Chloroplast DNA phylogeography of a distylous shrub (Palicourea padifolia, Rubiaceae) reveals past fragmentation and demographic expansion in Mexican cloud forests

Several phylogeographic studies in northern Mesoamerica have examined the influence of Pleistocene glaciations on the genetic structure of temperate tree species with their southern limit by the contact zone between species otherwise characteristic of North or South America, but few have featured plant species that presumably colonized northern Mesoamerica from South America. A phylogeographical study of Palicourea padifolia, a fleshy-fruited, bird dispersed distylous shrub, was conducted to investigate genetic variation at two chloroplast regions (trnS-trnG and rpl32-trnL) across cloud forest areas to determine if such patterns are consistent with the presence of Pleistocene refugia and/or with the historical fragmentation of the Mexican cloud forests. We conducted population and spatial genetic analyses as well as phylogenetic and isolation with migration analyses on 122 individuals from 22 populations comprising the distribution of P. padifolia in Mexico to gain insight of the evolutionary history of these populations. Twenty-six haplotypes were identified after sequencing 1389 bp of chloroplast DNA. These haplotypes showed phylogeographic structure (N(ST) = 0.508, G(ST) = 0.337, N(ST) > G(ST), P < 0.05), including a phylogeographic break at the Isthmus of Tehuantepec, with private haplotypes at either side of the isthmus, and a divergence time of the split in the absence of gene flow dating back c. 309,000-103,000 years ago. The patterns of geographic structure found in this study are consistent with past fragmentation and demographic range expansion, supporting the role of the Isthmus of Tehuantepec as a biogeographical barrier in the dispersal of P. padifolia. Our data suggest that P. padifolia populations were isolated throughout glacial cycles by the Isthmus of Tehuantepec, accumulating genetic differences due to the lack of migration across the isthmus in either direction, but the results of our study are not consistent with the existence of the previously proposed Pleistocene refugia for rain forest plant species in the region.     

Coalescent analyses show isolation without migration in two closely related tropical orioles: the case of Icterus graduacauda and Icterus chrysater

The Isthmus of Tehuantepec has played an important role in shaping the avian diversity of Mexico, as well as the rest of the Western Hemisphere. It has been both a barrier and a land connector between North and South America for many groups of birds. Furthermore, climatic change over the Pleistocene has resulted in ecological fluctuations that led to periods of connection and isolation of the highlands in this area. Here we studied the divergence of two species of orioles whose distribution in the highlands is separated by the lowlands of the Isthmus of Tehuantepec: Icterus graduacauda (west of the Isthmus) and Icterus chrysater (east of the Isthmus). We sequenced multiple loci (one mitochondrial gene and six nuclear introns) and performed coalescent analyses (Isolation with Migration) to test whether their divergence resulted from prior occupancy of the ancestral area followed by a vicariant event or recent dispersal from one side or the other of this Isthmus. Results strongly indicate a vicariant event roughly 300,000 years ago in the Pleistocene followed by little or no gene flow. Both mitochondrial and nuclear genes show that the Isthmus of Tehuantepec is a strong barrier to gene flow. Thus, these two species appear to not exchange genes despite their recent divergence and the close geographic proximity of their ranges.     

Do the Oaxacan Highlands represent a natural biotic unit? A cladistic biogeographical test based on vertebrate taxa

Aim  We analysed the distributional patterns of six terrestrial vertebrate taxa from the Oaxacan Highlands (Sierra Mazateca, Nudo de Zempoaltépetl and Sierra de Juárez) through a cladistic biogeographical approach, in order to test their naturalness as a biotic unit.
Location  The Oaxacan Highlands, Mexico.
Methods  The cladistic biogeographical analysis was based on the area cladograms of the Pseudoeurycea bellii species group (Amphibia: Plethodontidae), the genus Chlorospingus (Aves: Thraupidae), the genera Microtus , Reithrodontomys and Habromys , and the Peromyscus aztecus species group (Mammalia: Rodentia). We obtained paralogy-free subtrees, from which the components were coded in a data matrix for parsimony analysis. The data matrix was analysed with N ona through W in C lada .
Results  The parsimony analysis resulted in a single general area cladogram in which areas were fragmented following the sequence Sierra Madre Occidental, Trans-Mexican Volcanic Belt, Chiapas, Sierra Madre Oriental + Sierra Mazateca, Sierra Madre del Sur, Nudo de Zempoaltépetl and Sierra de Juárez.
Main conclusions  The general area cladogram shows that the Oaxacan Highlands do not constitute a natural unit. The Sierra Mazateca is the sister area to the Sierra Madre Oriental, whereas the Nudo de Zempoaltépetl and the Sierra de Juárez are closely related to the Sierra Madre del Sur. The events that might have caused these patterns include cycles of expansion and contraction of mountain pinyon, juniper and oak woodlands during the Pleistocene.     

Phylogeography of Middle American gophersnakes: mixed responses to biogeographical barriers across the Mexican Transition Zone

Aim We used inferences of phylogeographical structure and estimates of divergence times for three species of gophersnakes (Colubridae: Pituophis) distributed across the Mexican Transition Zone (MTZ) to evaluate the postulated association of three Neogene geological events (marine seaway inundation of the Isthmus of Tehuantepec, formation of the Transvolcanic Belt across central Mexico, and secondary uplifting of the Sierra Madre Occidental) and of Pleistocene climate change with inter‐ and intraspecific diversification. Location Mexico, Guatemala, and the western United States. Methods We combined range‐wide sampling (67 individuals representing three putative species distributed across northern Middle America and western North America) and phylogenetic analyses of 1637 base pairs of mitochondrial DNA to estimate genealogical relationships and divergence times. The hypothesized concordance of inferred gene trees with geological histories was assessed using topology tests. Results We identified three major lineages of Middle American gophersnakes, and strong phylogeographical structure within each lineage. Gene trees were statistically congruent with hypothesized geological histories for two of the three postulated geological events. Estimated divergence dates and the geographical distribution of genetic variation further support mixed responses to these geological events. Considerable phylogeographical structure appears to have been generated during the Pleistocene. Main conclusions Phylogenetic and phylogeographical structure in gophersnakes distributed across northern Middle America and western North America highlights the influence of both Neogene vicariance events and Pleistocene climate change in shaping genetic diversity in this region. Despite the presence of two major geographical barriers in southern Mexico, extreme geological and environmental heterogeneity in this area may have differentially structured genetic diversity in highland taxa. To the north, co‐distributed taxa may display a more predictable pattern of diversification across the warm desert regions. Future studies should incorporate nuclear data to disentangle inferred lineage boundaries and further elucidate patterns of mitochondrial introgression.     

Molecular and iridescent feather reflectance data reveal recent genetic diversification and phenotypic differentiation in a cloud forest hummingbird

The present day distribution and spatial genetic diversity of Mesoamerican biota reflects a long history of responses to habitat change. The hummingbird Lampornis amethystinus is distributed in northern Mesoamerica, with geographically disjunct populations. Based on sampling across the species range using mitochondrial DNA (mtDNA) sequences and nuclear microsatellites jointly analysed with phenotypic and climatic data, we (1) test whether the fragmented distribution is correlated with main evolutionary lineages, (2) assess body size and plumage color differentiation of populations in geographic isolation, and (3) evaluate a set of divergence scenarios and demographic patterns of the hummingbird populations. Analysis of genetic variation revealed four main groups: blue‐throated populations (Sierra Madre del Sur); two groups of amethyst‐throated populations (Trans‐Mexican Volcanic Belt and Sierra Madre Oriental); and populations east of the Isthmus of Tehuantepec (IT) with males showing an amethyst throat. The most basal split is estimated to have originated in the Pleistocene, 2.39–0.57 million years ago (MYA), and corresponded to groups of populations separated by the IT. However, the estimated recent divergence time between blue‐ and amethyst‐throated populations does not correspond to the 2‐MY needed to be in isolation for substantial plumage divergence, likely because structurally iridescent colors are more malleable than others. Results of species distribution modeling and Approximate Bayesian Computation analysis fit a model of lineage divergence west of the Isthmus after the Last Glacial Maximum (LGM), and that the species’ suitable habitat was disjunct during past and current conditions. These results challenge the generality of the contraction/expansion glacial model to cloud forest‐interior species and urges management of cloud forest, a highly vulnerable ecosystem to climate change and currently facing destruction, to prevent further loss of genetic diversity or extinction.     

Ephemeral Pleistocene woodlands connect the dots for highland rattlesnakes of the Crotalus intermedius group

Aim To test how Pleistocene climatic changes affected diversification of the Crotalus intermedius species complex. Location Highlands of Mexico and the south‐western United States (Arizona). Methods We synthesize the matrilineal genealogy based on 2406 base pairs of mitochondrial DNA sequences, fossil‐calibrated molecular dating, reconstruction of ancestral geographic ranges, and climate‐based modelling of species distributions to evaluate the history of female dispersion. Results The presently fragmented distribution of the C. intermedius group is the result of both Neogene vicariance and Pleistocene pine–oak habitat fragmentation. Most lineages appear to have a Quaternary origin. The Sierra Madre del Sur and northern Sierra Madre Oriental are likely to have been colonized during this time. Species distribution models for the Last Glacial Maximum predict expansions of suitable habitat for taxa in the southern Sierra Madre Occidental and northern Sierra Madre Oriental. Main conclusions Lineage diversification in the C. intermedius group is a consequence of Pleistocene climate cycling. Distribution models for two sister taxa in the northern and southern Sierra Madre Occidental and northern Sierra Madre Oriental during the Last Glacial Maximum provide evidence for the expansion of pine–oak habitat across the Central Mexican Plateau. Downward displacement and subsequent expansions of highland vegetation across Mexico during cooler glacial cycles may have allowed dispersal between highlands, which resulted in contact between previously isolated taxa and the colonization of new habitats.     

Diversification of the arboreal mice of the genus Habromys (Rodentia: Cricetidae: Neotominae) in the Mesoamerican highlands

The arboreal mice of the genus Habromys (Rodentia: Cricetidae: Neotominae) are among the most poorly known Neotropical rodents. We investigated species-level phylogenetic relationships among the seven described Habromys species using 1331 aligned bases from the mitochondrial ND3 and ND4 regions. Sequences were obtained from 30 specimens of the seven known species of Habromys and we performed maximum parsimony, maximum likelihood, and Bayesian probabilities analyses. The monophyly of the genus Habromys within the Neotomines was verified. The northernmost H. simulatus is sister to the remaining species of the group; within the latter, the southernmost clade (Oaxaca to Central America) is sister to the Transmexican Volcanic Belt clade. Four major clades are clearly distinguished: H. simulatus from the Sierra Madre Oriental and the closely associated Sierra Mazateca; H. delicatulus and H. schmidlyi from the Transmexican Volcanic Belt; H. lepturus, H. chinanteco, and H. ixtlani from the northern Oaxacan highlands; and H. lophurus from Nuclear Central America. Within species, the analyses suggest that H. simulatus and H. lophurus are each composed by two different taxa.     

Historical biogeography of lowland species of toads (Bufo) across the Trans-Mexican Neovolcanic Belt and the Isthmus of Tehuantepec

Aim In this study, we investigate phylogeographic structure in two different species groups of lowland toads. First, we further investigate strict parapatry of the Pliocene‐vicariant Bufo valliceps/B. nebulifer species pair. Secondly, we test for similar phylogeographic structure in the distantly related toad B. marinus, a species we hypothesize will show a Pleistocene dispersal across the same area. Location The eastern extension of the Trans‐Mexican Neovolcanic Belt (TMNB) contacts the Atlantic Coast in central Veracruz, Mexico. Although it is not a massive structure at this eastern terminus, the TMNB has nonetheless effected vicariance and subsequent speciation in several groups of animals. The Isthmus of Tehuantepec unites the North American continent with Nuclear Central America and is also known to be a biogeographic barrier for many taxa. Methods We use sequence data from two mitochondrial DNA genes (c. 550 base‐pairs (bp) of 16S and c. 420 bp of cyt b) from 58 individuals of the B. valliceps/nebulifer complex, collected from 24 localities. We also present homologous sequence data from 23 individuals of B. marinus, collected from 12 localities. We conduct maximum‐parsimony, maximum‐likelihood and Bayesian analyses to investigate phylogeographic structure. We then use parsimony‐ and likelihood‐based topology tests to assess alternative phylogenetic hypotheses and use a previously calibrated molecular rate of evolution to estimate dates of divergence. Results Our results further define the parapatric contact zone across the TMNB between the Pliocene‐vicariant sister species B. valliceps and B. nebulifer. In contrast, phylogenetic structure among populations of B. marinus across the TMNB is much shallower, suggesting a more recent Pleistocene dispersal in this species. In addition, we found phylogeographic structure associated with the Isthmus of Tehuantepec in both species groups. Main conclusions The existence of a Pliocene–Pleistocene seaway across the Isthmus of Tehuantepec has been controversial. Our data depict clades on either side of the isthmus within two distinct species (B. valliceps and B. marinus), although none of the clades associated with the isthmus, for either species, are reciprocally monophyletic. In the B. valliceps/B. nebulifer complex, the TMNB separation appears to predate the isthmian break, whereas in B. marinus dispersal across the TMNB has occurred subsequent to the presence of a barrier at the Isthmus of Tehuantepec.     

Historical biogeography of the genus Rhadinaea (Squamata: Dipsadinae)

Multiple geological and climatic events have created geographical or ecological barriers associated with speciation events, playing a role in biological diversification in North and Central America. Here, we evaluate the influence of the Neogene and Quaternary geological events, as well as the climatic changes in the diversification of the colubrid snake genus Rhadinaea using molecular dating and ancestral area reconstruction. A multilocus sequence dataset was generated for 37 individuals of Rhadinaea from most of the biogeographical provinces where the genus is distributed, representing 19 of the 21 currently recognized species, and two undescribed species. Our analyses show that the majority of the Rhadinaea species nest in two main clades, herein identified as “Eastern” and “Southern”. These clades probably diverged from each other in the early Miocene, and their divergence was followed by 11 divergences during the middle to late Miocene, three divergences during the Pliocene, and six divergences in the Pleistocene. The ancestral distribution of Rhadinaea was reconstructed across the Sierra Madre del Sur. Our phylogenetic analyses do not support the monophyly of Rhadinaea. The Miocene and Pliocene geomorphology, perhaps in conjunction with climate change, appears to have triggered the diversification of the genus, while the climatic changes during the Miocene probably induced the diversification of Rhadinaea in the Sierra Madre del Sur. Our analysis suggests that the uplifting of the Trans‐Mexican Volcanic Belt and Chiapan–Guatemalan highlands in this same period resulted in northward and southward colonization events. This was followed by more recent, independent colonization events in the Pliocene and Pleistocene involving the Balsas Basin, Chihuahuan Desert, Pacific Coast, Sierra Madre Occidental, Sierra Madre Oriental, Sierra Madre del Sur, Trans‐Mexican Volcanic Belt, and Veracruz provinces, probably driven by the climatic fluctuations of the time.     

Phylogeography of the Buarremon brush-finch complex (Aves, Emberizidae) in Mesoamerica

The Buarremon brush-finches represent a complex suite of populations distributed in the montane New World Tropics from Mexico south to South America. Traditional taxonomic arrangements have separated populations of this genus into three species, based on plumage variation, although plumage patterns are well known to exhibit homoplasy. We present a first detailed phylogeographic and phylogenetic study, focused on Mesoamerican populations, and signal the existence of strong differentiation among populations with a clear geographic structure. We find well differentiated clades for (1) the Sierra Madre Oriental and Sierra Madre del Sur in Oaxaca, (2) western Mexican populations, including the B. brunneinucha populations in the Sierra Madre del Sur and B. virenticeps, (3) Sierra Madre Oriental and Sierra de los Tuxtlas, (4) northern Central America, (5) southern Central America, (6) middle Central America, and (7) South America. We demonstrate a lack of concordance with plumage patterns, and argue for several additional species to be recognized in the complex.     

Speciation in the highlands of Mexico: genetic and phenotypic divergence in the Mexican jay (Aphelocoma ultramarina)

The pine-oak woodlands of the Mexican highlands harbour significant biological diversity, yet little is known about the evolutionary history of organisms inhabiting this region. We assessed genetic and phenotypic differentiation in 482 individuals representing 27 populations of the Mexican jay ( Aphelocoma ultramarina ) — a widespread bird species of the Mexican highlands — to test whether populations in the central and northern Mexican sierras display discrete breaks between groups, which would be consistent with a role for the different mountain chains in divergence and speciation. We found abrupt breaks in mitochondrial DNA (mtDNA; ND2 and control region) delineating four major genetic groups found in the Sierra Madre Occidental, Sierra Madre Oriental, southern Central Plateau (Bajio), and Transvolcanic Belt. These mtDNA groups were largely corroborated by data from nuclear microsatellites and phenotypic data, except that clades from the Central Plateau and Sierra Madre Oriental showed clinal change in these data sets. Uncertainty about the mutation rate for our mitochondrial markers warrants considerable caution with regard to estimating divergence times, but the major genetic groups appear to have split before the most extreme period of glacial cycling that marked the last 0.7 million years and after Mexico's period of major mountain formation. The fact that some genetic breaks do not coincide with well-known geographic barriers suggests a role for ecology in divergence and speciation, and we discuss implications for taxonomy and conservation.     

Biogeographical analysis of two Polypodium species complexes (Polypodiaceae) in Mexico and Central America

We analyzed the geographical and elevational distributions of two Polypodium complexes from Mexico and Central America. Distribution data of nine species of the Polypodium colpodes complex and the Polypodium plesiosorum complex were obtained from almost 1500 herbarium specimens, field collections in Mexico and Costa Rica, and literature studies. The presence of each species was recorded for each Mesoamerican country, in 1° × 1° grid‐cells and biogeographical provinces. The rarity of species was also evaluated. Although the two complexes show extensive overlap, the P. colpodes complex is distributed mainly along the Pacific versant of Mexico and Central America, whereas the P. plesiosorum complex occurs mainly along the Atlantic versant. Those biogeographical provinces with maximum species diversity are Chiapas (seven species), Sierra Madre del Sur (six species), and the Trans‐Mexican Volcanic belt (six species). Grid‐cells with more species are located mainly in the mountains of central‐southern Mexico and northern Central America. Richness does not decrease or increase with latitude. Elevation distributions showed that most Polypodium species are concentrated in the montane interval and three species groups were recognized based on elevational preferences. Polypodium colpodes and P. plesiosorum are the most widely distributed species, whereas Polypodium castaneum and Polypodium flagellare are the only two species that possess the three attributes of rarity (narrow geographical distribution, high habitat specificity, and scarce local populations). Polypodium species of both complexes are present mainly in the montane regions of the study area and show some degree of geographical sympatry, especially in southern Mexico and northern Central America. This overlapping is explained by the elevation tolerance within montane systems and because most species inhabit three or more vegetation types. The distributional patterns of these complexes coincided with the three regional highlands of Mesoamerica, which are separated from each other by the Isthmus of Tehuantepec and by the lowlands of Nicaragua. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Phylogeography of Peromyscus furvus (Rodentia; muridae) based on cytochrome b sequence data

We conducted phylogenetic analyses of cytochrome b sequence data to assess genetic variation within and among the three allopatric segments of the distribution of Peromyscus furvus from the Sierra Madre Oriental in eastern Mexico. We identified 24 unique haplotypes among the 54 individuals examined and genetic distances ranged up to 0.078 substitutions per site. Populations from the central portion of the range formed a monophyletic unit, whereas samples from the southern distributional unit were polyphyletic. Furthermore, the southernmost population sampled may represent a distinct species. This high degree of genetic differentiation among populations, currently recognized as conspecific, mirrors the result of other genetic studies of highland rodents in Mesoamerica. Together these studies indicate that the region, already considered hyperdiverse on the basis of species diversity and endemism, may contain considerably greater diversity than is currently appreciated.     

Phylogeography of Podocarpus matudae (Podocarpaceae): pre‐Quaternary relicts in northern Mesoamerican cloud forests

Aim Cloud forests of northern Mesoamerica represent the northern and southern limit of the contact zone between species otherwise characteristic of North or South America. Several phylogeographic studies featuring temperate conifer species have improved our understanding of species responses to environmental changes. In contrast, conifer species that presumably colonized northern Mesoamerica from South America are far less studied. A phylogeographic study of Podocarpus matudae (Podocarpaceae) was conducted to identify any major evolutionary divergences or disjunctions across its range and to determine if its current distribution is associated with pre‐Quaternary climatic and/or long‐distance dispersal events. Location Northern Mesoamerica (Mexico and Guatemala). Methods Sixteen populations (157 individuals) of P. matudae were screened for variation at two plastid DNA markers. The intra‐specific phylogenetic relationships among haplotypes were reconstructed using Bayesian inference. Population genetic analyses were undertaken to gain insight into the evolutionary history of these populations. To test whether genetic divergence among populations occurred at different time‐scales plastid DNA sequence data and fossil‐ and coalescent‐based calibrations were integrated. Results The combination of plastid markers yielded 11 haplotypes. Differentiation among populations based on DNA variation (G_ST) (0.707, SE 0.0807) indicated a clear population structure in P. matudae. Differentiation for ordered alleles (N_ST) (0.811, SE 0.0732) was higher than that for G_ST, indicating phylogeographical structure in P. matudae. Most of the total variation (81.3%, P < 0.0001) was explained by differences among populations. The estimated divergence time between the unique haplotypes from a Guatemalan population and the two most common haplotypes from the Sierra Madre Oriental in Mexico was between 10 and 20 Ma, and further haplotype divergence in the poorly resolved clade of the Sierra Madre Oriental occurred between 3 and 0.5 Ma. Main conclusions Divergence estimations support the hypothesis that extant Podocarpus matudae populations are pre‐Quaternary relicts. This finding is consistent with fossil and pollen data that support a Miocene age for temperate floristic elements in Mesoamerican cloud forests, whereas further haplotype divergence within the Sierra Madre Oriental, Chiapas and Guatemala occurred more recently, coinciding with Pleistocene cloud forest refugia.     

Population genetics and geometric morphometrics of the <Emphasis Type="Italic">Bombus ephippiatus</Emphasis> species complex with implications for its use as a commercial pollinator

Mexico and Central America are among the most biodiverse regions on Earth, harboring many species with high levels of interpopulation morphological and genetic diversity. The mountainous topography of this region contains isolated sky island habitats that have the potential to promote speciation. This has been studied in vertebrates, yet few studies have examined the phylogeographic and genetic structure of insect species encompassing this region. Here we investigate geographic patterns of genetic and morphological divergence and speciation among widespread populations of the highly polymorphic bumble bee Bombus ephippiatus and its closest relative B. wilmattae. We used DNA sequences from a fragment of cytochrome oxidase I (COI), genotypes for twelve microsatellite markers, and morphometric data from wings to construct a well-supported inference of the divergences among these taxa. We have found complex patterns of genetic isolation and morphological divergence within B. ephippiatus across its geographic range and present evidence that B. ephippiatus comprises multiple independent evolutionary lineages. The pattern of their diversification corresponds to geographic and environmental isolating mechanisms, including the Mexican highlands, the lowlands of the Isthmus of Tehuantepec in southern Mexico, the Nicaraguan Depression, the patchily distributed volcanic ranges in Nuclear Central America and Pleistocene glacial cycles. These results have important implications for the development and distribution of B. ephippiatus as a commercial pollinator in Mexico and Central America.     

Complex phylogeographic patterns indicate Central American origin of two widespread Mesoamerican <Emphasis Type="Italic">Quercus</Emphasis> (Fagaceae) species

The northern Neotropical region is characterized by a heterogeneous geological and climatic history. Recent studies have shown contrasting patterns regarding the role of geographic elements as barriers that could have determined phylogeographic structure in various species. Recently, the phylogeography and biogeography of Quercus species have been studied intensively, and the patterns observed so far suggest contrasting evolutionary histories for Neotropical species in comparison with their Holarctic relatives. The goal of this study was to describe the phylogeographic structure of two Neotropical oak species (Quercus insignis and Quercus sapotifolia) in the context of the geological and palaeoclimatic history of the northern Neotropics. Populations through the distribution range of both species were collected and characterized using nine chloroplast DNA microsatellite loci. Both oak species showed high levels of genetic diversity and strong phylogeographic structure. The distribution of genetic variation in Q. insignis suggested an influence of two major barriers, the Isthmus of Tehuantepec and the Nicaraguan Depression, while Q. sapotifolia exhibited a genetic structure defined by the heterogeneity of the Chortis highlands. The haplotype networks of both species indicated complex histories, suggesting that colonization from the Sierra Madre de Chiapas to central Mexico and from the north of the Nicaraguan Depression to the Costa Rican mountains may have occurred during different stages, and apparently more than one time. In conclusion, the phylogeographic structure of Neotropical oak species seems to be defined by a combination of geological and climatic events.     

Moss endemism in the Mexican flora

Although the moss flora of Mexico consists of nearly 1000 species, only 77 are endemic. The country has many poorly collected or unexplored areas, but the number of endemic mosses is not expected to undergo a substantial increase; percent endemism has in fact decreased with taxonomic revisions and monographs and better exploration in other countries. Literature and herbarium records (n?=?584) were used to obtain an updated list of endemic mosses and their state distribution in Mexico. Cluster analysis and mapping indicate that there are three main areas of endemism: Lowland areas in various states, the mountain area along 19–20°N lat., and the highlands in Oaxaca and Chiapas. Similarity by province shows that Trans-Mexican Volcanic Belt, Sierra Madre Oriental, Chihuahuan Desert, and Sierra Madre del Sur have the highest numbers of endemic species. Five monotypic genera and 76 species (including two infraspecific taxa), many of which have comparatively narrow geographical ranges, suggest that speciation is recent, that species have had little time to disperse, and were formed by Pleistocene environmental climates in the highlands; older speciation may be represented by widespread disjunct species that still are found in the highlands of Mexico.     

Phylogeography and systematics of the Peromyscus eremicus species group and the historical biogeography of North American warm regional deserts

Phylogeographic relationships among 26 populations from throughout the geographic range of the Peromyscus eremicus species group are described based on sequence data for a 699-bp fragment of the mitochondrial DNA COIII gene. Distance, maximum-likelihood, and maximum-parsimony analyses of phylogenetic trees generated under four separate character-weighting strategies and representing five alternative biogeographic hypotheses revealed the existence of a cryptic species (Peromyscus fraterculus, previously included under P. eremicus) on the Baja California Peninsula and adjacent southwestern California and two distinct forms of P. eremicus, one from the Mojave, Sonoran, and northwestern Chihuahuan regional deserts (West) and one from the remainder of the Chihuahuan Desert (East). Distinctiveness of P. fraterculus is supported by previous morphometric and allozyme analyses, including comparisons with neighboring P. eremicus and parapatric P. eva, with which P. fraterculus shares a sister taxon relationship. Divergence of the eva + fraterculus, West + East eremicus, and P. merriami haplotype lineages likely occurred in the late Neogene (3 Ma), in response to northern extension of the Sea of Cortéz and elevation of the Sierra Madre Occidental; divergence of eva from fraterculus is concordant with the existence of a trans-Peninsular seaway during the Pleistocene (1 Ma); and divergence of West from East eremicus occurred during the Pleistocene pluvial-interpluvial cycles, but well before the Wisconsinan glacial interval. The sequence of divergence within the eremicus species group and causal association of geological events of the Neogene and Holocene provide a working hypothesis against which phylogeographic patterns among other arid-adapted species of the warm regional deserts of North America may be compared.     

Molecular systematics of Middle American harvest mice Reithrodontomys (Muridae), estimated from mitochondrial cytochrome b gene sequences

We estimated phylogenetic relationships among 16 species of harvest mice using sequences from the mitochondrial cytochrome b (cyt b) gene. Gene phylogenies constructed using maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) optimality criteria were largely congruent and arranged taxa into two groups corresponding to the two recognized subgenera (Aporodon and Reithrodontomys). All analyses also recovered R. mexicanus and R. microdon as polyphyletic, although greater resolution was obtained using ML and BI approaches. Within R. mexicanus, three clades were identified with high nodal support (MP and ML bootstrap, Bremer decay and Bayesian posterior probabilities). One represented a subspecies of R. mexicanus from Costa Rica (R. m. cherrii) and a second was distributed in the Sierra Madre Oriental of Mexico. The third R. mexicanus clade consisted of mice from southern Mexico southward to South America. Polyphyly between the two moieties of R. microdon corresponded to the Isthmus of Tehuantepec in southern Mexico. Populations of R. microdon microdon to the east of the isthmus (Chiapas, Mexico) grouped with R. tenuirostris, whereas samples of R. m. albilabris to the west in Oaxaca, Mexico, formed a clade with R. bakeri. Within the subgenus Reithrodontomys, all analyses recovered R. montanus and R. raviventris as sister taxa, a finding consistent with earlier studies based on allozymes and cyt b data. There was also strong support (ML and BI criteria) for a clade consisting of ((R. megalotis, R. zacatecae) (R. sumichrasti)). In addition, cytb gene phylogenies (MP, ML, and BI) recovered R. fulvescens and R. hirsutus (ML and BI) as basal taxa within the subgenus Reithrodontomys. Constraint analyses demonstrated that tree topologies treating the two subgenera (Aporodon and Reithrodontomys) as monophyletic (ML criterion) was significantly better (p>0.036) and supported polyphyly of R. mexicanus (both ML and MP criteria - p>0.013) and R. microdon (MP criterion only for certain topologies; p>0.02). Although several species-level taxa were identified based on multiple, independent data sets, we recommended a conservative approach which will involve thorough analyses of museum specimens including material from type localities together with additional sampling and data from multiple, nuclear gene markers.     

Cladistic biogeography of the Mexican transition zone

Biogeographic relationships among nine montane areas of endemism across the transition zone between North and South America are analysed cladistically based on phylogenetic hypotheses of thirty‐three resident monophyletic taxa of insects, fish, reptiles, and plants. Areas of endemism include the Arizona mountains (AZ), Sonoran Desert (SD), Sierra Madre Occidental (OCC), southern Sierra Madre Occidental (SOC), Sierra Madre Oriental (ORI), Sierra Transvolcanica (TRAN), Sierra Madre del Sur (SUR), Chiapan‐Guatemalan Highlands (CGH), and Talamancan Cordillera (TC). Area relationships are summarized using Brooks Parsimony Analysis and Assumption 0, with the former resulting in more defensible biogeographic hypotheses. Areas of endemism are dividable into two monophyletic groups; a northern group including AZ, SD, OCC, and ORI, and a southern group consisting of TC, CGH, TRAN, SUR, and the isolated southern regions of the Sierra Madre Occidental (SOC). The northern set of areas are characterized by recent, probably Pleistocene, isolation and prevalent widespread species, whereas the southerly areas probably diverged after Pliocene closure of the Panamanian isthmus. The southern areas are redundantly represented on many of the taxon‐area cladograms by endemic species, indicative of much higher levels of endemism in the Sierra Transvolcanica and further south. Use of a general area cladogram in such a transition zone permits explicit exploration of biogeographic patterns and establishes a predictive framework for taxonomy and conservation prioritization.