The Casiquiare river acts as a corridor between the Amazonas and Orinoco river basins: biogeographic analysis of the genusCichla

Phylogeography and population genetic structure of the cardinal tetra (Paracheirodon axelrodi) in the Orinoco basin and Negro River (Amazon basin): evaluating connectivity and historical patterns of diversification

The Neotropics contain one of the most diverse assemblages of freshwater fishes worldwide. Part of this diversity is shared between the Orinoco and Amazon basins. These basins have been separated for a long time due to the Vaupes Arch, rising between 10-11 Ma. Today, there is only one permanent connection between the Orinoco and Negro (Amazon) basins, known as the Casiquiare Canal. However, alternative corridors allowing fish dispersion between both basins have been proposed. The cardinal tetra (Paracheirodon axelrodi), the most important fish in the ornamental world market, is distributed in both basins. Here we investigated P. axelrodi phylogeography, population structure, and potential routes of migration and connectivity between the two basins. A total of 468 bp of the mitochondrial gene (COI), 555 bp of the nuclear gene fragment (MYH6), and eight microsatellite loci were analyzed. As a result, we found two major genetic clusters as the most likely scenario (K = 2), but they were not discreetly distributed between basins. A gradient of genetic admixture was observed in Cucui and São Gabriel da Cachoeira, between the upper Negro River and the upper Orinoco. Samples from the middle-lower Negro River were highly structured. Cucui (Negro basin) was more similar to the Orinoco than to the rest of the Negro basin populations. However, substructure was also observed by the discriminant analysis, fixation indices and other hierarchichal structure analyses (K = 3 - 6), showing three major geographic clusters: Orinoco, Cucui, and the remaining Negro basin. Unidirectional migration patterns were detected between basins: via Cucui toward Orinoco and via the remaining of the Negro basin toward Orinoco. Results from the Relaxed Random Walk analysis support a very recent origin of this species in the headwater Orinoco basin (Western Guiana Shield, at late Pleistocene) with a later rapid colonization of the remaining Orinoco basin and almost simultaneously the Negro River via Cucui, between 0.115 until about 0.001 Ma. Historical biogeography and population genetic patterns observed here for Cardinal tetra, seem to be better explained by river capture, physical, or ecological barriers than due to the geographic distance.

Genomic analyses of the scorpion mud turtle (Kinosternon scorpioides) (Linnaeus, 1766) in insular and continental Colombia: Evidence for multiple conservation and taxonomic units

The turtle genus Kinosternon is widespread with at least 25 species distributed from Mexico to northern Argentina. The taxonomy of this genus is controversial and requires a full revision using both morphological and molecular approaches. In this study, we did a genomic analysis on the species Kinosternon scorpioides distributed in insular and continental Colombia in order to define conservation units. Total DNA was extracted from 24 tissue samples and RADseq genotyping analysis was done. In addition, the intron R35 was amplified and sequenced for a subset of samples. A total of 35,507 SNPs combined with 1,047 bp of the intron were used for spatiotemporal colonization pattern reconstruction and phylogenetic analyses. In addition, SNPs were used for population structure inferences and allele frequency-based analyses. Reciprocal monophyly, significant differences in allele frequencies (Fst = 0.32 - 0.78), and evidence of reproductive isolation (no admixture/geneflow), indicate long-term divergence between groups (2-8 MYA), possibly due to geographical barriers. Four Evolutionarily Significant Units (ESUs) were defined within our samples. One ESU was represented by the insular subspecies K. scorpioides albogulare, found on San Andrés island, and three ESUs were defined for the subspecies K. s. scorpioides in continental Colombia: one trans-Andean, found in northwestern Colombia (Caribbean region) and two cis-Andean, found in eastern and southeastern Colombia in the Orinoco and Amazon regions, respectively. Colonization of this species occurred from an ancestral area on South of Central America region (~ 8.43 MYA), followed by an establishing of current populations on San Andrés Island and then, in the continent. First, in the Colombian Caribbean, next, in the Orinoco, and more recently, in the Amazon. We hypothesize that the emergence of the Panamá Isthmus, as well as the final uplift of the North Eastern Andes and Vaupes Arch, were key event leading to the differentiation of these ESUs. For management and conservation purposes, each of these ESUs should be considered as a separate management unit. A full revision of the taxonomy of the genus Kinosternon is warranted.

Biology of the Big-headed Amazon River Turtle, Peltocephalus dumerilianus (Schweigger, 1812) (Testudines, Pleurodira): the basal extant Podocnemididae species

We review the extent and nature of scientific knowledge of the Big-headed Amazon River Turtle, Peltocephalus dumerilianus, covering distribution, morphology, taxonomy, diet, behaviour, reproduction, and ecology. We discuss the phylogenetic position of the species and its evolutionary relationships with the other podocnemidids, comparing morphological, karyological and molecular information. Also, we describe the importance of this species and its relationship with traditional Amazonian communities, including capture techniques, uses, beliefs and taboos. Finally, we comment on the conservation status of the species and the urgent need for additional studies. Besides discussing and reinterpreting published data, we provide new information from recent genetic studies, field activities and captive observations.

Razak IH, Shahimi S, Pati S, Edinur HA, John AB, Ahmad A, Kumaran JV, Martin MB, Chong JL, Chowdhury AJK, Nelson BR. A review on introduced Cichla spp. and emerging concerns

Peacock bass (Cichla spp.) originates from the Neotropical environments of Brazil and Venezuela but, through trade and smuggling for aquarium keeping, sport fishing and aquaculture, it is now an emerging concern. Yet, less is known for Cichla spp. distribution and its ability to invade new environments. Aimed to communicate on Cichla spp. ecology, biology and introduction schemes from Scopus, Web of Science, Google Scholar and also National Centre for Biotechnology Information, this review also contains management strategies for invading fish species. While Cichla spp. can displace native fish populations, this concern is explained using ecological functions, physiological demands, direct and secondary invasion, disease tolerance and parasite spillover. Briefly, Cichla spp. has rapid embryogenesis (72 h) and matures in short periods (11-12 months), giving it an advantage to colonize new environments. With a large appetite, this true piscivore gains territorial control over water bodies by making it their feeding and nursery grounds. Perceived as an emerging concern after becoming introduced, seal-off or sport fishing were used to manage Cichla spp. but, this practice is not sustainable for the entire ecosystem. Hence, we recommend bottom-up management that involves community participation because they interact with the fish and have knowledge about their environment.

Comparative cytogenetic of six species of Amazonian Peacock bass (Cichla, Cichlinae): intrachromosomal variations and genetic introgression among sympatric species

Cytogenetic data for the genus Cichla Bloch et Schneider, 1801 are still very limited, with only four karyotype descriptions to date. The sum of the available cytogenetic information for Cichla species, points to a maintenance of the diploid number of 48 acrocentric chromosomes, considered a typical ancestral feature in cichlids. In the current study, we performed molecular and classical cytogenetic analyses of the karyotype organization of six species of Cichla, the earliest-diverging genus of Neotropical cichlids. We cytogenetically analysed Cichla kelberi Kullander et Ferreira, 2006, Cichla monoculus Agassiz, 1831, Cichla piquiti Kullander et Ferreira, 2006, Cichla temensis Humboldt, 1821, Cichla vazzoleri Kullander et Ferreira, 2006 and Cichla pinima Kullander et Ferreira, 2006, including three individuals that showed mixed morphological characteristics, likely from different species, suggesting they were hybrid individuals. All individuals analysed showed 2n = 48 acrocentric chromosomes, with centromeric heterochromatic blocks on all chromosomes and a terminal heterochromatic region on the q arm of the 2^nd pair. Mapping 18S rDNA gave hybridization signals, correlated with the nucleolus organizer regions, on the 2^nd pair for all analyzed individuals. However, we found distinct patterns for 5S rDNA: interstitially at the proximal position on 6^th pair of four species (C. kelberi, C. pinima, C. piquiti and C. vazzoleri), and on the distal of the 4^th pair in two (C. monoculus and C. temensis). Accordingly, we present here new data for the genus and discuss the evolutionary trends in the karyotype of this group of fish. In addition, we provide data that supports the occurrence of hybrid individuals in the Uatumã River region, mainly based on 5S rDNA mapping.

Using community phylogenetics to assess phylogenetic structure in the Fitzcarrald region of Western Amazonia

ABSTRACT Here we explore the use of community phylogenetics as a tool to document patterns of biodiversity in the Fitzcarrald region, a remote area in Southwestern Amazonia. For these analyses, we subdivide the region into basin-wide assemblages encompassing the headwaters of four Amazonian tributaries (Urubamba, Yuruá, Purús and Las Piedras basins), and habitat types: river channels, terra firme (non-floodplain) streams, and floodplain lakes. We present a robust, well-documented collection of fishes from the region including 272 species collected from 132 field sites over 63 field days and four years, comprising the most extensive collection of fishes from this region to date. We conduct a preliminary community phylogenetic analysis based on this collection and recover results largely statistically indistinguishable from the random expectation, with only a few instances of phylogenetic structure. Based on these results, and of those published in other recent biogeographic studies, we conclude that the Fitzcarrald fish species pool accumulated over a period of several million years, plausibly as a result of dispersal from the larger species pool of Greater Amazonia.

On the importance of geographic and taxonomic sampling in phylogeography: A reevaluation of diversification and species limits in a Neotropical thrush (Aves, Turdidae)

Phylogeographic studies seeking to describe biogeographic patterns, infer evolutionary processes, and revise species-level classification should properly characterize the distribution ranges of study species, and thoroughly sample genetic variation across taxa and geography. This is particularly necessary for widely distributed organisms occurring in complex landscapes, such as the Neotropical region. Here, we clarify the geographic range and revisit the phylogeography of the Black-billed Thrush (Turdus ignobilis), a common passerine bird from lowland tropical South America, whose evolutionary relationships and species limits were recently evaluated employing phylogeographic analyses based on partial knowledge of its distribution and incomplete sampling of populations. Our work employing mitochondrial and nuclear DNA sequences sampled all named subspecies and multiple populations across northern South America, and uncovered patterns not apparent in earlier work, including a biogeographic interplay between the Amazon and Orinoco basins and the occurrence of distinct lineages with seemingly different habitat affinities in regional sympatry in the Colombian Amazon. In addition, we found that previous inferences about the affinities and taxonomic status of Andean populations assumed to be allied to populations from the Pantepui region were incorrect, implying that inferred biogeographic and taxonomic scenarios need re-evaluation. We propose a new taxonomic treatment, which recognizes two distinct biological species in the group. Our findings illustrate the importance of sufficient taxon and geographic sampling to reconstruct evolutionary history and to evaluate species limits among Neotropical organisms. Considering the scope of the questions asked, advances in Neotropical phylogeography will often require substantial cross-country scientific collaboration.

One species or four? Yes!...and, no. Or, arbitrary assignment of lineages to species obscures the diversification processes of Neotropical fishes

Species are fundamental units in many biological disciplines, but there is continuing disagreement as to what species are, how to define them, and even whether the concept is useful. While some of this debate can be attributed to inadequate data and insufficient statistical frameworks in alpha taxonomy, an equal part results from the ambiguity over what species are expected to represent by the many who use them. Here, mtDNA data, microsatellite data, and sequence data from 17 nuclear loci are used in an integrated and quantitative manner to resolve the presence of evolutionary lineages, their contemporary and historical structure, and their correspondence to species, in a species complex of Amazonian peacock "bass" cichlids (Cichla pinima sensu lato). Results suggest that the historical narrative for these populations is more complex than can be portrayed by recognizing them as one, two, or four species: their history and contemporary dynamics cannot be unambiguously rendered as discrete units (taxa) at any level without both choosing the supremacy of one delimitation criterion and obscuring the very information that provides insight into the diversification process. This calls into question the utility of species as a rank, term, or concept, and suggests that while biologists may have a reasonable grasp of the structure of evolution, our methods of conveying these insights need updating. The lack of correspondence between evolutionary phenomena and discrete species should serve as a null hypothesis, and researchers should focus on quantifying the diversity in nature at whatever hierarchical level it occurs.

Molecular and morphological differentiation between two Miocene-divergent lineages of Amazonian shrimps, with the description of a new species (Decapoda, Palaemonidae, Palaemon)

Palaemoncarteri (Gordon, 1935) and Palaemonivonicus (Holthuis, 1950) are morphologically similar species of South American freshwater shrimps. Past studies have questioned the taxonomic status of both species, which are supposed to have partially sympatric geographic distributions in the Amazon basin. We analyzed a 550 bp fragment of the mitochondrial 16S rRNA gene from these Amazonian Palaemon species as well as from 11 palaemonids as the outgroup. Additionally, we checked diagnostic characters of the genus and family as well as other morphological characters that have been little explored before. Palaemoncarteri and Palaemonivonicus are allocated in two sister lineages, with wide genetic divergence and little morphological differentiation. The divergence time between these lineages was estimated as approximately 10 million years ago. Both molecular and morphological data support the taxonomic validity of both Palaemoncarteri and Palaemonivonicus, refuting the hypothesis of synonymy. In addition, a new species, Palaemonyunasp. n., closely related to Palaemonivonicus, is described. Our findings indicate that these species can be differentiated using the projection of the anterolateral margin and anterolateral spine of the first antennular segment, shape of the rostrum, and relative size of the appendix masculina.

A time-calibrated, multi-locus phylogeny of piranhas and pacus (Characiformes: Serrasalmidae) and a comparison of species tree methods

The phylogeny of piranhas, pacus, and relatives (family Serrasalmidae) was inferred on the basis of DNA sequences from eleven gene fragments that include the mitochondrial control region plus 10 nuclear genes (two exons and eight introns). The new data were obtained for a representative sampling of 53 specimens, collected from all major South American rivers, accounting for over 40% of the valid species and all genera excluding Utiaritichthys. Two fossil calibration points and relaxed-clock Bayesian analyses were used to estimate the timing of diversification. The new multilocus dataset also is used to compare several species-tree approaches against the results obtained using the concatenated alignment analyzed under maximum likelihood and Bayesian inference. Individual gene trees showed substantial topological discordance, but analyses based on concatenation and Bayesian and maximum likelihood-based species trees approaches converged onto a single phylogeny. The resulting phylogenetic hypothesis is robust and supports a division of the family into three major clades, consistent with previous results based on mitochondrial DNA alone. The earliest branching event separated a "pacu" clade (Colossoma, Mylossoma and Piaractus) from the rest of the family in the Late Cretaceous (over 68 Ma). The other two clades, that contain most of the diversity, are formed by the "true piranhas" (Metynnis, Pygopristis, Pygocentrus, Pristobrycon, Catoprion, and Serrasalmus) and the Myleus-like pacus (the Myleus clade). The "true" piranha clade originated during the Eocene (∼53 Ma) but the most recent diversification of flesh-eating piranhas within the genera Serrasalmus and Pygocentrus did not start until the Miocene (∼17 Ma). A comparison of species tree approaches indicates that most methods tested are consistent with results obtained by concatenation, suggesting that the gene-tree incongruence observed is mild and will not produce misleading results under simple concatenation analysis. Non-monophyly of several genera (Pristobrycon, Tometes, Myloplus, Mylesinus) and putative species (Serrasalmus rhombeus) was obtained, suggesting that further study of this family is necessary.

First record of the freshwater copepod Eucyclops titicacae Kiefer, 1957, new rank (Copepoda, Cyclopoida) in Colombia

The freshwater cyclopoid copepod Eucyclops titicacaeKiefer, 1957, new rank, was previously known as a subspecies of E. neumani (Pesta, 1927). Hitherto, it was recorded only from Lake Titicaca in Peru and Lake Valencia in Venezuela. This species is here recorded from Laguna Navío Quebrado, La Guajira, northern Colombia. This is the first record of E. titicacae in Colombia and the third locality in which this species has been reported from. We provide comparative data on the morphology of this copepod. The Colombian specimens have the combination of diagnostic features of E. neumani titicacae as reported in both the original description and subsequent taxonomical accounts, including: 1) spinules on caudal rami not reaching halfway the outer margin; 2) caudal rami length/width ratio= 6.0; 3) length/width ratio of third endopodal segment of fourth leg=1.66; 4) inner spine of fifth leg being shorter than the two adjacent setae. The consistent morphologic differences and the isolation of E. neumani titicacae with respect to E. neumani neumani, each related to a different biogeographic subregion in South America, support the notion that these are two separate species, E. neumani and E. titicacae. Considering this interesting addition, the number of species of Eucyclops known from Colombia increases to 8; a key for the identification of these species is also provided.

Phylogeographical patterns shed light on evolutionary process in South America

The South American continent is composed of several biogeographical regions harbouring the highest biodiversity on the globe, encompassing five of the world's biodiversity 'hot spots'. Nonetheless, the patterns and processes responsible for shaping its astonishing species diversity are largely unknown. Here, we present a review of current South American phylogeographical knowledge based on published articles on this topic. An appraisal of the literature reveals emerging phylogeographical patterns in the biota of South America. The striking phylogeographical divergence observed among organism lineages in South American studies is suggestive of high levels of undocumented species diversity. The interplay between Pleistocene climatic oscillations and Pliocene/Miocene orogenic events has contributed to shaping the current diversity and distribution of modern lineages in both the tropical and temperate regions of South America. Although older divergence times were observed for a range of species, most herpetofauna underwent an intraspecific lineage split much earlier than other organisms. The geographical ranges of species associated with forest habitats were reduced mainly during glacial cycles, whereas species associated with open vegetation domains have shown variable responses to climatic oscillations. The results suggest a highly complex mosaic of phylogeographical patterns in South America. We suggest future research directions to promote a better understanding of the origin and maintenance of the South American biota.

Simultaneous delimitation of species and quantification of interspecific hybridization in Amazonian peacock cichlids (genus cichla) using multi-locus data

Background

Introgression likely plays a significant role in evolution, but understanding the extent and consequences of this process requires a clear identification of species boundaries in each focal group. The delimitation of species, however, is a contentious endeavor. This is true not only because of the inadequacy of current tools to identify species lineages, but also because of the inherent ambiguity between natural populations and species paradigms. The result has been a debate about the supremacy of various species concepts and criteria. Here, we utilized multiple separate sources of molecular data, mtDNA, nuclear sequences, and microsatellites, to delimit species under a polytypic species concept (PTSC) and estimate the frequency and genomic extent of introgression in a Neotropical genus of cichlid fishes (Cichla). We compared our inferences of species boundaries and introgression under this paradigm to those when species are identified under a diagnostic species concept (DSC).

Results

We find that, based on extensive molecular data and an inclusive species concept, 8 separate biological entities should be recognized rather than the 15 described species of Cichla. Under the PTSC, fewer individuals are expected to exhibit hybrid ancestry than under the DSC (~2% vs. ~12%), but a similar number of the species exhibit introgression from at least one other species (75% vs. 60%). Under either species concept, the phylogenetic breadth of introgression in this group is notable, with both sister species and species from different major mtDNA clades exhibiting introgression.

Conclusions

Introgression was observed to be a widespread phenomenon for delimited species in this group. While several instances of introgressive hybridization were observed in anthropogenically altered habitats, most were found in undisturbed natural habitats, suggesting that introgression is a natural but ephemeral part of the evolution of many tropical species. Nevertheless, even transient introgression may facilitate an increase in genetic diversity or transfer of adaptive mutations that have important consequences in the evolution of tropical biodiversity.

Color pattern variation in Cichla temensis (Perciformes: Cichlidae): resolution based on morphological, molecular, and reproductive data

Morphological variants of Cichla temensis, readily differentiated by their striking color pattern differences, are found in several Amazon basin flood pulse river systems. The adult variants have at times been thought to represent different species or sexual dimorphism. A three part study was performed in two regions in Brazil (rio Igapó Açú and rio Caures) to elucidate the nature of the variants. In part one; selected diagnostic morphometric characters were compared intraspecifically among the variants and interspecifically with C. monoculus and C. orinocensis. All of the C. temensis variants were found to differ significantly from their sympatric congeners while not differing among each other. In part two, mitochondrial DNA samples were compared intraspecifically among the variants and interspecifically with their sympatric congeners. There were no diagnostic molecular synapomorphies that would unambiguously distinguish the variants and all C. temensis variants were clearly diagnosable and divergent from their sympatric congeners. In part three, color pattern variation in both sexes was compared to a gonadosomatic index (GSI). A significant correlation between color pattern variation and gonadosomatic index was found. The results of this study demonstrate that Cichla temensis variants are confirmed to be members of a single species and that the variation does not represent a sexual dimorphism. The color pattern variation is a cyclically occurring secondary sexual characteristic and is indicative of the specific degree of an individual's seasonal sexual maturation.

A molecular perspective on systematics, taxonomy and classification amazonian discus fishes of the genus symphysodon

With the goal of contributing to the taxonomy and systematics of the Neotropical cichlid fishes of the genus Symphysodon, we analyzed 336 individuals from 24 localities throughout the entire distributional range of the genus. We analyzed variation at 13 nuclear microsatellite markers, and subjected the data to Bayesian analysis of genetic structure. The results indicate that Symphysodon is composed of four genetic groups: group PURPLE—phenotype Heckel and abacaxi; group GREEN—phenotype green; group RED—phenotype blue and brown; and group PINK—populations of Xingú and Cametá. Although the phenotypes blue and brown are predominantly biological group RED, they also have substantial contributions from other biological groups, and the patterns of admixture of the two phenotypes are different. The two phenotypes are further characterized by distinct and divergent mtDNA haplotype groups, and show differences in mean habitat use measured as pH and conductivity. Differences in mean habitat use is also observed between most other biological groups. We therefore conclude that Symphysodon comprises five evolutionary significant units: Symphysodon discus (Heckel and abacaxi phenotypes), S. aequifasciatus (brown phenotype), S. tarzoo (green phenotype), Symphysodon sp. 1 (blue phenotype) and Symphysodon sp. 2 (Xingú group).

Guianacara dacrya, a new species from the rio Branco and Essequibo River drainages of the Guiana Shield (Perciformes: Cichlidae)

A new species of Guianacara is described from tributaries of the Essequibo River and the rio Branco in Guyana and northern Brazil. Guianacara dacrya, new species, can be diagnosed from all congeners by the possession of a unique infraorbital stripe and by the shape of the lateral margin of the lower pharyngeal jaw tooth plate. Guianacara dacrya can be further distinguished from G. geayi, G. owroewefi, G. sphenozona and G. stergiosi by the possession of a thin midlateral bar, from G. cuyunii by the possession of dusky branchiostegal membranes and from G. oelemariensis by the possession of two supraneurals. This species differs from most congeners by the presence of white spots on the spiny portion of the dorsal fin, the placement of the midlateral spot, the presence of filaments on the dorsal, anal and in rare cases the caudal-fin and from at least the Venezuelan species by several morphometric variables. Guianacara dacrya is known from the Essequibo, Takutu and Ireng River basins of Guyana and possibly from the rio Uraricoera in the rio Branco basin in Brazil. A key to the species is provided.