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Fulltext Pleistocene divergence across a mountain range and the influence of selection on mitogenome evolution in threatened Australian freshwater cod species

Harrisson K, Pavlova A, Gan HM, Lee YP, Austin CM, Sunnucks P

Heredity (Edinb), 2016 Jun;116(6):506-15.
PMID: 26883183 DOI: 10.1038/hdy.2016.8

Climatic differences across a taxon's range may be associated with specific bioenergetic demands and may result in genetics-based metabolic adaptation, particularly in aquatic ectothermic organisms that rely on heat exchange with the environment to regulate key physiological processes. Extending down the east coast of Australia, the Great Dividing Range (GDR) has a strong influence on climate and the evolutionary history of freshwater fish species. Despite the GDR acting as a strong contemporary barrier to fish movement, many species, and species with shared ancestries, are found on both sides of the GDR, indicative of historical dispersal events. We sequenced complete mitogenomes from the four extant species of the freshwater cod genus Maccullochella, two of which occur on the semi-arid, inland side of the GDR, and two on the mesic coastal side. We constructed a dated phylogeny and explored the relative influences of purifying and positive selection in the evolution of mitogenome divergence among species. Results supported mid- to late-Pleistocene divergence of Maccullochella across the GDR (220-710 thousand years ago), bringing forward previously reported dates. Against a background of pervasive purifying selection, we detected potentially functionally relevant fixed amino acid differences across the GDR. Although many amino acid differences between inland and coastal species may have become fixed under relaxed purifying selection in coastal environments rather than positive selection, there was evidence of episodic positive selection acting on specific codons in the Mary River coastal lineage, which has consistently experienced the warmest and least extreme climate in the genus.

Matched MeSH terms: Endangered Species
Benzofurans and dibenzofurans from galls on twigs of the endangered Chinese endemic tree Parrotia subaequalis and their inhibitory properties against Staphylococcus aureus and ATP-citrate lyase

Zhou PJ, Wu XY, Zhao ZY, Zang Y, Sun ZS, Li YL, et al.

Phytochemistry, 2025 Jan;229:114309.
PMID: 39427693 DOI: 10.1016/j.phytochem.2024.114309

Parrotia subaequalis, an endangered Tertiary relict tree native to China and a member of the Hamamelidaceae family, is one of several host plant species in this family that exhibit unique ecological habits, such as gall formation. Tree galls are the results of complex interactions between gall-inducing insects and their host plant organs. The formation of galls may serve to protect other regions of the plant from potential damage, often through the production of phytoalexins. In this study, a preliminary investigation was carried out on the metabolites of the 90% MeOH extract derived from the closed spherical galls on the twigs of P. subaequalis. Consequently, nine previously undescribed benzofuran-type and dibenzofuran-type phytoalexins (parrotiagallols A-I, 1-9, respectively) were isolated and characterized, along with several known miscellaneous metabolites (10-17). Their chemical structures and absolute configurations were elucidated using spectroscopic methods, a combination of calculated and experimental electronic circular dichroism data, and single crystal X-ray diffraction analyses. Among these compounds, 1 and 2 are identified as neolignan derivatives, while compounds 3-5 are classified as 9,10-dinorneolignans. Compound 6 represents a rare 2,3-seco-neolignan, and compounds 7-9 are dihydroxy-dimethyl-dibenzofuran derivatives. Parrotiagallol A (1) showed considerable antibacterial activity against Staphylococcus aureus, with an MIC value of 14 μM. Additionally, parrotiagallol E (5) and methyl gallate (17) exhibited inhibitory effects against ATP-citrate lyase (ACL), a potential therapeutic target for hyperlipidemia, with IC50 values of 5.1 and 9.8 μM, respectively. The findings underscore that galls not only serve as physical defense barriers but also benefit from the chemical defense system of the host plants. These insights provide avenues for exploring potential new therapeutic agents for S. aureus infections and ACL-related diseases, while also promoting scientific conservation strategies for P. subaequalis.

Matched MeSH terms: Endangered Species
Fulltext Using DNA metabarcoding and direct behavioural observations to identify the diet of proboscis monkeys (Nasalis larvatus) in the Kinabatangan Floodplain, Sabah

Thiry V, Boom AF, Stark DJ, Hardy OJ, Beudels-Jamar RC, Vercauteren Drubbel R, et al.

PLoS One, 2025;20(1):e0316752.
PMID: 39752478 DOI: 10.1371/journal.pone.0316752

Characterizing the feeding ecology of threatened species is essential to establish appropriate conservation strategies. We focused our study on the proboscis monkey (Nasalis larvatus), an endangered primate species which is endemic to the island of Borneo. Our survey was conducted in the Lower Kinabatangan Wildlife Sanctuary (LKWS), a riverine protected area that is surrounded by oil palm plantations. We aimed to determine the diet of multiple proboscis monkey groups by using two methods. First, we conducted boat-based direct observations (scan and ad libitum sampling) and identified 67 plant species consumed by the monkeys at their sleeping sites in early mornings and late afternoons. Secondly, we used the DNA metabarcoding approach, based on next-generation sequencing (NGS, MiSeq Illumina) of faecal samples (n = 155), using the short chloroplast sequence, the trnL (UAA) P6 loop. In addition, we built a DNA reference database with the local plants available in the LKWS. When combining feeding data from both methods, we reported a diverse dietary ecology in proboscis monkeys, with at least 89 consumed plant taxa, belonging to 76 genera and 45 families. Moreover, we were able to add 22 new genera as part of the diet of this endangered colobine primate in the LKWS. The two methods provided congruent and complementary results, both having their advantages and limitations. This study contributed to enhance the knowledge on the feeding ecology of proboscis monkeys, highlighting the significance of several plant species that should further be considered in habitat restoration plans or corridor establishment.

Matched MeSH terms: Endangered Species
Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species

Nater A, Mattle-Greminger MP, Nurcahyo A, Nowak MG, de Manuel M, Desai T, et al.

Curr Biol, 2017 Nov 20;27(22):3487-3498.e10.
PMID: 29103940 DOI: 10.1016/j.cub.2017.09.047

Six extant species of non-human great apes are currently recognized: Sumatran and Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos [1]. However, large gaps remain in our knowledge of fine-scale variation in hominoid morphology, behavior, and genetics, and aspects of great ape taxonomy remain in flux. This is particularly true for orangutans (genus: Pongo), the only Asian great apes and phylogenetically our most distant relatives among extant hominids [1]. Designation of Bornean and Sumatran orangutans, P. pygmaeus (Linnaeus 1760) and P. abelii (Lesson 1827), as distinct species occurred in 2001 [1, 2]. Here, we show that an isolated population from Batang Toru, at the southernmost range limit of extant Sumatran orangutans south of Lake Toba, is distinct from other northern Sumatran and Bornean populations. By comparing cranio-mandibular and dental characters of an orangutan killed in a human-animal conflict to those of 33 adult male orangutans of a similar developmental stage, we found consistent differences between the Batang Toru individual and other extant Ponginae. Our analyses of 37 orangutan genomes provided a second line of evidence. Model-based approaches revealed that the deepest split in the evolutionary history of extant orangutans occurred ∼3.38 mya between the Batang Toru population and those to the north of Lake Toba, whereas both currently recognized species separated much later, about 674 kya. Our combined analyses support a new classification of orangutans into three extant species. The new species, Pongo tapanuliensis, encompasses the Batang Toru population, of which fewer than 800 individuals survive. VIDEO ABSTRACT.

Matched MeSH terms: Endangered Species
Fulltext Behavioral studies and veterinary management of orangutans at Bukit Merah Orang Utan Island, Perak, Malaysia

Hayashi M, Kawakami F, Roslan R, Hapiszudin NM, Dharmalingam S

Primates, 2018 Mar;59(2):135-144.
PMID: 29383576 DOI: 10.1007/s10329-018-0650-2

The Bukit Merah Orang Utan Island (OUI) Foundation has been conducting behavioral and veterinary research on orangutans as an attempt at ex situ conservation. Since 2010, the Primate Research Institute, Kyoto University has been collaborating with OUI to promote environmental enrichment and infant rearing by biological mothers in addition to the continuous efforts of refining the veterinary management of the endangered species. In 2011, three Bornean orangutans (Pongo pygmaeus pygmaeus) were released on an island, called BJ Island, adjacent to OUI. This island is approximately 5.6 ha in size, and 635 trees belonging to 102 plant species were identified prior to their release. Behavioral monitoring of the released individuals has been conducted to evaluate their behavioral adaptation to the new environment. Two of the three released orangutans were born in the wild, whereas the youngest individual was born on OUI and expected to learn forest survival strategies from the two older individuals. One of the orangutans was pregnant at the time of release and subsequently gave birth to two male infants on BJ Island. The behavioral monitoring indicated that these orangutans traveled more and spent more time on trees following their release onto BJ Island. However, resting was longer for two females both on OUI and BJ Island when compared to other populations. The orangutans consumed some natural food resources on BJ Island. The release into a more naturalistic environment may help the orangutans to develop more naturalistic behavioral patterns that resemble their wild counterparts.

Matched MeSH terms: Endangered Species
A new species of karst forest Bent-toed Gecko (genus Cyrtodactylus Gray) not yet threatened by foreign cement companies and a summary of Peninsular Malaysia's endemic karst forest herpetofauna and the need for its conservation

Grismer LL, Wood PL, Anuar S, Davis HR, Cobos AJ, Murdoch ML

Zootaxa, 2016 Jan 04;4061(1):1-17.
PMID: 27395475 DOI: 10.11646/zootaxa.4061.1.1

A new species of Bent-toed Gecko, Cyrtodactylus gunungsenyumensis sp. nov. of the sworderi complex, is described from Hutan Lipur Gunung Senyum, Pahang, Peninsular Malaysia and is differentiated from all other species in the sworderi complex by having a unique combination of characters including a maximum SVL of 74.7 mm; low, rounded, weakly keeled, body tubercles; 34-40 paravertebral tubercles; weak ventrolateral body fold lacking tubercles; 38-41 ventral scales; an abrupt transition between the posterior and ventral femoral scales; 20-23 subdigital lamellae on the fourth toe; enlarged femoral scales; no femoral or precloacal pores; no precloacal groove; wide caudal bands; and an evenly banded dorsal pattern. Cyrtodactylus gunungsenyumensis sp. nov. is a scansorial, karst forest-adapted specialist endemic to the karst ecosystem surrounding Gunung Senyum and occurs on the vertical walls of the limestone towers as well as the branches, trunks, and leaves of the vegetation in the associated karst forest. Cyrtodactylus gunungsenyumensis sp. nov. is the seventh species of karst forest-adapted Cyrtodactylus and the sixteenth endemic species of karst ecosystem reptile discovered in Peninsular Malaysia in the last seven years from only 12 different karst forests. This is a clear indication that many species remain to be discovered in the approximately 558 isolated karst ecosystems in Peninsular Malaysia not yet surveyed. These data continue to underscore the importance of karst ecosystems as reservoirs of biodiversity and microendemism and that they constitute an important component of Peninsular Malaysia's natural heritage and should be protected from the quarrying interests of foreign industrial companies.

Matched MeSH terms: Endangered Species
Fulltext A standardized dataset for conservation prioritization of songbirds to support CITES

Juergens J, Bruslund S, Staerk J, Oegelund Nielsen R, Shepherd CR, Leupen B, et al.

Data Brief, 2021 Jun;36:107093.
PMID: 34041313 DOI: 10.1016/j.dib.2021.107093

In this article we present a standardized dataset on 6659 songbirds (Passeriformes) highlighting information relevant to species conservation prioritization with a main focus to support the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Data were collected from both scientific and grey literature as well as several online databases. The data are structured into six knowledge categories: Conventions and Treaties, Human Use, Extinction Risk, Management Opportunities, Biological Information, and Intrinsic Values. The Conventions and Treaties category includes the listings for two international conventions, CITES and the Convention on the Conservation of Migratory Species of Wild Animals (CMS), as well as EU listings for the EU Wildlife Trade Regulations and the EU Birds Directive. The Human Use category contains information on both regulated trade collected from the CITES Trade Database and the United States' Law Enforcement Management Information System (LEMIS), and highly aggregated data on seizures which we obtained from TRAFFIC, the United Nations Office on Drugs and Crime (UNODC) and two data sources on traditional medicine. We also present, for the first time, the complete Songbirds in Trade Database (SiTDB), a trade database curated by taxon expert S. Bruslund based on expert knowledge, literature review, market surveys and sale announcements. Data on the types of human use, including traditional medicine are also provided. The knowledge area on Extinction Risk contains data on the species' IUCN Red List status, the Alliance for Zero Extinction Trigger Species status, site and population at the site, the species' IUCN Climate Change Vulnerability Assessment, and the listing of priority species at the Asian Songbird Crisis Summit. In the Management Opportunities category, we gathered data on ex-situ management from Species360 zoo holdings as well as species management plans from the European and North American Zoo Associations (EAZA and AZA, respectively). Biological Information includes data on body mass, clutch size, diet, availability of data from the IUCN Red List on habitat systems, extent of occurrence, generation length, migration pattern, distribution, and biological data from the Demographic Species Knowledge Index, number of occurrences recorded by the Global Biodiversity Information Facility (GBIF) as well as genomic data from the Bird 10 000K Genomes (B10K) project, Vertebrate Genome Project (VGP) and GenBank. Information on invasive species is also part of this knowledge area. The Intrinsic Value category refers to two measures of the species' intrinsic value, namely Ecological and Evolutionary Distinctiveness. In order to make these knowledge areas comparable, we standardized data following the taxonomy of the Handbook of the Birds of the World and Birdlife (Version 4, 2019). The data enable a broad spectrum of analyses and will be useful to scientists for further research and to policymakers, zoos and other conservation stakeholders for future prioritization decisions.

Matched MeSH terms: Endangered Species
Fulltext Blood meal analysis of tabanid fly after it biting the rare Sumatran rhinoceros

Rovie-Ryan JJ, Zainuddin ZZ, Marni W, Ahmad AH, Ambu LN, Payne J

Asian Pac J Trop Biomed, 2013 Feb;3(2):95-9.
PMID: 23593586 DOI: 10.1016/S2221-1691(13)60031-3

To demonstrate a noninvasive large mammalian genetic sampling method using blood meal obtained from a tabanid fly.

Matched MeSH terms: Endangered Species
The complete mitogenome of the endangered freshwater crayfish Cherax tenuimanus (Smith 1912) (Crustacea: Decapoda: Parastacidae)

Austin CM, Tan MH, Gan HY, Gan HM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4176-4177.
PMID: 25630729

Next-Gen sequencing was used to recover the complete mitochondrial genome of Cherax tenuimanus. The mitogenome consists of 15,797 base pairs (68.14% A + T content) containing 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs, and a 779 bp non-coding AT-rich region. Mitogenomes have now been recovered for all six species of Cherax native to Western Australia.

Matched MeSH terms: Endangered Species
Fulltext DNA Barcoding of the Endangered Aquilaria (Thymelaeaceae) and Its Application in Species Authentication of Agarwood Products Traded in the Market

Lee SY, Ng WL, Mahat MN, Nazre M, Mohamed R

PLoS One, 2016;11(4):e0154631.
PMID: 27128309 DOI: 10.1371/journal.pone.0154631

The identification of Aquilaria species from their resinous non-wood product, the agarwood, is challenging as conventional techniques alone are unable to ascertain the species origin. Aquilaria is a highly protected species due to the excessive exploitation of its precious agarwood. Here, we applied the DNA barcoding technique to generate barcode sequences for Aquilaria species and later applied the barcodes to identify the source species of agarwood found in the market. We developed a reference DNA barcode library using eight candidate barcode loci (matK, rbcL, rpoB, rpoC1, psbA-trnH, trnL-trnF, ITS, and ITS2) amplified from 24 leaf accessions of seven Aquilaria species obtained from living trees. Our results indicated that all single barcodes can be easily amplified and sequenced with the selected primers. The combination of trnL-trnF+ITS and trnL-trnF+ITS2 yielded the greatest species resolution using the least number of loci combination, while matK+trnL-trnF+ITS showed potential in detecting the geographical origins of Aquilaria species. We propose trnL-trnF+ITS2 as the best candidate barcode for Aquilaria as ITS2 has a shorter sequence length compared to ITS, which eases PCR amplification especially when using degraded DNA samples such as those extracted from processed agarwood products. A blind test conducted on eight agarwood samples in different forms using the proposed barcode combination proved successful in their identification up to the species level. Such potential of DNA barcoding in identifying the source species of agarwood will contribute to the international timber trade control, by providing an effective method for species identification and product authentication.

Matched MeSH terms: Endangered Species
Characterizing the gastrointestinal microbiome diversity in endangered Malayan Siamang (Symphalangus syndactylus): Insights into group composition, age variability and sex-related patterns

Sariyati NH, Othman N, Abdullah-Fauzi NAF, Chan E, Md-Zain BM, Karuppannan KV, et al.

J Med Primatol, 2024 Oct;53(5):e12730.
PMID: 39148344 DOI: 10.1111/jmp.12730

BACKGROUND: The gut morphology of Symphalangus syndactylus exhibits an intermediate structure that aligns with its consumption of fruit and ability to supplement its diet with leaves. The Siamang relies on its gut microbiome for energy extraction, immune system development, and the synthesis of micronutrients. Gut microbiome composition may be structured based on several factors such as age, sex, and habitat. No study has yet been carried out on the gut microbiota of the Hylobatidae members in Malaysia especially S. syndactylus.
METHODS: This study aims to resolve the gut microbiome composition of S. syndactylus by using a fecal sample as DNA source, adapting high-throughput sequencing, and 16S rRNA as the targeted region.
RESULTS: A total of 1 272 903 operational taxonomic units (OTUs) reads were assigned to 22 phyla, 139 families, and 210 genera of microbes. The {Unknown Phylum} Bacteria-2 is the dominant phyla found across all samples. Meanwhile, {Unknown Phylum} Bacteria-2 and Firmicutes are genera that have the highest relative abundance found in the Siamang gut.
CONCLUSIONS: This study yields nonsignificance relationship between Siamang gut microbiome composition with these three factors: group, sex, and age.

Matched MeSH terms: Endangered Species
Profiling the Gut Microbiome of Hylobatidae and Cercopithecinae: Insights Into the Health of Primates in Captivity

Tingga RCT, Mohd-Ridwan AR, Denel A, Md-Zain BM

J Med Primatol, 2025 Apr;54(2):e70008.
PMID: 39994494 DOI: 10.1111/jmp.70008

BACKGROUND: A healthy gut microbiome is essential for digestion in primates, for developing the gut immune system, and for defense against pathogen invasion. Next-generation sequencing allows for determining the microbiome composition and enables the continuous monitoring of primate health.
METHODS: To comprehensively analyze the gut microbiome diversity of three endangered primate species at Matang Wildlife Centre-Hylobates abbotti, Macaca fascicularis, and Macaca nemestrina, using high-throughput sequencing of the 16S rRNA gene.
RESULTS: A total of 18 phyla, 84 families, 188 genera, and 46 species were successfully classified. H. abbotti exhibited the highest microbial diversity with a distinct microbiome profile from the Macaca species. The presence of Treponema (nonpallidum), Bifidobacterium, and Faecalibacterium prausnitzii is critical for gut health, promoting digestion and maintaining the microbial balance.
CONCLUSION: This study highlights the importance of monitoring microbial diversity in captive primates to better understand their health and facilitate the early detection of potential pathogens. This also offers insights into microbiome-based strategies for improving overall animal welfare.

Matched MeSH terms: Endangered Species
Fulltext Transcriptome Profiling of Haloxylon persicum (Bunge ex Boiss and Buhse) an Endangered Plant Species under PEG-Induced Drought Stress

Thayale Purayil F, Rajashekar B, S Kurup S, Cheruth AJ, Subramaniam S, Hassan Tawfik N, et al.

Genes (Basel), 2020 06 10;11(6).
PMID: 32531994 DOI: 10.3390/genes11060640

Haloxylon persicum is an endangered western Asiatic desert plant species, which survives under extreme environmental conditions. In this study, we focused on transcriptome analysis of H. persicum to understand the molecular mechanisms associated with drought tolerance. Two different periods of polyethylene glycol (PEG)-induced drought stress (48 h and 72 h) were imposed on H. persicum under in vitro conditions, which resulted in 18 million reads, subsequently assembled by de novo method with more than 8000 transcripts in each treatment. The N50 values were 1437, 1467, and 1524 for the control sample, 48 h samples, and 72 h samples, respectively. The gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis resulted in enrichment of mitogen-activated protein kinase (MAPK) and plant hormone signal transduction pathways under PEG-induced drought conditions. The differential gene expression analysis (DGEs) revealed significant changes in the expression pattern between the control and the treated samples. The KEGG analysis resulted in mapping transcripts with 138 different pathways reported in plants. The differential expression of drought-responsive transcription factors depicts the possible signaling cascades involved in drought tolerance. The present study provides greater insight into the fundamental transcriptome reprogramming of desert plants under drought.

Matched MeSH terms: Endangered Species
Fulltext Sustainable Syntheses of (-)-Jerantinines A & E and Structural Characterisation of the Jerantinine-Tubulin Complex at the Colchicine Binding Site

Smedley CJ, Stanley PA, Qazzaz ME, Prota AE, Olieric N, Collins H, et al.

Sci Rep, 2018 Jul 13;8(1):10617.
PMID: 30006510 DOI: 10.1038/s41598-018-28880-2

The jerantinine family of Aspidosperma indole alkaloids from Tabernaemontana corymbosa are potent microtubule-targeting agents with broad spectrum anticancer activity. The natural supply of these precious metabolites has been significantly disrupted due to the inclusion of T. corymbosa on the endangered list of threatened species by the International Union for Conservation of Nature. This report describes the asymmetric syntheses of (-)-jerantinines A and E from sustainably sourced (-)-tabersonine, using a straight-forward and robust biomimetic approach. Biological investigations of synthetic (-)-jerantinine A, along with molecular modelling and X-ray crystallography studies of the tubulin-(-)-jerantinine B acetate complex, advocate an anticancer mode of action of the jerantinines operating via microtubule disruption resulting from binding at the colchicine site. This work lays the foundation for accessing useful quantities of enantiomerically pure jerantinine alkaloids for future development.

Matched MeSH terms: Endangered Species

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