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Abstract

The diversity of the freshwater-fish genus Rasbora (Cyprinidae) on Sri Lanka (five species) is high compared with the four species reported from the peninsula of India, from which the island's cyprinid fauna is derived. The paucity of characters by which species of Rasbora can be phenotypically distinguished renders field identification difficult, adversely affecting the estimation of populations and distributions, with consequences for conservation and management, increasing also the risk of taxonomic inflation. From a sampling of 90 sites across Sri Lanka and based on phylogenetic and haplotype analyses of sequences of cox1 and cytb mitochondrial, and rag1 and irbp nuclear markers, we review the species diversity and phylogeography of Rasbora on the island. Molecular analyses recover, in addition to the five species previously reported, a new (cryptic) species: Rasbora adisi sp. nov. Uncorrected pairwise cox1 genetic distances between species range from 2.0 to 12.3 percent. The Sri Lankan diversification derives from a common ancestor which arrived from India during a sea-level low-stand in the mid-Miocene (15.1 Ma [95% HPD: 11.5–19.8 Ma]), when the present-day island was subaerially connected to the Indian subcontinent by a broad isthmus. This gave rise to a clade comprising five species—R. adisi sp. nov., Rasbora armitagei, Rasbora microcephalus, Rasbora naggsi and Rasbora wilpita—with a crown age of 9.9 Ma (95% HPD: 7.1–13.3 Ma) and to a clade comprising Indian and Sri Lankan populations of Rasbora dandia, which themselves are reciprocally monophyletic. Morphological analysis of 334 specimens discriminates between most species which, however, are most reliably diagnosed by chromatic characters. The four endemic species exhibit a pattern of inter-basin dispersal via headwater capture, followed by vicariance, explaining the high diversity of the genus on the island.

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... Hence, much of the island's remarkable biodiversity derives from insular diversifications stemming from a small number of immigrant dispersals, as in the case of its 59 endemic treefrog species and 50 endemic crab species, shown to be monophyletic by Meegaskumbura et al. [12] and Beenaerts et al. [13], respectively. The same has been shown to be true also for several freshwater-fish diversifications, such as in the cypriniform genera Devario, Rasbora and Systomus [11,14,15]. ...
... bandula, P. nigrofasciata, P. cumingii and P. reval) exhibiting a similar morphology and being confined to the island's south-western wet and intermediate zones (rainfall > 2.5 m/y and 1.8-2.5 m/y, respectively). The wetzone diversifications of several other cypriniform genera have been shown to be monophyletic [e.g., Systomus: 11, Devario: 14, and Rasbora: 15], whereas such diversifications are rare in the dry zone [15,39]. Of the four species of Pethia endemic to the island's south-western wet zone, only one, P. reval, has a range extending into the western intermediate zone, as far north as the Deduru basin. ...
... Thus, our phylogeny suggests that the five species of Sri Lankan Pethia derive from two or three discrete colonization events from the Indian mainland. Multiple colonization events have been recovered also in the case of other freshwater-fish diversifications in Sri Lanka, such as Laubuka, Rasbora, Devario and Systomus [11,14,15,39]. In those cases, the diversifications in the island's wet zone within each genus were shown to stem from a single colonization from India. ...
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Background Sri Lanka is a continental island separated from India by the Palk Strait, a shallow-shelf sea, which was emergent during periods of lowered sea level. Its biodiversity is concentrated in its perhumid south-western ‘wet zone’. The island’s freshwater fishes are dominated by the Cyprinidae, characterized by small diversifications of species derived from dispersals from India. These include five diminutive, endemic species of Pethia ( P. bandula , P. cumingii , P. melanomaculata , P. nigrofasciata , P. reval ), whose evolutionary history remains poorly understood. Here, based on comprehensive geographic sampling, we explore the phylogeny, phylogeography and morphological diversity of the genus in Sri Lanka. Results The phylogenetic analyses, based on mitochondrial and nuclear loci, recover Sri Lankan Pethia as polyphyletic. The reciprocal monophyly of P. bandula and P. nigrofasciata , and P. cumingii and P. reval , is not supported. Pethia nigrofasciata , P. cumingii , and P. reval show strong phylogeographic structure in the wet zone, compared with P. melanomaculata , which ranges across the dry and intermediate zones. Translocated populations of P. nigrofasciata and P. reval in the Central Hills likely originate from multiple sources. Morphological analyses reveal populations of P. nigrofasciata proximal to P. bandula , a narrow-range endemic, to have a mix of characters between the two species. Similarly, populations of P. cumingii in the Kalu basin possess orange fins, a state between the red-finned P. reval from Kelani to Deduru and yellow-finned P. cumingii from Bentara to Gin basins. Conclusions Polyphyly in Sri Lankan Pethia suggests two or three colonizations from mainland India. Strong phylogeographic structure in P. nigrofasciata , P. cumingii and P. reval , compared with P. melanomaculata , supports a model wherein the topographically complex wet zone harbors greater genetic diversity than the topographically uniform dry-zone. Mixed morphological characters between P. bandula and P. nigrofasciata , and P. cumingii and P. reval , and their unresolved phylogenies, may suggest recent speciation scenarios with incomplete lineage sorting, or hybridization.
... Indeed, by comparison with the Western Ghats, the island's fish fauna is notably depauperate: eight families and some 25 genera that occur in southern peninsular India, including widespread generalist taxa such as Sperata (Bagridae), and Cirrhinus (Cyprinidae), are absent from Sri Lanka. Lineages that did succeed in crossing the Palk Isthmus to reach Sri Lanka appear to have done so during two widely spaced temporal windows, in the late Oligocene-early Miocene, and the Plio-Pleistocene (Sudasinghe, et al., 2020a(Sudasinghe, et al., , 2020b(Sudasinghe, et al., , 2020c. The former event involved the ancestors of 'relict' genera that contain between one and three species each: Malpulutta, Belontia, Rasboroides and Systomus (Sudasinghe, 2018a(Sudasinghe, , 2020a. ...
... All of these are broadly associated with the island's wet zone rainforest region, and their deeper relationships are with Southeast Asian lineages absent from the Indian peninsula (Rüber et al., 2006;Sudasinghe et al., 2020a;Wu et al., 2019). The Plio-Pleistocene dispersers, however, comprise genera widespread in the plains of southern peninsular India, which show only modest autochthonous diversifications on the island, such as the cyprinids Rasbora, Devario and Laubuka (Sudasinghe et al., 2020b(Sudasinghe et al., , 2020c(Sudasinghe et al., , 2020d. ...
... Fig. S10) than genetic divergence attributable to Sri Lanka's insularity. A similar phylogeographic structure has also been observed in other Sri Lankan cyprinids with comparable distributions and Pleistocene separations between India and Sri Lanka, such as in Devario malabaricus and Rasbora dandia (Sudasinghe et al., 2020b(Sudasinghe et al., , 2020c. Recent taxonomic and molecular work on freshwater fishes has further supported the close genetic and morphological similarity between widespread Sri Lankan species with those of Southeast India (Sudasinghe et al., 2019. ...
Article
The cyprinid genus Dawkinsia comprises 13 species distributed in lowland streams and rivers in southern peninsular India and Sri Lanka. Eleven species are endemic to India, largely restricted to streams draining the Western Ghats, while one is confined to the Knuckles Hills of Sri Lanka. One species, D. filamentosa, has a wide range, straddling the island and mainland. Here, based on 135 samples representative of all 13 species, collected from 45 locations in India and 17 in Sri Lanka, we present phylogenetic and phylogeographic analyses of Dawkinsia. We use two mitochondrial markers—cytochrome b and cytochrome c oxidase subunit 1. Dawkinsia is recovered as paraphyletic with respect to Sahyadria, with strong node support. The ‘filamentosa group’ which includes both Sri Lankan and Indian taxa (D. filamentosa, D. crassa, D. rohani, D. exclamatio, D. srilankensis, D. tambraparniei, D. arulius, D. rubrotincta and D. uttara) is recovered as the sister group of Sahyadria, a genus confined to the Western Ghats. The ‘assimilis group’, which consists entirely of Indian endemics (D. assimilis, D. austellus, D. apsara and D. lepida), is recovered as the sister group of the ‘filamentosa group’ + Sahyadria. Ancestral-range estimates indicate two colonization events from India to Sri Lanka, across the Palk Isthmus. The first of these, in the Pliocene, involved the common ancestor of D. tambraparniei and D. srilankensis, while the second was of D. filamentosa in the late Pleistocene. Dawkinsia filamentosa shows little phylogeographic structure within or between Sri Lanka and India. Ancestral-range analyses suggest that neither the Palghat nor Shencottah Gaps acted as barriers to the north–south dispersal of Dawkinsia along the Western Ghats. Instead, these valleys appear to have offered lowland passages for west–east colonization by some ancestral species across the Western Ghats ridge. Despite the Palk Isthmus having been subaerial for much of the Plio-Pleistocene and serving as the only terrestrial biotic corridor connecting Sri Lanka to the Asian mainland, it appears to have served also as a climatic filter to dispersal following the aridification of south-eastern India during the Late Miocene/early Pliocene.
... The circumstance allows cryptic species to exist among them. Genetic distances of up to 12.3% as a cryptic species on Rasbora adisi (Sudasinghe et al. 2020). Bali Strait, which separated Java and Bali Islands formed in the same period as the Karimata Strait ( Figure 5A), was predicted to cause cryptic species Rasbora lateristriata from the Java and Bali islands (Kusuma et al. 2016). ...
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Kurniawan A, Hariati AM, Kurniawan A, Kurniawan N, Nugroho TW, Bidayani E, Syarif AF, wiadnya DGR. 2022. Genetic diversity analysis and phylogeography of Osteochilus spilurus (Cyprinidae: Labeoninae) from Bangka, Belitung, and Kalimantan Islands using Cytochrome b gene. Biodiversitas 23: 4738-4746. The Sundaland fish species, Osteochilus spilurus is only utilized commercially in the Belitung Islands and has yet to be domesticated. This species can characterize freshwater fish phylogeography because have a minimum of human influence. This study aimed to analyze the genetic diversity and phylogeography of O. spilurus from the Bangka, Belitung, and Kalimantan Islands using Cytochrome b gene. Twenty fish samples were collected from the Sebangau and Kapuas Rivers in Kalimantan, the Lenggang River in Belitung Island, and the Lebak River in Bangka Island. Forward LA-cyp and reverse HA-cyp primers were used for amplification Cytochrome b gene. Mega 10.0 applications were used to construct of the phylogenetic tree. The phylogeographic analysis uses a comparative phylogenetic tree approach with geographical history. The cytochrome b gene showed variations in the nucleotides of O. spilurus from the three islands. Phylogeography of O. spilurus showed that there are two different clades with intraspecific variation according to a geographic area with bootstrap values of 99-100%. One clade contains fish samples from Bangka and Belitung islands, while the other clade comes from Kalimantan island. The formation of the Karimata Strait (between Bangka-Belitung and Kalimantan Islands) and the pattern of paleo rivers are predicted to influence the disparity.
... Studies on the genetic diversity of widespread freshwater taxa, largely applying DNA barcoding methods, are increasingly revealing complex patterns of cryptic variation. Apart from investigations of freshwater fishes [2] and other macroscopic taxa [3], studies on the phylogeny of smaller freshwater crustaceans, such as cladocerans [4][5][6], isopods [7], amphipods [8][9][10], and copepods [11] have demonstrated the presence of hidden genetic diversity and occurrence of cryptic species across presumed conspecific populations. ...
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Comparative phylogeography has become a powerful approach in exploring hidden or cryptic diversity within widespread species and understanding how historical and biogeographical factors shape the modern patterns of their distribution. Most comparative phylogeographic studies so far focus on terrestrial and vertebrate taxa, while aquatic invertebrates (and especially freshwater invertebrates) remain unstudied. In this article, we explore and compare the patterns of molecular diversity and phylogeographic structure of four widespread freshwater copepod crustaceans in Eu-ropean water bodies: the harpacticoids Attheyella crassa, Canthocamptus staphylinus and Nitokra hiber-nica, and the cyclopoid Eucyclops serrulatus, using sequence data from mtDNA COI and nuclear ITS/18S rRNA genes. The three taxa A. crassa, C. staphylinus and E. serrulatus each consist of deeply diverged clusters and are deemed to represent complexes of species with largely (but not completely) non-overlapping distributions, while in N. hibernica only little differentiation was found, which may however reflect the geographically more restricted sampling. However, the geographical patterns of subdivision differ. The divisions in A. crassa and E. serrulatus follow an east-west pattern in Northern Europe whereas that in C. staphylinus has more of a north-south pattern, with a distinct Fennoscandian clade. The deep mitochondrial splits among populations of A. crassa, C. staphylinus and E. serrulatus (model-corrected distances 26-36%) suggest that divergence of the lin-eages predate the Pleistocene glaciations. This study provides an insight into cryptic diversity and biogeographic distribution of freshwater copepods.
... Research that addresses these population components from a phylogenetic perspective is becoming more common, not only among tropical reef fishes but also in coastal and freshwater fishes (e.g. Mennesson et al., 2018;Rodríguez-Rey et al., 2018;Sudasinghe et al., 2020). ...
Article
Marine species that are widely distributed in the Tropical Eastern Pacific (TEP) has served as a model for studying biogeographic patterns resulting from the effects of intraregional habitat discontinuities and oceanographic processes on the diversification and evolution of cryptobenthic reef fishes. Tomicodon petersii, a clingfish (Gobiesocidae) endemic to the TEP, is found on very shallow rocky reefs from central Mexico to northern Peru, and in the Cocos and Galapagos islands. We evaluated the effect of likely biogeographic barriers in different parts of the TEP on the diversification process of this species. We used one mitochondrial and three nuclear DNA markers from 112 individuals collected across the distribution range of T. petersii. Our phylogenetic results showed the samples constituted a monophyletic group, with three well-supported, allopatric subgroups: in the Mexican province, the Panamic province (from El Salvador to Ecuador), and the Galapagos Islands. The split between the Mexican and more southerly clades was estimated to occur at the end of the Miocene ca. 5.74 Mya, and the subsequent cladogenetic event separating the Galapagos population from the Panamic population at the junction of the Pliocene and Pleistocene, ca. 2.85 Mya. The species tree, Bayesian species delimitation tests (BPP), STACEY, and substantial genetic distances separating these three populations indicate that these three independent evolutionary units likely include two unnamed species. The cladogenetic events that promoted the formation of those genetically differentiated groups are consistent with disruptive effects on gene flow of habitat discontinuities and oceanographic processes along the mainland shoreline in the TEP and of ocean-island isolation, in conjunction with the species intrinsic life-history characteristics.
... The vertebrates recorded include, three species of fish Devario memorialis (Aranayake Devario from Aranayake) 2 (Figure 1), Laubuka hema ( from Nilgala) 37 and Rasbora adisi (from Kotagama) 3 , four species of snakes [Rhinophis mendisi (Mendis's shieldtail from Balangoda) 4 , Rhinophis gunasekarai (Gunasekara's shieldtail from Knuckles) 5 , Dryocalamus chithrasekarai (Chithrasekara's bridle snake from Peak Wilderness) 6 and Dendrelaphis wickrorum (Wickramasinghe's bronzeback from Pundalu Oya) 7 ]; three species of skinks [Lankascincus merrill (Merrill's Lanka-skink from Rakwana hills) 8 , Lankascincus sameerai (Sameera's Lanka-skink from Morningside) 9 , Eutropis resetarii (Resetar's Skink from Agarapatana) 10 ]; one species of lizard Ceratophora ukuwelai (Ukuwela's rough-horn lizard ( Figure 2) from Salgala) 11 ; one species of gecko Cnemaspis manoae (Mano's day-gecko from Pilikuttuwa) 12 . ...
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Provides a comprehensive report on the status of species in Sri Lanka, including new species discovered during 2020, species recorded for the first time in Sri Lanka, changes in the distribution status of species, changes in nomenclature, new invasive species recorded and overall update on the statistics of the species.
... Recent taxonomic assessments of Sri Lankan and Peninsular-Indian freshwater fishes based on multiple lines of evidence suggest that some widespread species hitherto considered as endemic to the island are in fact shared between the two landmasses (Sudasinghe et al., 2019b(Sudasinghe et al., , 2020aKatwate et al., 2020b) with, however, some exceptions (Sudasinghe et al., 2018b(Sudasinghe et al., , 2019a. In the present study, we recover strong support for the monophyly of G. ceylonensis from both nuclear and mitochondrial data, and our timing analysis suggests a Pliocene divergence from ancestral G. mullya (clade A). ...
Article
Despite exhibiting multiple morphological adaptations to living in swiftly flowing water (rheophily), Garra ceylonensis is one of the most widely distributed freshwater fish in Sri Lanka. It is thus an ideal organism to reconstruct the evolutionary history of a widespread, yet morphologically specialized, freshwater fish in a tropical-island setting. We analysed the phylogenetic and phylogeographic relationships of G. ceylonensis based on two mitochondrial and one nuclear genes. G. ceylonensis is shown to be monophyletic, with a sister-group relationship to the Indian species Garra mullya. Our results suggest a single colonization of Sri Lanka by ancestral Garra, in the late Pliocene. This suggests that the Palk Isthmus, which was exposed for most of the Pleistocene, had a hydroclimate unsuited to the dispersal of fishes such as Garra. G. ceylonensis exhibits strong phylogeographic structure: six subclades are distributed as genetically distinct populations in clusters of contiguous river basins, albeit with two exceptions. Our data reveal one or more Pleistocene extirpation events, evidently driven by aridification, with relict populations subsequently re-colonizing the island. The phylogeographic structure of G. ceylonensis suggests inter-basin dispersal largely through headwater capture, likely facilitated by free-swimming post-larvae. The Peninsular-Indian species G. mullya comprises two genetically distinct parapatric clades, which may represent distinct species. ADDITIONAL KEYWORDS: biogeography-dispersal-freshwater fish-Labeoninae-phylogeny-Pleistocene-torrent fish.
... Recent taxonomic assessments of Sri Lankan and Peninsular-Indian freshwater fishes based on multiple lines of evidence suggest that some widespread species hitherto considered as endemic to the island are in fact shared between the two landmasses (Sudasinghe et al., 2019b(Sudasinghe et al., , 2020aKatwate et al., 2020b) with, however, some exceptions (Sudasinghe et al., 2018b(Sudasinghe et al., , 2019a. In the present study, we recover strong support for the monophyly of G. ceylonensis from both nuclear and mitochondrial data, and our timing analysis suggests a Pliocene divergence from ancestral G. mullya (clade A). ...
Article
Despite exhibiting multiple morphological adaptations to living in swiftly flowing water (rheophily), Garra ceylonensis is one of the most widely distributed freshwater fish in Sri Lanka. It is thus an ideal organism to reconstruct the evolutionary history of a widespread, yet morphologically specialized, freshwater fish in a tropical-island setting. We analysed the phylogenetic and phylogeographic relationships of G. ceylonensis based on two mitochondrial and one nuclear genes. G. ceylonensis is shown to be monophyletic, with a sister-group relationship to the Indian species Garra mullya. Our results suggest a single colonization of Sri Lanka by ancestral Garra, in the late Pliocene. This suggests that the Palk Isthmus, which was exposed for most of the Pleistocene, had a hydroclimate unsuited to the dispersal of fishes such as Garra. G. ceylonensis exhibits strong phylogeographic structure: six subclades are distributed as genetically distinct populations in clusters of contiguous river basins, albeit with two exceptions. Our data reveal one or more Pleistocene extirpation events, evidently driven by aridification, with relict populations subsequently re-colonizing the island. The phylogeographic structure of G. ceylonensis suggests inter-basin dispersal largely through headwater capture, likely facilitated by free-swimming post-larvae. The Peninsular-Indian species G. mullya comprises two genetically distinct parapatric clades, which may represent distinct species.
... The absence of shared haplotypes between populations of L. varuna in the major river basins sampled (Attanagalu, Kalu, Gin, and Nilwala: Fig. 3), all of which debouch into the Indian Ocean across a common floodplain, suggest restricted gene-flow even between adjacent basins of this evidently 'forest-adapted' species. Similar phylogeographic pattern has been observed also in other Sri Lankan cyprinids, such as Devario and Rasbora in the southwestern wet zone (Sudasinghe et al., 2020b;Sudasinghe, et al., 2020c). ...
Article
The freshwater-fish genus Laubuka contains ∼13 species distributed through the lowlands of tropical South and South-east Asia. Four of these species (Laubuka lankensis, L. varuna, L. ruhuna, and L. insularis) are reported as endemic to Sri Lanka, a remarkable datum given the island’s small size. We sampled populations of Laubuka at 56 locations in 14 of the island’s principal river basins and analysed their morphological, meristic, phylogenetic, and phylogeographic relationships using the mitochondrial genes cytochrome b and cytochrome c oxidase subunit 1 and the nuclear recombination activating protein 1. We investigated the geographic structure, and delineated species using molecular species delimitation methods and morphological analysis within the general lineage concept of species. Molecular and morphological analyses failed to identify L. ruhuna and L. insularis as distinct species; we show them to be synonyms of L. varuna and L. lankensis, respectively. Taxonomic inflation in previous literature is attributed as a result of limited sampling and negligence of size allometry. Additionally, a third, cryptic species discovered in this study is described as L. hema sp. nov. which is evidently confined to the headwaters of the Gal basin in eastern Sri Lanka. Phylogenetic and haplotype network analyses suggest phylogeographic structure within both the southwest-endemic L. varuna and the dry-zone endemic L. lankensis, but the former shows strong phylogeographic structure between adjacent basins. The Sri Lankan species of Laubuka do not form a monophyletic group: they stem from two dispersal or vicariance events, one involving the lineage that led to L. varuna in south-western Sri Lanka, and the other, of [L. lankensis + L. hema] in the dry zone. http://zoobank.org/urn:lsid:zoobank.org:pub:D2A29329-E0E7-447E-B316-81049212CCCB http://zoobank.org/urn:lsid:zoobank.org:act:920E5DC0-CEDC-4243-98C7-12CCF829CBCD
... Research that addresses these population components from a phylogenetic perspective is becoming more common, not only among tropical reef fishes but also in coastal and freshwater fishes (e.g. Mennesson et al., 2018;Rodríguez-Rey et al., 2018;Sudasinghe et al., 2020). ...
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Ricefishes of the genus Oryzias occur commonly in the fresh and brackish waters in coastal lowlands ranging from India across Southeast Asia and on to Japan. Among the three species of Oryzias recorded from peninsular India, two widespread species, O. carnaticus and O. dancena, have previously been reported from Sri Lanka based on museum specimens derived from a few scattered localities. However, members of the genus are widespread in the coastal lowlands of Sri Lanka, a continental island separated from India by the shallow Palk Strait. Although recent molecular phylogenies of Adrianichthyidae represent near-complete taxon representation, they lack samples from Sri Lanka. Here, based on sampling at 13 locations representative of the entire geographic and climatic regions of the island's coastal lowlands, we investigate for the first time the molecular phylogenetic relationships and phylogeography of Sri Lankan Oryzias based on one nuclear and two mitochondrial markers. Sri Lankan Oryzias comprise two distinct non-sister lineages within the javanicus species group. One of these is represented by samples exclusively from the northern parts of the island; it is recognized as O. dancena. This lineage is recovered as the sister group to the remaining species in the javanicus group. The second lineage represents a species that is widespread across the island's coastal lowlands. It is recovered as the sister group of O. javanicus and is identified as O. cf. carnaticus. Ancestral-range estimates suggest two independent colonizations of Indian subcontinent and Sri Lanka by widespread ancestral species of Oryzias during two discrete temporal windows: late Miocene and Plio-Pleistocene. No phylogeographic structure is apparent in Sri Lankan Oryzias, suggesting that there are no strong barriers to gene flow and dispersal along the coastal floodplains, as is the case also for other generalist freshwater fishes in the island
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Despite advances in biodiversity exploration, the origins of Sri Lanka's fauna and flora have never yet been treated in a synthetic work. This book draws together the threads that make up that fascinating 100-million year story. Encompassing the island's entire biota while emphasising the ecology, biogeography and phylogeography of freshwater fishes, it provides a comprehensive context for understanding how the island's plants and animals came to be as they are. The 258-page text contains more than 200 figures, photographs and maps. It provides a clear account of how, when and from where the ancestors of the plants and animals that now inhabit Sri Lanka came. For the first time, the island's unique biodiversity can be understood and appreciated in its historical and evolutionary context in this invaluable sourcebook, designed for scientists, students and biodiversity enthusiasts alike.
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Fish genetic resources and diversity are very important aspects of environmental management and fisheries and are vital for making decisions on their commercial exploitation as well as conservation. The snakehead fishes in the world have significant economic importance as food and ornamental fish. A clear understanding of species’ taxonomic status and genetic diversity is important for the utilization and implementation of conservation and management practices. Channa orientalis is a snakehead endemic to Sri Lanka that is heavily utilized in the ornamental fish export trade. Its genetic diversity has not yet been fully understood and it is difficult to distinguish it from closely resembling species. Therefore, we examined the genetic diversity of C. orientalis and developed a DNA-based marker that permits accurate, low cost, and reliable identification of C. orientalis. Determination of genetic diversity was mainly carried out through genetic analysis of the mitochondrial cytochrome c oxidase subunit 1 (MT-CO1) gene. The development of the DNA-based marker for the identification of C. orientalis was done through Polymerase Chain Reaction and Restriction Fragment Length Polymorphism (PCR-RFLP) analysis. Our analyses confirmed the presence of two distinct genetically divergent and geographically separated lineages of C. orientalis in Sri Lanka. The fast cost-effective gel-based PCR-RFLP marker method developed by us was successful in diagnosing C. orientalis from its closely resembling species. Thus, we believe our findings on the cryptic diversity and diagnostic methods will have important implications for the conservation and management of this endemic species.
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The South and SouthEast Asian freshwater fish genus Systomus (Cyprinidae) comprises 17 valid species. Six nominal species, including three endemics, have been reported from Sri Lanka, a continental island separated from India by a shallow-shelf sea. The species diversity of Systomus on the island has until now not been assessed; neither has an evaluation been made of their phylogenetic history. Here, based on an analysis of the nuclear recombination activating protein 1 (rag1), and mitochondrial cytochrome c oxidase subunit 1 (cox1) and cytochrome b (cytb) gene markers, and a morphological examination of 143 specimens from 49 locations in Sri Lanka, we reassess the diversity of Systomus on the island and analyse patterns of their evolution and biogeography. Divergence-time estimates, based on a substitution rate calibration , date the basal split between Systomus and its sister group, the Afrotropical small barbs, to 30.0 Ma (95% highest posterior density: 25.4-35.2 Ma). The species of Systomus belong to two distinct clades. The first includes the Sri Lankan endemics S. asoka, S. martenstyni and S. pleurotaenia, which comprise an insular diversification following the immigration of a common ancestor during the Oligocene. The second, which includes the remaining species of Indian, Sri Lankan and SouthEast Asian Systomus, has a crown age dating to the Late Miocene. Morphological and molecular species delimitation analyses failed to validate the two nominal species, S. spilurus and S. timbiri, previously reported from Sri Lanka: both are considered synonyms of S. sarana, as are the nomina S. chryseus, S. chrysopoma, S. laticeps, S. rufus, S. pinnauratus and S. subnasutus. Four genetically and geographically discrete line-ages of S. sarana occur in the island, and three in India. Molecular species delimita-tion analysis suggests these all belong to a single species, S. sarana. The genetically distinct Sri Lankan populations of S. sarana result from Plio-Pleistocene dispersal or vicariance events between India and Sri Lanka-as a result of emergence and in-undation of the now submerged isthmus connecting the two landmasses-as well as autochthonous insular diversification.
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As the type species of the genus Channa, the identity of the pelvic-finless snakehead Channa orientalis Bloch is important to channid systematics. Although this name has been attached to a Sri Lankan species for the past 160 years, its vaguely specified type locality, ‘India Orientali’, has long cast doubt as to its origin. Here, based on a collection across its range in the island and analysis of the cytochrome c oxidase subunit 1 (cox1) barcoding gene, we show that the Sri Lankan pelvic-finless Channa is composed of two geographically discrete lineages separated by an uncorrected pairwise cox1 genetic distance of 6.9–8.1%. The minimum genetic distance between these two lineages and other species of the Gachua group of Channa is 5.1%. Despite their genetic divergence, the two lineages exhibit remarkable morphological stasis: they are indistinguishable from each other in external morphology. We argue that the type locality of C. orientalis is south-western Sri Lanka, to which the species is endemic. Channa orientalis is distinguished from other species of Channa by the absence of pelvic fins, adult coloration in life, dorsal- and anal-fin ray counts, number of vertebrae, and scale counts.
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The dwarf snakehead Channa gachua (Hamilton, 1822) (type locality Bengal) has been reported from a vast range, from Iran to Taiwan, and northern India to Sri Lanka. Here, adopting an integrative taxonomic approach, we show that the Sri Lankan snakehead previously referred to as C. gachua is in fact a distinct species, for which the name C. kelaartii (Günther, 1861) is available. Widely distributed in streams and ponds throughout Sri Lanka's lowlands, and also recorded here from the east-flowing drainages of southern peninsular India, C. kelaartii is distinguished from all the other species of the C. gachua species group by the combination of head shape, dorsal-and anal-fin ray counts, scale counts, the presence of pelvic fins, and live adult coloration. Further, C. kelaartii is genetically distinct from topotypical C. gachua by an uncorrected pairwise distance of 7.9-8.8 % for the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene.
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We present the latest version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, MEGA has been optimized for use on 64-bit computing systems for analyzing bigger datasets. Researchers can now explore and analyze tens of thousands of sequences in MEGA. The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit MEGA is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OSX. The command line MEGA is available as native applications for Windows, Linux, and Mac OSX. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
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Sundaland constitutes one of the largest and most threatened biodiversity hotspots; however, our understanding of its biodiversity is afflicted by knowledge gaps in taxonomy and distribution patterns. The subfamily Rasborinae is the most diversified group of freshwater fishes in Sundaland. Uncertainties in their taxonomy and systematics have constrained its use as a model in evolutionary studies. Here, we established a DNA barcode reference library of the Rasborinae in Sundaland to examine species boundaries and range distributions through DNA-based species delimitation methods. A checklist of the Rasborinae of Sundaland was compiled based on online catalogs and used to estimate the taxonomic coverage of the present study. We generated a total of 991 DNA barcodes from 189 sampling sites in Sundaland. Together with 106 previously published sequences, we subsequently assembled a reference library of 1097 sequences that covers 65 taxa, including 61 of the 79 known Rasborinae species of Sundaland. Our library indicates that Rasborinae species are defined by distinct molecular lineages that are captured by species delimitation methods. A large overlap between intraspecific and interspecific genetic distance is observed that can be explained by the large amounts of cryptic diversity as evidenced by the 166 Operational Taxonomic Units detected. Implications for the evolutionary dynamics of species diversification are discussed.
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Biodiversity hotspots have provided useful geographic proxies for conservation efforts. Delineated from a few groups of animals and plants, biodiversity hotspots do not reflect the conservation status of freshwater fishes. With hundreds of new species described on a yearly basis, fishes constitute the most poorly known group of vertebrates. This situation urges for an acceleration of the fish species inventory through fast and reliable molecular tools such as DNA barcoding. The present study focuses on the freshwater fishes diversity in the Sundaland biodiversity hotspot in Southeast Asia. Recent studies evidenced large taxonomic gaps as well as unexpectedly high levels of cryptic diversity, particularly so in the islands of Java and Bali. The Cypriniformes genera Rasbora and Nemacheilus account for most of the endemic species in Java and Bali, however their taxonomy is plagued by confusion about species identity and distribution. This study examines the taxonomic status of the Rasbora and Nemacheilus species in Java, Bali and Lombok islands through DNA barcodes, with the objective to resolve taxonomic confusion and identify trends in genetic diversity that can be further used for conservation matters. Several species delimitation methods based on DNA sequences were used and confirmed the status of most species, however several cases of taxonomic confusion and two new taxa are detected. Mitochondrial sequences argue that most species range distributions currently reported in the literature are inflated due to erroneous population assignments to the species level, and further highlight the sensitive conservation status of most Rasbora and Nemacheilus species on the islands of Java, Bali and Lombok.
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Morphological and molecular analyses of specimens representative of the geographic range of the cyprinid genus Amblypharyngodon in Sri Lanka suggest the presence of only a single species in the island, for which the name Amblypharyngodongrandisquamis Jordan & Starks, 1917, is available. Amblypharyngodongrandisquamis is a species endemic to Sri Lanka, distributed across the lowlands of both of the island’s main climatic zones. It is distinguished from all other species of Amblypharyngodon , including the three species recorded from peninsular India ( A.mola , A.microlepis , and A.melettinus ), by a suite of characters that includes a body depth of 26.9–31.2% of the standard length (SL), 42–56 scales in the lateral series (of which usually 8–16 are pored), 20–24 circumpeduncular scales, 14–17 scale rows between the origins of the dorsal and pelvic fins, a dorsal-fin height of 21.1–27.6% SL, 18–19 caudal vertebrae and an eye diameter of 22.7–30.5% of the head length. Amblypharyngodongrandisquamis differs from A.melettinus and A.mola by uncorrected pairwise genetic distances of more than 9% and 6%, respectively, for the mitochondrial cytochrome oxidase subunit 1 (COI) gene.
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A recent (2013) taxonomic review of the freshwater-fish genus Rasboroides, which is endemic to Sri Lanka, showed it to comprise four species: R. vaterifloris, R. nigro- marginatus, R. pallidus and R. rohani. Here, using an integrative-taxonomic analysis of morphometry, meristics and mitochondrial DNA sequences of cytochrome b (cytb) and cytochrome oxidase subunit 1 (coi), we show that R. nigromarginatus is a synonym of R. vaterifloris, and that R. rohani is a synonym of R. pallidus. The creation and recognition of unnecessary taxa (‘taxonomic inflation’) was in this case a result of selective sampling confounded by a disregard of allometry. The population referred to R. rohani in the Walawe river basin represents an undocumented trans-basin translocation of R. pallidus, and a translocation into the Mahaweli river of R. vaterifloris, documented to have occurred ca 1980, in fact involves R. pallidus. A shared haplotype suggests the latter introduction was likely made from the Bentara river basin and not from the Kelani, as claimed. To stabilize the taxonomy of these fishes, the two valid species, R. vaterifloris and R. pallidus, are diagnosed and redescribed, and their distributions delineated. We draw attention to the wasteful diversion of conservation resources to populations resulting from undocumented translocations and to taxa resulting from taxonomic inflation. We argue against translocations except where mandated by a conservation emergency, and even then, only when supported by accurate documentation.
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The taxonomy of the three native taxa assigned to the genus Labeo (L. dussumieri, L. fisheri and L. porcellus lankae) in Sri Lanka is reviewed. The population hitherto identified as L. dussumieri in Sri Lanka is shown to be a distinct species, here named L. heladiva. Labeo heladiva, new species, has a wide distribution in the low and mid-elevations of the island and is distinguished from its Indian congeners by the combination of having two pairs of barbels; 12-13 branched dorsal-fin rays; lateral line with 44-51 scales; ½8-½9+1+6-7 scales in transverse series; and 19-22 circumpeduncular scales. It differs from its closest relative, L. dussumieri, principally by having 44-51 vs. 50-60 lateral-line scales, 19-22 vs. 22-27 circumpeduncular scales, and by uncorrected pairwise genetic distances of 1.27-2.22% and 1.88-2.91% for the two mi-tochondrial genes COI and cytb, respectively. Labeo fisheri, which is endemic to the upper reaches of the Mahaweli River basin in the Knuckles mountain range and the central hills in the vicinity of Kandy, is distinguished from Indian congeners by having (in combination) only a single pair of barbels; dorsal fin with 10-12 branched rays; lateral line with 37-39 scales; 7+1+4½-6 scales in transverse series; and 17-20 circumpeduncular scales. Labeo lankae is recognized as a valid species endemic to Sri Lanka. Long suspected to have become extinct, or known only from spurious records, an extant population is reported from the northern dry zone of the island. Labeo lankae is the sister species of L. porcellus of pen-insular India; it can be distinguished from its congeners by having, in combination, 10-12 branched dorsal-fin rays; 36-39 lateral-line scales; ½8+1+5-6½ scales in transverse series; and 21-24 circumpeduncular scales. It differs from L. por-cellus principally by having ½8 (vs. ½6-½7) scales between the origin of the dorsal fin and the lateral line, 21-24 (vs. 20-21) circumpeduncular scales and uncorrected pairwise genetic distances of 1.27% and 1.41% for the mitochondrial genes COI and cytb, respectively. The three species of Labeo in Sri Lanka do not form a monophyletic group.
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The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package has become a primary tool for Bayesian phylogenetic and phylodynamic inference from genetic sequence data. BEAST unifies molecular phylogenetic reconstruction with complex discrete and continuous trait evolution, divergence-time dating, and coalescent demographic models in an efficient statistical inference engine using Markov chain Monte Carlo integration. A convenient, cross-platform, graphical user interface allows the flexible construction of complex evolutionary analyses.
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As we collect range-wide genetic data for morphologically-defined species, we increasingly unearth evidence for cryptic diversity. Delimiting this cryptic diversity is challenging, both because the divergences span a continuum and because the lack of overt morphological differentiation suggests divergence has proceeded heterogeneously. Here, we address these challenges as we diagnose and describe species in three co-occurring species groups of Australian lizards. By integrating genomic and morphological data with data on hybridization and introgression from contact zones, we explore several approaches - and their relative benefits and weaknesses - for testing the validity of cryptic lineages. More generally, we advocate that genetic delimitations of cryptic diversity must consider whether these lineages are likely to be durable and persistent through evolutionary time.
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Species are fundamental units in biological research and can be defined on the basis of various operational criteria. There has been growing use of molecular approaches for species delimitation. Among the most widely used methods, the generalized mixed Yule-coalescent (GMYC) and Poisson tree processes (PTP) were designed for the analysis of single-locus data but are often applied to concatenations of multilocus data. In contrast, the Bayesian multispecies coalescent approach in the software BPP explicitly models the evolution of multilocus data. In this study, we compare the performance of GMYC, PTP, and BPP using synthetic data generated by simulation under various speciation scenarios. We show that in the absence of gene flow, the main factor influencing the performance of these methods is the ratio of population size to divergence time, while number of loci and sample size per species have smaller effects. Given appropriate priors and correct guide trees, BPP shows lower rates of species overestimation and underestimation, and is generally robust to various potential confounding factors except high levels of gene flow. The single-threshold GMYC and the best strategy that we identified in PTP generally perform well for scenarios involving more than a single putative species when gene flow is absent, but PTP outperforms GMYC when fewer species are involved. Both methods are more sensitive than BPP to the effects of gene flow and potential confounding factors. Case studies of bears and bees further validate some of the findings from our simulation study, and reveal the importance of using an informed starting point for molecular species delimitation. Our results highlight the key factors affecting the performance of molecular species delimitation, with potential benefits for using these methods within an integrative taxonomic framework.
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In South Asia, south-west Sri Lanka alone represents the sole surviving perhumid region where Mixed Dipterocarp Forests (MDF) harbour a number of relict signature taxa providing evidence of ancient plant migration routes from Gondwana to perhumid Far Eastern Sunda land, at least partially via southern Laurasia. Palynological and phylogenetic evidence now confirm that the Malesian rain forest flora overwhelmingly immigrated from tropical Africa/Madagascar and South Asia along an ever-wet equatorial corridor sometime before the collision of the Indian Plate with the Southern Laurasian coast in middle Eocene (c. 45 Ma). This ever-wet climatic and geological history has led to the evolution of a characteristic species composition and dynamics within SW Sri Lanka’s rain forest communities, which exhibit remarkable patterns of species distribution and habitat specialization, and which parallel those of Far Eastern sister taxa. We here examine the patterns of floristic variation in each of three MDF sites using classification and ordination methods to analyse tree data collected in 62 random plots, each 0.25ha, along an altitudinal gradient. In addition, a 25 ha forest dynamics plot (FDP) was established in the Sinharaja World Heritage Site, within the CTFS-ForestGEO network that addresses issues related to community ecology and phylogenetics incorporating large-scale biogeographic patterns of major clades of both plants and animals. In the above studies, ecologically distinct floristic assemblages were revealed, i) among the three MDF sites as well as, ii) among the ridge-, slope-, and valley habitats within each forest site. In the FDP too, >80% of the 125 species, with individuals >1 cm dbh and >100 individuals per species, are significantly more associated with one or more of eight topographic habitat categories than in others. These results suggest that ecological ranges and dispersion of tree species in SW Sri Lanka is primarily mediated by soil water and nutrient levels in topographically different catenal habitats mirroring those in the Far East.Many of these species are threatened relict endemics, and their distribution patterns have important conservation implications. Their spatial distributional features provide useful criteria in site-species matching or environmental filtering in forest restoration efforts.
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We present version 6 of the DnaSP (DNA Sequence Polymorphism) software, a new version of the popular tool for performing exhaustive population genetic analyses on multiple sequence alignments. This major upgrade incorporates novel functionalities to analyse large datasets, such as those generated by high-throughput sequencing (HTS) technologies. Among other features, DnaSP 6 implements: i) modules for reading and analysing data from genomic partitioning methods, such as RADseq or hybrid enrichment approaches, ii) faster methods scalable for HTS data, and iii) summary statistics for the analysis of multi-locus population genetics data. Furthermore, DnaSP 6 includes novel modules to perform single- and multi-locus coalescent simulations under a wide range of demographic scenarios. The DnaSP 6 program, with extensive documentation, is freely available at http://www.ub.edu/dnasp.
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Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group with those previously reported revealed several inconsistencies that prompted us to expand and improve on previous studies. By generating 343 novel snakehead coxI sequences and combining them with an additional 434 coxI sequences from GenBank we highlight several problems with previous efforts towards the assembly of a snakehead reference barcode library. We found that 16.3% of the channid coxI sequences deposited in GenBank are based on misidentifications. With the inclusion of our own data we were, however, able to solve these cases of perpetuated taxonomic confusion. Different species delimitation approaches we employed (BIN, GMYC, and PTP) were congruent in suggesting a potentially much higher species diversity within snakeheads than currently recognized. In total, 90 BINs were recovered and within a total of 15 currently recognized species multiple BINs were identified. This higher species diversity is mostly due to either the incorporation of undescribed, narrow range, endemics from the Eastern Himalaya biodiversity hotspot or the incorporation of several widespread species characterized by deep genetic splits between geographically well-defined lineages. In the latter case, over-lumping in the past has deflated the actual species numbers. Further integrative approaches are clearly needed for providing a better taxonomic understanding of snakehead diversity, new species descriptions and taxonomic revisions of the group.
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The adaptive radiation of the seven-spined gobies (Gobiidae: Gobiosomatini) represents a classic example of how ecological specialization and larval retention can drive speciation through local adaptation. However, geographically widespread and phenotypically uniform species also do occur within Gobiosomatini. This lack of phenotypic variation across large geographic areas could be due to recent colonization, widespread gene flow, or stabilizing selection acting across environmental gradients. We use a phylogeographic approach to test these alternative hypotheses in the naked goby Gobiosoma bosc, a widespread and phenotypically invariable intertidal fish found along the Atlantic Coast of North America. Using DNA sequence from 218 individuals sampled at 15 localities, we document marked intraspecific genetic structure in mitochondrial and nuclear genes at three main geographic scales: (i) between Gulf of Mexico and Atlantic Coast, (ii) between the west coast of the Florida peninsula and adjacent Gulf of Mexico across the Apalachicola Bay, and (iii) at local scales of a few hundred kilometers. Clades on either side of Florida diverged about 8 million years ago, whereas some populations along the East Cost show divergent phylogroups that have differentiated within the last 200,000 years. The absence of noticeable phenotypic or ecological differentiation among lineages suggests the role of stabilizing selection on ancestral phenotypes, together with isolation in allopatry due to reduced dispersal and restricted gene flow, as the most likely explanation for their divergence. Haplotype phylogenies and spatial patterns of genetic diversity reveal frequent population bottlenecks followed by rapid population growth, particularly along the Gulf of Mexico. The magnitude of the genetic divergence among intraspecific lineages suggests the existence of cryptic species within Gobiosoma and indicates that modes of speciation can vary among lineages within Gobiidae.
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Motivation: In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is a phylogeny-aware approach that does not rely on such thresholds. Yet, two weaknesses of PTP impact its accuracy and practicality when applied to large datasets; it does not account for divergent intraspecific variation and is slow for a large number of sequences. Results: We introduce the multi-rate PTP (mPTP), an improved method that alleviates the theoretical and technical shortcomings of PTP. It incorporates different levels of intraspecific genetic diversity deriving from differences in either the evolutionary history or sampling of each species. Results on empirical data suggest that mPTP is superior to PTP and popular distance-based methods as it, consistently yields more accurate delimitations with respect to the taxonomy (i.e., identifies more taxonomic species, infers species numbers closer to the taxonomy). Moreover, mPTP does not require any similarity threshold as input. The novel dynamic programming algorithm attains a speedup of at least five orders of magnitude compared to PTP, allowing it to delimit species in large (meta-) barcoding data. In addition, Markov Chain Monte Carlo sampling provides a comprehensive evaluation of the inferred delimitation in just a few seconds for millions of steps, independently of tree size. Availability and implementation: mPTP is implemented in C and is available for download at http://github.com/Pas-Kapli/mptp under the GNU Affero 3 license. A web-service is available at http://mptp.h-its.org . Contact: : paschalia.kapli@h-its.org or alexandros.stamatakis@h-its.org or tomas.flouri@h-its.org. Supplementary information: Supplementary data are available at Bioinformatics online.
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Rasbora lateristriata is a primary freshwater fish described from Java Island of Indonesia but its taxonomy, phylogeny, and distributional boundary have not been fully studied. Rasbora baliensis was described as a species endemic to Balinese lakes but its taxonomic status has been controversial in relation to R. lateristriata. Here, we collected Rasbora fishes from various freshwater localities of Java Island, as well as five neighboring islands to conduct molecular and morphological analyses on their phylogenetic relationships. Both molecular analyses using two mitochondrial and two nuclear gene sequences and morphological analyses featuring the body color pattern consistently support that the currently recognized R. lateristriata forms a species complex including at least four major lineages that possibly represent different species. In one of the major lineages, Balinese individuals cluster with those from East Javanese, Lombok and Sumbawa localities, calling for taxonomic revision on R. baliensis. The other three major lineages occur in distinct regions of central, west-central, and western Java and they can be clearly distinguished by the combination of pigmentation patterns in the basicaudal blotch and the supra anal pigment. Our molecular phylogeny suggests west-to-east divergences of the R. lateristriata species complex in Java Island from the late Miocene to Plio-Pleistocene before it finally crossed Wallace’s Line, colonizing Lombok and Sumbawa Islands very recently.
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There are 3108 valid and named native fish species in the inland waters of Southeast Asia between the Irrawaddy and Red River drainages, the small coastal drainages between the Red River and Hainan, the whole Indochinese Peninsula, Andaman and Nicobar Islands, Indonesia (excluding Papua Province, Waigeo, Aru [but Kai is included]), and the Philippines. They belong to 137 families. Their taxonomy and nomenclature are reviewed. The original descriptions of all 7047 recorded species-group names and 1980 genus-group names have been checked in the original works for correct spelling, types, type locality and bibliographic references. The bibliography includes about 4700 titles. Synonymies are given, based on published information as well as unpublished observations. The names of 49 introduced species and 347 extralimital taxa cited in the discussions have also been checked. The original descriptions of all species not present in the covered area but cited as type species of genera have been checked for availability, authorship, date and correct spelling. The availability of some family-group names has been checked when there was suspicion of possible nomenclatural problems. Bibliographic notes include new informations on the dates of publication of works by, among others, Bleeker, Bloch, Heckel and Steindachner and discussion of authorship of names in various works.
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In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix, is commonly accompanied by the assumption of partition models. Under such models each gene, or more generally partition, is allowed to evolve under its own evolutionary model. Though partition models provide a more comprehensive analysis of supermatrices, missing data may hamper the tree search algorithms due to the existence of phylogenetic (partial) terraces. Here we introduce the phylogenetic terrace aware (PTA) data structure for the efficient analysis under partition models. In the presence of missing data PTA exploits (partial) terraces and induced partition trees to save computation time. We show that an implementation of PTA in IQ-TREE leads to a substantial speedup of up to 4.5 and 8 times compared with the standard IQ-TREE and RAxML implementations, respectively. PTA is generally applicable to all types of partition models and common topological rearrangements thus can be employed by all phylogenomic inference software.
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Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3–97.1%. IQ-TREE is freely available at http://www.cibiv.at/software/iqtree.
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Four new species of the minnow genus Rasbora of the Sumatrana group, R. arundinata, R. haru, R. maninjau, and R. bindumatoga, are described from northern Sumatra. Rasbora arundinata is distinguished from all congeners in the Sumatrana group by the black midlateral stripe overall forming a reed-leaf-like profile. Rasbora haru differs from its congeners in the Sumatrana group in having the black midlateral stripe overall forming a stamen-like profile. The new species endemic to Lake Maninjau in central west Sumatra, Rasbora maninjau, is unique among all the congeners in the Sumatrana group in having a combination of the black midlateral stripe extending from the midhumeral region of uniform width, the prominent acutely triangular basicaudal blotch, and the oval supra-anal pigmentation. Rasbora bindumatoga is distinguished from all congeners in the Sumatrana group by a combination of the black rectangular subdorsal blotch, the absence of supra-anal pigmentation, and the somewhat oval basicaudal blotch. Rasbora arundinata, R. maninjau, and R. bindumatoga occur allopatrically in the northwestern coastal region of Sumatra, while R. haru is known from northeastern coastal area of Sumatra. A new diagnostic character for the Sumatrana group is described: partial exposure of the upper lip due to a submedial contact between the maxilla and the lower lip, which is marked posteriorly by a lachrymal groove.
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As a discipline, phylogenetics is becoming transformed by a flood of molecular data. These data allow broad questions to be asked about the history of life, but also present difficult statistical and computational problems. Bayesian inference of phylogeny brings a new perspective to a number of outstanding issues in evolutionary biology, including the analysis of large phylogenetic trees and complex evolutionary models and the detection of the footprint of natural selection in DNA sequences.
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A reassembly of the Precambrian fragments of central Gondwana is presented that is a refinement of a tight reassembly published earlier. Fragments are matched with conjugate sides parallel as far as possible and at a distance of 60–120 km from each other. With this amount of Precambrian crust now stretched into rifts and passive margins, a fit for all the pieces neighbouring Madagascar – East Africa, Somalia, the Seychelles, India, Sri Lanka and Mozambique – may be made without inelegant overlap or underlap. This works less well for wider de-stretched margins on such small fragments. A model of Gondwana dispersal is also developed, working backwards in time from the present day, confining the relative movements of the major fragments – Africa, Antarctica and India – such that ocean fracture zones collapse back into themselves until each ridge-reorganisation is encountered. The movements of Antarctica with respect to Africa and of India with respect to Antarctica are defined in this way by a limited number of interval poles to achieve the Gondwana ‘fit’ situation described above. The ‘fit’ offers persuasive alignments of structural and lithologic features from Madagascar to its neighbours. The dispersal model helps describe the evolution of Madagascar’s passive margins and the role of the Madagascar Rise as a microplate in the India–Africa–Antarctica triple junction. Intrusions, extrusions and dykes observed in Madagascar and its neighbours, largely from aeromagnetic survey data, are related to the outbreak of the Karoo/Bouvet mantle plume at ∼182 Ma, the Marion mantle plume at ∼88 Ma and the Reunion mantle plume at ∼66 Ma. The dispersal model may be viewed and downloaded as an animation at: http://www.reeves.nl/gondwana.
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We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.
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The taxonomic status of the large snakeheads of the Channa marulius group that occur in Sri Lanka is reviewed and clarified. Two species are recognized from the island, based on both morphological and molecular (cytochrome c oxidase subunit 1: cox1) differentiation: C. marulius Hamilton from the northern dry zone and C. ara Deraniyagala from the middle and lower regions of the Mahaweli basin. Channa ara is endemic to Sri Lanka and can be distinguished from its Marulius group congeners, C. marulius, C. aurolineata and C. auroflammea, by having fewer dorsal-and anal-fin rays, fewer lateral-line scales and fewer vertebrae; from C. marulioides by a different adult colour pattern; and from C. pseudomarulius by having more vertebrae. At the cox1 barcoding locus, Channa ara is at least 3.6% genetically different from C. marulius, and at least 8% different from the other described species in the group. Specimens collected from the southwestern wet zone in Sri Lanka are a puzzling third component of the Marulius group's diversity, uncovered in this study, and identified here as C. cf. ara. Whilst genetically more similar to C. marulius, C. cf. ara possesses fewer dorsal-and anal-fin rays, fewer lateral-line scales and fewer vertebrae and is therefore morphologically more similar to C. ara. Channa ara can be distinguished from C. cf. ara, however, by differences in circumpeduncular scale count, adult colour pattern, and by an uncorrected pairwise genetic distance of 3.7% in cox1 sequences. A neotype is designated for Ophicephalus marulius ara Deraniyagala.
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Molecular and morphological analyses show that Esomus thermoicos is the only species of Esomus in Sri Lanka. Esomus thermoicos is distinguished from its congeners by the combination of having a complete lateral line, a dark mediolateral stripe, a short pectoral fin that does not reach the anal-fin origin when adpressed, and by lacking conspicuous spots or blotches on the body. A limited series of specimens from southern peninsular India are also identified as E. thermoicos. Esomus brevibarbartus is a junior subjective synonym of E. thermoicos.
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Available online under http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp
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Pseudophilautus comprises an endemic diversification predominantly associated with the wet tropical regions of Sri Lanka that provides an opportunity to examine the effects of geography and historical climate change on diversification. Using a time-calibrated multi-gene phylogeny, we analyze the tempo of diversification in the context of past climate and geography to identify historical drivers of current patterns of diversity and distribution. Molecular dating suggests that the diversification was seeded by migration across a land-bridge connection from India during a period of climatic cooling and drying, the Oi-1 glacial maximum around the Eocene-Oligocene boundary. Lineage-through-time plots suggest a gradual and constant rate of diversification, beginning in the Oligocene and extending through the late Miocene and early Pliocene with a slight burst in the Pleistocene. There is no indication of an early-burst phase of diversification characteristic of many adaptive radiations, nor were there bursts of diversification associated with favorable climate shifts such as the intensification of monsoons. However, a late Miocene (8.8 MYA) back-migration to India occurred following the establishment of the monsoon. The back migration did not trigger a diversification in India similar to that manifest in Sri Lanka, likely due to occupation of available habitat, and consequent lack of ecological opportunity, by the earlier radiation of a sister lineage of frogs (Raorchestes) with similar ecology. Phylogenetic area reconstructions show a pattern of sister species distributed across adjacent mountain ranges or from different parts of large montane regions, highlighting the importance of isolation and allopatric speciation. Hence, local species communities are composed of species from disparate clades that, in most cases, have been assembled through migration rather than in situ speciation. Lowland lineages are derived from montane lineages. Thus, the hills of Sri Lanka acted as species pumps as well as refuges throughout the 31 million years of evolution, highlighting the importance of tropical montane regions for both the generation and maintenance of biodiversity.
Article
Humans have dramatically altered the planet over the course of a century, from the acidity of our oceans to the fragmentation of our landscapes and the temperature of our climate. Species find themselves in novel environments, within communities assembled from never before encountered mixtures of invasives and natives. The speed with which the biotic and abiotic environment of species has changed has already altered the evolutionary trajectory of species, a trend that promises to escalate. In this article, I reflect upon this altered course of evolution. Human activities have reshaped selection pressures, favouring individuals that better survive in our built landscapes, that avoid our hunting and fishing, and that best tolerate the species that we have introduced. Human-altered selection pressures have also modified how organisms live and move through the landscape, and even the nature of reproduction and genome structure. Humans are also shaping selection pressures at the species level, and I discuss how species traits are affecting both extinction and speciation rates in the Anthropocene.
Article
Zootaxa 4422 (4): 478-492 Abstract Schistura scripta, new species, is described from Nakiyadeniya in the southwestern lowlands of Sri Lanka. It can be distinguished from all other congeners from Sri Lankan and peninsular India by the combination of the following characters: an incomplete lateral line with 53-76 pores, ending beneath the dorsal-fin base or slightly beyond; 7-13 post-dorsal bars; 7½ branched dorsal-fin rays; absence of an axillary pelvic lobe; and absence of a suborbital flap.
Article
Cryptic species could represent a substantial fraction of biodiversity. However, inconsistent definitions and taxonomic treatment of cryptic species prevent informed estimates of their contribution to biodiversity and impede our understanding of their evolutionary and ecological significance. We propose a conceptual framework that recognizes cryptic species based on their low levels of phenotypic (morphological) disparity relative to their degree of genetic differentiation and divergence times as compared with non-cryptic species. We discuss how application of a more rigorous definition of cryptic species in taxonomic practice will lead to more accurate estimates of their prevalence in nature, better understanding of their distribution patterns on the tree of life, and increased abilities to resolve the processes underlying their evolution.
Article
Schistura madhavai, new species, is described from Suriyakanda, Sri Lanka. It is distinguished from all other species of Schistura in the peninsula of India and Sri Lanka by the combination of the following characters: 8–9 wide, brown post-dorsal bars separated by narrow, white interspaces; width of interspaces ¼–⅓ times width of bars; black bar at caudal-fin base wider than interspaces on the body; incomplete lateral line, ending beneath dorsal-fin base; absence of an axillary pelvic lobe; adpressed pelvic fin just reaching anus; origin of the pelvic fin on a vertical through the last unbranched dor-sal-fin ray. Schistura notostigma, the only other Sri Lankan species of Schistura, is redescribed. It can be distinguished from all other species of Schistura in the peninsula of India and Sri Lanka by the combination of the following characters: 6–7 wide, brown postdorsal bars; width of interspaces ½–1 times width of bars; complete, black bar at caudal-fin base narrower than width of interspaces between bars on body; emarginate caudal fin; incomplete lateral line ending beneath dorsal-fin base; adpressed pelvic fin surpassing anus; and origin of pelvic fin beneath first branched dorsal-fin ray. Schis-tura madhavai is separated from S. notostigma by an uncorrected pairwise distance of 3.0–3.8% for the 16S rRNA gene fragment.
Article
Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
Article
Premise of the study: Spermacoceae are mainly an herbaceous group in the Rubiaceae. However, a few lineages are woody and are found in a diverse range of habitat types. Three of the largest woody lineages (Arcytophyllum, Hedyotis, and Kadua) are characterized by their distribution in the moist tropical mountains and have disjunct distribution patterns with respect to their closest relatives. In this study, we explore the cases of derived woodiness in these three lineages and their diversification dynamics in the tropical mountains of Asia, the Pacific, and the Americas. Methods: By combining phylogenetic results with wood anatomical studies, we estimated timing of origin of the three woody groups, inferred their ancestral traits and ancestral distribution ranges, analyzed their associations with the tropical upland habitat, and elucidated their diversification across tropical mountains. Key results: The three woody clades originated and diversified from herbaceous ancestors in close association with the tropical upland habitat during the Miocene. The ancestral range for Asian-Pacific Hedyotis is Africa/Madagascar and continental Asia for Pacific Kadua. The complex geological history of tropical Asia allowed Hedyotis to diversify faster and create narrow endemics near oceans in the highlands of the Western Ghats in India, Sri Lanka, Southeast Asia including southeastern China, and New Guinea. Conclusions: The three major woody clades in Spermacoceae have gained their woodiness independently from one another, subsequent to colonization by their ancestors from a different geographic environment. The evolution and diversification along the tropical mountain orogeny is strongly linked with the formation of woody habit and many narrow endemic species.
Article
We evaluated the status of 16 of 22 recognized Sri Lankan Cnemaspis Strauch species, and flagged overlooked diversity with two mitochondrial (cyt b & ND2) and two nuclear markers (RAG1 & PDC) totalling 2829 base pairs. A fossil-calibrated timetree and sampling of other South Asian Cnemaspis provide insights into the diversification of the genus in peninsular India and Sri Lanka. Phylogenetic analyses consistently inferred two broad clades within South Asian Cnemaspis, with Sri Lankan species in two clades, which we call the podihuna and kandiana clades. Each Sri Lankan clade as a whole is sister to Indian taxa and nested within Indian lineages. Cnemaspis modigliani Das from Indonesia is a member of the kandiana clade. This suggests a minimum of two dispersal events between India and Sri Lanka and one between Sri Lanka/India and Southeast Asia. South Asian Cnemaspis date back to at least the Eocene, in Sri Lanka to the early Miocene, with late Miocene diversification in the kandiana clade. All but one of the named species we sampled is likely to be valid, and 10 divergent unnamed lineages may warrant specific recognition. A resolution of Sri Lankan Cnemaspis taxonomy will require thorough sampling and the use of both morphological and molecular data.
Article
PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder The source code is available at https://github.com/brettc/partitionfinder.
Article
In Bayesian phylogenetic analyses of genetic data, prior probability distributions need to be specified for the model parameters, including the tree. When Bayesian methods are used for molecular dating, available tree priors include those designed for species-level data, such as the pure-birth and birth-death priors, and coalescent-based priors designed for population-level data. However, molecular dating methods are frequently applied to data sets that include multiple individuals across multiple species. Such data sets violate the assumptions of both the speciation and coalescent-based tree priors, making it unclear which should be chosen and whether this choice can affect the estimation of node times. To investigate this problem, we used a simulation approach to produce data sets with different proportions of within- and between-species sampling under the multispecies coalescent model. These data sets were then analysed under pure-birth, birth-death, constant-size coalescent, and skyline coalescent tree priors. We also explored the ability of Bayesian model testing to select the best-performing priors. We confirmed the applicability of our results to empirical data sets from cetaceans, phocids, and coregonid whitefish. Estimates of node times were generally robust to the choice of tree prior, but some combinations of tree priors and sampling schemes led to large differences in the age estimates. In particular, the pure-birth tree prior frequently led to inaccurate estimates for data sets containing a mixture of inter- and intraspecific sampling, whereas the birth-death and skyline coalescent priors produced stable results across all scenarios. Model testing provided an adequate means of rejecting inappropriate tree priors. Our results suggest that tree priors do not strongly affect Bayesian molecular dating results in most cases, even when severely misspecified. However, the choice of tree prior can be significant for the accuracy of dating results in the case of data sets with mixed inter- and intraspecies sampling.
Article
Haplotype networks are an intuitive method for visualising relationships between individual genotypes at the population level. Here, we present popart, an integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication-ready figure production. popart also provides a platform for the implementation and distribution of new network-based methods – we describe one such new method, integer neighbour-joining. The software is open source and freely available for all major operating systems.
Article
Rasbora cryptica, new species, is described from Borneo in southern Sarawak (Malaysia). It is distinguished from all other species of the genus by a unique colour pattern consisting of a bold black longitudinally elongated blotch, made of a layer of deep pigment, appearing as a ventrad widening of the axial streak, on which the midlateral stripe is overimposed; the blotch extends from about midway between the pectoral- and pelvic-fin bases, until the middle of the dorsal-fin base. On the caudal peduncle, there is an elongate triangular blotch, with the apex pointed forwards, not extending onto the caudal fin. Rasbora cryptica was earlier misidentified as R. volzii fasciata, which is a synonym of R. volzii. A lectotype is designated for R. volzii.
Article
A complete introduction to discriminant analysis--extensively revised, expanded, and updated This Second Edition of the classic book, Applied Discriminant Analysis, reflects and references current usage with its new title, Applied MANOVA and Discriminant Analysis. Thoroughly updated and revised, this book continues to be essential for any researcher or student needing to learn to speak, read, and write about discriminant analysis as well as develop a philosophy of empirical research and data analysis. Its thorough introduction to the application of discriminant analysis is unparalleled. Offering the most up-to-date computer applications, references, terms, and real-life research examples, the Second Edition also includes new discussions of MANOVA, descriptive discriminant analysis, and predictive discriminant analysis. Newer SAS macros are included, and graphical software with data sets and programs are provided on the book's related Web site. The book features: Detailed discussions of multivariate analysis of variance and covariance An increased number of chapter exercises along with selected answers Analyses of data obtained via a repeated measures design A new chapter on analyses related to predictive discriminant analysis Basic SPSS(r) and SAS(r) computer syntax and output integrated throughout the book Applied MANOVA and Discriminant Analysis enables the reader to become aware of various types of research questions using MANOVA and discriminant analysis; to learn the meaning of this field's concepts and terms; and to be able to design a study that uses discriminant analysis through topics such as one-factor MANOVA/DDA, assessing and describing MANOVA effects, and deleting and ordering variables. © 2006 by JohnWiley & Sons, Inc., Hoboken, New Jersey. All rights reserved.