Article

Comparative phylogeography of livebearing fishes in the genera Poeciliopsis and Poecilia (Poeciliidae: Cyprinodontiformes) in Central Mexico

Journal of Biogeography

May 2005
32(5):775 - 780

DOI:10.1111/j.1365-2699.2005.01236.x

Authors:

Mariana Mateos

Texas A&M University

Aim To test the hypothesis that the vicariant event responsible for north–south divergences in two clades of the fish genus Poeciliopsis Regan was also responsible for north–south divergences in the fish Poecilia butleri Jordan. Location Central Mexico. Methods Parsimony, distance, maximum likelihood and Bayesian phylogenetic analyses of a mitochondrial gene. Molecular clock test and Bayesian analyses of divergence time. Results We report concordant phylogeographical patterns between two clades in the genus Poeciliopsis (i.e. the other formed by P. latidens Garman and P. fasciata Meek, and the other formed by P. presidionis Jordan and P. turneri Miller) and the clade of Poecilia butleri, with northern and southern individuals within each clade grouping into separate lineages. There is also evidence for slower substitution rates in Poecilia compared with Poeciliopsis. After taking into account these substitution rate discrepancies with Bayesian relaxed molecular clock analyses, north–south divergences in Poecilia butleri were equivalent to those reported for Poeciliopsis latidens-fasciata and P. presidionis-turneri. Main conclusions The same Plio-Pleistocene vicariant event associated with geological activity of the Trans-Mexican Volcanic Belt (TMVB) appears to have caused divergence in three different freshwater fish lineages. This study is an example of how comparative phylogeography can strengthen inferences about vicariant events in regions of high biological diversity and complex geological history such as the TMVB.

Population level genetic divergence and phylogenetic placement of Mexican shortfin mollies (Mollienesia: Poecilia: Poeciliidae)

Article

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May 2023
NEOTROP ICHTHYOL

Mexico is a megadiverse region with a complex geological history, but it remains unclear to what extent the distribution of freshwater fish has been influenced by geographic barriers. This study examines the population level genetic divergence and phylogenetic relationships of species in the shortfin group of the subgenus Mollienesia (genus Poecilia), a group of live-bearing fishes that are widely distributed across Mexico, with sampling at a small geographic scale. Samples from over 50 locations were analyzed for six species by using phylogenetic and haplotype network approaches to assess genetic diversity across geographic ranges and to refine the distributions of species in this group. The results indicate that Mexican species have diversified following multiple, independent invasions from Middle America. Two species found north of the Trans-Mexican Volcanic Belt (TMVB) and one transversal species exhibited weak phylogenetic structure, likely due to the lack of physiographic barriers, recent colonization, and high dispersal rates among regions. In contrast, three species found south of the TMVB exhibited strong phylogenetic structure, reflecting a longer presence in the area and multiple physiographic barriers that isolated populations. This study identified mechanisms driving divergence and speciation, expanded the known range of several species, and resolved taxonomic uncertainties of populations.

A multilocus phylogeny of the fish genus Poeciliopsis: Solving taxonomic uncertainties and preliminary evidence of reticulation

Article

Full-text available

Jan 2019

The fish genus Poeciliopsis constitutes a valuable research system for evolutionary ecology, whose phylogenetic relationships have not been fully elucidated. We conducted a multilocus phylogenetic study of the genus based on seven nuclear and two mitochondrial loci with a thorough set of analytical approaches, that is, concatenated (also known as super‐matrix), species trees, and phylogenetic networks. Although several relationships remain unresolved, the overall results uncovered phylogenetic affinities among several members of this genus. A population previously considered of undetermined taxonomic status could be unequivocally assigned to P. scarlli; revealing a relatively recent dispersal event across the Trans‐Mexican Volcanic Belt (TMVB) or Pacific Ocean, which constitute a strong barrier to north–south dispersal of many terrestrial and freshwater taxa. The closest relatives of P. balsas, a species distributed south of the TMVB, are distributed in the north; representing an additional north–south split in the genus. An undescribed species of Poeciliopsis, with a highly restricted distribution (i.e., a short stretch of the Rio Concepcion; just south of the US‐Mexico border), falls within the Leptorhaphis species complex. Our results are inconsistent with the hypothesis that this species originated by “breakdown” of an asexual hybrid lineage. On the other hand, network analyses suggest one or more possible cases of reticulation within the genus that require further evaluation with genome‐wide marker representation and additional analytical tools. The most strongly supported case of reticulation occurred within the subgenus Aulophallus (restricted to Central America), and implies a hybrid origin for P. retropinna (i.e., between P. paucimaculata and P. elongata). We consider that P. balsas and P. new species are of conservation concern.

Evolutionary History of the Fish Genus Astyanax Baird & Girard (1854) (Actinopterygii, Characidae) in Mesoamerica Reveals Multiple Morphological Homoplasies

Chapter

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Apr 2011

Background: Mesoamerica is one of the world's most complex biogeographical regions, mostly due to its complex geological history. This complexity has led to interesting biogeographical processes that have resulted in the current diversity and distribution of fauna in the region. The fish genus Astyanax represents a useful model to assess biogeographical hypotheses due to it being one of the most diverse and widely distributed freshwater fish species in the New World. We used mitochondrial and nuclear DNA to evaluate phylogenetic relationships within the genus in Mesoamerica, and to develop historical biogeographical hypotheses to explain its current distribution.

Evolutionary history of the Evolutionary history of the fish genus Astyanax Baird and Girard (1854) (Actinopterygii, Characidae)

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Jan 2008

Do freshwater ecoregions and continental shelf width predict patterns of historical gene flow in the freshwater fish Poecilia butleri? Dryad Digital Repository

Article

Jul 2014
BIOL J LINN SOC

We examined historical patterns of gene flow in the freshwater fish Poecilia butleri in western Mexico. We tested the hypothesis that the boundaries between four freshwater ecological communities (ecoregions) might have limited the movement of P. butleri because changes in species compositions might restrict establishment between adjacent ecoregions, even in situations where a physical barrier is absent. Hence, we predicted that boundaries between ecoregions should correspond to phylogeographical breaks in P. butleri. We also tested the hypothesis that the width of the continental shelf affected historical gene flow in P. butleri because a broad continental shelf provides a greater opportunity for rivers to coalesce during historical episodes of low sea levels as opposed to a narrow continental shelf that should restrict the potential for gene flow among adjacent rivers. Hence, we predicted greater amounts of historical gene flow among neighbouring river basins in the region of western Mexico where the continental shelf is wider, whereas, in the region where the continental shelf is narrower, we expected to detect limited levels of historical gene flow. We analyzed mitochondrial DNA sequence data (cytochrome b) taken from 264 individuals of P. butleri collected from 34 locations distributed across four different ecoregions in western Mexico. To examine patterns of phylogenetic diversification and historical gene flow in P. butleri, we employed several analytical approaches, including traditional tree-based phylogenetic analyses (likelihood and parsimony), haplotype network reconstruction, analyses of molecular variance, and spatial analysis of molecular variance. We found genetic breaks coinciding with two out of three different ecoregion boundaries, suggesting limited historical gene flow. In addition to different species compositions between these adjacent ecoregions, geological features such as the Trans-Mexican Volcanic Belt and the mountainous topography in south-western Mexico, likely contributed to these observed genetic breaks. By contrast, no genetic break was evident between two other ecoregions, a result that partially rejects our first hypothesis. Several results were consistent with our second hypothesis. Changes in the width of the continental shelf in western Mexico are associated with the observed patterns of historical gene flow. Our results indicate that the interactions among multiple geological and biological factors affect the spatial patterns of genetic diversity of widespread freshwater species. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, ●●, ●●–●●.

Comparative Phylogeography: Designing Studies while Surviving the Process

Article

Full-text available

Nov 2011

Comparative phylogeography (CP) can be defined as the study of the effects of evolutionary history and biogeography on the distribution of genetic variation of codistributed species. CP studies have intensified in recent years, which is a natural progression from an extensive history of intraspecific phylogeography research. On the basis of a thorough review of published studies that specifically deal with CP, our objective in the present review is to provide a comprehensive guide to the discipline that will help those wishing to develop a CP project. We describe the characteristics that shape a CP study and summarize the field's prime theoretical, methodological, and analytical requirements; frequent hypotheses tested; and current achievements and limitations, including a variety of illustrative examples throughout. We finally highlight some new approaches in CP and briefly discuss future directions for the field.

Patterns of Genetic Differentiation Among Populations of Smilisca fodiens

Article

Full-text available

Jun 2012
HERPETOLOGICA

The Trans-Mexican Volcanic Belt and surrounding areas contain substantial biological diversity. The mountains that make up the Trans-Mexican Volcanic Belt are a hypothesized biogeographic barrier for the terrestrial fauna found in the region. Several phylogeographic studies have provided genetic evidence in support of this historical narrative; however, the species examined represent a small percentage of the diversity found in this part of Mexico. Thus, additional studies are needed to identify concordant phylogeographic patterns and infer the historic species composition of particular ecoregions. In this study we investigated genetic variation in the Lowland Burrowing Treefrog, Smilisca fodiens, a species that occurs on both sides of the Trans-Mexican Volcanic Belt. We used mitochondrial (12S and 16S ribosomal subunits; 1039 base pairs [bp]) and nuclear (tyrosinase precursor; 513 bp) DNA to perform phylogenetic analyses on frogs from several localities in Mexico. Mitochondrial DNA supported two well-defined clades that correspond to populations found north and south of the Trans-Mexican Volcanic Belt, respectively. These analyses of matrilineal lineages also found higher levels of genetic diversity south of the Trans-Mexican Volcanic Belt. Although our nuclear DNA analysis did not reveal a phylogeographic split at the Trans-Mexican Volcanic Belt, we observed higher genetic variation among our southern samples, similar to the mitochondrial analyses. Our results are consistent with studies in other sympatric taxa that propose the Trans-Mexican Volcanic Belt as a biogeographic barrier. Additionally, our results suggest recent northern range expansion of S. fodiens. We suggest retaining S. fodiens as a single species until future work can clarify the amount and direction of gene flow between the mitochondrial clades.

“Colonization routes and demographic history of Chirostoma humboldtianum in the central Mexican plateau”

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Aug 2020
J FISH BIOL

In the present study we evaluate the population structure and potential colonization routes of the silverside Chirostoma humboldtianum through approximate Bayesian computations. Six microsatellite loci were amplified in a total of 288 individuals from six different locations covering the complete geographic distribution of the species. Additionally, two mitochondrial DNA markers, a D loop control region and cytochrome b were amplified in a subset of 107 individuals. The results found with microsatellites allow recovering well‐structured populations that have experienced a drastic reduction in the effective population size. On the other hand, mtDNA sequences showed a moderate phylogeographic structure with shared haplotypes between geographic localities and signalsof a slight increase in the effective population size. Finally, the approximate Bayesian computation analysis performed with both datasets suggested a west‐to‐east colonization route for the species in Central Mexico.

Molecular clocks, biogeography and species diversity in Herichthys with evaluation of the role of Punta del Morro as a vicariant brake along the Mexican Transition Zone in the context of local and global time frame of cichlid diversification

Article

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Apr 2020

Using molecular dated phylogenies and biogeographic reconstructions, the species diversity, biogeography and time frame of evolution of the genus Herichthys were evaluated. In particular, we test the role of Punta del Morro (PdM) as a vicariant brake along the Mexican Transition Zone in the context of local and global time frame of cichlid diversification using several sets of calibrations. Species diversity in Herichthys is complex and the here employed dating methods suggest young age and rapid divergence for many species while species delimitation methods did not resolve these young species including both sympatric species pairs. Based on our molecular clock dating analyses, Herichthys has colonized its present distribution area significantly prior to the suggested vicariance by PdM (10-17.1 Ma vs. 5 to 7.5 Ma). The PdM constraint is in conflict with all other paleogeographic and fossil constraints including novel ones introduced in this study that are, however, congruent among each other. Our study demonstrates that any cichlid datings significantly older or younger than the bounds presented by our analyses and discussion have to be taken as highly questionable from the point of view of Middle American paleogeography and cichlid biogeography unless we allow the option that cichlid biogeography is completely independent from ecological and geological constraints.

Multilocus phylogeography and morphology give insights into the recent evolution of a Mexican endemic songbird: Vireo hypochryseus

Article

May 2014

We used multilocus phylogeographic analyses, morphometric measurements, and environmental niche models (ENMs) to analyze the recent evolution of the golden vireo Vireo hypochryseus, a Mexican endemic species. Vireo hypochryseus is made up of two phylogeographically structured mitochondrial DNA clades that probably diverged 132 000 yr ago. One clade comprised individuals from mainland Sinaloa and the Tres Mar í as islands in the northwest, and the other included individuals from the remaining range of the species. Th is marked phylogeographic structure contrasts with the low genetic structure reported for temperate North American vireos. The nuclear DNA markers also showed some geographic diﬀerences in allele frequency, but did not exhibit a clearphylogeographic structure. The morphometric analyses suggested a decreasing north to south cline, with the largest individuals located in the Tres Marías islands. The ENMs did not support a scenario of geographic fragmentation of the environmental conditions of the area in which V. hypochryseus has inhabited over the last 130 000 yr. However, a model of isolation by resistance based on the actual conﬁguration of climatic conditions in western Mexico did explain a major proportion of both the mitochondrial DNA distances and the diﬀerences in size, while a model of isolation by distance explain a low proportion of such diﬀerences. Therefore, the recent history of V. hypochryseus was likely shaped by historical habitat fragmentation due to ﬂuctuating environmental conditions in the mainland that produced a phylogeographic print, and natural selection on morphological traits in the insular population, suggesting an active diversiﬁ cation of endemic lineages in the Mexican dry forest.

Phylogeography and demographic history of the swordtail fish Xiphophorus multilineatus

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May 2025
ENVIRON BIOL FISH

Geographical features and climatic oscillations that occurred in the Quaternary are among the main factors shaping the genetic diversity of both terrestrial and aquatic taxa. Rivers are naturally discontinuous and heterogeneous habitats due to interruptions and connections of water flow that resulted from tectonic activity and Pleistocene climatic fluctuations. These factors, in combination with the biological characteristics of the species, can affect the dispersal of organisms that are restricted to rivers, which can, in turn, influence their genetic diversity, genetic structure, and gene flow. Here, we investigate the phylogeographic patterns and demographic history of the high-backed pygmy swordtail fish Xiphophorus multilineatus to understand the effects that geography and climatic fluctuations of the Pleistocene had on the genetic patterns of this species. We amplified the control region of the mitochondrial DNA of 62 individuals from six sites in the Tampaón basin (the only distribution area of the species) in San Luis Potosí, Mexico. We found relatively high genetic diversity and limited genetic structure, as well as demographic expansions occurring during glacial and interglacial periods of the Pleistocene. The phylogeographic patterns exhibited by X. multilineatus seem to reflect cycles of isolation and connection of its populations as a result of the climatic oscillations that occurred during the Pleistocene. This study constitutes a first approximation of geographic patterns of genetic variation in the high-backed pygmy swordtail fish Xiphophorus multilineatus.

The evolution of a placenta accelerates the evolution of post-copulatory reproductive isolation

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Dec 2024
EVOLUTION

The evolution of placentation is predicted to intensify intergenomic conflicts between mothers and offspring over optimal levels of maternal investment by providing offspring opportunities to manipulate mothers into allocating more resources. Parent-offspring conflicts can result in the evolution of reproductive isolation among populations when conflicts resolve in different ways. Postzygotic reproductive isolation is hypothesized to evolve more rapidly following the evolution of placentation due to the predicted increase in conflict. We tested this hypothesis by performing interpopulation crosses within placental and non-placental species of Poeciliopsis to determine if the relationship between genetic distance and measures of postzygotic reproductive success differed as function of reproductive mode. We did not observe any differences in offspring viability or sterility among crosses. Offspring size declined rapidly as a function of interpopulation genetic distance within the placental species, but not among our non-placental species. The decrease in offspring size in the placental species was beyond normal variation, likely representing a major fitness cost, consistent with the prediction that negative epistatic interactions are evolving more quickly among populations in our placental species than the non-placental species. We discuss how our results support the role parent-offspring conflicts play in the evolution of reproductive isolation and reproductive mode.

Evidence for gene flow and trait reversal during radiation of Mexican Goodeid fish

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Understanding the phylogeographic history of a group and identifying the factors contributing to speciation is an important challenge in evolutionary biology. The Goodeinae are a group of live-bearing fishes endemic to Mexico. Here, we develop genomic resources for species within the Goodeinae and use phylogenomic approaches to characterise their evolutionary history. We sequenced, assembled and annotated the genomes of four Goodeinae species, including Ataeniobius toweri , the only matrotrophic live-bearing fish without a trophotaenia in the group. We estimated timings of species divergence and examined the extent and timing of introgression between the species to assess if this may have occurred during an early radiation, or in more recent episodes of secondary contact. We used branch-site models to detect genome-wide positive selection across Goodeinae , and we specifically asked whether this differs in A. toweri , where loss of placental viviparity has recently occurred. We found evidence of gene flow between geographically isolated species, suggesting vicariant speciation was supplemented by limited post-speciation gene flow, and gene flow may explain previous uncertainties about Goodeid phylogeny. Genes under positive selection in the group are likely to be associated with the switch to live-bearing. Overall, our studies suggest that both volcanism-driven vicariance and changes in reproductive mode influenced radiation in the Goodeinae .

Comparative phylogeography of two codistributed species of the genus Herichthys (Actinopterygii: Cichliformes: Cichlidae) in northeastern Mexico

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Phylogeographic patterns of freshwater fishes in coastal regions are highly susceptible to eustatic sea level changes associated with Pleistocene glaciations. In this context, the Plain Coastal Gulf in northeastern Mexico represents an ideal study area due to its low elevation. Herein, we compare the phylogeographic structures of two cichlid species of the genus Herichthys Baird et Girard, 1854 widely distributed in the Pánuco-Tamesí system in northeastern Mexico using two mitochondrial markers. The species studied were: Herichthys carpintis (Jordan et Snyder, 1899) and Herichthys pantostictus (Taylor et Miller, 1983). We estimate their genetic diversity, gene flow, and demographic history and perform biogeographic reconstructions using a Bayesian computation approach and environmental niche modeling. The biogeographic reconstruction suggests a different history for each species. Environmental niche modeling indicates that both species experienced a demographic expansion during the Pleistocene but responded differently to Pleistocene climatic changes. In summary, their current sympatric distribution could be the outcome of contemporary and not historical processes reflecting a pseudo-incongruent pattern.

Patterns of Distribution in Helminth Parasites of Freshwater Fish of Mexico: Can We Detect Hotspots of Richness and Endemism?

Chapter

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Speciation on a complex landscape; phylogeny and demography of Mexican Goodeid fish

Preprint

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Understanding the phylogeographic history of a group and identifying the factors contributing to speciation is an important challenge in evolutionary biology. Vicariance has clearly played a major role in diversification across diverse groups of organisms, but how this interacts with intrinsic biological features such as changes in reproductive system or sexual selection is less well understood. The Goodeinae are a Mexican endemic group of live-bearing fish. Here, we develop genomic resources for species within the Goodeinae and use phylogenomic approaches to characterise their evolutionary history. We sequenced, assembled and annotated the genomes of four new Goodeinae genomes, including A. toweri, the only matrotrophic live-bearing fish without a trophotaenia in the group. We produced a phylogeny of the Goodeinae and estimate timings of species divergence. We determined the extent and timing of introgression between the species to assess if this may have occurred during an early radiation, or in more recent episodes of secondary contact. We also analyse patterns in the changes of effective population size for the species and examine the time course of expansion and decline. We used branch-site models to detect genome-wide positive selection across Goodeinae, and we specifically ask if this differs in A. toweri, where reversal of placental viviparity has recently occurred. We find that Goodeinae diverged rapidly, with reductions in effective population size after each split. Contrary to expectations, we find evidence of gene flow between geographically isolated species, suggesting vicariant speciation was supplemented by limited post-speciation gene flow, potentially as a result of river piracy. Genes under positive selection in the group are likely to be associated with the switch to live-bearing. Overall, our studies suggest that both volcanism driven vicariance and changes in reproductive mode influenced radiation in the Goodeinae.

Evolutionary history of the Aztec shiner Aztecula sallaei (Günther, 1868) (Teleostei: Cyprinidae): An endemic and monotypic species of Mexico

Article

Oct 2021

The distribution and diversification processes of freshwater fishes have been influenced by tecto-volcanic and climatic events that have in turn promoted genesis, destruction, and numerous changes in the drainage networks, leaving complex phylogeographic patterns in the ichthyofauna of highly dynamic regions such as central Mexico. In this study, we evaluated the evolutionary history of the Aztec shiner Aztecula sallaei, which is distributed in currently isolated drainages in the highlands of central Mexico, performing phylogenetic, biogeographic, and phylogeographic analyses using three genes: the mitochondrial cytb and two nuclear genes, S7 and ACTB. The studied populations show three genetically divergent and structured lineages: two are exclusive to the Panuco biogeographic region and the third is widely distributed in the Upper Lerma, Middle Lerma, Cuitzeo, and Balsas (Zempoala Lakes) biogeographic regions, as well as one population in Panuco. This widely distributed lineage also presents a genetic structure that is congruent with these biogeographic regions supported by the cytb gene and partially supported by the S7 gene. The divergence time of these lineages was dated to the Pleistocene period (0.56–2.79 Mya) and was associated with temporally or spatially independent events of river capture, which promoted the exchange of fishes between the river headwaters followed by subsequent isolation, explaining the current distribution of this cyprinid in neighboring but currently isolated basins. Our results indicate that, in the highlands of central Mexico, tecto-volcanic activity has shaped the geographic ranges, diversification, and phylogeographic patterns of freshwater fishes.

Sex chromosomes in meiotic, hemiclonal, clonal and polyploid hybrid vertebrates: Along the 'extended speciation continuum'

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We review knowledge about the roles of sex chromosomes in vertebrate hybridization and speciation, exploring a gradient of divergences with increasing reproductive isolation (speciation continuum). Under early divergence, well-differentiated sex chromosomes in meiotic hybrids may cause Haldane-effects and introgress less easily than autosomes. Undifferentiated sex chromosomes are more susceptible to introgression and form multiple (or new) sex chromosome systems with hardly predictable dominance hierarchies. Under increased divergence, most vertebrates reach complete intrinsic reproductive isolation. Slightly earlier, some hybrids (linked in ‘the extended speciation continuum’) exhibit aberrant gametogenesis, leading towards female clonality. This facilitates the evolution of various allodiploid and allo- polyploid clonal (‘asexual’) hybrid vertebrates, where ‘asexuality’ might be a form of intrinsic reproductive isolation. A comprehensive list of ‘asexual’ hybrid vertebrates shows that they all evolved from parents with divergences that were greater than at the intraspecific level (K2P-distances of greater than 5–22% based on mtDNA). These ‘asexual’ taxa inherited genetic sex determi- nation by mostly undifferentiated sex chromosomes. Among the few known sex-determining systems in hybrid ‘asexuals’, female heterogamety (ZW) occurred about twice as often as male heterogamety (XY). We hypothesize that pre-/meiotic aberrations in all-female ZW-hybrids present Haldane- effects promoting their evolution. Understanding the preconditions to produce various clonal or meiotic allopolyploids appears crucial for insights into the evolution of sex, ‘asexuality’ and polyploidy. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.

Genetic and morphological differentiation in the green swordtail fish, Xiphophorus hellerii: the influence of geographic and environmental factors

Article

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Jul 2021
HYDROBIOLOGIA

Genetic and morphological variation within species are determined by intrinsic and extrinsic factors, which jointly or separately can promote population divergence. In freshwater systems, the structure of the basins, geographic distance, climatic fluctuations of the Pleistocene as well as extant environmental variation are important drivers of population divergence. Xiphophorus hellerii is a fish widely distributed in basins of the Gulf of Mexico slope. We used mitochondrial DNA sequences, geometric morphometrics and ecological niche modeling to investigate the roles of geographic and environmental factors in population divergence of X. hellerii. We found strong genetic structure conforming to the Stream Hierarchy and isolation by distance models. Demographic tests and ecological niche modeling suggested that the niche and populations of the species underwent contractions and expansions during the Pleistocene. Body shape of X. hellerii varied among basins and hydrological regions. Temperature seems to affect body shape, as individuals with shallow bodies were found in basins with low temperature and high altitudes. We found significant relationships between genetics, morphology, geography and the environment. Our study suggests that X. hellerii from different basins and hydrological regions have followed independent evolutionary routes and that environmental and geographical factors have played an important role in population divergence.

Revista Mexicana de Biodiversidad Diversity and divergence of 10 amphibian species from the Santiago River Basin as a result of vulcanism in the Trans-Mexican Volcanic Belt

Article

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May 2019

During the Trans-Mexican Volcanic Belt history, geological events related to its formation have produced barriers for highland species, favoring isolation and population diversification. In this study, we investigated the phylogenetic relationships between amphibian populations from the highlands of the Santiago River Basin in Jalisco and Nayarit, Mexico. We sampled 33 individuals belonging to 10 species, from 10 volcanoes and mountains, and along altitudinal gradients from 1,400 to 2,915 m asl. Additionally, 55 samples from populations outside of the study area were included. We amplified a fragment of the cytb gene and using fossils and secondary calibrations we estimated divergence times between species and their populations, using a Bayesian approach. Divergence estimates suggest that separations between species occurred during the Neogene, probably due to geological episodes in the region, while intraspecific divergences occurred mainly during the Quaternary. Our results reveal new patterns that can help the understanding of evolutionary history in highland species.

Sequence-based species delineation and molecular phylogenetics of the transitional Nearctic–Neotropical grasshopper genus Taeniopoda (Orthoptera, Romaleidae)

Article

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May 2017

Taeniopoda is a genus of grasshoppers currently represented by 12 species distributed from southern USA to Panama, with most of them occurring along the transitional Nearctic–Neotropical region in central and southern Mexico. Despite being a small group of conspicuous, colourful species, the systematics of Taeniopoda has been largely neglected, including its phylogenetic affinity with the morphologically similar, monotypic genus Romalea. Here, we assessed the species limits in 11 of the species of Teniopoda based on two mitochondrial (mt) markers (COI, cyt b). Phylogenetic relationships were reconstructed adding two nuclear gene markers (28S, H3). A relaxed molecular clock analysis was performed based on the mt markers. We detected nuclear mt paralogues (numts) and the probable introgression of T. tamaulipensis mtDNA in specimens of T. eques from central Mexico. Between six and 14 species of Taeniopoda were delimited by the sequence-based approaches performed (COI divergence with thresholds of 1 and 2%; General Mixed Yule-Coalescent (GMYC) model). The GMYC and 1% threshold analyses with COI were more congruent with the currently recognized morphology-based taxonomy with 10 and 11 putative species, respectively. Four of these species were regarded as ‘stable’, since they were supported by at least one of the molecular analyses and by diagnostic morphological features. The species-based phylogeny recovered Taeniopoda as paraphyletic with respect to the monotypic genus Romalea. Three morphologically and geographically congruent major clades were recovered, two with species having a considerably elevated pronotal crest and one with its members having it less elevated. The origin and subsequent diversification of Taeniopoda were estimated to occur from the mid and late Miocene to Pliocene, respectively. The current species diversity in Taeniopoda was estimated to occur during the Pleistocene, which was probably influenced by the climatic oscillations that occurred during this period and the uplift of mountain ranges in Central America.

The origin and biogeographic diversification of fishes in the family Poeciliidae

Article

Full-text available

Mar 2017
PLOS ONE

The fish subfamily Poeciliinae (sensu Parenti, 1981) is widely distributed across the Western Hemisphere and a dominant component of the fish communities of Central America. Poeciliids have figured prominently in previous studies on the roles of dispersal and vicariance in shaping current geographic distributions. Most recently, Hrbek et al. combined a DNA-based phylogeny of the family with geological models to provide a biogeographic perspective that emphasized the role of both vicariance and dispersal. Here we expand on that effort with a database enlarged in the quantity of sequence represented per species, in the number of species included, and in an enlarged and more balanced representation of the order Cyprinodontiformes. We combine a robust timetree based upon multiple fossil calibrations with enhanced biogeographic analyses that include ancestral area reconstructions to provide a detailed biogeographic history of this clade. Key features of our results are that the family originated in South America, but its major diversification dates to a later colonization of Central America. We also resolve additional colonizations among South, Central and North America and the Caribbean and consider how this reconstruction contributes to our understanding of the mechanisms of dispersal.

Sympatry Predicts Spot Pigmentation Patterns and Female Association Behavior in the Livebearing Fish Poeciliopsis baenschi

Article

Full-text available

Jan 2017
PLOS ONE

In this study, we explored the possibility that differences in pigmentation patterns among populations of the fish Poeciliopsis baenschi were associated with the presence or absence of the closely related species P. turneri. If reproductive character displacement is responsible, spotting patterns in these two species should diverge in sympatry, but not allopatry. We predicted that female P. baenschi from sympatric sites should show a preference for associating with conspecifics vs. heterospecific males, but females from allopatric sites should show no such preferences. To evaluate these predictions, we compared spotting patterns and female association behaviors in populations of P. baenschi from Central Mexico. We found that both of our predictions were supported. Poeciliopsis baenschi that co-occured with P. turneri had spotting patterns significantly different than their counterparts from allopatric sites. Using a simultaneous choice test of video presentations of males, we also found that female P. baenschi from populations that co-occured with P. turneri spent significantly more time with males of their own species than with P. turneri males. In contrast, females from allopatric populations of P. baenschi showed no differences in the amount of time they spent with either conspecific or heterospecific males. Together, our results are consistent with the hypothesis that reproductive character displacement may be responsible for behavioral and spotting pattern differences in these populations of P. baenschi.

Phylogenetic analyses of the subgenus Mollienesia (Poecilia, Poeciliidae, Teleostei) reveal taxonomic inconsistencies, cryptic biodiversity, and spatio-temporal aspects of diversification in Middle America

Article

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The subgenus Mollienesia is a diverse group of freshwater fishes, including species that have served as important models across multiple biological disciplines. Nonetheless, the taxonomic history of this group has been conflictive and convoluted, in part because the evolutionary relationships have not been rigorously resolved. We conducted a comprehensive molecular phylogenetic analysis of the subgenus Mollienesia to identify taxonomic discrepancies and potentially identify undescribed species, estimate ancestral areas of origin and estimate dates of divergence, as well as explore biogeographical patterns. Our findings confirm the presence of three main clades composed of the P. latipinna, P. sphenops, and P. mexicana species complexes. Unlike previously hypothesized morphology-based analyses, species found on the Caribbean Islands are not part of Mollienesia, but are more closely related to species of the subgenus Limia. Our study also revealed several taxonomic inconsistencies and distinct lineages in the P. mexicana species complex that may represent undescribed species. The diversity in the subgenus Mollienesia is a result of dynamic geologic activity leading to vicariant events, dispersal across geologic blocks, and ecological speciation.

Contrasting genetic structure in two codistributed freshwater fish species of highly seasonal systems

Article

Apr 2009

Given the seasonal nature of ecosystems such as permanent sinkholes ('cenotes') and temporary wetlands, their fish fauna experience yearly local extinction and colonization processes, with strong fluctuations in population size. We evaluated the genetic diversity, population genetic structure and degree of isolation of populations of Poecilia orri and Gambusia yucatana among and within wetlands and cenotes. We also assessed some abiotic characteristics of the water bodies and their potential relationship with average genetic diversity. Both species showed low genetic diversity, but this was twice as low in P. orri. Populations of G. yucatana showed no genetic structure, whereas those of P. orri did. The genetic divergence results were consistent with isolation between cenotes and wetlands, where the different types of water bodies had a distinctive genetic composition. We suggest that our genetic diversity and differentiation results are associated with the successive, seasonal-yearly population size shrinkage and expansion events (i.e. extinction and recolonization) that occur in these systems, and also with the environmental tolerance, body size, and reproduction characteristics of both species. Our results show how these codistributed species can have markedly different genetic structuring and diversity, most likely determined by their particular biological and ecological characteristics, and provide baseline information for future studies.

How Long Does Evolution of the Troglomorphic Form Take? Estimating Divergence Times in Astyanax Mexicanus

Article

Full-text available

Apr 2007

Features including colonization routes (stream capture) and the existence of both epigean and cave-adapted bypogean populations make Astyanax mexicanus an attractive system for investigating the subterranean evolutionary time necessary for acquisition of the troglomorphic form. Using published sequences, we have estimated divergence times for A. mexicanus using: 1) two different population-level mitochondrial datasets (cytochrome b and NADH dehydrogenase 2) with both strict and relaxed molecular clock methods, and 2) broad phylogenetic approaches combining fossil calibrations and with four nuclear (recombination activating gene, seven in absentia, forkhead, and αt-tropomyosin) and two mitochondrial (16S rDNA and cytochrome b) genes. Using these datasets, we have estimated divergence times for three events in the evolutionary history of troglomorphic A. mexicanus populations. First, divergence among cave haplotypes occurred in the Pleistocene, possibly correlating with fluctuating water levels allowing the colonization and subsequent isolation of new subterranean habitats. Second, in one lineage, A. mexicanus cave populations experienced introgressive hybridization events with recent surface populations (0.26-2.0 Ma), possibly also correlated with Pleistocene events. Finally, using divergence times from surface populations in the lineage without evidence of introgression as an estimate, the acquisition of the troglomorphic form in A. mexicanus is younger than 2.2 (fossil calibration estimates) - 5.2 (cytb estimate) Ma (Pliocene).

Taxonomic composition of the helminth parasites of ictalurids and heptapterids (Osteichthyes: Siluriformes) in Mexico, with a hypothesis of biogeographical primary homology

Article

Dec 2008

Ictaluridae and Heptapteridae (Siluriformes) are 2 families of freshwater fishes distributed in Mexico, with a nearctic and neotropical origin, respectively. This generates a particular interest in the study of its parasitic helminths from the biogeographical point of view. In this study we present a checklist of the helminth parasites of these freshwater fishes, obtained from bibliographical sources as well as field work conducted during the last few years, and we use this information to describe host-parasite patterns, to uncover the biogeographical history of these associates. Altogether, both fish families are infected with 89 species of helminths, 49 as adults and 40 as larvae, and only 2 occur as both adults and larvae. Track analysis (panbiogeography) is used to propose a biogeographical hypothesis by considering the distribution of 16 of the 89 helminth species recorded in these hosts. The hypothesis indicates that the associates have a common biogeographical history and in the case of some species of Ictalurus, the taxonomic composition of their helminth fauna is partly a result of the speciation events of their hosts. We corroborate the general pattern of the helminth parasites of Mexican freshwater fishes, which is the circumscription of helminth species to a particular host family, with limited host-sharing even when hosts occurr in sympatry.

Hacia una biogeografía evolutiva

Article

Full-text available

Dec 2007

Juan Morrone

The proliferation of methods in the last decades has led some authors to question whether biogeography is a coherent discipline. Biotas are complex mosaics due to dispersal (expansion of distributions) and vicariance (fragmentation of distributions), having complex, reticulate histories, which necessarily need to be studied through the integration of different methodologies. An evolutionary biogeographical analysis may involve five steps: (1) recognition of biotic components (sets of spatio-temporally integrated taxa due to common history), through panbiogeography and methods used to identify areas of endemism; (2) contrastation of the biotic components and identification of the vicariant events that fragmented them, through cladistic biogeography and comparative phylogeography; (3) establishment of a hierarchic arrangement of the components in a biogeographic system of realms, regions, dominions, provinces and districts; (4) identification of cenocrons (sets of taxa with similar origins and ages), dated using intraspecific phylogeography, molecular clocks and fossils; and (5) formulation of a geobiotic scenario, that explains the evolution of the biotic components and cenocrons, integrating geological and tectonical information.

La perspectiva biogeográfica histórica

Article

Full-text available

Dec 2008

Mitochondrial DNA diversity, genetic structure, and demographic history of the Neotropical otter (Lontra longicaudis) in Mexico

Article

Jan 2015

Jimena Guerrero

Mitochondrial DNA diversity, genetic structure, and demographic history of the Neotropical otter (Lontra longicaudis) in Mexico

Article

Full-text available

Dec 2015

Genetic diversity represents the evolutionary potential of a population, and allows insights into its demographic history and genetic structure; understanding these aspects of a population is crucial for conservation planning. The Neotropical otter (Lontra longicaudis) is distributed from Argentina to Northern Mexico and is currently listed as ‘data deficient’ by the International Union for the Conservation of Nature (IUCN). To contribute to conservation planning for the species, we used non-invasive sampling to obtain mtDNA control region sequences from 44 individuals from across Mexico. We examined country-wide genetic diversity and demographic history, as well as genetic structure among 3 regions: North Pacific, South Pacific, and Atlantic. Haplotypes identified in Mexico were combined with Central and South American haplotypes in order to examine phylogeographic patterns and identify evolutionary significant units (ESUs). Results show lower genetic diversity in Mexico compared to recent estimates for South American populations. Analyses of demographic history in Mexico indicated an expansion coinciding with climatic changes at the end of the Pleistocene. Genetic structure was high among North Pacific/South Pacific (FST = 0.48) and North Pacific/Atlantic (FST = 0.49), potentially due to mountain chains acting as barriers to female gene flow among these regions. On the other hand, we identified a potential corridor for gene flow among South Pacific and Atlantic. Phylogeographic analyses identified a distinct lineage distributed in North and Central America. We propose this represents a distinctive ESU which should be considered for separate conservation management.La diversidad genética está directamente ligada al potencial evolutivo de una población y permite obtener información acerca de su historia demográfica y estructura genética; el comprender estos aspectos de una población es crucial para su conservación. La nutria neotropical (Lontra longicaudis) se distribuye desde Argentina hasta México y actualmente está clasificada como ‘deficiente en datos’ por la UICN. A fin de contribuir a la conservación de esta especie, se realizó muestreo no-invasivo para obtener secuencias de la región control del DNA mitocondrial de 44 individuos en México. En el presente estudio, se examinó la diversidad genética e historia demográfica a nivel nacional, así como la estructura genética entre tres regiones: Norte del Pacifico (NP), Sur del Pacifico (SP) y Atlántico (AT). Los haplotipos identificados en México se combinaron con haplotipos de Centro y Sudamérica a fin de identificar patrones filogeográficos y Unidades Evolutivamente Significativas (UES). En México, la diversidad genética estimada fue menor que en estudios recientes en poblaciones de Sudamérica; los análisis de historia demográfica en México indicaron una expansión que coincide con cambios climáticos al final del Pleistoceno. La estructura genética entre NP y SP/AT fue alta (FST = 0.49), posiblemente debido a la presencia de sierras que actúan como barrera al flujo genético entre estas regiones. En contraste, se identificó un potencial corredor de flujo genético entre SP y AT. Mediante análisis filogeográficos, se identificó un linaje monofilético distribuido en Norte y Centro América (NCAM). Se propone que éste representa una Unidad Evolutivamente Significativa (UES), por lo que para su conservación deberá ser manejada de manera independiente.

Checklist of the species of Neoechinorhynchus (Acanthocephala: Neoechinorhynchidae) in fishes and turtles in Middle-America, and their delimitation based on sequences of the 28S rDNA

Article

Full-text available

Jul 2015

Among the acanthocephalans, Neoechinorhynchus is one of the most speciose genera, with 116 described species distributed worldwide. The adults of Neoechinorhynchus are found in the intestine of freshwater and brackish water fish, as well as in freshwater turtles. In this study, a checklist of the congeneric species of Neoechinorhynchus occurring in Middle-American fish and turtles is presented. The checklist contains the records established in all published accounts, as well as novel data from survey work conducted in the region comprising Neotropical areas of Mexico, as well as some localities in Central America. The species delimitation criteria used to discriminate among species is based on molecular data. In the last years, a large database derived from sequences of the D2 + D3 domains of the large subunit of rDNA (28S) was generated for 262 specimens corresponding to nine species of Neoechinorhynchus. This molecular marker has shown to be useful in establishing species limits within Neoechinorhynchus and in resolving phylogenetic relationships at species level. Based on our results, the domains D2 + D3 of the 28S rDNA could be considered as potential DNA barcodes to complement mitochondrial DNA to discriminate among acanthocephalan species.

A new species of Xenosaurus (Squamata: Xenosauridae) from the Sierra Gorda Biosphere Reserve of Querétaro, Mexico

Article

Full-text available

Jun 2013

A new species of Xenosaurus from the Sierra Gorda Biosphere Reserve of northeastern Queretaro, Mexico, is described. The new species differs from all of the other described species of the genus by having usually 2 postrostral scales on each side of the midline (in 84.6% of the specimens, n=26); largest supraoculars that are not, or only slightly, wider than long; postorbital and zygomatic ridges that are widely separated from each other by an intervening row of scales; labiomental rows that usually extend posteriorly from the second or third chinshield (in 92.3% of the specimens, n=26); 23-26 lamellae under the fourth toe ((x) over bar =24.3, n=25); a venter that is immaculate or with only diffuse, scattered dark specks on the sides, and a postorbital region rounded, lacking a canthus temporalis demarcated by enlarged or well-defined scales. The new species inhabits oak forest and a transitional zone between oak forest and subperennial tropical forest at approximately 1 100-1 400 m of elevation. The new species is morphologically most similar to X. platyceps from Tamaulipas, but does not appear to be its sister taxon.

Comparative historical biogeography of three groups of Nearctic freshwater fishes across central Mexico

Article

Full-text available

Feb 2015
J FISH BIOL

Biogeographic patterns of the three main Nearctic groups of continental fishes inhabiting river drainages in central Mexico (livebearing goodeids, southern Mexican notropins and species of Algansea, the last two representing independent lineages of cyprinids) were obtained and compared by following two approaches: an estimate of divergence times and using a well-defined biogeographic method. Three concordant biogeographic events were identified among the three groups, showing some evidence of a partially congruent evolutionary history. The analysed groups show at least three independent colonization events into central Mexico: two western routes, followed by the Goodeinae and members of Algansea, and an early Plateau route followed by southern notropins. The most recent common ancestor (MRCA) of each of the three freshwater fish groups diversified in central Mexico in the Late Miocene. The lack of a strong congruence in their biogeographic patterns, and the differences in species richness among the three clades might be evidence for distinct patterns of diversification.

Sympatric populations of sister species of Brachyrhaphis

Article

Dec 2014
J FISH BIOL

Spencer J Ingley

The first records of sympatric populations of the poorly studied sister species Brachyrhaphis roseni and Brachyrhaphis terrabensis are presented. Sympatric populations were found in a total of 14 localities in four river drainages throughout the Pacific slopes of western Panama, and they occurred in a wide range of elevations, from 90 to 651 m. These data expand the elevation range of each species, and provide the first case of sympatric sister species within the genus. (C) 2014 The Fisheries Society of the British Isles

Size doesn't matter, sex does: A test for boldness in sister species of Brachyrhaphis fishes

Article

Full-text available

Oct 2014

The effect of divergent natural selection on the evolution of behavioral traits has long been a focus of behavioral ecologists. Predation, due to its ubiquity in nature and strength as a selective agent, has been considered an important environmental driver of behavior. Predation is often confounded with other environmental factors that could also play a role in behavioral evolution. For example, environments that contain predators are often more ecologically complex and “risky” (i.e., exposed and dangerous). Previous work shows that individuals from risky environments are often more bold, active, and explorative than those from low-risk environments. To date, most comparative studies of environmentally driven behavioral divergence are limited to comparisons among populations within species that occur in divergent selective environments but neglect comparisons between species following speciation. This limits our understanding of how behavior evolves post-speciation. The Central American live-bearing fish genus Brachyrhaphis provides an ideal system for examining the relationship between selective environments and behavior, within and between species. Here, we test for differences in boldness between sister species B. roseni and B. terrabensis that occur in streams with and without piscivorous predators, respectively. We found that species do differ in boldness, with species that occur with predators being bolder than those that do not. Within each species, we found that sexes differed in boldness, with males being bolder than females. We also tested for a relationship between size (a surrogate for metabolic rate) and boldness, but found no size effects. Therefore, sex, not size, affects boldness. These results are consistent with the hypothesis that complex and risky environments favor individuals with more bold behavioral traits, but they are not consistent with the hypothesis that size (and therefore metabolic rate) drives divergence in boldness. Finally, our results provide evidence that behavioral trait divergence continues even after speciation is complete.

Repeated geographic divergence in behavior: A case study employing phenotypic trajectory analyses

Article

Full-text available

Jul 2014
BEHAV ECOL SOCIOBIOL

Environmental effects on behavior have long been a focus of behavioral ecologists. Among the important drivers of behavior is predation environment, which can include the presence/absence of predators, differences in resource availability, and variation in individual density. Environments with predators are often more ecologically complex and “risky” than those without predators. Populations from these environments are sometimes more active and explorative than populations from low-risk, less complex environments. To date, most comparative studies of behavior are limited to within-species comparisons of populations from divergent environments, but neglect comparisons between species following speciation, thus limiting our understanding of post-speciation behavioral evolution. Brachyrhaphis fishes provide an ideal system for studying correlations between divergent environments and behavior within and between species. Here, we test for differences in two behavioral traits—activity and exploration —between sister species Brachyrhaphis roseni and Brachyrhaphis terrabensis that occur in divergent predation environments. Species differed in activity and exploration, with higher activity and exploration levels in populations that co-occur with predators. Furthermore, we found drainage-by-species interactions, indicating that the nature of divergence varied geographically. Using the recently developed phenotypic trajectory analysis (PTA), we quantified this difference and found that, while the geographically isolated populations of sister species tended to evolve in parallel, the magnitude of divergence between species differed between drainages. Our results highlight the utility of PTA for multivariate behavioral data and corroborate past predictions that complex and risky environments are correlated with increased activity and exploration levels and that divergence continues post-speciation.

Relaciones filogenéticas de la familia Profundulidae

Conference Paper

Full-text available

Nov 2012

La familia Profundulidae comprende un género nominal, Profundulus Hubbs, 1924, el cual a su vez se subdivide en dos subgéneros: Profundulus Hubbs, 1924 y Tlaloc Álvarez y Carranza, 1951. Entre los dos subgéneros, Profundulus es el que presenta una distribución más amplia y mayor diversidad específica, con seis especies reconocidas. Mientras que Tlaloc cuenta con una distribución más restringida a la zonas altas con tres especies reconocidas. Con fines de llevar a cabo una reconstrucción filogenética así como una revisión biogeográfica, se analizaron los genes mitocondriales ATP 8/6(850 pb), y un fragmento del gen mitocondrial ND2 (1047 pb), así como el 1er y el 2do intron del gen nuclear S7 (998 pb). En el presente estudio se incluyeron un total de 35 poblaciones, las cuales abarcaron una muestra representativa de la familia. Nuestros resultados dan evidencia de que la familia es monofilética, además de que la divergencia genética entre ambos subgéneros es considerablemente alta, por lo que proponemos su consideración como géneros distintos. Con base en nuestros resultados la distribución del género Profundulus comprende en la vertiente Pacífica desde la cuenca del Mixteco Balsas (México), hasta la cuenca del río Lempa (Honduras). En este género fueron recuperados dos clados, de los cuales uno comprende exclusivamente la región Mixteca en México, mientras que el segundo linaje presenta al menos dos grupos diferentes. Mientras que el género Tlaloc se encuentra restringido a las cuencas de las tierras altas en la vertiente del Atlántico, desde el río Jacate (México) hasta la cuenca del río Motagua (Guatemala). Para este género fueron recuperados dos linajes bien definidos. Finalmente con base en un reloj molecular fue propuesto un escenario biogeográfico para la familia.

Estructura genética contrastante en dos especies codistribuidas de peces de agua dulce que habitan sistemas marcadamente estacionales

Article

Full-text available

Apr 2009

Given the seasonal nature of ecosystems such as permanent sinkholes ('cenotes') and temporary wetlands, their fish fauna experience yearly local extinction and colonization processes, with strong fluctuations in population size. We evaluated the genetic diversity, population genetic structure and degree of isolation of populations of Poecilia orri and Gambusia yucatana among and within wetlands and cenotes. We also assessed some abiotic characteristics of the water bodies and their potential relationship with average genetic diversity. Both species showed low genetic diversity, but this was twice as low in P. orri. Populations of G. yucatana showed no genetic structure, whereas those of P. orri did. The genetic divergence results were consistent with isolation between cenotes and wetlands, where the different types of water bodies had a distinctive genetic composition. We suggest that our genetic diversity and differentiation results are associated with the successive, seasonalyearly population size shrinkage and expansion events (i.e. extinction and recolonization) that occur in these systems, and also with the environmental tolerance, body size, and reproduction characteristics of both species. Our results show how these codistributed species can have markedly different genetic structuring and diversity, most likely determined by their particular biological and ecological characteristics, and provide baseline information for future studies.

Morphological Divergence Driven by Predation Environment within and between Species of Brachyrhaphis Fishes

Article

Full-text available

Feb 2014
PLOS ONE

Natural selection often results in profound differences in body shape among populations from divergent selective environments. Predation is a well-studied driver of divergence, with predators having a strong effect on the evolution of prey body shape, especially for traits related to escape behavior. Comparative studies, both at the population level and between species, show that the presence or absence of predators can alter prey morphology. Although this pattern is well documented in various species or population pairs, few studies have tested for similar patterns of body shape evolution at multiple stages of divergence within a taxonomic group. Here, we examine morphological divergence associated with predation environment in the livebearing fish genus Brachyrhaphis. We compare differences in body shape between populations of B. rhabdophora from different predation environments to differences in body shape between B. roseni and B. terrabensis (sister species) from predator and predator free habitats, respectively. We found that in each lineage, shape differed between predation environments, consistent with the hypothesis that locomotor function is optimized for either steady swimming (predator free) or escape behavior (predator). Although differences in body shape were greatest between B. roseni and B. terrabensis, we found that much of the total morphological diversification between these species had already been achieved within B. rhabdophora (29% in females and 47% in males). Interestingly, at both levels of divergence we found that early in ontogenetic development, females differed in shape between predation environments; however, as females matured, their body shapes converged on a similar phenotype, likely due to the constraints of pregnancy. Finally, we found that body shape varies with body size in a similar way, regardless of predation environment, in each lineage. Our findings are important because they provide evidence that the same source of selection can drive similar phenotypic divergence independently at multiple divergence levels.

Phylogenetic Diversity of Live-Bearing Fishes (Poeciliidae) Peaks on Peninsulas, Isthmuses, and in Deserts

Article

Dec 2024
J BIOGEOGR

Aim Poeciliids are ecologically important, are widely used as pets, and also have value as model organisms. To understand diversity within this family, we study their phylogenetic diversity (PD) at regional and local scales to delimit bioregions and identify patterns of biodiversity. Location The Americas. Taxon Poeciliidae (Actinopterygii: Cyprinodontiformes). Methods We expanded an existing dated phylogeny from 164 to 261 species with distributional data for 1 o × 1 o latitude × longitude cells (~111 km ² ) and conducted a cluster analysis (phylo‐jaccard distance) to delineate bioregions. For individual cells, we mapped species richness (SR), phylogenetic diversity (PD), weighted endemism (WE) and phylogenetic endemism (PE). We used randomisation tests to map phylogenetic clustering and over‐representation of short‐branch species by cell. We used categorical analysis of neo‐ and palaeo‐endemism to map neo‐, palaeo‐, mixed and super (mixed) endemism. Results We delineated six bioregions. Highest regional species density and density of PD occurred on the Isthmus of Panamá (IOP). At the grid‐cell scale, the Grijalva–Usumacinta drainage is a hotspot for SR, PD, PE and WE; the IOP has high PD and PE; the Isthmus of Tehuantepec (IOT) has high PD, WE and moderately high SR; and western Hispaniola has high WE and moderately high SR. The Grijalva–Usumacinta drainage also includes cells of super (mixed) and palaeoendemism, while mixed endemism is widespread in Middle America and the Greater Antilles. Phylogenetic clustering is widespread, whereas over‐representation of short‐branch species is concentrated in the Chihuahuan Desert–Sierra Madre Oriental region and in western Hispaniola, both hotspots of neoendemism. Main Conclusions We found widespread diversification of genera intermixed with relict species (mixed endemism). Furthermore, SR and PD were strongly correlated. Centres of endemism include the Chihuahuan Desert–Sierra Madre Oriental, western Hispaniola, the IOT, the IOP and (most of all) the Grijalva–Usumacinta drainage. However, conservation efforts must occur within each bioregion and for each genus.

Environmental and anthropogenic factors mediating the functional connectivity of the mesquite lizard along the eastern Trans-Mexican Volcanic Belt

Article

Full-text available

Jul 2024
MOL ECOL

Functional connectivity, the extent to which a landscape facilitates or impedes the dispersal of individuals across the landscape, is a key factor for the survival of species. Anthropogenic activities, such as urbanization, agriculture and roads, negatively impact functional connectivity of most species, particularly low-vagility species like lizards. Here, we examine how a landscape modified by anthropogenic activities affects the functional connectivity, at both broad and fine scales, of a widely distributed generalist lizard Sceloporus grammicus in the eastern Trans-Mexican Volcanic Belt, Mexico. We estimated for the first time the species' genetic structure, gene flow and functional connectivity in agricultural and forest zones using genomic data, a comprehensive landscape characterization and novel methods including gravity models. Our results showed not only marked genetic differentiation across the study region but also that functional connectivity is maintained for tens of kilometres despite S. gram-micus low vagility. Specifically, we found that substrate and air temperature facilitated connectivity over broad and fine scales, respectively, while agricultural cover, relative humidity and slope were important for connectivity and gene flow. Contrastingly, forest cover and roads favoured (broad-scale) and limited (fine-scale) connectivity, likely associated with movement facilitated by small forest patches and with thermoregula-tion. Altogether, these results support that S. grammicus alternates its thermoregula-tory behaviour depending on the distance travelled and the habitat environmental conditions, and that it can disperse through relatively modified landscapes, mainly using agricultural zones. The information obtained is crucial to understanding the response of lizards to current anthropogenic pressures and their potential to adapt. K E Y W O R D S functional connectivity,

Genomic data support the taxonomic validity of Middle American livebearers Poeciliopsis gracilis and Poeciliopsis pleurospilus (Cyprinodontiformes: Poeciliidae)

Article

Full-text available

Jan 2022
PLOS ONE

Poeciliopsis (Cyprinodontiformes: Poeciliidae) is a genus comprised of 25 species of freshwater fishes. Several well-known taxonomic uncertainties exist within the genus, especially in relation to the taxonomic status of Poeciliopsis pleurospilus and P. gracilis. However, to date, no studies have been conducted to specifically address the taxonomic status of these two species. The goal of this study was to examine the taxonomic validity of P. pleurospilus and P. gracilis using genomic data (ddRADseq) in phylogenetic, population genetic, and species delimitation frameworks. Multiple analyses support the recognition of both taxa as distinct species and also permits us to revise their respective distributions. A species delimitation analysis indicates that P. pleurospilus and P. gracilis are distinct species, each of which consists of two distinct lineages that are geographically structured. Phylogenetic and population genetic analyses provide clear evidence that individuals of P. gracilis are distributed north and west of the Isthmus of Tehuantepec in both Pacific and Atlantic river systems in Mexico, whereas individuals of P. pleurospilus are distributed in both Atlantic and Pacific river systems south and east of the Isthmus of Tehuantepec, from southern Mexico to Honduras.

Phylogeny and taxonomy of the genus Ilyodon Eigenmann, 1907 (Teleostei: Goodeidae), based on mitochondrial and nuclear DNA sequences

Article

Aug 2017
J ZOOL SYST EVOL RES

Taxonomy of the live-bearing fish of the genus Ilyodon Eigenmann, 1907 (Goodeidae), in Mexico, is controversial, with morphology and mitochondrial genetic analyses in disagreement about the number of valid species. The present study accumulated a comprehensive DNA sequences dataset of 98 individuals of all Ilyodon species and mitochondrial and nuclear loci to reconstruct the evolutionary history of the genus. Phylogenetic inference produced five clades, one with two sub-clades, and one clade including three recognized species. Genetic distances in mitochondrial genes (cytb: 0.5%–2.1%; coxI: 0.5%–1.1% and d-loop: 2.3%–10.2%) were relatively high among main clades, while, as expected, nuclear genes showed low variation (0.0%–0.2%), with geographic concordance and few shared haplotypes among river basins. High genetic structure was observed among clades and within basins. Our genetic analyses, applying the priority principle, suggest the recognition only of Ilyodon whitei and Ilyodon furcidens, with I. cortesae relegated to an invalid species, the populations of which belong to I. whitei.

Lineage Diversification of Lizards (Phrynosomatidae) in Southwestern North America: Integrating Genomics and Geology

Thesis

Full-text available

Aug 2015

Andrew Gottscho

In the first chapter of my dissertation, I provide an ultimate tectonic hypothesis for several well-studied zoogeographic boundaries along the west coast of North America, specifically along the San Andreas Fault system. Reviewing the literature, I demonstrate that four Great Pacific Fracture Zones correspond with spatially concordant phylogeographic breaks for a variety of marine and terrestrial animals. I hypothesize that the four zoogeographic boundaries reviewed here ultimately originated via the same tectonic process (triple junction evolution along the San Andreas Fault system), and I suggest how a comparative phylogeographic approach can be used to test this hypothesis. In the second chapter, I investigate the systematics and species delimitation of fringe-toed lizards of the Uma notata complex in the deserts of southwestern North America. Ten nuclear loci were Sanger sequenced and genome-wide sequence and single-nucleotide polymorphism (SNP) data were collected using restriction-associated DNA (RAD) sequencing. I validated five species-level lineages within the U. notata complex, three of which were previously described as full species, one originally described as a subspecies but later synonymized, and one previously documented yet undescribed species from Mohawk Dunes, Arizona, USA. The results support the hypothesis that Pleistocene glacial cycles promoted allopatric speciation via dispersal across a landscape matrix shaped by older tectonic events, but I also recovered evidence for a vicariant role of the Colorado River during the Pleistocene epoch. In the third chapter, I studied the comparative phylogeography of lizards (Phrynosomatidae) of the Baja California Peninsula, including the genera Callisaurus, Petrosaurus, Urosaurus, and Sceloporus. I collected sequence/SNP data from 228 individual lizards from the peninsula and eight islands using RADseq. The estimated divergence dates across co-distributed clades revealed that for each of the five regions where comparisons are possible, at least two or three episodes of divergence are required to explain the observed patterns. I tested for range expansions or bottlenecks associated with Pleistocene glacial cycles or continent-to-peninsula invasions. The results are consistent with the hypothesis that plate tectonic events established a complex landscape matrix with numerous barriers to dispersal that ultimately facilitated divergence, generating the idiosyncratic patterns observed among co-distributed lineages.

Phylogenetic relationships and evolutionary history of the Mesoamerican endemic freshwater fish family Profundulidae (Cyprinodontiformes: Actinopterygii)

Article

Sep 2015
MOL PHYLOGENET EVOL

Freshwater fishes of Profundulidae, which until now was composed of two subgenera, represent one of the few extant fish families endemic to Mesoamerica. In this study we investigated the phylogenetic relationships and evolutionary history of the eight recognized extant species (from 37 populations) of Profundulidae using three mitochondrial and one nuclear gene markers (∼2.9 Kbp). We applied a Bayesian species delimitation method as a first approach to resolving speciation patterns within Profundulidae considering two different scenarios, eight-species and twelve-species models, obtained in a previous phylogenetic analysis. Based on our results, each of the two subgenera was resolved as monophyletic, with a remarkable molecular divergence of 24.5% for mtDNA and 7.8% for nDNA uncorrected p distances, and thus we propose that they correspond to separate genera. Moreover, we propose a conservative taxonomic hypothesis with five species within Profundulus and three within Tlaloc, although both eight-species and twelve-species models were highly supported by the bayesian species delimitation analysis, providing additional evidence of higher taxonomic diversity than currently recognized in this family. According to our divergence time estimates, the family originated during the Upper Oligocene 26 Mya, and Profundulus and Tlaloc diverged in the Upper Oligocene or Lower Miocene about 20 Mya.

Zoogeography of the San Andreas Fault system: Great Pacific Fracture Zones correspond with spatially concordant phylogeographic boundaries in western North America

Article

Feb 2016
BIOL REV

Andrew Gottscho

The purpose of this article is to provide an ultimate tectonic explanation for several well-studied zoogeographic boundaries along the west coast of North America, specifically, along the boundary of the North American and Pacific plates (the San Andreas Fault system). By reviewing 177 references from the plate tectonics and zoogeography literature, I demonstrate that four Great Pacific Fracture Zones (GPFZs) in the Pacific plate correspond with distributional limits and spatially concordant phylogeographic breaks for a wide variety of marine and terrestrial animals, including invertebrates, fish, amphibians, reptiles, birds, and mammals. These boundaries are: (1) Cape Mendocino and the North Coast Divide, (2) Point Conception and the Transverse Ranges, (3) Punta Eugenia and the Vizcaíno Desert, and (4) Cabo Corrientes and the Sierra Transvolcanica. However, discussion of the GPFZs is mostly absent from the zoogeography and phylogeography literature likely due to a disconnect between biologists and geologists. I argue that the four zoogeographic boundaries reviewed here ultimately originated via the same geological process (triple junction evolution). Finally, I suggest how a comparative phylogeographic approach can be used to test the hypothesis presented here.

Comparative Phylogeography: Concepts, Methods and General Patterns in Neotropical Birds

Article

Full-text available

Apr 2012

Enrique Arbeláez-Cortés

Understanding the patterns and processes involved in intraspecific lineages diversification in time and space is the aim of phylogeography. The comparison of those phylogeographic patterns among co-distributed species shows insights of a community history. Here I review the concepts and methodologies of comparative phylogeography, an active research field that has heterogeneous analytical methods. In order to present a framework for phylogeography in the Neotropics, I comment the general phylogeographic patterns of the birds from this region. This review is based on more than 100 studies conducted during the last 25 years and indicate that despite different co-distributed species seem to share some points in their phylogeographic pattern they have idiosyncratic aspects, indicating an unique history for each one.

Evolutionary conservation biology of Poeciliid fishes

Chapter

Full-text available

Jan 2011

Sujan Henkanaththegedara

Multilocus analysis of intraspecific differentiation in three endemic bird species from the northern Neotropical dry forest

Article

Jan 2014
MOL PHYLOGENET EVOL

Among-species phylogeographic concordance provides insight into the common processes driving lineage divergence in a particular region. However, identifying the processes that caused phylogeographic breaks is not always straight forward, and inferring past environmental conditions in combination with documented geologic events is sometimes necessary to explain current patterns. We searched for concordant phylogeographic patterns and investigated their causes in three bird species (Momotus mexicanus, Melanerpes chrysogenys, and Passerina leclancherii) that belong to three different avian orders and are endemic to the northernmost range of the Neotropical dry forest. We obtained mitochondrial DNA (ND2 and COI or cyt b) and nuclear DNA (20454, GAPDH, MUSK, and TGFB) sequences for at least one locus from 162 individuals across all species and defined climatically stable areas using environmental niche model projections for the last 130,000 years to have a paleoenvironmental framework for the phylogeographic results. All three species showed marked phylogeographic structure, with breaks found in roughly similar areas, such as the border between the Mexican states of Guerrero and Oaxaca, and between southern Jalisco and Michoacán. Both of these regions are known biogeographic breaks among other taxa. Patterns of genetic diversity and differentiation were partially compatible with climatically stable areas. Coalescent analyses revealed recent population growth and estimated the deeper haplogroup divergence of all three taxa to have occurred within the last 600,000 years. The phylogeographic patterns found are noteworthy because they are maintained in a relatively small area for bird species with continuous ranges, and highlight a unique situation when compared to phylogeographic patterns found in other studies of Neotropical birds that have stressed the role of geographic barriers to explain intraspecific differentiation. Our results point to a scenario of population isolation resulting in the present phylogeographic structure, likely a result of historical climate fluctuations that have fragmented and reconnected the Neotropical dry forest. This study contributes to a growing body of evidence indicating active diversification of endemic lineages in the northern Neotropical dry forest region.

Space-time patterns of Cenozoic arc volcanism in central Mexico: From the Sierra Madre Occidental to the Mexican Volcanic Belt

Article

Full-text available

Apr 1999
GEOLOGY

A histogram of 778 isotopic ages of magmatic rocks younger than Eocene in central Mexico shows a multimodal distribution with peaks at about 30 Ma, 23 Ma, 10 Ma, and 5 Ma. The sample suite displays systematic spatial variations with age that likely reflect the protracted transition from the north-northwest trending arc of the Sierra Madre Occidental to the east-west trending Mexican Volcanic Belt. The reorientation of the arc is accompanied by a change in the dominant composition of the products from silicic ignimbrites and rhyolites to andesitic and basaltic lavas. The observed transition is related to the Miocene reorganization of the subduction system following the cessation of subduction off Baja California and the eastward motion of the Caribbean Farallon North America triple junction along the southeastern margin of Mexico. Our data support an early middle Miocene age for the initiation of subhorizontal subduction in southern Mexico and confirm that the locus of arc volcanism was primarily controlled by the geometry of plate boundaries and the thermal structure of the subducting slab.

Phylogenetic Relationships in the North American Cyprinid Genus Cyprinella (Actinopterygii: Cyprinidae) Based on Sequences of the Mitochondrial ND2 and ND4L Genes

Article

Full-text available

Feb 2000
COPEIA

Shiners of the cyprinid genus Cyprinella are abundant and broadly distributed in eastern and central North America. Thirty species are currently placed in the genus: these include six species restricted to Mexico and three barbeled forms formerly placed in different cyprinid genera (primarily Hybopsis). We conducted a molecular phylogenetic analysis of all species of Cyprinella found in the United States, using complete nucleotide sequences of the mitochondrial, protein-coding genes ND2 and ND4L. Maximum-parsimony analysis recovered a single most-parsimonious tree for Cyprinella. Among historically recognized, nonbarbeled Cyprinella, the mitochondrial (mt) DNA tree indicated that basal lineages in Cyprinella are comprised largely of species with linear breeding tubercles and that are endemic to Atlantic and/or Gulf slope drainages, whereas derived lineages are comprised of species broadly distributed in the Mississippi basin and the American Southwest. The Alabama Shiner, C. callistia, was basal in the mtDNA tree, although a monophyletic Cyprinella that included C. callistia was not supported in more than 50% of bootstrap replicates. There was strong bootstrap support (89%) for a clade that included all species of nonbarbeled Cyprinella (except C. callistia) and two barbeled species, C. labrosa and C. zanema. The third barbeled species, C. monacha, fell outside of Cyprinella sister to a species of Hybopsis. Within Cyprinella were a series of well-supported species groups, although in some cases bootstrap support for relationships among groups was below 50%. A derived clade consisting of C. spiloptera, C. whipplei, C. venusta, and the southwestern C. lutrensis group was strongly supported. The species C. lutrensis and C. lepida were not monophyletic, suggesting further study and revision within this group are warranted. In general, the most-parsimonious mtDNA tree was similar in terms of relationships among species to those proposed more than 40 years ago by R. H. Gibbs.

Simultaneous analysis of basal Hymenoptera (Insecta): Introducing robust-choice sensitivity analysis

Article

Full-text available

Jun 2003
BIOL J LINN SOC

Susanne Schulmeister

Molecular characters are analysed on their own and in combination with morphological data to examine the phylogenetic relationships of the basal lineages of Hymenoptera (‘Symphyta’). This study covers 47 sawfly genera and nine apocritan families and includes molecular sequences from five genes − 12S, 16S, 18S and 28S ribosomal genes and cytochrome oxidase 1 − as well as 343 morphological characters. A robust-choice sensitivity analysis is performed with the data. First, the simultaneous analysis is repeated three times, each time employing a different step matrix for weighting the transformations of the molecular characters. Then, the results of all three simultaneous analyses are summarized in a strict consensus in order to avoid basing the conclusions on a narrow set of assumptions. This methodology is discussed in the paper. The relationships among superfamilies largely confirm previous hypotheses, being (Xyeloidea (Tenthredinoidea s.l. (Pamphilioidea (Cephoidea (Siricoidea (Xiphydrioidea (Orussoidea Apocrita))))))), where Siricoidea is understood as Siricidae+Anaxyelidae. However, the relationships within Tenthredinoidea s.s. proposed here are novel: ({Argidae Pergidae}[Athalia{(Diprionidae Cimbicidae) Tenthredinidae minus Athalia}]). © 2003 The Linnean Society of London. Biological Journal of the Linnean Society, 2003, 79, 245–275.

MRBAYES: Bayesian inference of phylogenetic trees

Article

Full-text available

Sep 2001

The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. Availability: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html. Contact: johnh{at}brahms.biology.rochester.edu

Evolution of NADH Dehydrogenase Subunit 2 in East African Cichlid Fish

Article

Full-text available

Jan 1996

The complete sequence (1047 bp) of the mitochondrially encoded ND2 gene was obtained from 31 species of cichlid fishes to investigate the evolutionary history of the species flocks of the East African lakes. The observed pattern of nucleotide substitution in this sequence is typical of mitochondrial genes, showing a high transition bias and rapid mutational saturation, especially at codon positions where base frequencies are unequal. The base composition of the third position of codons is heterogeneous among species, suggesting frequent shifts in the pattern of substitution. Phylogenetic analysis of the sequences shows that the mtDNA variation in Lake Malawi cichlids is nested monophyletically within the range of variation shown by Tanganyikan cichlids. The closest Tanganyikan relatives of the Malawi flock are members of the tribe Tropheini. Classifications based on morphology are generally supported by the mtDNA data, with some significant exceptions in the Tropheini and Lamprologini. Because of an apparently rapid radiation of the Tanganyikan lineages, it is difficult to assess the basal topology of the Tanganyikan radiation at this time. Divergences among tribes are consistent with an intralacustrine radiation within the past 10 million years.

Phylogenetic Methods Come of Age: Testing Hypotheses in an Evolutionary Context

Article

Full-text available

May 1997

The use of molecular phylogenies to examine evolutionary questions has become commonplace with the automation of DNA sequencing and the availability of efficient computer programs to perform phylogenetic analyses. The application of computer simulation and likelihood ratio tests to evolutionary hypotheses represents a recent methodological development in this field. Likelihood ratio tests have enabled biologists to address many questions in evolutionary biology that have been difficult to resolve in the past, such as whether host-parasite systems are cospeciating and whether models of DNA substitution adequately explain observed sequences.

Estimating the rate of evolution of the rate of molecular evolution

Article

Full-text available

Jan 1999

A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction with any of the widely used models for nucleotide substitution or amino acid replacement. It is illustrated by analyzing a data set of rbcL protein sequences.

Modeltest: testing the model of DNA substitution

Article

Full-text available

Feb 1998

The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. AVAILABILITY: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu. edu/zoology/crandall_lab/modeltest.html.

Performance of a Divergence Time Estimation Method under a Probabilistic Model of Rate Evolution

Article

Full-text available

Apr 2001

Rates of molecular evolution vary over time and, hence, among lineages. In contrast, widely used methods for estimating divergence times from molecular sequence data assume constancy of rates. Therefore, methods for estimation of divergence times that incorporate rate variation are attractive. Improvements on a previously proposed Bayesian technique for divergence time estimation are described. New parameterization more effectively captures the phylogenetic structure of rate evolution on a tree. Fossil information and other evidence can now be included in Bayesian analyses in the form of constraints on divergence times. Simulation results demonstrate that the accuracy of divergence time estimation is substantially enhanced when constraints are included.

Divergence Time and Evolutionary Rate Estimation with Multilocus Data

Article

Full-text available

Nov 2002

Bayesian methods for estimating evolutionary divergence times are extended to multigene data sets, and a technique is described for detecting correlated changes in evolutionary rates among genes. Simulations are employed to explore the effect of multigene data on divergence time estimation, and the methodology is illustrated with a previously published data set representing diverse plant taxa. The fact that evolutionary rates and times are confounded when sequence data are compared is emphasized and the importance of fossil information for disentangling rates and times is stressed.

MODELTEST: Testing the model of DNA substitution

Article

Full-text available

May 2003

Introduction to general state-space Markov chain theory. In W. R. Gilks, S. Richardson, and D. J. Spiegelhalter (Eds.), Markov Chain Monte Carlo in Practice, Chapter 4, pp. 59-74. London: Chapman and Hall. Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen (2000). Codon- substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155, 431-449. Yang, Z. and B. Rannala (1997). Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method. Molecular Biology and Evolution 1, 717-724. Yang, Z. H. (1993). Maximum-likelihood-estimation of phylogeny from DNA- sequences when substitution rates differ over sites. Molecular Biology and Evolution I0(6), 1396-1401. Zuckerkandl, E. (1987). On the molecular evolutionary clock. Journal of Molec- ular Evolution 26, 34-46. Zuckerkandl, E. and L. Pauling (1962). Molecular disease, evolution, and genic heterogeneity. In M. Kasha and B. Pullman (Eds.), Horizons in Biochem- istry, pp. 189-225. Ne

Phylogeography: The History and Formation of Species

Book

Jan 2000

JOHN C. AVISE

MRBAYES: Bayesian inference of phylogeny

Article

Jan 2001

The fresh-water fishes of Mexico north of the Isthmus of Tehuantepec

Article

S.E. Meek

Species of the Poecilia sphenops Complex (Pisces: Poeciliidae) in México

Article

Jun 1971
COPEIA

Poecilia sphenops alternately has been cast as several (or many) species, or as a single polytypic species. Laboratory, field, and morphological evidence gathered mainly from a mixed population of mollies in southern México, but also from other parts of México and Guatemala, indicates that "Poecilia sphenops" is not a single species but a complex of unknown magnitude. The name Poecilia butleri is resurrected from synonymy for the Pacific representative of P. mexicana in México and southern Guatemala. A natural hybrid between P. sphenops and P. butleri is described.

PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4.0b10

Book

Jan 2002

David L. Swofford

— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.

Marine ZooGeography

Book

Jan 1974

John Carmon Briggs

Global marine zoogeography and evolution.

Systematics and Biogeography: Cladistics and Vicariance

Book

Jan 1981
Syst Zool

Volcanism and tectonism in western Mexico: A contrast of style and substance

Article

Jan 1992
GEOLOGY

The Jalisco block of southwestern Mexico records the initial stages of continental rifting superimposed on a convergent continental margin. Pliocene- Quaternary eruptions in north-northwest-trending graben systems within the block produced extraordinarily diverse lava types, including minette, leucitite, absarokite, and andesite. Interspersed with these are several basaltic shield volcanoes that have compositional similarities to lavas from oceanic islands. Evidence of Miocene Basin and Range extension, which is seen around much of the Gulf of California, is found only along the northern margin of the Jalisco block. Large volumes of alkali basalt were also erupted during the late Miocene at several locations along this northern margin. We propose that Pliocene- Quaternary extension and associated volcanism within the confines of the Jalisco block are consequences of complex plate-boundary reorganizations that are causing the block to rift away from the Mexican mainland

Tectonic Control of the Volcano-Sedimentary Sequence of the Chapala Graben, Western Mexico

Article

Apr 1998

The Chapala graben forms part of a regional system of intra-arc and half-grabens located along the western and central portions of the Mexican Volcanic Belt. Results of a stratigraphic and tectonic study of the thick, widespread volcano-sedimentary sequence around the Chapala graben are reported. The study has concentrated on the distribution of lacustrine deposits and on the stratigraphy, geochronology, and deformation of the sequence. The volcano-sedimentary record suggests a probable link between the Tepic-Zacoalco and Chapala grabens through a basin system developed during late Miocene and early Pliocene time. The stratigraphic sections show a southward spatial migration of the basin (and lake) system. The main unit of the volcano-sedimentary succession is the Chapala Formation, which has been affected by northeast tilting, unlike the lacustrine deposits to the east in the Chapala plain (e.g., Ixtlan area), where the sequence is essentially flat lying. Two distinct units with different structural attitudes, separated by an angular unconformity, can be distinguished in the Chapala Formation. Based on differences between the stratigraphic sections and structural attitudes, we propose a model for development of the Chapala graben that involves a combination of left-lateral and extensional deformation, together with volcanic and erosional processes, all of which have contributed to shape the basin. Furthermore, we suggest that Lake Chapala is the remnant of a large Jalisco paleo-lake in west-central Mexico.

Molecular and morphological data reveal cryptic taxonomic diversity in the terrestrial slug complex Arion subfuscus/fuscus (Mollusca, Pulmonata, Arionidae) in continental north-west Europe

Article

Aug 2004
BIOL J LINN SOC

The importance and abundance of cryptic species among invertebrate taxa is well documented. Nowadays, taxonomic, phylogenetic and conservation biological studies frequently use molecular markers to delineate cryptic taxa. Such studies, however, often face the problem of the differential resolution of the molecular markers and techniques involved. This issue is explored in the present study of cryptic taxa within the terrestrial slug complex Arion subfuscus/fuscus in continental north-west Europe. To this end, morphological, allozyme and mitochondrial 16S rDNA sequence data have been jointly evaluated. Using allozyme data and gonad type, two distinct groups were consistently delineated, even under sympatric conditions. The 16S rDNA data strongly supported both those groups and even suggested the presence of three distinct taxa within one of them. However, in view of: (1) the allopatric distribution of three OTUs, (2) the lack of allozyme or morphological differentiation, and (3) the extremely high degree of intraspecific mtDNA variation reported in pulmonate gastropods, they are, for the time being, not regarded as valid species under the biological species concept. By means of 16S rDNA and allozyme data, the position of type and topotype material of A. subfuscus s.s. and A. fuscus relative to the newly defined OTUs was determined, thus clarifying the nomenclature of this species complex. Additionally, gonad type proved to be a useful character for distinguishing the two species in north-west Europe. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 83, 23–38.

The Colima volcanic complex, Mexico: Part II. Late-Quaternary cinder cones

Article

May 1981

Since the late Pleistocene, eleven cinder and lava cones have erupted on the floor of the southern Colima graben, NE and NW of the large, active, andesitic volcano Colima. Scoria and lava samples from nine of the cones form a completely transitional basic alkalic series including basanites (9), leucite-basanites (3), and minettes (15), the commonest variety of mica lamprophyre. These samples represent primitive, high temperature magmas with 47.6–50.3% SiO2, 7.4–15.3% MgO, 2.5–4.4% K2O, and 2.2–9.9% normative nepheline. All members of this basic alkalic suite contain Mg-olivine (Fo75–94), chromite, augite, and late plagioclase and titanomagnetite. The petrographic transition from basanite to minette is marked by the appearance of sanidine and the volatile-bearing phases phlogopite, apatite, and analcime during late stages of crystallization. As these phases increase in abundance, presumably reflecting a rise in magmatic volatile content, there are corresponding increases in the whole rock concentrations of 16 incompatible elements. Although these incompatible elements are relatively abundant even in the basanites, many are highly concentrated in the minettes: Ba≦ 4,200 ppm, Sr≦3,100 ppm, Zr≦ 550 ppm, Ce≦190 ppm, Hf ≦18 ppm. Among the incompatible elements, the degrees of enrichment in the minettes relative to the basanites decrease in the order: H, Th, Ce, La, Nd, Zr, Hf, U, Ba, Sm, Eu, Pb, P, Nb, Sr, Ti. These enrichments may reflect the increasing importance of minor, incompatible element rich mantle phases during partial melting. The concentrations of alkali metals K, Na, Rb, and Cs do not correlate with these other elemental enrichments. The leucite-basanties have similar incompatible element contents to many minettes, differing from them only in the presence of leucite rather than analcime, and Ti-F-rich groundmass phlogopite rather than hydrous phlogopite phenocrysts; thus the leucite-basanites represent relatively dry equivalents of minettes. Two of the eleven cinder cones are calc-alkaline in nature and do not belong to the basanite-minette group; the easternmost cone is constructed of high-Al basalt, and the northernmost of basaltic andesite. The high-Al basalt (49.5% SiO2, 9.3% MgO, 221 ppm Ni) closely approximates a parental magma to the post-caldera andesitic suite of V. Colima (56.5–61.6% SiO2). The basaltic-andesite is relatively enriched in incompatible elements compared to the high-Al basalt — V. Colima trend. The ne-normative basanite-minette samples are highly enriched in incompatible elements, while the contemporaneous hy — qz-normative calc-alkaline suite, encompassing the high-Al basalt and V. Colima's andesites, is characterized by relatively low abundances of these elements. No likely mineral assemblage can relate the alkaline and calc-alkaline suites through crystal fractionation; they probably represent fundamentally different melting events. During the Quaternary, the main focus of andesitic volcanism in the southern Colima graben has migrated southward with time. Volcán Colima marks its present position, 5 km south of the Pleistocene volcano Nevado de Colima, and another 15 km from the still older Volcán Cantaro. The eruptions of basic alkalic magma probably occurred during the late stages of Nevado's life and through the life of V. Colima. They generally migrated from west to east with time, towards V. Cantaro. The most recent cone, V. Apaxtepec, is the only one east of the andesitic Colima-Cantaro axis. The oldest and the two youngest cones produced basanites, while minettes dominated at cones of intermediate ages. The cinder cone eruptions may have coincided with a phase of lamprophyre dike injection into plutons solidifying beneath the extinct volcanoes north of V. Colima. The southern end of the Colima graben can be viewed, then, as the volcanic analog of many classical, post-plutonic, hypabyssal lamprophyre localities.

PAML: A program package for phylogenetic analysis by maximum likelihood

Article

Nov 1997

Ziheng Yang

PAML, currently in version 1.2, is a package of programs for phylogenetic analyses of DNA and protein sequences using the method of maximum likelihood (ML). The programs can be used for (i) maximum likelihood estimation of evolutionary parameters such as branch lengths in a phylogenetic tree, the transition/transversion rate ratio, the shape parameter of the gamma distribution for variable evolutionary rates at sites, and rate parameters for different genes; (ii) likelihood ratio test of hypotheses concerning sequence evolution, such as rate constancy and independence among sites and rate constancy among lineages (the molecular clock); (iii) calculation of substitution rates at sites and reconstruction of ancestral nucleotide or amino acid sequences; and (iv) phylogenetic tree reconstruction by maximum likelihood and Bayesian methods. The strength of PAML, in comparison with other phylogenetic packages currently available, is its implementation of a variety of evolutionary models. These include several models of variable evolutionary rates among sites, models for combined analyses of multiple gene sequence data and models for amino acid sequences. Multifurcating trees are supported, as well as trees in which some sequences are ancestral to some others. A heuristic tree search algorithm (star decomposition) is used in the package, but tree making is not a strong point of the current version, although work is under way to implement efficient search algorithms. Major programs in the package, as well as the types of analyses they perform, are listed in Table 1. More details are available in the documentation included in the package, written using Microsoft Word. PAML is distributed free of charge for academic use only. The package, including ANSI C source codes, documentation, example data sets, and control files, can be obtained by anonymous ftp at mw511.biol.berkeley.edu/pub, or from the Indiana molecular biology ftp site at ftp.bio.indiana.edu under the directory Incoming or molbio/evolve . MAC and PowerMac executables are also available, although DOS executables are not prepared yet. Further information about the package is available from the World Wide Web at

Historical biogeography of the livebearing fish genus Poeciliopsis (Poecilidae: Cyprinodontiformes)

Article

Jun 2002

To assess the historical biogeography of freshwater topminnows in the genus Poeciliopsis, we examined sequence variation in two mitochondrial genes, cytochrome b (1140 bp) and NADH subunit 2 (1047 bp). This widespread fish genus is distributed from Arizona to western Colombia, and nearly half of its 21 named species have distributions that border on the geologically active Trans-Mexican Volcanic Belt (TMVB), a region that defines the uplifted plateau (Mesa Central) of Mexico. We used the parametric bootstrap method to test the hypothesis that a single vicariant event associated with the TMVB was responsible for divergence of taxa found to the north and south of this boundary. Because the single-event hypothesis was rejected as highly unlikely, we hypothesize that at least two geological events were responsible for divergence of these species. The first (8-16 million years ago) separated ancestral populations that were distributed across the present TMVB region. A second event (2.8-6.4 million years ago) was associated with northward dispersal and subsequent vicariance of two independent southern lineages across the TMVB. The geological history of this tectonically and volcanically active region is discussed and systematic implications for the genus are outlined.

Phylogeography of the component species of broad-leaved evergreen forests in Japan, based on chloroplast DNA variation

Article

Mar 2004

In order to elucidate the past distribution and colonization routes of broad-leaved evergreen (lucidophyllous) forests, we investigated the intraspecific phylogeographic patterns of lucidophyllous forests in Japan and surrounding areas. We selected 6 component species with a similar geographic distributions growing in Castanopsis-dominant forests. We defined possible important refugia during the glacial periods as the regions rich in rare haplotypes (with a frequency of 5% or less), or as regions rich in the number of common haplotypes (with a frequency of more than 5%). We then located the sites of refuge by comparing the intraspecific phylogeographic patterns among 6 component species of lucidophyllous forests with respect to these two parameters (i.e., haplotype uniqueness and the number of haplotypes). The following results were obtained during the course of this study: (1) rare haplotypes were distributed among islands around the main islands of Japan; (2) rare subtypes and the greatest numbers of common haplotypes were observed in Kyushu, a finding which agreed with fossilized pollen data demonstrative of the past existence of refugia in southern Kyushu; and (3) rare haplotypes were found on the Muroto Peninsula, and the second greatest numbers of common haplotypes were observed on the Kii Peninsula, a finding which suggested the existence of additional important refugia along the Pacific coast of Japan during the glacial ages.

PAUP*: phylogenetic analysis using par-simony (*and other methods), version 4 Divergence time and evo-lutionary rate estimation with multilocus data

Jan 1998
689-702

D L Swofford
Associates
Ma Sunderland
J L Thorne
H Kishino

Swofford, D.L. (1998) PAUP*: phylogenetic analysis using par-simony (*and other methods), version 4. Sinauer Associates, Sunderland, MA. Thorne, J.L. & Kishino, H. (2002) Divergence time and evo-lutionary rate estimation with multilocus data. Systematic Biology, 51, 689–702.

Historical biogeography of the fish genus Poeciliopsis (Cyprinodontiformes)

Jan 2002
972

Mateos

Comparative phylogeography of livebearing fishes in the genera Poeciliopsis and Poecilia (Poeciliidae: Cyprinodontiformes) in Central Mexico

Abstract

No full-text available

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