Thoroughly sampled and well-supported phylogenetic trees are essential to taxonomy and to guide s... more Thoroughly sampled and well-supported phylogenetic trees are essential to taxonomy and to guide studies of evolution and ecology. Despite extensive prior inquiry, a comprehensive tree of heron relationships (Aves: Ardeidae) has not yet been published. As a result, the classification of this family remains unstable, and their evolutionary history remains poorly studied. Here, we sample genome-wide ultraconserved elements (UCEs) and mitochondrial DNA sequences (mtDNA) of >90% of extant species to estimate heron phylogeny using a combination of maximum likelihood, coalescent, and Bayesian inference methods. The UCE and mtDNA trees are mostly concordant with one another, providing a topology that resolves relationships among the 5 heron subfamilies and indicates that the genera Gorsachius, Botaurus, Ardea, and Ixobrychus are not monophyletic. We also present the first genetic data from the Forest Bittern Zonerodius heliosylus, an enigmatic species of New Guinea; our results suggest that it is a member of the genus Ardeola and not the Tigrisomatinae (tiger herons), as previously thought. Finally, we compare molecular rates between heron clades in the UCE tree with those in previously constructed mtDNA and DNA-DNA hybridization trees. We show that rate variation in the UCE tree corroborates rate patterns in the previously constructed trees-that bitterns (Ixobrychus and Botaurus) evolved comparatively faster, and some tiger herons (Tigrisoma) and the Boat-billed Heron (Cochlearius) more slowly, than other heron taxa.
The interspecific relationships and biogeography of seven southeast Asian tree shrew species in t... more The interspecific relationships and biogeography of seven southeast Asian tree shrew species in the genus Tupaia were examined by DNA hybridization and multivariate morphometric analysis. Urogale everetti served as the outgroup. DNA hybridization data indicate that T. tana is most closely related to T. montana, and they form a clade with T. minor. Morphometric comparisons indicate that T. tana and T. minor, and T. montana and T. palawanensis, form groups that, together, are most similar to T. glis. T. javanica and U. everetti cluster outside the rest of Tupaia. The DNA hybridization data support a model of Bornean speciation driven by sea-level changes. They also indicate either (1) that there is a large variation in the rate of tree shrew evolution or (2) that U. everetti may in fact be a member of the ingroup. When considered in light of the phylogenetic results, the morphometric data suggest substantial convergence in body size or correlation in character changes.
Occasional Papers of the Museum of Natural Science, 2023
Sarawak is Malaysia's largest state, covering most of northern Borneo. It has a remarkable histor... more Sarawak is Malaysia's largest state, covering most of northern Borneo. It has a remarkable history of scientific bird study, starting in the 1840s and growing ever since. To set the stage for the gazetteer, which is the core of this paper, we start with a review of this history and discuss various forces that have influenced the direction of bird research in the state. Following this introduction comes the gazetteer, which is an annotated list of c. 865 sites in Sarawak where birds have been collected, studied, or regularly observed. The gazetteer provides the latitude, longitude, and elevation of each site, and it lists publications, reports, and museum collections associated with each site. The purpose of the gazetteer is to help interested parties locate sites and investigate their research history. It is also intended to help museum curators geolocate specimens for various kinds of studies, including the assessment of bird distributions in relation to habitat change over time. A notable byproduct of the historical review and gazetteer is a bibliography of c. 750 references related to Sarawak ornithology. Another is the identification of areas in Sarawak where birds are better known and areas where they are not.
The chapter explores three fundamental issues: phylogenetic accuracy, adaptation, and phylogeneti... more The chapter explores three fundamental issues: phylogenetic accuracy, adaptation, and phylogenetic constraint. These issues are central to historical ecology and cover a broad range of subjects in the field. The most important step to successful historical ecology is the collection of appropriate, accurate, ecological, and phylogenetic data. Although obvious, this assertion is remarkably underemphasized in ecophylogenetic studies. Emphasis is placed primarily on the quality of ecological data, which are viewed as dependent variables, instead of on the accuracy of phylogeny, which is generally viewed as an independent variable without error. However, phylogenetic estimates have error distributions, but these are commonly ignored because they are too complicated to quantify. Historical ecology is burgeoning because it provides structure to the study of ecological patterns and evolutionary processes. Emphasis on the use of accurate phylogenetic data is crucial because the interpretation of evolutionary patterns obviously changes as relationships among taxa change. Although progress may be limited without knowledge of the quantitative genetics of specific traits, initial hypothesis testing is possible with prudent use of the phylogenetic approach, provided that multiple examples of potential evolutionary phenomena are examined.
... We thank AJ Baker, EA Cardiff, SW Cardiff, Mario Cohn-Haft, DL Dittmann, NK Klein, MB Robbins... more ... We thank AJ Baker, EA Cardiff, SW Cardiff, Mario Cohn-Haft, DL Dittmann, NK Klein, MB Robbins, RS Ridgely, F. Sornoza Molina, Paul Sweet, Katherine Wallace, Bret Whitney, Academy of Natural ...Daniel F. Lane provided advice on plumage variation in Gray-breasted Martin. ...
Els, Paul van, Chua, Vivien L., Burner, Ryan C., Rahman, Mustafa Abdul, Sheldon, Frederick H. (20... more Els, Paul van, Chua, Vivien L., Burner, Ryan C., Rahman, Mustafa Abdul, Sheldon, Frederick H. (2016): Notes on the life history of Harpactes whiteheadi (Aves: Trogonidae), with a description of the juvenile plumage. Raffles Bulletin of Zoology 64: 76-78
Pegan, Teresa M., Gulson-Castillo, Eric R., Biun, Alim, Byington, Joseph I., Moyle, Robert G., Yu... more Pegan, Teresa M., Gulson-Castillo, Eric R., Biun, Alim, Byington, Joseph I., Moyle, Robert G., Yu, Fred Tuh Yit, Wood, Eric M., Winkler, David W., Sheldon, Frederick H. (2018): An assessment of avifauna in a recovering lowland forest at Kinabalu National Park, Malaysian Borneo. Raffles Bulletin of Zoology 66: 110-131
Mahood, S. P., John, A. J. I., Eames, J. C., Oliveros, C. H., Moyle, R. G., Chamnan, Hong, Poole,... more Mahood, S. P., John, A. J. I., Eames, J. C., Oliveros, C. H., Moyle, R. G., Chamnan, Hong, Poole, C. M., Sheldon, F. H. (2013): A new species of lowland tailorbird (Passeriformes: Cisticolidae: Orthotomus) from the Mekong floodplain of Cambodia. Forktail 29: 1-14, DOI: 10.5281/zenodo.2764030
Herons (Aves: Ardeidae) are a cosmopolitan family of birds that comprises ~65 species and is foun... more Herons (Aves: Ardeidae) are a cosmopolitan family of birds that comprises ~65 species and is found on all continents except Antarctica. Despite being well-studied by ornithologists, phylogenetic relationships within the family are uncertain. For example, the earliest diverging lineages have not been confidently identified, and the monophyly of some genera has been questioned. Here, I present the results of a molecular phylogenetic analysis of herons that includes ~70 percent of species diversity. Analyses of thousands of genomic loci yielded a fully resolved and well-supported phylogeny for the herons. Phylogenetic relationships were broadly congruent across all analytical methods and clarified the composition and placement of several genera that have been traditionally difficult to place. For example, I identified the tiger-herons as the sister-group to all other herons and recovered non-monophyly for some tribes (Nycticoracini and Egrettini) and genera (e.g. Gorsachius and Ixobrychus). iv ACKNOWLEDGMENTS I am heavily indebted to my collaborators. Kevin McCracken and Philip Lavretsky, thank you for graciously contributing the majority of the tissue samples and extracts used in this first sequencing run. Fred Sheldon and Kevin, thank you for contributing the bulk of our knowledge on the systematics and evolutionary history of this fascinating and overlooked family. This thesis would have been much poorer without the background you've helped build. I sincerely hope this work will continue to build upon that legacy. Carl Oliveros, I am very grateful for the patience and your willingness to help, particularly on all matters UCEs. My apologies for the bevy of elementary questions. I aim to be a less of a burden for you from here on out. Adding you as a co-author was definitely one of the best decisions I've made. Rob, many thanks for the helpful discussions regarding the preparation and analysis of UCEs, as well as the recommendations on where to take the project moving forward.
Occasional Papers of the Museum of Natural Science, Louisiana State University, 2014
Collaborative Governance merupakan kerjasama antar Stakeholder yang memuat pihak pemerintah, swas... more Collaborative Governance merupakan kerjasama antar Stakeholder yang memuat pihak pemerintah, swasta dan masyarakat. Kota Yogyakarta sangat memerlukan kerjasama antar Stakeholder untuk dapat mewujudkan pembangunan dan pengelolaan RTHP, mengingat luas wilayah Kota Yogyakarta yang relatif kecil dan pentingnya keberadaan RTHP yang bukan hanya menjadi penghijauan tetapi juga untuk menjaga keseimbangan di lingkungan perkotaan. Oleh karena itu, DLH Kota Yogyakarta yang menjadi pemeran kunci dalam pengelolaan RTHP mengajak instansi lain seperti Dinas Komunikasi, Informasi dan Persandian Kota Yogyakarta dan pihak swasta seperti CV Sarana Mega Konstruksi, serta mengajak masyarakat sekitar untuk bekerjasama dalam membangun dan mengelolaan RTHP. Penelitian ini bertujuan untuk mengetahui bagaimana proses Collaborative Governance yang selama ini dijalin antar Stakeholder untuk mewujudkan pengelolaan RTHP yang baik. Jenis penelitian yang digunakan yaitu kualitatif dengan pendekatan deskriptif. Teknik pengumpulan data yang digunakan dalam penelitian ini yaitu wawancara dan dokumentasi. Penelitian ini menggunakan hasil analisa dari teori yang digunakan. Hasil penelitian yakni Collaborative Governance melalui 4 proses yakni adanya tahapan assesment, tahapan initiation, tahapan deliberation dan tahapam implementation.
Aim Our understanding of population diversification in the lowlands of Sundaland has improved sub... more Aim Our understanding of population diversification in the lowlands of Sundaland has improved substantially over the last 20 years through phylogeographical study, but we know almost nothing about population diversification in the mountains of the region. Here, we apply genomic analysis and habitat modelling to the phylogeography of Chlorocharis emiliae, the Mountain Blackeye, an endemic montane bird of Borneo with a sky-island distribution, to investigate the structure and interconnectivity of its populations. In the process, we consider factors driving population diversification in the mountains versus lowlands on the island, and how population structure of C. emiliae compares with structure of previously studied lowland species. Location Borneo. Methods Using RAD-seq, we produced thousands of SNPs in 25 individuals from five sky-island populations of C. emiliae. These populations represent the species entire range across Borneo. Genetic structure and species tree analyses were applied to measure population relationships and connectivity. Ecological niche modelling was used to estimate habitat distributions during current and LGM time periods. Results We identified slight to moderate genetic distinctiveness among all populations. Based on demographic models, isolation with migration was the main pattern of divergence, and the most admixture occurred among three populations in northeastern Borneo: Kinabalu, Trus Madi and Murud. The most divergent population, Pueh, in northwestern Borneo, has low genetic diversity and a small effective population size, is geographically isolated and has diverged in isolation without notable gene flow. These results, based on a large genomic dataset, contradict the evolutionary relationships identified in an earlier mitochondrial DNA study. Main conclusions Genomic phylogeographical comparisons indicate that diversification among sky-island populations of C. emiliae was driven largely by distance and historical habitat distribution, resulting in isolation but also some inter-population gene flow. During Pleistocene glacial events, cooler temperatures would have caused montane forest to descend and spread, thereby increasing connectivity among sky-island populations. However, despite increased montane habitat, the northwestern population of Pueh remained isolated. This montane pattern contrasts with phylogeographical patterns in the Bornean lowlands, where populations often display evidence of vicariance followed by secondary contact.
:Altitudinal gradients provide tractable, replicated systems in which to study changes in species... more :Altitudinal gradients provide tractable, replicated systems in which to study changes in species richness and community composition over relatively short distances. Previously, richness was often assumed to follow a monotonic decline with altitude, but recent meta-analyses show that more complex patterns, including mid-altitude richness peaks, are also prevalent in birds. In this study, we used point counts to survey birds at multiple altitudes on three mountains on the island of Borneo in Sundaland, an area for which quantitative analyses of avian altitudinal distribution are unavailable. In total we conducted 1088 point counts and collected associated habitat data at 527 locations to estimate species richness by altitude on Mt Mulu (2376 m), Mt Pueh (1550 m) and Mt Topap Oso (1450 m). On Mulu, the only mountain with an intact habitat gradient, bird species richness peaks at 600 m. Richness appeared to peak at 600 m on Totap Oso as well, but on Pueh it peaked several hundred metres higher. The richness peak on Mulu differs from that predicted by null models and is instead caused by the overlap of distinct lowland and montane avifaunas, supporting the faunal overlap hypothesis. This finding provides further evidence that a lack of coincidence between peak turnover and peak richness is not sufficient evidence to rule out faunal overlap as a causal factor.
Bulletin of the British Ornithologists' Club, 2018
BioOne Complete (complete.BioOne.org) is a full-text database of 200 subscribed and open-access t... more BioOne Complete (complete.BioOne.org) is a full-text database of 200 subscribed and open-access titles in the biological, ecological, and environmental sciences published by nonprofit societies, associations, museums, institutions, and presses.
The bulbuls comprise an ecologically important group of frugivorous, seed-dispersing birds found ... more The bulbuls comprise an ecologically important group of frugivorous, seed-dispersing birds found in Asia and Africa. Although several studies have examined the phylogenetic relationships of subsets of bulbul species, a comprehensive phylogeny of the family Pycnonotidae has hitherto been lacking. We used publicly available sequences generated from previous phylogenetic studies, augmented by new sequences from several unstudied taxa, to create a supermatrix from which to infer the phylogeny of the family. In all, we compared 121 of the 130 bulbul species. Our tree supports the monophyly of the family and comprises an exclusively African and a predominantly Asian clade. Several genera were found not to be monophyletic and we suggest taxonomic changes to provide a more accurate classification based on phylogeny.
Aim: A current model of rain forest population diversification in Sundaland specifies east-west v... more Aim: A current model of rain forest population diversification in Sundaland specifies east-west vicariance into refugia during the early Pleistocene. In some taxa, this division was followed by dispersal and apparent secondary contact on Borneo in the late Pleistocene. To investigate genetic, morphological, spatial and temporal characteristics of the model, we compared genomic population and plumage variation among four bird species with east-west mtDNA and plumage structure. Location: Borneo and western Sundaland (Sumatra and the Malay Peninsula). Methods: We quantified plumage patterns among populations of two muscicapids (Copsychus saularis and Kittacincla malabarica) and two timaliids (Mixornis gularis and Trichastoma malaccense), and compared them with population genetic patterns determined from (1) SNPs produced by RAD-Seq and (2) previously sequenced mtDNA. Results: All four species exhibit east-west variation in morphological and some genetic characters, but patterns are idiosyncratic. Copsychus saularis' mtDNA and plumage change gradually across Borneo, but RAD-Seq comparisons indicate no population structure. In K. malabarica, all three characteristics change abruptly and concurrently on Borneo. In M. gularis, the main east-west break occurs between Borneo and western Sundaland, with marginal mtDNA, plumage and RAD-Seq structure on Borneo. T. malaccense exhibits two distinct mtDNA and genomic transitions, an early Pleistocene break between western Sundaland and Borneo, and a Pliocene break between the northeast and the rest of Borneo. Despite this deep genetic division, its plumage changes clinally across Borneo. Main conclusions: MtDNA, plumage and RAD-Seq patterns may vary depending on such factors as pre-Pleistocene distribution, habitat requirements and dispersal propensity, differential introgression among the three character types, selection on plumage and phylogenetic relationships.
Molecular phylogenetic studies of woodpeckers (Picidae) have generally focused on relationships w... more Molecular phylogenetic studies of woodpeckers (Picidae) have generally focused on relationships within specific clades or have sampled sparsely across the family. We compared DNA sequences of six loci from 203 of the 217 recognized species of woodpeckers to construct a comprehensive tree of intrafamilial relationships. We recovered many known, but also numerous unknown, relationships among clades and species. We found, for example, that the three picine tribes are related as follows (Picini, (Campephilini, Melanerpini)) and that the genus Dinopium is paraphyletic. We used the tree to analyze rates of diversification and biogeographic patterns within the family. Diversification rate increased on two occasions during woodpecker history. We also tested diversification rates between temperate and tropical species but found no significant difference. Biogeographic analysis supported an Old World origin of the family and identified at least six independent cases of New World-Old World sister relationships. In light of the tree, we discuss how convergence, mimicry, and potential cases of hybridization have complicated woodpecker taxonomy.
ABSTRACT Mount Mulu, an isolated 2,376 m peak in eastern Sarawak, Malaysian Borneo, has not been ... more ABSTRACT Mount Mulu, an isolated 2,376 m peak in eastern Sarawak, Malaysian Borneo, has not been thoroughly surveyed for bird species since shortly after the creation of Mount Mulu National Park in 1974. The Park is of particular interest for its isolation, spectacular limestone structures, bat flights, and extensive primary forest that ranges from near sea level to the mountain’s peak. We spent 2.5 months surveying, observing, and mist-netting birds in the Park and recorded 244 species across its elevational gradient from 50–1,850 m, including 32 species new to the 1979–82 Mt. Mulu checklists. Here, we report the elevational range of each species we observed, compare our list with these earlier Mt. Mulu checklists compiled 25 years ago, and comment on unique observations.
During the last 15-20 years, phylogenetic, phylogeographic, paleontological, geological, and habi... more During the last 15-20 years, phylogenetic, phylogeographic, paleontological, geological, and habitat modeling studies have improved our knowledge of Sundaic biogeography dramatically. In light of these advances, we review (or postulate) where Sundaic rainforest birds came from, the causes of their endemism, and the influence of Pleistocene climatic perturbations on their diversification. We suggest that four scenarios make up a coherent, plausible explanation of patterns of extant diversity. First, relictual lineages, which represent hangovers from the warm, wet Eocene, survived the hard climatic times of the colder, drier Oligocene and Pliocene in the mountains and adjacent lowlands of eastern Borneo, where rainforest has existed continuously for the last 20-30 million years. Second, most modern SE Asian genera developed during the Miocene. Third, the rainforest of Sundaland and its avifauna were largely isolated from the rest of SE Asia during the late Miocene and Pliocene by seasonal habitats in southern Indochina and ocean boundaries elsewhere, increasing regional endemism. Finally, the advent of global glaciation in the Pleistocene introduced a different diversification dynamic to Sundaland. Early glacial events caused sufficient drying in central Sundaland to fragment rainforest and its avifauna into refugia in eastern and western Sundaland and to allow dry-habitat taxa to reach Java from Indochina. More recent glacial events resulted in sufficient perhumid habitat in central Sundaland to reconnect previously vicariated rainforest populations, creating the lowland and elevational parapatry we see today. This Pleistocene dynamic was probably not simply one period of separation and one period of connection, but rather a complex interplay of isolation and colonization, influenced by highly variable population sizes, changing levels of gene flow, and behavioral idiosyncrasies of the species involved. Throughout all of these events, Borneo played a seminal role in rainforest bird evolution by providing the habitat necessary for diversification and the long-term survival of taxa.
Thoroughly sampled and well-supported phylogenetic trees are essential to taxonomy and to guide s... more Thoroughly sampled and well-supported phylogenetic trees are essential to taxonomy and to guide studies of evolution and ecology. Despite extensive prior inquiry, a comprehensive tree of heron relationships (Aves: Ardeidae) has not yet been published. As a result, the classification of this family remains unstable, and their evolutionary history remains poorly studied. Here, we sample genome-wide ultraconserved elements (UCEs) and mitochondrial DNA sequences (mtDNA) of >90% of extant species to estimate heron phylogeny using a combination of maximum likelihood, coalescent, and Bayesian inference methods. The UCE and mtDNA trees are mostly concordant with one another, providing a topology that resolves relationships among the 5 heron subfamilies and indicates that the genera Gorsachius, Botaurus, Ardea, and Ixobrychus are not monophyletic. We also present the first genetic data from the Forest Bittern Zonerodius heliosylus, an enigmatic species of New Guinea; our results suggest that it is a member of the genus Ardeola and not the Tigrisomatinae (tiger herons), as previously thought. Finally, we compare molecular rates between heron clades in the UCE tree with those in previously constructed mtDNA and DNA-DNA hybridization trees. We show that rate variation in the UCE tree corroborates rate patterns in the previously constructed trees-that bitterns (Ixobrychus and Botaurus) evolved comparatively faster, and some tiger herons (Tigrisoma) and the Boat-billed Heron (Cochlearius) more slowly, than other heron taxa.
The interspecific relationships and biogeography of seven southeast Asian tree shrew species in t... more The interspecific relationships and biogeography of seven southeast Asian tree shrew species in the genus Tupaia were examined by DNA hybridization and multivariate morphometric analysis. Urogale everetti served as the outgroup. DNA hybridization data indicate that T. tana is most closely related to T. montana, and they form a clade with T. minor. Morphometric comparisons indicate that T. tana and T. minor, and T. montana and T. palawanensis, form groups that, together, are most similar to T. glis. T. javanica and U. everetti cluster outside the rest of Tupaia. The DNA hybridization data support a model of Bornean speciation driven by sea-level changes. They also indicate either (1) that there is a large variation in the rate of tree shrew evolution or (2) that U. everetti may in fact be a member of the ingroup. When considered in light of the phylogenetic results, the morphometric data suggest substantial convergence in body size or correlation in character changes.
Occasional Papers of the Museum of Natural Science, 2023
Sarawak is Malaysia's largest state, covering most of northern Borneo. It has a remarkable histor... more Sarawak is Malaysia's largest state, covering most of northern Borneo. It has a remarkable history of scientific bird study, starting in the 1840s and growing ever since. To set the stage for the gazetteer, which is the core of this paper, we start with a review of this history and discuss various forces that have influenced the direction of bird research in the state. Following this introduction comes the gazetteer, which is an annotated list of c. 865 sites in Sarawak where birds have been collected, studied, or regularly observed. The gazetteer provides the latitude, longitude, and elevation of each site, and it lists publications, reports, and museum collections associated with each site. The purpose of the gazetteer is to help interested parties locate sites and investigate their research history. It is also intended to help museum curators geolocate specimens for various kinds of studies, including the assessment of bird distributions in relation to habitat change over time. A notable byproduct of the historical review and gazetteer is a bibliography of c. 750 references related to Sarawak ornithology. Another is the identification of areas in Sarawak where birds are better known and areas where they are not.
The chapter explores three fundamental issues: phylogenetic accuracy, adaptation, and phylogeneti... more The chapter explores three fundamental issues: phylogenetic accuracy, adaptation, and phylogenetic constraint. These issues are central to historical ecology and cover a broad range of subjects in the field. The most important step to successful historical ecology is the collection of appropriate, accurate, ecological, and phylogenetic data. Although obvious, this assertion is remarkably underemphasized in ecophylogenetic studies. Emphasis is placed primarily on the quality of ecological data, which are viewed as dependent variables, instead of on the accuracy of phylogeny, which is generally viewed as an independent variable without error. However, phylogenetic estimates have error distributions, but these are commonly ignored because they are too complicated to quantify. Historical ecology is burgeoning because it provides structure to the study of ecological patterns and evolutionary processes. Emphasis on the use of accurate phylogenetic data is crucial because the interpretation of evolutionary patterns obviously changes as relationships among taxa change. Although progress may be limited without knowledge of the quantitative genetics of specific traits, initial hypothesis testing is possible with prudent use of the phylogenetic approach, provided that multiple examples of potential evolutionary phenomena are examined.
... We thank AJ Baker, EA Cardiff, SW Cardiff, Mario Cohn-Haft, DL Dittmann, NK Klein, MB Robbins... more ... We thank AJ Baker, EA Cardiff, SW Cardiff, Mario Cohn-Haft, DL Dittmann, NK Klein, MB Robbins, RS Ridgely, F. Sornoza Molina, Paul Sweet, Katherine Wallace, Bret Whitney, Academy of Natural ...Daniel F. Lane provided advice on plumage variation in Gray-breasted Martin. ...
Els, Paul van, Chua, Vivien L., Burner, Ryan C., Rahman, Mustafa Abdul, Sheldon, Frederick H. (20... more Els, Paul van, Chua, Vivien L., Burner, Ryan C., Rahman, Mustafa Abdul, Sheldon, Frederick H. (2016): Notes on the life history of Harpactes whiteheadi (Aves: Trogonidae), with a description of the juvenile plumage. Raffles Bulletin of Zoology 64: 76-78
Pegan, Teresa M., Gulson-Castillo, Eric R., Biun, Alim, Byington, Joseph I., Moyle, Robert G., Yu... more Pegan, Teresa M., Gulson-Castillo, Eric R., Biun, Alim, Byington, Joseph I., Moyle, Robert G., Yu, Fred Tuh Yit, Wood, Eric M., Winkler, David W., Sheldon, Frederick H. (2018): An assessment of avifauna in a recovering lowland forest at Kinabalu National Park, Malaysian Borneo. Raffles Bulletin of Zoology 66: 110-131
Mahood, S. P., John, A. J. I., Eames, J. C., Oliveros, C. H., Moyle, R. G., Chamnan, Hong, Poole,... more Mahood, S. P., John, A. J. I., Eames, J. C., Oliveros, C. H., Moyle, R. G., Chamnan, Hong, Poole, C. M., Sheldon, F. H. (2013): A new species of lowland tailorbird (Passeriformes: Cisticolidae: Orthotomus) from the Mekong floodplain of Cambodia. Forktail 29: 1-14, DOI: 10.5281/zenodo.2764030
Herons (Aves: Ardeidae) are a cosmopolitan family of birds that comprises ~65 species and is foun... more Herons (Aves: Ardeidae) are a cosmopolitan family of birds that comprises ~65 species and is found on all continents except Antarctica. Despite being well-studied by ornithologists, phylogenetic relationships within the family are uncertain. For example, the earliest diverging lineages have not been confidently identified, and the monophyly of some genera has been questioned. Here, I present the results of a molecular phylogenetic analysis of herons that includes ~70 percent of species diversity. Analyses of thousands of genomic loci yielded a fully resolved and well-supported phylogeny for the herons. Phylogenetic relationships were broadly congruent across all analytical methods and clarified the composition and placement of several genera that have been traditionally difficult to place. For example, I identified the tiger-herons as the sister-group to all other herons and recovered non-monophyly for some tribes (Nycticoracini and Egrettini) and genera (e.g. Gorsachius and Ixobrychus). iv ACKNOWLEDGMENTS I am heavily indebted to my collaborators. Kevin McCracken and Philip Lavretsky, thank you for graciously contributing the majority of the tissue samples and extracts used in this first sequencing run. Fred Sheldon and Kevin, thank you for contributing the bulk of our knowledge on the systematics and evolutionary history of this fascinating and overlooked family. This thesis would have been much poorer without the background you've helped build. I sincerely hope this work will continue to build upon that legacy. Carl Oliveros, I am very grateful for the patience and your willingness to help, particularly on all matters UCEs. My apologies for the bevy of elementary questions. I aim to be a less of a burden for you from here on out. Adding you as a co-author was definitely one of the best decisions I've made. Rob, many thanks for the helpful discussions regarding the preparation and analysis of UCEs, as well as the recommendations on where to take the project moving forward.
Occasional Papers of the Museum of Natural Science, Louisiana State University, 2014
Collaborative Governance merupakan kerjasama antar Stakeholder yang memuat pihak pemerintah, swas... more Collaborative Governance merupakan kerjasama antar Stakeholder yang memuat pihak pemerintah, swasta dan masyarakat. Kota Yogyakarta sangat memerlukan kerjasama antar Stakeholder untuk dapat mewujudkan pembangunan dan pengelolaan RTHP, mengingat luas wilayah Kota Yogyakarta yang relatif kecil dan pentingnya keberadaan RTHP yang bukan hanya menjadi penghijauan tetapi juga untuk menjaga keseimbangan di lingkungan perkotaan. Oleh karena itu, DLH Kota Yogyakarta yang menjadi pemeran kunci dalam pengelolaan RTHP mengajak instansi lain seperti Dinas Komunikasi, Informasi dan Persandian Kota Yogyakarta dan pihak swasta seperti CV Sarana Mega Konstruksi, serta mengajak masyarakat sekitar untuk bekerjasama dalam membangun dan mengelolaan RTHP. Penelitian ini bertujuan untuk mengetahui bagaimana proses Collaborative Governance yang selama ini dijalin antar Stakeholder untuk mewujudkan pengelolaan RTHP yang baik. Jenis penelitian yang digunakan yaitu kualitatif dengan pendekatan deskriptif. Teknik pengumpulan data yang digunakan dalam penelitian ini yaitu wawancara dan dokumentasi. Penelitian ini menggunakan hasil analisa dari teori yang digunakan. Hasil penelitian yakni Collaborative Governance melalui 4 proses yakni adanya tahapan assesment, tahapan initiation, tahapan deliberation dan tahapam implementation.
Aim Our understanding of population diversification in the lowlands of Sundaland has improved sub... more Aim Our understanding of population diversification in the lowlands of Sundaland has improved substantially over the last 20 years through phylogeographical study, but we know almost nothing about population diversification in the mountains of the region. Here, we apply genomic analysis and habitat modelling to the phylogeography of Chlorocharis emiliae, the Mountain Blackeye, an endemic montane bird of Borneo with a sky-island distribution, to investigate the structure and interconnectivity of its populations. In the process, we consider factors driving population diversification in the mountains versus lowlands on the island, and how population structure of C. emiliae compares with structure of previously studied lowland species. Location Borneo. Methods Using RAD-seq, we produced thousands of SNPs in 25 individuals from five sky-island populations of C. emiliae. These populations represent the species entire range across Borneo. Genetic structure and species tree analyses were applied to measure population relationships and connectivity. Ecological niche modelling was used to estimate habitat distributions during current and LGM time periods. Results We identified slight to moderate genetic distinctiveness among all populations. Based on demographic models, isolation with migration was the main pattern of divergence, and the most admixture occurred among three populations in northeastern Borneo: Kinabalu, Trus Madi and Murud. The most divergent population, Pueh, in northwestern Borneo, has low genetic diversity and a small effective population size, is geographically isolated and has diverged in isolation without notable gene flow. These results, based on a large genomic dataset, contradict the evolutionary relationships identified in an earlier mitochondrial DNA study. Main conclusions Genomic phylogeographical comparisons indicate that diversification among sky-island populations of C. emiliae was driven largely by distance and historical habitat distribution, resulting in isolation but also some inter-population gene flow. During Pleistocene glacial events, cooler temperatures would have caused montane forest to descend and spread, thereby increasing connectivity among sky-island populations. However, despite increased montane habitat, the northwestern population of Pueh remained isolated. This montane pattern contrasts with phylogeographical patterns in the Bornean lowlands, where populations often display evidence of vicariance followed by secondary contact.
:Altitudinal gradients provide tractable, replicated systems in which to study changes in species... more :Altitudinal gradients provide tractable, replicated systems in which to study changes in species richness and community composition over relatively short distances. Previously, richness was often assumed to follow a monotonic decline with altitude, but recent meta-analyses show that more complex patterns, including mid-altitude richness peaks, are also prevalent in birds. In this study, we used point counts to survey birds at multiple altitudes on three mountains on the island of Borneo in Sundaland, an area for which quantitative analyses of avian altitudinal distribution are unavailable. In total we conducted 1088 point counts and collected associated habitat data at 527 locations to estimate species richness by altitude on Mt Mulu (2376 m), Mt Pueh (1550 m) and Mt Topap Oso (1450 m). On Mulu, the only mountain with an intact habitat gradient, bird species richness peaks at 600 m. Richness appeared to peak at 600 m on Totap Oso as well, but on Pueh it peaked several hundred metres higher. The richness peak on Mulu differs from that predicted by null models and is instead caused by the overlap of distinct lowland and montane avifaunas, supporting the faunal overlap hypothesis. This finding provides further evidence that a lack of coincidence between peak turnover and peak richness is not sufficient evidence to rule out faunal overlap as a causal factor.
Bulletin of the British Ornithologists' Club, 2018
BioOne Complete (complete.BioOne.org) is a full-text database of 200 subscribed and open-access t... more BioOne Complete (complete.BioOne.org) is a full-text database of 200 subscribed and open-access titles in the biological, ecological, and environmental sciences published by nonprofit societies, associations, museums, institutions, and presses.
The bulbuls comprise an ecologically important group of frugivorous, seed-dispersing birds found ... more The bulbuls comprise an ecologically important group of frugivorous, seed-dispersing birds found in Asia and Africa. Although several studies have examined the phylogenetic relationships of subsets of bulbul species, a comprehensive phylogeny of the family Pycnonotidae has hitherto been lacking. We used publicly available sequences generated from previous phylogenetic studies, augmented by new sequences from several unstudied taxa, to create a supermatrix from which to infer the phylogeny of the family. In all, we compared 121 of the 130 bulbul species. Our tree supports the monophyly of the family and comprises an exclusively African and a predominantly Asian clade. Several genera were found not to be monophyletic and we suggest taxonomic changes to provide a more accurate classification based on phylogeny.
Aim: A current model of rain forest population diversification in Sundaland specifies east-west v... more Aim: A current model of rain forest population diversification in Sundaland specifies east-west vicariance into refugia during the early Pleistocene. In some taxa, this division was followed by dispersal and apparent secondary contact on Borneo in the late Pleistocene. To investigate genetic, morphological, spatial and temporal characteristics of the model, we compared genomic population and plumage variation among four bird species with east-west mtDNA and plumage structure. Location: Borneo and western Sundaland (Sumatra and the Malay Peninsula). Methods: We quantified plumage patterns among populations of two muscicapids (Copsychus saularis and Kittacincla malabarica) and two timaliids (Mixornis gularis and Trichastoma malaccense), and compared them with population genetic patterns determined from (1) SNPs produced by RAD-Seq and (2) previously sequenced mtDNA. Results: All four species exhibit east-west variation in morphological and some genetic characters, but patterns are idiosyncratic. Copsychus saularis' mtDNA and plumage change gradually across Borneo, but RAD-Seq comparisons indicate no population structure. In K. malabarica, all three characteristics change abruptly and concurrently on Borneo. In M. gularis, the main east-west break occurs between Borneo and western Sundaland, with marginal mtDNA, plumage and RAD-Seq structure on Borneo. T. malaccense exhibits two distinct mtDNA and genomic transitions, an early Pleistocene break between western Sundaland and Borneo, and a Pliocene break between the northeast and the rest of Borneo. Despite this deep genetic division, its plumage changes clinally across Borneo. Main conclusions: MtDNA, plumage and RAD-Seq patterns may vary depending on such factors as pre-Pleistocene distribution, habitat requirements and dispersal propensity, differential introgression among the three character types, selection on plumage and phylogenetic relationships.
Molecular phylogenetic studies of woodpeckers (Picidae) have generally focused on relationships w... more Molecular phylogenetic studies of woodpeckers (Picidae) have generally focused on relationships within specific clades or have sampled sparsely across the family. We compared DNA sequences of six loci from 203 of the 217 recognized species of woodpeckers to construct a comprehensive tree of intrafamilial relationships. We recovered many known, but also numerous unknown, relationships among clades and species. We found, for example, that the three picine tribes are related as follows (Picini, (Campephilini, Melanerpini)) and that the genus Dinopium is paraphyletic. We used the tree to analyze rates of diversification and biogeographic patterns within the family. Diversification rate increased on two occasions during woodpecker history. We also tested diversification rates between temperate and tropical species but found no significant difference. Biogeographic analysis supported an Old World origin of the family and identified at least six independent cases of New World-Old World sister relationships. In light of the tree, we discuss how convergence, mimicry, and potential cases of hybridization have complicated woodpecker taxonomy.
ABSTRACT Mount Mulu, an isolated 2,376 m peak in eastern Sarawak, Malaysian Borneo, has not been ... more ABSTRACT Mount Mulu, an isolated 2,376 m peak in eastern Sarawak, Malaysian Borneo, has not been thoroughly surveyed for bird species since shortly after the creation of Mount Mulu National Park in 1974. The Park is of particular interest for its isolation, spectacular limestone structures, bat flights, and extensive primary forest that ranges from near sea level to the mountain’s peak. We spent 2.5 months surveying, observing, and mist-netting birds in the Park and recorded 244 species across its elevational gradient from 50–1,850 m, including 32 species new to the 1979–82 Mt. Mulu checklists. Here, we report the elevational range of each species we observed, compare our list with these earlier Mt. Mulu checklists compiled 25 years ago, and comment on unique observations.
During the last 15-20 years, phylogenetic, phylogeographic, paleontological, geological, and habi... more During the last 15-20 years, phylogenetic, phylogeographic, paleontological, geological, and habitat modeling studies have improved our knowledge of Sundaic biogeography dramatically. In light of these advances, we review (or postulate) where Sundaic rainforest birds came from, the causes of their endemism, and the influence of Pleistocene climatic perturbations on their diversification. We suggest that four scenarios make up a coherent, plausible explanation of patterns of extant diversity. First, relictual lineages, which represent hangovers from the warm, wet Eocene, survived the hard climatic times of the colder, drier Oligocene and Pliocene in the mountains and adjacent lowlands of eastern Borneo, where rainforest has existed continuously for the last 20-30 million years. Second, most modern SE Asian genera developed during the Miocene. Third, the rainforest of Sundaland and its avifauna were largely isolated from the rest of SE Asia during the late Miocene and Pliocene by seasonal habitats in southern Indochina and ocean boundaries elsewhere, increasing regional endemism. Finally, the advent of global glaciation in the Pleistocene introduced a different diversification dynamic to Sundaland. Early glacial events caused sufficient drying in central Sundaland to fragment rainforest and its avifauna into refugia in eastern and western Sundaland and to allow dry-habitat taxa to reach Java from Indochina. More recent glacial events resulted in sufficient perhumid habitat in central Sundaland to reconnect previously vicariated rainforest populations, creating the lowland and elevational parapatry we see today. This Pleistocene dynamic was probably not simply one period of separation and one period of connection, but rather a complex interplay of isolation and colonization, influenced by highly variable population sizes, changing levels of gene flow, and behavioral idiosyncrasies of the species involved. Throughout all of these events, Borneo played a seminal role in rainforest bird evolution by providing the habitat necessary for diversification and the long-term survival of taxa.
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