital in the current context of an increasing pace of environmental changes. Through this knowledge, it is possible to predict their potential to adapt and/or evolve in face of new environmental conditions such as climate change, and/or to understand their ecological range expansion. In Patagonian rocky salt-marshes, one of the most abundant invertebrate species is the scorched mussel Perumytilus purpuratus. In this system, this mussel can be found inhabiting both vegetated and non-vegetated patches, which differ in critical environmental conditions. We performed a field study evaluating whether mussels growing in vegetated patches differ in shell shape from those growing in adjacent non-vegetated patches. We sampled individuals from both patch types and assessed their shell shape and size using geometric morphometrics. The results showed that mussels from vegetated patches had shells that were more dorsoventrally expanded, anterodorsally restricted and globose in shape than those from non-vegetated patches, which showed the opposite traits resulting in a more elongated shell. The differences found could be driven by the different conditions of temperature, desiccation rate, wave action and population density to which mussels are exposed in each patch type. These results revealed the striking phenotypic plasticity of shell form of this native species at a fine-grained scale, which could be one of the explanations for its success in its ecological range expansion.

The Cheilosia canicularis group (Diptera: Syrphidae): species delimitation and evolutionary relationships based on wing geometric morphometrics

Zootaxa ◽  
2008 ◽  
Vol 1825 (1) ◽  
pp. 40 ◽  
Author(s):  
JASMINA LUDOŠKI ◽  
LJUBINKA FRANCUSKI ◽  
ANTE VUJIĆ ◽  
VESNA MILANKOV
Keyword(s):  
Sequence Data ◽  
Balkan Peninsula ◽  
Wing Shape ◽  
Canonical Variate ◽  
Wing Size ◽  
Shape Variation ◽  
Geometric Morphometric ◽  
Mahalanobis Distances ◽  
Size And Shape ◽  
Upgma Cluster Analysis

A landmark-based geometric morphometric approach was used to assess differences in the size and shape of wing among/within three species of the Cheilosia canicularis group (Diptera: Syrphidae): C. canicularis, C. himantopus and C. orthotricha. Wing size and shape variation was observed from 25, 176 and 41 specimens of C. canicularis, C. himantopus and C. orthotricha, respectively, collected from six localities on the Balkan Peninsula. Significant differences in wing size were obtained among the analysed species and canonical variate analysis showed that wing shape was sufficiently different to allow the correct classification of 73% individuals of C. canicularis, 80% of C. orthotricha and 94% of C. himantopus, and clear delimitation of the species pairs C. canicularis/C. orthotricha and C. himantopus/C. orthotricha. In all analysed species, the consistent sex dimorphism in wing shape was observed indicating that female specimens had shorter and broader wings than males. The UPGMA cluster analysis based on squared Mahalanobis distances revealed close accordance with previously published phylogenetic relationships of these species indicated by allozyme and DNA sequence data analysis. Our results suggested that wing parameters contain useful information in quantification phenotypic variation and identification of species in this challenging group for taxonomy and systematics.

scholarly journals Planktonic foraminifera genomic variations reflect paleoceanographic changes in the Arctic: evidence from sedimentary ancient DNA

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Joanna Pawłowska ◽  
Jutta E. Wollenburg ◽  
Marek Zajączkowski ◽  
Jan Pawlowski
Keyword(s):  
Ancient Dna ◽  
Sequence Data ◽  
Planktonic Foraminifera ◽  
Molecular Ecology ◽  
The Arctic ◽  
Marine Biodiversity ◽  
Neogloboquadrina Pachyderma ◽  
Rna Genes ◽  
The Last Glacial Maximum ◽  
The Last Glacial

Abstract Deciphering the evolution of marine plankton is typically based on the study of microfossil groups. Cryptic speciation is common in these groups, and large intragenomic variations occur in ribosomal RNA genes of many morphospecies. In this study, we correlated the distribution of ribosomal amplicon sequence variants (ASVs) with paleoceanographic changes by analyzing the high-throughput sequence data assigned to Neogloboquadrina pachyderma in a 140,000-year-old sediment core from the Arctic Ocean. The sedimentary ancient DNA demonstrated the occurrence of various N. pachyderma ASVs whose occurrence and dominance varied through time. Most remarkable was the striking appearance of ASV18, which was nearly absent in older sediments but became dominant during the last glacial maximum and continues to persist today. Although the molecular ecology of planktonic foraminifera is still poorly known, the analysis of their intragenomic variations through time has the potential to provide new insight into the evolution of marine biodiversity and may lead to the development of new and important paleoceanographic proxies.

scholarly journals Vertigo shimochii Kuroda & Amano 1960 synonymized with Gastrocopta servilis (Gould, 1843) based on conchological and DNA sequence data

Zootaxa ◽  
2012 ◽  
Vol 3161 (1) ◽  
pp. 48 ◽  
Author(s):  
JEFFREY C. NEKOLA ◽  
ALEX JONES ◽  
GABE MARTINEZ ◽  
SARAH MARTINEZ ◽  
KHAYMAN MONDRAGON ◽  
...  
Keyword(s):  
Sequence Data ◽  
Shell Shape ◽  
Dna Sequence Data ◽  
Red Data Book ◽  
Kagoshima Prefecture ◽  
Data Book ◽  
Environment Agency ◽  
Deep Suture ◽  
Threatened Status ◽  
Near Threatened

Kuroda (1960) noted that his new species, Vertigo shimochii Kuroda & Amano, 1960, was distinct from other members of the genus in Japan by possessing a “relatively large and long shell with deep suture and much inflated whorls” (p. 77). While shell shape was noted to be similar to a Gastrocopta, they assigned the species to Vertigo based on its “shell color and lamella characteristics” (p. 77). Vertigo shimochii has since been considered endemic to the southern parts of Japan (The Environment Agency 1988; Minato 1988; Azuma 1995; Biodiversity Center of Japan 2002), and of near threatened status in the Kagoshima Prefecture Red Data Book (Kagoshima Prefectural Government 2003).

A new species of big-headed, fanged dicroglossine frog (Genus Limnonectes) from Thailand

Zootaxa ◽  
2008 ◽  
Vol 1807 (1) ◽  
pp. 26 ◽  
Author(s):  
DAVID S. McLEOD
Keyword(s):  
New Species ◽  
Dna Sequence ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Type Material ◽  
Base Pairs ◽  
Dna Sequence Data ◽  
16S Gene ◽  
A New Species

A new species of the dicroglossine genus Limnonectes from eastern Thailand and its tadpole are described. Analysis of DNA sequence data from 2518 base-pairs of the mitochondrial 12S and 16S gene regions places the species within the complex of frogs currently referred to as Limnonectes kuhlii and demonstrates it to be a separate lineage (>18% sequence divergence from type-material of L. kuhlii from Java). The new species differs from L. kuhlii by having nuptial pads, a greater snout–vent length, and different relative finger lengths than specimens from Java. It has more extensive toe webbing, a different arrangement of nuptial pads, and a greater snout–vent length than Limnonectes laticeps. The new species, which lacks vocal slits, also can be distinguished from the morphologically similar Limnonectes namiyei from Japan, which possesses vocal slits.

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