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A Landscape Approach to Conservation Genetics: Conserving Evolutionary Processes in the African Bovidae
... The purpose of this article is to answer this question by worked examples that make use of the evolutionary time dimension provided by haplotype trees. Traditional F statistics do not use temporal information on allelic variation, but several new statistical procedures can make use of haplotype trees (Hudson et al. 1992; Slatkin 1989 Slatkin , 1993 Slatkin & Maddison 1989 Templeton 1993; Templeton et al. 1995; Templeton & Georgiadis 1996). This article provides worked examples demonstrating that these new approaches have enhanced power over F statistics, allow greater precision of geneflow estimation, and can separate population structure (recurrent forces such as gene flow) from historical events (fragmentation and range expansion events). ...
... Indeed, the primary advantage of using the haplotype tree information is not the quantitative advantage of enhanced power and precision; rather, it is the qualitative advantage of discriminating among various biological explanations for any detected geographical association. To show that haplotype trees can discriminate among cases that appear identical to the nonhistorical F-statistic analyses, consider the study of Templeton & Georgiadis (1996) on mitochondrial DNA (mtDNA) restriction site variation in Eastern African populations of buffalo (Syncerus caffeer) and impala (Aepyceros melampus). The F-statistic estimator of Davis et al. (1990) yields an F ST of 0.08 for the buffalo and 0.10 for the impala. ...
... found in the other locations, and it was the Chobe samples that were primarily responsible for the significant F ST values in both cases. Hence, this F-statistic analysis implies that both species are equally subdivided, have comparable rates of gene flow, and display restricted gene flow primarily between the Chobe vs. Kenya/ Tanzania localities. Templeton & Georgiadis (1996) also estimated haplotype trees for the mtDNA, as shown here inFig. 2.Figure 2 also indicates the haplotypes found only in Chobe in both species. Even a cursory glance atFig. 2 reveals that the pattern of distribution of the Chobe-only haplotypes in the haplotype trees are completely different in these two species which appear indistingu ...
Since the 1920s, population geneticists have had measures that describe how genetic variation is distributed spatially within a species' geographical range. Modern genetic survey techniques frequently yield information on the evolutionary relationships among the alleles or haplotypes as well as information on allele frequencies and their spatial distributions. This evolutionary information is often expressed in the form of an estimated haplotype or allele tree. Traditional statistics of population structure, such as F statistics, do not make use of evolutionary genealogical information, so it is necessary to develop new statistical estimators and tests that explicitly incorporate information from the haplotype tree. One such technique is to use the haplotype tree to define a nested series of branches (clades), thereby allowing an evolutionary nested analysis of the spatial distribution of genetic variation. Such a nested analysis can be performed regarding the geographical sampling locations either as categorical or continuous variables (i.e. some measure of spatial distance). It is shown that such nested phylogeographical analyses have more power to detect geographical associations than traditional, nonhistorical analyses and, as a consequence, allow a broader range of gene-flow parameters to be estimated in a precise fashion. More importantly, such nested analyses can discriminate between phylogeographical associations due to recurrent but restricted gene flow vs. historical events operating at the population level (e.g. past fragmentation, colonization, or range expansion events). Restricted gene flow and historical events can be intertwined, and the cladistic analyses can reconstruct their temporal juxtapositions, thereby yielding great insight into both the evolutionary history and population structure of the species. Examples are given that illustrate these properties, concentrating on the detection of range expansion events.
... The biology of Ambystoma macrodactylum facilitates cohesion among closely related individuals that would maintain phylogeographic structure over time (Cruzan and Templeton 2000). Much of the natural history of A. macrodactylum indicates that populations are fairly resilient to extinction and thus should reflect processes that have been operating over evolutionary time (Templeton and Georgiadis 1996). It persists in disturbed habitats (Powell et al. 1997a), thus limiting haplotype loss due to contemporary declines (Templeton and Georgiadis 1996;Fisher and Shaffer 1996;Alford and Richards 1999;Houlahan et al. 2000). ...
... Much of the natural history of A. macrodactylum indicates that populations are fairly resilient to extinction and thus should reflect processes that have been operating over evolutionary time (Templeton and Georgiadis 1996). It persists in disturbed habitats (Powell et al. 1997a), thus limiting haplotype loss due to contemporary declines (Templeton and Georgiadis 1996;Fisher and Shaffer 1996;Alford and Richards 1999;Houlahan et al. 2000). Like other salamanders (Petranka 1998), it exhibits philopatric behavior towards breeding ponds (Beneski et al. 1986;Fukumoto and Herrero 1998). ...
The long-toed salamander (Ambystoma macrodactylum) is a widespread inhabitant of the Cordilleran Region of western North America. The Cordilleran ice sheet retreated when climates changed at the end of the Pleistocene. This setting provides a natural experiment for phylogeographic tests of post-glacial migration. As migration occurs, the demographics of populations change; these changes are imprinted into the gene frequencies of descendant populations. Species ranges shifted as migrants inhabited tolerable post-glacial environments, and new genealogical mixtures formed as populations came into secondary contact. Historical climate, ecology, and geography impacted the range dynamics and consequent population genetics of the long-toed salamander. This systematic study of mitochondrial DNA tests biogeographic patterns using phylogenetic trees, nested phylogeographic clade analysis, and mismatch distributions. Phylogenetic congruence is tested first in a partitioned versus an intersected arrangement of two mitochondrial loci, including 95 cytochrome b and 103 intergenic spacer sequences. Nested phylogeographic clade analysis provides an explicit system to correlate lineages and their mismatch distributions. Although mismatch distributions operate ideally in high-migration species, and the long-toed salamander migrates little among contemporary populations, there is reason to suspect that waif dispersal increased with changes in fluvial dynamics following glacial retreat. Clade patterns support a deep vicariance across the central interior and reveal seven Pleistocene refugia. Waves in mismatch distributions indicate that population sizes increased in lineages residing in refugia near the ice margins at this time. The phylogenetic identities that spread away from refugia and their genetic patterns are placed into a historical pre- and post-glaciated context.
... The biology of Ambystoma macrodactylum facilitates cohesion among closely related individuals that would maintain phylogeographic structure over time (Cruzan and Templeton 2000). Much of the natural history of A. macrodactylum indicates that populations are fairly resilient to extinction and thus should reflect processes that have been operating over evolutionary time (Templeton and Georgiadis 1996). It persists in disturbed habitats (Powell et al. 1997a), thus limiting haplotype loss due to contemporary declines (Templeton and Georgiadis 1996;Fisher and Shaffer 1996;Alford and Richards 1999;Houlahan et al. 2000). ...
... Much of the natural history of A. macrodactylum indicates that populations are fairly resilient to extinction and thus should reflect processes that have been operating over evolutionary time (Templeton and Georgiadis 1996). It persists in disturbed habitats (Powell et al. 1997a), thus limiting haplotype loss due to contemporary declines (Templeton and Georgiadis 1996;Fisher and Shaffer 1996;Alford and Richards 1999;Houlahan et al. 2000). Like other salamanders (Petranka 1998), it exhibits philopatric behavior towards breeding ponds (Beneski et al. 1986;Fukumoto and Herrero 1998). ...
... A pattern with older (interior) haplotypes typically found at the most distant sites of the Tajo basin, provides indications for site refugia and from where subsequently the tip haplotypes of the species expanded in Extremadura. Private haplotype distributions with interior and tip at Ambroz and Jerte Valleys, respectively, explain the current proneness to fragmentation of this specialist species [43]. Thus, a widespread status of at most a single founder female can occur under restricted dispersal because it favors the lack of admixtures of mitochondrial types even without a visible geographic barrier [2] causing mtDNA monomorphism by drift and lineage sorting [44]. ...
Background
Currently, many micromammals are important targets for study. The endangered Galemys pyrenaicus is an outstanding example. Globally, their populations have suffered a substantial decline in last 20 years. In the surveyed area, the capture of desman is legally forbidden due to the high conservation concerns. Reason by non-invasive sampling through faeces is proposed for its monitoring. Furthermore, the confusion between faeces from desman and Mediterranean water shrews must be considered. Thus, the aim of this study was focused on developing RT-PCR assays to determine the presence of Galemys pyrenaicus and N. a. anomalus from non-invasive samples.
Methods and results
The study was conducted in the mountains of the System Central of Extremadura (Spain). A total of 186 samples were collected from 2018 to 2021 by experts where historically reported and/or our previous studies confirmed their presence. RT-PCR assays using hydrolysis probes were designed to detect genetic material from both desman and Mediterranean water shrews and its specificity was confirmed. The reliability of the method was further assessed by PCR sequencing of mitochondrial Cyb and d-loop, resulting fully compatible with the RT-PCR approach. Intraspecific phylogenetic relationship was reported to improve knowledge about mtDNA variability in the desman from the Central System.
Conclusions
We demonstrated that RT-PCR gives a gold opportunity to further map the species using faeces which minimizes disturbance and reports both population status and individual presence. Cost-effective RT-PCR combined with field-collected faeces allows us to better investigate the full range of occurrence of the species.
... Searches for concordant phylogeographic evidence soon led researchers into broader comparative analyses that involve, for example, examination of the genealogical content of multiple unlinked genes within a species (Hare, 2001), and of phylogeographic patterns across multiple species within a regional biota. The latter has been termed the "regional" (Avise, 1996), "landscape" (Templeton & Georgiadis, 1996), or comparative (Bermingham & Moritz, 1998) logeography, and it is likely to become a focus of much more phylogeographic research in the future. A fourth general realization was that genealogical outcomes within and among conspecific populations are inextricably linked to the demographic histories of those populations. ...
... This work was stimulated by a multi-investigator study of the impact of forest ecosystem management on biodiversity, called the Missouri Ozark Forest Ecosystem Project (MOFEP), and administered through the Missouri Department of Conservation (Brookshire and Hauser 1993). Given evidence that landscape fragmentation and reductions in population size could jeopardize gene flow and connectivity (for example, see Hamrick et al. 1991;Ledig 1992;Templeton and Georgiadis 1996;Nason and Hamrick 1997), my role was to assess whether forest management practices would have an impact on genetic diversity of tree populations in 200+ ha plots. In contrast to the other MOFEP studies that looked at immediate impacts of forest-cutting practices on insect, bird, and mammal biodiversity (Brookshire and Hauser 1993;Brookshire et al. 1997), because of the longevity of trees, our project would not be able to measure changes in diversity for at least 50 years. ...
A central question in evolutionary biology is how gene flow and natural selection shape geographic patterns of genotypic and phenotypic variation. My overall research program has pursued this question in tree populations through complementary lines of inquiry. First, through studies of contemporary pollen and seed movement, I have studied how limited gene movement creates fine-scale genetic structure, while long-distance gene flow promotes connectivity. My collaborators and I have provided new tools to study these processes at a landscape scale as well as statistical tests to determine whether changes in landscape conditions or dispersal vectors affect gene movement. Second, my research on spatial patterns of genetic variation has investigated the interacting impacts of geography and climate on gene flow and selection. Third, using next generation genomic tools, I am now studying genetic variation on the landscape to find initial evidence of climate-associated local adaptation and epigenetic variation to explore its role in plant response to the climate. By integrating these separate lines of inquiry, this research provides specific insight into real-world mechanisms shaping evolution in tree populations and potential impacts of landscape transformation and climate change on these populations, with the prospective goal of contributing to their management and conservation.This article is protected by copyright. All rights reserved.
... Phylogeography-the analysis of information integrating allele genealogies, allele frequencies, and geographic distribution of alleles-provides insight into the historical factors generating extant geographic patterns of genetic variation (Avise, 1994). By using a phylogeographic approach in several codistributed species, it is possible to infer some historical processes at the landscape level (Templeton & Georgiadis, 1996;Zink, 1996). Many Holarctic phylogeographic studies focus on taxa from Europe or North America (review Hewitt, 1996), but little is known about phylogeographic structure in species from the Eurasian Arctic on a continental scale. ...
The geographic pattern of mtDNA variation in lemmings from 13 localities throughout the Eurasian Arctic was studied by using eight restriction enzymes and sequencing of the cytochromebregion. These data are used to reveal the vicariant history ofLemmus, and to examine the effect of the last glaciation on mtDNA variation by comparing diversity in formerly glaciated areas to the diversity in non-glaciated areas. Phylogenetic congruence across different Arctic taxa and association between observed discontinuities, and probable Pleistocene barriers, suggest that glacial-interglacial periods were crucial in the vicariant history ofLemmus. Differences in amount of divergence (2.1–9.1%) across different historical barriers indicate chronologically separate vicariant events during the Quaternary. Populations from a formerly glaciated area are no less variable than those in the non-glaciated area. Regardless of glaciation history, no population structure and high haplotype diversity were found within geographic regions. The lack of population structure indicates that populations with high ancestral haplotype diversity shifted their distribution during the Holocene, and that lemmings tracked a changing environment during the Quaternary without reduction of effective population size.
... Searches for concordant phylogeographic evidence soon led researchers into broader comparative analyses that involve, for example, examination of the genealogical content of multiple unlinked genes within a species (Hare, 2001), and of phylogeographic patterns across multiple species within a regional biota. The latter has been termed the "regional" (Avise, 1996), "landscape" (Templeton & Georgiadis, 1996), or comparative (Bermingham & Moritz, 1998) approach to phy-Avise • What is biogeography? 53 (4) • November 2004: 893-898 logeography, and it is likely to become a focus of much more phylogeographic research in the future. ...
... Phylogeography-the analysis of information integrating allele genealogies, allele frequencies, and geographic distribution of alleles-provides insight into the historical factors generating extant geographic patterns of genetic variation (Avise, 1994). By using a phylogeographic approach in several codistributed species, it is possible to infer some historical processes at the landscape level (Templeton & Georgiadis, 1996; Zink, 1996). Many Holarctic phylogeographic studies focus on taxa from Europe or North America (review Hewitt, 1996), but little is known about phylogeographic structure in species from the Eurasian Arctic on a continental scale. ...
The geographic pattern of mtDNA variation in lemmings from 13 localities throughout the Eurasian Arctic was studied by using eight restriction enzymes and sequencing of the cytochrome b region. These data are used to reveal the vicariant history of Lemmus, and to examine the effect of the last glaciation on mtDNA variation by comparing diversity in formerly glaciated areas to the diversity in non‐glaciated areas. Phylogenetic congruence across different Arctic taxa and association between observed discontinuities, and probable Pleistocene barriers, suggest that glacial‐interglacial periods were crucial in the vicariant history of Lemmus. Differences in amount of divergence (2.1–9.1%) across different historical barriers indicate chronologically separate vicariant events during the Quaternary. Populations from a formerly glaciated area are no less variable than those in the non‐glaciated area. Regardless of glaciation history, no population structure and high haplotype diversity were found within geographic regions. The lack of population structure indicates that populations with high ancestral haplotype diversity shifted their distribution during the Holocene, and that lemmings tracked a changing environment during the Quaternary without reduction of effective population size.
... We recognize that human threats often require immediate action to save individuals from disease, poaching or encroachment. However, an immediate genetic survey and historical analysis of existing populations would help guide management decisions and avoid translocations that would be detrimental to long-term survival of these species (Templeton & Georgiatis, 1996). ...
Although some African rhinoceros populations are currently increasing, others are critically endangered. Even healthy populations are extensively managed in the wild and in captivity. While political and demographic considerations are of primary concern, many decisions are made in the name of genetic management. Such decisions should be informed by a full understanding of the multiple meanings of inbreeding and effective population size. In this essay, we examine inbreeding and effective size of wild and captive populations of African rhinoceroses. We conclude by showing how misunderstanding of effective size and Franklin's 50 ⁄ 500 rule can make a crucial difference in informing management decisions. Résumé Bien que certaines populations de rhinocéros africains soient actuellement en augmentation, d'autres sont en danger critique. Même les populations saines sont gérées très activement dans la nature et en captivité. Alors que les considérations politiques et démographiques soient les principaux motifs d'inquiétude, de nombreuses décisions sont prises au nom de la gestion génétique. Ces décisions devraient se faire en pleine connaissance des multiples implications de l'inbreeding et de ce qu'est une taille de population nécessaire. Dans cet essai, nous examinons l'inbreeding et la taille nécessaire des populations sauvages et captives de rhinocéros africains. Nous concluons en montrant comment une mauvaise compréhension de la taille nécessaire et de la règle 50 ⁄ 500 de Franklin peut entraıˆnerentraıˆner une différence cruciale lorsqu'il s'agit de prendre, en connaissance de cause, les décisions opportunes.
... Even though isolation-by-distance appears to be an unlikely force maintaining divergence between parapatric taxa, simulations suggest that under some circumstances parapatric speciation is possible solely due to limited dispersal distances and the accumulation of genetic incompatibilities[13,14]. Hypothesis II – Geographic barriers to dispersal – and as a result gene flow – between the three giraffe species are not obvious, but they have been implicated – most notably the Rift Valley – in the divergence of other large mammals, including wildebeest (Connochaetes taurinus)[15]and impala (Aepyceros melampus)[16]. Thus, even though the ranges of giraffe species abut, dispersal might be limited by the steep topographical gradients of the Rift Valley and other habitat discontinuities associated with steep terrain. ...
Masai (Giraffa tippelskirchi), Reticulated (G. reticulata) and Rothschild's (G. camelopardalis) giraffe lineages in East Africa are morphologically and genetically distinct, yet in Kenya their ranges abut. This raises the question of how divergence is maintained among populations of a large mammal capable of long-distance travel, and which readily hybridize in zoos. Here we test four hypotheses concerning the maintenance of the phylogeographic boundaries among the three taxa: 1) isolation-by-distance; 2) physical barriers to dispersal; 3) general habitat differences resulting in habitat segregation; or 4) regional differences in the seasonal timing of rainfall, and resultant timing of browse availability. We used satellite remotely sensed and climate data to characterize the environment at the locations of genotyped giraffes. Canonical variate analysis, random forest algorithms, and generalized dissimilarity modelling were employed in a landscape genetics framework to identify the predictor variables that best explained giraffes' genetic divergence. We found that regional differences in the timing of precipitation, and resulting green-up associated with the abundance of browse, effectively discriminate between taxa. Local habitat conditions, topographic and human-induced barriers, and geographic distance did not aid in discriminating among lineages. Our results suggest that selection associated with regional timing of events in the annual climatic cycle may help maintain genetic and phenotypic divergence in giraffes. We discuss potential mechanisms of maintaining divergence, and suggest that synchronization of reproduction with seasonal rainfall cycles that are geographically distinct may contribute to reproductive isolation. Coordination of weaning with green-up cycles could minimize the costs of lactation and predation on the young. Our findings are consistent with theory and empirical results demonstrating the efficacy of seasonal or phenologically dictated selection pressures in contributing to the reproductive isolation of parapatric populations.
... However, inferring the history of population structure using present genetic structures is problematic when the method is applied to reconstruct the population histories of species that have experienced severe population bottlenecks. This is because allele frequencies may have been influenced by genetic drift and historical information on the population structure can be lost Excoffier and Schneider 1999;Knowles and Maddison 2002;Templeton and Georgiadis 1995). For example, Crandall et al. (2000) found that two recently divided small (e.g. ...
The history of population structure is a key to effective wildlife management and conservation. However, inferring the history of population structure using present genetic structures is problematic when the method is applied to species that have experienced severe population bottlenecks. Ancient DNA analysis seemed to be a promising, direct method for inferring ancient population structures. However, the usual methods for inferring modern population structure, i.e. the phylogeographic approach using mitochondrial DNA and the Bayesian approach using microsatellite DNA, are often unsuitable for ancient samples. In this study, we combined ancient DNA obtained from zooarchaeological bones with carbon/nitrogen stable isotope ratios and morphological variations to infer ancient population structure of the short-tailed albatross Phoebastria albatrus. The results showed that the bird existed in two populations, between which the genetic distance was greater than that of distinct sister albatross species, although no subspecies of P. albatrus have been proposed. Our results suggest that the birds at the present two breeding regions (Torishima in the Izu Islands and two islets of the Senkaku Islands) are descended from these two ancient populations, and that reevaluation of the status and conservation strategy for the species is required. Our results also indicate that lineage breeding on the Senkaku Islands has drastically reduced genetic diversity, while that on Torishima has not. The approach proposed in this study would be useful for inferring ancient population structure, using samples of highly mobile animals and/or samples from archaeological sites, and the reconstructed ancient population structure would be useful for conservation and management recommendations.
... All of these calculations depend upon the assumption of neutrality. Deleterious mutations will cause this procedure to underestimate effective size, and such mutations are known to exist (Hey 1997;Nachman et al. 1996;Templeton 1996). Therefore, all of the above calculations are lower bounds given this demonstrated violation of assumptions. ...
Race is generally used as a synonym for subspecies, which traditionally is a geographically circumscribed, genetically differentiated population. Sometimes traits show independent patterns of geographical variation such that some combination will distinguish most populations from all others. To avoid making "race" the equivalent of a local population, minimal thresholds of differentiation are imposed. Human "races" are below the thresholds used in other species, so valid traditional subspecies do not exist in humans. A "subspecies" can also be defined as a distinct evolutionary lineage within a species. Genetic surveys and the analyses of DNA haplotype trees show that human "races" are not distinct lineages, and that this is not due to recent admixture; human "races" are not and never were "pure." Instead, human evolution has been and is characterized by many locally differentiated populations coexisting at any given time, but with sufficient genetic contact to make all of humanity a single lineage sharing a common evolutionary fate.
... This has included extensions and refinements of coalescent theory for populations of varying demographies (Hudson 1990;Slatkin & Hudson 1991;Rogers & Harpending 1992;Nee et al. 1995;Eller & Harpending 1996; see also several articles in this issue of Molecular Ecology), improvements in statistical and cladistic procedures for extracting phylogeographic information from empirical data on gene genealogies (e.g. Slatkin 1989;Neigel et al. 1991;Templeton et al. 1995;Templeton & Georgiadis 1996;this issue), and a great plethora of empirical applications primarily involving mtDNA (Fig. 3) Brown provides an initial report on human mtDNA variation 1983 ...
Last year marked the 10th anniversary of the birth of phylogeography as a formal discipline. However, the field’s gestation began in the mid-1970s with the introduction of mitochondrial (mt) DNA analyses to population genetics, and to the profound shift toward genealogical thought at the intraspecific level (now formalized as coalescent theory) that these methods prompted. This paper traces the early history and explosive growth of phylogeography, and closes with predictions about future challenges for the field that centre on several facets of genealogical concordance.
... More specifically, Reitz & Leonard (1994) found that females of the European hare are more sedentary than males. In general, therefore, estimates of the number of migrants between the populations have to be interpreted cautiously all the more so since non-zero values can also be produced by retention of ancestral polymorphism (Templeton & Georgiadis, 1996;Griswold & Baker, 2002). ...
Genetic differentiation among populations of the South African scrub hare Lepus saxatilis was examined using hypervariable mitochondrial DNA control region I (CR-I) sequences. Neighbour-joining analysis revealed a pattern that did not correspond to the current subspecies delineations. The CR-I sequence data delimit scrub hares into three major maternal lineages. The three phylogenetic assemblages exhibited different geographical distributions. AMOVA analyses and exact tests for population differentiation confirmed this phylogeographic partitioning. One lineage (SW) was confined to the south-western Cape, the second lineage (N) was exclusively found in the northern part of South Africa and in the neighbouring countries, and the third lineage (C) was predominant in the central parts of South Africa. This spatial distribution did not coincide with the ranges of the 10 described subspecies covered by our sampling regime. The lineages C and N overlapped in an area including eastern parts of South Africa and southern Namibia. The presence of both lineages in that area of overlap was interpreted as the result of secondary contact due to recent range expansions after the two lineages had undergone a population restriction approximately 18 000 years ago. Analyses of contemporary gene flow disclosed an exchange of migrants between N and C, which was biased towards a movement from C to N. The SWgroup represents a very distinct evolutionary lineage that has been isolated for more than 45 000 years. It does not exchange female migrants with the other two groups. Mismatch distribution analyses indicated sudden population size expansions in the history of all three
populations.
... The extreme morphological variability within the species therefore allows us to test the congruence between phylogenetic-based and morphological-based classification. Although several genetic studies on African buffalo have already been conducted, these were generally focused at smaller spatial scales, mainly in East and Southern Africa (S. c. caffer), using various molecular markers such as mitochondrial DNA, autosomal microsatellites, Y-chromosomal microsatellites and the histocompatibility complex (MHC) DRB3 gene333435363738394041424344. Partial exceptions include the studies by Van Hooft [36,37], which include a few samples (n = 14) from Central Africa. ...
The African buffalo (Syncerus caffer) exhibits extreme morphological variability, which has led to controversies about the validity and taxonomic status of the various recognized subspecies. The present study aims to clarify these by inferring the pan-African spatial distribution of genetic diversity, using a comprehensive set of mitochondrial D-loop sequences from across the entire range of the species. All analyses converged on the existence of two distinct lineages, corresponding to a group encompassing West and Central African populations and a group encompassing East and Southern African populations. The former is currently assigned to two to three subspecies (S. c. nanus, S. c. brachyceros, S. c. aequinoctialis) and the latter to a separate subspecies (S. c. caffer). Forty-two per cent of the total amount of genetic diversity is explained by the between-lineage component, with one to seventeen female migrants per generation inferred as consistent with the isolation-with-migration model. The two lineages diverged between 145 000 to 449 000 years ago, with strong indications for a population expansion in both lineages, as revealed by coalescent-based analyses, summary statistics and a star-like topology of the haplotype network for the S. c. caffer lineage. A Bayesian analysis identified the most probable historical migration routes, with the Cape buffalo undertaking successive colonization events from Eastern toward Southern Africa. Furthermore, our analyses indicate that, in the West-Central African lineage, the forest ecophenotype may be a derived form of the savanna ecophenotype and not vice versa, as has previously been proposed. The African buffalo most likely expanded and diverged in the late to middle Pleistocene from an ancestral population located around the current-day Central African Republic, adapting morphologically to colonize new habitats, hence developing the variety of ecophenotypes observed today.
... As elaborated by Avise et al. (1992b) and Templeton & Georgiadis (1996), important object lessons come from contrasts between alternative classes of information on population structure. Direct contemporary observations on individual dispersal and gene flow (e.g. from tag returns) offer an incomplete picture of population structure because they fail to address genealogical aspects of population connectedness. ...
Sooty tern (Sterna fuscata) rookeries are scattered throughout the tropical oceans. When not nesting, individuals wander great distances across open seas, but, like many other seabirds, they tend to be site-faithful to nesting locales in successive years. Here we examine the matrilineal history of sooty terns on a global scale. Assayed colonies within an ocean are poorly differentiated in mitochondrial DNA sequence, a result indicating tight historical ties. However, a shallow genealogical partition distinguishes Atlantic from Indo-Pacific rookeries. Phylogeographic patterns in the sooty tern are compared to those in other colonially nesting seabirds, as well as in the green turtle (Chelonia mydas), an analogue of tropical seabirds in some salient aspects of natural history. Phylogeographic structure within an ocean is normally weak in seabirds, unlike the pronounced matrilineal structure in green turtles. However, the phylogeographic partition between Atlantic and Indo-Pacific rookeries in sooty terns mirrors, albeit in shallower evolutionary time, the major matrilineal subdivision in green turtles. Thus, global geology has apparently influenced historical gene movements in these two circumtropical species.
... Allelic differentiation, as expressed by the fixation indices G ST and γ, was most pronounced between Kruger NP and the three NPs located in eastern Africa. This is not surprising given the distant location of the South African population (average distance over 2000 km) and fits the notion of genetic isolation by distance in buffalo, previously inferred from the distribution of polymorphisms in the mitochondrial genome (Templeton & Georgiadis 1995). Population differentiation measures should not be overvaluated, as they are derived from only a single locus. ...
Historical population collapses caused by rinderpest epidemics are hypothesized to have resulted in notable genetic losses in populations of the African buffalo. Polymorphism in the major histocompatibity complex (MHC) DRB3 gene was probed by means of restriction analysis of the sequence encoding the peptide-binding region. Nucleotide substitution patterns agreed with a positive selection acting on this fitness-relevant locus. Buffalo populations from four National Parks, situated in eastern and southern Africa, each revealed a surprisingly high allelic diversity. Current high levels of heterozygosity may be reconciled with historical bottlenecks by assuming that local extinctions were followed by fast recolonization, in accordance with the high dispersive capabilities of buffalo. The specific amplification of DRB3 alleles also enabled the assignment of individual genotypes. For each population sample a deficiency in the expected number of heterozygous animals was found. As overdominant selection on the MHC is predicted to yield an excess of heterozygous individuals, this may not be a locus-specific effect. Several other explanations are discussed, of which increased homozygosity caused by nonrandom mating of buffalo in populations seems the most probable.
... We recognize that human threats often require immediate action to save individuals from disease, poaching or encroachment. However, an immediate genetic survey and historical analysis of existing populations would help guide management decisions and avoid translocations that would be detrimental to long-term survival of these species (Templeton & Georgiatis, 1996). ...
Although some African rhinoceros populations are currently increasing, others are critically endangered. Even healthy populations are extensively managed in the wild and in captivity. While political and demographic considerations are of primary concern, many decisions are made in the name of genetic management. Such decisions should be informed by a full understanding of the multiple meanings of inbreeding and effective population size. In this essay, we examine inbreeding and effective size of wild and captive populations of African rhinoceroses. We conclude by showing how misunderstanding of effective size and Franklin’s 50/500 rule can make a crucial difference in informing management decisions.
Bien que certaines populations de rhinocéros africains soient actuellement en augmentation, d’autres sont en danger critique. Même les populations saines sont gérées très activement dans la nature et en captivité. Alors que les considérations politiques et démographiques soient les principaux motifs d’inquiétude, de nombreuses décisions sont prises au nom de la gestion génétique. Ces décisions devraient se faire en pleine connaissance des multiples implications de l’inbreeding et de ce qu’est une taille de population nécessaire. Dans cet essai, nous examinons l’inbreeding et la taille nécessaire des populations sauvages et captives de rhinocéros africains. Nous concluons en montrant comment une mauvaise compréhension de la taille nécessaire et de la règle 50/500 de Franklin peut entraîner une différence cruciale lorsqu’il s’agit de prendre, en connaissance de cause, les décisions opportunes.
... The lion haplotype from Tsavo, Kenya was identical to the haplotype from the Transvaal region, yet differed considerably from the haplotype found at Aberdares National Park in western Kenya. A similar pattern of variation across the Rift Valley was also reported for sable (Hippotragus niger) (Pitra et al. 2002); wildebeest (Connochaetes taurinus) and impala (Aepyceros melampus) (Templeton & Georgiadis 1996; Arctander et al. 1999); and African wild dogs (Lycaon pictus) (Girman et al. 2001). The distinctness and basal position of the Ugandan haplotype suggest isolation and independent evolution by lion populations north of the Congo Basin and west of the Rift, or reflect an ancestral polymorphism alternately fixed by lineage sorting (Lieberman & Vrba 1995; Tosi et al. 2000 ). ...
We examined sequence variation in the mitochondrial cytochrome b and NADH dehydrogenase subunit 5 genes (2,360 bp total) for 26 lions from eleven locations throughout sub-Saharan Africa. Six distinct haplotypes were observed in the combined sequences, forming two clades: the eastern and the western savannas. The Uganda-Western Kenya haplotype grouped at a basal position with the eastern clade of lions from Tsavo south to the Transvaal and Natal regions. The phylogenetic position of the haplotype from Sabi Sands in the southern part of Kruger National Park remained poorly resolved. The haplotypes found in Namibia and Botswana formed the western clade. The modest genetic variation documented here argues against taxonomic distinctions among living African lions.
... Understanding these changes is fundamental for developing policies to reduce species extinction and environmental deterioration (e.g. [38]). Errors in haplotype inference could compromise these policies. ...
Phasing genotype data to identify the composite haplotype pairs is a widely-studied problem due to its value for understanding genetic contributions to diseases, population genetics research, and other significant endeavors. The accuracy of the phasing is crucial as identification of haplotypes is frequently the first step of expensive and vitally important studies. We present a combinatorial approach to this problem which we call SplittingHeirs. This approach is biologically motivated as it is based on three widely accepted principles: there tend to be relatively few unique haplotypes within a population, there tend to be clusters of haplotypes that are similar to each other, and some haplotypes are relatively common. We have tested SplittingHeirs, along with several popular existing phasing methods including PHASE, HAP, EM, and Pure Parsimony, on seven sets of haplotype data for which the true phase is known. Our method yields the highest accuracy obtainable by these methods in all cases. Furthermore, SplittingHeirs is robust and had higher accuracy than any of the other approaches for the two datasets with high recombination rates. The success of SplittingHeirs validates the assumptions made by the dense graph model and highlights the benefits of finding globally optimal solutions.
... Another application of nested clade phylogeographic analysis to conservation is to infer how environmental factors in a landscape and the ecological attributes of the species living in this landscape affect the population structures of the species. For example, nested clade phylogeographic analysis was performed on several bovid species and elephants, all inhabiting the same general area in Eastern Africa [58]. Some species displayed a pattern of isolation-by-distance over this landscape, whereas others displayed significant fragmentation with strong barriers to gene flow. ...
The genetic variation found in small regions of the genomes of many species can be arranged into haplotype trees that reflect the evolutionary genealogy of the DNA lineages found in that region and the accumulation of mutations on those lineages. This review demonstrates some of the many ways in which clades (branches) of haplotype trees have been applied in recent years, including the study of genotype/phenotype associations at candidate loci and in genome-wide association studies, the phylogeographic history of species, human evolution, the conservation of endangered species, and the identification of species.
... 241-243): Cape buffalo on the savannahs of eastern and southern Africa ( S. c. caffer ), Forest buffalo in the rain forests of western and central Africa ( S. c. nanus ) and West African buffalo from the Sahel-Sudan savannahs ( S. c. brachyceros ) (Fig. 1). The population genetics (Templeton & Georgiadis 1996;O'Ryan et al . 1998;Simonsen et al . ...
Population genetics and phylogeography of the African buffalo (Syncerus caffer) are inferred from genetic diversity at mitochondrial D-loop hypervariable region I sequences and a Y-chromosomal microsatellite. Three buffalo subspecies from different parts of Africa are included. Nucleotide diversity of the subspecies Cape buffalo at hypervariable region I is high, with little differentiation between populations. A mutation rate of 13 –18% substitutions/million years is estimated for hypervariable region I. The nucleotide diversity indicates an estimated female effective population size of 17 000–32 000 individuals. Both mitochondrial and Y-chromosomal diversity are considerably higher in buffalo from central and southwestern Africa than in Cape buffalo, for which several explanations are hypothesized. There are several indications that there was a late middle to late Pleistocene population expansion in Cape buffalo. This also seems to be the period in which Cape buffalo evolved as a separate subspecies, according to the net sequence divergence with the other subspecies. These two observations are in agreement with the hypothesis of a rapid evolution of Cape buffalo based on fossil data. Additionally, there appears to have been a population expansion from eastern to southern Africa, which may be related to vegetation changes. However, as alternative explanations are also possible, further analyses with autosomal loci are needed.
... In theory, historical dispersal and demography consort to shape the phylogeographic architectures of neutral loci within and among closely related species. Thus, phylogenetic methods applied to gene lineages and their geographic distributions provide an opportunity to examine evolutionary processes underlying contemporary population genetic patterns (Crandall and Templeton 1993;Templeton and Georgiadis 1996). By focusing on relationships of alleles as well as allele frequencies, phylogeographic approaches have helped to bridge the formerly distinct fields of systematic biology and population genetics (Avise 1989). ...
Multiple haplotypes from each of three nuclear loci were isolated and sequenced from geographic populations of the American oyster, Crassostrea virginica. In tests of alternative phylogeographic hypotheses for this species, nuclear gene genealogies constructed for these haplotypes were compared to one another, to a mitochondrial gene tree, and to patterns of allele frequency variation in nuclear restriction site polymorphisms (RFLPs) and allozymes. Oyster populations from the Atlantic versus the Gulf of Mexico are not reciprocally monophyletic in any of the nuclear gene trees, despite considerable genetic variation and despite large allele frequency differences previously reported in several other genetic assays. If these populations were separated vicariantly in the past, either insufficient time has elapsed for neutral lineage sorting to have achieved monophyly at most nuclear loci, or balancing selection may have inhibited lineage extinction, or secondary gene flow may have moved haplotypes between regions. These and other possibilities are examined in light of available genetic evidence, and it is concluded that no simple explanation can account for the great variety of population genetic patterns across loci displayed by American oysters. Regardless of the source of this heterogeneity, this study provides an empirical demonstration that different sequences of DNA within the same organismal pedigree can have quite different phylogeographic histories.
... Contrastingly, in A. buselaphus, no differentiation is found among these three populations, which belong to the cokei subspecies. Habitat discontinuity has been proposed to be responsible for the fragmentation of C. taurinus and Aepyceros melampus (impala) populations across the Rift Valley, as inferred from restriction fragment length polymorphism data (Templeton and Georgiadis 1996). For the buffalo, a broader ecological[1993]niche is invoked by the same authors to explain the observed pattern of isolation by distance. ...
The phylogeography of three species of African bovids, the hartebeest (Alcelaphus buselaphus), the topi (Damaliscus lunatus), and the wildebeest (Connochaetes taurinus), is inferred from sequence variation of 345 sequences at the control region (d-loop) of the mtDNA. The three species are closely related (tribe Alcelaphini) and share similar habitat requirements. Moreover, their former distribution extended over Africa, as a probable result of the expansion of open grassland on the continent during the last 2.5 Myr. A combination of population genetics (diversity and structure) and intraspecific phylogeny (tree topology and relative branch length) methods is used to substantiate scenarios of the species history. Population dynamics are inferred from the distribution of sequence pairwise differences within populations. In the three species, there is a significant structuring of the populations, as shown by analysis of molecular variance (AMOVA) pairwise and hierarchical differentiation estimations. In the wildebeest, a pattern of colonization from southern Africa toward east Africa is consistent with the asymmetric topology of the gene tree, showing a paraphyletic position of southern lineages, as well as their relatively longer branch lengths, and is supported by a progressive decline in population nucleotide diversity toward east Africa. The phylogenetic pattern found in the topi and the hartebeest differs from that of the wildebeest: lineages split into monophyletic clades, and no geographical trend is detected in population diversity. We suggest a scenario where these antelopes, previously with wide pan-African distributions, became extinct except in a few refugia. The hartebeest, and probably also the topi, survived in refugia north of the equator, in the east and the west, respectively, as well as one in the south. The southern refugium furthermore seems to have been the only place where the wildebeest has survived.
... The inspection of how geography overlays a haplotype tree is classical in intraspecific phylogeography (e.g., Avise, 1994). However, using the NCA, Templeton and Georgiadis (1996) have shown that such an approach may be misleading in the inference of evolutionary forces shaping genetic variation. Inferring evolutionary processes at the intraor interspecific level from the shapes of phylogenetic trees is just beginning to develop (but without geographical consideration; see Mooers and Heard, 1997 for a review of literature). ...
Phylogenetic relationships among Greek populations of the chub, Leuciscus cephalus, were investigated using 600 bp of the cytochrome b gene. The aim of this study was to test the assumption that the main difference in ichthyological composition between both sides of the Balkan Peninsula is directly linked to differences in the dispersion mechanisms used by fish in order to extend their distribution range. Phylogenetic and nested clade analyses clearly showed that populations in Greece are significantly differentiated. Greek populations were found to descend from three lineages in three geographical provinces: Western, Central, and Eastern Greece. The chub reached Western Greece at the beginning of the Pleistocene and Eastern Greece during the mid-Pleistocene. Chub dispersion occurred mainly by river confluence due to sea level lowering and river capture in Western Greece and sea dispersal with low-salinity conditions within the Aegean Sea in Eastern Greece. However, in Central Greece, the original mtDNA lineage has presumably been lost owing to a genetic introgression following a second invasion from the Danube during the final stage of the last glaciation. This study provides new elements for a better understanding of the composition of the contemporary ichthyofauna in Greece and highlights possible evolutionary mechanisms responsible for the high endemism rate in the Western Greek biogeographic province.
... The expected patterns under each model of restricted gene flow, range expansion and population fragmentation are described elsewhere (Templeton 1993;Templeton et al . 1995;Templeton & Georgiadis 1996;1998a). The geographical distance analysis using permutation testing which was mentioned was performed using version 2.0 of the program GeoDis written by D. Posada, K. Crandall and A. Templeton. ...
The Timarcha goettingensis complex is a monophyletic assemblage of closely related leaf beetles (Chrysomelidae), distributed from the north half of the Iberian Peninsula to Central Europe. Oligophagy, mountainous habitat and apterism are factors which are assumed to promote speciation in these beetles. We have used cytochrome oxidase subunit II mitochondrial DNA genealogies obtained from 31 sampling localities and a nested geographical distance analysis to assess the population structure and demographic factors explaining the geographical distributions of the mtDNA haplotypes in the T. goettingensis complex. The results show that there is a significant association between genetic structuring and geography. Inferences about the historical population processes in the species complex are discussed, being in general in accordance with contiguous range expansions and past fragmentations. The use of the cohesion species concept approach suggests the existence of several systematic ranks among the different T. goettingensis populations, which is in part supported by ecological traits such as trophic selection and altitudinal distribution.
... There were subsequent rinderpest epidemics during the remainder of the 20th century, but they were less severe with mortality not exceeding 50% (Plowright 1982). Recently, different population genetic studies on African buffalo have been conducted (Grobler & Van der Bank 1996; Templeton & Georgiadis 1996; O'Ryan et al . 1998; Simonsen et al . ...
Genetic diversity in nine African buffalo (Syncerus caffer) populations throughout Africa was analysed with 14 microsatellites to study the effects of rinderpest epidemics and habitat fragmentation during the 20th century. A gradient of declining expected heterozygosity was observed among populations in Save Valley Conservancy (Zimbabwe), and northern and southern Kruger National Park (South Africa). This was explained by a high mortality in northern Kruger National Park during the rinderpest pandemic at the end of the 19th century followed by recolonization from neighbouring populations, resulting in intermediate heterozygosity levels in northern Kruger National Park. In other populations expected heterozygosity was very high, indicating that rinderpest and recent habitat fragmentation had a limited effect on genetic diversity. From expected heterozygosity, estimates of long-term effective population size were derived. Migration rates among populations in eastern and southern Africa were very high, as shown by a weak isolation by distance and significant correlation in allele frequencies between populations. However, there were indications that dry habitats could limit migration. Genetic distances within buffalo in central Africa were relatively large, supporting their status as distinct subspecies. Finally, it was observed that the higher polymorphic microsatellites were less sensitive at detecting isolation by distance and differences in Ne, which may be a result of the high mutation pressure at these loci.
Unlike most of the other members of the wild cattle family, the aurochs is extinct. That means that not all data concerning this animal and its life history can be described, and that some aspects will be examined here in a different way than in other wild cattle species. Linnaeus (1758) described domestic cattle under the name of Bos taurus. He mentioned that at the time its wild ancestor was briefly described by the Roman commander-in-chief Julius Caesar under the name of urus (derived from the Germanic word ‘ur’). In 1827, Bojanus made the first osteological research on an aurochs skeleton and gave to this species the name Bos primigenius. Because he thought it came ‘before the Flood’, he added the word antediluvialis. Though the name given by Bojanus is widely used so far, more correctly the name given by Linnaeus should be employed, because he described the species first. The Spanish word for this animal, ‘uro’, comes directly from the Latin word urus. In both the English and the French languages the word ‘aurochs’ comes from the German word ‘auerochs’. For centuries, this latter word was mistakenly used for the wisent (Bison bonasus). Around the twelfth and thirteenth centuries, during which the original aurochs became extinct in Germany, the word ‘ur’ gradually changed into ‘auer’ and ‘auerochs’ (Szalay 1915). When people were no longer aware of the original aurochs its name passed to a related animal, similarly impressive-the wisent. Such a process has been observed in other species too.
Except in rare instances where DNA might be extracted from a well-preserved and well-dated fossil series, molecular genetic assays normally are confined to living organisms sampled from the present-day horizon in time. Nevertheless, temporal aspects of evolution can be recovered from extant organisms using genomic differences accumulated since shared ancestry. This temporal, phylogenetic dimension of evolution has traditionally been the province of macroevolutionary studies that deal with relationships among species and higher taxa. Phylogenetic perspectives were rarely applied, or even perceived as relevant, at the intraspecific level because of a lack of empirical approaches to assess historical relationships, and because of a widespread perception that phylogeny had no real meaning for potentially interbreeding assemblages of populations. In the last two decades, studies of mitochondrial (mt) DNA have changed this view dramatically by demonstrating that the matriarchal component of intraspecific phylogeny can be estimated empirically (Avise 1989).
The distribution, abundance, and demographic make up of primates living within fragments are an important component for understanding conservation needs of the species. Species response to habitat fragmentation and disturbance occurs in two phases (Wilcove et al., 1986). In the first phase, the species will try to adjust to modified habitats, while in the second phase, changes will occur in the demography of the population. The initial response to fragmentation includes changes in activity pattern, feeding, ranging, and other behaviors (Marsh, 1981; Johns, 1987; Johns and Skorupa, 1987; Menon, 1993), which in turn changes the demographics. Of primary concern is the genetic welfare of any species that remains in genetic or demographic isolation.
Names Genus: Bubalus C. H. Smith, 1827 Species: Tamaraw Bubalus mindorensis Heude, 1888 Names in other languages: French: Tamarau, Tamarao; German: Mindoro-Büffel; Spanish: Tamarao, Búfalo de Mindoro; Italian: Tamaraw Other common names: Mindoro dwarf buffalo. Taxonomy Bubalus mindorensis Heude (1888), type specimen Mindoro Island, Philippines. Despite early debates on its proper taxonomic classification (Everett 1878; Meyer 1878; Bartlett 1878), the tamaraw is classified as a distinct species within the genus Bubalus based on morphological characteristics (Groves 1969; Custodio et al. 1996; Braun et al. 2002; Wilson & Reeder 2005) and genetic analyses (Namikawa et al. 1995; Tanaka et al. 1996, 2000). Steere (1888a) also independently described the tamaraw, placing it in the genus Anoa, but was superseded by Heude (1888). Heude’s type specimen was lost and then rediscovered (Braun et al. 2002) in Xujiahui, China, in the Shanghai Natural History Museum, which acquired the museum Heude founded (Zikawei Museum of Natural History). Subspecies and distribution The tamaraw is endemic to the island of Mindoro, Philippines (Plate 9; Heaney et al. 1987; Custodio et al. 1996). Thought to be previously widely distributed in Mindoro (Everett 1878; Steere 1888b, 1891), by 1949 there appears to have been fewer than 1000 animals left on the island, with an estimated 244 in Occidental Mindoro (Manuel 1957) in at least three areas (Harrisson 1969a). By 2007 the three areas where tamaraw are now thought to remain are in Mounts Iglit-Baco National Park (MIBNP), the Mount Calavite Wildlife Sanctuary and the Aruyan-Malati area (R. M. Boyles, unpublished; J. de Leon, unpublished).
Inferring the past, recent and future evolutionary history of species At the end of the last century, the renowned scientist John Avise introduced the phylogeography concept in reference to the study of the historical principles and processes that govern the geographical distribution of genealogical lineages (Avise et al. 1987; Avise 2000). Considered as a biogeography subdiscipline, phylogeography emphasizes historical aspects of the contemporary distribution of lineages (Avise & Hamrick 1996; Avise 2000; Hewitt & Butlin 1997). Widely studied, climatic changes have been shown to engender major fluctuations in the demography and distribution of wild species on an evolutionary time scale. Climatic changes (e.g. influence of Quaternary climatic fluctuations) sometimes entail long-lasting isolation of populations, subsequently leading to ecological differentiation or speciation (Lister 2004; Vrba 1995a, 1995b). These phylogeographic patterns shape the evolutionary history of contemporary taxa. Phylogeographical studies have flourished over the last few decades, especially in Europe, but not in Africa, although this continent still hosts large megafaunal communities (Barnosky et al. 2004). Understanding how African wildlife responded to climatic changes in the past facilitates the identification of biodiversity hotspots (i.e. glacial refugia), forecasting future population dynamics and developing adapted management strategies.
Systematists and population geneticists can both use molecular data sets to construct evolutionary trees (species and gene trees, respectively), and then use the resulting historical framework to test a variety of hypotheses. The greatest prospect for future advances in our understanding of speciation is to extend these historical approaches to the species/population interface, for only by straddling this interface can we actually study the processes involved in the origin of a new species. This chapter illustrates how the bottomup historical approaches used in population genetics can be extended upward to this critical interface in order to separate the effects of population structure from population history, to rigorously test the species status of a group and to test hypotheses about the process of speciation by using gene trees to define a nested, statistical analysis of biogeographic and other types of data.
The cohesion species concept defines a species as an evolutionary lineage whose boundaries arose from the forces that create reproductive communities. Such forces are collectively called cohesion mechanisms and consist of two main subtypes: genetic exchangeablity and ecological interchangeablity. To make this definition operational, populations that behaved as separate evolutionary lineages are first identified. A method is reviewed for inferring lineages using explicit statistical criteria from geographical overlays upon gene trees and is illustrated with data from the Spalax ehrenbergi superspecies complex. This step infers three statistically significant lineages of mole rats and several range expansion events within this group. Once lineages have been identified, the next step is to use the cohesion mechanisms to identify candidate traits that should contribute to genetic exchangeability and/or ecological interchangeability. The cohesion species are then identified by performing overlays upon gene trees to identify significant transitions in the candidate traits. Cohesion species are recognized only when statistically significant genetic/ecological transitions occur that are concordant with the lineages defined earlier. All three mole rat lineages reject the null hypotheses of both genetic exchangeability and ecological interchangeability among the lineages, and hence there is statistically significant evidence for three cohesion species in this complex. More species could exist, and the testing procedure provides detailed guidance for future research on species status in these mole rats. This data-rich method of recognizing species automatically generates much information about the biogeography, population structure, historical events, and ecology and/or reproductive biology of the group under study. This information in turn provides much insight into the process of speciation.
Conceptual connections between ecology and population genetics have been an integral part of the field of conservation biology from its beginnings. The conservation of genes, the perpetuation of microevolutionary processes (e.g., natural selection, mutation, genetic drift, and gene flow) within populations, and the conservation of demographic and landscape-scale processes make up the three pillars of modern conservation biology (see Brussard 1991). This chapter reviews how population genetic processes interact with landscape processes in a conservation biology context and suggests practical ways that managers can address these interactions. Although extremely important in the preservation of biological diversity, these interactions are obscured by differences in scale that exist between genetic processes operating at the population level, and landscape processes operating at much broader spatial scales and significantly smaller temporal scales.
Thunnus albacares is an important fishery species throughout the world. Polymorphisms of sequence variations in mtDNA COI genes were assessed to explore the genetic differentiations among 11 populations of T. albacares sampled from the central Pacific Ocean. Sixty-one mtDNA haplotypes and 38 variable sites were detected. Analysis of mtDNA COI sequences revealed that tuna from the 11 localities were characterized by moderately high haplotype diversity (h = 0.650 ± 0.040), while sequence divergence between haplotypes was relatively low (π = 0.00364 ± 0.00044). Analyses of molecular variance and F
ST analysis supported that significant genetic differentiations existed between some of the sampled populations. Tests of neutral evolution and mismatch distribution analysis suggested that T. albacares might have experienced a population expansion, which possibly occurred within the last 0.82 million years. Our study unraveled the genetic structure of the extant population of T. albacares and addressed the related fishery management issues including fishery stock identification and management.
Genetic differentiation among populations of the South African scrub hare Lepus
saxatilis was examined using hypervariable mitochondrial DNA control region I (CR-I) sequences. Neighbour-joining analysis revealed a pattern that did not correspond to the current subspecies delineations. The CR-I sequence data delimit scrub hares into three major maternal lineages. The three phylogenetic assemblages exhibited different geographical distributions. AMOVA analyses and exact tests for population differentiation confirmed this phylogeographic partitioning. One lineage (SW) was confined to the south-western Cape, the second lineage (N) was exclusively found in the northern part of South Africa and in the neighbouring countries, and the third lineage (C) was predominant in the central parts of South Africa. This spatial distribution did not coincide with the ranges of the 10 described subspecies covered by our sampling regime. The lineages C and N overlapped in an area including eastern parts of South Africa and southern Namibia. The presence of both lineages in that area of overlap was interpreted as the result of secondary contact due to recent range expansions after the two lineages had undergone a population restriction approximately 18 000 years ago. Analyses of contemporary gene flow disclosed an exchange of migrants between N and C, which was biased towards a movement from C to N. The SW group represents a very distinct evolutionary lineage that has been isolated for more than 45 000 years. It does not exchange female migrants with the other two groups. Mismatch distribution analyses indicated sudden population size expansions in the history of all three populations.
Nonequilibrium conditions due to either allopatry followed by secondary contact or recent range expansion can confound measurements of gene flow among populations in previously glaciated regions. We determined the scale at which gene flow can be estimated among breeding aggregations of bullfrogs (Rana catesbeiana) at the northern limit of their range in Ontario, Canada, using seven highly polymorphic DNA microsatellite loci. We first identified breeding aggregations that likely share a common history, determined from the pattern of allelic richness, factorial correspondence analysis, and a previously published mtDNA phylogeography, and then tested for regional equilibrium by evaluating the association between pairwise F-ST and geographic distance. Regional breeding aggregations in eastern Ontario separated by less than or equal to100 km were determined to be at or near equilibrium. High levels of gene flow were measured using traditional 1 statistics and likelihood estimates of Nm. Similarly high levels of recent migration (past one to three generations) were estimated among the breeding aggregations rising nonequilibrium methods. We also show that, in many cases, breeding aggregations separated by tip to tens of kilometers are not genetically distinct enough to be considered separate genetic populations. These results have important implications both for the identification of independent "populations" and in assessing the effect of scale in detecting patterns of genetic equilibrium and gene flow.
Evolutionary trees can be constructed from the haplotypes observed with molecular surveys of sequence or restriction site variation. Such gene trees can be constructed regardless of whether or not all of the individual specimens came from one or many species. Hence, these gene trees can straddle the species/population interface, thereby providing a powerful tool for studying the meaning of species and the process of specia-tion. We illustrate how historical approaches using gene trees can be used to separate the effects of population structure from population history, in order to rigorously test the species status of a group, and to test hypotheses about the process of speciation. A worked example of species status in the Piriqueta caroliniana complex is presented. Species status is evaluated under the cohesion species concept that defines a species as an evolutionary lineage with boundaries arising from the forces that create reproductive communities. Such forces are collectively called cohesion mechanisms and consist of two main sub-types: (i) genetic exchangeability, and (ii) ecological interchangeability. To make this def-inition operational, populations that behave as separate evolutionary lineages are first identified. A method is reviewed for inferring lineages using explicit statistical criteria from geographic overlays upon gene trees. Once lineages have been identified, the next step is to use the cohesion mechanisms to identify candidate traits that should contribute to genetic exchangeability and/or ecological interchangeability. The cohesion species are then identified by performing overlays upon gene trees in order to identify significant transitions in the candidate traits. Cohesion species are recognized only when statisti-cally significant reproductive/ecological transitions occur that are concordant with the lineages defined earlier. This data-rich method of recognizing species automatically gen-erates much information about the biogeography, population structure, historical events, and ecology and/or reproductive biology of the group under study. In turn, this infor-mation provides much insight into the process of speciation. It also makes the criteria, data, methods of analysis and degree of support for the species inference completely explicit, thereby avoiding confusion, inconsistency and artificial controversies that plague much of the literature on species concepts.
Variation in mitochondrial and microsatellite DNA was used to define the genetic structure of hartebeest populations straddling a transition zone between two morphotypes (Alcelaphus buselaphus cokei and A. b. lelwel) in Kenya. Previous analyses of mtDNA from hartebeest populations across Africa supported the refugium hypothesis; that present day hartebeest morphotypes diverged in allopatry, due to climatic changes. In this analysis of morphologically distinct populations in close geographical proximity, majority of genetic variation was found within populations, with relatively little distinction, and varying levels of subdivision, among populations. Patterns of shared alleles, and reduced tendency for mtDNA haplotypes to cluster phylogenetically according to morphotype, depicted gene flow between populations. There was sharp disparity between apparently seamless genetic transition between populations and marked disjunction in gross morphology over short distances (<100km). Hartebeest in the transitional zone between A. b. lelwel and A. b. cokei, including populations in Ruma, Meru National Parks and Laikipia, are the only remaining examples, each genetically and morphologically different from the other, of what appears to be resumed contact between two lineages that diverged in allopatry. Our results underscore the importance of using genetic and morphological information to explicitly define evolutionary processes as targets for conservation in Africa.
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.
Sexual differences in herding behaviour ofAfrican buffalo (Syncerus caffer) werestudied by analysing at the herd levelmitochondrial D-loop hypervariable region I andfourteen autosomal microsatellites. Three herdsfrom Arusha National Park in Tanzania wereanalysed with mtDNA and five herds from KrugerNational Park in South Africa with mtDNA andmicrosatellites. Significant mtDNAdifferentiation was observed among herds inArusha NP (FST = 0.12, based on haplotypefrequencies). Assignment tests withmicrosatellite data from Kruger NP showed thatmost frequent migration between herds is bymales two years. This was confirmed bytests for herd differentiation and analyseswith Lynch and Ritland's relatedness estimator.Within a herd, males younger than two years andfemales showed a higher relationship through acommon father rather than a common mother,indicating that female herd members mate withonly a few dominant males. This in turnsuggests a female:male sex ratio larger than5:1. The migration rate per generation betweenherds was estimated to be 5–2% for femalesand close to 100% for males. Finally, theimplications for the management of buffalopopulations are being discussed.
The application of principles from coalescence theory to genealogical relationships within species can provide insights into the process of diversification and the influence of biogeography on distributional patterns. There are several features that make some organisms more suitable for detailed studies of historical processes; in particular, limited dispersal, which serves to conserve the patterns of genetic variation that developed during colonization. We describe the potential benefits of studies that integrate analyses of genetic variation with information from the fossil pollen record and present recent examples of the application of quantitative methods of phylogeographic analysis.
The African buffalo (Syncerus caffer) is widespread throughout sub-Saharan Africa and is found in most major vegetation types, wherever permanent sources of water are available, making it physically able to disperse through a wide range of habitats. Despite this, the buffalo has been assumed to be strongly philopatric and to form large aggregations that remain within separate home ranges with little interchange between units, but the level of differentiation within the species is unknown. Genetic differences between populations were assessed using mitochondrial DNA (control region) sequence data and analysis of variation at six microsatellite loci among 11 localities in eastern and southern Africa. High levels of genetic variability were found, suggesting that reported severe population bottlenecks due to outbreak of rinderpest during the last century did not strongly reduce the genetic variability within the species. The high level of genetic variation within the species was found to be evenly distributed among populations and only at the continental level were we able to consistently detect significant differentiation, contrasting with the assumed philopatric behaviour of the buffalo. Results of mtDNA and microsatellite data were found to be congruent, disagreeing with the alleged male-biased dispersal. We propose that the observed pattern of the distribution of genetic variation between buffalo populations at the regional level can be caused by fragmentation of a previous panmictic population due to human activity, and at the continental level, reflects an effect of geographical distance between populations.
Nonrandom associations of alleles or haplotypes with geographical location can arise from restricted gene flow, historical events (fragmentation, range expansion, colonization), or any mixture of these factors. In this paper, we show how a nested cladistic analysis of geographical distances can be used to test the null hypothesis of no geographical association of haplotypes, test the hypothesis that significant associations are due to restricted gene flow, and identify patterns of significant association that are due to historical events. In this last case, criteria are given to discriminate among contiguous range expansion, long-distance colonization, and population fragmentation. The ability to make these discriminations depends critically upon an adequate geographical sampling design. These points are illustrated with a worked example: mitochondrial DNA haplotypes in the salamander Ambystoma tigrinum. For this example, prior information exists about restricted gene flow and likely historical events, and the nested cladistic analyses were completely concordant with this prior information. This concordance establishes the plausibility of this nested cladistic approach, but much future work will be necessary to demonstrate robustness and to explore the power and accuracy of this procedure.
A questionnaire survey was conducted in Tanzania of 1396 local people living adjacent to Arusha, Kilimanjaro, Tarangire, Lake Manyara, and Mikumi National Parks and the Selous Game Reserve. Over 71% of local people surveyed reported problems with wildlife. The relative frequency of reported conflict with wildlife was significantly and inversely related to human density on lands adjacent to a protected area. Of those local people who reported having problems with wildlife, 86% reported crop damage, while 10% reported the killing of livestock and poultry. The problematic wildlife species also varied significantly with human density. Large animals were more problematic at low human densities, while small animals were more problematic at high human densities. Local people were generally less effective in controlling small-bodied species than large-bodied species. The relative frequency of reported success in controlling wildlife varied significantly with human density and was bimodal: local people were less effective in controlling wildlife at lower and higher human densities. This bimodal relationship suggests that, even if all protected areas in Tanzania were abolished, local people would continue to experience problems with wildlife at high human densities. To minimize the conflict between wildlife and local people, land uses associated with low human density that are non-attractive to wildlife should be encouraged on lands adjacent to protected areas in Tanzania.
Because phylogenies play a central role in many evolutionary and population genetic questions, it is vital to have confidence in phylogeny reconstructions for particular data sets. An algorithm recently introduced by Templeton et al. (1992, Genetics 132:619-633) simultaneously estimates cladograms from a given set of restriction site or nucleotide sequence data and calculates a confidence set of alternatives while allowing for the possibility of recombination within the data set. This method was developed for use at the intraspecific level, where mutational differences between operational taxonomic units are few. Because of the strengths of this method, it would be desirable to use it at higher levels of phylogenetic analysis. I tested the accuracy of the method of Templeton et al. using a known phylogeny from bacteriophage T7, which simulates higher levels of diversification. This method has greater statistical power and more accurately reconstructs phylogenetic relationships than does maximum parsimony when few molecular characters are available for analysis, even at higher levels of diversification.
In Tanzania, in the dry season, Tarangire National Park is second only to Ngorongoro in the concentrations of wildlife to be seen there. But there is a bleak outlook for the species that traditionally migrate to pastures outside the park in the rainy season. Over the last 10 years many of their routes out of the park have been blocked by farms and ranches, and further expansion of agricultural schemes could threaten the remainder. Part of the zebra and wildebeest populations that migrate north have already been lost. The author, who has been carrying out wildlife surveys in Tanzania for the Frankfurt Zoological Society for seven years, proposes some remedies to prevent the park from becoming the domain of only a few resident species.
We previously developed a cladistic approach to identify subsets of haplotypes defined by restriction endonuclease mapping or DNA sequencing that are associated with significant phenotypic deviations. Our approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site or sequence data that represents the evolutionary steps that interrelate the observed haplotypes. The cladogram is used to define a nested statistical design to identify mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that any undetected mutation causing a phenotypic effect is embedded within the same evolutionary history that is represented by the cladogram. The power of this approach depends upon the confidence one has in the particular cladogram used to draw inferences. In this paper, we present a strategy for estimating the set of cladograms that are consistent with a particular sample of either restriction site or nucleotide sequence data and that includes the possibility of recombination. We first evaluate the limits of parsimony in constructing cladograms. Once these limits have been determined, we construct the set of parsimonious and nonparsimonious cladograms that is consistent with these limits. Our estimation procedure also identifies haplotypes that are candidates for being products of recombination. If recombination is extensive, our algorithm subdivides the DNA region into two or more subsections, each having little or no internal recombination. We apply this estimation procedure to three data sets to illustrate varying degrees of cladogram ambiguity and recombination.
Nonrandom associations of alleles or haplotypes with geographical location can arise from restricted gene flow, historical events (fragmentation, range expansion, colonization), or any mixture of these factors. In this paper, we show how a nested cladistic analysis of geographical distances can be used to test the null hypothesis of no geographical association of haplotypes, test the hypothesis that significant associations are due to restricted gene flow, and identify patterns of significant association that are due to historical events. In this last case, criteria are given to discriminate among contiguous range expansion, long-distance colonization, and population fragmentation. The ability to make these discriminations depends critically upon an adequate geographical sampling design. These points are illustrated with a worked example: mitochondrial DNA haplotypes in the salamander Ambystoma tigrinum. For this example, prior information exists about restricted gene flow and likely historical events, and the nested cladistic analyses were completely concordant with this prior information. This concordance establishes the plausibility of this nested cladistic approach, but much future work will be necessary to demonstrate robustness and to explore the power and accuracy of this procedure.
Patterns of restriction site variation within mitochondrial DNA (mtDNA) of 270 individuals were used to examine the current structure of savanna elephant populations and to infer historical patterns of gene flow across eastern and southern Africa. Elephants have a complex population structure characterized by marked subdivision at the continental level (Fst = 0.39; 95% confidence interval 0.19-0.58), and isolation by distance at the regional level. However, phylogeographic analysis revealed evidence of protracted gene flow across the continent. First, one relatively derived haplotype was found at all sampling locations. Second, haplotypes representing exceptionally divergent (up to 8.3%) mitochondrial clades were found to coexist at distant (> 2,000 km) sampling locations. In the few other species characterized by sympatric individuals bearing such divergent haplotypes, all such individuals were found to coexist within limited geographical regions. Accordingly, pronounced mitochondrial divergence within populations is often attributed to ancestral isolation in allopatry, followed by secondary contact. The patterns within elephants do not accord with ancestral isolation in allopatry. Given the exceptional mobility of elephants, a geographical barrier is unlikely to have obstructed gene flow between regions for long enough to produce the observed mitochondrial divergence. Rather, the patterns are consistent with the more parsimonious hypothesis, based on neutral coalescent theory, that gene flow has maintained a sufficiently large effective population size (> 50,000 females) for representatives of clades that diverged at least 4 million years ago to have persisted by chance within a population that was subdivided, but not strictly isolated in allopatry.
Empirical data sets of intraspecific restriction site polymorphism in Drosophila have been gathered in order to test hypotheses derived from coalescent theory. Three main ideas are tested: (1) haplotype frequency in the sample contains information on the topological position of a given haplotype in a cladogram, (2) the frequency of a haplotype is related to the number of mutational connections to other haplotypes in the cladogram and (3) geographic location can be used to infer topological positioning of haplotypes in a cladogram. These relationships can then be used to better estimate intraspecific phylogenies in two ways: (1) rooting the phylogeny and (2) resolving ambiguities in a cladogram. This information will allow one to reduce the number of alternative phylogenies and incorporate the uncertainties involved in reconstructing intraspecific phylogenies into subsequent analyses that depend heavily on the topology of the tree.
Phylogenetic reconstruction--the method by which biologists examine the relationship between living and extinct organisms in an effort to identify evolutionary pathways--has seen radical changes in the last ten years. But as rapid advances in mathematical, molecular, developmental, and cladistic techniques have greatly improved reconstruction efforts, they have also sparked controversy, especially with regard to the assumptions and data underlying the cladistic method. This book brings together contributions from a wide range of practitioners in order to find common ground. By examining numerous models from a variety of fields, the book serves as a guide to the latest methods of classification and phylogeny reconstruction and provides insights into the relative merits that each approach has to offer. In particular, developmental studies emerge as a significant factor in cladogram construction. Splendidly written and wide-ranging in scope, Models in Phylogeny Reconstruction will be welcomed by students and researchers in systematic and evolutionary biology.
Preface. Part I: Background: 1. Introduction. Why Employ Molecular Genetic Markers? Why Not Employ Molecular Genetic Markers? 2. History of Molecular Phylogenetics. Debates and Diversions from Molecular Systematics. Molecular Phylogenetics. 3. Molecular Tools. Protein Assays. DNA Assays. References to Laboratory Protocols. 4. Interpretative Tools. Categorical Subdivisions of Molecular Genetic Data. Molecular Clocks. Procedures for Phylogeny Reconstruction. Gene Trees versus Species Trees. Part II: Applications: 5. Individuality and Parentage. Genetic Identity versus Non-Identity. Parentage. 6. Kinship and Intraspecific Phylogeny. Close Kinship and Family Structure. Geographic Population Structure and Gene Flow. Phylogeography. Microtemporal Phylogeny. 7. Speciation and Hybridization. The Speciation Process. Hybridization and Introgression. 8. Species Phylogenies and Macroevolution. Rationales for Phylogeny Estimation. Special Approaches to Phylogeny Estimation. Prospectus for a Global Phylogeny. Special Topics in Molecular Phylogenetics. 9. Conservation Genetics. Issues of Heterozygosity. Issues of Phylogeny. Literature Cited. Index to Taxonomic Genera. General Index.
Genetics can be applied to many problems in the area of conservation biology, and four such uses will be illustrated in this paper. First is conservation forensics in which genetic techniques are used to aid the enforcement of laws concerning endangered species. An example of this application is the use of DNA “fingerprinting” to identify the geographical source of tusks as part of an effort to restrict poaching of African elephants. A second application is in systematics. Before a conservation program can be designed, we obviously need to know what it is we are trying to conserve. Genetic techniques are emerging as a major tool in systematics and have proven to be useful in identifying taxa that behave as independently evolving genetic lineages (i.e., species). An example of this is provided by studies on wild cattle species. The cattle also illustrate a third application of genetics in conservation: the detection and monitoring of hybridization. Hybridization can cause genotypic extinction through extensive gene flow, and the incidence of hybridization has been greatly increased by human activities through the introduction of exotics and the disturbance of natural environments and isolating barriers. The final area is genetic management of natural and captive populations of endangered species. Genetic management is necessary both for the short-term health of the species (e.g., inbreeding depressions) and the long-term adaptive flexibility of the species (e.g., preserving genetic diversity). Examples of genetic management of both captive and natural populations will be given.
The natural habitats of many species have become fragmented into small "islands," principally by human activities. In this paper we discuss the long-term genetic and evolutionary consequences of fragmentation as inferred from studies on populations that have undergone natural habitat fragmentation in the Ozark Mountains. The Ozarks are the highest land formation found in the midwestern United States. Because of the absence of major geographical barriers around the Ozarks, plants and animals from diverse parts of the continent have been able to invade the area during post-Pleistocene climatic periods. Many of these invasions were short-lived, but the geological and topographical complexity of the Ozarks provided numerous relictual habitats. As a consequence, natural habitat fragmentation occurred for many species, and the fragmentation has often persisted for thousands of years. The genetic and ecological consequences of habitat fragmentation depend critically upon whether or not habitat fragmentation results in a complete cessation of dispersal between the habitat islands. If habitat fragmentation results in the complete genetic isolation of habitat islands, then each "island" becomes demographically independent and local extinction can occur. When there is no opportunity for recolonization, an "extinction ratchet" is possible in which each local extinction brings the global population irreversibly one step closer to total extinction. It is therefore critical to know if habitat fragmentation actually prevents dispersal or not. Unfortunately, studying dispersal patterns directly is usually not feasible. We show how genetic surveys can be used to answer this question. Given demographic fragmentation, we also show how genetic surveys can pinpoint species at high risk for local extinction. These suffer the most severe genetic consequences from habitat fragmentation, such as a drastic loss of genetic variability within habitat islands and inbreeding depression. On the positive side, the genetic variation of a fragmented species is not totally lost but is often present as fixed differences between different local populations. Indeed, a fragmented population is subject to less global loss of genetic variation than an equally sized panmictic population. Consequently, as long as the rate of local extinction is relatively small or counteracted by a recolonization program, a fragmented species can preserve almost all of its genetic variation at the global level for long periods of time. We discuss the optimal design for a recolonization program to prevent global extinction and to maintain high levels of global genetic variation.
Six variable protein loci and one variable ribosomal DNA restriction site were used for an analysis of population structure in five species of Polistes from Texas. A sample-reuse algorithm was developed that estimated FST, FIS, and ⊘ (the coefficient of kinship) from probabilities of identity. Of the four species analyzed in detail only one, Polistes exclamans, had statistically significant values of FST. These values may reflect natural constraints on successful nesting for migrants of this species. Three of the four species had significant values of FIS and three of the four species had significant values of ⊘. In many cases ⊘ also differed from the expected value under haplodiploidy and random mating. Values of ⊘ did not differ from expectations under haplodiploidy and local inbreeding. These results emphasize that theories of social behavior and evolution based on coefficients of kinship should include some explicit consideration of population structure.
The botanical composition of diets was determined for Thomson's (Gazella thomsoni) and Grant's gazelles (G. granti), impala (Aepyceros melampus), topi (Damaliscus lunatus topi), kongoni (Alcelaphus buselaphus cokii), wildebeest (Connochaetes taurinus), zebra (Equus burchelli), buffalo (Syncerus caffer), giraffe (Giraffe camelopardalis), and elephant (Loxodonta africana) in Masai Mara National Reserve by microhistological analyses of feces. The non-grazers (>50% dicotyledons) were Grant's gazelle, giraffe, and elephant. Thomson's gazelle, topi, kongoni, wildebeest, zebra, and buffalo were grazers (>50% monocots). The impala's diet consisted of equal percentages of dicots and grasses. No relation was found between diversity in diet and body mass among the ungulates studied. The buffalo, kongoni, wildebeest, topi, and Thomson's gazelle preferred the same grasses. The giraffe's diet was extremely dissimilar (11% overlap) to the other ungulates. Dietary similarities were not frequently higher in the dry season than in the wet season. The elephant was the only ungulate studied that did not select a bontanical diet which was in significant disagreement with that of another.
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Canopy interception data from 105 grassland stands in the Serengeti National Park in Tanzania and the Masai Mara Game Reserve in Kenya were used to evaluate community organization within an ecosystem defined by the annual movements of large herds of nomadic ungulates. Other studies tested hypotheses about factors influencing species composition and diversity of the communities. The herbaceous vegetation was principally C"4 grasses, which commonly contributed over 90% of total abundance. Ninety-nine stands were classified into 17 communities, using a numerical clustering method. Sixteen communities were principally perennial grasses; one was dominated by an annual species. Short grasslands predominated below 700 mm mean annual rainfall and in heavily grazed sites on hilltops at higher-rainfall locations. Much of the savanna understory at intermediate rainfall levels was medium-height Themeda triandra grassland; six variants were recognized by clustering. Tall grasslands dominated by Hyparrhenia filipendula occurred as a savanna understory in locations with >900 mm of annual rainfall. Two ordination axes revealed a shortgrass continuum that graded into a medium-to tallgrass continuum, and an outlying floodplain tall grassland dominated by Echinochloa haploclada. The latter and the short grasslands dominated by Andropogon greenwayi were very different in species composition from the other communities. The first ordination axis was related to grazing intensity, and the second to soil texture. Spatial heterogeneity was an important attribute of the grasslands from the level of local stands to the level of landscape regions. Spatial pattern, rather than point diversity, was the major vegetation property correlated with @a-diversity. Higher @a-diversity was accompanied by low dominance concentration and more clumped species distributions. Individuals of rare species were more aggregated than members of common species. @b-diversity also was a significant feature of the vegetation, leading to pronounced @c-diversity and a variety of different grassland types in local areas. Coenoclines were evident only in more arid locations. @c-diversity was associated with topographic and geological heterogeneity. Animals, soils, the overlying tree canopy in savannas, and fire influence @a-diversity through their contribution to creating spatial pattern. Animals have particularly complicated effects, in addition to defoliating areas. Grazing is a major environmental factor affecting the grasslands, but it is a composite factor interacting in complex ways with other environmental factors.
Some African mammal clades are used to analyse evolutionary processes. The clades chosen are especially suitable for this purpose because they include both extant species, for which there is an abundant literature, and fossil records from various Miocene-Recent strata mainly in Eastern and Southern Africa. The monophyletic groups in this sample differ considerably in speciation rates and in the magnitudes of long-term trends. I take a number of rival hypotheses as to why such disparate macroevolutionary patterns should have evolved (the Birth Rate, Gene Flow, Resource-Use, Extrinsic and Random Hypotheses) and test their predictions. The tests involve comparisons of phylogenetic patterns with biological variation (in life histories, population structure, mobility and habitat-specificity) among the extant species. The results accord best with the Resource-Use Hypothesis.
The evolving concept of ecosystem management is the focus of much current debate. To clarify discussion and provide a framework for implementation, I trace the historical development of ecosystem management, provide a working definition, and summarize dominant themes taken from an extensive literature review. The general goal of maintaining ecological integrity is discussed along with five specific goals: maintaining viable populations, ecosystem representation, maintaining ecological process (ie., natural disturbance regimes), protecting evolutionary potential of species and ecosystems, and accommodating human use in light of the above. Short-term policy implications of ecosystem management for several groups of key actors (scientists, policymakers, managers, citizens) are discussed. Long-term (> 100 years) policy implications are also reviewed including reframing environmental values, fostering cooperation, and evaluating success. Ecosystem management is not just about science nor is it simply an extension of traditional resource management; it offers a fundamental reframing of bow humans may work with nature.
"Wright's views about population genetics and evolution are so fundamental and so comprehensive that every serious student must examine these books firsthand. . . . Publication of this treatise is a major event in evolutionary biology."-Daniel L. Hartl, BioScience
Because some genes have been cloned that have a known biochemical or physiological function, genetic variation can be measured in a population at loci that may directly influence a phenotype of interest. With this measured genotype approach, specific alleles or haplotypes in the probed DNA region can be assigned phenotypic effects. In this paper we address several problems encountered in implementing the measured genotype approach with restriction site data. A number of analytical problems arise in part as a consequence of the linkage disequilibrium that is commonly encountered when dealing with small DNA regions: 1) different restriction site polymorphisms are not statistically independent, 2) the sites being measured are not likely to be the direct cause of the associated phenotypic effects, 3) haplotype classes may be phenotypically heterogeneous, and 4) the sites that are most strongly associated with phenotypic effects are not necessarily the most closely linked to the actual genetic cause of the effects. When recombination and gene conversion are rare, the primary cause of linkage disequilibrium is history (mutational origin, genetic drift, hitchhiking, etc.). We deal with historical association directly by producing a cladogram that partially reconstructs the evolutionary history of the present-day haplotype variability. The cladogram defines a nested analysis of variance that simultaneously detects phenotypic effects, localizes the effects within the cladogram, and identifies haplotypes that are potentially heterogeneous in their phenotypic associations. The power of this approach is illustrated by an analysis of the associations between alcohol dehydrogenase (ADH) activity and restriction site variability in a 13-kb fragment surrounding the ADH locus in Drosophila melanogaster.
Genetic variation is the basis of adaptive flexibility in populations and is the ultimate evolutionary basis of much species and community-level diversity. Accordingly, the preservation and maintenance of genetic diversity has a high priority in many conservation programmes. This paper discusses how genetic diversity is measured at the molecular level, including some newer measures made possible with restriction site or DNA sequence data as well as the development of a phylogenetic approach to assessing the significance of genetic variation within a species. These measures of genetic diversity are then used to re-examine the validity of the 50/500 rule of conservation biology; a rule that states that populations should have no fewer than 50 individuals for short-term maintenance of genetic variation and no fewer than 500 individuals for long-term maintenance. Both the 50 and 500 parts of this rule are found to be invalid and frequently misleading. Instead of invoking 'universal' rules, conservation biologists should recognize the role of biodiversity in management policies. Not all species are the same, and we need more research and a willingness to try novel approaches rather than naively apply a 'rule' that has no demonstrable generality.
Systematists and population geneticists can both use molecular data sets to construct evolutionary trees (species and gene trees, respectively), and then use the resulting historical framework to test a variety of hypotheses. The greatest prospect for future advances in our understanding of speciation is to extend these historical approaches to the species/population interface, for only by straddling this interface can we actually study the processes involved in the origin of a new species. This chapter illustrates how the bottom-up historical approaches used in population genetics can be extended upwards to this critical interface in order to separate the effects of population structure from population history, to rigorously test the species status of a group, and to test hypotheses about the process of speciation by using gene trees to define a nested, statistical analysis of biogeographic and other types of data.
The rooting of intraspecific gene or haplotype trees has proven to be difficult using the traditional techniques of rooting species trees such as outgroups. As an alternative, we apply neutral coalescent theory to the problems of determining the root of an intraspecific gene tree and the relative ages of the haplotypes. By using a recursive equation, exact root probabilities can be calculated for small cladograms and sample sizes. These exact probabilities indicate that root probabilities are not very sensitive to the parameter theta, which is four times the mutation rate times the inbreeding effective size. The exact probabilities also indicate that root probabilities are not very sensitive to the absolute numbers of each haplotype (allele) class, only their relative proportions. The exact method, unfortunately, is not feasible for implementation with larger data sets with present algorithms and computers. However, the exact results suggested a simple heuristic for determining outgroup weights; that is, finding the haplotype that is the oldest in the sample and that can serve as an outgroup for the remainder of the haplotype tree. Computer simulations revealed that these outgroup weights are strongly correlated with actual age and are much better indicators of haplotype age than is the haplotype frequency, another commonly used indicator of relative age.
We previously developed an analytical strategy based on cladistic theory to identify subsets of haplotypes that are associated with significant phenotypic deviations. Our initial approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site data to estimate the evolutionary steps that interrelate the observed haplotypes to one another. The cladogram is then used to define a nested statistical design for identifying mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that a mutation responsible for a particular phenotypic effect is embedded within the evolutionary history that is represented by the cladogram. The power of this approach depends on the accuracy of the cladogram in portraying the evolutionary history of the DNA region. This accuracy can be diminished both by recombination and by uncertainty in the estimated cladogram topology. In a previous paper, we presented an algorithm for estimating the set of likely claodgrams and recombination events. In this paper we present an algorithm for defining a nested statistical design under cladogram uncertainty and recombination. Given the nested design, phenotypic associations can be examined using either a nested analysis of variance (for haploids or homozygous strains) or permutation testing (for outcrossed, diploid gene regions). In this paper we also extend this analytical strategy to include categorical phenotypes in addition to quantitative phenotypes. Some worked examples are presented using Drosophila data sets. These examples illustrate that having some recombination may actually enhance the biological inferences that may derived from a cladistic analysis. In particular, recombination can be used to assign a physical localization to a given subregion for mutations responsible for significant phenotypic effects.