Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The Theory of Island Biogeography

Since their inception, DNA barcodes have become a powerful tool for understanding the biodiversity and biology of aquatic species, with multiple applications in diverse fields such as food security, fisheries, environmental DNA, conservation, and exotic species detection. Nevertheless, most aquatic ecosystems, from marine to freshwater, are understudied, with many species disappearing due to environmental stress, mostly caused by human activities. Here we highlight the progress that has been made in studying aquatic organisms with DNA barcodes, and encourage its further development in assisting sustainable use of aquatic resources and conservation.

Aquatic Organisms Research with DNA Barcodes

Specific status and species boundaries of several freshwater prawns in the Macrobrachium pilimanus species group remain ambiguous, despite the taxonomic re-description of type materials and additional specimens collected to expand the boundaries of some species. In this study, the "pilimanus" species group of Macrobrachium sensu Johnson (1958) was studied using specimens collected from montane streams of Thailand. Molecular phylogenetic analyses based on sequences of three molecular markers (COI, 16S and 18S rRNA) were performed. The phylogenetic results agreed with morphological identifications, and indicated the presence of at least nine putative taxa. Of these, six morphospecies were recognised as M. malayanum, M. forcipatum, M. dienbienphuense, M. hirsutimanus, M. eriocheirum, and M. sirindhorn. Furthermore, three morphologically and genetically distinct linages were detected, and are described herein as M. naiyanetri Siriwut sp. nov. , M. palmopilosum Siriwut sp. nov. and M. puberimanus Siriwut sp. nov. The taxonomic comparison indicated wide morphological variation in several species and suggested additional diagnostic characters that are suitable for use in species diagnoses, such as the shape and orientation of fingers, the rostrum form, and the presence or absence of velvet pubescence hairs and tuberculated spinulation on each telopodite of the second pereiopods. The "pilimanus" species group was portrayed as non-monophyletic in both ML and BI analyses. The genetic structure of different geographical populations in Thailand was detected in some widespread species. The species delimitation based on the four delimitation methods (BIN, ABGD, PTP and GMYC) suggested high genetic diversity of the "pilimanus" species group and placed the candidate members much higher than in previous designations based on traditional morphology. This finding suggests that further investigation of morphological and genetic diversity of Southeast Asian freshwater prawns in the genus Macrobrachium is still required to provide a comprehensive species list to guide efforts in conservation and resource management.

/pdf/molecular-phylogeny-and-species-delimitation-of-the-2vtvx9sddi.pdf

Molecular phylogeny and species delimitation of the freshwater prawn Macrobrachium pilimanus species group, with descriptions of three new species from Thailand.

The diversity of Indochinese prawns in genus Macrobrachium is enormous due to the habitat diversification and broad tributary networks of two river basins: the Chao Phraya and the Mekong. Despite long-standing interest in SE-Asian decapod diversity, the subregional Macrobrachium fauna is still not yet comprehensively clarified in terms of taxonomic identification or genetic diversification. In this study, integrative taxonomic approaches including morphological examination, DNA barcoding, and molecular species delimitation were used to emphasize the broad scale systematics of Macrobrachium prawns in Indochina. Twenty-seven nominal species were successfully re-verified by traditional and molecular taxonomy. Barcode gap analysis supported broad overlapping of species boundaries. Taxonomic ambiguity of several deposited samples in the public database is related to inter- and intraspecific genetic divergence as indicated by BOLD discordance. Diagnostic nucleotide positions were found in six Macrobrachium species. Eighteen additional putative lineages are herein assigned using the consensus of species delimitation methods. Genetic divergence indicates the possible existence of cryptic species in four morphologically complex and wide-ranging species: M. lanchesteri, M. niphanae, M. sintangense, and some members of the M. pilimanus group. The geographical distribution of some species supports the connections and barriers attributed to paleo-historical events of SE-Asian rivers and land masses. Results of this study show explicitly the importance of freshwater ecosystems in Indochinese subregions, especially for the Mekong River Basin due to its high genetic diversity and species composition found throughout its tributaries.

/pdf/evidence-of-cryptic-diversity-in-freshwater-macrobrachium-1sdhmot2b7.pdf

Evidence of cryptic diversity in freshwater Macrobrachium prawns from Indochinese riverine systems revealed by DNA barcode, species delimitation and phylogenetic approaches.

Ohta-MatSubaYaShi, Y., KataKura, H., KahOnO, S. and KiKuchi, N. 2017. A taxonomic review of the phytophagous ladybird beetles of the Diekeana alternans complex (Coleoptera: Coccinellidae: Epilachnini) with descriptions of eight new species and one new subspecies. Ins. matsum. n. s. 73: 1–37, 14 figs, 1 table, 3 online supplementary figs. A group of phytophagous ladybird beetles utilizing diverse host plants in South and Southeast Asia was reviewed as the Diekeana alternans complex. Ten species (one with two subspecies) including seven new species and one new subspecies were described or redescribed under this species complex. Diekeana hopeiana (Miyatake) was synonymized with D. grayi (Mulsant). Two other species were also incorporated into this complex based on literature information. Additionally, another species closely related to this species complex was described as new to science. Species of the D. alternans complex constituted a part of the Diekeana admirabilis group and were characterized by a “blade” situated at the apical part of penis of male genitalia. Almost all the species could be identified by the species-specific conditions of male genitalia. The species that utilize cucurbitaceous plants of the tribes Benincaseae, Sicyoeae and/or Cucurbiteae were widespread in South and Southeast Asia comprising at least four allopatric species. On the other hand, the species specialized to other taxonomic groups of host plants were localized in either Sumatra or Java with a possible exception of D. glochinosa (Pang & Mao) in South China. They often sympatrically occurred with each other or with one of the cucurbitaceous plant feeders. Authors’ addresses. Ohta-Matsubayashi, Y.: Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan. Katakura, H.: The Hokkaido University Museum, Hokkaido University, Sapporo 060-0810, Japan (corresponding author: haruo_katakura@ nifty.com). Kahono, S.: Zoology Division (Museum Zoologicum Bogoriense), Research Center for Biology, Indonesian Institute of Science (LIPI), Cibinong 16911, Indonesia. KiKuchi, N.: Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.

/pdf/a-taxonomic-review-of-the-phytophagous-ladybird-beetles-of-1gejeo1jwt.pdf

A taxonomic review of the phytophagous ladybird beetles of the Diekeana alternans complex (Coleoptera: Coccinellidae: Epilachnini) with descriptions of eight new species and one new subspecies

The Cikaniki resort is one of the most accessible research stations located in the Gunung Halimun Salak National Park (GHSNP). It is in adjacent with Citalahab village. The Research Center for Biology, Indonesian Institute of Sciences and other institutions have conducted intensive research on the fauna diversity of GHSNP from this station. Here we formulate a checklist on fauna diversity surrounding the Cikaniki Research Station and Citalahab, GHNSP from various sources, i.e. field work, museum collections (Museum Zoologicum Bogoriense), scientific publications, and technical report. The study was conducted from October 2019 until October 2020. The latest field work was conducted from 8-10 October 2019 under the framework of the Jungle Survival and Biological Collection Management 2019 program. In total, 821 fauna species were recorded in Cikaniki-Citalahab areas which comprises of 48 species of Mollusca, five species of Malacostraca, 523 species of Insects, 22 species of Actinopterygii, 63 species of Amphibia and Reptiles, 115 species of Aves and 45 species of Mammals. The diversity contributes 62.1% of the total 1,323 known fauna species in GHSNP. Five number of species were assigned as endangered and three species critical endangered by IUCN. In addition, 123 species were endemic to Java and 34 species protected by Regulation of the Ministry of Environment and Forestry Republic of Indonesia Number P.106/MENLHK/SETJEN/KUM.1/12/2018. The areas of Cikaniki and Citalahab are rich in biodiversity. Although both areas are in close intact with human activity, research and ecotourism, the need of continuously spreading awareness and enforce species and area conservation is inevitable.

https://e-journal.biologi.lipi.go.id/index.php/zoo_indonesia/article/download/4037/3278

CHECKLIST ON FAUNA DIVERSITY GUNUNG HALIMUN SALAK NATIONAL PARK: Cikaniki-Citalahab

Species proliferate through evolutionary mechanisms but coexist through ecological dynamics. As such, it might be expected that mechanisms of speciation and species maintenance jointly influence the settlement of ecological communities, a process called community assembly. Disentangling the relative contribution of evolutionary and ecological dynamics might be a difficult task, particularly so for the tropical biotas due to their extreme diversity and large knowledge gaps. Here, we explore genetic diversity and distribution of 23 freshwater shrimp species of the genera Caridina and Macrobrachium in Sundaland to examine patterns of species co-occurrence based on 1583 observations across 19 sites in Java and Bali islands. DNA-based species delimitation methods applied to 204 cytochrome oxidase I sequences detected 30 operational taxonomic units and a few cases of deep intraspecific divergence. Species co-occurrence and phylogenetic community structure show no departure from expectations under a random distribution of species in landscapes and support a lottery model of community assembly. Species age estimates expand beyond the geological settlement of Sundaland, suggesting that species proliferation and community assembly are driven by mechanisms acting at distinct spatial and temporal scales.

Exploring community assembly among Javanese and Balinese freshwater shrimps (Atyidae, Palaemonidae) through DNA barcodes

Mangrove ecosystem is one of the unique ecological niches and the ideal habitat for several groups of fishes. The total area of mangroves in Indonesia is estimated at 3,489,140.68 ha. Although many studies have been conducted, there are still many fish species of this ecosystem that have not been revealed. This study aims to determine the fish community in several mangrove hotspots in Banyuasin Regency, South Sumatra. Specimen collection was carried out in May–June 2021 by using various fishing gears including hand net, seine net, and gill net. Water parameters, e.g., pH, salinity, and temperature, were also measured. This research has succeeded in collecting 31 fish species consisting of 20 families and 26 genera with a total of 145 individuals. Gobiidae and Butidae are the two most abundant families in term of number of species with 7 and 4 species, respectively. The remaining families each were represented by 1 species. Oryzias javanicus, Planiliza subviridis, and Ambassis macracanthus had the highest relative abundance values compared to other species. This study also found the first record for Bostrychus cf. scalaris from Indonesian water which B. scalaris was previously known only from Peninsular Malaysia.

https://iopscience.iop.org/article/10.1088/1755-1315/1191/1/012005/pdf

Update on fish community in the mangrove ecosystems of Banyuasin Regency, South Sumatra, Indonesia, with the addition of the first record of the genus Bostrychus

Rena Tri Hernawati

Papers

CHECKLIST ON FAUNA DIVERSITY GUNUNG HALIMUN SALAK NATIONAL PARK: Cikaniki-Citalahab

Exploring community assembly among Javanese and Balinese freshwater shrimps (Atyidae, Palaemonidae) through DNA barcodes

Update on fish community in the mangrove ecosystems of Banyuasin Regency, South Sumatra, Indonesia, with the addition of the first record of the genus Bostrychus