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The subterranean Aenigmachanna gollum, a new genus and species of snakehead (Teleostei: Channidae) from Kerala, South India
Abstract
Aenigmachanna gollum, new genus and species, is described from Kerala, South India. It is the first subterranean species of the family Channidae. It has numerous derived and unique characters, separating it from both the Asian Channa Scopoli and the African Parachanna Teugels & Daget. Uniquely among channids, A. gollum has a very slender (maximum body depth only 11.1–11.3% SL), eel-like body (head length 20.8–21.6% SL), large mouth (jaw length 60.4–61.1 % HL), 43–44 anal-fin rays, 83–85 scales in a lateral series, an unusual colour pattern and it lacks pored lateral-line scales on the body and body buoyancy. In addition, it is distinguished by its DNA barcode sequence, which is 15.8–24.2% divergent from other species of the family Channidae. Morphological modifications usually associated with a subterranean life, such as reduction of eyes and enhancement of non-visual senses (taste, smell, mechanosensory systems) are absent in A. gollum. However, it shares with subterranean fishes a slight reduction of its pigmentation in comparison to epigean channids.
... The new species can be distinguished from its congener in possessing fewer dorsal fin rays (53 vs 56-57), fewer total vertebrae (61 vs 64), fewer scales in lateral series (76 vs 83-85) and in the pectoral-fin rays being extended beyond the margin of the membrane into filaments. , Britz et al. 2019). ...
... Counts and measurements follow Musikasinthorn (1998). Terminology for cephalic pores follows Britz et al. (2019). Measurements up to 100mm were taken with digital callipers to the nearest tenth of a millimetre; those greater than 100mm were taken to the nearest millimetre. ...
... Rather, it either stayed at the bottom under a piece of sponge or remained still at an angle, head upwards, under the filter. We also note that, unlike what is reported for A. gollum (Britz et al. 2019), the specimen of A. mahabali did not appear to lack buoyancy, and was able to maintain its position in the water column. An x-radiograph also revealed a large swim bladder within the body cavity (Fig. 5). ...
Aenigmachanna mahabali, a new species of troglophilic snakehead is described on the basis of a single specimen recovered from a well in Kerala, India, over 200km south of the type locality for the only known species in the genus. The new species can be distinguished from its congener in possessing fewer dorsal fin rays (53 vs 56-57), fewer total vertebrae (61 vs 64), fewer scales in lateral series (76 vs 83-85) and in the pectoral-fin rays being extended beyond the margin of the membrane into filaments.
... Our discovery of Pangio bhujia in the laterite areas of Kerala follows closely that of two other remarkable subterranean fishes, Aenigmachanna gollum (Britz et al. 2019) and A. mahabali (Kumar et al. 2019) raises the number of subterranean fishes from this part of India to ten. Among the species of Pangio, P. bhujia is easily recognized by the absence of both dorsal and pelvic fins and their skeletal supports (basipterygia and dorsal-fin pterygiophores). ...
... As we pointed out previously (Britz et al. 2019), the aquifers of Kerala, though well-known for their unique subterranean fauna, are still poorly explored and comprehensive surveys are required to uncover the true diversity of this unique habitat. Such a survey must rely on the help and support of the local villagers who are much more likely to encounter these peculiar subterranean animals, which cannot be sampled with traditional collecting methods. ...
A unique, new species of eel loach, Pangio bhujia, is described from Kerala, India. It is the first species of Pangio to be described from subterranean waters. It possesses several unusual characters including absence of both dorsal and pelvic fins, the presence of only 3 pectoral-fin rays, 6 anal-fin rays and a unique count of 38 precaudal + 24 caudal vertebrae.
... The Channidae include some 50 valid species in three genera: Channa, with 46 valid species distributed from the Middle East to South-East and Far-East Asia, Parachanna with three species restricted to Africa, and Aenigmachanna with one species from the Western Ghats of India (Conte-Grand et al., 2017;Praveenraj et al., 2018a, b, c;Adamson & Britz, 2018;Praveenraj et al., 2019;Britz et al., 2019). Known popularly as snakeheads, the genus Channa includes medium to large-sized predatory freshwater fishes capable of both aquatic and aerial respiration owing to the possession of accessory air-breathing organs housed in the suprabranchial cavity. ...
... Twenty-two valid species of snakeheads are reported from India, 19 of them from the Eastern Himalayan region (Lalramliana et al., 2018;Praveenraj et al., 2018 a, b;Praveenraj et al. 2019;Britz et al., 2019). The more vividlycoloured ones are popular in the aquarium trade and are regularly exported from India (Bleher, 1998). ...
Channa brunnea, a new species of snakehead fish lacking pelvic fins, from West Bengal, India, is distinguished from its pelvic fin-less congeners by possessing an uniform dark brown body, ochre to bright-orange blotches on the caudal fin, fewer dorsal and anal-fin rays (35–37 vs. 47–51 and 24 vs. 28–32, respectively), fewer vertebrae (43 vs. 45–57), and fewer lateral-line scales (43–46 vs. 51–63). Though Channa brunnea superficially resembles C. bleheri, it can be distinguished from the latter by possessing dark-brown oblique markings on the upper half of the body; transverse scale rows (4½–5½ vs. 3½); pre-anal scales (22–26 vs. 17–20); 2 rows of teeth in the fifth ceratobranchial, the outer row with 16 large conical teeth (vs. 3 rows of teeth, the outer row with 13 large conical teeth); dentary with 20 large, stout, conical teeth in the inner row (vs. 32 medium-sized conical teeth); and a Kimura’s two parameter (K2P) distance of 9.8–10.6%.
... T HE family Channidae is represented by 53 species in three genera, Channa with 48 valid species distributed from the Middle East to South-East and Far-East Asia, Parachanna with three species restricted to tropical Africa, and Aenigmachanna with two species from the laterite areas of Western Ghats of India (Britz et al., 2019aKumar et al., 2019;Praveenraj et al., 2019a;Sudasinghe et al., 2020aSudasinghe et al., , 2020b. The Eastern Himalayan region possess a remarkable diversity of endemic snakeheads. ...
A new species of colorful snakehead from Meghalaya, northeastern India is distinguished from all its congeners by possessing a uniform bright blue to bluish-green body, bright-blue dorsal, anal, and caudal fins, submarginally black with white distal margin, series of brown to maroon-red, rounded, oblong or clover-shaped blotches or spots on dorsolateral, postorbital, and ventrolateral region of head, continued on body forming oblique pattern or randomly distributed. The new species superficially resembles C. pardalis and C. bipuli in appearance, but it can be distinguished from both in having brown to maroon-red, rounded, oblong or clover-shaped blotches or spots on head and sides of the body (vs. possession of well-defined, black to brown, rounded to oblong spots), fewer pre-dorsal scales (7 vs. 8-9), more caudal-fin rays (15 vs. 13), and more vertebrae (49 vs. 45). The new species differs from both C. pardalis and C. bipuli by Kimura's two-parameter (K2P) distance of 4.2-4.8 and 4.9-6.0% in the coxI gene sequence. A key to the snakehead Gachua group of the Eastern Himalayan region is provided herein.
... Lineage G10: Parachanna (Table 1; Figs 4,13A,D;Supporting Information Fig. S4) The Afrotropical snakehead genus Parachanna includes three species and is the sister group of the Oriental and more species-rich genus Channa (Adamson, Hurwood & Mather, 2010), together with the Oriental genus Aenigmachanna (Britz et al., 2019), they form the family Channidae. The Channidae belongs to a larger freshwater clade, the Anabantiformes, mostly distributed in the Orient . ...
The Afrotropics house a diverse freshwater ichthyofauna with > 3000 species, almost all of which are endemic. Recent progress in dated phylogenetics and palaeontology of several groups of Afrotropical freshwater fishes (AFFs) has allowed the testing of palaeoecology- and palaeogeography-based hypotheses explaining their early presence in Africa. Seven hypotheses were tested for 37 most-inclusive monophyletic groups of AFFs. Results indicated that ten lineages originated from direct, but asynchronous, marine-to-freshwater shifts. These lineages contribute < 2% to the current AFF species richness. Eleven lineages colonized the Afrotropics from the Orient after the Afro-Arabian plate collided with Eurasia in the early Oligocene. These lineages contribute ~20% to the total diversity. There are seven sister relationships between Afrotropical and Neotropical taxa. For only three of them (4% of the species diversity), the continental drift vicariance hypothesis was not rejected. Distributions of the other four younger trans-Atlantic lineages are better explained by post-drifting long-distance dispersal. In those cases, I discuss the possibility of dispersal through the Northern Hemisphere as an alternative to direct trans-Atlantic dispersal. The origins of ten AFF lineages, including the most species-rich Pseudocrenilabrinae (> 1100 species), are not yet established with confidence.
... The Western Ghats mountain region is an area with a high level of freshwater fish endemism (Abell et al. 2008) and new species are being described from this part of Peninsular India on a regular basis (Katwate et al. 2014(Katwate et al. , 2018Dahanukar et al. , 2016Britz & Ali 2015;Kumkar et al. 2016;Britz et al. 2018Britz et al. , 2019Kumar et al. 2019). counts were obtained from specimens under transmitted light with the aid of a stereomicroscope. ...
Channa rara, new species, is described from the Jagbudi River in Maharashtra, India. It belongs to the Gachua group and differs from all its members by the possession of one or more ocelli in the posterior part of the dorsal fin in adults (vs. ocelli absent or 1, rarely 2–3 ocelli in juveniles only). It is further distinguished from most species of the C. gachua group by having 6–7 dark concentric bands on the pectoral fins. We review recent descriptions of species of the genus Channa and conclude that C. royi is a synonym of Channa harcourtbutleri, that the diagnosis of C. shingon from C. harcourtbutleri is seriously flawed and that C. torsaensis is not sufficiently diagnosed from C. quinquefasciata. The recently described C. amari is a junior synonym of C. brunnea.
Pronounced organism-wide morphological stasis in evolution has resulted in taxa with unusually high numbers of primitive characters. These ‘living fossils’ hold a prominent role for our understanding of the diversification of the group in question. Here we provide the first detailed osteological analysis of Aenigmachanna gollum based on high-resolution nano-CT scans and one cleared and stained specimen of this recently described snakehead fish from subterranean waters of Kerala in South India. In addition to a number of derived and unique features, Aenigmachanna has several characters that exhibit putatively primitive conditions not encountered in the family Channidae. Our morphological analysis provides evidence for the phylogenetic position of Aenigmachanna as the sister group to Channidae. Molecular analyses further emphasize the uniqueness of Aenigmachanna and indicate that it is a separate lineage of snakeheads, estimated to have split from its sister group at least 34 or 109 million years ago depending on the fossil calibration employed. This may indicate that Aenigmachanna is a Gondwanan lineage, which has survived break-up of the supercontinent, with India separating from Africa at around 120 mya. The surprising morphological disparity of Aenigmachanna from members of the Channidae lead us to erect a new family of snakehead fishes, Aenigmachannidae, sister group to Channidae, to accommodate these unique snakehead fishes.
Purpose : Fish species of the family Channidae, commonly known as snakeheads, represent biggest and most caught native freshwater species in Sri Lanka. Despite importance for biodiversity and fisheries in Sri Lanka, members of this family are one of the least studied on taxonomic status and geographic distribution. Research Method : As an initial step of a study to revise the taxonomy and biogeography of freshwater fish in the family Channidae based on molecular phylogenetic and morphological relationships and biogeographical affinities, authors reviewed all the available published information and examined the specimens available at the National Museum of Sri Lanka. Findings : Six valid species have been recorded; Channa ara (Deraniyagala, 1945), C. marulius (Hamilton, 1822) C. kelaartii (Gunther,1861), C. orientalis Bloch and Schneider 1801 C. punctata (Bloch, 1794) and C. striata (Bloch, 1793). Current review suggests the exiting knowledge on the phylogeny and biogeography of Channidae in Sri Lanka is far from complete, identifying specific gaps to be prioritized in future research. Limitations : Current regional studies on the family Chanidae highlight the importance of a complete systematic revision of Sri Lankan species with an integrative approach. Literature review shows the necessity of a fresh analysis on the distribution data with ecological niche modeling and molecular phylogenetic studies to understand biogeographical and evolutionary history of the family. Originality / Value : Provides a consolidated account of the current knowledge on the taxonomy and biogeography of the Sri Lankan members of the family Channidae.
Morphology of sagittal otoliths of seven species of genus Channa from upper Assam, India was studied to obtain baseline information for their prospective role in taxonomic studies. In the present study, variations were recorded in morphological characteristics of sagittal otolith among the studied species. Of all the studied parameters, otolith shape, sulcus acusticus, ostium, and cauda, in particular, were found to be taxonomically important features for the identification of the species. The pentagonal shape of sagitta in Channa punctata, pseudo-ostiocaudal sulcus acusticus in C. marulius, bent concave ostium in C. stewartii, straight cauda in C. bleheri were found to be species-specific features. Sagitta size was smallest in C. gachua while the largest was recorded in C. striata. The proposed taxonomic keys enumerated through the combination of different otolith characters from the present investigation will be useful in the identification of these species when standard methodologies fail to deliver satisfactory results.
The collision of the Indian and Eurasian landmasses in the Cenozoic was a decisive factor in shaping biodiversity patterns in Southern and Southeastern Asia. While most studies thus far have focused on the biotic interchange between India and Eurasia and evolutionary diversification on or around the Tibetan Plateau, little attention has been paid to the biodiversity buildup in the Eastern Himalaya biodiversity hotspot (EHH) which harbors over 540 freshwater fish species with a high degree of endemicity. An important component of the regional ichthyofauna are snakehead fishes of the family Channidae comprising throughout their African‐Asian distribution 47 valid species, but a poorly known species‐level diversity. In order to evaluate channid intrarelationships and biogeography, a temporal and geographic framework of channid evolution in conjunction with a critical reevaluation of the channid fossil record is warranted. Based on molecular data, we provide a comprehensive species‐level phylogeny based on 223 channid individuals belonging to 37 species and one additional currently undescribed species. The first split within channids separates the African genus Parachanna from the Asian genus Channa which can be divided into eight distinct species groups (Argus, Asiatica, Gachua, Lucius, Marulius, Micropeltes, Punctata, and Striata groups). Large intraspecific divergences were observed within several species and potentially indicate additional species‐level diversity. Almost 40% of the channid species are narrow‐range endemics belonging to the Gachua group. These are found in the EHH making this area an outstanding hotspot for endemic channid diversity. The large majority of the EHH endemics are restricted to the southern foothills of the Eastern Himalaya and the Shillong‐Mikir Hills Plateau, areas west of the Indoburman Ranges. Our results reveal complex and difficult to interpret biogeographic patterns indicating that both vicariance and dispersal events have potentially been responsible in shaping current distribution patterns in Asian channids. We recognize †Parachanna fayumensis as the oldest reliable channid fossil and argue that the three oldest so‐called channid fossils (i.e., †Eochanna chlorakkiensis, †Anchichanna kuldanensis, and †Ophiocephalus lydekkeri) lack clear diagnostic features that would allow them to be unequivocally placed within Channidae. Based on a comprehensive molecular multilocus study of 223 individuals, we provide a species‐level hypothesis of phylogenetic relationships among snakeheads. Eight species groups are distinguished within the Asian snakeheads of the genus Channa and large intraspecific divergences indicate additional species diversity in several clades. We provide a temporal and spatial framework of channid evolution and show that almost 40% of the snakehead species are narrow range endemics of the Eastern Himalaya biodiversity hotspot.
The "bullseye" or "cobra" snakehead is a large, predatory freshwater fish of South Asian origin. Until recently, only one bullseye species has been recognised, Channa marulius, but new studies on the 'Marulius group' have revealed that there are at least four species with different native ranges in rivers of mainland South Asia, as well as Channa marulioides (the "emperor snakehead") from Sundaland. New data, generated as part of this wider taxonomic investigation and reported here for the first time, reveal that Marulius group specimens collected in the Mae Khlong Basin of Western Thailand are similar genetically and in appearance to the recently revalidated Channa aurolineata, that occurs in Myanmar's Salween, Sittang and Ayeyarwady River Basins. Thus, the Mae Klong bullseye snakehead should now rightly be referred to by the scientific name C. aurolineata. Furthermore, C. aurolineata from western Thailand are a direct DNA barcode match to publicly available data for the feral bullseye snakehead population in Florida, North America. This identifies the Mae Khlong Basin as the probable source for the feral population in Florida. Identifying Thailand as the likely origin for the feral North American population may further have implications for understanding historical invasion pathways into the USA.
The Western Ghats (WG) is an escarpment on the west coast of Peninsular India, housing one of the richest assemblages of frogs in the world, with three endemic families. Here, we report the discovery of a new ancient lineage from a high-elevation massif in the Wayanad Plateau of the southern WG. Phylogenetic analysis
reveals that the lineage belongs to Natatanura and clusters with Nyctibatrachidae, a family endemic to the WG/Sri Lanka biodiversity hotspot. Based on geographic distribution, unique morphological traits, deep genetic divergence, and phylogenetic position that distinguishes the lineage from the two nyctibatrachid subfamilies Nyctibatrachinae Blommers-Schlösser, 1993 and Lankanectinae Dubois & Ohler, 2001, we erect a new subfamily Astrobatrachinae subfam. nov. (endemic to the WG, Peninsular India), and describe a new genus Astrobatrachus gen. nov. and species, Astrobatrachus kurichiyana sp. nov. The discovery of this species adds to the
list of deeply divergent and monotypic or depauperate lineages with narrow geographic ranges in the southern massifs of the WG. The southern regions of the WG have long been considered geographic and climatic refugia, and this new relict lineage underscores their evolutionary significance. The small range of this species exclusively outside protected areas highlights the significance of reserve forest tracts in the WG in housing evolutionary novelty. This reinforces the need for intensive sampling to uncover new lineages and advance our understanding of the historical biogeography of this ancient landmass.
We report molecular phylogenetic and dating analyses of snakes that include new mitochondrial and nuclear DNA sequence data for three species of the peninsular Indian endemic Xylophis. The results provide the first molecular genetic test of and support for the monophyly of Xylophis. Our phylogenetic results support the findings of a previous, taxonomically restricted phylogenomic analysis of ultraconserved nuclear sequences in recovering the fossorial Xylophis as the sister taxon of a clade comprising all three recognised extant genera of the molluscivoran and typically arboreal pareids. The split between Xylophis and ‘pareids’ is estimated to have occurred on a similar timescale to that between most (sub)families of extant snakes. Based on phylogenetic relationships, depth of molecular genetic and estimated temporal divergence, and on the external morphological and ecological distinctiveness of the two lineages, we classify Xylophis in a newly erected subfamily (Xylophiinae subfam. nov.) within Pareidae.
urn:lsid:zoobank.org:pub:43BDE72C-6823-4D6A-8601-482862556D78
urn:lsid:zoobank.org:act:AD3486DF-D874-4CFD-8EAE-14FF3E403AF9
A new genus and species of Euryrhynchidae is described from Kerala, India. This freshwater shrimp family was previously only known from northern South America and West Africa. Although the inclusion of the genus in Euryrhynchidae is unequivocal (e.g. shape of the accessory ramus of the antennular flagellum, frontal margin of the carapace, telson ornamentation), the presence of a number of unique characters makes the relative placement of the genus within the family unclear, but likely basal to the other genera. The new genus can be easily distinguished from all others within the family by these characters, e.g. the upper antennular flagellum and its accessory ramus being joined over three divisions, the presence of a reduced carpo-propodal brush and a well-developed branchiostegal groove.
Monopterus luticolus, new species, is described from Cameroon. Most of the seven known individuals were discovered in inundated soil while digging for caecilian amphibians. Monopterus luticolus differs from the two other nominal African synbranchid species in the number of vertebrae and details of its osteology. The spatial dissociation of ceratobranchial 1 from hypobranchial 1 and its close association with hypobranchial 2 and ceratobranchial 2 demonstrate that M. luticolus is a member of the 'Amphipnous group'.
The Asian (nandid) and Afro-Neotropical (polycentrid) leaffishes represent two superficially similar, but historically poorly diagnosed families – a situation resulting in a convoluted systematic history. Here, and including for the first time in a molecular study all leaffish genera, we generate a hypothesis of the phylogenetic history of both groups. We analyse a multilocus molecular data set encompassing 257 acanthomorph taxa, carry out a survey and assessment of selected osteological characters for the polycentrid leaffishes and also provide a reanalysis of previously published morphological data. Our results confirm: (1) that the Polycentridae and Nandidae are only remotely related, and hence, the classic leaffishes are diphyletic; (2) that the Polycentridae is monophyletic, with new skeletal synapomorphies being congruent with molecular data in placing the enigmatic Afronandus – a taxon that thus far has never been included in any molecular study – as sistergroup to the remaining genera; (3) the monophyly of the Nandidae + Badidae and their inclusion into a larger monophyletic group – along with the Pristolepididae, Anabantoidei and Channoidei – comprising the Labyrinthici sensu Rosen & Patterson. We also review the morphological and molecular evidence for both the conflicting placement of Pristolepis and the putative sistergroup relationship between the labyrinth fishes (Anabantoidei) and snakeheads (Channoidei).
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.
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.
The Nilgiri Mystus, Hemibagrus punctatus, a rare bagrid catfish endemic to the Western Ghats, has been currently listed in the IUCN Red List, as ‘Critically Endangered’ with a possibility that it could be extinct. The last validated record of H. punctatus was known to be in 1998, and several surveys since then have not been able to collect the species from its native range. In this paper, we provide information on new records of this rare catfish from the Western Ghats after a period of 14 years, and discuss its distribution, ecology and conservation. An updated conservation assessment of this species following the IUCN Red List Criteria is also provided.
The Western Ghats of India and Sri Lanka biodiversity hotspot is often regarded as one unit because of shared biogeographical history. However, recent studies suggest that certain faunal components, particularly in the wet zones are distinct. This article looks at the existing information on species richness and endemicity of taxa in both regions. Data are available on some taxa but not on others, and many taxa have not received equal attention in both regions. The natural ecosystems of this hotspot are under threat and urgent conservation action is needed, especially in augmenting the protected area network. There is also the need for increasing the level of scientific collaboration in biodiversity studies between the two countries.
BACKGROUND OF THE WORK: The phylogenetic position and evolution of Hemidactylus anamallensis (family Gekkonidae) has been much debated in recent times. In the past it has been variously assigned to genus Hoplodactylus (Diplodactylidae) as well as a monotypic genus 'Dravidogecko' (Gekkonidae). Since 1995, this species has been assigned to Hemidactylus, but there is much disagreement between authors regarding its phylogenetic position within this genus. In a recent molecular study H. anamallensis was sister to Hemidactylus but appeared distinct from it in both mitochondrial and nuclear markers. However, this study did not include genera closely allied to Hemidactylus, thus a robust evaluation of this hypothesis was not undertaken.
The objective of this study was to investigate the phylogenetic position of H. anamallensis within the gekkonid radiation. To this end, several nuclear and mitochondrial markers were sequenced from H. anamallensis, selected members of the Hemidactylus radiation and genera closely allied to Hemidactylus. These sequences in conjunction with published sequences were subjected to multiple phylogenetic analyses. Furthermore the nuclear dataset was also subjected to molecular dating analysis to ascertain the divergence between H. anamallensis and related genera.
Results showed that H. anamallensis lineage was indeed sister to Hemidactylus group but was separated from the rest of the Hemidactylus by a long branch. The divergence estimates supported a scenario wherein H. anamallensis dispersed across a marine barrier to the drifting peninsular Indian plate in the late Cretaceous whereas Hemidactylus arrived on the peninsular India after the Indian plate collided with the Eurasian plate. Based on these molecular evidence and biogeographical scenario we suggest that the genus Dravidogecko should be resurrected.
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.
We present a new map depicting the first global biogeographic regionalization of Earth's freshwater systems. This map of freshwater
ecoregions is based on the distributions and compositions of freshwater fish species and incorporates major ecological and
evolutionary patterns. Covering virtually all freshwater habitats on Earth, this ecoregion map, together with associated species
data, is a useful tool for underpinning global and regional conservation planning efforts (particularly to identify outstanding
and imperiled freshwater systems); for serving as a logical framework for large-scale conservation strategies; and for providing
a global-scale knowledge base for increasing freshwater biogeographic literacy. Preliminary data for fish species compiled
by ecoregion reveal some previously unrecognized areas of high biodiversity, highlighting the benefit of looking at the world's
freshwaters through a new framework.
Global changes, from habitat loss and invasive species to anthropogenic climate change, have initiated the sixth great mass
extinction event in Earth’s history. As species become threatened and vanish, so too do the broader ecosystems and myriad
benefits to human well-being that depend upon biodiversity. Bringing an end to global biodiversity loss requires that limited
available resources be guided to those regions that need it most. The biodiversity hotspots do this based on the conservation
planning principles of irreplaceability and vulnerability. Here, we review the development of the hotspots over the past two
decades and present an analysis of their biodiversity, updated to the current set of 35 regions. We then discuss past and
future efforts needed to conserve them, sustaining their fundamental role both as the home of a substantial fraction of global
biodiversity and as the ultimate source of many ecosystem services upon which humanity depends.
The Malabar snakehead Channa diplogramma is one of the most enigmatic and least understood species within the family Channidae, which comprise one of the most important groups of freshwater food fish in tropical Asia. Since its description from peninsular India in 1865, it has remained a taxonomic puzzle with many researchers questioning its validity, based on its striking similarity with the South East Asian C. micropeltes. In this study, we assessed the identity of the Malabar snakehead, C. diplogramma, using morphological and molecular genetic analyses, and also evaluated its phylogenetic relationships and evolutionary biogeography.
The morphometric and meristic analysis provided conclusive evidence to separate C. diplogramma and C. micropeltes as two distinct species. Number of caudal fin rays, lateral line scales, scales below lateral line; total vertebrae, pre-anal length and body depth were the most prominent characters that can be used to differentiate both the species. Channa diplogramma also shows several ontogenic color phases during its life history, which is shared with C. micropeltes. Finally, the genetic distance between both species for the partial mitochondrial 16S rRNA and COI sequences is also well above the intra-specific genetic distances of any other channid species compared in this study.
The current distribution of C. diplogramma and C. micropeltes is best explained by vicariance. The significant variation in the key taxonomic characters and the results of the molecular marker analysis points towards an allopatric speciation event or vicariant divergence from a common ancestor, which molecular data suggests to have occurred as early as 21.76 million years ago. The resurrection of C. diplogramma from the synonymy of C. micropeltes has hence been confirmed 146 years after its initial description and 134 years after it was synonymised, establishing it is an endemic species of peninsular India and prioritizing its conservation value.
A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
Two hundred and seven species of fish, mostly Australian marine fish, were sequenced (barcoded) for a 655 bp region of the mitochondrial cytochrome oxidase subunit I gene (cox1). Most species were represented by multiple specimens, and 754 sequences were generated. The GC content of the 143 species of teleosts was higher than the 61 species of sharks and rays (47.1% versus 42.2%), largely due to a higher GC content of codon position 3 in the former (41.1% versus 29.9%). Rays had higher GC than sharks (44.7% versus 41.0%), again largely due to higher GC in the 3rd codon position in the former (36.3% versus 26.8%). Average within-species, genus, family, order and class Kimura two parameter (K2P) distances were 0.39%, 9.93%, 15.46%, 22.18% and 23.27%, respectively. All species could be differentiated by their cox1 sequence, although single individuals of each of two species had haplotypes characteristic of a congener. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data. In the neighbour-joining tree for all 754 sequences, four major clusters were apparent: chimaerids, rays, sharks and teleosts. Species within genera invariably clustered, and generally so did genera within families. Three taxonomic groups-dogfishes of the genus Squalus, flatheads of the family Platycephalidae, and tunas of the genus Thunnus-were examined more closely. The clades revealed after bootstrapping generally corresponded well with expectations. Individuals from operational taxonomic units designated as Squalus species B through F formed individual clades, supporting morphological evidence for each of these being separate species. We conclude that cox1 sequencing, or 'barcoding', can be used to identify fish species.
About 96% of the more than 4,800 living anuran species belong to the Neobatrachia or advanced frogs. Because of the extremely poor representation of these animals in the Mesozoic fossil record, hypotheses on their early evolution have to rely largely on extant taxa. Here we report the discovery of a burrowing frog from India that is noticeably distinct from known taxa in all anuran families. Phylogenetic analyses of 2.8 kilobases of mitochondrial and nuclear DNA unambiguously designate this frog as the sister taxon of Sooglossidae, a family exclusively occurring on two granitic islands of the Seychelles archipelago. Furthermore, molecular clock analyses uncover the branch leading to both taxa as an ancient split in the crown-group Neobatrachia. Our discovery discloses a lineage that may have been more diverse on Indo-Madagascar in the Cretaceous period, but now only comprises four species on the Seychelles and a sole survivor in India. Because of its very distinct morphology and an inferred origin that is earlier than several neobatrachian families, we recognize this frog as a new family.
Life in caves means life in perpetual darkness. This has two dramatic effects on animals: it eliminates the need to see and reduces the availability of food as there is no local photosynthesis. Food availability for cave dwellers is often seasonal, episodic or unscheduled. Like other cave animals, fish species adapted for cave life exhibit a suite of sensory, morphological, physiological and behavioral traits that are shared among species from phylogenetically distant families. Most cave fishes are entirely or partially blind. The most extreme of them, the obligatory cave-dwelling fish that spend their entire life in caves, are the subject of this primer. At present, over 200 such cavefish species have been described, and all of them have evolved independently from surface ancestors. Thus, each cavefish species is a replicate of the same natural experiment, testing the evolutionary response of a sighted surface fish to the absence of light and the limitations on food in a subterranean environment. The evolutionary responses converge on loss of eyes and pigmentation and the augmentation of other senses, such as taste, smell or mechanosensation, as well as a more efficient metabolism, changes in feeding behavior, altered activity levels, loss of circadian rhythmicity and increased wakefulness. However, not all of these troglomorphic traits are present in every cavefish species.
This book provides fascinating insights into the development and genetics of evolutionary processes on the basis of animals living in the dark, such as the Astyanax cave fish.
Biologically functionless traits show high variability, which results from neutral deleterious mutations no longer being eliminated by natural selection, which normally acts to preserve functional capability. These negative mutations accumulate until the traits they are responsible for become rudimentary or even lost.
The random genetic basis of regressive evolution is in accordance with Nei’s Neutral Theory of Molecular Evolution, which applies to the molecular level. Such processes are particularly conspicuous in species living in constant darkness, where, for example in Astyanax, all traits depending on the exposure to light, like eyes, pigmentation, visually triggered aggressive behaviour, negative phototaxis, and several peripheral outcomes of circadian rhythmicity, are useless and diminish. In compensation constructive traits like taste, olfaction or the lateral line senses are improved by selection and do not show variability. Regressive and constructive traits inherit independently, proving that the rudimentation process is not driven by pleiotropic linkage between them. All these traits are subject to mosaic evolution and exhibit unproportional epistatic gene effects, which play an important role in evolutionary adaptation and improvement.
Offering valuable evolutionary insights and supplemented by a wealth of illustrations, this book will appeal to evolutionary and developmental biologists alike.
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.
Physiologists, ecologists, ethologists and evolutionary biologists have long been interested in the phenomenon of air breathing in fishes. Aside from the intrinsic significance of understanding the numerous and intriguing multiple adaptations that have evolved in air breathing fishes, biologists hope to find the biological solutions to the environmental problems associated with the transition of aquatic to terrestrial life in vertebrates. Since some recent air breathing fishes possess fairly primitive gas exchange systems, and exhibit distinct behavioral and ecological responses to the fluctuating environmental factors characterizing their habitats, they offer extraordinary opportunities to gain understanding of the early evolution of air breathing in the vertebrates.
Kryptoglanis shajii was recently described from a public well in Kerala, India. Its systematic position among cat- fishes has remained unresolved partly due to lack of morphological information. We present here a detailed osteological description of the skeleton of K. shajii and discuss its unusual skeletal features. Unlike most other catfishes Kryptoglanis has a fifth vertebra that is well-separated from the Weberian complex, a character shared only with the Diplomystidae, Helogenes and with the troglobitic or phreatic ictalurids Trogloglanis, Prietella and Satan. There is no trace of the dorsal fin or its supporting skeleton and the caudal fin skeleton consists of a single hypural plate articulating with five rays. Kryptoglanis has a number of reductive features, which may be interpreted as developmental truncations. It lacks the vomer, metapterygoid, all infraorbital bones except the antorbital, the mesocoracoid, and the pectoral fin spine. The phylogenetic position of Kryptoglanis remains unclear, even though the reduced condition of the palatine may point to a closer relationship with the Siluridae. Our osteological analysis of Kryptoglanis demonstrates that this genus cannot be accommodated into any known catfish family and we therefore propose the new family Kryptoglanidae for it.
Channa ornatipinnis, new species, from Waloun Chaung, northern Rakhine State, Myanmar, differs from all its congeners by a unique colour pattern that consists of numerous large black spots on the cheeks, golden-orange lips, a red posterior rim of the opercular flap, five to seven narrow alternating white and dark brown to black semicircular bands on the pectoral fin, three dorsal fin blotches, and red and bluish-grey scales with numerous black spots on the body. Channa pulchra, new species, from Kyeintali Chaung, southern Rakhine State, Myanmar, is also distinguished by a unique colour pattern consisting of numerous small black spots on the cheek and body, usually four semicircular white bands on the pectoral fin, one anterior dorsal fin blotch, and a series of reddish-orange blotches and numerous black spots on the body.
This is the report of a new species of catfish, Kryptoglanis shajii nov. gen. and nov. sp., distinguished from all other genera of siluriform fishes by the combination of the following morphological
characters: viz. the absence of dorsal fin; the presence of four pairs of barbels; an upwardly directed mouth, with a distinctly
projecting lower jaw; subcutaneous eyes; anal fin completely confluent with the caudal fin; anal and caudal fins together
carry 70–74 fin rays; and no spines in any of the fins. Kryptoglanis, which has a maximum recorded size of 59.1 mm in standard length, was collected from a well fed by subterranean springs.
The type locality is a well located at the extreme western part of Western Ghats, near Chalakudy in Thrissur district, Kerala
State, India.
In phylogenetic analyses of molecular sequence data, partitioning involves estimating independent models of molecular evolution for different sets of sites in a sequence alignment. Choosing an appropriate partitioning scheme is an important step in most analyses because it can affect the accuracy of phylogenetic reconstruction. Despite this, partitioning schemes are often chosen without explicit statistical justification. Here, we describe two new objective methods for the combined selection of best-fit partitioning schemes and nucleotide substitution models. These methods allow millions of partitioning schemes to be compared in realistic time frames and so permit the objective selection of partitioning schemes even for large multilocus DNA data sets. We demonstrate that these methods significantly outperform previous approaches, including both the ad hoc selection of partitioning schemes (e.g., partitioning by gene or codon position) and a recently proposed hierarchical clustering method. We have implemented these methods in an open-source program, PartitionFinder. This program allows users to select partitioning schemes and substitution models using a range of information-theoretic metrics (e.g., the Bayesian information criterion, akaike information criterion [AIC], and corrected AIC). We hope that PartitionFinder will encourage the objective selection of partitioning schemes and thus lead to improvements in phylogenetic analyses. PartitionFinder is written in Python and runs under Mac OSX 10.4 and above. The program, source code, and a detailed manual are freely available from www.robertlanfear.com/partitionfinder.
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.
Le genre #Parachanna$ a été révisé à partir de caractères morphologiques de 245 exemplaires, y compris les specimens types de toutes les espèces nominales. Trois espèces valides, #Parachanna obscura, P. insignis$ et #P. africana$ ont été retenues. Une clé de détermination ainsi que des descriptions détaillées comprenant des données sur la distribution géographique et la biologie sont fournies pour chaque espèce. (Résumé d'auteur)
http://deepblue.lib.umich.edu/bitstream/2027.42/57162/1/OP726.pdf
Conservationists are far from able to assist all species under threat, if only for lack of funding. This places a premium on priorities: how can we support the most species at the least cost? One way is to identify 'biodiversity hotspots' where exceptional concentrations of endemic species are undergoing exceptional loss of habitat. As many as 44% of all species of vascular plants and 35% of all species in four vertebrate groups are confined to 25 hotspots comprising only 1.4% of the land surface of the Earth. This opens the way for a 'silver bullet' strategy on the part of conservation planners, focusing on these hotspots in proportion to their share of the world's species at risk.
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.
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