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Phylogeography and species delimitation in convict cichlids (Cichlidae: Amatitlania): Implications for taxonomy and Plio-Pleistocene evolutionary history in Central America
Abstract
We investigate phylogeographic patterns and delimit species boundaries within Amatitlania, a genus of CentralAmerican cichlid fishes. Phylogenetic analyses of mitochondrial DNA sequences from 318 individuals spanningthe geographical ranges of all three currently recognized Amatitlania species strongly supported one major clade,with a relatively diverged subclade corresponding to A. kanna samples from eastern Costa Rica and Panama.Gene trees and networks revealed marked incongruences between phylogeographic structure and morpho-speciestaxonomy as a result of species-level polyphyly. Bayes factor comparisons of species delimitation modelsaccounting for incomplete lineage sorting under the multispecies coalescent decisively supported the recognitionof two distinct species within Amatitlania corresponding to Amatitlania nigrofasciata and A. kanna lineages. Theonly clearly genetically and morphologically diagnosable species was A. kanna. These results strongly suggestthat incomplete lineage sorting provides the best explanation for the polyphyly of A. kanna, whereas thepolyphyly of A. siquia is likely a result of an imperfect taxonomy. Additional insights from coalescent-dating,network, and historical demographic analyses suggested that the two species of Amatitlania diversified only sincethe early Pleistocene, and that A. nigrofasciata experienced population expansions from approximately 200 000years ago in the mid-late Pleistocene onward. We discuss implications of our results for the taxonomy andevolutionary history of Amatitlania and, more broadly, of Central American freshwater fishes.
... A. coatepeque, A. kanna, A. nigrofasciata and A. siquia. However, McMahan, Matamoros, Barraza, Kutz, and Chakrabarty (2014) identified A. coatepeque as a junior synonym of A. nigrofasciata, and recent molecular studies have shown that only two species are valid (Bagley et al., 2017). Nevertheless, the taxonomy of the genus has not been fully clarified: online platforms still list nine species under the genus (Fricke, Eschmeyer, & Van der Laan, 2019;Froese & Pauly, 2019), some of which should be moved to other genera (Schmitter-Soto, 2007). ...
... The captured specimens were identified in our laboratory based on meristic and morphometric traits. Following Bagley et al. (2017) and Schmitter-Soto (2007), we registered the number of spines and soft rays in the dorsal and anal fins (Table 1) We determined the sex of each animal based on the morphology of the genital papilla and macroscopic aspects of the gonads. Individuals of uncertain sex were classified as juveniles. ...
... SL ratio was smaller for our specimens of A. nigrofasciata (39-46%) than for A. kanna (48-58%) (Schmitter-Soto, 2007), the two valid species of the genus, according to Bagley et al. (2017). ...
Several fish species from Central America and other regions have been introduced into Brazil. In this study, we evaluated the bioecological aspects of a non‐native cichlid of the genus Amatitlania (convict cichlid) and its possible establishment in high‐altitude forest enclaves of semi‐arid Northeastern Brazil. Specimens of Amatitlania nigrofasciata (Günther, 1867) were captured in a local stream displaying abiotic conditions like those of its natural range of distribution. The individuals collected were predominantly adult, insectivorous and displayed normal length–weight relationships, although we observed some phenotypical plasticity (variation in body depth, and a morphologically abnormal dorsal fin in three cases). Our results indicate that A. nigrofasciata has successfully colonized an Atlantic forest enclave in the Brazilian semi‐arid region, making it necessary to adopt measures to prevent the species from spreading to other water bodies in the surroundings.
... In recent years, Neotropical research in the Fish Section has included the description of new species (Matamoros et al., 2012(Matamoros et al., , 2013Walsh and Chakrabarty, 2016), higher taxonomy (McMahan et al., 2015), discovery of invasives and nonnatives (Matamoros et al., 2016;Elías et al., 2018), biogeography and phylogeography (Bacon et al., 2015a(Bacon et al., , 2015bMatamoros et al., 2015;Bagley et al., 2016;McMahan et al., 2017;Ludt et al., 2015Ludt et al., , 2018Tagliacollo et al., 2017) phylogenomic research Burress et al., 2018;Alda et al., 2019), mitogenomics (Alda et al., 2017(Alda et al., , 2018, morphological studies (McMahan et al., 2017b;Evans et al., 2017) and behavior (Oldfield et al., 2015). The main focus of the LSU MNS Fish Section is to carry out collections-based research to better understand the Fish Tree of Life in order to explain Earth history and evolution. ...
... In recent years, Neotropical research in the Fish Section has included the description of new species (Matamoros et al., 2012(Matamoros et al., , 2013Walsh and Chakrabarty, 2016), higher taxonomy (McMahan et al., 2015), discovery of invasives and nonnatives (Matamoros et al., 2016;Elías et al., 2018), biogeography and phylogeography (Bacon et al., 2015a(Bacon et al., , 2015bMatamoros et al., 2015;Bagley et al., 2016;McMahan et al., 2017;Ludt et al., 2015Ludt et al., , 2018Tagliacollo et al., 2017) phylogenomic research Burress et al., 2018;Alda et al., 2019), mitogenomics (Alda et al., 2017(Alda et al., , 2018, morphological studies (McMahan et al., 2017b;Evans et al., 2017) and behavior (Oldfield et al., 2015). The main focus of the LSU MNS Fish Section is to carry out collections-based research to better understand the Fish Tree of Life in order to explain Earth history and evolution. ...
This edition in which the article is included counts with articles about 22 Brazilian fish collections and 17 other collections distributed around the world. Despite the different localities, one thing all articles have in common: our investment in sampling the neotropical fish biodiversity and an urge to discuss the slow (or rapid) dismounting of scientific collections, due to limited investment to their maintenance and care. Our former SBI President, Luiz Malabarba opens this bulletin with an article that questions the “chronicles of a death foretold” of museums and scientific collections, urging us to review our values regarding scientific and cultural patrimony.
... In recent years, Neotropical research in the Fish Section has included the description of new species (Matamoros et al., 2012(Matamoros et al., , 2013Walsh and Chakrabarty, 2016), higher taxonomy (McMahan et al., 2015), discovery of invasives and nonnatives (Matamoros et al., 2016;Elías et al., 2018), biogeography and phylogeography (Bacon et al., 2015a(Bacon et al., , 2015bMatamoros et al., 2015;Bagley et al., 2016;McMahan et al., 2017;Ludt et al., 2015Ludt et al., , 2018Tagliacollo et al., 2017) phylogenomic research Burress et al., 2018;Alda et al., 2019), mitogenomics (Alda et al., 2017(Alda et al., , 2018, morphological studies (McMahan et al., 2017b;Evans et al., 2017) and behavior (Oldfield et al., 2015) ...
... In recent years, Neotropical research in the Fish Section has included the description of new species (Matamoros et al., 2012(Matamoros et al., , 2013Walsh and Chakrabarty, 2016), higher taxonomy (McMahan et al., 2015), discovery of invasives and nonnatives (Matamoros et al., 2016;Elías et al., 2018), biogeography and phylogeography (Bacon et al., 2015a(Bacon et al., , 2015bMatamoros et al., 2015;Bagley et al., 2016;McMahan et al., 2017;Ludt et al., 2015Ludt et al., , 2018Tagliacollo et al., 2017) phylogenomic research Burress et al., 2018;Alda et al., 2019), mitogenomics (Alda et al., 2017(Alda et al., , 2018, morphological studies (McMahan et al., 2017b;Evans et al., 2017) and behavior (Oldfield et al., 2015) ...
... In recent years, Neotropical research in the Fish Section has included the description of new species (Matamoros et al., 2012(Matamoros et al., , 2013Walsh and Chakrabarty, 2016), higher taxonomy (McMahan et al., 2015), discovery of invasives and nonnatives (Matamoros et al., 2016;Elías et al., 2018), biogeography and phylogeography (Bacon et al., 2015a(Bacon et al., , 2015bMatamoros et al., 2015;Bagley et al., 2016;McMahan et al., 2017;Ludt et al., 2015Ludt et al., , 2018Tagliacollo et al., 2017) phylogenomic research Burress et al., 2018;Alda et al., 2019), mitogenomics (Alda et al., 2017(Alda et al., , 2018, morphological studies (McMahan et al., 2017b;Evans et al., 2017) and behavior (Oldfield et al., 2015). The main focus of the LSU MNS Fish Section is to carry out collections-based research to better understand the Fish Tree of Life in order to explain Earth history and evolution. ...
... In recent years, Neotropical research in the Fish Section has included the description of new species (Matamoros et al., 2012(Matamoros et al., , 2013Walsh and Chakrabarty, 2016), higher taxonomy (McMahan et al., 2015), discovery of invasives and nonnatives (Matamoros et al., 2016;Elías et al., 2018), biogeography and phylogeography (Bacon et al., 2015a(Bacon et al., , 2015bMatamoros et al., 2015;Bagley et al., 2016;McMahan et al., 2017;Ludt et al., 2015Ludt et al., , 2018Tagliacollo et al., 2017) phylogenomic research Burress et al., 2018;Alda et al., 2019), mitogenomics (Alda et al., 2017(Alda et al., , 2018, morphological studies (McMahan et al., 2017b;Evans et al., 2017) and behavior (Oldfield et al., 2015). The main focus of the LSU MNS Fish Section is to carry out collections-based research to better understand the Fish Tree of Life in order to explain Earth history and evolution. ...
... To further explore the factors that influence group mate choice, we explored the shoalmate choices of juvenile convict cichlids (Amatitlania nigrofasciata; Bagley et al., 2016;Schmitter-Soto, 2007). ...
... We studied convict cichlids, Amatitlania nigrofasciata (Günther, 1867), from laboratory-bred stocks originally purchased from commercial suppliers. Under a recent taxonomic arrangement, convict cichlids from various populations in Central America have been ascribed to various species, such as A. siquia, A. nigrofasciata, and A. kanna (Schmitter-Soto, 2007); however, subsequent genetic results suggest that this species is polytypic due to imperfect taxonomy, and it is likely that domestic stock populations, such as those used within this experiment, belong to A. nigrofasciata (Bagley et al., 2016). ...
Many animals form groups and socialize in response to evolutionary pressures such as predation, food availability, and mate acquisition. Evidence of social choice based on various phenotypic characters (Group Phenotypic Composition [GPC]) has been observed in several animal species. In addition to the physical characteristics of the social group, it is also interesting to consider how decisions of who to socialize with might be expected to change for an individual over time. Younger individuals with limited life experience may discriminate differently between social groups than older conspecifics who have had the opportunity to learn and who may be faced with different ecological or environmental pressures. Here, we used a traditional two‐choice design to explore the shoaling behavior of juvenile convict cichlids and determine whether the number of fish and/or the size/life stage of the individuals within a shoal influenced social choices. We found that juvenile convict cichlids spent more time shoaling with similarly sized juvenile individuals and also preferred to shoal with larger shoals, but not when shoals were comprised of adult fish. The size of the individuals in a shoal was a more influential factor than the size of the shoal itself. Size of individual juveniles was correlated with tendency to visit shoals, but was not correlated with overall time spent shoaling, regardless of shoal composition. As juveniles, convict cichlids can make discriminatory choices that are influenced by specific aspects of shoal composition.
... Source of variation Reeves and Richards, 2011). This approach has been quite useful when dealing with genetically divergent populations and cryptic species (Unmack et al., 2012;Arteaga et al., 2016;Bagley et al., 2016;Fennessy et al., 2016;Schield et al., 2018). Populations of Rhoadsia in Ecuador were split into two main lineages allopatrically distributed in northern and southern regions of western Ecuador based on the analysis of mtDNA (Fig. 5). ...
... Under the taxonomic arrangement of Schmitter-Soto (2007), convict cichlids from Nicaragua were ascribed to the species A. siquia. However, recent genetic analysis suggests that this species is polytypic due to imperfect taxonomy and more likely belongs to A. nigrofasciata (Bagley et al. 2016). Therefore, we follow the taxonomy in Bussing (1998) and Allgayer (2001), which is consistent with the genetic data. ...
Carotenoid pigments have myriad functions in fish, including coloration and immunity. The “carotenoid trade-off hypothesis” posits that dietary limitation of carotenoids imposes constraints on animals to allocate to one function at the expense of another. This hypothesis rarely has been tested in fish. We quantified tissue carotenoids in breeding and non-breeding female convict cichlids in Lake Xiloá, Nicaragua. This species is reverse sexually dichromatic such that females possess carotenoid-based coloration that males lack. We also collected algae samples near nest sites to assess carotenoid availability, recorded water depth, and examined cichlids’ behavioral interactions with pair mates, conspecifics, heterospecific competitors, and predators. Each of these, we predicted, would mediate potential carotenoid trade-offs. We found that non-breeding females had significantly higher levels of carotenoids in their integument, liver, and gonads compared to breeding fish. We found that algae and total carotenoids declined with depth across our study transects at 9, 11, 13, and 15 m, but the concentration of carotenoids (ng carotenoid g⁻¹ algae, or algal quality) did not vary with depth. Furthermore, relationships among carotenoid concentrations of the three tissue types did not vary with depth, and female color status (orange or not) was not affected by behavioral interactions with other community members, reproductive status, or water depth. Our results support previous studies showing that carotenoid pigmentation may serve a signal function that facilitates the establishment of non-breeding females within the breeding population. Our study also uncovered no evidence indicating that carotenoids are limiting in the diet of breeding female convict cichlids.
... The Neotropical region shows exceptional species richness and endemism due to diversifications associated with its unique geological history resulting in a complex topography and climatic history, but is still poorly understood (Bagley et al., 2016). The family Cichlidae, which occur in the region, are the most diverse group within the order Perciformes. ...
Cichlids constitute a diverse monophyletic group that have developed adaptive strategies to thrive in diverse environments. Andinoacara represents an example of diversification on the South American Andean uplift, providing a key model for understanding the evolution of biogeographic patterns. In this study, we analyzed the species Andinoacara latifrons using two mitochondrial markers (COI, cytb) and one nuclear marker (RAG1) in a populational level. Sequences were obtained through tissue collection and from the GenBank database. Populational analysis showed significant structuration among populations, also corroborated with population pairwise F
st
results. Fu's Fs and Tajima's D results showed populations that seems to be under populational expansion. We identified 22 haplotypes using cytb. The population associations in the Cauca haplotype are related to the Momposina depression and the mixture of the Cauca-Magdalena river basins in the lower Cauca-Magdalena region. We constructed a new phylogenetic tree, which grouped mainly two A. latifrons lineages: (1) an upper Magdalena and Catatumbo clade and (2) an upper Cauca and upper Magdalena clade. Thus, A. latifrons represents a diverse entity that contributes to our understanding of the evolutionary history of northern South America. Our findings provide insight into devising public policies in determining refuges for the preservation of biodiversity in the lower Cauca and Magdalena regions in Colombia.
... Under the general lineage concept of species (de Queiroz 2007), we agree with Bagley et al. (2016) that genealogical and statistical evidence from genetic data should be sufficient for species identification. Species delimitation analyses (mtDNA-nuDNA combined and nuDNA data sets) identify at least three independently evolving lineages within M. pennsylvanicus that we suggest should be recognized as distinct species. ...
Conservation efforts rely on robust taxonomic assessments that should be based on critical assessment of interspecific boundaries, infraspecific variation, and potentially distinctive peripheral populations. The meadow vole (Microtus pennsylvanicus) is widely distributed across North America, including 28 morphologically defined subspecies and numerous isolated populations. Because some subspecies are of high conservation concern, we examined geographic variation across the range of the species to test existing infraspecific taxonomy in terms of local and regional diversification. We sequenced mitochondrial DNA (mtDNA) from 20 subspecies of M. pennsylvanicus and contextualized infraspecific variation through comparison of pairwise genetic distances derived from an extended data set of 63 species of Microtus. We found strong support for at least three divergent clades within M. pennsylvanicus, with observed intraspecific clade divergence exceeding that between several pairwise comparisons of sister species within Microtus. Six nuclear genes were then sequenced to test the validity of mtDNA structure and to further evaluate the possibility of cryptic, species-level diversity using Bayes factor species delimitation (BFD) analyses. BFD consistently and decisively supported multiple species based on the multilocus approach. We propose that taxonomic revision of the meadow vole is required, with the eastern clade now identified as M. pennsylvanicus (Ord 1815), the western clade as M. drummondii (Audubon and Bachman 1853), and the coastal Florida clade as M. dukecampbelli (Woods, Post, and Kilpatrick 1982). We suggest that such an arrangement would more closely reflect evolutionary history and provide critical context for further examination of distinctive southern peripheral populations that harbor novel evolutionary legacies and adaptive potential.
... References [3,36,48,49]. ...
The introduction of exotic fishes in streams and water reservoirs has modified autochthonous freshwater fish communities in Puerto Rico. There are approximately 46 fish species in inland waters, and most of them were introduced during the last century. We here summarize relevant information on 46 freshwater fish species reported for the island. Approximately 80% of the species are non-native. An evaluation of the local trade revealed another 128 freshwater fish species are sold locally as pets. This raises serious concerns, as we detected a potential pool of non-native species that are either considered invasive elsewhere, or that, based on their ecology, could become invasive on the island in the near future. We also found that cichlids as a group pose the highest risk to freshwater ecosystems, with 13 species established in the wild, and another 38 potential invaders in the local pet trade. This study may be used as a baseline for the conservation and management purposes of both native and non-native fish species, including the development of strategies for preventing the release of live fish pets into the wild. More specific management for non-native fish, especially those identified here that pose significant threats to Puerto Rico’s native fish and their ecosystems, are warranted.
... In recent years, Neotropical research in the Fish Section has included the description of new species (Matamoros et al., 2012(Matamoros et al., , 2013Walsh and Chakrabarty, 2016), higher taxonomy , discovery of invasives and nonnatives Elías et al., 2018), biogeography and phylogeography (Bacon et al., 2015a(Bacon et al., , 2015bMatamoros et al., 2015;Bagley et al., 2016;McMahan et al., 2017;Ludt et al., 2015Ludt et al., , 2018Tagliacollo et al., 2017) phylogenomic research Burress et al., 2018;Alda et al., 2019), mitogenomics (Alda et al., 2017, morphological studies (McMahan et al., 2017b;Evans et al., 2017) and behavior (Oldfield et al., 2015). The main focus of the LSU MNS Fish Section is to carry out collections-based research to better understand the Fish Tree of Life in order to explain Earth history and evolution. ...
... The molecular data demonstrate this morph is not genetically distinct and it was recovered nested inside other individuals of the species, confirming that this species is extremely polymorphic. Polymorphism in Middle American heroine cichlids has been well documented in other species, e.g. the convict cichlid Amatitlania nigrofasciata ( McMahan et al. 2014, Bagley et al. 2016), the Midas cichlid Amphilophus citrinellus species complex ( Barluenga & Meyer 2004) and the Cuatro Ciénegas cichlid Herichthys minckleyi ( Kornfield & Taylor 1983, Cohen et al. 2005). Some species of the genus Herichthys described by De la Maza Benignos et al. (2013) may also be polymophisms ( Říčan et al. 2016). ...
Vieja hartwegi was described by Taylor and Miller in 1980 based on 45 juvenile and sub-adult specimens, but this species shows an enormous variation in coloration patterns during ontogenic development and between individuals. Additionally, morphological data have demonstrated the existence of two forms in V. hartwegi: the typical morph of a moderately deep to slightly elongated body shape with midlateral band, and a rheophilic morph with an elongated to slightly deep body shape and lack of midlateral band. Herein we redescribe V. hartwegi adding adults and individuals from broad geographic ranges, as well as a rheophilic morph recently discovered in the upper reaches of the Grijalva River basin in Mexico. The set of characters include coloration, meristic, morphometric and osteological features. Vieja hartwegi is a polymorphic species whose forms may be segregating because of habitat preferences and food habits.
... However, demographically, genetic data indicate population expansion for V. maculicauda based on the significant and negative Tajima's D and Fu's F values, as well as unimodal distribution and low nonsignificant Harpending's Raggedness index from mismatch distribution. This has also been illustrated in other Middle American cichlids based on cyt b sequences (genus Amatitlania, [43]) Niche modeling corroborated distributional evidence from collections that suggested this species is typically found in lowland habitats. Present-day ENM analyses projected onto the geographic range of the species, in addition to the percent occurrence plot with altitude, supports this relatively narrow habitat preference of this species within its wide distribution. ...
The distributions of many Northern Hemisphere organisms have been influenced by fluctuations in sea level and climatic conditions during Pleistocene interglacial periods. These cycles are associated with range contraction and refugia for northern-distributed organisms as a response to glaciers. However, lower sea levels in the tropics and sub-tropics created available habitat for expansion of the ranges of freshwater organisms. The goal of this study was to use ecological niche modeling to test the hypothesis of north to south range expansion of Vieja maculicauda associated with Pleistocene glacial cycles. Understanding the biogeography of this widespread species may help us better understand the geology and interconnectivity of Central American freshwaters. Occurrence data for V. maculicauda was based on georeferencing of all museum records of specimens recovered from FishNet2. General patterns of phylogeographic structure were assessed with mtDNA. Present day niche models were generated and subsequently projected onto paleoclimatic maps of the region during the Last Interglacial, Last Glacial Maximum, and mid-Holocene. Phylogenetic analysis of mtDNA sequence data showed no phylogeographic structure throughout the range of this widespread species. Present day niche models were congruent with the observed distribution of V. maculicauda in Central America. Results showed a lack of suitable freshwater habitat in northern Central America and Mexico during the Last Interglacial, with greatest range expansion during the Last Glacial Maximum and mid-Holocene. Results support the hypothesis of a north to south range expansion of V. maculicauda associated with glacial cycles. The wide distribution of this species compared to other closely related cichlids indicates the latter did not respond to the degree of V. maculicauda in expansion of their distributions. Future work aimed at comparisons with other species and modeling of future climatic scenarios will be a fruitful area of investigation. © 2017 McMahan et al.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
... Similar results have been found for needlefishes [85], shovelnose catfishes [86], discus cichlids [87], several groups of Central American cichlids (e.g. [88,89]), among others. Some of these incongruences can be explained by inadequate sampling and scrutiny, and some to previous use of questionable methods to recognize species, but other cases show nested patterns of divergence and gene exchange not unlike those observed in Cichla. ...
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.
(1) Predation selects for antipredator competence in prey. For fishes with parental care, brood predators exert selection on the morphological phenotype of offspring, and also exert strong selection pressure to promote parental care behavior of adults. (2) This review summarizes field and lab studies on the ontogeny of antipredator competence in convict cichlids, a freshwater fish with extended biparental care of their free-swimming young. (3) Here, data show that differences in swimming performance between small and large young are exploited by parents when they adopt (smaller) young. Velocity and acceleration of startle responses improves nonlinearly with body size, increasing rapidly at a point when the skeleton rapidly ossifies from cartilage to bone, at the size at which discrimination by adopting parents shifts, and the timing of change in the rate of change in area protected by parents. Convict cichlids in a Nicaraguan lake population showed a similar correlation among these traits, but these traits are delayed relative to Costa Rican fish. (4) Population divergence is likely explained by relatively more intense brood predation in the lake, which selects for different optima of larval antipredator competence and parental brood defense.
This introductory chapter explains the coverage of this book, which is about freshwater fishes in South and Central America. It summarizes the major geographical features of tropical South and Central America, provides a brief overview of the earth history context in which modern fauna underwent its diversification, and reviews the development of ideas on the origins of the rich fauna. This book addresses questions concerning the evolutionary forces underlying the formation of highly diverse tropical aquatic ecosystems.
Introns may accumulate much higher genetic variation than exons. Universal primers were designed from the conservative nucleotide sequences of exons to amplify the flanking intron. Length variations in the S7 ribosomal protein (RP) gene intron 1 and mitochondrial creatine kinase (CK) gene intron 6 of the swordfish Xiphias gladius were found. Single or two banded fragment patterns in each individual were observed by agarose gel electrophoresis. Nucleotide sequence analysis revealed that highly polymorphic fragment patterns observed in the RP gene intron 1 were due to different numbers of a TG repeat (microsatellite). The length of the CK gene intron 6 was dimorphic, in which presence or absence of a 24 bp block was responsible for longer or shorter introns. Additional minor nucleotide insertion/deletions were observed independent of the RP microsatellite and the CK 24 bp block regions. The results of this investigation indicate that introns may be good sources of intraspecific genetic variation for population genetic studies and that the same set of primers can be used to amplify homologous intron regions even among distant species. Further, the conserved exon primed PCR strategy may be useful to prevent appearance of priming site polymorphism (null allele).
The fish faunas of continental South and Central America constitute one of the greatest concentrations of aquatic diversity on Earth, consisting of about 10 percent of all living vertebrate species. Historical Biogeography of Neotropical Freshwater Fishes explores the evolutionary origins of this unique ecosystem. The chapters address central themes in the study of tropical biodiversity: why is the Amazon basin home to so many distinct evolutionary lineages? What roles do ecological specialization, speciation, and extinction play in the formation of regional assemblages? How do dispersal barriers contribute to isolation and diversification? Focusing on whole faunas rather than individual taxonomic groups, this volume shows that the area's high regional diversity is not the result of recent diversification in lowland tropical rainforests. Rather, it is the product of species accumulating over tens of millions of years and across a continental arena.
As part of a revision of the cichlid genus Archocentrus, a new genus, Amatitlania, was erected comprising four species: A. nigrofasciata (the type species), A. siquia, A. kanna, and A. coatepeque. Amatitlania coatepeque is an endemic and an eponym of Lago Coatepeque in the interior highlands of western El Salvador. This species was diagnosed by a Y-shaped pattern formed by the ventral fusion of bars four and five on the body; a triple-spined, squarish, or blunt appearance of the dentigerous arm of the dentary; the presence of a posterior projection at the dorsal corner of the lower lip; the presence of a double medial-loop in the gut; sparsely uniform pigmentation of the peritoneum, and 5-5.5 scale rows from the lateral line to the origin of the dorsal fin. Here we examined the taxonomic status of A. coatepeque using molecular and morphological characters. We found that A. coatepeque is phylogenetically nested within the clade of A. nigrofasciata. Additionally, our re-examination of the reported diagnostic morphological characters failed (even in combination) to diagnose A. coatepeque. We instead found that some of those characters were highly variable within A. coatepeque and are sometimes present in members of A. nigrofasciata. Based on our results, we conclude that A. coatepeque is a junior synonym of A. nigrofasciata. © 2014 by the American Society of Ichthyologists and Herpetologists.
Accurately delimiting species is fundamentally important for understanding species diversity and distributions and devising effective strategies to conserve biodiversity. However, species delimitation is problematic in many taxa, including 'non-adaptive radiations' containing morphologically cryptic lineages. Fortunately, coalescent-based species delimitation methods hold promise for objectively estimating species limits in such radiations, using multilo-cus genetic data. Using coalescent-based approaches, we delimit species and infer evolutionary relationships in a morphologically conserved group of Central American freshwater fishes, the Poecilia sphenops species complex. Phylogenetic analyses of multiple genetic markers (sequences of two mitochondrial DNA genes and five nuclear loci) from 10/15 species and genetic lineages recognized in the group support the P. sphenops species complex as monophyletic with respect to outgroups, with eight mitochondrial 'major-line-ages' diverged by !2% pairwise genetic distances. From general mixed Yule-coalescent models, we discovered (conservatively) 10 species within our concatenated mitochondrial DNA dataset, 9 of which were strongly supported by subsequent multilocus Bayesian species delimitation and species tree analyses. Results suggested species-level diversity is underestimated or overestimated by at least ~15% in different lineages in the complex. Nonparametric statistics and coalescent simulations indicate genealogical discordance among our gene tree results has mainly derived from interspecific hybridization in the nuclear genome. However, mitochondrial DNA show little evidence for introgression, and our species delimitation results appear robust to effects of this process. Overall, our findings support the utility of combining multiple lines of genetic evidence and broad phylogeogra-phical sampling to discover and validate species using coalescent-based methods. Our
A central goal of comparative phylogeography is determining whether codistributed species experienced (1) concerted evolutionary responses to past geological and climatic events, indicated by congruent spatial and temporal patterns (“concerted-response hypothesis”); (2) independent responses, indicated by spatial incongruence (“independent-response hypothesis”); or (3) multiple responses (“multiple-response hypothesis”), indicated by spatial congruence but temporal incongruence (“pseudocongruence”) or spatial and temporal incongruence (“pseudoincongruence”). We tested these competing hypotheses using DNA sequence data from three livebearing fish species codistributed in the Nicaraguan depression of Central America (Alfaro cultratus, Poecilia gillii, and Xenophallus umbratilis) that we predicted might display congruent responses due to co-occurrence in identical freshwater drainages. Spatial analyses recovered different subdivisions of genetic structure for each species, despite shared finer-scale breaks in northwestern Costa Rica (also supported by phylogenetic results). Isolation-with-migration models estimated incongruent timelines of among-region divergences, with A. cultratus and Xenophallus populations diverging over Miocene–mid-Pleistocene while P. gillii populations diverged over mid-late Pleistocene. Approximate Bayesian computation also lent substantial support to multiple discrete divergences over a model of simultaneous divergence across shared spatial breaks (e.g., Bayes factor [B10] = 4.303 for Ψ [no. of divergences] > 1 vs. Ψ = 1). Thus, the data support phylogeographic pseudoincongruence consistent with the multiple-response hypothesis. Model comparisons also indicated incongruence in historical demography, for example, support for intraspecific late Pleistocene population growth was unique to P. gillii, despite evidence for finer-scale population expansions in the other taxa. Empirical tests for phylogeographic congruence indicate that multiple evolutionary responses to historical events have shaped the population structure of freshwater species codistributed within the complex landscapes in/around the Nicaraguan depression. Recent community assembly through different routes (i.e., different past distributions or colonization routes), and intrinsic ecological differences among species, has likely contributed to the unique phylogeographical patterns displayed by these Neotropical fishes.
http://onlinelibrary.wiley.com/doi/10.1111/brv.12076/abstract
http://onlinelibrary.wiley.com/doi/10.1111/brv.12076/full
Lower Central America (LCA) provides a geologically complex and dynamic, richly biodiverse model for studying the recent assembly and diversification of a Neotropical biota. Here, we review the growing literature of LCA phylogeography studies and their contribution to understanding the origins, assembly, and diversification of the LCA biota against the backdrop of regional geologic and climatic history, and previous biogeographical inquiry. Studies to date reveal that phylogeographical signal within taxa of differing distributions reflects a diversity of patterns and processes rivalling the complexities of LCA landscapes themselves. Even so, phylogeography is providing novel insights into regional diversification (e.g. cryptic lineage divergences), and general evolutionary patterns are emerging. Congruent multi-taxon phylogeographic breaks are found across the Nicaraguan depression, Chorotega volcanic front, western and central Panama, and the Darién isthmus, indicating that a potentially shared history of responses to regional-scale (e.g. geological) processes has shaped the genetic diversity of LCA communities. By contrast, other species show unique demographic histories in response to overriding historical events, including no phylogeographic structure at all. These low-structure or incongruent patterns provide some evidence for a role of local, ecological factors (e.g. long-distance dispersal and gene flow in plants and bats) in shaping LCA communities. Temporally, comparative phylogeographical structuring reflects Pliocene–Pleistocene dispersal and vicariance events consistent with the timeline of emergence of the LCA isthmus and its major physiographic features, e.g. cordilleras. We emphasise the need to improve biogeographic inferences in LCA through in-depth comparative phylogeography projects capitalising on the latest statistical phylogeographical methods. While meeting the challenges of reconstructing the biogeographical history of this complex region, phylogeographers should also take up the critical service to society of applying their work to the conservation of its fascinating biodiversity.
Current molecular methods of species delimitation are limited by the types of species delimitation models and scenarios that can be tested. Bayes factors allow for more flexibility in testing non-nested species delimitation models and hypotheses of individual assignment to alternative lineages. Here, we examined the efficacy of Bayes factors in delimiting species through simulations and empirical data from the Sceloporus scalaris species group. Marginal likelihood scores of competing species delimitation models, from which Bayes factor values were compared, were estimated with four different methods: harmonic mean estimation, smoothed harmonic mean estimation, path-sampling/thermodynamic integration, and stepping-stone analysis. We also performed model selection using a posterior simulation-based analog of the Akaike information criterion through Markov chain Monte Carlo analysis (AICM). Bayes factor species delimitation results from the empirical data were then compared with results from the reversible-jump MCMC (rjMCMC) coalescent-based species delimitation method Bayesian Phylogenetics and Phylogeography (BP&P). Simulation results show that harmonic and smoothed harmonic mean estimators perform poorly compared to path sampling and stepping stone marginal likelihood estimators when identifying the true species delimitation model. Furthermore, Bayes factor delimitation (BFD) of species showed improved performance when species limits are tested by reassigning individuals between species, as opposed to either lumping or splitting lineages. In the empirical data, BFD through path sampling and stepping-stone analyses, as well as the rjMCMC method, each provide support for the recognition of all scalaris group taxa as independent evolutionary lineages. Bayes factor species delimitation and BP&P also support the recognition of three previously undescribed lineages. In both simulated and empirical datasets, harmonic and smoothed harmonic mean marginal likelihood estimators provided much higher marginal likelihood estimates than path sampling and stepping-stone estimators. The AICM displayed poor repeatability in both simulated and empirical datasets, and produced inconsistent model rankings across replicate runs with the empirical data. Our results suggest that species delimitation through the use of Bayes factors with marginal likelihood estimates via path-sampling or stepping-stone analyses provide a useful and complementary alternative to existing species delimitation methods.
We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements our RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
Estimating genealogical relationships among genes at the population level presents a number of difficulties to traditional methods of phylogeny reconstruction. These traditional methods such as parsimony, neighbour-joining, and maximum-likelihood make assumptions that are invalid at the population level. In this note, we announce the availability of a new software package, TCS, to estimate genealogical relationships among sequences using the method of Templeton et al. (1992) .
Bootstrapping is a common method for assessing confidence in phylogenetic analyses. Although bootstrapping was first applied in phylogenetics to assess the repeatability of a given result, bootstrap results are commonly interpreted as a measure of the probability that a phylogenetic estimate represents the true phylogeny. Here we use computer simulations and a laboratory-generated phylogeny to test bootstrapping results of parsimony analyses, both as measures of repeatability (i.e., the probability of repeating a result given a new sample of characters) and accuracy (i.e., the probability that a result represents the true phylogeny). Our results indicate that any given bootstrap proportion provides an unbiased but highly imprecise measure of repeatability, unless the actual probability of replicating the relevant result is nearly one. The imprecision of the estimate is great enough to render the estimate virtually useless as a measure of repeatability. Under conditions thought to be typical of most phylogenetic analyses, however, bootstrap proportions in majority-rule consensus trees provide biased but highly conservative estimates of the probability of correctly inferring the corresponding clades. Specifically, under conditions of equal rates of change, symmetric phylogenies, and internodal change of less-than-or-equal-to 20% of the characters, bootstrap proportions of greater-than-or-equal-to 70% usually correspond to a probability of greater-than-or-equal-to 95% that the corresponding clade is real. However, under conditions of very high rates of internodal change (approaching randomization of the characters among taxa) or highly unequal rates of change among taxa, bootstrap proportions >50% are overestimates of accuracy.
▪ Abstract Many uses of gene trees implicitly assume that nominal species are monophyletic in their alleles at the study locus. However, in well-sampled gene trees, certain alleles in one species may appear more closely related to alleles from different species than to other conspecific alleles. Such deviations from species-level monophyly have a variety of causes and may lead to erroneous evolutionary interpretations if undetected. The present paper describes the causes and consequences of these paraphyletic and polyphyletic patterns. It also provides a detailed literature survey of mitochondrial DNA studies on low-level animal phylogeny and phylogeography, results from which reveal the frequency of nonmonophyly and patterns of interpretation and sampling. This survey detected species-level paraphyly or polyphyly in 23% of 2319 assayed species, demonstrating this phenomenon to be statistically supported, taxonomically widespread, and far more common than generally recognized. Our findings call for increa...
Phylogeography has become a powerful approach for elucidating contemporary geographical patterns of evolutionary subdivision within species and species complexes. A recent extension of this approach is the comparison of phylogeographic patterns of multiple co-distributed taxonomic groups, or ‘comparative phylogeography.’ Recent comparative phylogeographic studies have revealed pervasive and previously unrecognized biogeographic patterns which suggest that vicariance has played a more important role in the historical development of modern biotic assemblages than current taxonomy would indicate. Despite the utility of comparative phylogeography for uncovering such ‘cryptic vicariance’, this approach has yet to be embraced by some researchers as a valuable complement to other approaches to historical biogeography. We address here some of the common misconceptions surrounding comparative phylogeography, provide an example of this approach based on the boreal mammal fauna of North America, and argue that together with other approaches, comparative phylogeography can contribute importantly to our understanding of the relationship between earth history and biotic diversification.
The freshwater fauna of Southern Australia is primarily restricted to the southwestern and southeastern corners of the continent, and is separated by a large, arid region that is inhospitable to this biota. This geographic phenomenon has attracted considerable interest from biogeographers looking to explain evolutionary diversification in this region. Here, we employed phylogenetic and phylogeographic approaches to evaluate the effect of this barrier on a group of four galaxiid fish species (Galaxiella) endemic to temperate Southern Australia. We also tested if continental shelf width has influenced connectivity among populations during low sea levels when rivers, now isolated, could have been connected. We addressed these questions by sampling each species across its range using multiple molecular markers (mitochondrial cytochrome b sequences, nuclear S7 intron sequences, and 49 allozyme loci). These data also allowed us to assess species boundaries, to refine phylogenetic affinities, and to estimate species ages. Interestingly, we found compelling evidence for cryptic species in G. pusilla, manifesting as allopatric eastern and western taxa. Our combined phylogeny and dating analysis point to an origin for the genus dating to the early Cenozoic, with three of the four species originating during the Oligocene-Miocene. Each Galaxiella species showed high levels of genetic divergences between all but the most proximate populations. Despite extensive drainage connections during recent low sea levels in southeastern Australia, populations of both species within G. pusilla maintained high levels of genetic structure. All populations experienced Late Pleistocene-Holocene population growth, possibly in response to the relaxation of arid conditions after the last glacial maximum. High levels of genetic divergence and the discovery of new cryptic species have important implications for the conservation of this already threatened group of freshwater species.
Coalescent theory has provided a basis for evolutionary biologists to build sophisticated methods for inferring population history from variation in genetic markers, but these methods leave out a major conceptual cornerstone of modern evolutionary theory: natural selection. I provide the first quantitative analysis of the effects of selection on genealogical patterns in a continuously distributed population in which the selective optimum for a trait linked to the marker varies gradually and continuously across the landscape. Simulations show that relatively weak selection for local adaptation can lead to strong phylogeographic structure, in which highly divergent genealogical groups (i.e., clades) are geographically localized and differentially adapted, and dramatically increased standing variation (e.g., coalescence time) compared to neutral expectations. This pattern becomes more likely with increasing population size and with decreasing dispersal distances, mutation rates, and mutation sizes. Under some conditions, the system alternates between a nearly neutral behavior and a behavior in which highly divergent clades are locally adapted. Natural selection on markers commonly used in phylogeographic studies (such as mitochondrial DNA) presents a major challenge to the inference of biogeographic history but also provides exciting opportunities to study how selection affects both between- and within-species biodiversity.
The statistical rigor of species delimitation has increased dramatically over the past decade. Coalescent theory provides powerful models for population genetic inference, and is now increasingly important in phylogenetics and speciation research. By applying probabilistic models, coalescent-based species delimitation provides clear and objective testing of alternative hypotheses of evolutionary independence. As acquisition of multilocus data becomes increasingly automated, coalescent-based species delimitation will improve the discovery, resolution, consistency, and stability of the taxonomy of species. Along with other tools and data types, coalescent-based species delimitation will play an important role in an integrative taxonomy that emphasizes the identification of species limits and the processes that have promoted lineage diversification.
The emergence of low-frequency, high-amplitude, quasi-periodic (∼100-kyr) glacial variability during the middle Pleistocene in the absence of any significant change in orbital forcing indicates a fundamental change internal to the climate system. This middle Pleistocene transition (MPT) began 1250 ka and was complete by 700 ka. Its onset was accompanied by decreases in sea surface temperatures (SSTs) in the North Atlantic and tropical-ocean upwelling regions and by an increase in African and Asian aridity and monsoonal intensity. During the MPT, long-term average ice volume gradually increased by ∼50 m sea-level equivalent, whereas low-frequency ice-volume variability experienced a 100-kyr lull centered on 1000 ka followed by its reappearance ∼900 ka, although as a broad band of power rather than a narrow, persistent 100-kyr cycle. Additional changes at 900 ka indicate this to be an important time during the MPT, beginning with an 80-kyr event of extreme SST cooling followed by the partial recovery and subsequent stabilization of long-term North Atlantic and tropical ocean SSTs, increasing Southern Ocean SST variability primarily associated with warmer interglacials, the loss of permanent subpolar sea-ice cover, and the emergence of low-frequency variability in Pacific SSTs and global deep-ocean circulation. Since 900 ka, ice sheets have been the only component of the climate system to exhibit consistent low-frequency variability. With the exception of a near-universal organization of low-frequency power associated with marine isotope stages 11 and 12, all other components show an inconsistent distribution of power in frequency-time space, suggesting a highly nonlinear system response to orbital and ice-sheet forcing.
The marginal likelihood is commonly used for comparing different evolutionary models in Bayesian phylogenetics and is the central quantity used in computing Bayes Factors for comparing model fit. A popular method for estimating marginal likelihoods, the harmonic mean (HM) method, can be easily computed from the output of a Markov chain Monte Carlo analysis but often greatly overestimates the marginal likelihood. The thermodynamic integration (TI) method is much more accurate than the HM method but requires more computation. In this paper, we introduce a new method, steppingstone sampling (SS), which uses importance sampling to estimate each ratio in a series (the "stepping stones") bridging the posterior and prior distributions. We compare the performance of the SS approach to the TI and HM methods in simulation and using real data. We conclude that the greatly increased accuracy of the SS and TI methods argues for their use instead of the HM method, despite the extra computation needed.
Species delimitation and species tree inference are difficult problems in cases of recent divergence, especially when different
loci have different histories. This paper quantifies the difficulty of jointly finding the division of samples to species
and estimating a species tree without constraining the possible assignments a priori. It introduces a parametric and a nonparametric
method, including new heuristic search strategies, to do this delimitation and tree inference using individual gene trees
as input. The new methods were evaluated using thousands of simulations and 4 empirical data sets. These analyses suggest
that the new methods, especially the nonparametric one, may provide useful insights for systematists working at the species
level with molecular data. However, they still often return incorrect results.
Genealogical data are an important source of evidence for delimiting species, yet few statistical methods are available for calculating the probabilities associated with different species delimitations. Bayesian species delimitation uses reversible-jump Markov chain Monte Carlo (rjMCMC) in conjunction with a user-specified guide tree to estimate the posterior distribution for species delimitation models containing different numbers of species. We apply Bayesian species delimitation to investigate the speciation history of forest geckos (Hemidactylus fasciatus) from tropical West Africa using five nuclear loci (and mtDNA) for 51 specimens representing 10 populations. We find that species diversity in H. fasciatus is currently underestimated, and describe three new species to reflect the most conservative estimate for the number of species in this complex. We examine the impact of the guide tree, and the prior distributions on ancestral population sizes () and root age (τ(0)), on the posterior probabilities for species delimitation. Mis-specification of the guide tree or the prior distribution for can result in strong support for models containing more species. We describe a new statistic for summarizing the posterior distribution of species delimitation models, called speciation probabilities, which summarize the posterior support for each speciation event on the starting guide tree.
The scientific study of fishes of the Great Lakes of Nicaragua began in 1864 with the description by Gunther of Heros labiatus (=Cichlasoma labiatum) from Lake Managua. Subsequently, Gunther reported on several other species collected in the Great Lakes by Captain J. M. Dow. Astorqui (1967) reviewed the sparse ichthyological literature dealing with Nicaraguan fishes and pointed out the paucity of recent studies. Since then Villa (1971) has produced a provisional list of the freshwater and brackish water fishes of Nicaragua and Astorqui (1972) has analyzed the ichthyofauna of the Great Lakes Basin. Riedel (1972) discussed the geological history of the Great Lakes in relation to the composition and evolution of its fish fauna.
This chapter highlights the biogeography of fishes with perspectives from the Panamanian isthmus as it provides a rich landscape to study the evolution of fish and molecules. It focuses on fish biogeography, particularly the geography of conspecific populations of tropical marine and freshwater fishes. It provides an insight into the mechanics and reliability of mitochondrial molecular clocks functioning across shallow spans of time. Conspecific populations, if differentiated, can provide historical information about a region. Molecules, particularly mtDNA, are well suited for reconstructing the evolutionary relationships among conspecific populations. For species or species groups demonstrating little or no phylogenetically informative morphological variation, molecules can provide a taxonomy that can be easily and immediately placed in a phylogenetic context. Tabular representations are provided for the geographic scaling of species groups like the Panama Isthmus, the circumtropical Abudefduf, and Neotropical freshwater fishes. A reasonable conclusion follows that molecular and genetic analysis can provide rapid means for surveying regional biotic diversity. Phylogenetic history and/or genetic diversity should be used in biodiversity indices to emphasize the phylogenetic and genetic distinctiveness of some groups compared to others.
The distribution of freshwater fishes in Central America is reviewed. Major parts of the region, especially in Honduras and Nicaragua, have yet to be explored ichthyologically, and systematic revision of important groups, notably the cichlids, is long overdue. The continental area from the Isthmus of Tehuantepec to the Colombian border contains approximately 456 species, of which over 75% comprise the Cyprinodontidae, Poeciliidae, Cichlidae, and marine invaders (peripheral fishes); about one-third of the latter (57 species) have taken up more or less permanent residence in fresh water. There are 104 primary species in 10 families, 165 secondary forms in 6 families, and 187 peripheral species distributed among 30 families (nearly half of the latter are ariids, atherinids, gerrids, and gobies). Poeciliids and cichlids are particularly rich and diverse, together comprising 139 species. Characins are numerous only in the Panamanian region, into which they and five South American catfish families have recently penetrated. Except for gars, no North American family has reached beyond northern Guatemala. There are no non-ostariophysan primary fishes in the area.
In a 1935 paper and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null is one-half. Although there has been much discussion of Bayesian hypothesis testing in the context of criticism of P-values, less attention has been given to the Bayes factor as a practical tool of applied statistics. In this article we review and discuss the uses of Bayes factors in the context of five scientific applications in genetics, sports, ecology, sociology, and psychology. We emphasize the following points:
Aim We present a molecular phylogenetic and biogeographical analysis of Brachyhypopomus occidentalis, one of the few gymnotiform electric fish in Central America, to further understand the colonization and diversification processes of primary freshwater fishes over the Central American Isthmus.LocationLower Central America.
Methods We used Bayesian and maximum-likelihood phylogenetic reconstructions using mitochondrial [cytochrome c oxidase subunit I (COI) and ATP synthase 6 and 8 (ATPase 8/6)] and nuclear (RAG1 and rhodopsin) genes and extensive geographical sampling, together with molecular clock analyses and tests of biogeographical scenarios to assess the timing and mode of dispersal and diversification.
Results We identified high levels of phylogeographical structure, with a highly divergent lineage composed of individuals from western Atlantic Panama (Bocas), sister to all trans-Andean South American and Central American lineages. The Pacific slope of Panama showed surprisingly little genetic structure compared with the Atlantic slope. Molecular-clock and biogeographical analyses support two waves of colonization originating from South America: a first dispersal event in the late Miocene with the Bocas lineage as the only relict, and a second major colonization in the late Pliocene leading to the establishment of B. occidentalis in all central and eastern Panama drainages.
Main conclusions The genetic structure of B. occidentalis over the Isthmian landscape reflects the progressive, complex and dynamic geological evolution of the region. Our results support multiple colonization events, with an ancient Miocene dispersal event followed by a recent rapid expansion in the late Pliocene, probably facilitated by the final closure of the Isthmus, which provided an important corridor.
Biogeographic patterns displayed by obligate freshwater organisms are intimately related to the nature and extent of connectivity between suitable habitats. Two of the more significant barriers to freshwater connections are seawater and major drainage divides. South-eastern Australia provides a contrast between these barriers as it has discrete areas that are likely influenced to a greater or lesser extent by each barrier type. We use continental shelf width as a proxy for the potential degree of river coalescence during low sea levels. Our specific hypothesis is that the degree of phylogeographic divergence between coastal river basins should correspond to the continental shelf width of each region. This predicts that genetic divergences between river basins should be lowest in regions with a wider continental shelf and that regions with similar continental shelf width should have similar genetic divergences. Pygmy perches (Nannoperca australis and Nannoperca 'flindersi') in south-eastern Australia provide an ideal opportunity to test these biogeographic hypotheses. Phylogeographic patterns were examined based on range-wide sampling of 82 populations for cytochrome b and 23 polymorphic allozyme loci. Our results recovered only limited support for our continental shelf width hypothesis, although patterns within Bass clade were largely congruent with reconstructed low sea-level drainage patterns. In addition, we identified several instances of drainage divide crossings, typically associated with low elevational differences. Our results demonstrate high levels of genetic heterogeneity with important conservation implications, especially for declining populations in the Murray-Darling Basin and a highly restricted disjunct population in Ansons River, Tasmania.
A phylogeny for 28 cichlid species that have been included in or near the same clade as Archocentrus centrarchus (type species of the genus) in previous phylogenetic analyses is presented, based on 98 morphological characters (osteology, gut-coiling pattern, pigmentation, squamation, meristics, and others), plus one cytogenetic character. Monophyly is supported for Archocentrus sensu stricto, Cryptoheros, Hypsophrys, Amatitlania, and Rocio; the relationships among these genera are not resolved. The three subgenera of Cryptoheros are also supported; Cr. panamensis is the sister group of the rest of the species in the genus. Within Cryptoheros (Cryptoheros), Cr. chetumalensis is the sister group of the clade Cr. spilurus + Cr. cutteri. Within Amatitlania the pattern is: (Am. coatepeque (Am. nigrofasciata (Am. siquia + Am. kanna))).
The cichlid genus Archocentrus has been considered one of the most promising (i.e., possibly natural) genera resurrected to receive some of the species formerly included in Cichlasoma. Evidence is presented to justify generic recognition of Archocentrus, as well as eight other closely related genera (Caquetaia, Hypsophrys, Parachromis, Amphilophus, Archocentrus, Cryptoheros, Amatitlania, and Rocio). Of these, Amatitlania (type species, A. nigrofasciata) and Rocio (type species, R. octofasciata) are described as new. The present revision treats all nominal species ever assigned to Archocentrus, as well as species that have been included in or near the same clade as Archocentrus centrarchus (type species of the genus) in available phylogenetic analyses. Geographical variation in morphology of the more widespread species was examined, which has resulted in the description of six new species {Cryptoheros chetumalensis, Amatitlania coatepeque, A. kanna, A. siquia, Rocio gemmata, and R. ocotal) with a seventh resurrected from synonymy (Cryptoheros cutteri). Archocentrus includes the type species (Ar. centrarchus), plus Ar. spinosissimus and Ar. multispinosus. Cryptoheros is restricted to the species complexes of Cr. spilurus (= subgenus Cryptoheros, including also Cr. chetumalensis and Cr. cutteri) and Cr. septemfasciatus (= Bussingius n. subgen., including also Cryptoheros altoflavus, Cr. nanoluteus, Cr. myrnae, and Cr. sajica); Cryptoheros panamensis is placed in Panamius n. subgen. Herotilapia is synonymized with Archocentrus, and Neetroplus is synonymized with Hypsophrys, which now includes the type species H. nicaraguensis and H. nematopus. Lectotypes are designated for Amatitlania nigrofasciata, Archocentrus spinosissimus, Cryptoheros septemfasciatus, Cr. spilurus, and Rocio octofasciata. Cichlasoma immaculatum is considered to be a synonym of Archocentrus spilurus, not of Ar. spinosissimus.
http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8312.2011.01720.x/full
For groups of animals with limited or unstable taxonomic resolution, congeneric phylogeographical sampling represents a way to potentially increase resolution of species limits and internal branches during phylogenetic inference. We investigated species limits and whether there was better support for hypothesized relationships among Micropterus (black basses) using wide geographical sampling. Bayesian and maximum likelihood estimates of Micropterus phylogeny including 205 mitochondrial DNA cytochrome b (1140 bp) sequences (150 haplotypes) representing eight extant species and one subspecies recovered eight well-supported clades. Haplotypes from fish identified as Micropterus coosae, Micropterus henshalli, Micropterus punctulatus, Micropterus salmoides, and Micropterus treculii created eight forms of broad-sense polyphyly in the tree, which we hypothesized were the result of incomplete lineage sorting and hybridization-mediated introgression (natural and anthropogenic, i.e. associated with stocking). Our findings mostly agree with hypothesized relationships. However, they provide a more complex view of Micropterus biodiversity, highlighting population-level processes. Our data also provide a useful guide for expanding character sampling (nuclear loci and morphology) to evaluate the history, distinctiveness, and geographical distributions of genetic lineages within and among black basses. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104, 346–363.
Delineating species boundaries correctly is crucial to the discovery of life's diversity because it determines whether or not different individual organisms are members of the same entity. The gap in communication between the dif-ferent disciplines currently involved in delimiting species is an important and overlooked problem in the so-called 'taxonomy crisis'. To solve this problem, it is suggested that taxonomy become integrative, and this integration is seen as the real challenge for the future of taxonomy. 'Integrative taxonomy' is defined as the science that aims to delimit the units of life's diversity from multiple and complementary perspectives (phylogeography, comparative morphology, population genetics, ecology, development, behaviour, etc.). Some workers have already collaborated and successfully adopted an integrative approach to taxonomy. However, it is now time for the whole discipline to evolve. A radical change in mentality is needed concerning the creation of names in order to achieve this integration and to prevent the over-abundance of both synonyms and names of doubtful application from worsening. Integrative tax-onomy gives priority to species delineation over the creation of new species names. Furthermore, it is emphasized that describing morphological diversity, referred to as 'morphodiversity', does not require the naming of any single set of specimens. Seven guidelines are proposed to help integrative taxonomists recognize cases when species are supported by broad biological evidence and therefore are deserving of an official name.
We present a phylogeographical analysis of four genera of Mesoamerican primary freshwater fish (Brycon, Bryconamericus, Eretmobrycon, and Cyphocharax). Three hundred and thirty-nine individuals were genotyped into one of 31 operational taxonomic units (OTUs) based on the nucleotide sequence of their mitochondrial ATPase 6 & 8 genes (842–839 bp). Contrary to inference based on the species-level taxonomy of these genera, molecular data identified only a single case of sympatry between closely related OTUs, despite extensive parapatry. Polytomies dominate the mtDNA-based phylogenies and demonstrate multiple, noncontemporaneous waves of rapid expansion across Mesoamerica from South American sources. Analyses based on genetic distances observed among congeneric species of Mesoamerican primary freshwater fishes in comparison to divergence between transisthmian marine fishes permit the strong inference that the Pliocene rise of the Panama land bridge provided the first opportunity for the colonization of Mesoamerica by Characiform fishes. We develop a priority-effect model, based on the assumption that genetically closely related OTUs share similar ecological niches, to reconcile the general lack of contemporary sympatry between closely related OTUs with the substantial historical connectivity among Mesoamerican drainages demonstrated by the rapid expansion of Brycon, Bryconamericus, and Cyphocharax. Finally, in most cases, we infer that the westerly limits of freshwater fish distributions in Mesoamerica are more consistent with being defined by ecological factors rather than by dispersal limitation. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 88, 235–255.
The literature about species concepts might be larger than that about any other subject in evolutionary biology, but the issue of empirically testing species boundaries has been given little attention relative to seemingly endless debates over what species are. The practical issue of delimiting species boundaries is nevertheless of central importance to many areas of evolutionary biology. The number of recently described methods for delimiting species suggests renewed interest in the topic, and some methods are explicitly quantitative. Here, we review nine of these methods by summarizing the relevant biological properties of species amenable to empirical evaluation, the classes of data required and some of the strengths and limitations of each.
Recent developments in marginal likelihood estimation for model selection in the field of Bayesian phylogenetics and molecular evolution have emphasized the poor performance of the harmonic mean estimator (HME). Although these studies have shown the merits of new approaches applied to standard normally distributed examples and small real-world data sets, not much is currently known concerning the performance and computational issues of these methods when fitting complex evolutionary and population genetic models to empirical real-world data sets. Further, these approaches have not yet seen widespread application in the field due to the lack of implementations of these computationally demanding techniques in commonly used phylogenetic packages. We here investigate the performance of some of these new marginal likelihood estimators, specifically, path sampling (PS) and stepping-stone (SS) sampling for comparing models of demographic change and relaxed molecular clocks, using synthetic data and real-world examples for which unexpected inferences were made using the HME. Given the drastically increased computational demands of PS and SS sampling, we also investigate a posterior simulation-based analogue of Akaike's information criterion (AIC) through Markov chain Monte Carlo (MCMC), a model comparison approach that shares with the HME the appealing feature of having a low computational overhead over the original MCMC analysis. We confirm that the HME systematically overestimates the marginal likelihood and fails to yield reliable model classification and show that the AICM performs better and may be a useful initial evaluation of model choice but that it is also, to a lesser degree, unreliable. We show that PS and SS sampling substantially outperform these estimators and adjust the conclusions made concerning previous analyses for the three real-world data sets that we reanalyzed. The methods used in this article are now available in BEAST, a powerful user-friendly software package to perform Bayesian evolutionary analyses.
Genetic diversity is recognized as a fundamental component of biodiversity and its protection is incorporated in several conventions and policies. However, neither the concepts nor the methods for assessing conservation value of the spatial distribution of genetic diversity have been resolved. Comparative phylogeography can identify suites of species that have a common history of vicariance. In this study we explore the strengths and limitations of Faith’s measure of ‘Phylogenetic Diversity’ (PD) as a method for predicting from multiple intraspecific phylogeographies the underlying feature diversity represented by combinations of areas. An advantage of the PD approach is that information on the spatial distribution of genetic diversity can be combined across species and expressed in a form that allows direct comparison with patterns of species distributions. It also seeks to estimate the same parameter, feature diversity, regardless of the level of biological organization. We extend the PD approach by using Venn diagrams to identify the components of PD, including those unique to or shared among areas and those which represent homoplasy on an area tree or which are shared across all areas. PD estimation should be complemented by analysis of these components and inspection of the contributing phylogeographies. We illustrate the application of the approach using mtDNA phylogeographies from vertebrates resident in the wet tropical rainforests of north-east Queensland and compare the results to biodiversity assessments based on the distribution of endemic vertebrate species. The genetic vs. species approaches produce different assessments of conservation value, perhaps reflecting differences in the temporal and spatial scale of the determining processes. The two approaches should be seen as complementary and, in this case, conservation planning should incorporate information on both dimensions of biodiversity.
The origin of extant neotropical biodiversity has been a controversial topic since the time of Darwin. In this review, I discuss the timing of, and potential driving factors associated with, diversification using recent evidence from molecular phylogenetics. Although these studies provide new insights into the subject, they are sensitive to dating approaches and targets, and can eventually lead to biased conclusions. A careful analysis suggests that the origin of extant neotropical biodiversity cannot be attributed to the action of one or few events during key time intervals. Rather, it is the result of complex ecological and evolutionary trends initiated by Neogene tectonic events and palaeogeographical reorganisations, and maintained by the action of Pleistocene climatic changes.
Historical biogeography and comparative phylogeography have much in common. Both seek to discover common historical patterns in the elements of biotas, although typically at different tiers of evolutionary history. Comparative phylogeography is based on phylogeographic analyses of multiple taxa, usually widespread species. By comparing the phylogeographic structures of numerous widespread sympatric species, one can infer whether the current fauna has been historically stable, as evidenced by the relative frequency of geographically congruent reciprocally monophyletic groups. Alternatively, if species distributions are ephemeral over evolutionary time, a mixture of phylogeographic structures is expected. Coalescence analyses contribute information about history irrespective of whether haplotype phylogenies are structured or not. In the aridlands of North America, several isolating events are evident in the phylogeographic patterns of birds, mammals and herps. A mid-peninsular seaway in Baja California, dated at ca. one million years before present, had a pervasive effect, with 13 of 16 assayed species showing a concordant split. Hence, this community appears to have been a stable assemblage of species over the past one million years. In contrast, the avifauna of the Sonoran-Chihuahuan deserts consists of two species with a concordant split and three other species that are undifferentiated across both deserts. Hence, the species in this area have had different histories. The Baja biota appears to resemble its ancestral configuration to a greater degree than the Sonoran-Chihuahuan one. A deeper evolutionary event separated taxa in Baja California from the eastern deserts, showing that the aridlands fauna was affected by events at different times resulting in overlain tiers of history.
As DNA sequences have become more readily available, it has become increasingly desirable to infer species phylogenies from multigene data sets. Much recent work has centered around the recognition that substantial incongruence in single-gene phylogenies necessitates the development of statistical procedures to estimate species phylogenies that appropriately model the process of evolution at the level of the individual genes. One process that gives rise to variation in the histories of individual genes is incomplete lineage sorting, which is commonly modeled by the coalescent, and thus much current work is focused on proper estimation of species phylogenies under the coalescent model. A second common source of discord in single-gene phylogenies is hybridization, a process that is ubiquitous in many groups of plants and animals. Although methods to incorporate hybridization into phylogenetic estimation have also been developed, only a handful of methods that address both coalescence and hybridization have been proposed. Here, I propose an extension of an existing model that incorporates both of these processes simultaneously by utilizing gene trees for inference in a likelihood framework. The model allows examination of the evidence for hybridization in the presence of incomplete lineage sorting due to deep coalescence via model selection using standard information criteria (e.g., Akaike information criterion and Bayesian information criterion). The potential of the method is evaluated using simulated data.