Transposable elements (TEs) are mobile genetic elements in the genome and broadly distributed across both prokaryotes and eukaryotes, and play an important role in shaping the genome evolution of their hosts. hAT elements are thought to be the most widespread cut-and-paste DNA transposon found throughout the tree of life. Buster is a recently recognized family of hAT. However, the evolutionary profile of the Buster family, such as its taxonomic distribution, evolutionary pattern, and activities, remains largely unknown. We conducted a systematic analysis of the evolutionary landscape of the Buster family and found that most Buster transposons are 1.72-4.66 kilobases (kb) in length, encode 500-736-amino acid (aa) transposases and are flanked by short (10-18 bp) terminal inverted repeats (TIRs) and 8 bp target site duplications (TSDs). Buster family is widely distributed in 609 species, involving eight classes of invertebrates and most lineage of vertebrates (including mammals). Horizontal transfer events were detected across multiple phyla and classes of animals, which may have contributed to their wide distribution, and both parasites and invasive species may facilitate HT events of Buster in vertebrates. Our data also suggest that Buster transposons are young, highly active, and appear as intact copies in multiple lineages of animals. High percentages of intact copies (>30%) were identified in some Arthropoda, Actinopterygii, Agnatha, and reptile species, and some of these may be active. These data will help increase understanding of the evolution of the hAT superfamily and its impact on eukaryotic genome evolution.

DNA transposons play a significant role in shaping the size and structure of eukaryotic genomes. The Tc1/mariner transposons are the most diverse and widely distributed superfamily of DNA transposons and the structure and distribution of several Tc1/mariner families, such as DD35E/TR, DD36E/IC, DD37E/TRT, and DD41D/VS, have been well studied. Nonetheless, a greater understanding of the structure and diversity of Tc1/mariner transposons will provide insight into the evolutionary history of eukaryotic genomes. Here, we conducted further analysis of DD37D/maT and DD39D (named Guest, GT), which were identified by the specific catalytic domains DD37D and DD39D. Most transposons of the maT family have a total length of approximately 1.3 kb and harbor a single open reading frame encoding a ~ 346 amino acid (range 302-398 aa) transposase protein, flanked by short terminal inverted repeats (TIRs) (13-48 base pairs, bp). In contrast, GTs transposons were longer (2.0-5.8 kb), encoded a transposase protein of ~400 aa (range 140-592 aa), and were flanked by short TIRs (19-41 bp). Several conserved motifs, including two helix-turn-helix (HTH) motifs, a GRPR (GRKR) motif, a nuclear localization sequence, and a DDD domain, were also identified in maT and GT transposases. Phylogenetic analyses of the DDD domain showed that the maT and GT families each belong to a monophyletic clade and appear to be closely related to DD41D/VS and DD34D/mariner. In addition, maTs are mainly distributed in invertebrates (144 species), whereas GTs are mainly distributed in land plants through a small number of GTs are present in Chromista and animals. Sequence identity and phylogenetic analysis revealed that horizontal transfer (HT) events of maT and GT might occur between kingdoms and phyla of eukaryotes; however, pairwise distance comparisons between host genes and transposons indicated that HT events involving maTs might be less frequent between invertebrate species and HT events involving GTs may be less frequent between land plant species. Overall, the DD37D/maT and DD39D/GT families display significantly different distribution and tend to be identified in more ancient evolutionary families. The discovery of intact transposases, perfect TIRs, and target site duplications (TSD) of maTs and GTs illustrates that the DD37D/maT and DD39D/GT families may be active. Together, these findings improve our understanding of the diversity of Tc1/mariner transposons and their impact on eukaryotic genome evolution.

A new cyprinid gudgeon,Saurogobio punctatussp. nov., is described based on specimens collected from the Yangtze River, China. The new species can be distinguished from its congeners by differences in both morphology and the cytochromeb(cytb) gene sequence. Numerous minute blackish spots are scattered on dorsal and caudal fins inS. punctatussp. nov.v. absent in the other seven validSaurogobiospecies. The new species can be further distinguished from its congeners by the following unique combination of characters: a dorsal fin with eight branched rays; absence of scales in chest area before pectoral origin; upper and lower lips thick, covered with papillae; and a papillose mental pad approximately triangular. Morphologically, the new species most resembles the Chinese lizard gudgeonSaurogobio dabryi, but the new species lays yellowish adhesive eggsv. white pelagic eggs inS. dabryi. A phylogenetic analysis of allSaurogobiospecies based oncytbgene sequences indicated thatS. punctatussp. nov was distinctly separated from its congeners, with mean sequence divergence ranging from 12·6 to 21·0%. Therefore, molecular data further supported the distinctiveness of the new species.

Balitoridae, a family within the Cypriniformes, inhabit torrential mountain streams in Asia. Although they have long fascinated ichthyologists for their numerous adaptations to this tumultuous environment, the evolutionary history of this group remains poorly understood. In this study, we investigate the evolutionary relationships of the balitorids with particular attention to the phylogenetic placement of two balitorid species, Yaoshania pachychulis and Erromyzon kalotaenia . Both species have extremely limited distributions, they are limited to Mt. Dayaoshan of the Pearl River in China and require dedicated conservation plans. However, little is known about their evolutionary relationships to other balitorids. Here, we examined the evolutionary relationships of Y. pachychulis and E. kalotaenia to each other and other balitorids through sequencing the complete mitochondrial genomes of nine balitorid individuals. For the newly sequenced balitorids, the length of the whole mitogenome, gene arrangement and their base composition are similar to those of other bony fishes. Analyses based on these newly sequenced mitogenomes and an additional 50 previously published mitogenomes show that Y. pachychulis and E. kalotaenia cluster as different clade within the subfamily Gastromyzontinae. The genetic distance between these two species ranges from 0.127 ± 0.003 to 0.132 ± 0.004 which is slightly higher than that between some genera (e.g. the distance between Vanmanenia and Metahomaloptera is 0.127 ± 0.004). Therefore, it is reasonable to assign Y. pachychulis and E. kalotaenia to different genera. Phylogenetic signal assessment suggested that ND 1 , ND 4 and ND 5 genes as well as their concatenated subsets perform relatively well in reconstructing the Cobitoidea phylogeny. The divergence time estimation indicated that the balitorids distributed in Mt. Dayaoshan might have originated and evolved following the flattening and uplifting of the Yunnan–Guizhou Plateau during the late Miocene to late Pliocene.

Ecological speciation, which relies heavily on selection driving the emergence of new species, has become the primary paradigm through which rapid species radiations are understood. In this way, selection, particularly ecological selection, is assumed to be the driver of most species radiations. However, in many radiations, such as the radiation of Lake Malawi’s cichlids, the assumption of selection as the driver of speciation has rarely been explicitly tested, and drift, often, has completely been ignored as potential factor. In order to understand the forces driving the divergence of Lake Malawi cichlids at the microevolutionary level, we studied the genetic and phenotypic divergence of ten allopatric populations of Maylandia zebra. We estimated effective population sizes as proxy for drift. Further, we compared neutral genetic differentiation to divergence in three phenotypic traits: body size, body shape, and melanophore counts. We found small, yet significant, population differentiation in all the studied traits across most populations. Population sizes were small rendering the potential for drift to be high. However, phenotypic differentiation exceeded neutral expectations for all traits suggesting divergent local selection. Our data suggest that natural, and potentially also sexual, selection may be the dominant force driving population differentiation in Lake Malawi’s rock-dwelling cichlids, despite the potential for drift in small populations.

In this study, water temperature longitudinal and temporal patterns were investigated in four locations of the Yangtze River to identify their influence on spawning of the Chinese sturgeon (Acipenser sinensis Gray 1835). The results showed that, historically (1960-1980), the four locations, Pingshan (PS, 2,687river kilometres [rkm]), Yichang (YC, 1,640rkm), Chenglingji (CLJ, 1,265rkm), and Hukou (HK, 805rkm), all had similar average annual water temperatures (around 18.0 degrees C) but very different amplitudes: The upper two locations, PS (11.4-23.2 degrees C) and YC (9.1-25.9 degrees C), were relatively stable and had smaller amplitude than the lower two ones, CLJ (6.0-30.0 degrees C) and HK (5.9-30.8 degrees C). On the basis of the physiological effects for Chinese sturgeon, we defined three water temperature ranges: stressing (>23 degrees C), holding (23-20 degrees C), and spawning (20-16 degrees C). We found that the upper two locations with successful spawning of the Chinese sturgeon (PS and YC) had short or no stressing period but long holding and spawning periods. Currently (2013-2016), the impoundment of the Three Gorges Reservoir increases the time for water temperature decreasing to 20 degrees C at the current spawning ground (YC) in autumn, which increases the stressing and holding periods, and has significant negative impact on the spawning of Chinese sturgeon. Nonetheless, considering the very high stressing temperature and the short duration of the holding and spawning periods at CLJ and HK, we propose that YC is still the most suitable spawning location for the Chinese sturgeon.

Phenotypic differences may have genetic and plastic components. Here, we investigated the contributions of both for differences in body shape in two species of Lake Malawi cichlids using wild-caught specimens and a common garden experiment. We further hybridized the two species to investigate the mode of gene action influencing body shape differences and to examine the potential for transgressive segregation. We found that body shape differences between the two species observed in the field are maintained after more than 10 generations in a standardized environment. Nonetheless, both species experienced similar changes in the laboratory environment. Our hybrid cross experiment confirmed that substantial variation in body shape appears to be genetically determined. The data further suggest that the underlying mode of gene action is complex and cannot be explained by simple additive or additive-dominance models. Transgressive phenotypes were found in the hybrid generations, as hybrids occupied significantly more morphospace than both parentals combined. Further, the body shapes of transgressive individuals resemble the body shapes observed in other Lake Malawi rock-dwelling genera. Our findings indicate that body shape can respond to selection immediately, through plasticity, and over longer timescales through adaptation. In addition, our results suggest that hybridization may have played an important role in the diversification of Lake Malawi cichlids through creating new phenotypic variation.

Understanding the factors that regulate species diversity remains an important goal in ecology, conservation and evolutionary biology. Speciose communities, like the cichlid fishes in the East African Great Lakes, offer useful opportunities to examine these factors. For example, Lake Malawi supports well over 700 cichlid fish species which likely descended from a common ancestor within the past 2–4 million years. One consequence of this remarkable radiation is the high species diversity of Lake Malawi’s cichlid communities. However, the factors facilitating the assembly and maintenance of species rich cichlid communities have yet to be fully identified. In this study, we examine the diversity of Lake Malawi’s rock-dwelling cichlid communities and investigate the roles that several environmental variables have played in maintaining such high diversity. We surveyed 82 quadrats spanning seven sites and observed 54 species from 12 genera. Most environmental variables that we measured varied significantly within, but did not differ significantly among sampled sites, suggesting that habitat heterogeneity is locally high, but at the lake-wide scale habitats are uniformly heterogeneous. Community diversity was strongly influenced by habitat complexity, while community similarity was strongly dependent on the geographical distance between communities. At the genus level, no relationship between geographic distance and community similarity was found, but community composition was also determined by habitat complexity. Our findings demonstrate that habitat complexity predicts both cichlid species diversity and functional diversity, whereas geographic separation determines the similarities among communities at the species but not at the generic level.

We estimated the effective population sizes (Ne) and tested for short‐term temporal demographic stability of populations of two Lake Malawi cichlids: Maylandia benetos, a micro‐endemic, and Maylandia zebra, a widespread species found across the lake. We sampled a total of 351 individuals, genotyped them at 13 microsatellite loci and sequenced their mitochondrial D‐loop to estimate genetic diversity, population structure, demographic history and effective population sizes. At the microsatellite loci, genetic diversity was high in all populations. Yet, genetic diversity was relatively low for the sequence data. Microsatellites yielded mean Ne estimates of 481 individuals (±99 SD) for M. benetos and between 597 (±106.3 SD) and 1524 (±483.9 SD) individuals for local populations of M. zebra. The microsatellite data indicated no deviations from mutation–drift equilibrium. Maylandia zebra was further found to be in migration–drift equilibrium. Temporal fluctuations in allele frequencies were limited across the sampling period for both species. Bayesian Skyline analyses suggested a recent expansion of M. zebra populations in line with lake‐level fluctuations, whereas the demographic history of M. benetos could only be estimated for the very recent past. Divergence time estimates placed the origin of M. benetos within the last 100 ka after the refilling of the lake and suggested that it split off the sympatric M. zebra population. Overall, our data indicate that micro‐endemics and populations in less favourable habitats have smaller Ne, indicating that drift may play an important role driving their divergence. Yet, despite small population sizes, high genetic variation can be maintained.

Patterns of colonization and diversification on islands provide valuable insights into evolutionary processes. Due to their unique geographic position and well known history, the Galapagos Islands are an important model system for evolutionary studies. Here we investigate the evolutionary history of a winged grasshopper genus to infer its origin and pattern of colonization in the Galapagos archipelago. The grasshopper genus Sphingonotus has radiated extensively in the Palaearctic and many species are endemic to islands. In the New World, the genus is largely replaced by the genus Trimerotropis. Oddly, in the Caribbean and on the Galapagos archipelago, two species of Sphingonotus are found, which has led to the suggestion that these might be the result of anthropogenic translocations from Europe. Here, we test this hypothesis using mitochondrial and nuclear DNA sequences from a broad sample of Sphingonotini and Trimerotropini species from the Old World and New World. The genetic data show two distinct genetic clusters representing the New World Trimerotropini and the Old World Sphingonotini. However, the Sphingonotus species from Galapagos and the Caribbean split basally within the Old World Sphingonotini lineage. The Galapagos and Caribbean species appear to be related to Old World taxa, but are not the result of recent anthropogenic translocations as revealed by divergence time estimates. Distinct genetic lineages occur on the four investigated Galapagos Islands, with deep splits among them compared to their relatives from the Palaearctic. A scenario of a past wider distribution of Sphingonotus in the New World with subsequent extinction on the mainland and replacement by Trimerotropis might explain the disjunct distribution.

Genetic variation was evaluated for spotted bass (Micropterus punctulatus) at the edge of the species native range in central Texas. We analyzed mitochondrial D-Loop sequences from 64 individuals representing nine sites within the Brazos and Trinity River watersheds. Our primary objectives were to 1) compare the genetic diversity of spotted bass in central Texas to genetic diversity estimates of conspecifics in other geographic regions and to other species from similar geographic regions, to 2) determine whether there was evidence for within or between drainage genetic structure, and to 3) test whether the D-Loop sequence was a reliable marker for discriminating among native and introduced Texas micropterids. Genetic diversity was low relative to sympatric micropterids, as well as for the marker in general, but our results are similar to patterns observed for this species in Oklahoma and fit with broader multi-species patterns observed for this geographic area. AMOVA, SAMOVA, and isolation by distance analyses provided evidence that genetic differentiation exists among population groups. The sequence data suggests the D-Loop would be useful for discriminating among M. floridanus, M. salmoides, and M. dolomieu, but not among M. punctulatus, M. coosae, M. henshalli, and M. treculii.

The traits involved in sexual selection, such as male secondary sexual characteristics and female mate choice, often co-evolve which can promote population differentiation. However, the genetic architecture of these phenotypes can influence their evolvability and thereby affect the divergence of species. The extraordinary diversity of East African cichlid fishes is often attributed to strong sexual selection and thus this system provides an excellent model to test predictions regarding the genetic architecture of sexually selected traits that contribute to reproductive isolation. In particular, theory predicts that rapid speciation is facilitated when male sexual traits and female mating preferences are controlled by a limited number of linked genes. However, few studies have examined the genetic basis of male secondary sexual traits and female mating preferences in cichlids and none have investigated the genetic architecture of both jointly. In this study, we artificially hybridized a pair of behaviorally isolated cichlid fishes from Lake Malawi and quantified both melanistic color pattern and female mate choice. We investigated the genetic architecture of both phenotypes using quantitative genetic analyses. Our results suggest that 1) many non-additively acting genetic factors influence melanistic color patterns, 2) female mate choice may be controlled by a minimum of 1-2 non-additive genetic factors, and 3) F2 female mate choice is not influenced by male courting effort. Furthermore, a joint analysis of color pattern and female mate choice indicates that the genes underlying these two traits are unlikely to be physically linked. These results suggest that reproductive isolation may evolve rapidly owing to the few genetic factors underlying female mate choice. Hence, female mate choice likely played an important role in the unparalleled speciation of East African cichlid fish.

The cichlid fishes of Lake Malawi represent one of the most diverse adaptive radiations of vertebrates known. Among the rock-dwelling cichlids (mbuna), closely related sympatric congeners possess similar trophic morphologies (i.e. cranial and jaw structures), defend overlapping or adjacent territories, but can be easily distinguished based on male nuptial coloration. The apparent morphological similarity of congeners, however, leads to an ecological conundrum: theory predicts that ecological competition should lead to competitive exclusion. Hence, we hypothesized that slight, yet significant, ecological differences accompanied the divergence in sexual signals and that the divergence of ecological and sexual traits is correlated. To evaluate this hypothesis, we quantified body shape, a trait of known ecological importance, in populations of Maylandia zebra, a barred, widespread mbuna, and several sympatric nonbarred congeners. We found that the barred populations differ in body shape from their nonbarred sympatric congeners and that the direction of shape differences was consistent across all barred vs. nonbarred comparisons. Barred populations are generally deeper bodied which may be an adaptation to the structurally complex habitat they prefer, whereas the nonbarred species have a more fusiform body shape, which may be adaptive in their more open microhabitat. Furthermore, M.zebra populations sympatric with nonbarred congeners differ from populations where the nonbarred phenotype is absent and occupy less morphospace, indicating potential ecological character displacement. Mitochondrial DNA as well as published AFLP data indicated that the nonbarred populations are not monophyletic and therefore may have evolved multiple times independently. Overall our data suggest that the evolution of coloration and body shape may be coupled as a result of correlational selection. We hypothesize that correlated evolution of sexually selected and ecological traits may have contributed to rapid speciation as well as the maintenance of diversity in one of the most diverse adaptive radiations known.