Historical biogeography and molecular systematics of the Indo-Pacific genus Dascyllus (Teleostei: Pomacentridae)

The phylogeographical and systematic relationships among species in the tropical marine fish genus Dascyllus were inferred using mitochondrial DNA (mtDNA) sequence data. Although our results were generally consistent with previously published phylogenies based on both morphological and mitochondrial data, our broad taxonomic and geographical sampling design revealed novel insights into the phylogenetic history of Dascyllus that had escaped previous notice. These results include: (a) the polyphyletic nature of D. reticulatus mtDNAs, representing two divergent and geographically separated lineages, one shared with D. flavicaudus and the second forming the sister lineage of D. carneus; (b) the paraphyly of D. trimaculatus relative to the closely related D. abisella; and (c) phylogeographical structure within the widespread taxa D. aruanus and D. trimaculatus. Application of a molecular clock permits us to posit a causative role for tectonic and oceanic changes regarding some Dascyllus speciation events. Finally, we mapped body size and the presence or absence of protogynous sex change on the mtDNA tree, and tested published hypotheses regarding determinants of the evolution of mating system and protogyny in the genus. Our data rejected a model based on body size but not one based on phylogenetic inertia. The ability to change sex arose once in the ancestor to the entire genus, and was lost once in the ancestor of the D. trimaculatus complex. For taxa that are as geographically widespread as many Indo-Pacific genera, this study highlights the importance of adequate geographical sampling when inferring patterns of species diversification and life history evolution.     

Phylogenetic systematics and historical biogeography of the Neotropical electric fish Sternopygus (Teleostei: Gymnotiformes)

Interrelationships among 10 extant species of the Neotropical electric fish Sternopygus are inferred from phylogenetic analysis of 66 morphological characters, including features of pigmentation, body proportions, meristics and osteology. A total of 287 lots containing 677 specimens were examined. The important findings of this study are: (1) S. branco is the most basal species unique among congeners in being restricted to whitewater rivers in the Central Amazon Basin, (2) S. sp. ‘cau’ from the Rio Caura of Venezuela is the sister taxon to (S. obtusirostris + S. astrabes), (3) S. castroi is a junior synonym of S. astrabes, (4) S. macrurus is the sister taxon to (S. arenatus + S. xingu + S. aequilabiatus species group) and (5) S. arenatus is the sister taxon to (S. xingu + S. aequilabiatus species group). A key to the adults of Sternopygus species is provided. Several features of S. astrabes previously thought to be plesiomorphic are now considered derived, including: short body cavity, paedomorphic cranial osteology, and the habitat restriction to terra firme streams. Sternopygus species assemblages in the Pacific (trans‐Andean) and Atlantic (cis‐Andean) slopes of northwestern South America are not monophyletic and do not result exclusively from local or regional radiations. The clade composed of S. macrurus, S. arenatus, S. xingu and the S. aequilabiatus species group is inferred to predate the Middle Miocene uplift of the Eastern Cordillera (c. 11.8–12.2 Ma). As currently recognized S. macrurus is the most widely distributed and most eurytopic gymnotiform species, inhabiting all hydrogeographical regions of tropical South America and most lowland aquatic habitats. Other Sternopygus species have much more restricted geographic and ecological distributions. Perceptions of phylogenetic patterns in Sternopygus are shown to be highly sensitive to taxon sampling.     

Biogeographical revision of Argentina (Andean and Neotropical Regions): an analysis using freshwater fishes

Aim  To provide an objective geographic framework displaying the distribution patterns of freshwater fishes from Argentina.
Location  Argentina, southern South America.
Methods  Parsimony analysis of endemicity (PAE) and similarity and cluster analyses were applied to presence and absence data on 440 fish species from 52 localities in Argentina. Both 50% majority consensus and strict consensus analyses were undertaken in the first case, and the Jaccard similarity index was used in the second.
Results  Five ichthyogeographic provinces are described based on a PAE of the 52 localities. A cluster analysis provided similar results.
Main conclusions  The following zoogeographic provinces are proposed for Argentine freshwater fish fauna following the International Code of Area Nomenclature: Andean Cuyan, Patagonian, Aymaran, Great Rivers and Pampean. The former two are placed within the Andean Subregion of the Austral Region, and the latter three within the Neotropical Subregion of the Holotropical Region. These provinces, based on results coinciding with PAE and cluster analysis, represent the first classification of Argentine provinces based on objective methods. Some small regions of endemism and some localities remain separated from the proposed regions. The new scheme includes valuable empirical information from previous schemes, and is in agreement with ecological zones and other environmental arrangements proposed earlier.     

Integrative taxonomy of calcareous sponges (subclass Calcinea) from the Peruvian coast: morphology,molecules, and biogeography

Understanding of evolution and systematics of Calcarea (Porifera) have not yet met a corresponding increase in the knowledge of diversity and distribution of these sponges in several parts of the world. Peru is an emblematic example of this lack of taxonomic knowledge, as only three shallow‐water species of sponges have hitherto been reported from its 3000 km coast. With the aim of studying sponges of Peru, an integrative taxonomy approach (morphology, molecules, and biogeography) was used in order to achieve sound species identifications. The first findings of Peruvian calcareous sponges are presented here. Eight species are described in the subclass Calcinea, of which five are new to science. The retrieved biogeographical patterns are either locally endemic, widespread, or discontinuous over large areas. Clathrina antofagastensis was previously known from Chile, while C. aurea and Ernstia tetractina had been reported from the Atlantic (Brazil), and thus represent the first genetically confirmed tropical amphi‐American distributions of species not yet found on both sides of the Isthmus of Panama. Our results reveal a richer Tropical East Pacific sponge fauna than the Warm Temperate South‐Eastern Pacific one. © 2015 The Linnean Society of London     

Comparative morphology,phylogenetic relationships,and historical biogeography of plesiolebiasine seasonal killifishes (Teleostei: Cyprinodontiformes: Rivulidae)

Phylogenetic and biogeographical analyses were performed for the Plesiolebiasini, a group of 20 small and rare species of South American annual killifishes, some threatened with extinction, occurring in river basins of Brazil, Bolivia, Paraguay, and Argentina. The results of a maximum parsimony analysis of 142 morphological characters highly corroborate monophyly of the Plesiolebiasini. Monophyly of each plesiolebiasine genus is supported and Plesiolebias is hypothesized to be the sister group to a clade comprising the remaining plesiolebiasine genera (Papiliolebias, Pituna, Maratecoara, and Stenolebias), corroborating studies based on mitochondrial genes. The phylogenetic analysis supports sister group relationships between Papiliolebias and the clade containing Pituna, Maratecoara, and Stenolebias, and between Maratecoara and Stenolebias. The biogeographical analysis indicates a complex historical biogeographical scenario for plesiolebiasines. A vicariance event between the western Paraguay area and northern river basins may be related to the isolation of the Chaco region from the Amazon between the Late Oligocene and Early Miocene. A vicariance event involving the Paraguay River basin and northern rivers, and the multiple occurrence of area hybridism along the Araguaia depression are tentatively identified as a consequence of tectonic subsidence events occurring during the Pleistocene. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 162 , 131–148.     

Phylogeography of the flag cabrilla Epinephelus labriformis (Serranidae): implications for the biogeography of the Tropical Eastern Pacific and the early stages of speciation in a marine shore fish

Aim To examine the role of previously described biogeographical boundaries in shaping phylogeographical relationships within and among two putative eastern Pacific sibling species, the flag cabrilla, Epinephelus labriformis and the Clipperton grouper, Epinephelus clippertonensis (Serranidae). Location Tropical Eastern Pacific (TEP). Methods Sequence data from the mitochondrial cytochrome b gene were obtained from samples throughout the range of the species. Coalescence analysis, mismatch distributions and an analysis of molecular variance (amova ) were used to infer population differentiation. Results Overall, 49 haplotypes were found among 304 specimens, and there was significant structure corresponding to geographical locality (amova , Φ_ct = 0.198, P < 0.001; Φ_st = 0.207, P < 0.001; F_st = 0.169, P < 0.001; F_ct = 0.151, P = 0.036). Coalescence analysis indicates a population expansion at Clipperton Atoll during the mid‐Pleistocene. Main conclusions Our results suggest that previously described barriers to dispersal along the mainland of the TEP may not impinge on the dispersal ability of marine species, such as these groupers, that have long‐lived pelagic larvae. In contrast, gene flow between mainland and island populations of the readily distinguishable morphospecies E. labriformis and E. clippertonensis is restricted. The low level of genetic differentiation between the two species indicates that changes in external colour patterns may evolve more rapidly than genetic markers commonly used to delimit species boundaries. Thus a combination of colour differences and a lack of reciprocal monophyly may act as good indicators of incipient speciation in the marine environment.     

Comparative historical biogeography of Plateumaris leaf beetles (Coleoptera: Chrysomelidae) in Japan: interplay between fossil and molecular data

Aim In an attempt to use molecular and fossil data interactively in historical biogeography, we studied the phylogeography of five Plateumaris leaf beetles in Japan using mitochondrial cytochrome oxidase subunit I (COI) sequence data to explore interspecific differences in phylogeographical patterns and estimate the timings of colonization and geographical differentiation. Location A total of 461 beetles from five species on Hokkaido, Honshu and Kyushu islands of Japan were analysed with 117 beetles from three conspecies and two congeners from the mainland (Russia, including Sakhalin; Korea; Mongolia; Belgium; France; hereafter, the continent). Methods Using the sequence data from a 750‐bp portion of the COI gene, we studied the phylogeny of COI haplotypes, intraspecific population differentiation using analysis of molecular variance and the Mantel test, and intraspecific phylogeography using nested clade analysis. In addition, divergence times between the continental and Japanese lineages, as well as among the various Japanese lineages, were estimated using a Bayesian approach with node constraints based on fossil records of extant species. Results Three widely distributed species showed different degrees of geographical differentiation corresponding to their different colonization history in Japan. Bayesian estimates of divergence time revealed that one of two endemic species, which originated before the late Pliocene, attained intraspecific differentiation through the Pliocene and Pleistocene, whereas another endemic species has been confined in one locality, and three non‐endemic species colonized Japan after the mid‐Pleistocene. Main conclusions Molecular analyses of an insect group with relatively abundant fossil data can contribute greatly to the understanding of diverse biogeographical histories of related species in a region. Bayesian estimates of divergence time could be used to assess the variable evolutionary rates of the COI gene, and may be applied to other related insect species.     

Phylogeny, diversity, and distribution inExostema (Rubiaceae): Implications of morphological and molecular analyses

The neotropical genusExostema comprises 25 species of trees and shrubs, ranging in distribution from Bolivia to Mexico and throughout the West Indies, with most species endemic to the Greater Antilles. Infrageneric relationships and species-level patterns of evolution were investigated in phylogenetic analyses using morphological, molecular, and combined data sets. All data sets resolved three main species groups which correspond to the three sections recognized byMcDowell (1996). However, the analyses of ITS sequence data placed the two South American species basal to the three main clades. Otherwise, the morphological and molecular data are highly compatible, and produce a more robust yet consistent phylogeny in the combined data analysis. Morphological evolution inExostema involves many specializations for xeric habitats, reflecting repeated ecological shifts from moist forest to exposed, seasonally dry environments during the diversification of the genus. Both moth and bee pollination syndromes are found inExostema, and shifts in pollination ecology appear pivotal to the differentiation of the three sections. Biogeographically,Exostema likely originated in South America and migrated via Central America to the Greater Antilles, where the morphological diversification and speciation are most extensive.     

A re‐examination of the molecular phylogeny and biogeography of the genus Schizothorax (Teleostei: Cyprinidae) through enhanced sampling,with emphasis on the species in the Yunnan–Guizhou Plateau,China

The mitochondrial DNA cytochrome b sequences of 36 Schizothorax species from 51 localities in the Yunnan–Guizhou Plateau (YGP) and its adjacent areas were analysed. Maximum parsimony, Maximum likelihood and Bayesian phylogenetic analyses were performed to examine the relationships of Schizothorax species. A hypothesis of the phylogenetic relationships of the species is given. A relaxed molecular clock based on Bayesian evolutionary analysis was used to tentatively calculate the divergence times of Schizothorax. Samples from the YGP were tentatively grouped into three geographically distributed clades: the Tsangpo‐Irrawaddy, the Mekong‐Salween and the Trans‐Jinsha River (including Jinsha, Red, Nanpan and Beipan Rivers). Calibration of the molecular clock revealed that two geological periods, the late Miocene about 10 million years before present (Myr BP) and the Pliocene (4.0 Myr BP), were important times in the vicariant speciation of Schizothorax. The phylogenetic history of the species is congruent with events caused by the uplift of the Tibetan Plateau and the YGP. The divergence of Schizothorax species in YGP began in the Pliocene. Our phylogenetic trees did not support the hypothesis that the paleo Jinsha River was drained through the Yangtze River‐Jianchuan Lake‐Erhai Lake to the Red River. Schizothorax in the Beipan River were derived from the Jinsha River.     

Compilation of morphological and molecular data,a necessity for taxonomy: The case of Hormogaster abbatissae sp. n. (Annelida,Clitellata, Hormogastridae)

Conflict among data sources can be frequent in evolutionary biology, especially in cases where one character set poses limitations to resolution. Earthworm taxonomy, for example, remains a challenge because of the limited number of morphological characters taxonomically valuable. An explanation to this may be morphological convergence due to adaptation to a homogeneous habitat, resulting in high degrees of homoplasy. This sometimes impedes clear morphological diagnosis of species. Combination of morphology with molecular techniques has recently aided taxonomy in many groups difficult to delimit morphologically. Here we apply an integrative approach by combining morphological and molecular data, including also some ecological features, to describe a new earthworm species in the family Hormogastridae, Hormogaster abbatissae sp. n., collected in Sant Joan de les Abadesses (Girona, Spain). Its anatomical and morphological characters are discussed in relation to the most similar Hormogastridae species, which are not the closest species in a phylogenetic analysis of molecular data. Species delimitation using the GMYC method and genetic divergences with the closest species are also considered. The information supplied by the morphological and molecular sources is contradictory, and thus we discuss issues with species delimitation in other similar situations. Decisions should be based on a profound knowledge of the morphology of the studied group but results from molecular analyses should also be considered.