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Resolving an unnoticed diversity within the Schistura robertsi species complex (Teleostei: Nemacheilidae) using molecules and morphology
Abstract
The Schistura robertsi species complex is a group of freshwater fish inhabiting streams in southeast Myanmar as well as in western and southern Thailand. In southern Thailand, the distribution exceeds the biogeographically important ‘Surat Thani – Krabi line’. The complex is believed to include five described and one undescribed species, but monophyly and systematics of the group have never been studied explicitly. The present study aims to resolve the number of species within the Schistura robertsi group as well as their distribution areas and phylogenetic relations. We analysed mitochondrial and nuclear sequence data of 86 specimens from 47 localities and 18 morphological characters of 193 specimens. The phylogenetic analyses revealed the S. robertsi complex to be monophyletic and to be composed of ten major lineages. Six of them correspond to the known described or undescribed species, but another four newly identified clades reveal the existence of an overlooked diversity within the group. All genetic lineages are statistically highly supported and all are morphologically diagnosable, suggesting that they represent distinct species. The distribution areas of several clades overlap, the cases of direct co-occurrence show no sign of hybridisation.
... DNA was extracted from fin or muscle tissue either by Dneasy Blood & Tissue kit (QIAGEN N.V., Venlo, Netherlands) or by the phenol-chloroform method [38]. As an outgroup, we used published sequences of various Nemacheilidae and Cobitis taenia from the closely related loach family Cobitidae [24,25,35]. ...
... The species Paracanthocobitis zonalternans from eastern Myanmar and western Thailand were supposed either to represent a single species [27] or three species [70], however, a molecular databased phylogeny showed it to be composed of six genetic clades, two of them sympatric, and the others allopatric [24]. A phylogenetic study on the Schistura robertsi species complex revealed at least ten species in the group instead of the four originally anticipated ones [25]. A phylogenetic investigation of the genus Nemacheilus revealed that at least five species do not belong to Nemacheilus, but to three different clades within Nemacheilidae [17]. ...
... The second mechanism is by contact of the lower courses of rivers, which happens particularly during geologic periods with lowered sea levels. Both mechanisms have been shown to have shaped the present diversity of Nemacheilidae [24,25]. Since recent geologic studies deny a river contact between the north Indian Yarlung-Brahmaputra and the Burmese Chindwin-Irrawaddy during the Miocene [72,[79][80][81], no potential colonisation pathway from north India to Myanmar is known. ...
Simple Summary
Since large animal families with unresolved taxonomy are difficult to study, it is better to focus on smaller units. In the present study, we test if we can define a restricted group of species within a large and unsorted fish family (Nemacheilidae). In the beginning, we selected 17 candidate species that share a rare and specific pigmentation pattern, and 29 comparative species with a different pattern. We studied their relationships and the ages of pedigree branches using molecular genetic markers. It turned out that the candidate and comparative species are intermixed in two main groups, meaning that the specific pigmentation pattern is not diagnostic. However, the genetic lineages themselves are smaller units within the large family Nemacheilidae and can be used for further studies. For example, one group revealed its evolutionary history: it expanded 12 million years ago from India into Myanmar and later further to Thailand, Laos, and China. They also revealed more than 20% of undescribed species, a very high rate in vertebrates. Our results show that species groups can be a helpful tool to approach large and unsorted animal units. This finding offers species groups as a new tool for future studies exploring the diversity of life on earth.
Abstract
Large animal families with unresolved taxonomy are notoriously difficult to handle with respect to their biodiversity, systematics, and evolutionary history. We approach a large and taxonomically unresolved family of freshwater fishes (Nemacheilidae, >600 species) by proposing, on the basis of morphologic data, a species group within the family and study its phylogeny with conclusions regarding its diversity, taxonomy, and biogeographic history. Phylogenetic analyses of two mitochondrial and three nuclear genes of 139 specimens, representing about 46 species (17 candidate species from the proposed species-group, plus 29 comparative species), revealed that the proposed species group does not form a distinct monophyletic lineage, but that the candidate and comparative species mixed in three different lineages. However, the results revealed more than 20% of undescribed species within the ingroup and showed that species do not cluster according to the presently recognised genera. At least one of the genetic clades shows signs of an eastward range expansion during the second half of Miocene from north India via Myanmar into Laos, western China, and western Thailand. We conclude that the approach of picking monophyletic lineages to study biodiversity, systematics, and evolutionary history helps to open the door to large animal families.
... Lens contradens individuals occurring on either side of this important biogeographic barrier are molecularly very similar, suggesting that this putative capture event occurred recently (Fig. 12). This recent stream capture is also supported by the disjunct distributions and shallow molecular divergences of the freshwater fish Paracanthocobitis zonalternans and Schistura auranantiaca in the Moei (Salween drainage) and Khwae Yai (Mae Klong drainage), and has been estimated to have occurred 1.5 million years ago (Bohlen et al. 2020a(Bohlen et al. , 2020b. Similar to our phylogenomic reconstruction ( Fig. 9) but with greater taxon sampling, our COI phylogeny shows a diverse radiation of at least six Lens species, all of which are endemic to the Mekong drainage (Fig. 12). ...
... Each of the isolated populations in the Mekong (Kok, Ing, Loei) and Salween (Moei) drainages are restricted to relatively small watersheds that generally flow from south to north, the opposite direction in comparison to the drainage's general flow, creating drainage network geometries that are often characteristic of stream capture (Bishop 1995). All three of the Mekong tributaries, the Kok, Ing and Loei, have been previously hypothesised as areas of drainage rearrangement (Hutchison 1989;Rainboth et al. 2012), and the Moei has Revision of some South-east Asian freshwater mussels Invertebrate Systematics recently been hypothesised to have captured the upper reaches of the Mae Klong (Bohlen et al. 2020a(Bohlen et al. , 2020b. The molecular divergences between the Mekong and Chao Phraya samples and Salween and Chao Phraya samples are very shallow, suggesting that the stream captures are recent (Fig. 12). ...
... This disjunct population of L. contradens in the Salween suggests a stream-capture event caused part of the Mae Klong or Chao Phraya to start draining to the Salween. Bohlen et al. (2020aBohlen et al. ( , 2020b hypothesised that the Salween drainage recently captured part of the Mae Klong drainagẽ 1.5 million years ago and that this event effected the distribution of at least two freshwater fish species. These putative stream-capture events occur in relatively small, high-gradient watersheds very near a drainage divide, which are likely areas of drainage rearrangement especially 'bottom up' processes such as headwater extension (Bishop 1995). ...
The tribes Contradentini and Rectidentini (Unionidae) comprise a diverse clade of freshwater mussels endemic to South-east Asia. Our understanding of the diversity and phylogeny of this radiation has improved dramatically in recent years, but this systematic transformation has not yet benefited from comprehensive museum sampling or phylogenomic methods. A synthetic taxonomic revision of the Contradentini+Rectidentini that leverages these useful and accessible methods is needed. We set out to (1) generate a phylogenomic reconstruction of the supraspecific relationships of the Contradentini+Rectidentini using anchored hybrid enrichment, (2) revise the taxonomy and geographic boundaries of the generic and species-level diversity of the radiation, and (3) identify patterns of freshwater mussel diversity and distribution in this clade and discuss the processes that may have precipitated them. Our phylogenomic reconstruction using over 1600 loci, with a total alignment length of over a half a million nucleotides, recovers a well supported phylogeny of the clade that resolves four independent multispecies radiations endemic to the Mekong drainage. We examined, digitised, and imaged 1837 records from 15 natural history museums that provided the necessary data to document the morphological variation and geographic distributions of the focal taxa. We also analysed 860 COI sequences, 519 of which were generated in this study, to better understand the species boundaries and geographic distributions of the recovered clades. We recognise 54 valid species in the tribes Contradentini and Rectidentini, including 9 described herein as new to science. Out of this revision emerged several interesting biogeographic patterns that appear to have resulted from recent stream capture, historical confluence, and intradrainage barriers to dispersal. We hypothesise that these phenomena shaped the diversity and distribution of the Contradentini+Rectidentini, contributing to the formation of several characteristic freshwater mussel provinces in South-east Asia.
... As a result, taxonomists traditionally resorted to the use of weak synapomorphies to identify and delineate species, and group them under 'catch-all' and inclusive genera such as Schistura McClelland 1838 and Nemacheilus Bleeker 1863. The advent of molecular phylogenetic studies integrating mitochondrial and nuclear DNA sequences have revealed a surprising taxonomic complexity within Nemacheilidae (Šlechtová et al. 2021;Dvořák et al. 2022Dvořák et al. , 2023, including evidence of multiple, independent, diversification events and the presence of cryptic lineages, thus challenging traditional classifications (Bohlen et al. 2020). From 2001 until the end of 2023, as many as nineteen new genera have been described within the family, including Dzihunia Prokofiev 2001;Traccatichthys Freyhof & Serov 2001;Paracanthocobitis Grant 2007;Afronemacheilus golubtsov & Prokofiev 2009;Iskandaria Prokofiev 2009;Paraschistura Prokofiev 2009;Claea Kottelat 2011;Pteronemacheilus Bohlen & Šlechtová 2011;Draconectes Kottelat 2012;Speonectes Kottelat 2012;Eidinemacheilus Segherloo, ghaedrahmati & Freyhof 2016;Sasanidus Freyhof, Geiger, Golzarianpour & Patimar 2016;Troglonectes Zhang, Zhao & Tang 2016;Malihkaia Kottelat 2017;Mustura Kottelat 2018;Rhyacoschistura Kottelat 2019;Kayahschistura Kottelat & Grego 2020;Guinemachilus Du, li, Xu, luo, luo, Yu &Karstsinnectes Zhou, luo, Wang, Zhou &Xiao 2023. ...
Koima, a new genus of nemacheilid loach, is described for Mesonoemacheilus remadevii Shaji 2002, and Nemacheilus monilis Hora 1921, both of which are endemic to the Western Ghats of southern peninsular India. Koima is distinguished from all other genera of family Nemacheilidae by its unique colour pattern comprising a yellowish-brown ground colour, single row of black spots on lateral line, all fins hyaline, and absence of a uniform banding pattern on dorsal side. Koima remadevii was initially identified as a species of Mesonoemacheilus Bănărescu & Nalbant 1982, from which it can be distinguished by the presence of a lower adipose crest, and an absence of a banding pattern on the dorsal side and on the caudal fin, while Koima monilis was initially identified as a species of Nemacheilus Bleeker 1863, from which it can be distinguished by the presence of a lower adipose crest, a narrow and deeply incised upper lip and having the fins hyaline. In the multi-gene phylogenetic analysis based on concatenated mitochondrial and nuclear gene sequences, Koima remadevii and K. monilis were recovered in a monophyletic group, sister to the endemic peninsular Indian nemacheilid, Schistura denisoni. Resolution of the identity of Koima remadevii and K. monilis contributes to our understanding of the phylogenetics of family Nemacheilidae, which is widely considered to be a polyphyletic group.
... For instance, Nemacheilidae in the superfamily Cobitoidea exhibits inconsistencies between traditional morphological and molecular phylogenetic taxonomy [1]. Schistura McClelland, 1838, is the largest genus in Nemacheilidae [2][3][4], and is found throughout a large portion of South and Southeast Asia [5]. Because of their charming color stripe pattern and size, Schistura species are very popular in the ornamental fish trade [6]. ...
The inconsistency between traditional morphological taxonomy and molecular phylogenetic data is a major issue that puzzles the study of fish classification and evolution. Although mitochondrial genes are commonly used in phylogenetic analyses to compare fish species, the mitochondrial evolution and diversity of Schistura are still not well understood. To better understand the evolution of Schistura, we sequenced the mitochondrial genome of Schistura fasciolata and compared it with other species of Schistura. A 16,588 bp circular mitochondrial genome of S. fasciolata was obtained and it contains 13 protein-coding, 22 transfer RNA, and two ribosomal RNA genes, and a non-coding control region. The gene arrangement in the mitochondrial genomes of all Schistura species was consistent. However, we also found that S. fasciolata was not monophyletic. Although mitochondrial genes can be effectively used for Schistura species identification, they may not be suitable for inferring the evolutionary process of Schistura species. These results provide support for the use of mitochondrial genes in identifying Schistura species, and also serve as a warning against mistakenly using them to evaluate the evolution process of Schistura species.
... Few researchers have tried to identify natural groups of related species of manageable size within the genus in order to analyse their taxonomy and, biogeography, and to contribute to their conservation. This is an unfortunate situation and experience shows that it is feasible to distinguish a number of groups of species that share distinctive morphological feature 11,15,16 . It is predictable that several such species groups might once be recognised as distinct genera. ...
To approach the taxonomy of large and complex animal groups it is of advantage to focus on species groups with shared derived character state. We investigate the composition, morphological characteristics and relationships of and within the Schistura cincticauda species group, whose members are small freshwater fishes that inhabit streams and rivers in eastern Myanmar and western and southern Thailand. A phylogenetic analysis using molecular genetic markers demonstrated the monophyly of this group; a combined genetic and morphological analysis revealed the inclusion of at least twelve species. They share the presence of a pair of black marks on the lower lip, one on each side of the median interruption (these marks may be reduced to few melanophores or even missing in some individuals). Additionally, all species share a small body size (max. 60 mm SL), an incomplete lateral line reaching at most to vertical through anal-fin base, and the absence of sexual dimorphism. Each of the 12 species is diagnosed by a unique combination of character states in fin ray numbers, anus position, presence/absence of an axillary pelvic lobe, and colour pattern. The distribution areas of several species overlap and five cases of syntopic occurrence are known. Five unnamed species are described herein.
... Although the genetic data for cox1 gene are not available for I. telanganaensis, both I. neeleshi and I. rajeevi are distinct from it in cytb gene sequence. For loaches, the interspecific genetic distances for cytb gene have been observed to range from 2.0% in Balitoridae (Tang et al. 2006) and 3.0% in Cobitidae (Perd-ices et al. 2018) to 5.4% in Nemacheilidae (Bohlen et al. 2020). As a result, the pairwise genetic distance of more than 5.7% between I. neeleshi from all its known congeners and 11.8% between I. rajeevi from all its congeners is high. ...
The hill stream loach genus Indoreonectes is endemic to peninsular India south of the Satpura hill ranges and is represented by three species I. evezardi , I. keralensis and I. telanganaensis . Indoreonectes evezardi has been suggested as a species complex based on recent genetic studies; however, due to lack of type material the species delimitation has been difficult. Here we redescribe I. evezardi collected from its type locality and describe two new species from the northern Western Ghats of India. Indoreonectes neeleshi , described from Mula River tributary of Godavari river system, can be diagnosed from all its congeners based on a combination of characters: inner rostral barbel reaching middle of nostril; maxillary barbel reaching midway between eye and posterior border of operculum; dorsal hump behind nape; bars on lateral side of the body wider than inter-bar space; total vertebrae 35 and dorsal fin insertion between 13 th and 14 th abdominal vertebrae. Indoreonectes rajeevi , described from Hiranyakeshi River of the Krishna river system, differs from all its congeners based on a combination of characters: inner rostral barbel reaching anterior margin of eye; maxillary barbel reaching posterior border of operculum; conspicuous black markings on lower lip, dorsal hump absent; total vertebrae 36 and dorsal fin insertion between 12 th and 13 th abdominal vertebrae. Further, I. neeleshi differs from its congeners by the raw genetic distance of 6.8–14.4% for the cox1 gene and 5.7–16.2% for the cytb gene, while I. rajeevi differs from its congeners by the raw genetic distance of 10.9–14.0% for the cox1 gene and 11.8–15.8% for the cytb gene.
... Examining the R. pulmo timetree (Figure 6), it took as much as 740,000 years (from 5.33 to 4.59 mya, Figure 6) for the revived MS to stabilize and to produce some environmental (Woodruff, 2003) that indicates that sea levels were 100 m above the present sea level during the early Pliocene (5.5-4.5 mya). Such a big decline in the sea level ending at the time we see genetic divergence at 4.59 mya could be a result of an environmental change and indicative of a long dry period (Bohlen et al., 2020;Woodruff, 2003). ...
Jellyfish are useful genetic indicators for aquatic ecosystems as they have limited mobility and are highly exposed to the water column. By using comparative genomics and the molecular clock (timetree) of Rhizostoma pulmo, we revealed a divergence point between the East and West Mediterranean Sea (MS) populations that occurred 4.59 million years ago (mya). It is suggested that the two distinct ecological environments we know today were formed at this time. We propose that before this divergence, the highly mixed Atlantic and Mediterranean waters led to the wide dispersal of different species including R. pulmo. At 4.59 mya, the Western and Eastern MS were formed, indicating the possibility of a dramatic environmental event. For the first time, we find that for the jellyfish we examined, the division of the MS in east and west is not at the Straits of Sicily as generally thought, but significantly to the east. Using genomics of the Aurelia species, we examined contemporary anthropogenic impacts with a focus on migration of scyphozoa across the Suez Canal (Lessepsian migration). Aurelia sp. is among the few scyphozoa we find in both the MS and the Red Sea, but our DNA analysis revealed that the Red Sea Aurelia sp. did not migrate or mix with MS species. Phyllorhiza punctata results showed that this species was only recently introduced to the MS as a result of anthropogenic transportation activity, such as ballast water discharge, and revealed a migration vector from Australia to the MS. Our findings demonstrate that jellyfish genomes can be used as a phylogeographic molecular tool to trace past events across large temporal scales and reveal invasive species introduction due to human activity.
... It is possible that records of L. "doriae" from extreme southern Thailand and Peninsular Malaysia are actually L. pseudodoriae sp. nov., and that the two species are separated by the Khlong Mauri Fault south of the Isthmus of Kra [63,64], a known historical barrier to dispersal and stimulant for vicariant speciation in many organisms (e.g., [65][66][67]). Additional field sampling for L. doriae and L. pseudodoriae sp. ...
Simple Summary
New species of frogs continue to be discovered at a rapid rate in Southeast Asia, often as a result of reexamining populations of geographically widespread species using new molecular and bioacoustic tools. Here, we show that members of the fanged frog genus Limnonectes from Ko Pha-ngan, Ko Samui, and Ko Lanta Yai Islands in southern Thailand can be distinguished from the morphologically similar species Limnonectes doriae in molecular, advertisement call, morphometric, and qualitative morphological characters. On the basis of these multiple lines of evidence, we describe the insular populations in southern Thailand as a new species, Limnonectes pseudodoriae sp. nov. The new species occurs near small streams in low to mid-elevation forests and breeds in terrestrial nests consisting of moist, clay depressions in which the eggs and larvae develop.
Abstract
A new species in the dicroglossid frog genus Limnonectes is described from Ko Pha-ngan, Ko Samui, and Ko Lanta Yai Islands in southern Thailand. Males of Limnonectes pseudodoriae sp. nov. lack a caruncle on top of the head and very closely resemble L. doriae (Boulenger, 1887) from Myanmar and western and southern Thailand. However, the new species is distinguished from L. doriae and its congeners using an integrative taxonomic approach of morphology, mitochondrial DNA, and bioacoustics. Limnonectes pseudodoriae sp. nov. differs from L. doriae and its congeners by having a unique combination of morphological characters, including body size; skin texture of the interorbital region, dorsum, and shank; toe webbing; relative size of the inner metatarsal tubercle; and coloration of the tympanum, venter, and ova. The advertisement call of the new species is also readily differentiated from that of L. doriae in temporal parameters. Limnonectes pseudodoriae sp. nov. is highly divergent in mitochondrial DNA from L. doriae and its congeners, but its phylogenetic position within the genus is not resolved. The natural history of the new species is presented, and the geographic range of L. doriae in Thailand is clarified.
... Genetically, I. telanganaensis forms reciprocally monophyletic clade from its congeners I. evezardi and I. keralensis with genetic distance of 6.6% or more. In the case of loaches, interspecific genetic distances have been observed to be as low as 2.0% in Balitoridae (Tang et al. 2006) and 3.0% in Cobitidae (Perdices et al. 2018) to as high as 5.4% in Nemacheilidae (Bohlen et al. 2020). As a result, the genetic distance of 6.6% is consistent with the intraspecific distances associated with loach species. ...
A new species of hill-stream loach, Indoreonectes telanganaensis, is described from a seasonal tributary of the Godavari
River at Maisamma Loddi, within the Kawal Tiger Reserve, Telangana State, India. The new species is distinguished from
its congeners by a combination of characters including caudal peduncle as long as deep; eye large, its diameter about onefifth
head length; pectoral fin as long as head; nasal barbel reaching the middle of the eye; dorsal-fin origin on vertical
through pelvic-fin origin; and bars on the lateral side of the body well defined and wide. We also provide multivariate
morphometric, and DNA analysis based on the mitochondrial cytochrome b gene sequence to support the distinction of
the new species.
Eurasia has undergone substantial tectonic, geological, and climatic changes throughout the Cenozoic, primarily associated with tectonic plate collisions and a global cooling trend. The evolution of present-day biodiversity unfolded in this dynamic environment, characterised by intricate interactions of abiotic factors. However, comprehensive, large-scale reconstructions illustrating the extent of these influences are lacking. We reconstructed the evolutionary history of the freshwater fish family Nemacheilidae across Eurasia and spanning most of the Cenozoic on the base of 471 specimens representing 279 species and 37 genera plus outgroup samples. Molecular phylogeny using six genes uncovered six major clades within the family, along with numerous unresolved taxonomic issues. Dating of cladogenetic events and ancestral range estimation traced the origin of Nemacheilidae to Indochina around 48 mya. Subsequently, one branch of Nemacheilidae colonised eastern, central, and northern Asia, as well as Europe, while another branch expanded into the Burmese region, the Indian subcontinent, the Near East, and northeast Africa. These expansions were facilitated by tectonic connections, favourable climatic conditions, and orogenic processes. Conversely, aridification emerged as the primary cause of extinction events. Our study marks the first comprehensive reconstruction of the evolution of Eurasian freshwater biodiversity on a continental scale and across deep geological time.
Eurasia has undergone substantial tectonic, geological, and climatic changes throughout the Cenozoic era, primarily associated with tectonic plate collisions and a global cooling trend. The evolution of present-day biodiversity unfolded in this dynamic environment, characterised by intricate interactions of abiotic factors. However, comprehensive, large-scale reconstructions illustrating the extent of these influences are lacking. We reconstructed the evolutionary history of the freshwater fish family Nemacheilidae across Eurasia and spanning most of the Cenozoic era on the base of 471 specimens representing 279 species and 37 genera. Molecular phylogeny using 6 genes uncovered six major clades within the family, along with numerous unresolved taxonomic issues. Dating of cladogenetic events and ancestral range estimation traced the origin of Nemacheilidae to Indochina around 48 million years ago. Subsequently, one branch of Nemacheilidae colonised eastern, central, and northern Asia, as well as Europe, while another branch expanded into the Burmese region, the Indian subcontinent, the Near East, and northeast Africa. These expansions were facilitated by tectonic connections, favourable climatic conditions, and orogenic processes. Conversely, aridification emerged as the primary cause of extinction events. Our study marks the first comprehensive reconstruction of the evolution of Eurasian freshwater biodiversity on a continental scale and across deep geological time.
Eurasia has undergone substantial tectonic, geological, and climatic changes throughout the Cenozoic era, primarily associated with tectonic plate collisions and a global cooling trend. The evolution of present-day biodiversity unfolded in this dynamic environment, characterised by intricate interactions of abiotic factors. However, comprehensive, large-scale reconstructions illustrating the extent of these influences are lacking. We reconstructed the evolutionary history of the freshwater fish family Nemacheilidae across Eurasia and spanning most of the Cenozoic era. Molecular phylogeny uncovered six major clades within the family, along with numerous unresolved taxonomic issues. Dating of cladogenetic events and ancestral range estimation traced the origin of Nemacheilidae to Indochina around 48 million years ago. Subsequently, one branch of Nemacheilidae colonised eastern, central, and northern Asia, as well as Europe, while another branch expanded into the Burmese region, the Indian subcontinent, the Near East, and northeast Africa. These expansions were facilitated by tectonic connections, favourable climatic conditions, and orogenic processes. Conversely, aridification emerged as the primary cause of extinction events. Our study marks the first comprehensive reconstruction of the evolution of Eurasian freshwater biodiversity on a continental scale and across deep geological time.
Eurasia has undergone substantial tectonic, geological, and climatic changes throughout the Cenozoic era, primarily associated with tectonic plate collisions and a global cooling trend. The evolution of present-day biodiversity unfolded in this dynamic environment, characterised by intricate interactions of abiotic factors. However, comprehensive, large-scale reconstructions illustrating the extent of these influences are lacking. We reconstructed the evolutionary history of the freshwater fish family Nemacheilidae across Eurasia and spanning most of the Cenozoic era. Molecular phylogeny uncovered six major clades within the family, along with numerous unresolved taxonomic issues. Dating of cladogenetic events and ancestral range estimation traced the origin of Nemacheilidae to Indochina around 48 million years ago. Subsequently, one branch of Nemacheilidae colonised eastern, central, and northern Asia, as well as Europe, while another branch expanded into the Burmese region, the Indian subcontinent, the Near East, and northeast Africa. These expansions were facilitated by tectonic connections, favourable climatic conditions, and orogenic processes. Conversely, aridification emerged as the primary cause of extinction events. Our study marks the first comprehensive reconstruction of the evolution of Eurasian freshwater biodiversity on a continental scale and across deep geological time.
The taxonomy of the Parachela–Oxygaster–Macrochirichthys clade of Xenocyprididae has been confused since the original descriptions of Parachela oxygastroides and Parachela hypophthalmus in the mid‐19th century. The confusion seems attributable to the substantial intraspecific variation in color and other morphological characteristics of species of Oxygaster and Parachela. Morphological data on 401 specimens from throughout the range of Parachela and molecular phylogenetic analyses indicate that six available species names for Parachela are valid: Parachela cyanea, P. hypophthalmus, Parachela ingerkongi, Parachela johorensis (removed from the synonymy of P. oxygastroides), P. oxygastroides, and Parachela williaminae. In addition, two new species of Parachela, Parachela melanosticta and Parachela microlepis, are described. Chela pointoni is a synonym of P. oxygastroides, not a valid species of Oxygaster as previously hypothesized, and Parachela maculicauda is a synonym of Parachela johorensis. Considerable morphological and genetic variation is present in all well‐sampled species of Parachela.
Motivation
Phylogenetic analysis like Bayesian MCMC or bootstrapping result in a collection of trees. Trees are discrete objects and it is generally difficult to get a mental grip on a distributions over trees. Visualisation tools like DensiTree can give good intuition on tree distributions. It works by drawing all trees in the set transparently thus highlighting areas where the tree in the set agrees. In this way, both uncertainty in clade heights and uncertainty in topology can be visualised. In our experience, a vanilla DensiTree can turn out to be misleading in that it shows too much uncertainty due to wrongly ordering taxa or due to unlucky placement of internal nodes.
Results
DensiTree is extended to allow visualisation of meta-data associated with branches such as population size and evolutionary rates. Furthermore, geographic locations of taxa can be shown on a map, making it easy to visually check there is some geographic pattern in a phylogeny. Taxa orderings have a large impact on the layout of the tree set, and advances have been made in finding better orderings resulting in significantly more informative visualisations. We also explored various methods for positioning internal nodes, which can improve the quality of the image. Together, these advances make it easier to comprehend distributions over trees.
Availability
DensiTree is freely available from http://compevol.auckland.ac.nz/software/ .
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.
Western Southeast Asia is hosting one of the world’s most diverse faunas, and one of the reasons for this huge diversity is the complex geologic past of the area, increasing the frequency of isolation and expansion events over evolutionary time scale. As an example case, the present study reveals the phylogeny and biogeographic history of the Paracanthocobitis zonalternans species complex, small benthic freshwater fish (Teleostei: Nemacheilidae) that are commonly occurring across western Southeast Asia (from central Myanmar through western and southern Thailand to northern Malaysia). The group is particularly interesting since it occurs in three biogeographic subdivisions (Burmese, Indochinese, Malay/Sundaic) and across all of the major biogeographic barriers in the region. Basing on mitochondrial and nuclear sequence data of 93 samples from about 50 localities we found six major clades, most with exclusive geographic distribution. Divergence time dated the origin of the P. zonalternans species complex to early Miocene (17.8 MYA) and a biogeographic analysis identified the Tenasserim region as the ancestral region. From this region the fish spread during periods of lowered global sea level, particularly during late Miocene (11-8 MYA) northwards into all Burmese river basins and southwards into south Thailand and northern Malaysia. Besides lowered global sea level periods, local stream capture events allowed the complex to expand, e.g. into the Mae Klong basin. Strong fragmentations during periods with elevated sea level during the Pliocene and Pleistocene repeatedly restricted populations to refuges and shaped the observed major lineages. Our results document a higher diversity within the P. zonalternans species complex than formerly believed and a strong impact of global sea level on its evolutionary history. Low sea levels promoted dispersal and elevated sea levels fragmentation events. A very similar impact of sea level changes can be expected in all stationary fauna (freshwater and terrestrial) in all non-mountainous coastal regions worldwide.
Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.
There is a general consensus that the genus Schistura (Nemacheilidae), currently with 241 species, is not monophyletic. However, weak morphological synapomorphies and a lack of genetic data for most species of Schistura and their presumptive relatives have prevented meaningful diagnoses of species groups within this genus. To aid in deciphering evolutionary relationships, sequence data from two mitochondrial genes (cytochrome b and D-loop) were implemented in phylogenetic analyses for species of Schistura and other nemacheilids for which data from earlier studies and recently collected material were available. This analysis of 67 nemacheilid species, including 28 species of Schistura, provides the most comprehensive phylogeny of Nemacheilidae to date. In the phylogenetic tree for the combined data set, species of Schistura clustered in three clades. One clade contained 14 species of Schistura and Sectoria heterognathos and was sister to Homatula. A second clade of 11 species of Schistura was in a larger clade with Turcinoemacheilus kosswigi and Nemacheilus corica. The third clade contained three species, all from the Mae Khlong basin of Thailand. Taxonomic implications of these results are discussed; however, a more taxon-rich dataset and nuclear sequence data are needed before making taxonomic changes.
Fully Bayesian multispecies coalescent (MSC) methods like *BEAST estimate species trees from multiple sequence alignments. Today thousands of genes can be sequenced for a given study, but using that many genes with *BEAST is intractably slow. An alternative is to use heuristic methods which compromise accuracy or completeness in return for speed. A common heuristic is concatenation, which assumes that the evolutionary history of each gene tree is identical to the species tree. This is an inconsistent estimator of species tree topology, a worse estimator of divergence times, and induces spurious substitution rate variation when incomplete lineage sorting is present. Another class of heuristics directly motivated by the MSC avoids many of the pitfalls of concatenation but cannot be used to estimate divergence times. To enable fuller use of available data and more accurate inference of species tree topologies, divergence times, and substitution rates, we have developed a new version of *BEAST called StarBEAST2. To improve convergence rates we add analytical integration of population sizes, novel MCMC operators and other optimisations. Computational performance improved by 13.5× to 13.8× when analysing empirical data sets, and an average of 33.1× across 30 simulated data sets. To enable accurate estimates of perspecies substitution rates we introduce species tree relaxed clocks, and show that StarBEAST2 is a more powerful and robust estimator of rate variation than concatenation. StarBEAST2 is available through the BEAUTi package manager in BEAST 2.4 and above.
PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder The source code is available at https://github.com/brettc/partitionfinder.
Background:
Loaches of the family Nemacheilidae are one of the most speciose elements of Palearctic freshwater ichthyofauna and have undergone rapid ecological adaptations and colonizations. Their cytotaxonomy is largely unexplored; with the impact of cytogenetical changes on this evolutionary diversification still unknown. An extensive cytogenetical survey was performed in 19 nemacheilid species using both conventional (Giemsa staining, C- banding, Ag- and Chromomycin A3/DAPI stainings) and molecular (fluorescence in situ hybridization with 5S rDNA, 45S rDNA, and telomeric (TTAGGG)n probes) methods. A phylogenetic tree of the analysed specimens was constructed based on one mitochondrial (cytochrome b) and two nuclear (RAG1, IRBP) genes.
Results:
Seventeen species showed karyotypes composed of 2n = 50 chromosomes but differentiated by fundamental chromosome number (NF = 68-90). Nemachilichthys ruppelli (2n = 38) and Schistura notostigma (2n = 44-48) displayed reduced 2n with an elevated number of large metacentric chromosomes. Only Schistura fasciolata showed morphologically differentiated sex chromosomes with a multiple system of the XY1Y2 type. Chromomycin A3 (CMA3)- fluorescence revealed interspecific heterogeneity in the distribution of GC-rich heterochromatin including its otherwise very rare association with 5S rDNA sites. The 45S rDNA sites were mostly located on a single chromosome pair contrasting markedly with a pattern of two (Barbatula barbatula, Nemacheilus binotatus, N. ruppelli) to 20 sites (Physoschistura sp.) of 5S rDNA. The cytogenetic changes did not follow the phylogenetic relationships between the samples. A high number of 5S rDNA sites was present in species with small effective population sizes.
Conclusion:
Despite a prevailing conservatism of 2n, Nemacheilidae exhibited a remarkable cytogenetic variability on microstructural level. We suggest an important role for pericentric inversions, tandem and centric fusions in nemacheilid karyotype differentiation. Short repetitive sequences, genetic drift, founder effect, as well as the involvement of transposable elements in the dispersion of ribosomal DNA sites, might also have played a role in evolutionary processes such as reproductive isolation. These remarkable dynamics of their genomes qualify river loaches as a model for the study of the cytogenetic background of major evolutionary processes such as radiation, endemism and colonization of a wide range of habitats.
Schistura aurantiaca, new species, is described from the Mae Khlong basin in western Thailand. It is distinguished from all other species of Schistura by a unique color pattern of 3-9 orange bars on the side of the body, with the 1st bar immediately behind the head and the 2nd bar near the dorsal-fin origin and widely separated so that most of the nape and the anterior side of the body are uniformly brown. The species reaches only 41 mm SL and in-habits shallow gravel and rubble riffles in small streams.
Understanding the evolutionary history of living organisms is a central problem in biology. Until recently the ability to infer evolutionary relationships was limited by the amount of DNA sequence data available, but new DNA sequencing technologies have largely removed this limitation. As a result, DNA sequence data are readily available or obtainable for a wide spectrum of organisms, thus creating an unprecedented opportunity to explore evolutionary relationships broadly and deeply across the Tree of Life. Unfortunately, the algorithms used to infer evolutionary relationships are NP-hard, so the dramatic increase in available DNA sequence data has created a commensurate increase in the need for access to powerful computational resources. Local laptop or desktop machines are no longer viable for analysis of the larger data sets available today, and progress in the field relies upon access to large, scalable high-performance computing resources. This paper describes development of the CIPRES Science Gateway, a web portal designed to provide researchers with transparent access to the fastest available community codes for inference of phylogenetic relationships, and implementation of these codes on scalable computational resources. Meeting the needs of the community has included developing infrastructure to provide access, working with the community to improve existing community codes, developing infrastructure to insure the portal is scalable to the entire systematics community, and adopting strategies that make the project sustainable by the community. The CIPRES Science Gateway has allowed more than 1800 unique users to run jobs that required 2.5 million Service Units since its release in December 2009. (A Service Unit is a CPU-hour at unit priority).
Biogeographic boundaries are characterised by distinct faunal and floral assemblages restricted on either side, but patterns among groups of taxa often vary and may not be discrete. Historical biogeography as a consequence, while providing crucial insights into the relationship between biological diversity and earth history, has some limitations. Patterns of intraspecific molecular variation, however, may show unambiguous evidence for such historical divides, and can be used to test competing biogeographic hypotheses (often based on the dispersal-vicariance debate). Here, we utilise this method to test the hypothesis that a major biogeographic transition zone between the Sundaic and Indochinese biotas, located just north of the Isthmus of Kra in SE Asia, is the result of Neogene marine transgressions that breached the Isthmus in two locations for prolonged periods of time (>1 million year duration). Phylogeographic analyses of a freshwater decapod crustacean, the giant freshwater prawn Macrobrachium rosenbergii, strongly supports the historical existence of the more northerly postulated seaway. Results presented here highlight the power of utilising intraspecific molecular variation in testing biogeographical hypotheses.
MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g. morphological, nucleotide, and protein—and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
Availability: http://morphbank.ebc.uu.se/mrbayes
Contact: fredrik.ronquist@ebc.uu.se
*
To whom correspondence should be addressed.
Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (< 1-2 Myr) mutation rate and the low, long-term substitution rate. The relationship between the age of the calibration and the rate of change can be described by a vertically translated exponential decay curve, which may be used for correcting molecular date estimates. The phylogenetic substitution rates in mitochondria are approximately 0.5% per million years for avian protein-coding sequences and 1.5% per million years for primate protein-coding and d-loop sequences. Further analyses showed that purifying selection offers the most convincing explanation for the observed relationship between the estimated rate and the depth of the calibration. We rule out the possibility that it is a spurious result arising from sequence errors, and find it unlikely that the apparent decline in rates over time is caused by mutational saturation. Using a rate curve estimated from the d-loop data, several dates for last common ancestors were calculated: modern humans and Neandertals (354 ka; 222-705 ka), Neandertals (108 ka; 70-156 ka), and modern humans (76 ka; 47-110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution.
Advances in sequence stratigraphy and the development of depositional models have helped explain the origin of genetically
related sedimentary packages during sea level cycles. These concepts have provided the basis for the recognition of sea level
events in subsurface data and in outcrops of marine sediments around the world. Knowledge of these events has led to a new
generation of Mesozoic and Cenozoic global cycle charts that chronicle the history of sea level fluctuations during the past
250 million years in greater detail than was possible from seismic-stratigraphic data alone. An effort has been made to develop
a realistic and accurate time scale and widely applicable chronostratigraphy and to integrate depositional sequences documented
in public domain outcrop sections from various basins with this chronostratigraphic framework. A description of this approach
and an account of the results, illustrated by sea level cycle charts of the Cenozoic, Cretaceous, Jurassic, and Triassic intervals,
are presented.
The absence of obvious morphological differences between species impedes species identification in many groups of organisms. Such cryptic species appear to be particularly common in small-bodied animals, impacting species richness estimates.
In this study we aimed at characterizing the molecular diversity of the Palearctic arboreal oribatid mite species Cymbaeremaeus cymba across large parts of Europe. Phylogenetic analyses of three molecular markers, including the COI barcoding region, identified eight well supported, fairly divergent clades within C. cymba, which we consider to represent distinct species based on molecular species delimitation methods. Intraspecific variation of the COI gene was extremely low in all putative species, contradicting previous assumptions of high intraspecific diversity in oribatid mites. The frequent co-occurrence of two species on a single tree suggests an ecological micro-niche differentiation. Contrary to previous studies on oribatid mites, we find that COI is a good marker for species delimitation and its further use for barcoding of oribatids is highly recommended. Furthermore, we provide descriptions of six new Cymbaeremaeus species and designate a neotype of C. cymba.
Atyid shrimps, a key component of tropical freshwater ecosystems, face multiple anthropogenic threats and thus need special attention. With more than 300 described species, the genus Caridina is the most speciose of all the Caridea infra-order. Caridina spp. occupy diverse habitats in tropical freshwaters of the Indo-West Pacific region. Several species complexes have been recognized, based on common morphological features, but little is known about how well these morphological characteristics align with phylogenetic characteristics. Furthermore, no phylogeny of the genus Caridina published so far has provided well-resolved and supported relationships among different species, thus impeding the possibility of proposing evolutionary hypotheses. In this study we used next generation sequencing (NGS) to provide new insights into the phylogenetic relationships among the genus Caridina, focusing on two complexes: ‘Caridina nilotica’ and ‘Caridina weberi’. We collected 92 specimens belonging to these two groups from most of their known geographical range, representing 50 species, for which we sequenced seven mitochondrial genes and two nuclear markers using ion torrent NGS. We performed a phylogenetic
analysis, which yielded the first well-supported tree for the genus Caridina. On this tree were mapped the geographic ranges and the habitats used by the different species, and a time calibration was tested. We found the driving factors that most likely account for separation of clades are differences in habitat and to a lesser extent
geography. This work provides new insights into the taxonomy of this group and identifies opportunities for further studies in order to fill knowledge gaps that currently impede the management and conservation of atyid species.
Mustura celata, new genus and species, is described from small tributaries of Lake Indawgyi, Myanmar. Mustura is distinguished from other genera of Nemacheilidae by having: the male pectoral fin slanted upwards, with branched ray 1 wider than following rays, branched once and branches close together, without membrane between them except near tip; wide, thickened unculiferous pad extending along anterior branched pectoral-fin rays, covered dorsally by small conical tubercles; two air bladder capsules connected by a manubrium and posterior chamber small and circular, or absent; lower lip with wide median interruption, two halves forming an acute angle, not in contact medially, wide and fleshy medially, forming a triangular ‘cushion’, partly free from jaw and connected to throat by a frenum; suborbital flap present, with small tubercles on posterior extremity. Most species earlier placed in Physoschistura in fact belong to Mustura. Physoschistura is diagnosed by having the two halves of the air bladder capsule joined medially (without manubrium) and the posterior chamber free, well developed and in direct contact with the capsule; it presently includes only P. brunneana (type species), P. pseudobrunneana, and possibly P. elongata, P. raoi and P. rivulicola. Mustura celata is distinguished from the other species of Mustura by, among others, the colour pattern (6-10 [usually 7] very irregular blotches or bars on flank, alternating with irregular saddles); 9 + 8 branched caudal-fin rays; 8 ¹/2 branched dorsal-fin rays; lateral line complete; caudal peduncle depth 1.3-1.7 times in its length. Schistura shuensis, S. maepaiensis and S. bella belong to Mustura. Physoschistura absumbra belongs to Schistura s. l.; P. shuangjiangensis belongs to a distinct genus, apparently unnamed. Mustura, Pteronemacheilus, Physoschistura and Petruichthys seem to be closely related; they share features of the mouth morphology and unique features of the male pectoral fin and suborbital flap.
Schistura crocotula, a new species, is described from Khanan River, Prachuap Khiri Khan Province, southern Thailand. It is distinguished from other species of Schistura in Southeast Asia by a depressed head; 6-11 dark brown bars against an orange background; the first bar is the widest, two bars are under dorsal fin; interspaces are often indistinct on posterior part of body; a thick black bar at the base of the caudal fin.
Aim The aim of this review is to contribute to our understanding of the origination of the Sundaic and Indochinese biotas in Southeast Asia. Numerous unsolved problems surround the origination of the differences between these biotas and the determinants of the breadth and current position of the transition between them.
Location Literature reviews show that phytogeographical and zoogeographical transitions between the Sundaic and Indochinese subregions lie on the Thai–Malay peninsula just north of the Isthmus of Kra. A second, more widely recognized botanical transition lies 500 km further south at the Kangar–Pattani line near the Thai–Malay border.
Results The phytogeographical transition involves 575 genera of plants, and a change from wet seasonal evergreen dipterocarp rain forest to moist mixed deciduous forest. The zoogeographical transition is best characterized for forest birds, and more than half the species present in this region have species boundaries north of the Isthmus of Kra, at 11–13° N latitude. Although the phytogeographical transition is climate‐related today, and the avifaunal transition is viewed as being associated with the vegetation change, there is no obvious present day geological, physiographical or environmental feature to account for the origination of the provincial biotas. Similarly, known Neogene palaeoenvironmental changes on the tectonically stable peninsula, including those associated with periods of lower sea levels and the emergence of Sundaland, fail to account for either the origination of the provincial differences or the current position of the transition.
Main conclusions Contrary to earlier palaeogeographical reconstructions, it is suggested that Neogene marine transgressions flooded the peninsula in two areas and created circumstances leading to the biogeographical patterns of the present day. The Vail global eustatic curve, supported by the oxygen isotope record, indicates that sea levels were c. 100 m above the present‐day level during the early/middle Miocene (24–13 Ma) and again during the early Pliocene (5.5–4.5 Ma). Present topography suggests such high sea stands would have created 30–100‐km wide seaways north and south of the Nakhon si Thammarat Range in the central peninsula (southern Thailand). Geological, palaeontological and phylogenetic evidence for such hypothetical seaways is scant (there have been no focussed searches) but does not preclude their occurrence. The role of such Neogene highstands in explaining present day biogeographical patterns in Southeast Asia and elsewhere requires assessment.
The only known fossil representative of the genus Triplophysa, T. opinata from the middle-upper Miocene of Kirgizia is redescribed. It is suggested that this species is closest to the species groups
“dorsalis” and “labiata” (sensu Prokofiev, 2002, 2004a). The fossil finding clearly suggests that Triplophysa developed no later than in the middle of the Neogene.
Phylogenetic relationships and classification of nemacheiline loaches belonging to the line with lost preethmoideum I are
investigated. With consideration of the analysis of 29 apomorphous states of 23 characters, the following hypothesis of relationships
within this line is suggested: Oxynoemacheilus + Indoreonectes + Dzihunia + (Seminemacheilus (Afronemacheilus + Nun)) + Iskandaria (Paracobitis + Troglocobitis) + Metaschistura + Paraschistura + (Schistura gr. B (Acanthocobitis + Nemacheilus s. str. + Schistura gr. A)))). Revision of the generic classification of loaches of this line inhabiting water bodies from the Near East and
Ethiopia to middle Asia and the Indus upper reaches is made. Key to genera of this region is suggested. Four new genera are
described: Afronemacheilus Golubtsov and Prok., g. n. (type species A. abyssinicus), Iskandaria Prok., g. n. (type species I. kuschakewitschi), Metaschistura Prok., g. n. (type species M. cristata), and Paraschistura Prok., g. n. (type species P. sargadensis). Independence of the genera Oxynoemacheilus and Troglocobitis is confirmed. The Oriental Schistura are subdivided into two groups (A and B). Schistura gr. A form a monophyletic line with the genera Acanthocobitis and Nemacheilus s. str. It is noted that the south-China genus Homatula cannot be related to Paracobitis or Schistura as it has no ventral axillar lobe, but it may turn out to be identical to the genus Oreias from the same region.
[1] A new regional compilation of the drainage history in southeastern Tibet suggests that the modern rivers draining the plateau margin were once tributaries to a single, southward flowing system which drained into the South China Sea. Disruption of the paleo-drainage occurred by river capture and reversal prior to or coeval with the initiation of Miocene (?) uplift in eastern Tibet, including similar to 2000 m of surface uplift of the lower plateau margin since reversal of the flow direction of the Yangtze River. Despite lateral changes in course due to capture and reversal, the superposition of eastward and southward draining rivers that cross the southeastern plateau margin suggests that uplift has occurred over long wavelengths (> 1000 km), mimicking the present low-gradient topographic slope. Thus reorganization of drainage lines by capture and reversal events explains most of the peculiar patterns of the eastern plateau rivers, without having to appeal to large-magnitude tectonic shear.
After the completion of several entire genome projects and a remarkable increase in public genetic databases in the recent years the results of post-genomic analyses can facilitate a better understanding of the genomic evolution underlying the diversity of organisms and the complexity of gene function. This influx of genomic information and resources is also beneficial to the discipline of systematic biology. In this paper, we describe a set of 6 previous and 22 new PCR/sequencing primers for RAG1, Rhodopsin and four novel nuclear markers from IRBP, EGR1, EGR2B and EGR3 that we developed through an approach making use of public genetic/genomic data mining for one of the ongoing tree of life projects aimed at understanding the evolutionary relationships of the planet's largest clade of freshwater fishes — the Cypriniformes. The primers and laboratory protocols presented here were successfully tested in 33 species comprising all cypriniform family and subfamily groups. Phylogenetic performance of each gene, as well as their implications in the investigation of the evolution of cypriniform fishes were assessed and discussed.
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 freshwater fish family Botiidae is represented by seven genera on the Indian subcontinent and in East and Southeast Asia and includes diploid as well as evolutionary tetraploid species. We present a phylogeny of Botiidae including 33 species representing all described genera using the mitochondrial cytochrome b and 12s rRNA genes to reconstruct the phylogenetic relationships among the genera and to estimate the number of polyploidisation events during their evolution. Our results show two major lineages, the subfamilies Leptobotiinae with the genera Leptobotia and Parabotia and Botiinae with the genera Botia, Chromobotia, Sinibotia, Syncrossus, and Yasuhikotakia. Our results suggest that two species that were traditionally placed into the genus Yasuhikotakia form a monophyletic lineage with the species of Sinibotia. A review of the data on the ploidy level of the included species shows all diploid species to belong to Leptobotiinae and all tetraploid species to Botiinae. A single polyploidisation event can therefore be hypothesised to have occurred in the ancestral lineage leading to the Botiinae.
The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate
the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest
versions of Linux, Macintosh and Windows operating systems.
Availability: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/
Contact: clustalw{at}ucd.ie
A new loach of Schistura and comments on the genus
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