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Phylogenetic position and relationships of mountain loaches (Teleostei: Balitoridae) of the Western Ghats as revealed by CO1 sequences
Abstract
The teleostean family Balitoridae comprises small-sized freshwater fishes adapted to swift-flowing torrential mountain streams in South and South-East Asia. Little is known about their molecular phylogenetics and evolutionary biogeography, and much of the scientific literature that references them is focused on morphological taxonomy. In this paper, we generate CO1 sequences for the endemic balitorid lineages of the Western Ghats (WG) Hotspot in India, particularly for the endemic genera, Bhavania, Ghatsa and Travancoria. Integration of these data into a phylogeny revealed that the endemic WG genera together form a well-supported monophyletic clade that shows, subject to our limited taxon sampling, a sister-group relationship to the Southeast Asian genus Pseudohomaloptera. Three WG endemic species of the genus Balitora, namely B. chipkali, B. jalpalli and B. laticauda, though morphologically distinct, have low genetic divergence and barcode gap, suggestive of recent speciation. Interestingly, a fourth WG endemic, B. mysorensis, formed a clade with two species of Balitora from Eastern-Himalaya and Indo-Burma. We also show that all available CO1 sequences assigned to WG endemic balitorid genera in GenBank are misidentifications, and provide diagnostic characters for the accurate identification of these taxa in the future.
... Channidae, Conte-Grand et al. 2017), has subsequently resulted in descriptions of several new species of snakeheads -helping reduce the Linnean Shortfall, while others have revealed the possibility of 'cryptic species' (Sidharthan et al. 2021). Despite this utility, there also exist several issues and challenges in the use of molecular datasets for understanding freshwater fish taxonomy in India, the most important of which is the large-scale misidentifications of sequences in GenBank (see Sidharthan et al. 2021;Chakraborty & Ghosh 2014). ...
... Channidae, Conte-Grand et al. 2017), has subsequently resulted in descriptions of several new species of snakeheads -helping reduce the Linnean Shortfall, while others have revealed the possibility of 'cryptic species' (Sidharthan et al. 2021). Despite this utility, there also exist several issues and challenges in the use of molecular datasets for understanding freshwater fish taxonomy in India, the most important of which is the large-scale misidentifications of sequences in GenBank (see Sidharthan et al. 2021;Chakraborty & Ghosh 2014). For example, all available cox1 sequences assigned to Western Ghats endemic species of the family Balitoridae in GenBank were revealed to be misidentifications of various other species (see discussion in Sidharthan et al. 2021). ...
... Despite this utility, there also exist several issues and challenges in the use of molecular datasets for understanding freshwater fish taxonomy in India, the most important of which is the large-scale misidentifications of sequences in GenBank (see Sidharthan et al. 2021;Chakraborty & Ghosh 2014). For example, all available cox1 sequences assigned to Western Ghats endemic species of the family Balitoridae in GenBank were revealed to be misidentifications of various other species (see discussion in Sidharthan et al. 2021). ...
... In India, a little studies used DNA barcoding technique for molecular identification and documentation of freshwater and marine fishes (Lakra et al. 2011(Lakra et al. , 2016Khedkar et al. 2014; Barman et al. 2018). Some ornamental and common fish species in Northeast India have been identified by DNA barcoding (Dhar and Ghosh 2015;Barman et al. 2018;Pandey et al. 2020) and Western Ghat (Sidharthan et al. 2021). ...
The loss of fish biodiversity in the coastal ecosystem of West Bengal, India, due to adverse environmental impacts both natural and anthropogenic, poses significant threats to the stability of the coastal ecosystem and economy. Therefore, accurate fish species identification and documentation is the first step toward fish biodiversity conservation. The challenges of relying solely on morphological identification and the lack of DNA barcoding-based molecular identification of fish are the impetus for the present study. The present study aims to address these challenges by identifying and barcoding fish species collected from coastal areas near the Sundarbans mangrove using morpho-molecular characterization and genetic analysis with partial mitochondrial cytochrome c oxidase subunit I (COI). Out of 110 collected fish samples, 20 representative species were identified and classified into 19 species, 17 genera, 12 families and 6 orders. The DNA sequences of these species showed 98 to 100% similarity match with the GenBank database. Notably, the International Union for Conservation of Nature’s (IUCN) Red List indicates that Ompok pabda is considered near threatened, while other species are listed as least concern. In conclusion, the selected 19 fish samples belonged to distinct species with unique barcodes, which will serve as a strong reference for a fish diversity database in the studied coastal ecosystem. Morpho-molecular identification emerges as a reliable approach for understanding fish biodiversity and supporting sustainable management of coastal fish bioresources.
... The mitochondrial genome is an important model system used to understand genome structure, molecular evolution and phylogenetic relationships amongst vertebrates (Moritz and Brown 1986;Pääbo et al. 1991;Inoue et al. 2003;Krishnan et al. 2004;Jiang et al. 2007;Qian et al. 2018). Specific mitochondrial genes, such as the 12S ribosomal RNA (12S rRNA), 16S ribosomal RNA (16S rRNA), NADH dehydrogenase subunit 4 (ND4), cytochrome c oxidase subunit I (COI) and cytochrome b (Cytb) have been often used to compare phylogenetic relationships between vertebrates (Malhotra and Thorpe 2004;Rivera et al. 2018;Sidharthan et al. 2021). Although phylogenetic studies using mitochondrial sequences have both advantages and disadvantages (Rubinoff and Holland 2005), using the complete mitochondrial genome may provide higher phylogenetic resolution between species (Inoue et al. 2003;Nardi et al. 2003;Qian et al. 2018). ...
Studies using complete mitochondrial genome data have the potential to increase our understanding on gene organisations and evolutionary species relationships. In this study, we compared complete mitochondrial genomes between all 22 squamate species listed in South Korea. In addition, we constructed Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian Inference (BI) phylogenetic trees using 13 mitochondrial protein-coding genes. The mitochondrial genes for all six species in the suborder Sauria followed the same organisation as the sequenced Testudines (turtle) outgroup. In contrast, 16 snake species in the suborder Serpentes contained some gene organisational variations. For example, all snake species contained a second control region ( CR2 ), while three species in the family Viperidae had a translocated tRNA-Pro gene region. In addition, the snake species, Elaphe schrenckii , carried a tRNA-Pro pseudogene. We were also able to identify a translocation of a tRNA-Asn gene within the five tRNA ( WANCY gene region) gene clusters for two true sea snake species in the subfamily Hydrophiinae. Our BI phylogenetic tree was also well fitted against currently known Korean squamate phylogenetic trees, where each family and genus unit forms monophyletic clades and the suborder Sauria is paraphyletic to the suborder Serpentes. Our results may form the basis for future northeast Asian squamate phylogenetic studies.
... As an adaptation to their life in fast-flowing streams, balitorid loaches have a dorsoventrally flattened body, and an enlarged ventral area to aid adhesion by enhanced friction (De Meyer & Geerinckx, 2014). Despite being one of the most widespread and diverse families in South and South East Asia (Kottelat, 2012;Sidharthan, Raghavan, Anoop, Keskar, & Dahanukar, 2021), very little is known about life history and ecology of balitorid loaches (Yang & Dudgeon, 2009). ...
Riverscape genetics of fish, though extensively studied in temperate regions, have received limited interest in tropical rivers, especially in montane systems which not only harbour several endemic and threatened species, but are also subjected to extensive habitat modifications. We determine the population genetic structure of two endemic balitorid loaches (Bhavania australis and Travancoria elongata) in response to natural (25 m high waterfall) and artificial (23 m high and 290 m long hydropower dam) barriers in a small mountain riverscape in the Western Ghats Hotspot. Population genetics analysis using mitochondrial cytochrome b gene sequence showed low nucleotide diversity, haplotype diversity and genetic differentiation among populations, for both species, suggesting that barriers did not influence genetic structuring. Though migration analysis also revealed that barriers did not affect movement of the two species through the riverscape, patterns in mutation‐scaled immigration rates and population sizes differed between the two species supporting our observation that they rarely co‐exist in the same habitat, likely as an effect of competitive exclusion. Mismatch distribution and Bayesian skyline plot suggested recent expansion in the populations of B. australis and corresponding population decline in T. elongata in the last 100 years, which probably explains the widespread and abundant distribution of B. australis as opposed to the narrow endemism and rarity of T. elongata. Our results provide novel insights into the ecology of balitorid loaches and their response to riverine barriers in a tropical mountain landscape.
... Species names and identities in clade V are also likely to be erroneous due to morphological ambiguities. Studies on generating reference DNA barcodes without morphological taxonomy could often lead to species misidentification [38,39], which has been demonstrated recently in hill stream loaches of the Western Ghats [40]. Due to overlapping diagnostic characters and morphological similarities, various authors could have misidentified M. tengara, M. vittatus, and M. carcio resulting in the deposition of erroneous sequences in NCBI GenBank. ...
Background
The taxonomic status and geographical distribution of M. tengara are vague. No genetic diversity and phylogenetic study have been done till now to resolve its identity and distribution. In the present study, an integrated taxonomic approach has been applied to clarify the taxonomic status, identity, and distribution of bagrid catfish, Mystus tengara.
Methods and results
Comparative morphometric evaluation of M. tengara identified in the present study from distant geographical locations revealed variations of the traits in response to body length and environment, without significant genetic distance. The observed morphometric traits of M. tengara were found to be overlapping with available morphometric traits of M. tengara, M. carcio and M. vittatus. Maximum likelihood and Bayesian phylogenetic analysis based on mitochondrial cytochrome c oxidase (COI) gene also could not resolve their identity, and five paraphyletic clades comprising of M. tengara, M. vittatus, and M. carcio from India, Nepal, and Bangladesh were observed. Morphological and genetic evidence along with comparative evaluation of M. tengara, from its type locality, we consider M. tengara identified in the present study to be true, with its distribution extending from North East India to West Bengal, North India, Central India, Northern peninsular India, and Bangladesh.
Conclusion
The observation of paraphyletic subclades and evaluation of genetic distance between subclades reveals the presence of four cryptic species. Further confirmation on the identity of M. vittatus and M. carcio, by an integrated taxonomic approach based on fresh specimens collected from the type locality, is required.
... During the breakup of Gondwana, the Indian subcontinent became isolated from Africa around 130-160 Ma, drifted northwards, and eventually collided with Eurasia, which originated from Laurasia, around 35-55 Ma (figure 1a) [2][3][4][5][6][7]. Though the origin of the Indian subcontinent differs geologically from that of Eurasia, many terrestrial animal and plant species on it have congeneric or sister species in other parts of Asia, especially in the Southeast [8][9][10][11][12][13][14][15]. ...
The Indian subcontinent has an origin geologically different from Eurasia, but many terrestrial animal and plant species on it have congeneric or sister species in other parts of Asia, especially in the Southeast. This faunal and floral similarity between India and Southeast Asia is explained by either of the two biogeographic scenarios, ‘into-India’ or ‘out-of-India’. Phylogenies based on complete mitochondrial genomes and five nuclear genes were undertaken for ricefishes (Adrianichthyidae) to examine which of these two biogeographic scenarios fits better. We found that Oryzias setnai , the only adrianichthyid distributed in and endemic to the Western Ghats, a mountain range running parallel to the western coast of the Indian subcontinent, is sister to all other adrianichthyids from eastern India and Southeast–East Asia. Divergence time estimates and ancestral area reconstructions reveal that this western Indian species diverged in the late Mesozoic during the northward drift of the Indian subcontinent. These findings indicate that adrianichthyids dispersed eastward ‘out-of-India’ after the collision of the Indian subcontinent with Eurasia, and subsequently diversified in Southeast–East Asia. A review of geographic distributions of ‘out-of-India’ taxa reveals that they may have largely fuelled or modified the biodiversity of Eurasia.
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.
Aim
The Western Ghats Hotspot in peninsular India harbours remarkable diversity and endemism of freshwater fish. However, the ichthyofauna's evolutionary histories and biogeography are poorly known. Here, we investigate (a) the diversity, evolutionary history and biogeography of endemic mountain loaches and (b) the potential influence of the physiography of hill ranges, geological barriers and river systems on the diversification and cladogenesis of loaches, in the Western Ghats Biodiversity Hotspot.
Location
Southern Western Ghats mountain ranges (8–13°N latitudes), Western Ghats‐Sri Lanka Biodiversity Hotspot.
Taxa
Mountain loaches Bhavania annandalei and B. australis (Cypriniformes: Balitoridae).
Methods
We carried out a multigene phylogenetic analysis with mitochondrial and nuclear markers using Bhavania specimens collected throughout the genus' range. The Automated Barcode Gap Analysis, Poisson Tree Process and Generalized Mixed Yule‐Coalescent Model were used to delimit species. A Bayesian chronogram was constructed to estimate the time elapsed since the most recent common ancestor of the distinct lineages of Bhavania. Ancestral ranges of distinct lineages of Bhavania were reconstructed using the dispersal–extinction–cladogenesis model.
Results
Phylogenetic analysis of combined mitochondrial and nuclear data, as well species delimitation using the Poisson Tree Process and Generalized Mixed Yule‐Coalescent Model analyses supported eight distinct lineages, which included the narrowly distributed B. annandalei and widely distributed B. australis. The Barcode Gap Analysis, however, supported only seven lineages. Bayesian divergence time dating suggests that the genus originated early in the Neogene and diversified in the Miocene. Ancestral state reconstruction indicated Bhavania diversifed as a result of sympatric, subset and vicariant speciation with five dispersal and one vicariant events across biogeographic barriers and river systems.
Main conclusions
Bhavania australis is a ‘species complex’. Miocene‐associated climatic changes including intensification of the south‐west monsoon likely triggered dispersal and range expansion; subsequent aridification would have led to drying up of riverine connections, formation of land barriers and fragmentation of streams, resulting in cladogenesis. Our results also provide preliminary evidence that Cauvery, one of the largest east flowing rivers of Western Ghats, facilitates an east‐west pathway for dispersal and diversification of endemic lineages of the region.
Bhavania annandalei Hora 1920, is resurrected from the synonymy of B. australis (Jerdon, 1849) based on examination of freshly collected topotypic specimens. The two species can be distinguished by a combination of morphological characters including low, dense, and sparsely distributed tubercles on dorsal surface of head and operculum, rostral barbels reaching anterior border of upper lip, rostral flaps between the rostral barbels fleshier, 11–12 scale rows above the lateral line, and caudal peduncle stout with its depth to width ratio less than 2.5. The two species formed significantly distinct clusters in multivariate space. Further, the two species have a raw genetic distance of 6.4% in the mitochondrial cytochrome oxidase subunit 1 gene. The distribution of B. annandalei is restricted to the river systems draining the Agasthyamalai Hills, below the Shencottah Gap in southern Western Ghats, while B. australis occurs in rivers north of the Shencottah Gap.
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.
The whole mitochondrial genome sequence of Lepturichthys fimbriata was amplified by primer walking sequence method, and then the whole genome genetic map of mitochondrion was obtained and mapped. The mitochondrial genome of L. fimbriata is a double-strand ring-like molecule with a total length of 16,567bp. It contains 2 rRNA genes (12SrRNA and 16SrRNA), 13 protein-coding genes (COI, COII, COIII, ATP6, ATP8, ND1, ND2, ND3, ND4, ND4L, ND5, ND6, Cytb), 22 tRNA coding genes, and one non-coding control region (D-loop control region). The overall nucleotide composition was A: 30.4%, T: 24.4%, C: 28.7%, and G: 16.5%, exhibiting an A + T bias of 54.8%. Phylogeny showed the phylogenetic relationships of different genera in the family Balitoridae and found the genus Lepturichthys is clustered with the genus Jinshaia, which suggested the intergeneric hybridization has likely occurred in both lineages.
DNA barcodes analyzed by using relevant techniques provide an imperative approach towards validation of prevailing taxa and putative species. Here, molecular methods were used for assessment of 246 barcodes belonging to 81 fish species from northern Western Ghats of India, using, Barcode gap analysis, barcode index number, automatic barcode gap discovery, Poisson tree processes and general mixed Yule-coalescent, these methods had their potential to discriminate 97.53%, 93.90% 95.06%, 93.82% and 92.59% of species respectively. But, some of them tended to estimate the inconsistent number of species leading to discrepancies between the morphological concept and inference from molecular phylogenetic reconstructions. So, we took a standard approach to recognize those methods that produced consistent results, three of five such methods were identified that revealed three hidden cryptic species complexes in Monopterus indicus, Parambassis ranga and Systomus sarana. Further, to validate these three genetically diverged species, we used diagnostic character based approach along with nine unidentified species through BLOG and WEKAs SMO classifier. Those methods were unable to identify these species, which might be due to the limited number of specimens used for the analysis. This is the first effort to generate the DNA barcode reference library of freshwater fishes from northern Western Ghats of India, one of the world’s biodiversity hotspots. These barcodes when analyzed through the defined workflow, will provide valuable measures to prove the efficiency of molecular species delimitation methods in taxonomic discrimination which aid conservation of biodiversity.
Balitoridae, a family within the Cypriniformes, inhabit torrential mountain streams in Asia. Although they have long fascinated ichthyologists for their numerous adaptations to this tumultuous environment, the evolutionary history of this group remains poorly understood. In this study, we investigate the evolutionary relationships of the balitorids with particular attention to the phylogenetic placement of two balitorid species, Yaoshania pachychulis and Erromyzon kalotaenia. Both species have extremely limited distributions, they are limited to Mt. Dayaoshan of the Pearl River in China and require dedicated conservation plans. However, little is known about their evolutionary relationships to other balitorids. Here, we examined the evolutionary relationships of Y. pachychulis and E. kalotaenia to each other and other balitorids through sequencing the complete mitochondrial genomes of nine balitorid individuals. For the newly sequenced balitorids, the length of the whole mitogenome, gene arrangement and their base composition are similar to those of other bony fishes. Analyses based on these newly sequenced mitogenomes and an additional 50 previously published mitogenomes show that Y. pachychulis and E. kalotaenia cluster as different clade within the subfamily Gastromyzontinae. The genetic distance between these two species ranges from 0.127 ± 0.003 to 0.132 ± 0.004 which is slightly higher than that between some genera (e.g. the distance between Vanmanenia and Metahomaloptera is 0.127 ± 0.004). Therefore, it is reasonable to assign Y. pachychulis and E. kalotaenia to different genera. Phylogenetic signal assessment suggested that ND1, ND4 and ND5 genes as well as their concatenated subsets perform relatively well in reconstructing the Cobitoidea phylogeny. The divergence time estimation indicated that the balitorids distributed in Mt. Dayaoshan might have originated and evolved following the flattening and uplifting of the Yunnan–Guizhou Plateau during the late Miocene to late Pliocene.
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches.
Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested datasets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
Balitora chipkali, a new species of stone loach, is described from the westward-flowing Astoli tributary of the Kali River system in the northern part of the Western Ghats, India. The species differs from its congeners in a combination of characters that includes: a single pair of maxillary barbels; a large eye, of diameter greater than 15% head length (HL); snout length less than 4 times eye diameter; gape of mouth less than 30% HL; upper lip with 9–12 papillae in first series and 3–8 papillae in second series; flattened body, of depth less than 15% standard length; caudal-peduncle length less than three times its depth, 66–68 lateral line scales, 11 caudal vertebrae excluding compound centrum, third infraorbital sensory canal tube straight; and a distinct color pattern with almost round 7 dorsal saddles not reaching lateral irregular crossbar markings. Balitora chipkali forms a monophyletic group with B. laticauda as its sister taxon in a phylogeny based on a concatenated cytochrome b (Cytb) and cytochrome oxidase subunit 1 (COI) gene fragments. Raw genetic distance between B. chipkali and B. laticauda was 1.9–2.2% based on COI and 3.4–4.3% based on Cytb partial gene sequences, which was far more than the intra-species variation in widely separated populations of B. laticauda. Based on molecular and morphological analysis, we also provide new locality records for B. laticauda and delimit its distribution to eastward-flowing tributaries of the Krishna River system in the northern Western Ghats.
Homaloptera van Hasselt 1823 as treated historically exhibits substantial morphological diversity and is paraphyletic based on both morphological and molecular data. The morphological diversity and phylogenetic relationships of Homaloptera, Homalopteroides Fowler 1905, Homalopterula Fowler 1940, and Balitoropsis Smith 1945, are elucidated. Pseudohomaloptera Silas 1953 is removed from the synonymy of Homaloptera. Homalopteroidini is created for the monophyly of Homalopteroides and Homalopterula; it is the sister group to balitorini Swainson 1839. Ghatsa n. gen. is created for species previously assigned to Homaloptera from the Western Ghats of India, and a redescription of Ghatsa montana (Herre 1945) is provided.
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.
Travancoria elongata is a rare balitorid loach endemic to the Kerala part of the Western Ghats, where it was till date known to occur in two locations, one each in the Chalakudy and Periyar River. The species was listed in the IUCN Red List as Endangered as a result of its restricted distribution, and continuing decline in the quality of habitats in its range. Here we present new records of this species from three locations (Mlappara, Thanikkudy and Mankulam) in the Periyar River. Although Mlappara and Thanikkudy are located within the highly protected Periyar Tiger Reserve, the third site (Mankulam) does not have any legal protection, and is subjected to threats such as agro-based pollution and proliferation of exotic species.
Lepidopygopsis, known as the peninsular-Indian hill trout, is a monotypic genus endemic to the Periyar stream-reservoir system, in the Western Ghats. Due to the morphological similarity of its only species, L. typus, with the Himalayan schizothoracine fishes, it was considered to be a relict species and a classic example of disjunct distribution. Using mitochondrial and nuclear gene sequence datasets, we show that L. typus is not allied to the schizothoracine fishes. Phylogenetic hypothesis-testing unequivocally supports a scenario in which L. typus and a clade comprising various genera of Asian and African barbins such as Tor, Gonoproktopterus, Kosswigobarbus and Varicorhinus are sister groups. Based on our results, we suggest that the sheath of tile-like scales covering the anal-fin base of schizothoracine fishes and Lepidopygopsis typus could be a symplesiomorphy or a homoplasy.
A new species of stone loach (Cypriniformes: Balitoridae), Balitora jalpalli, is described from Kunthi tributary of Bharatapuzha River located inside Silent Valley National Park in the southern Western Ghats of Kerala, India. It can be distinguished from known Indian species of Balitora by five major characters: head length, caudal peduncle depth, maximum head width and difference in number and pattern of bands on the dorsal side. The new species is distinct in having two unbranched and 8–9 branched ventral fin rays, nine unbranched and 10–11 branched pectoral fin rays and 66 lateral line scales, a caudal peduncle length to depth ratio of 2.3–2.7, anal fin to anus distance 3.3–4.7 % SL, least depth of caudal peduncle 6.3–6.7 % SL, length of caudal peduncle 15.4–17.2 % SL, length of upper caudal lobe 22.1–22.8 % SL, maximum head width 67.9–74.1 % HL, eye diameter 12.1–14.2 % HL, and gape 31.3–31.5 % HL.
A new species of stone loach Balitora laticauda is described from the Krishna River, northern Western Ghats, India. It differs from all known species of the genus in a combination of characters including: 10 transverse bands on the dorsal surface, deeper caudal peduncle, two prominent rows of papilla encircling upper lip where the proximate row has small papillae while distal row has larger papillae, 66–68 lateral line scales, 8–9 simple rays in pectoral fin, two simple rays in the pelvic fin and pectoral fin not surpassing pelvic fin base. The new species also differs from its related species in the ratios such as caudal peduncle length to depth (2.21–2.89), standard length to body depth (7.48–8.72), head length to head depth (2.11–2.50), head length to interorbital distance (2.20–2.96), head depth to head length (0.42–0.47), eye diameter to head length (0.13–0.17) and head width to gape of mouth (3.12–4.78). As percent of standard length B. laticauda sp. nov. differs from other related species with respect to caudal peduncle depth (6.3–7.4%), caudal peduncle length (15.0–20.0%), body width at anus (8.7–11.5%), body depth at anus (9.1–11.4%), pre-dorsal fin length (43.7–47.4%), pre-pectoral fin length (12.9–16.2%), pre-anal fin length (74.3–79.3%), pre-pelvic fin length (44.4–48.3%), pelvic fin length (19.3–23.7%), pectoral fin length (24.1–28.9%) and body depth at dorsal (11.5–13.4%).
It is widely accepted that mitochondrial DNA (mtDNA) control region evolves faster than protein encoding genes with few exceptions. In the present study, we sequenced the mitochondrial cytochrome b gene (cyt b) and control region (CR) and compared their rates in 93 specimens representing 67 species of loaches and some related taxa in the Cobitoidea (Order Cypriniformes). The results showed that sequence divergences of the CR were broadly higher than those of the cyt b (about 1.83 times). However, in considering only closely related species, CR sequence evolution was slower than that of cyt b gene (ratio of CR/cyt b is 0.78), a pattern that is found to be very common in Cypriniformes. Combined data of the cyt b and CR were used to estimate the phylogenetic relationship of the Cobitoidea by maximum parsimony, neighbor-joining, and Bayesian methods. With Cyprinus carpio and Danio rerio as outgroups, three analyses identified the same four lineages representing four subfamilies of loaches, with Botiinae on the basal-most clade. The phylogenetic relationship of the Cobitoidea was ((Catostomidae+Gyrinocheilidae)+(Botiinae+(Balitorinae+(Cobitinae+Nemacheilinae)))), which indicated that Sawada's Cobitidae (including Cobitinae and Botiinae) was not monophyletic. Our molecular phylogenetic analyses are in very close agreement with the phylogenetic results based on the morphological data proposed by Nalbant and Bianco, wherein these four subfamilies were elevated to the family level as Botiidae, Balitoridae, Cobitidae, and Nemacheilidae.
Available online under
http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp
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.
Ecological opportunities and physical challenges of fast-water habitats have dramatically shaped the evolution of freshwater fish lineages from a broad diversity of clades globally, often leading to the convergent or parallel evolution of highly similar morphologies. In this chapter, we present a patch dynamics model of how longitudinal shifts in geomorphological and ecological processes from small headwater torrents to large river rapids may differentially affect gene flow among, and evolutionary specialization within, resident rheophilic fish populations. Fast-water habitats offer ecological advantages including predator avoidance and increased foraging efficiency, but require that organisms resist downstream displacement and avoid shifting, crushing substrates. We review the specialized morphological and behavioral characteristics associated with life in fast waters and the taxonomic distribution of these specializations across fishes. We also report results of specific functional studies where available and summarize empirical evolutionary, phylogenetic support for our model and for specific mechanisms or pathways by which rheophilic specializations may arise.
The superfamily Cobitoidea of the order Cypriniformes is a diverse group of fishes, inhabiting freshwater ecosystems across Eurasia and North Africa. The phylogenetic relationships of this well-corroborated natural group and diverse clade are critical to not only informing scientific communities of the phylogeny of the order Cypriniformes, the world's largest freshwater fish order, but are key to every area of comparative biology examining the evolution of traits, functional structures, and breeding behaviors to their biogeographic histories, speciation, anagenetic divergence, and divergence time estimates. In the present study, two mitochondrial gene sequences (COI, ND4+5) and four single-copy nuclear gene segments (RH1, RAG1, EGR2B, IRBP) were used to infer the phylogenetic relationships of the Cobitoidea as reconstructed from maximum likelihood (ML) and partitioned Bayesian Analysis (BA). Analyses of the combined mitochondrial/nuclear gene datasets revealed five strongly supported monophyletic Cobitoidea families and their sister-group relationships: Botiidae+(Vaillantellidae+(Cobitidae+(Nemacheilidae+Balitoridae))). These recovered relationships are in agreement with previous systematic studies on the order Cypriniformes and/or those focusing on the superfamily Cobitoidea. Using these relationships, our analyses revealed pattern lineage- or ecological-group-specific evolution of these genes for the Cobitoidea. These observations and results corroborate the hypothesis that these group-specific-ancestral ecological characters have contributed in the diversification and/or adaptations within these groups. Positive selections were detected in RH1 of nemacheilids and in RAG1 of nemacheilids and genus Vaillantella, which indicated that evolution of RH1 (related to eye's optic sense) and RAG1 (related to immunity) genes appeared to be important for the diversification of these groups. The balitorid lineage (those species inhabiting fast-flowing riverine habitats) had, as compared with other cobitoid lineages, significantly different dN/dS, dN and dS values for ND4 and IRBP genes. These significant differences are usually indicative of weaker selection pressure, and lineage-specific evolution on genes along the balitorid lineage. Furthermore, within Cobitoidea, excluding balitorids, species living in subtropics had significantly higher dN/dS values in RAG1 and IRBP genes than those living in temperate and tropical zones. Among tropical cobitoids, genes COI, ND5, EGR2B, IRBP and RH1, had a significantly higher mean dS value than those species in subtropical and temperate groups. These findings suggest that the evolution of these genes could also be ecological-group-specific and may have played an important role in the adaptive evolution and diversification of these groups. Thus, we hypothesize that the genes included in the present study were actively involved in lineage- and/or ecological-group-specific evolutionary processes of the highly diverse Cobitoidea. These two evolutionary patterns, both subject to further testing, are hypothesized as integral in the diversification with this major clade of the world's most diverse group of freshwater fishes.
The problem of selecting one of a number of models of different dimensions is treated by finding its Bayes solution, and evaluating the leading terms of its asymptotic expansion. These terms are a valid large-sample criterion beyond the Bayesian context, since they do not depend on the a priori distribution.
We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm
include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log‐expectation score, and refinement using tree‐dependent
restricted partitioning. The speed and accuracy of MUSCLE are compared with T‐Coffee, MAFFT and CLUSTALW on four test sets
of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest,
rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable
from T‐Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences
of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely
available at http://www.drive5. com/muscle.
Homalopterid fishes from peninsular India. Records of the Indian Museum
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The Freshwater Fishes of the Indian Region. 2 nd Edition
- K C Jayaram
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Fishes of the genus Homaloptera van Hasselt, 1823 in Kerala, with description of a new species Homaloptera silasi
- B M Kurup
- K V Radhakrishnan
Kurup, B.M. & Radhakrishnan, K.V. (2011) Fishes of the genus Homaloptera van Hasselt, 1823 in Kerala, with description of
a new species Homaloptera silasi. Journal of the Bombay Natural History Society, 107, 224-226.
Homaloptera menoni-a new homalopterid fish (Pisces: Homalopteridae) from Kerala
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