scholarly journals A molecular phylogeny of the spiny lobster Panulirus homarus highlights a separately evolving lineage from the Southwest Indian Ocean

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3356 ◽  
Author(s):  
Sohana P. Singh ◽  
Johan C. Groeneveld ◽  
Abdulaziz Al-Marzouqi ◽  
Sandi Willows-Munro
Keyword(s):  
Indian Ocean ◽  
Species Delimitation ◽  
Statistical Power ◽  
Life Stage ◽  
Larval Settlement ◽  
Spiny Lobster ◽  
Separate Species ◽  
Southwest Indian Ocean ◽  
Mitochondrial Data ◽  
Divergence Dating

Accurate species description in the marine environment is critical for estimating biodiversity and identifying genetically distinct stocks. Analysis of molecular data can potentially improve species delimitations because they are easily generated and independent, and yield consistent results with high statistical power. We used classical phylogenetic (maximum likelihood and Bayesian inference) and coalescent-based methods (divergence dating with fossil calibrations and coalescent-based species delimitation) to resolve the phylogeny of the spiny lobster Panulirus homarus subspecies complex in the Indo-West Pacific. Analyses of mitochondrial data and combined nuclear and mitochondrial data recovered Panulirus homarus homarus and Panulirus homarus rubellus as separately evolving lineages, while the nuclear data trees were unresolved. Divergence dating analysis also identified Panulirus homarus homarus and Panulirus homarus rubellus as two distinct clades which diverged from a common ancestor during the Oligocene, approximately 26 million years ago. Species delimitation using coalescent-based methods corroborated these findings. A long pelagic larval life stage and the influence of ocean currents on post-larval settlement patterns suggest that a parapatric mode of speciation drives evolution in this subspecies complex. In combination, the results indicate that Panulirus homarus rubellus from the Southwest Indian Ocean is a separately evolving lineage and possibly a separate species.

scholarly journals Phylogeography of the scalloped spiny-lobster Panulirus homarus rubellus in the southwest Indian Ocean

2014 ◽  
Vol 34 (6) ◽  
pp. 773-781 ◽  
Author(s):  
Maggie M. Reddy ◽  
Angus H. H. Macdonald ◽  
Johan C. Groeneveld ◽  
Michael H. Schleyer
Keyword(s):  
Indian Ocean ◽  
Spiny Lobster ◽  
Southwest Indian Ocean

scholarly journals Circulation pattern controls of wet days and dry days in Free State, South Africa

2021 ◽  
Author(s):  
Chibuike Chiedozie Ibebuchi
Keyword(s):  
South Africa ◽  
Indian Ocean ◽  
Atmospheric Circulation ◽  
Southern Africa ◽  
Austral Summer ◽  
Free State ◽  
Austral Spring ◽  
Study Region ◽  
Southwest Indian Ocean ◽  
South Indian

AbstractAtmospheric circulation is a vital process in the transport of heat, moisture, and pollutants around the globe. The variability of rainfall depends to some extent on the atmospheric circulation. This paper investigates synoptic situations in southern Africa that can be associated with wet days and dry days in Free State, South Africa, in addition to the underlying dynamics. Principal component analysis was applied to the T-mode matrix (variable is time series and observation is grid points at which the field was observed) of daily mean sea level pressure field from 1979 to 2018 in classifying the circulation patterns in southern Africa. 18 circulation types (CTs) were classified in the study region. From the linkage of the CTs to the observed rainfall data, from 11 stations in Free State, it was found that dominant austral winter and late austral autumn CTs have a higher probability of being associated with dry days in Free State. Dominant austral summer and late austral spring CTs were found to have a higher probability of being associated with wet days in Free State. Cyclonic/anti-cyclonic activity over the southwest Indian Ocean, explained to a good extent, the inter-seasonal variability of rainfall in Free State. The synoptic state associated with a stronger anti-cyclonic circulation at the western branch of the South Indian Ocean high-pressure, during austral summer, leading to enhanced low-level moisture transport by southeast winds was found to have the highest probability of being associated with above-average rainfall in most regions in Free State. On the other hand, the synoptic state associated with enhanced transport of cold dry air, by the extratropical westerlies, was found to have the highest probability of being associated with (winter) dryness in Free State.

Minimal clustering and species delimitation based on multi-locus alignments vs SNPs: the case of the Seriphium plumosum L. complex (Gnaphalieae: Asteraceae)

2021 ◽  
Author(s):  
Zaynab Shaik ◽  
Nicola Georgina Bergh ◽  
Bengt Oxelman ◽  
Anthony George Verboom
Keyword(s):  
Species Delimitation ◽  
Bayes Factor ◽  
Cape Floristic Region ◽  
Parametric Models ◽  
Western Cape ◽  
Nucleotide Polymorphisms ◽  
Sequence Alignments ◽  
Separate Species ◽  
Multiple Sequence ◽  
Data Set

We applied species delimitation methods based on the Multi-Species Coalescent (MSC) model to 500+ loci derived from genotyping-by-sequencing on the South African Seriphium plumosum (Asteraceae) species complex. The loci were represented either as multiple sequence alignments or single nucleotide polymorphisms (SNPs), and analysed by the STACEY and Bayes Factor Delimitation (BFD)/SNAPP methods, respectively. Both methods supported species taxonomies where virtually all of the 32 sampled individuals, each representing its own geographical population, were identified as separate species. Computational efforts required to achieve adequate mixing of MCMC chains were considerable, and the species/minimal cluster trees identified similar strongly supported clades in replicate runs. The resolution was, however, higher in the STACEY trees than in the SNAPP trees, which is consistent with the higher information content of full sequences. The computational efficiency, measured as effective sample sizes of likelihood and posterior estimates per time unit, was consistently higher for STACEY. A random subset of 56 alignments had similar resolution to the 524-locus SNP data set. The STRUCTURE-like sparse Non-negative Matrix Factorisation (sNMF) method was applied to six individuals from each of 48 geographical populations and 28023 SNPs. Significantly fewer (13) clusters were identified as optimal by this analysis compared to the MSC methods. The sNMF clusters correspond closely to clades consistently supported by MSC methods, and showed evidence of admixture, especially in the western Cape Floristic Region. We discuss the significance of these findings, and conclude that it is important to a priori consider the kind of species one wants to identify when using genome-scale data, the assumptions behind the parametric models applied, and the potential consequences of model violations may have.

Current-controlled, abyssal microtopography and sedimentation in Mozambique Basin, southwest Indian Ocean

1980 ◽  
Vol 34 (3-4) ◽  
pp. 171-206 ◽  
Author(s):  
Venkatarathnam Kolla ◽  
Stephen Eittreim ◽  
Lawrence Sullivan ◽  
John A Kostecki ◽  
Lloyd H Burckle
Keyword(s):  
Indian Ocean ◽  
Southwest Indian Ocean

scholarly journals Effect of deep convection on the tropical tropopause layer composition over the southwest Indian Ocean during austral summer

2020 ◽  
Vol 20 (17) ◽  
pp. 10565-10586
Author(s):  
Stephanie Evan ◽  
Jerome Brioude ◽  
Karen Rosenlof ◽  
Sean M. Davis ◽  
Holger Vömel ◽  
...  
Keyword(s):  
Water Vapor ◽  
Indian Ocean ◽  
Tropical Cyclones ◽  
Austral Summer ◽  
Lagrangian Model ◽  
Southwest Indian Ocean ◽  
Tropical Tropopause Layer ◽  
Tropical Tropopause ◽  
Tropopause Region ◽  
The Impact

Abstract. Balloon-borne measurements of cryogenic frost-point hygrometer (CFH) water vapor, ozone and temperature and water vapor lidar measurements from the Maïdo Observatory on Réunion Island in the southwest Indian Ocean (SWIO) were used to study tropical cyclones' influence on tropical tropopause layer (TTL) composition. The balloon launches were specifically planned using a Lagrangian model and Meteosat-7 infrared images to sample the convective outflow from tropical storm (TS) Corentin on 25 January 2016 and tropical cyclone (TC) Enawo on 3 March 2017. Comparing the CFH profile to Aura's Microwave Limb Sounder's (MLS) monthly climatologies, water vapor anomalies were identified. Positive anomalies of water vapor and temperature, and negative anomalies of ozone between 12 and 15 km in altitude (247 to 121 hPa), originated from convectively active regions of TS Corentin and TC Enawo 1 d before the planned balloon launches according to the Lagrangian trajectories. Near the tropopause region, air masses on 25 January 2016 were anomalously dry around 100 hPa and were traced back to TS Corentin's active convective region where cirrus clouds and deep convective clouds may have dried the layer. An anomalously wet layer around 68 hPa was traced back to the southeast Indian Ocean where a monthly water vapor anomaly of 0.5 ppmv was observed. In contrast, no water vapor anomaly was found near or above the tropopause region on 3 March 2017 over Maïdo as the tropopause region was not downwind of TC Enawo. This study compares and contrasts the impact of two tropical cyclones on the humidification of the TTL over the SWIO. It also demonstrates the need for accurate balloon-borne measurements of water vapor, ozone and aerosols in regions where TTL in situ observations are sparse.

scholarly journals Species delimitation and life stage association of Propsilocerus Kieffer, 1923 (Diptera, Chironomidae) using DNA barcodes

ZooKeys ◽  
2020 ◽  
Vol 975 ◽  
pp. 79-86
Author(s):  
Hai-Jun Yu ◽  
Xiao-Long Lin ◽  
Rui-Lei Zhang ◽  
Qian Wang ◽  
Xin-Hua Wang
Keyword(s):  
Species Delimitation ◽  
Life Stage ◽  
Dna Barcodes ◽  
Neighbor Joining ◽  
Index Numbers ◽  
Nj Tree ◽  
Barcode Gap

The utility of COI DNA barcodes in species delimitation is explored as well as life stage associations of five closely related Propsilocerus species: Propsilocerus akamusi (Tokunaga, 1938), Propsilocerus paradoxus (Lundström, 1915), Propsilocerus saetheri Wang, Liu et Paasivirta, 2007, Propsilocerus sinicus Sæther et Wang, 1996, and Propsilocerus taihuensis (Wen, Zhou et Rong, 1994). Results revealed distinctly larger interspecific than intraspecific divergences and indicated a clear “barcode gap”. In total, 42 COI barcode sequences including 16 newly generated DNA barcodes were applied to seven Barcode Index Numbers (BINs). A neighbor-joining (NJ) tree comprises five well-separated clusters representing five morphospecies. Comments on how to distinguish the larvae of P. akamusi and P. taihuensis are provided.

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