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.     

Evolutionary drivers of phylogeographical diversity in the highlands of Mexico: a case study of the Crotalus triseriatus species group of montane rattlesnakes

Aim To assess the genealogical relationships of widespread montane rattlesnakes in the Crotalus triseriatus species group and to clarify the role of Late Neogene mountain building and Pleistocene pine–oak forest fragmentation in driving the diversification of Mexican highland taxa. Location Highlands of mainland Mexico and the south‐western United States (Texas, New Mexico, and Arizona). Methods A synthesis of inferences was used to address several associated questions about the biogeography of the Mexican highlands and the evolutionary drivers of phylogeographical diversity in co‐distributed taxa. We combined extensive range‐wide sampling (130 individuals representing five putative species) and mixed‐model phylogenetic analyses of 2408 base pairs of mitochondrial DNA to estimate genealogical relationships and divergence times within the C. triseriatus species group. We then assessed the tempo of diversification using a maximum likelihood framework based on the birth–death process. Estimated times of divergences provided a probabilistic temporal component and questioned whether diversification rates have remained constant or varied over time. Finally, we looked for phylogeographical patterns in other co‐distributed taxa. Results We identified eight major lineages within the C. triseriatus group, and inferred strong correspondence between maternal and geographic history within most lineages. At least one cryptic species was detected. Relationships among lineages were generally congruent with previous molecular studies, with differences largely attributable to our expanded taxonomic and geographic sampling. Estimated divergences between most major lineages occurred in the Late Miocene and Pliocene. Phylogeographical structure within each lineage appeared to have been generated primarily during the Pleistocene. Although the scale of genetic diversity recognized affected estimated rates of diversification, rates appeared to have been constant through time. Main conclusions The biogeographical history of the C. triseriatus group implies a dynamic history for the highlands of Mexico. The Neogene formation of the Transvolcanic Belt appears responsible for structuring geographic diversity among major lineages. Pleistocene glacial–interglacial climatic cycles and resultant expansions and contractions of the Mexican pine–oak forest appear to have driven widespread divergences within lineages. Climatic change, paired with the complex topography of Mexico, probably produced a myriad of species‐specific responses in co‐distributed Mexican highland taxa. The high degree of genetic differentiation recovered in our study and others suggests that the Mexican highlands may contain considerably more diversity than currently recognized.     

Diversification in the Mexican horned lizard Phrynosoma orbiculare across a dynamic landscape

The widespread montane Mexican horned lizard Phrynosoma orbiculare (Squamata: Phrynosomatidae) represents an ideal species to investigate the relative impacts of Neogene vicariance and Quaternary climate change on lineage diversification across the Mexican highlands. We used mitochondrial DNA to examine the maternal history of P. orbiculare and estimate the timing and tempo of lineage diversification. Based on our results, we inferred 11 geographically structured, well supported mitochondrial lineages within this species, suggesting P. orbiculare represents a species complex. Six divergences between lineages likely occurred during the Late Miocene and Pliocene, and four splits probably happened during the Pleistocene. Diversification rate appeared relatively constant through time. Spatial and temporal divergences between lineages of P. orbiculare and co-distributed taxa suggest that a distinct period of uplifting of the Transvolcanic Belt around 7.5-3 million years ago broadly impacted diversification in taxa associated with this mountain range. To the north, several river drainages acting as filter barriers differentially subdivided co-distributed highland taxa through time. Diversification patterns observed in P. orbiculare provide additional insight into the mechanisms that impacted differentiation of highland taxa across the complex Mexican highlands.     

Sky island diversification meets the multispecies coalescent – divergence in the spruce‐fir moss spider (Microhexura montivaga,Araneae, Mygalomorphae) on the highest peaks of southern Appalachia

Microhexura montivaga is a miniature tarantula‐like spider endemic to the highest peaks of the southern Appalachian mountains and is known only from six allopatric, highly disjunct montane populations. Because of severe declines in spruce‐fir forest in the late 20th century, M. montivaga was formally listed as a US federally endangered species in 1995. Using DNA sequence data from one mitochondrial and seven nuclear genes, patterns of multigenic genetic divergence were assessed for six montane populations. Independent mitochondrial and nuclear discovery analyses reveal obvious genetic fragmentation both within and among montane populations, with five to seven primary genetic lineages recovered. Multispecies coalescent validation analyses [guide tree and unguided Bayesian Phylogenetics and Phylogeography (BPP), Bayes factor delimitation (BFD)] using nuclear‐only data congruently recover six or seven distinct lineages; BFD analyses using combined nuclear plus mitochondrial data favour seven or eight lineages. In stark contrast to this clear genetic fragmentation, a survey of secondary sexual features for available males indicates morphological conservatism across montane populations. While it is certainly possible that morphologically cryptic speciation has occurred in this taxon, this system may alternatively represent a case where extreme population genetic structuring (but not speciation) leads to an oversplitting of lineage diversity by multispecies coalescent methods. Our results have clear conservation implications for this federally endangered taxon and illustrate a methodological issue expected to become more common as genomic‐scale data sets are gathered for taxa found in naturally fragmented habitats.     

Deep intra‐island divergence of a montane forest endemic: phylogeography of the Puerto Rican frog Eleutherodactylus portoricensis (Anura: Eleutherodactylidae)

Aim Hypotheses proposed for lineage diversification of tropical montane species have rarely been tested within oceanic islands. Our goal was to understand how basin barriers and Pleistocene climatic fluctuations shaped the distribution of diversity in Eleutherodactylus portoricensis (Eleutherodactylidae), a frog endemic to the montane rain forests of Puerto Rico. Location The north‐eastern (Luquillo) and south‐eastern (Cayey) mountains of Puerto Rico. Methods We generated mitochondrial DNA (mtDNA) control region sequences (c. 565 bp) from 144 individuals of E. portoricensis representing 16 localities, and sequenced 646 bp of cytochrome b and 596 bp of nuclear DNA (nDNA) rhodopsin exon and intron 1 from a subset of individuals. We conducted a phylogenetic analysis on the mtDNA sequence data and explored population substructure with maximum parsimony networks, a spatial analysis of molecular variance, and pairwise F_ST analysis. Coalescent simulations were performed to test alternative models of population divergence in response to late Pleistocene interglacial periods. Historical demography was assessed through coalescent analyses and Bayesian skyline plots. Results We found: (1) two highly divergent groups associated with the disjunct Luquillo and Cayey Mountains, respectively; (2) a shallow mtDNA genetic discontinuity across the La Plata Basin within the Cayey Mountains; (3) phylogeographic congruence between nDNA and mtDNA markers; (4) divergence dates for both mtDNA and nDNA pre‐dating the Holocene interglacial (c. 10 ka), and nDNA suggesting divergence in the penultimate interglacial (c. 245 ka); and (5) historical demographic stability in both lineages. Main conclusions The low‐elevation Caguas Basin is a long‐term barrier to gene flow between the two montane frog populations. Measures of genetic diversity for mtDNA were similar in both lineages, but lower nDNA diversity in the Luquillo Mountains lineage suggests infrequent dispersal between the two mountain ranges and colonization by a low‐diversity founder population. Population divergence began prior to the Holocene interglacial. Stable population sizes over time indicate a lack of demonstrable demographic response to climatic changes during the last glacial period. This study highlights the importance of topographic complexity in promoting within‐island vicariant speciation in the Greater Antilles, and indicates long‐term persistence and lineage diversification despite late Pleistocene climatic oscillations.     

Divergence and gene flow in the globally distributed blue‐winged ducks

The ability to disperse over long distances can result in a high propensity for colonizing new geographic regions, including uninhabited continents, and lead to lineage diversification via allopatric speciation. However, high vagility can also result in gene flow between otherwise allopatric populations, and in some cases, parapatric or divergence‐with‐gene‐flow models might be more applicable to widely distributed lineages. Here, we use five nuclear introns and the mitochondrial control region along with Bayesian models of isolation with migration to examine divergence, gene flow, and phylogenetic relationships within a cosmopolitan lineage comprising six species, the blue‐winged ducks (genus Anas), which inhabit all continents except Antarctica. We found two primary sub‐lineages, the globally‐distributed shoveler group and the New World blue‐winged/cinnamon teal group. The blue‐winged/cinnamon sub‐lineage is composed of sister taxa from North America and South America, and taxa with parapatric distributions are characterized by low to moderate levels of gene flow. In contrast, our data support strict allopatry for most comparisons within the shovelers. However, we found evidence of gene flow from the migratory, Holarctic northern shoveler A. clypeata and the more sedentary, African Cape shoveler A. smithii into the Australasian shoveler A. rhynchotis, although we could not reject strict allopatry. Given the diverse mechanisms of speciation within this complex, the shovelers and blue‐winged/cinnamon teals can serve as an effective model system for examining how the genome diverges under different evolutionary processes and how genetic variation is partitioned among highly dispersive taxa.     

Cryptic diversity within the endemic prehensile‐tailed gecko Urocotyledon inexpectata across the Seychelles Islands: patterns of phylogeographical structure and isolation at the multilocus level

The deciphering of the process of genetic differentiation of species with insular distributions is relevant for biogeographical and conservation reasons. Despite their importance as old gondwanic islands and part of the western Indian Ocean biodiversity hotspot, little is known about the genetic structure of taxa from the Seychelles Islands. We have examined the patterns of structure and isolation within Urocotyledon inexpectata (Reptilia: Geckkonidae), an endemic species from this archipelago. Genetic diversity was screened from populations across the archipelago for both mitochondrial and nuclear genes. Gene genealogies and model‐based inference were used to explore patterns and timings of isolation between the main lineages. High levels of genetic diversity were found for the mitochondrial and some of the nuclear markers. This species harbours at least two highly differentiated lineages, exclusively distributed across the northern and southern groups of the islands. The main split between these was dated back to the Miocene–late Pliocene, but isolation events throughout the Pliocene and Pleistocene were also inferred. Migration between groups of islands was apparently nonexistent, except for one case. The low dispersal capabilities of this species, together with the intrinsic fragmented nature of its geographical distribution, seem to have resulted in highly structured populations, despite the cyclic periods of contact between the different island groups. These populations may currently represent more than one species, making U. inexpectata another example of a morphologically cryptic lineage with deep genetic divergence within gekkonids. The observed patterns suggest a hypothetical biogeographic scenario (of a main north–south phylogeographic break) for the Seychelles that can be further tested with the exploration of the phylogeographic structure of other Seychellois taxa. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 177–191.     

Relative roles of Neogene vicariance and Quaternary climate change on the historical diversification of bunchgrass lizards (Sceloporus scalaris group) in Mexico

Neogene vicariance during the Miocene and Pliocene and Quaternary climate change have synergistically driven diversification in Mexican highland taxa. We investigated the impacts of these processes on genetic diversification in the widely distributed bunchgrass lizards in the Sceloporus scalaris group. We searched for correlations between timing in diversification and timing of (1) a period of marked volcanism across the Trans-Mexican Volcanic Belt in central Mexico 3-7.5 million years ago (Ma) and (2) a transition to larger glacial-interglacial cycles during the mid-Pleistocene. From our phylogenetic analyses of mitochondrial DNA we identified two major clades that contained 13 strongly supported lineages. One clade contained lineages from the two northern sierras of Mexico, and the other clade included lineages associated with the Trans-Mexican Volcanic Belt and Central Mexican Plateau. Results provided support for Neogene divergences within the S. scalaris group in response to uplift of the Trans-Mexican Volcanic Belt, a pattern observed in several co-distributed taxa, and suggested that Quaternary climate change likely had little effect on diversification between lineages. Uplift of the Trans-Mexican Volcanic Belt during specific time periods appears to have strongly impacted diversification in Mexican highland taxa.     

Genetic divergence of the Mesoamerican azure‐crowned hummingbird (Amazilia cyanocephala,Trochilidae) across the Motagua‐Polochic‐Jocotán fault system

The cloud forests of Mesoamerica are highly endangered habitats and the existence of narrowly distributed cryptic endemics will increase the number of taxa at potential risk of extinction. Here, we investigate genetic divergence between populations of the azure‐crowned hummingbird (Amazilia cyanocephala), a species complex of endemic hummingbirds to the montane forests of Mesoamerica, by analysing DNA sequences of four mitochondrial markers, morphological data and ecological niche modelling. Our results revealed the presence of two mtDNA lineages corresponding to subspecies A. c. cyanocephala distributed from Tamaulipas to Chiapas in Mexico and Amazilia c. guatemalensis distributed from southern Chiapas to Guatemala. The lineage split can be explained as a consequence of relative isolation of the populations in the different mountain ranges separated by the Motagua‐Polochic‐Jocotán fault system and corresponds to differences in morphology and to the lack of overlap in environmental space between subspecies. The divergence time estimates do not support the proposed model of a highly constrained temporal window at the end of the Pliocene as divergence at this barrier between cyanocephala and guatemalensis and splits of other bird taxa occurred during the Pleistocene.     

Secondary contact followed by gene flow between divergent mitochondrial lineages of a widespread Neotropical songbird (Zonotrichia capensis)

Understanding how genetic and phenotypic differences that arise in geographically isolated populations influence the outcome of secondary contact advances our knowledge of speciation. In the present study, we investigate the secondary contact between divergent lineages of a widespread Neotropical songbird, the Rufous‐collared sparrow (Zonotrichia capensis). Zonotrichia capensis is morphologically and behaviourally diverse, and shows a pattern of lineage diversification produced by a Pleistocene expansion and colonization of South America from a probable Central American origin. Consistent with previous results, we find three lineages throughout the species range, showing between 1.5% and 2.5% divergence in mitochondrial control region sequences. These lineages come into secondary contact in the Dominican Republic, La Paz (Bolivia), and North‐eastern Argentina. We use DNA microsatellite data to study a broad secondary contact zone in North‐eastern Argentina, finding that Bayesian clustering analyses do not assign individuals to their respective mitochondrial lineages. Overall, we did not observe nuclear genetic discontinuities in the study area. We conclude that, if genetic, morphological, and/or cultural differences accumulated among lineages during isolation, they were insufficient to prevent gene flow after secondary contact. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 863–868.     

Comparative phylogeography of pitvipers suggests a consensus of ancient Middle American highland biogeography

Aim  We used inferences of phylogenetic relationships and divergence times for three lineages of highland pitvipers to identify broad-scale historical events that have shaped the evolutionary history of Middle American highland taxa, and to test previous hypotheses of Neotropical speciation.
Location  Middle America (Central America and Mexico).
Methods  We used 2306 base pairs of mitochondrial gene sequences from 178 individuals to estimate the phylogeny and divergence times of New World pitviper lineages, focusing on three genera ( Atropoides , Bothriechis and Cerrophidion ) that are broadly co-distributed across Middle American highlands.
Results  We found strong correspondence across three highland lineages for temporally and geographically coincident divergences in the Miocene and Pliocene, and further identified widespread within-species divergences across multiple lineages that occurred in the early–middle Pleistocene.
Main conclusions  Available data suggest that there were at least three major historical events in Middle America that had broad impacts on species divergence and lineage diversification among highland taxa. In addition, we find widespread within-species genetic structure that may be attributable to the climatic changes that affected gene flow among highland taxa during the middle–late Pleistocene.     

DEEP DIVERSIFICATION AND LONG‐TERM PERSISTENCE IN THE SOUTH AMERICAN ‘DRY DIAGONAL’: INTEGRATING CONTINENT‐WIDE PHYLOGEOGRAPHY AND DISTRIBUTION MODELING OF GECKOS

The relative influence of Neogene geomorphological events and Quaternary climatic changes as causal mechanisms on Neotropical diversification remains largely speculative, as most divergence timing inferences are based on a single locus and have limited taxonomic or geographic sampling. To investigate these influences, we use a multilocus (two mitochondrial and 11 nuclear genes) range‐wide sampling of Phyllopezus pollicaris, a gecko complex widely distributed across the poorly studied South American ‘dry diagonal’ biomes. Our approach couples traditional and model‐based phylogeography with geospatial methods, and demonstrates Miocene diversification and limited influence of Pleistocene climatic fluctuations on P. pollicaris. Phylogeographic structure and distribution models highlight that persistence across multiple isolated regions shaped the diversification of this species complex. Approximate Bayesian computation supports hypotheses of allopatric and ecological/sympatric speciation between lineages that largely coincide with genetic clusters associated with Chaco, Cerrado, and Caatinga, standing for complex diversification between the ‘dry diagonal’ biomes. We recover extremely high genetic diversity and suggest that eight well‐supported clades may be valid species, with direct implications for taxonomy and conservation assessments. These patterns exemplify how low‐vagility species complexes, characterized by strong genetic structure and pre‐Pleistocene divergence histories, represent ideal radiations to investigate broad biogeographic histories of associated biomes.     

Phylogeny and evolution of dorsal pattern in the Mexican endemic lizard genus Barisia (Anguidae: Gerrhonotinae)

The phylogeny of the Mexican lizard genus Barisia was assessed using an 878 bp fragment of the mtDNA ND4 gene and a section of associated tRNA genes, as well as 16 external morphological characters. The terminal taxa comprised the currently recognized members of Barisia, including the four subspecies of the polytypic Barisia imbricata and individuals from different populations of the widespread B. i. imbricata and Barisia i. ciliaris, although for Barisia levicollis only morphology could be examined. The ‘step‐matrix frequency’ and the ‘step‐matrix gap‐weighting’ coding approaches were employed simultaneously for the morphological data set, and three different scaling methods were evaluated for the last approach. Maximum parsimony (MP) analyses were performed for the separate and combined data sets and Bayesian analysis was also performed for the mtDNA sequence data. The hypothesis obtained from the simultaneous MP analysis strongly supports the monophyly of Barisia, but the ‘exclusivity’ of B. imbricata as well as of B. i. imbricata and B. i. ciliaris were not recovered. Moreover, inclusion of the morphological data showed B. levicollis nested within a clade together with the taxa assigned to B. i. ciliaris. This, together with the genetic distances and geographic concordance among the haplotypes examined, confirms that B. imbricata represents several species, although the actual species limits in this composite taxon are still unclear. Applying previously published rates of molecular evolution to the mtDNA data gives ages of divergence similar to the times proposed for some Pleistocene–Miocene geological and climatic phenomena that occurred in the Mexican territory. Variation of the dorsal pattern within Barisia was mapped onto the simultaneous morphological and molecular phylogeny, indicating that the two main states present in the taxa assigned to B. imbricata, an adult dorsal pattern present in females and absent in males and the absence of any pattern in both sexes, occur each in separate lineages. This suggests a possible scenario, where sexual dichromatism within Barisia has been repeatedly lost in different lineages.     

Host conservatism,geography, and elevation in the evolution of a Neotropical moth radiation

The origins of evolutionary radiations are often traced to the colonization of novel adaptive zones, including unoccupied habitats or unutilized resources. For herbivorous insects, the predominant mechanism of diversification is typically assumed to be a shift onto a novel lineage of host plants. However, other drivers of diversification are important in shaping evolutionary history, especially for groups residing in regions with complex geological histories. We evaluated the contributions of shifts in host plant clade, bioregion, and elevation to diversification in Eois (Lepidoptera: Geometridae), a hyper‐diverse genus of moths found throughout the Neotropics. Relationships among 107 taxa were reconstructed using one mitochondrial and two nuclear genes. In addition, we used a genotyping‐by‐sequencing approach to generate 4641 SNPs for 137 taxa. Both datasets yielded similar phylogenetic histories, with relationships structured by host plant clade, bioregion, and elevation. While diversification of basal lineages often coincided with host clade shifts, more recent speciation events were more typically associated with shifts across bioregions or elevational gradients. Overall, patterns of diversification in Eois are consistent with the perspective that shifts across multiple adaptive zones synergistically drive diversification in hyper‐diverse lineages.     

Phylogeographic structuring and volant mammals: the case of the pallid bat (Antrozous pallidus)

Aim To examine the phylogeographic pattern of a volant mammal at the continental scale. The pallid bat (Antrozous pallidus) was chosen because it ranges across a zone of well‐studied biotic assemblages, namely the warm deserts of North America. Location The western half of North America, with sites in Mexico, the United States, and Canada. Methods PCR amplification and sequencing of the mitochondrial control region was performed on 194 pallid bats from 36 localities. Additional sequences at the cytochrome‐b locus were generated for representatives of each control‐region haplotype. modeltest was used to determine the best set of parameters to describe each data set, which were incorporated into analyses using paup *. Statistical parsimony and measurements of population differentiation (amova , F_ST) were also used to examine patterns of genetic diversity in pallid bats. Results We detected three major lineages in the mitochondrial DNA of pallid bats collected across the species range. These three major clades have completely non‐overlapping geographic ranges. Only 6 of 80 control‐region haplotypes were found at more than a single locality, and sequences at the more conserved cytochrome‐b locus revealed 37 haplotypes. Statistical parsimony generated three unlinked networks that correspond exactly to clades defined by the distance‐based analysis. On average there was c. 2% divergence for the combined mitochondrial sequences within each of the three major clades and c. 7% divergence between each pair of clades. Molecular clocks date divergence between the major clades at more than one million years, on average, using the faster rates, and at more than three million years using more conservative rates of evolution. Main conclusions Divergent haplotypic lineages with allopatric distributions suggest that the pallid bat has responded to evolutionary pressures in a manner consistent with other taxa of the American southwest. These results extend the conclusions of earlier studies that found the genetic structuring of populations of some bat species to show that a widespread volant species may comprise a set of geographically replacing monophyletic lineages. Haplotypes were usually restricted to single localities, and the clade showing geographic affinities to the Sonoran Desert contained greater diversity than did clades to the east and west. While faster molecular clocks would allow for glacial cycles of the Pleistocene as plausible agents of diversification of pallid bats, evidence from co‐distributed taxa suggests support for older events being responsible for the initial divergence among clades.     

Phylogeography of the Australian freshwater turtle Chelodina expansa reveals complex relationships among inland and coastal bioregions

We examined range‐wide mitochondrial phylogeographical structure in the riverine freshwater turtle Chelodina expansa to determine whether this species exhibits deep genetic divergence between coastal and inland hydrological provinces, as seen in co‐distributed freshwater taxa. We sequenced two mitochondrial loci, genealogical relationships were assessed using a network approach, and relationships among biogeographical regions were tested using analyses of molecular variance. Population history was evaluated using neutrality tests, indices of demographic expansion, and mismatch analyses. Twenty‐one haplotypes were recovered across two mitochondrial haplogroups separated by approximately 4% nucleotide divergence. The haplogroups have discrete geographical boundaries but only partially support a hypothesis of deep divergence between coastal and inland bioregions. The first haplogroup comprises populations from the inland Murray‐Darling Basin and from coastal catchments south of the Mary River in south‐east Queensland. The second haplogroup comprises populations from coastal catchments north of the Mary River. Cryptic phylogeographical barriers separating adjacent coastal populations are congruent with those demonstrated for other freshwater taxa and may result from the combined influences of the Conondale Range and alluvial deposits at the mouth of the Mary River. The findings of the present study demonstrate that freshwater taxa commonly display genetic differentiation within a biogeographical region where no boundaries have been recognized, highlighting the need to uncover cryptic microbiogeographical regions to aid conservation of freshwater biota. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 789–805.     

Phylogeographic diversification of antelope squirrels (Ammospermophilus) across North American deserts

We investigated the biogeographic history of antelope squirrels, genus Ammospermophilus, which are widely distributed across the deserts and other arid lands of western North America. We combined range‐wide sampling of all currently recognized species of Ammospermophilus with a multilocus data set to infer phylogenetic relationships. We then estimated divergence times within identified clades of Ammospermophilus using fossil‐calibrated and rate‐calibrated molecular clocks. Lastly, we explored generalized distributional changes of Ammospermophilus since the last glacial maximum using species distribution models, and assessed responses to Quaternary climate change by generating demographic parameter estimates for the three wide‐ranging clades of A. leucurus. From our phylogenetic estimates we inferred strong phylogeographic structure within Ammospermophilus and the presence of three well‐supported major clades. Initial patterns of historical divergence were coincident with dynamic alterations in the landscape of western North America, and the formation of regional deserts during the Late Miocene and Pliocene. Species distribution models and demographic parameter estimates revealed patterns of recent population expansion in response to glacial retreat. When combined with evidence from co‐distributed taxa, the historical biogeography of Ammospermophilus provides additional insight into the mechanisms that impacted diversification of arid‐adapted taxa across the arid lands of western North America. We propose species recognition of populations of the southern Baja California peninsula to best represent our current understanding of evolutionary relationships among genetic units of Ammospermophilus. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 949–967.     

Mitochondrial genomes reveal the global phylogeography and dispersal routes of the migratory locust

The migratory locust, Locusta migratoria, is the most widely distributed grasshopper species in the world. However, its global genetic structure and phylogeographic relationships have not been investigated. In this study, we explored the worldwide genetic structure and phylogeography of the locust populations based on the sequence information of 65 complete mitochondrial genomes and three mitochondrial genes of 263 individuals from 53 sampling sites. Although this locust can migrate over long distances, our results revealed high genetic differentiation among the geographic populations. The populations can be divided into two different lineages: the Northern lineage, which includes individuals from the temperate regions of the Eurasian continent, and the Southern lineage, which includes individuals from Africa, southern Europe, the Arabian region, India, southern China, South‐east Asia and Australia. An analysis of population genetic diversity indicated that the locust species originated from Africa. Ancestral populations likely separated into Northern and Southern lineages 895 000 years ago by vicariance events associated with Pleistocene glaciations. These two lineages evolved in allopatry and occupied their current distributions in the world via distinct southern and northern dispersal routes. Genetic differences, caused by the long‐term independent diversification of the two lineages, along with other factors, such as geographic barriers and temperature limitations, may play important roles in maintaining the present phylogeographic patterns. Our phylogeographic evidence challenged the long‐held view of multiple subspecies in the locust species and tentatively divided it into two subspecies, L. m. migratoria and L. m. migratorioides.     

Three‐dimensional post‐glacial expansion and diversification of an exploited oceanic fish

Vertical divergence in marine organisms is being increasingly documented, yet much remains to be carried out to understand the role of depth in the context of phylogeographic reconstruction and the identification of management units. An ideal study system to address this issue is the beaked redfish, Sebastes mentella – one of four species of ‘redfish’ occurring in the North Atlantic – which is known for a widely distributed ‘shallow‐pelagic’ oceanic type inhabiting waters between 250 and 550 m, and a more localized ‘deep‐pelagic’ population dwelling between 550 and 800 m, in the oceanic habitat of the Irminger Sea. Here, we investigate the extent of population structure in relation to both depth and geographic spread of oceanic beaked redfish throughout most of its distribution range. By sequencing the mitochondrial control region of 261 redfish collected over a decadal interval, and combining 160 rhodopsin coding nuclear sequences and previously genotyped microsatellite data, we map the existence of two strongly divergent evolutionary lineages with significantly different distribution patterns and historical demography, and whose genetic variance is mostly explained by depth. Combined genetic data, analysed via independent approaches, are consistent with a Late Pleistocene lineage split, where segregation by depth probably resulted from the interplay of climatic and oceanographic processes with life history and behavioural traits. The ongoing process of diversification in North Atlantic S. mentella may serve as an ‘hourglass’ to understand speciation and adaptive radiation in Sebastes and in other marine taxa distributed across a depth gradient.     

Niche divergence promotes rapid diversification of East African sky island white‐eyes (Aves: Zosteropidae)

The Eastern Afromontane biodiversity hotspot composed of highly fragmented forested highlands (sky islands) harbours exceptional diversity and endemicity, particularly within birds. To explain their elevated diversity within this region, models founded on niche conservatism have been offered, although detailed phylogeographic studies are limited to a few avian lineages. Here, we focus on the recent songbird genus Zosterops, represented by montane and lowland members, to test the roles of niche conservatism versus niche divergence in the diversification and colonization of East Africa's sky islands. The species‐rich white‐eyes are a typically homogeneous family with an exceptional colonizing ability, but in contrast to their diversity on oceanic islands, continental diversity is considered depauperate and has been largely neglected. Molecular phylogenetic analysis of ~140 taxa reveals extensive polyphyly among different montane populations of Z. poliogastrus. These larger endemic birds are shown to be more closely related to taxa with divergent habitat types, altitudinal distributions and dispersal abilities than they are to populations of restricted endemics that occur in neighbouring montane forest fragments. This repeated transition between lowland and highland habitats over time demonstrate that diversification of the focal group is explained by niche divergence. Our results also highlight an underestimation of diversity compared to morphological studies that has implications for their taxonomy and conservation. Molecular dating suggests that the spatially extensive African radiation arose exceptionally rapidly (1–2.5 Ma) during the fluctuating Plio‐Pleistocene climate, which may have provided the primary driver for lineage diversification.