Phylogeography and historical demography of the Pacific Sierra mackerel (Scomberomorus sierra) in the Eastern Pacific

<p>Abstract</p> <p>Background</p> <p>Testing connectivity among populations of exploited marine fish is a main concern for the development of conservation strategies. Even though marine species are often considered to display low levels of population structure, barriers to dispersal found in the marine realm may restrict gene flow and cause genetic divergence of populations. The Pacific Sierra mackerel (<it>Scomberomorus sierra</it>) is a pelagic fish species distributed throughout the tropical and subtropical waters of the eastern Pacific. Seasonal spawning in different areas across the species range, as well as a limited dispersal, may result in a population genetic structure. Identification of genetically discrete units is important in the proper conservation of the fishery.</p> <p>Results</p> <p>Samples collected from the Eastern Pacific, including the areas of main abundance of the species, presented high levels of mtDNA genetic diversity and a highly significant divergence. At least two genetically discrete groups were detected in the northern (Sinaloa) and central areas (Oaxaca and Chiapas) of the species range, exhibiting slight genetic differences with respect to the samples collected in the southern region (Peru), together with a "chaotic genetic patchiness" pattern of differentiation and no evidence of isolation by distance. Historical demographic parameters supported the occurrence of past population expansions, whereas the divergence times between populations coincided with the occurrence of glacial maxima some 220 000 years ago.</p> <p>Conclusions</p> <p>The population genetic structure detected for the Pacific Sierra mackerel is associated with a limited dispersal between the main abundance areas that are usually linked to the spawning sites of the species. Population expansions have coincided with glacial-interglacial episodes in the Pleistocene, but they may also be related to the increase in the SST and with upwelling areas in the EEP since the early Pleistocene.</p

Phylogenetic relationships among five marine Catfish species (Pisces: Ariidae) from Mexico

La sistemática de los bagres marinos pertenecientes a la familia Ariidae es controversial, porque hasta la actualidad, no se conoce con exactitud el número de especies y géneros existentes en la familia, ni las relaciones que se establecen entre ellos. En el presente trabajo se estudiaron las relaciones filogenéticas entre cinco especies representativas de bagres marinos de la familia Ariidae, de ambas costas del Pacífico y del Atlántico Mexicano. El mencionado análisis se llevó a cabo mediante el análisis de la variabilidad en 21 loci aloenzimáticos y a través de la comparación de patrones electroforéticos de proteínas totales de músculo. Los niveles de divergencia interespecífica obtenidos por ambos métodos electroforéticos mostraron una clara separación entre los géneros Cathorops, Bagre y Ariopsis, así como entre las especies estudiadas de Cathorops y Ariopsis con Bagre marinus, mostrando una mayor similitud genética con el grupo Ariopsis. Los resultados obtenidos en este estudio contribuyen al establecimiento de la presencia de estas especies a lo largo de las costas del Golfo de México.The systematics of the marine catfish of the family Ariidae is controversial because at the present time the number of species and genera in the family, or their relationships, remain uncertain. Phylogenetic relationships among five representative species of marine catfish of the family Ariidae from both the Pacific and the Atlantic coasts of Mexico were assessed by the analysis of the variability in 21 alloenzymatic loci, and by the comparison of the electrophoretic patterns of whole muscle proteins. Interspecific genetic divergence levels obtained by both electrophoretic methods showed a clear separation among the genera Cathorops, Bagre and Ariopsis, as well as in the studied species of Cathorops and Ariopsis, with Bagre marinus showing a greater genetic similarity with the Ariopsis group. Finally, our results contribute to the definition of the presence of this species in the coasts of the Gulf of Mexic

Phylogenetic relationships among five marine Catfish species (Pisces: Ariidae) from Mexico

The systematics of the marine catfish of the family Ariidae is controversial because at the present time the number of species and genera in the family, or their relationships, remain uncertain. Phylogenetic relationships among five representative species of marine catfish of the family Ariidae from both the Pacific and the Atlantic coasts of Mexico were assessed by the analysis of the variability in 21 alloenzymatic loci, and by the comparison of the electrophoretic patterns of whole muscle proteins. Interspecific genetic divergence levels obtained by both electrophoretic methods showed a clear separation among the genera Cathorops, Bagre and Ariopsis, as well as in the studied species of Cathorops and Ariopsis, with Bagre marinus showing a greater genetic similarity with the Ariopsis group. Finally, our results contribute to the definition of the presence of this species in the coasts of the Gulf of Mexic

Improved eDNA assay evidences further refugia for critically endangered smalltooth sawfish (Pristis pectinata) in Mexico

Sawfishes are considered one of the most threatened marine fish taxa globally, with major contractions in their geographic range documented over the last 50 years across all oceans. Two sawfish species used to be found in Mexico, but a historical lack of research and first-hand baseline information recently raised concerns about the fate of both species there. Recent Local Ecological Knowledge (LEK) and environmental DNA (eDNA) research has shown that: a) Pristis pectinata and P. pristis were formerly abundant and widely distributed in the Mexican Atlantic coast, and the latter also in the Mexican Pacific coast, and b) sawfishes (at least P. pectinata) are still found in some coastal refugia in central Veracruz state and Campeche state on the Atlantic coast. In the present research we developed improved primers that allow for better species ID resolution for Pristis pectinata and P. pristis through successful sequencing of eDNA samples by amplifying a 270 bp fragment of the CO1 gene. Our results based on the analysis of 305 eDNA samples showed an improved positive species identification rate through sequencing, demonstrate that P. pectinata occurs in other coastal refugia along the Yucatán Peninsula in the Mexican Caribbean, and suggest this species might be extirpated from southern Veracruz, while no P. pristis eDNA has been found along the Atlantic coast

A genomic approach for the identification of population management units for the dolphinfish (Coryphaena hippurus) in the eastern Pacific

In the Tropical Eastern Pacific dolphinfish (TEP) Corypahena hippurus is part of commercial, recreational, and artisanal fisheries and is also caught incidentally by the tuna purse-seine and longline fisheries. Defining the existence of differenced populations in exploited species for being considered independent management units is crucial for conservation plans. However, there is a great uncertainty about the species population genetic structure across the TEP. To investigate it and to identify possible management units for conservation purposes this study was carried out, based on two SNPs datasets of 3867 and 3220 SNPs for young of the year (YOY) and adult individuals, respectively, obtained through NGS protocols. Sampling covered the species’ range distribution in the Tropical Eastern Pacific and was structured into YOY and adult individuals in order to discard the effects of migrating individuals into sampled locations. Our results revealed slight but significant differences among locations occupying the latitudinal limits of the species distribution at transitional areas between tropical and subtropical waters. These areas are characterized by strong seasonal variations in sea surface temperature and limit the prevalence of populations in these extremes. Genetic differences also seem to be related to spatial separation of locations as the northernmost (Los Cabos) and southernmost (Peru) locations including a set of oceanic samples, showed the highest levels of genetic differentiation. Whereas were detected barriers to gene flow among spatially separated locations for YOY individuals probably related to site fidelity, clear limitations to gene flow between Mexico and Central America locations were observed probably related to oceanic circulation in the area. Design management strategies in countries where the dolphinfish is explored is of primary interest to preserve genetic resources. It is necessary to define the existence of genetic differences of populations for species that are highly dependent on environmental factors limiting its distributional range as is the case of the dolphinfish

Chromosomes of Cichlasoma istlanum (Perdformes: Cichlidae) and karyotype comparison oí two presumed subspecies

Cichlasoma istlanum (lordan &amp; Snyder, 1900) is a freshwater cichlid from the Balsas river province in the Pacific Basin. Two subspecies: C. istlana istlana, from lhe Ixtla river in ¡he state of Morelos, Mexico, and C. istlana fusca, from the Huámito river near the town of La Huacana, in the state of Michoacán, were named half a century ago on the basis of merisüe characters. In this work, the karyotype of the species was eslablished by conventional and G-banding cytogenetic procedures and a comparative analysis of karyotypes from the two populations, previously proposed as subspecies, was performed. Ten females were collected in the Amacuzac river, and nine specimens (two females), were eollected in the Huámito river. Based on the eount of 264 mitotie fields of the former and 203 of the latter, the modal number of 2n=48 was established in every sample and considered as ¡he diploid number of both populations. The karyotype analysis was based on ten karyotypes prepared from Morelos and eight from Michoacán, which included ¡hree from females and five from males. The chromosome formula thus established was of 8sm+40stt. The G-banding pattem was similar in both populations and the comparison of the mean Jengths of lhe chromosome pairs did not reveal statistically significant differences between both populations. The presence of a practically identical karyotype does not support the subspecific division. The morphometric analyses made by other authors, which detected overlappíng in the characters that were proposed as distinctive of the two subspecies, agree with the results of this study: not enough divergence has been found lo substantiate ¡he $ubdivision of C. istlanum. The lack of population divergence might have been brought about by an abated geographic isolation caused by gene flow among contiguous populations along their continuous distribution in the Balsas Basin regions, by the relatively small divergence time since their distribution in these regions, andlor, less probably, by a recent historie al replacement of one popuiation by the other. The absence of karyotype differences might also be attributed lo characteristics inherent to the genome organization in the genus Cichlasoma still to be identified and understood.Cichlasoma istlanum (Jordan &amp; Snyder, 1900) es un cíclido dulceacuícola que se encuentra en la provincia del Río Balsas en la Cuenca del Pacífico mexicano. De Buen (1946), basado en caracteres merísticos de la especie, propuso la división en dos subespecies: C. isrlana iSllana, procedente del Río Ixtla, en el estado de Morelos, y C. istlana fusca, del Río Huámito, Michoacán. En este trabajo se estableció el cariotipo de la especie por medio de procedimientos citogenéticos convencionales y de bandeo G, y se realizó un análisis comparativo de los cariotipos provenientes de las muestras de las dos poblaciones previamente propuestas como subespecies. Se recolectaron diez hembras en el Río Amacuzac, en el estado de Morelos, y nueve especímenes en el Río Huámito: dos hembras y siete machos. Mediante la cuenta de 264 campos mitóticos de la primera muestra y 203 de la segunda, se pudo establecer un número modal de 2n=48 en cada una, moda que se consideró correspondía al número diploide de la especie. El análisis cariotípico se basó en diez cariogramas preparados de la población de Morelos y de ocho de la de Michoacán, que incluyó tres provenientes de hembras y cinco de machos. La fórmula cromosómica encontrada fue de 8sm+40stt. El patrón de bandas G de ambas poblaciones fue similar y las comparaciones estadísticas de las longitudes promedio de los pares cromosómicos no mostraron diferencias significativas concluyentes entre ambas poblaciones. La existencia de un cariotipo prácticamente idéntico concuerda con la falta de diversificación subespecífica entre las poblaciones estudiadas. Los análisis morfométricos realizados por otros autores que encontraron sobreposición en los caracteres que fueron propuestos como distintivos de las dos subespecies, concuerdan con los resultados del presente estudio en que no se detectó divergencia suficiente para fundamentar la subdivisión de C. istlallum. La falta de divergencia poblacional encontrada puede deberse a un aislamiento geográfico disminuído por la existencia de flujo genético entre poblaciones contiguas a lo largo de su distribución en las diferentes regiones del Río Balsas, por un lapso de divergencia evolutiva relativamente corto a partir de su distribución en estas regiones y/o, con menor probabilidad, por un reemplazo de una población por la otra. La estabilidad carotípica encontrada pueda ser debida también a características, aun por identificarse y definirse, inherentes a la organización del genoma en este géner

Chromosomes of Cichlasoma istlanum (Perciformes: Cichlidae) and karyotype comparison of two presumed subspecies

Cichlasoma istlanum (Jordan & Snyder, 1900) is a freshwater cichlid from the Balsas river province in the Pacific Basin. Two subspecies: C. istlana istlana, from the Ixtla river in the state of Morelos, Mexico, and C. istlana fusca, from the Huámito river near the town of La Huacana, in the state of Michoacán, were named half a century ago on the basis of meristic characters. In this work, the karyotype of the species was established by conventional and G-banding cytogenetic procedures and a comparative analysis of karyotypes from the two populations, previously proposed as subspecies, was performed. Ten females were collected in the Amacuzac river, and nine specimens (two females), were collected in the Huámito river. Based on the count of 264 mitotic fields of the former and 203 of the latter, the modal number of 2n=48 was established in every sample and considered as the diploid number of both populations. The karyotype analysis was based on ten karyotypes prepared from Morelos and eight from Michoacán, which included three from females and five from males. The chromosome formula thus established was of 8sm+40stt. The G-banding pattern was similar in both populations and the comparison of the mean lengths of the chromosome pairs did not reveal statistically significant differences between both populations. The presence of a practically identical karyotype does not support the subspecific division. The morphometric analyses made by other authors, which detected overlapping in the characters that were proposed as distinctive of the two subspecies, agree with the results of this study: not enough divergence has been found to substantiate the subdivision of C. istlanum. The lack of population divergence might have been brought about by an abated geographic isolation caused by gene flow among contiguous populations along their continuous distribution in the Balsas Basin regions, by the relatively small divergence time since their distribution in these regions, and/or, less probably, by a recent historical replacement of one population by the other. The absence of karyotype differences might also be attributed to characteristics inherent to the genome organization in the genus Cichlasoma still to be identified and understood.Cichlasoma istlanum (Jordan & Snyder, 1900) es un cíclido dulceacuícola que se encuentra en la provincia del Río Balsas en la Cuenca del Pacífico mexicano. De Buen (1946), basado en caracteres merísticos de la especie, propuso la división en dos subespecies: C. istlana istlana, procedente del Río Ixtla, en el estado de Morelos, y C. istlana fusca, del Río Huámito, Michoacán. En este trabajo se estableció el cariotipo de la especie por medio de procedimientos citogenéticos convencionales y de bandeo G, y se realizó un análisis comparativo de los cariotipos provenientes de las muestras de las dos poblaciones previamente propuestas como subespecies. Se recolectaron diez hembras en el Río Amacuzac, en el estado de Morelos, y nueve especímenes en el Río Huámito: dos hembras y siete machos. Mediante la cuenta de 264 campos mitóticos de la primera muestra y 203 de la segunda, se pudo establecer un número modal de 2n=48 en cada una, moda que se consideró correspondía al número diploide de la especie. El análisis cariotípico se basó en diez cariogramas preparados de la población de Morelos y de ocho de la de Michoacán, que incluyó tres provenientes de hembras y cinco de machos. La fórmula cromosómica encontrada fue de 8sm+40stt. El patrón de bandas G de ambas poblaciones fue similar y las comparaciones estadísticas de las longitudes promedio de los pares cromosómicos no mostraron diferencias significativas concluyentes entre ambas poblaciones. La existencia de un cariotipo prácticamente idéntico concuerda con la falta de diversificación subespecífica entre las poblaciones estudiadas. Los análisis morfométricos realizados por otros autores que encontraron sobreposición en los caracteres que fueron propuestos como distintivos de las dos subespecies, concuerdan con los resultados del presente estudio en que no se detectó divergencia suficiente para fundamentar la subdivisión de C. istlanum. La falta de divergencia poblacional encontrada puede deberse a un aislamiento geográfico disminuído por la existencia de flujo genético entre poblaciones contiguas a lo largo de su distribución en las diferentes regiones del Río Balsas, por un lapso de divergencia evolutiva relativamente corto a partir de su distribución en estas regiones y/o, con menor probabilidad, por un reemplazo de una población por la otra. La estabilidad carotípica encontrada pueda ser debida también a características, aun por identificarse y definirse, inherentes a la organización del genoma en este género

The complete mitochondrial genome of the Mexican blind brotula Typhlias pearsei (Ophidiiformes: Dinematichthydae): an endemic and troglomorphic cavefish from the Yucatán Peninsula karst aquifer

In this study we report the first complete and annotated mitochondrial genome of the Mexican blind brotula, Typhlias pearsei, a troglobitic cavefish endemic to the Yucatán peninsula karst aquifer in southeastern Mexico. Genomic sequencing was accomplished via next generation sequencing (NGS). The resulting mitogenome is 16,813 bp long and, as in most vertebrates, consists of a total of 37 genes (13 PCGs, 2 rRNAs, 22 tRNAs) and two non-coding regions (control region and origin of the light strand replication). Other than a rearrangement in the position of two tRNAs (shuffling between tRNA-Ile and tRNA-Gln), the mitogenome of T. pearsei exhibits a genomic composition and organization similar to that of most teleost mitogenomes. Besides offering this valuable genomic resource for future studies, the resulting mitogenome was used in a comparative context to test the current higher-level taxonomy of ophidiiform fishes and to examine the phylogenetic position of T. pearsei among viviparous brotulas. Our phylogenetic results confirm those from the most comprehensive molecular phylogenetic study of the group

Variación morfológica del camarón café (Farfantepenaeus californiensis) en el Pacífico mexicano Morphological variation of brown shrimp (Farfantepenaeus californiensis) in Mexican Pacific

El análisis multivariado de datos morfométricos se ha utilizado ampliamente en especies comerciales para definir unidades de pesca independientes. En la presente investigación se analizó la diferenciación del camarón café Farfantepenaeus californiensis (Holmes, 1900) del Pacífico mexicano mediante el análisis morfométrico de 171 individuos recolectados en 4 localidades y se comparó con la subdivisión geográfica que el Instituto Nacional de la Pesca estableció para el monitoreo de sus poblaciones. La variación morfológica de cada muestra se estimó mediante el (CV%) promedio de 18 medidas. Se realizó un análisis discriminante utilizando proporciones estandarizadas de algunas de estas medidas y se calcularon las distancias de Manhattan entre las muestras; con éstas se obtuvo un dendrograma por el método UPGMA en el cual la agrupación de las localidades mostró una diferenciación morfológica clinal, relacionada con un gradiente geográfico. La baja variabilidad morfológica estimada al interior de las muestras permitió inferir que cada localidad conforma un grupo fenotípicamente homogéneo, aunque con claras diferencias entre sí, que podrían estar relacionadas con las características ambientales de cada localidad y con posibles variaciones genéticas entre las poblaciones. La diferenciación morfológica del camarón café del Pacífico mexicano que se encontró en esta investigación aporta elementos adicionales para sustentar la división geográfica que el Instituto Nacional de la Pesca ha establecido para el estudio de la pesquería del camarón.<br>Multivariate analyses of morphometric data have been widely used to define independent fishing units for exploited species. In this study we analyzed the morphometric variability of 4 brown shrimp Farfantepenaeus californiensis (Holmes, 1900) locations from the Mexican Pacific to assess whether differentiation agrees with the geographical subdivision established by the Instituto Nacional de la Pesca to monitoring the brown shrimp populations. The morphologic variation of each sample was estimated through the variation coefficient (CV%) averaged over 18 measurements. A discriminant analysis was made using the standardized ratios for some of the measurements. Manhattan distances among samples were calculated to obtain a dendrogram with the UPGMA method where localities grouping showed a clinal pattern of morphological differentiation related to a geographical gradient. The low estimated morphologic variability within samples allowed us to conclude that each sampled locality conforms a phenotypically homogeneous group, with clear differences to the others. These differences could be explained on basis of the environmental characteristics of each locality in addition to possible genetic variations between populations. Thus, the morphological differentiation of the brown shrimp populations of the Mexican Pacific detected in this study provides additional elements to sustain the geographical division that the Instituto Nacional de la Pesca established to survey the shrimp fishery

Phylogeography of Holothuria (Halodeima) inornata Semper, 1868 (Echinodermata: Holothuroidea)

Genetic structure of the populations of H. inornata was evaluated and the barriers for genetic flux and historic processes were investigated. Samples were collected trying to cover the distribution range of the species, from Mexico to northern Perú. Based on COI sequences, 118 haplotypes from 220 specimens were detected; the differences between such haplotypes were due to 97 variable sites (21.41%) of the 453 bp sequenced. A high haplotype diversity (h=0.979) and a moderate nucleotidic diversity were observed. The values of Fst, the exact test of population differentiation, and the molecular variance analysis (AMOVA) were used in order to analyze the genetic differentiation. These analyses suggest the existence of two populations: northern, off the coasts of Sinaloa, Jalisco, Michoacán, Guerrero, and Oaxaca, and southern, off the coasts of Chiapas, El Salvador, Panamá and Perú. Historic events and oceanographic patterns may be the main factors determining dispersion and structure of Hi populations. It seems probable that the original population have extended first in the south and then northern. Besides, the split between these two populations may be due to several tectonic and oceanographic events constituting a barrier for H. inornata settling