RFE-based feature selection to improve classification accuracy for morphometric analysis of craniodental characters of house rats

In conventional morphometrics, researchers often collect and analyze data using large numbers of morphometric features to study the shape variation among biological organisms. Feature selection is a fundamental tool in machine learning which is used to remove irrelevant and redundant features. Recursive feature elimination (RFE) is a popular feature selection technique that reduces data dimensionality and helps in selecting the subset of attributes based on predictor importance ranking. In this study, we perform RFE on the craniodental measurements of the Rattus rattus data to select the best feature subset for both males and females. We also performed a comparative study based on three machine learning algorithms such as Naïve Bayes, Random Forest, and Artificial Neural Network by using all features and the RFE-selected features to classify the R. rattus sample based on the age groups. Artificial Neural Network has shown to provide the best accuracy among these three predictive classification models

Molecular phylogeny of long-tailed giant rats (Muridae: genus leopoldamys) based on mitochondrial cytochrome B sequences

Two species of Leopoldamys long-tailed giant rats are found in Peninsular Malaysia. They are currently referred to as Leopoldamys ciliatus which inhabits montane habitat, and Leopoldamys vociferans which usually inhabits the lowland forest. To date, there is no report on the phylogenetic relationship of L. ciliatus with the other Leopoldamys taxa. The present study was carried out to determine its relationship, based on the mitochondrial cytochrome b (cyt b) gene sequence, with L. vociferans of Peninsular Malaysia and other congeners. Phylogenetic analysis shows that L. ciliatus is a sister-species to the lineage L1 of L. herberti and L. revertens, and is distantly related to L. edwardsi. L. vociferans, and L. sabanus form a distinct clade (lineage L5) from the other Leopoldamys taxa from Indochina. The Sumatra taxon currently known as L. sabanus is genetically distinct to L. vociferans with K2P distances between 0.065 and 0.069. Contrary to previous opinions, L. herberti, L. revertens, and L. neilli of Indochina are valid species based on more than 2.5% threshold genetic distance. Both the L. edwardsi and L. neilli species complexes are represented by several sibling species. A more extensive taxon sampling from various regions (particularly Sumatra and other regions of Indonesia) as well as the use of morphological and molecular (mitogenomes or multiple genes) data sets are needed to provide a robust phylogeny and systematics

Toxicity of Malaysian Medicinal Plant Extracts Against Sitophilus oryzae and Rhyzopertha dominica

The insecticidal activities of extracts from 22 Malaysian medicinal plant extracts from 8 botanical families were tested against rice weevil: Sitophilus oryzae (L.) and lesser grain borer: Rhyzopertha dominica (F.). The extracts were obtained using hexane, methanol, and dichloromethane to extract potential biopesticides from dried leaves. The toxicity levels were examined periodically based on antifeedant activity and contact toxicity assays using treated grain assay. Hexane extracts of Alpinia conchigera, Alpinia scabra, Curcuma mangga, Curcuma purpurascens, Goniothalamus tapisoides, Piper sarmentosum , and methanol extracts of Curcuma aeruginosa, C. mangga , and Mitragyna speciosa were the most potent extracts against S. oryzae and R. dominica with lethal concentration (LC50) values of ≤ 0.42 mg/mL and ≤ 0.49 mg/mL, respectively. The contact toxicity test results showed that methanol extracts of C. aeruginosa and C. mangga , dichloromethane extracts of Cryptocarya nigra , and hexane extracts of C. mangga, and C. purpurascens resulted in 100% mortality of both pests within 28 days exposure of 5 mg/cm2 concentration

Fig. 1 in Phylogenetic Relationships Of Malayan And Malagasy Pygmy Shrews Of The Genus Suncus (Soricomorpha: Soricidae) Inferred From Mitochondrial Cytochrome B Gene Sequences

Fig. 1. Male Malayan pygmy shrew (Suncus malayanus) captured in the Cameron Highlands, Pahang, Peninsular Malaysia, in a pitfall trap set on the forest floor. Notice the characteristic large ears and dark fine pelage.Published as part of <i>Omar, Hasmahzaiti, Adamson, Eleanor A. S., Bhassu, Subha, Goodman, Steven M. & Soarimalala, Voahangy, 2011, Phylogenetic Relationships Of Malayan And Malagasy Pygmy Shrews Of The Genus Suncus (Soricomorpha: Soricidae) Inferred From Mitochondrial Cytochrome B Gene Sequences, pp. 237-243 in Raffles Bulletin of Zoology 59 (2)</i> on page 238, DOI: <a href="http://zenodo.org/record/10107452">10.5281/zenodo.10107452</a&gt

Phylogenetic Relationships Of Malayan And Malagasy Pygmy Shrews Of The Genus Suncus (Soricomorpha: Soricidae) Inferred From Mitochondrial Cytochrome B Gene Sequences

Omar, Hasmahzaiti, Adamson, Eleanor A. S., Bhassu, Subha, Goodman, Steven M., Soarimalala, Voahangy (2011): Phylogenetic Relationships Of Malayan And Malagasy Pygmy Shrews Of The Genus Suncus (Soricomorpha: Soricidae) Inferred From Mitochondrial Cytochrome B Gene Sequences. Raffles Bulletin of Zoology 59 (2): 237-243, DOI: http://doi.org/10.5281/zenodo.1010745

Fig. 2 in Phylogenetic Relationships Of Malayan And Malagasy Pygmy Shrews Of The Genus Suncus (Soricomorpha: Soricidae) Inferred From Mitochondrial Cytochrome B Gene Sequences

Fig. 2. The neighbour-joining (A) and Bayesian (B) trees for Suncus inferred from 1140 base-pairs of cytochrome b gene sequence. Bootstrap and posterior probability values are given above branches.Published as part of <i>Omar, Hasmahzaiti, Adamson, Eleanor A. S., Bhassu, Subha, Goodman, Steven M. & Soarimalala, Voahangy, 2011, Phylogenetic Relationships Of Malayan And Malagasy Pygmy Shrews Of The Genus Suncus (Soricomorpha: Soricidae) Inferred From Mitochondrial Cytochrome B Gene Sequences, pp. 237-243 in Raffles Bulletin of Zoology 59 (2)</i> on page 241, DOI: <a href="http://zenodo.org/record/10107452">10.5281/zenodo.10107452</a&gt

Intraspecific phylogeny of the house shrews, Suncus murinus-S-montanus species complex, based on the mitochondrial cytochrome b gene

A phylogenetic tree was reconstructed based on the mitochondrial cytochrome b gene nucleotide sequences of 169 individuals of house shrews (Suncus murinus and S. montanus) from 44 localities in East Asia, Southeast Asia, West Asia, and islands in the western Indian Ocean. Shrews from China (Zhejiang), Japan (Okinawa), Vietnam, and Indonesia (Java) formed a monophyletic group with less genetic variation. Therefore, the shrews of these regions appeared to have originated from one or a few localities. Contrary to this, shrews from Sri Lanka, Myanmar, and Pakistan consisted of several haplogroups. This finding suggests immigration movements to these areas. Fascinating findings were also obtained concerning the islands in the western Indian Ocean. First, shrews on Zanzibar Island (Tanzania) had almost the same haplotype as those in southwestern Iran. Therefore, the house shrew in Zanzibar may have immigrated from Iran (or vice versa). Second, shrews from Madagascar and Grande Comore Island shared the same haplotype, whereas the shrews on Reunion Island were clearly different from those of Madagascar and Comoros. Thus, there appears to have been several immigration routes to the islands of the western Indian Ocean