No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
A molecular phylogeny of the genus Laubuka (Teleostei: Cyprinidae) in Sri Lanka reveals multiple origins and a cryptic species
Abstract
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
Supplementary resource (1)
... i DZ4452A, 36.9 mm SL (5). j DZ5352B, 39.0 mm SL (2). k DZ5350E, 42.6 mm SL (4). ...
... Pethia nigrofasciata in p-r. p DZ4403A, 39 The wet-zone species appear to comprise a monophyletic diversification, while P. melanomaculata seems more closely related to P. punctata, a South Indian species [27,30,31]. Additionally, the wet-zone species have unusual distributions. ...
... 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. ...
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.
... 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 . ...
... It was also established that Systomus spilurus and S. timbiri, once considered distinct endemic species, are synonyms of S. sarana and only represent two clades of the latter 36 . The revision of Sri Lankan Laubuka showed that L. ruhuna and L. insularis previously considered distinct species, to be synonyms of L. varuna and L. lankensis 37 . The Sri Lankan snakehead previously identified as Channa gachua was recognized as an endemic species, Channa kelaartii 35 . ...
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.
... Present day Sri Lankan Island has been a part of the Indian plate during the Gondwanan break-up and drifted away in Miocene from the mainland India to form an island (Biswas 2008). The Sri Lanka Island had several extended periods of land connection with mainland India during the Burdigalian age (~20-16 Mya) and the recent Pleistocene epoch as part of a series of glacial periods (Bossuyt et al. 2004;Epa et al. 2012;Sudasinghe et al. 2020). ...
... Hence, due to the lack of revisionary works, the taxonomic status of these species, their level of morphological variation etc. cannot be considered as confirmed. The Western Ghats and Sri Lanka have similar levels of endemism among various taxa such as trees, bryophytes, land snails, odonates, fishes, amphibians and reptiles, though the fauna of the wet evergreen forest zones have been found to be quite distinctive and forms endemic clades, where as the fauna and flora of lowland dry forests seems more similar (Bossuyt et al. 2004;Gunawardene et al. 2007;Sudasinghe et al. 2020). Earthworms are also not an exception for this; Megascolex and Notoscolex species show high level of endemism in Sri Lanka and Western Ghats south of Palghat (Palakkad) gap (Narayanan et al. 2016). ...
A comprehensive checklist of the earthworm species known from Sri Lanka, an island country in the Indian subcontinent, is presented. In total, 81 species and subspecies belonging to 20 genera and 8 families are recorded. Of these, 58 are Sri Lanka endemics, 2 near endemics and 21 exotics. The checklist includes the type locality, any significant subsequent generic placements, and the distributional pattern with province and districts for each species/subspecies within Sri Lanka.
... The methods of DNA extraction, PCR amplification and PCR product purification for the two mitochondrial markers follow Sudasinghe, Ranasinghe, et al. (2018), Ali, Dahanukar, Kanagavel, Philip, & Raghavan (2013) and Katwate, Paingankar, Jadhav, & Dahanukar (2013). Those for the nuclear marker follow Sudasinghe, Pethiyagoda, and Meegaskumbura (2020a). The newly generated sequences were verified using ChromasPro v1.34 (Technelysium Pty Ltd, Australia) and the consensus sequences of the 5′ and 3′ strands were prepared using MEGA v. 7.0 (Kumar, Stecher, & Tamura, 2016 Additional comparative genetic data for Smiliogastrinae Bleeker (sensu Tan & Armbruster, 2018) were downloaded from GenBank (Table S2). ...
... While haplotypes are not shared between these four haplogroups, compared with S. pleurotaenia, their haplotype and nucleotide diversities are low. Such a phylogeographic pattern has been observed also in other Sri Lankan cyprinids, such as Laubuka, Rasbora and Devario (Sudasinghe, Pethiyagoda, & Meegaskumbura, 2020a;2020b;Sudasinghe, Pethiyagoda, Ranasinghe, et al., 2020). Given that S. sarana are abundant in both lotic and lentic waters in the lowland floodplain that surrounds the island's central mountains, the barriers to dispersal across the basins remain to be determined. ...
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.
... The Western Ghats mountain range located in the southwestern portion of India along with Sri Lanka is known for its biodiversity hotspots [52,53] and contains several endemic species. The level of endemism in these regions is quite common among various taxa such as fishes, land snails, trees, amphibians, odonates, and reptiles [54,55]. This sort of endemism is also true for earthworms that exceptionally show a high level of endemism (71.6% in Sri Lanka and 77% in the Western Ghats) as reported by Narayanan et al. [6,56]. ...
Megascolex (Oligochaeta: Megascolecidae) are endemic species to India and Sri Lanka, however, to date their molecular taxonomy and phylogenetic relationships have not been reported. We applied the first integrative approach using morpho-anatomical features and a COI da-taset to unveil species delimitation (SD), molecular taxonomy, and phylogenetic relationships in Megascolex species. Our morpho-anatomical results revealed nine Megascolex species, namely, M. auriculata, M. cochinensis cochinensis, M. filiciseta, M. ratus, M. travancorensis travancorensis, M. trian-gularis, M. konkanensis konkanensis, M. polytheca polytheca, and M. polytheca zonatus. We also reported the occurrence of two new species, namely, M. papparensis sp. nov, and M. vazhichlensis sp. nov. Such findings were also supported by the analysed COI dataset, in which these new species appeared distinct on the phylogenetic trees with strong support. The studied Megascolex species appeared paraphyletic and formed three subclades on Bayesian inference (BI) and Maximum Likelihood (ML) phylogenetic trees. The first clade consisted of six species: M. cochinensis cochinensis, M. polytheca polytheca, M. polytheca zonatus, M. konkanensis konkanensis, M. filiciseta, and M. auriculata with strong posterior probability support. The second clade consisted of M. travancorensis travancorensis, M. pap-parensis sp. nov, and M. vazhichlensis sp. nov with strong support. The third clade consisted of M. ratus and M. triangularis with good support. In addition, the validation of species was confirmed by SD methods, in which the congruence among OTUs was observed with the clear barcode gap of 12-14% suggested by ABGD analysis. However, the species M. ratus and M. travancorensis travancorensis show deep intraspecific divergence and, therefore, require more sampling data. Such findings are essential to study the phylogenetics and evolution of the genus and, nonetheless, demand larger COI datasets to make concrete conclusions.
... Previous studies exploring comparative phylogeographic patterns and genetic structure in Sri Lankan freshwater fishes focused primarily on Cypriniformes, which are obligatorily confined to freshwater habitats Sudasinghe et al., 2020aSudasinghe et al., , 2020bSudasinghe, Herath, et al., 2018;Sudasinghe, Pethiyagoda, Ranasinghe, et al., 2020;Sudasinghe, Ranasinghe, et al., 2021). In contrast, Sri Lankan adrianichthyids offer us, for the first time, an opportunity to explore the phylogeography of a widespread, saline-tolerant species. ...
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
... 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. ...
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.
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.
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.
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.
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.
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.
Due to the low easterly gradient of the eastern slopes of the eastern and western ghats of Indian Peninsula, the easterly flowing Bay of Bengal bound rivers display well developed life histories with landforms of youthful stage in the western catchments, mature stage in the central plains and old stage along the eastern coastal region. The old stages of these rivers viz. Mahanadi, Godavari, Krishna, Cauvery and Vaigai rivers have developed broad, wide and characteristic deltas. Amidst these, the deltas of Tamil Nadu coast have been studied in detail which revealed (i) lobate morphology of Vaigai delta indicating total fluvial dominance in its evolution, (ii) Arcuate morphology of Cauvery delta suggesting dominant fluvial dynamics and marine dynamics all along the delta front (iii) cuspate nature of northern Vellar delta notifying equal energy of fluvial and marine dynamics, (iv) digitate architecture of Ponnaiyar delta signify dominance of marine dynamics over fluvial dynamics and (v) estuarine morphology of Tamiraparani notifying the total surrender of fluvial energy to the marine forces. The input of tectonics over the development of Tamil Nadu deltas brought out during the recent years elaborating the tectonic – fluvial – marine dynamics. However amongst these Tamil Nadu deltas, two deltas show abrupt truncation in their delta fronts. The significant one is the Vaigai lobate delta which cover over 2300 sq. km. with thousands of arcuately arranged concentric rings of crescent shaped sandy lobes and intervening depressions / water bodies encircling the apex in the northwest and spread over up to the coast in the southeast. This has been attributed to the constant tectonic uplift of the land and consequent progradation of the delta. But such huge prograding delta has been truncated along the Rameshwaram coast.. Similarly, the Tamiraparani river which has developed wider floodplains in the mature stage in the plains in the centre has not developed any major delta in the old stage in the east along the coast and rather the small delta too appears to be estuarine indicating the total surrender of the fluvial forces to marine dynamics. In this context, to unfurl the mysterious truncation of the life histories of Vaigi and Tamiraparani rivers, the offshore region was studied.
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.
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.
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.
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.
Laubuka tenella is a new species characterized by the colour pattern, consisting of short dark vertical bars anteriorly on the side, and a dark lateral band posteriorly on the side, combined with a relatively short pelvic fin and 29–30 lateral-line scales. It is separated from other Laubuka analysed by minimum 9 % uncorrected p -distance in the mitochondrial COI gene. The type series is composed of specimens from small streams in the Cox’s Bazar District in Bangladesh (the type locality), and the Thandwe River drainage in western Myanmar. Laubuka brahmaputraensis is strongly indicated to be a junior synonym of L. laubuca , the second known species of Laubuka in Bangladesh. Eustira ceylonensis , currently in the synonymy of Devario malabaricus , is a valid species of Laubuka .
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.
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.
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.
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.
Patterns of fish community composition in the Mahaweli ichthyological region of Sri Lanka were examined in agricultural tributaries of the Uma-oya catchment of the upper Mahaweli River in comparison to more pristine streams in a nature reserve in the Amban-ganga catchment. The Uma-oya catchment shows characteristics commonly observed in extensive agricultural exploitation such as impaired water quality and altered riparian vegetation. The most abundant fish species in the two regions were Garra ceylonensis, Devario malabaricus, and Rasbora daniconius, although their relative abundance differed between sites. G. ceylonensis and Neomacheilus notostigma were the only endemic fish species in common but the latter has been extremely depauperate. Endemism is higher in the reference sites (62.5%) than agricultural sites (ca. 25%); some of the reference streams showed greater diversity with unique fish species and a few species that have not been recorded previously in the catchment. The ichthyofaunal similarity between two catchments was 39% and fish species diversity was negatively correlated with stream gradients (Pearson correlation (-0.630); r 2 = 39.6% p = 0.028). Species density and biomass of G. ceylonensis and D. malabaricus were positively associated with some water quality parameters. The presence of exotic fish species were amongst the primary discriminants between human exploited and least-exploited (reference) streams. The possible negative impact of exotic Oreochromis niloticus (Nile tilapia) on indigenous G. ceylonensis is highlighted. This paper provides impetus for making several hypotheses for sustainability of stream fish assemblages in highly exploited agricultural catchments in Sri Lanka.
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.
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.
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.
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.
A comprehensive, but simple-to-use software package for executing a range of standard numerical analysis and operations used in quantitative paleontology has been developed. The program, called PAST (PAleontological STatistics), runs on standard Windows computers and is available free of charge. PAST integrates spreadsheettype data entry with univariate and multivariate statistics, curve fitting, time-series analysis, data plotting, and simple phylogenetic analysis. Many of the functions are specific to paleontology and ecology, and these functions are not found in standard, more extensive, statistical packages. PAST also includes fourteen case studies (data files and exercises) illustrating use of the program for paleontological problems, making it a complete educational package for courses in quantitative methods.
Sequence-based methods to delimit species are central to DNA taxonomy, microbial community surveys, and DNA meta-barcoding studies. Current approaches either rely on simple sequence similarity thresholds (OTU-picking) or on complex and compute-intensive evolutionary models. OTU-picking methods scale well on large data sets, but the results are highly sensitive to the similarity threshold. Coalescent-based species delimitation approaches often rely on Bayesian statistics and MCMC sampling, and can therefore only be applied to small data sets.
We introduce the Poisson Tree Processes (PTP) model to infer putative species boundaries on a given phylogenetic input tree. We also integrate PTP with our Evolutionary Placement Algorithm (EPA-PTP) to count the number of species in phylogenetic placements. We compare our approaches to popular OTU-picking methods and the General Mixed Yule Coalescent (GMYC) model. For de novo species delimitation, the stand-alone PTP model generally outperforms GMYC as well as OTU-picking methods when evolutionary distances between species are small. PTP neither requires an ultrametric input tree, nor a sequence similarity threshold as input. In the open reference species delimitation approach, EPA-PTP yields more accurate results than de novo species delimitation methods. Finally, EPA-PTP scales on large datasets because it relies on the parallel implementations of the EPA and RAxML, thereby allowing to delimit species in high-throughput sequencing data.
The code is freely available at www.exelixis-lab.org/software.html.
Alexandros.Stamatakis@h-its.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics on-line.
Despite numerous studies aimed at resolving relationships among basal euteleost lineages, many aspects of their phylogeny remain the subject of debate. The Esociformes have proven particularly difficult to place, and although a hypothesis of relationships within this group first proposed by Nelson has been generally accepted, a recent hypothesis based on evidence from mitochondrial DNA sequences is not congruent with it. We have assembled an expanded dataset of DNA sequences from the mitochondrial and nuclear genomes to test existing hypotheses of esociform inter- and intraordinal relationships. This dataset includes representatives from all extant esociform lineages and a wide diversity of potential outgroups (51 taxa in total). We also conducted a review of the morphological information that supports currently held hypotheses of esociform inter- and intraordinal relationships. This review revealed potential problems with character state coding and interpretation of character states. However, the molecular evidence, particularly the nuclear sequences, produced unambiguous support for a sister-group relationship between esociforms and salmonoids and also offer similarly strong corroboration of the hypothesis of esociform intraordinal relationships based on mitochondrial sequences and for the monophyly of the subgenera Esox and Kenoza of Esox. In addition to the conclusions regarding esociform relationships, the molecular evidence we present offers support for the monophyly of the Osmeridae, for a sister-group relationship between the Retropinnidae and the Osmeroidei (Osmeridae + Salangidae + Plecoglossidae) and for a close relationship of Stomiiformes and Osmeriformes.
Devario xyrops is described from small rivers on the western slope of the Rakhine Yoma in south-western Myanmar. It is distinguished from all other species in the genus except D. anomalus by its colour pattern including a dark blotch or condensed series of vertical bars anteriorly on the side, separate from a posterior dark horizontal band; and distinguished from D. anomalus in particular by deeper body (29.9-35.8% SL, vs. 25.0-26.8 % SL) and fewer lateral line scales (31-33, modally 32 vs. 33-35, modally 34).
Patterns of fish community composition in the Mahaweli ichthyological region of Sri Lanka were examined in agricultural tributaries of the Uma-oya catchment of the upper Mahaweli River in comparison to more pristine streams in a nature reserve in the Amban-ganga catchment. The Uma-oya catchment shows characteristics commonly observed in extensive agricultural exploitation such as impaired water quality and altered riparian vegetation. The most abundant fish species in the two regions were Garra ceylonensis, Devario malabaricus, and Rasbora daniconius, although their relative abundance differed between sites. G. ceylonensis and Neomacheilus notostigma were the only endemic fish species in common but the latter has been extremely depauperate. Endemism is higher in the reference sites (62.5%) than agricultural sites (ca. 25%); some of the reference streams showed greater diversity with unique fish species and a few species that have not been recorded previously in the catchment. The ichthyofaunal similarity between two catchments was 39% and fish species diversity was negatively correlated with stream gradients (Pearson correlation (-0.630); r 2 = 39.6% p = 0.028). Species density and biomass of G. ceylonensis and D. malabaricus were positively associated with some water quality parameters. The presence of exotic fish species were amongst the primary discriminants between human exploited and least-exploited (reference) streams. The possible negative impact of exotic Oreochromis niloticus (Nile tilapia) on indigenous G. ceylonensis is highlighted. This paper provides impetus for making several hypotheses for sustainability of stream fish assemblages in highly exploited agricultural catchments in Sri Lanka.
The species hitherto included in the genus Chela are shown to belong to two distinct genera, Chela (type species C. cachius) and Laubuca (type species L. laubuca). The Indian and Sri Lankan species of Laubuca (L. laubuca, L. fasdata, L. dadyburjori, L. lankensis and three new species, L. insularis, L. ruhuna and L. varuna) are distinguished from C. cachius, the type species of Chela (among other characters) by having 14 pre-caudal vertebrae (vs. 17 in C. cachius); 31-37 + 1-2 lateral-line scales (vs. 56-61 + 3-4); 7-11 scales in transverse line on body (vs. 17-19); and 14-20 branched anal-fin rays (vs. 21-23). Within Sri Lanka, the dry-zone species L. lankensis and L. insularis are distinguished from their wet-zone congeners L. varuna and L. ruhuna by having the skin over the dentary densely tuberculated (vs. tubercles minute, widely spaced). Laubuca lankensis is distinguished from L. insularis by its shorter pelvic fins (not reaching anal-fin origin, vs. reaching beyond base of third branched anal-fin ray in L. insularis); while L. ruhuna is distinguished from L. varuna by its deeper body (2.9-3.1 in SL, vs. 3.2-3.6 in L. varuna).
Aruwakkalu fossil bed is a part of Sri Lanka's Jaffna limestone, which underlies the whole of Jaffna Peninsula and extends southwards mostly along the west coast. Previous authors have suggested that Aruwakkalu contains a rich assemblage of vertebrate and invertebrate fossils. We sought to confirm the Burdigalian age of this northwestern Miocene deposit at Aruwakkalu on the basis of the foraminifer Pseudotaberina malabarica, an index fossil of the Burdigalian stage. General and timeline collections were made at seven selected sites and the fossils collected were identified. The study sites contained six sedimentary layers of which, third and sixth from top were fossiliferous. The sixth (deepest) layer was dominated by gastropod fossils while the third was dominated by fossils of giant oysters. Fossils of P. malabarica were recovered both from timeline and general collections. In the timeline collection, samples of this index fossil were recovered only from the gastropod layer, suggesting that P. malabarica existed during the time the gastropod layer was being laid down, thus confirming a Burdigalian age for the latter, and helping to date a substantial portion of the Sri Lankan fossil fauna with confidence.
DNA barcoding-type studies assemble single-locus data from large samples of individuals and species, and have provided new kinds of data for evolutionary surveys of diversity. An important goal of many such studies is to delimit evolutionarily significant species units, especially in biodiversity surveys from environmental DNA samples. The Generalized Mixed Yule Coalescent (GMYC) method is a likelihood method for delimiting species by fitting within- and between-species branching models to reconstructed gene trees. Although the method has been widely used, it has not previously been described in detail or evaluated fully against simulations of alternative scenarios of true patterns of population variation and divergence between species. Here, we present important reformulations to the GMYC method as originally specified, and demonstrate its robustness to a range of departures from its simplifying assumptions. The main factor affecting the accuracy of delimitation is the mean population size of species relative to divergence times between them. Other departures from the model assumptions, such as varying population sizes among species, alternative scenarios for speciation and extinction, and population growth or subdivision within species, have relatively smaller effects. Our simulations demonstrate that support measures derived from the likelihood function provide a robust indication of when the model performs well and when it leads to inaccurate delimitations. Finally, the so-called single threshold version of the method outperforms the multiple threshold version of the method on simulated data: we argue that this might represent a fundamental limit due to the nature of evidence used to delimit species in this approach. Together with other studies comparing its performance relative to other methods, our findings support the robustness of GMYC as a tool for delimiting species when only single-locus information is available.
Nonparametric bootstrap has been a widely used tool in phylogenetic analysis to assess the clade support of phylogenetic trees.
However, with the rapidly growing amount of data, this task remains a computational bottleneck. Recently, approximation methods
such as the RAxML rapid bootstrap (RBS) and the Shimodaira–Hasegawa-like approximate likelihood ratio test have been introduced
to speed up the bootstrap. Here, we suggest an ultrafast bootstrap approximation approach (UFBoot) to compute the support
of phylogenetic groups in maximum likelihood (ML) based trees. To achieve this, we combine the resampling estimated log-likelihood
method with a simple but effective collection scheme of candidate trees. We also propose a stopping rule that assesses the
convergence of branch support values to automatically determine when to stop collecting candidate trees. UFBoot achieves a
median speed up of 3.1 (range: 0.66–33.3) to 10.2 (range: 1.32–41.4) compared with RAxML RBS for real DNA and amino acid alignments,
respectively. Moreover, our extensive simulations show that UFBoot is robust against moderate model violations and the support
values obtained appear to be relatively unbiased compared with the conservative standard bootstrap. This provides a more direct
interpretation of the bootstrap support. We offer an efficient and easy-to-use software (available at http://www.cibiv.at/software/iqtree) to perform the UFBoot analysis with ML tree inference.
Background
Species are considered the fundamental unit in many ecological and evolutionary analyses, yet accurate, complete, accessible taxonomic frameworks with which to identify them are often unavailable to researchers. In such cases DNA sequence-based species delimitation has been proposed as a means of estimating species boundaries for further analysis. Several methods have been proposed to accomplish this. Here we present a Bayesian implementation of an evolutionary model-based method, the general mixed Yule-coalescent model (GMYC). Our implementation integrates over the parameters of the model and uncertainty in phylogenetic relationships using the output of widely available phylogenetic models and Markov-Chain Monte Carlo (MCMC) simulation in order to produce marginal probabilities of species identities.
Results
We conducted simulations testing the effects of species evolutionary history, levels of intraspecific sampling and number of nucleotides sequenced. We also re-analyze the dataset used to introduce the original GMYC model. We found that the model results are improved with addition of DNA sequence and increased sampling, although these improvements have limits. The most important factor in the success of the model is the underlying phylogenetic history of the species under consideration. Recent and rapid divergences result in higher amounts of uncertainty in the model and eventually cause the model to fail to accurately assess uncertainty in species limits.
Conclusion
Our results suggest that the GMYC model can be useful under a wide variety of circumstances, particularly in cases where divergences are deeper, or taxon sampling is incomplete, as in many studies of ecological communities, but that, in accordance with expectations from coalescent theory, rapid, recent radiations may yield inaccurate results. Our implementation differs from existing ones in two ways: it allows for the accounting for important sources of uncertainty in the model (phylogenetic and in parameters specific to the model) and in the specification of informative prior distributions that can increase the precision of the model. We have incorporated this model into a user-friendly R package available on the authors’ websites.
We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi-gene datasets. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into the program window. A multi-gene dataset is concatenated and displayed in a spreadsheet; each sequence is represented by a cell that provides information on sequence length, number of indels, the number of ambiguous bases (“Ns”), and the availability of codon information. Alternatively, GenBank numbers for the sequences can be displayed and exported. Matrices with hundreds of genes and taxa can be concatenated within minutes and exported in TNT, NEXUS, or PHYLIP formats, preserving both character set and codon information for TNT and NEXUS files. SequenceMatrix also creates taxon sets listing taxa with a minimum number of characters or gene fragments, which helps assess preliminary datasets. Entire taxa, whole gene fragments, or individual sequences for a particular gene and species can be excluded from export. Data matrices can be re-split into their component genes and the gene fragments can be exported as individual gene files. SequenceMatrix also includes two tools that help to identify sequences that may have been compromised through laboratory contamination or data management error. One tool lists identical or near-identical sequences within genes, while the other compares the pairwise distance pattern of one gene against the pattern for all remaining genes combined. SequenceMatrix is Java-based and compatible with the Microsoft Windows, Apple MacOS X and Linux operating systems. The software is freely available from http://code.google.com/p/sequencematrix/.
© The Willi Hennig Society 2010.
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.
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.
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.
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.
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.
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.
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.
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.
Laubuka parafasciata, new species, is described from the Sala River of Mizoram, northeast India. The species differs markedly from all its congeners, with the exception of L. fasciata, in having a broad, dark-brown, midlateral stripe from the posterior rim of the orbit to the middle of the caudal-fin base. It is further distinguished from all other species in the genus by the combination of the following characters: premaxillae not in contact at symphysis, 16 precaudal vertebrae, minute tubercles scattered on the lower jaw, 28–33 lateral-line scales, 16–18 predorsal scales, 8½ branched dorsal-fin rays, 2½ scales between lateral line and pelvic-fin origin, and 16½–19½ branched anal-fin rays.
Biodiversity reduction and loss continues to progress at an alarming rate, and thus there is widespread interest in utilizing rapid and efficient methods for quantifying and delimiting taxonomic diversity. Single-locus species-delimitation methods have become popular, in part due to the adoption of the DNA barcoding paradigm. These techniques can be broadly classified into tree-based and distance-based methods depending on whether species are delimited based on a constructed genealogy. Although the relative performance of these methods has been tested repeatedly with simulations, additional studies are needed to assess congruence with empirical data. We compiled a large data set of mitochondrial ND4 sequences from horned lizards (Phrynosoma) to elucidate congruence using four tree-based (single-threshold GMYC, multiple-threshold GMYC, bPTP, mPTP) and one distance-based (ABGD) species delimitation models. We were particularly interested in cases with highly uneven sampling and/or large differences in intraspecific diversity. Results showed a high degree of discordance among methods, with multiple-threshold GMYC and bPTP suggesting an unrealistically high number of species (29 and 26 species within the P. douglasii complex alone). The single-threshold GMYC model was the most conservative, likely a result of difficulty in locating the inflection point in the genealogies. mPTP and ABGD appeared to be the most stable across sampling regimes and suggested the presence of additional cryptic species that warrant further investigation. These results suggest that the mPTP model may be preferable in empirical data sets with highly uneven sampling or large differences in effective population sizes of species. This article is protected by copyright. All rights reserved.
Significance
Despite its widespread application to the species delimitation problem, our study demonstrates that what the multispecies coalescent actually delimits is structure. The current implementations of species delimitation under the multispecies coalescent do not provide any way for distinguishing between structure due to population-level processes and that due to species boundaries. The overinflation of species due to the misidentification of general genetic structure for species boundaries has profound implications for our understanding of the generation and dynamics of biodiversity, because any ecological or evolutionary studies that rely on species as their fundamental units will be impacted, as well as the very existence of this biodiversity, because conservation planning is undermined due to isolated populations incorrectly being treated as distinct species.
Fishes currently identified as Laubuka laubuca from the Cauvery River and its tributaries in the Western Ghats of India are shown to represent two different species: Laubuka trevori, sp. nov., and L. latens, sp. nov., distinguished from all spe-cies of Chela and Laubuka by possessing 71/2 branched dorsal-fin rays; 14 precaudal vertebrae; 17-18 predorsal scales; 5 branched pelvic-fin rays and 5+4+2 teeth on the fifth ceratobranchial. Laubuka trevori is further distinguished from its congeners by possessing 141/2-151/2 branched anal-fin rays; 1/26/1/11/2 scales in transverse line on body; a short pelvic fin (10.1-16.3% SL) and two longitudinal stripes: a golden and a bluish-green stripe on the body, running from behind the opercle to the base of the caudal fin, the latter broken and less distinct in the anterior half of the body. Laubuka latens is further distinguished by its long pelvic fin (23.2-26.9% SL) and the absence of any markings on the side of the body other than a humeral spot and a caudal-peduncle spot.
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.
In discussing the classification of the danios, Myers (1953,
Aquarium Jour., 24: 235-38) drew attention to
numerous gaps that still remain to be filled before
final word can be said as to their classification. Recently,
while studying the nomenclatorial status of
certain genera of Indian fishes, it was found that
one of the Ceylonese genera ascribed to different
positions in the system by various ichthyologists
needed more scrutiny
1. The generalized mixed Yule-coalescent (GMYC) model has become one of the most popular approaches for species delimitation based on single-locus data, and it is widely used in biodiversity assessments and phylogenetic community ecology. We here examine an array of factors affecting GMYC resolution (tree reconstruction method, taxon sampling coverage/taxon richness, and geographic sampling intensity/geographic scale).
2. We test GMYC performance based on empirical data (DNA barcoding of the Romanian butterflies) on a solid taxonomic framework (i.e. all species are thought to be described and can be determined with independent sources of evidence). The dataset is comprehensive (176 species), and intensely and homogeneously sampled (1303 samples representing the main populations of butterflies in this country). Taxonomy was assessed based on morphology, including linear and geometric morphometry when needed.
3. The number of GMYC entities obtained constantly exceeds the total number of morphospecies in the dataset. We show that approximately 80% of the species studied are recognised as entities by GMYC. Interestingly, we show that this percentage is practically the maximum that a single threshold method can provide for this dataset. Thus the ca. 20% of failures are attributable to intrinsic properties of the COI polymorphism: overlap in inter- and intraspecific divergences and non-monophyly of the species likely because of introgression or lack of independent lineage sorting.
4. Our results demonstrate that this method is remarkably stable under a wide array of circumstances, including most phylogenetic reconstruction methods, high singleton presence (up to 95%), taxon richness (above five species), and presence of gaps in intraspecific sampling coverage (removal of intermediate haplotypes). Hence, the method is useful to designate an optimal divergence threshold in an objective manner, and to pinpoint potential cryptic species that are worth being studied in detail. However, the existence of a substantial percentage of species wrongly delimited indicates that GMYC cannot be used as sufficient evidence for evaluating the specific status of particular cases without additional data.
5. Finally, we provide a set of guidelines to maximize efficiency in GMYC analyses and discuss the range of studies that can take advantage of the method.
Morphometric variation was used to examine the stock structure, in southern Australian waters, of the deepwater marine teleost Hoplostethus atlanticus, orange roughy. Seven samples were collected from non-spawning aggregations in 1989–1990. Three samples were also collected in the winter of 1992, two from the main spawning site off the eastern coast of Tasmania (St Helens), and the third from the other main fishing ground south of Tasmania. The 38 morphometric measurements taken from each of over 1300 fish were size-standardized by an allometric formula and analysed by univariate and multivariate statistics. The results indicate significant variation in the morphology of orange roughy caught from geographically distinct aggregations. They further suggest that the main spawning aggregation may consist of fish from different groups at different times of the spawning period. There appear to be at least seven morphologically distinguishable stocks of orange roughy in southern Australian waters, despite genetic data indicating appreciable levels of gene flow between them.